From 7ffeee0d5c774bb77e57667a07eefde89e257352 Mon Sep 17 00:00:00 2001 From: matuskalas Date: Tue, 1 Nov 2016 03:43:58 +0100 Subject: [PATCH] History of releases: 1.2 --- releases/EDAM.obo | 53432 ++++++++++++++++++++++++++++++---------------------- releases/EDAM.owl | 52059 ++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 82499 insertions(+), 22992 deletions(-) create mode 100644 releases/EDAM.owl diff --git a/releases/EDAM.obo b/releases/EDAM.obo index 11bef53..5947178 100644 --- a/releases/EDAM.obo +++ b/releases/EDAM.obo @@ -1,28808 +1,36256 @@ format-version: 1.2 -data-version: 1.1 -date: 05:07:2012 18:00 ! Always GMT (UTC) or British Summer Time -saved-by: Jon Ison -subsetdef: operations "EDAM operations" !{note="Singular, bioinformatics-specific operations that are functions of tools, workflows, or scripts, or can be performed manually."} -subsetdef: data "EDAM types of data" !{note="Types of data that are relevant in bioinformatics, commonly used as inputs, outputs, or intermediate data of analyses, or provided by databases and portals."} -subsetdef: topics "EDAM topics" !{note="Application domains of bioinformatics tools and resources; topics of research, studies, or analyses; approaches, techniques, and paradigms within - or directly related to - bioinformatics."} -subsetdef: formats "EDAM data formats" !{note="Data formats commonly used in - and specific to - bioinformatics. Many format concepts in EDAM include references to their definition and documentation."} -subsetdef: identifiers "EDAM types of identifiers" !{note="Types of identifiers that identify biological or computational entities; including resource-specific data accessions. Several identifier concepts in EDAM include regular expressions and examples."} -subsetdef: relations "EDAM relations" !{note="Types of relations - defined in EDAM - that apply between concepts, entities subject to semantic annotation, and entities and concepts (or possibly even vice versa)."} -subsetdef: concept_attributes "EDAM concept attributes" !{note="Types of concept attributes and attribute modifiers or qualifiers, that are defined and used in EDAM in addition to the standard attributes of the OBO format."} -idspace: EDAM_operation http://edamontology.org/operation_ "EDAM Operations" -idspace: EDAM_data http://edamontology.org/data_ "EDAM Types of Data" -idspace: EDAM_topic http://edamontology.org/topic_ "EDAM Topics" -idspace: EDAM_format http://edamontology.org/format_ "EDAM Data Formats" -idspace: EDAM http://edamontology.org/ "EDAM Relations and Concept Attributes" +ontology: http://edamontology.org +subsetdef: bioinformatics "Bioinformatics" +subsetdef: concept_properties "EDAM concept properties" +subsetdef: data "EDAM types of data" +subsetdef: edam "EDAM" +subsetdef: formats "EDAM data formats" +subsetdef: identifiers "EDAM types of identifiers" +subsetdef: operations "EDAM operations" +subsetdef: relations "EDAM relations" +subsetdef: topics "EDAM topics" +data-version: 1.2 +date: 13:12:2012 00:00 default-relationship-id-prefix: EDAM +idspace: EDAM http://edamontology.org/ "EDAM relations and concept properties" +idspace: EDAM_data http://edamontology.org/data_ "EDAM types of data" +idspace: EDAM_format http://edamontology.org/format_ "EDAM data formats" +idspace: EDAM_operation http://edamontology.org/operation_ "EDAM operations" +idspace: EDAM_topic http://edamontology.org/topic_ "EDAM topics" remark: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web. -remark: EDAM editors: Jon Ison and Matus Kalas. Co-authors: Inge Jonassen, Hamish McWilliam, James Malone, Rodrigo Lopez, Helen Parkinson, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE (FP6, EU), EMBOSS (BBSRC, UK), eSysbio and FUGE Bioinformatics Platform (both Research Council of Norway). See http://edamontology.org for documentation and licence. -next_id:3234 !{since=1.2} -remark: NB. This is a version for the NCBO BioPortal with all attribute modifiers commented out (due to a problem at BioPortal). Download the full, canonical version from http://edamontology.org/ontology?format=obo (always the latest stable version), or http://edamontology.org/EDAM.obo for latest stable and http://edamontology.org/EDAM_1.1.obo for version 1.1. - - - -! -! Relations -! - -[Typedef] -id: has_input -name: has input -subset: relations -def: "'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument." [http://edamontology.org] -comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. !{note="In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined."} -synonym: "has input" EXACT [http://wsio.org/has_input] -synonym: "has_specified_input" NARROW [http://purl.obolibrary.org/obo/OBI_0000293] !{note="'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant)."} -synonym: "has_participant" RELATED [OBO_REL:has_participant] !{note="'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject."} -inverse_of: is_input_of -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: true !{note="In very unusual cases"} -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_operation:0004 ! Operation -range: EDAM_data:0006 ! Data - -[Typedef] -id: is_input_of -name: is input of -subset: relations -def: "'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B." [http://edamontology.org] -comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. !{note="In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'."} -synonym: "is input of" EXACT [http://wsio.org/is_input_of] -synonym: "is_specified_input_of" NARROW [http://purl.obolibrary.org/obo/OBI_0000295] !{note="'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011)."} -synonym: "participates_in" RELATED [OBO_REL:participates_in] !{note="'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments."} -inverse_of: has_input -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: true !{note="In very unusual cases"} -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_data:0006 ! Data -range: EDAM_operation:0004 ! Operation - -[Typedef] -id: has_output -name: has output -subset: relations -def: "'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument." [http://edamontology.org] -comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. !{note="In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined."} -synonym: "has output" EXACT [http://wsio.org/has_output] -synonym: "has_specified_output" NARROW [http://purl.obolibrary.org/obo/OBI_0000299] !{note="'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant)."} -synonym: "has_participant" RELATED [OBO_REL:has_participant] !{note="'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it."} -inverse_of: is_output_of -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: true !{note="In very unusual cases"} -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_operation:0004 ! Operation -range: EDAM_data:0006 ! Data -! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statement, "An operation has_output An error" implies "An error is Data". -! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. - -[Typedef] -id: is_output_of -name: is output of -subset: relations -def: "'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B." [http://edamontology.org] -comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. !{note="In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'."} -synonym: "is output of" EXACT [http://wsio.org/is_output_of] -synonym: "is_specified_output_of" NARROW [http://purl.obolibrary.org/obo/OBI_0000312] !{note="'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011)."} -synonym: "participates_in" RELATED [OBO_REL:participates_in] !{note="'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it."} -inverse_of: has_output -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: true !{note="In very unusual cases"} -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_data:0006 ! Data -range: EDAM_operation:0004 ! Operation -! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'domain' statement, An error is_output_of An operation" implies "An error is Data". -! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. - -[Typedef] -id: has_topic -name: has topic -subset: relations -def: "'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B)." [http://edamontology.org] -comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. !{note="In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined."} -synonym: "hasTopic" RELATED [http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic] !{note="'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource."} -synonym: "has-quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality] -synonym: "has_quality" RELATED [http://purl.obolibrary.org/obo/OBI_0000298] !{note="'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject."} -synonym: "is about" RELATED [http://purl.obolibrary.org/obo/IAO_0000136] !{note="'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object."} -inverse_of: is_topic_of -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: true !{note="In very unusual cases"} -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_operation:0004 ! Operation -domain: EDAM_data:0006 ! Data -range: EDAM_topic:0003 ! Topic -! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'domain' statements, "My experiment has_topic Molecular mimicry" implies "My experiment is an Operation" and "My experiment is Data". -! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. -! NB: Second 'domain' line is not visible in OBO-Edit2 - -[Typedef] -id: is_topic_of -name: is topic of -subset: relations -def: "'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B)." [http://edamontology.org] -comment: Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. !{note="In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'."} -synonym: "inherent-in" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in] -synonym: "quality_of" RELATED [OBO_REL:quality_of] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object."} -inverse_of: has_topic -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: true !{note="In very unusual cases"} -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_topic:0003 ! Topic -range: EDAM_operation:0004 ! Operation -range: EDAM_data:0006 ! Data -! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statements, "Molecular mimicry is_topic_of My experiment" implies "My experiment is an Operation" and (even) "My experiment is Data". -! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. -! NB: Second 'range' line is not visible in OBO-Edit2 - -[Typedef] -id: has_format -name: has format -subset: relations -def: "'A has_format B' defines for the subject A, that it has the object B as its data format." [http://edamontology.org] -comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. !{note="In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'."} -synonym: "has-quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality] -synonym: "has_quality" RELATED [http://purl.obolibrary.org/obo/OBI_0000298] !{note="'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject."} -inverse_of: is_format_of -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: false -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_data:0006 ! Data -range: EDAM_format:1915 ! Format - -[Typedef] -id: is_format_of -name: is format of -subset: relations -def: "'A is_format_of B' defines for the subject A, that it is a data format of the object B." [http://edamontology.org] -comment: Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. !{note="In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined."} -synonym: "inherent-in" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in] -synonym: "quality_of" RELATED [OBO_REL:quality_of] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object."} -inverse_of: has_format -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: false -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_format:1915 ! Format -range: EDAM_data:0006 ! Data - -[Typedef] -id: has_identifier -name: has identifier -subset: relations -def: "'A has_identifier B' defines for the subject A, that it has the object B as its identifier." [http://edamontology.org] -comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. !{note="In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'."} -inverse_of: is_identifier_of -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: false -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_data:0006 ! Data -range: EDAM_data:0842 ! Identifier -! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statement, "My car has_identifier Licence plate number" implies "My car is Data". -! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. - -[Typedef] -id: is_identifier_of -name: is identifier of -subset: relations -def: "'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B." [http://edamontology.org] -comment: Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. !{note="In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined."} -inverse_of: has_identifier -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: false -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_data:0842 ! Identifier -range: EDAM_data:0006 ! Data -! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statement, "Licence plate number is_identifier_of My car" implies "My car is Data". -! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. - -[Typedef] -id: has_function -name: has function -subset: relations -def: "'A has_function B' defines for the subject A, that it has the object B as its function." [http://edamontology.org] -comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. !{note="In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts."} -synonym: "has function" EXACT [http://wsio.org/has_function] -synonym: "has_function" NARROW [http://purl.obolibrary.org/obo/OBI_0000306] !{note="'OBI:has_function' only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes, with objects that are a 'function' (snap:Function). It does not define explicitly that the object is a function of the subject."} -synonym: "has-quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality] -synonym: "bearer_of" RELATED [OBO_REL:bearer_of] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject."} -inverse_of: is_function_of -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: true !{note="In very unusual cases"} -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -range: EDAM_operation:0004 ! Operation -! NB. 'range' is defined in the following way in OBO format: According to that definition and the given 'range' statement, "My boss has_function Institute leadership" implies "Institute leadership is an Operation". -! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. - -[Typedef] -id: is_function_of -name: is function of -subset: relations -def: "'A is_function_of B' defines for the subject A, that it is a function of the object B." [http://edamontology.org] -comment: Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. !{note="Within EDAM itself, 'is_function_of' is not used."} -synonym: "is function of" EXACT [http://wsio.org/is_function_of] -synonym: "function_of" NARROW [OBO_REL:function_of] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object."} -synonym: "inherent-in" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in] -synonym: "inheres_in" RELATED [OBO_REL:inheres_in] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions."} -inverse_of: has_function -transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? -is_cyclic: true !{note="In very unusual cases"} -is_reflexive: false -is_symmetric: false -is_anti_symmetric: false -is_transitive: false -domain: EDAM_operation:0004 ! Operation -! NB. 'domain' is defined in the following way in OBO format: According to that definition and the given 'domain' statement, "Institute leadership is_function_of My boss" implies "Institute leadership is an Operation". -! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. - - - - - - - - -! -! Concept metadata tags, modifiers, and qualifiers -! - -[Typedef] -id: regex -name: Regular expression -subset: concept_attributes -def: "'Regular expression' concept attribute ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too." [http://edamontology.org] -is_metadata_tag: true - -[Typedef] -id: example -name: Example -subset: concept_attributes -def: "'Example' concept attribute ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too." [http://edamontology.org] -is_metadata_tag: true - -[Typedef] -id: documentation -name: Documentation -subset: concept_attributes -def: "'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format." [http://edamontology.org] -synonym: "Specification" NARROW [http.//edamontology.org] -is_metadata_tag: true - -[Typedef] -id: min_cardinality -name: Minimum cardinality -subset: concept_attributes -def: "'Minimum cardinality' trailing modifier ('min_cardinality') of 'has input' and 'has output' relations. Specificies the minimum number of data records consumed or produced by an operation." [http://edamontology.org] -is_metadata_tag: true - -[Typedef] -id: max_cardinality -name: Maximum cardinality -subset: concept_attributes -def: "'Maximum cardinality' trailing modifier ('max_cardinality') of 'has input' and 'has output' relations. Specificies the maximum number of data records consumed or produced by an operation." [http://edamontology.org] -comment: 'max_cardinality' is not (yet) defined among concepts in EDAM. -is_metadata_tag: true - -[Typedef] -id: cardinality -name: Cardinality -subset: concept_attributes -def: "'Cardinality' trailing modifier ('cardinality') of 'has input' and 'has output' relations. Specificies the number of data records consumed or produced by an operation." [http://edamontology.org] -comment: 'cardinality' is not (yet) defined among concepts in EDAM. -is_metadata_tag: true -is_a: min_cardinality -is_a: max_cardinality - -[Typedef] -id: note -name: Note -subset: concept_attributes -def: "'Note' trailing modifier ('note') of any concept or ontology attributes. Contains a note for a human reader related to the given attribute." [http://edamontology.org] -is_metadata_tag: true - -[Typedef] -id: since -name: Since -subset: concept_attributes -def: "'Since' trailing modifier ('since') of 'id' and 'is_obsolete: true' attributes (may be applicable to other attributes, too). Specificies the released version of the ontology in which the attribute received its current value/started to be valid. In case of 'id' this is the version in which the concept has been introduced, and in case of 'is_obsolete: true' the version in which the concept became obsolete." [http://edamontology.org] -is_metadata_tag: true - - - - - - - - - - - -! -! Top-level concepts (sub-ontologies) -! - -[Term] -id: EDAM_operation:0004 -name: Operation -namespace: operation -subset: operations -def: "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs)." [http://edamontology.org] -comment: A singular case is a constant operation (constant function) that consumes no input (has no input arguments). -xref: WSIO_operation:operation, http://wsio.org/operation -synonym: "Function" BROAD [http://edamontology.org] !{note="Operation is a function that has input(s) and output(s) that are data."} -synonym: "Computational operation" NARROW [http://edamontology.org] -synonym: "Computational procedure" NARROW [http://edamontology.org] -synonym: "Computational method" NARROW [http://edamontology.org] -synonym: "Computational subroutine" NARROW [http://edamontology.org] -synonym: "Function (programming)" NARROW [http://edamontology.org] -synonym: "Lambda abstraction" NARROW [http://edamontology.org] -synonym: "Mathematical operation" NARROW [http://edamontology.org] -synonym: "Mathematical function" NARROW [http://edamontology.org] -synonym: "Process" RELATED [http://edamontology.org] !{note="Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs."} -synonym: "Computational tool" RELATED [http://edamontology.org] !{note="Computational tool provides an operation with inputs and outputs."} -synonym: "Operation" EXACT [http://wsio.org/operation_001] -synonym: "function" BROAD [http://purl.org/biotop/biotop.owl#Function] !{note="Operation is a function that has input(s) and output(s) that are data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'."} -synonym: "function" BROAD [http://semanticscience.org/resource/SIO_000017] -synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] -synonym: "Function" BROAD [http://www.onto-med.de/ontologies/gfo.owl#Function] !{note="However, operation is not a GFO 'Concept' present only in someone's mind."} -synonym: "Subroutine" NARROW [http://en.wikipedia.org/wiki/Subroutine, http://en.wikipedia.org/wiki/Function_(computer_science)] -synonym: "Function (mathematics)" NARROW [http://en.wikipedia.org/wiki/Function_(mathematics)] -synonym: "function" RELATED [sumo:Function] ! Related external synonyms in EDAM without a note is usually almost exact. -synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials."} -synonym: "function" RELATED [http://purl.obolibrary.org/obo/BFO_0000034, http://www.ifomis.org/bfo/1.1/snap#Function] !{note="BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s)."} -synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] !{note="Function, including an operation, can be a quality/attribute of e.g. a computational tool."} -synonym: "quality" RELATED [http://purl.obolibrary.org/obo/BFO_0000019, http://www.ifomis.org/bfo/1.1/snap#Quality] !{note="Function, including an operation, can have a role of a quality/attribute in semantic annotation of e.g. a computational tool."} -synonym: "process" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} -synonym: "process" RELATED [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/span#Process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} -synonym: "Process" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} -synonym: "information processing" RELATED [http://www.ebi.ac.uk/swo/SWO_0000003] !{note="However, one may think that an operation is not a process."} -synonym: "information processing" RELATED [http://semanticscience.org/resource/SIO_000649] !{note="However, one may think that an operation is not a process and not a physical entity."} -synonym: "Method" RELATED [http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method] !{note="Method may in addition focus on how to achieve the result, not just on what to achieve as with operation."} -relationship: has_input EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. -relationship: has_output EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. -relationship: has_topic EDAM_topic:0003 ! Topic ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. - - -[Term] -id: EDAM_data:0006 -name: Data -namespace: data -subset: data -! alt_id: EDAM_data:3030 !{since=beta13} ! Not released -def: "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output." [http://edamontology.org] -synonym: "Datum" EXACT [http://edamontology.org] !{note="The multiplicity is not taken into account."} -synonym: "Data record" EXACT [http://edamontology.org] !{note="Currently we are for practical purposes not distinguishing a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable information)."} -synonym: "Data set" EXACT [http://edamontology.org] !{note="The multiplicity is not taken into account."} -synonym: "Data" EXACT [http://wsio.org/data_002] -synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] -synonym: "digital entity" RELATED [http://purl.org/biotop/biotop.owl#DigitalEntity] -synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual."} -synonym: "data item" RELATED [http://semanticscience.org/resource/SIO_000069] !{note="Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019)."} -synonym: "data item" RELATED [http://purl.obolibrary.org/obo/IAO_0000027] !{note="IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something."} -synonym: "information content entity" RELATED [http://purl.obolibrary.org/obo/IAO_0000030] !{note="IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity."} -synonym: "record" RELATED [http://semanticscience.org/resource/SIO_000088] !{note="Data does however not necessarily contain statements and not necessarily about an entity."} -relationship: has_topic EDAM_topic:0003 ! Topic ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. - - -[Term] -id: EDAM_topic:0003 -name: Topic -namespace: topic -subset: topics -def: "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other." [http://edamontology.org] -synonym: "quality" BROAD [http://purl.org/biotop/biotop.owl#Quality] -synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] -synonym: "field of study" RELATED [sumo:FiledOfStudy] ! Related external synonym in EDAM without a note is usually almost exact. -synonym: "Area of Research" RELATED [http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research] -synonym: "Category" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Category] !{note="GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated."} -synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials."} -synonym: "Method" RELATED [http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method] -synonym: "quality" RELATED [http://purl.obolibrary.org/obo/BFO_0000019, http://www.ifomis.org/bfo/1.1/snap#Quality] !{note="BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the topic."} -synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] !{note="Topic can be a quality of an entity."} - - -[Term] -id: EDAM_format:1915 -name: Format -namespace: format -subset: formats -def: "A specified way or layout of representing, structuring (and in some cases also encoding) data in a computer file, blob, string, message and so on." [http://edamontology.org] -synonym: "Data format" EXACT [http://edamontology.org] -synonym: "File format" NARROW [http://edamontology.org] !{note="File format denotes only formats of a computer file, but the same formats apply also to data blobs or messages. Thus the synonym is in practical terms exact."} -synonym: "Format" BROAD [http://purl.org/dc/elements/1.1/format] -synonym: "quality" BROAD [http://purl.org/biotop/biotop.owl#Quality] -synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] -synonym: "data format specification" RELATED [http://purl.obolibrary.org/obo/IAO_0000098] !{note="Closely related concept focusing on the specification of a data format."} -synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials."} -synonym: "Symbol structure" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure] -synonym: "File format" RELATED [http://en.wikipedia.org/wiki/File_format, http://en.wikipedia.org/wiki/List_of_file_formats] -synonym: "machine language" RELATED [http://purl.org/biotop/biotop.owl#MachineLanguage] -synonym: "Compression and encoding" RELATED [http://wsio.org/compression_004] !{note="'Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format."} -synonym: "standard" RELATED [http://semanticscience.org/resource/SIO_000618] -synonym: "representation" RELATED [http://semanticscience.org/resource/SIO_000612] -synonym: "quality" RELATED [http://purl.obolibrary.org/obo/BFO_0000019, http://www.ifomis.org/bfo/1.1/snap#Quality] !{note="BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format."} -synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] !{note="Format can be a quality of a data record."} -relationship: is_format_of EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. - - - - - - -[Term] -id: EDAM_data:0842 -name: Identifier -namespace: identifier -subset: identifiers -subset: data -! alt_id: EDAM_data:2860 -! alt_id: EDAM_data:2861 -! alt_id: EDAM_data:2926 -def: "Identifier is a datum identifying an entity and serving only the sole purpose of identification." [http://edamontology.org] -comment: An identifier is typically a rather short textual or numerical datum (string or integer). It is usually desired that an identifier identifies the entity uniquely and often also that it is persistent over time. -synonym: "ID" EXACT [http://edamontology.org] -synonym: "Identifier" EXACT [http://wsio.org/data_005] -synonym: "identifier" EXACT [http://semanticscience.org/resource/SIO_000115] -synonym: "Identifier" NARROW [http://purl.org/dc/elements/1.1/identifier] !{note="Almost exact but limited to identifying resources."} -is_a: EDAM_data:0006 ! Data -relationship: is_identifier_of EDAM_data:0006 !{note="However, NB. that an identifier may identify also other entities than data records."} ! Data - - - - - - -[Term] -id: EDAM_data:3031 !{since=beta13} -name: Core data -namespace: data -subset: data -def: "A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation." [http://edamontology.org] -comment: Core data entities typically have a format and may be identified by an accession number. -is_a: EDAM_data:0006 ! Data - - - - - - - - -! -! Topic -! - -[Term] -id: EDAM_topic:2807 -name: Tool topic -namespace: topic -subset: topics -def: "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:2809 -name: Study topic -namespace: topic -subset: topics -def: "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:3071 !{since=beta13} -name: Biological data resources -namespace: topic -subset: topics -! alt_id: EDAM_topic:2808 -def: "A topic concerning primarily a specific type of bioinformatics data, typically the broad category of content of a digital archives of biological data, including databanks, databases proper, web portals and other data resources." [http://edamontology.org] -synonym: "Biological databases" EXACT [http://edamontology.org] -synonym: "Biological data resource" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:0077 -name: Nucleic acid analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:3046 !{since=beta13} ! Not released -def: "Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis." [http://edamontology.org] -synonym: "Nucleic acids" EXACT [http://edamontology.org] -synonym: "Nucleic acid informatics" EXACT [http://edamontology.org] -synonym: "Nucleic acid bioinformatics" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - -[Term] -id: EDAM_topic:2839 -name: Molecules -namespace: topic -subset: topics -def: "Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [http://edamontology.org] -synonym: "molecular entity" RELATED [CHEBI:23367] -is_obsolete: true !{since=beta12orEarlier} - -[Term] -id: EDAM_topic:0078 -name: Protein analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:0586 -def: "Processing and analysis of protein data, typically molecular sequence and structural data." [http://edamontology.org] -synonym: "Protein informatics" EXACT [http://edamontology.org] -synonym: "Protein bioinformatics" EXACT [http://edamontology.org] -synonym: "Proteins" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - -[Term] -id: EDAM_topic:2225 -name: Protein databases -namespace: topic -subset: topics -def: "Topic concerning protein data resources." [http://edamontology.org] -synonym: "Protein data resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:3071 ! Biological data resources -is_a: EDAM_topic:0078 ! Protein analysis - - -[Term] -id: EDAM_topic:3174 !{since=1.1} -name: Metagenomics -namespace: topic -subset: topics -def: "Topic concerning the study of genetic material recovered from environmental samples." [http://edamontology.org] -synonym: "Environmental genomics" EXACT [http://edamontology.org] -synonym: "Ecogenomics" EXACT [http://edamontology.org] -synonym: "Community genomics" EXACT [http://edamontology.org] -is_a: EDAM_topic:0610 ! Ecoinformatics -is_a: EDAM_topic:0622 ! Genomics - - -[Term] -id: EDAM_topic:3172 !{since=1.1} -name: Metabolomics -namespace: topic -subset: topics -def: "Topic concerning the study of metabolites and the chemical processes they are involved in, especially the systematic study of the chemical fingerprints of specific cellular processes." [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - -[Term] -id: EDAM_topic:0079 -name: Metabolites -namespace: topic -subset: topics -def: "Topic concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." [http://edamontology.org] -comment: This concept excludes macromolecules such as proteins and nucleic acids. -is_a: EDAM_topic:0154 ! Small molecules -is_a: EDAM_topic:3172 ! Metabolomics - -[Term] -id: EDAM_topic:0080 -name: Sequence analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:2228 -! alt_id: EDAM_topic:0584 -def: "Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] -synonym: "Sequences" EXACT [http://edamontology.org] -xref: BioCatalogue:Sequence Analysis -is_a: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:3041 !{since=beta13} -name: Sequence databases -namespace: topic -subset: topics -def: "Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles." [http://edamontology.org] -synonym: "Sequence data" EXACT [http://edamontology.org] -synonym: "Sequence data resource" EXACT [http://edamontology.org] -synonym: "Sequence data resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:3071 ! Biological data resources -is_a: EDAM_topic:0080 ! Sequence analysis - -[Term] -id: EDAM_topic:0081 -name: Structure analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:0693 -! alt_id: EDAM_topic:2827 -! alt_id: EDAM_topic:0585 -def: "Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids." [http://edamontology.org] -comment: This includes related concepts such as structural properties, alignments and structural motifs. -synonym: "Structural bioinformatics" EXACT [http://edamontology.org] -synonym: "Computation structural biology" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:3038 !{since=beta13} -name: Structure databases -namespace: topic -subset: topics -! alt_id: EDAM_topic:3059 -def: "Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids." [http://edamontology.org] -synonym: "Structure data resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:3071 ! Biological data resources -is_a: EDAM_topic:0081 ! Structure analysis - - -[Term] -id: EDAM_topic:0082 -name: Structure prediction -namespace: topic -subset: topics -! alt_id: EDAM_topic:0171 -def: "Topic concerning the prediction of molecular (secondary or tertiary) structure." [http://edamontology.org] -is_a: EDAM_topic:0081 ! Structure analysis - - -[Term] -id: EDAM_topic:0083 -name: Alignment -namespace: topic -subset: topics -def: "Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0182 ! Sequence alignment -consider: EDAM_topic:0183 ! Structure alignment -consider: EDAM_topic:0184 ! Threading - -[Term] -id: EDAM_topic:0084 -! alt_id: EDAM_topic:0192 -! alt_id: EDAM_topic:0193 -name: Phylogenetics -namespace: topic -subset: topics -! alt_id: EDAM_topic:0636 -def: "Topic concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc." [http://edamontology.org] -comment: This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data. -xref: BioCatalogue:Phylogeny -xref: BioCatalogue:Statistical Robustness -synonym: "Phylogenetic simulation" EXACT [http://edamontology.org] -synonym: "Phylogenetic clocks, dating and stratigraphy" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - - - - - - - - -[Term] -id: EDAM_topic:0200 -name: Microarrays -namespace: topic -subset: topics -! alt_id: EDAM_topic:0206 -def: "Topic concerning microarrays, for example, to process microarray data or design probes and experiments." [http://edamontology.org] -xref: BioCatalogue:Microarrays -synonym: "DNA microarrays" EXACT [http://edamontology.org] -is_a: EDAM_topic:0607 ! Laboratory resources - -[Term] -id: EDAM_topic:0121 -name: Proteomics -namespace: topic -subset: topics -! alt_id: EDAM_topic:0764 -def: "Topic concerning the study of whole proteomes of organisms." [http://edamontology.org] -comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues). -synonym: "Protein expression" EXACT [http://edamontology.org] -xref: BioCatalogue:Proteomics -is_a: EDAM_topic:0003 ! Topic - - - - - -[Term] -id: EDAM_topic:0085 -name: Functional genomics -namespace: topic -subset: topics -def: "Topic concerning the study of gene or protein functions and their interactions." [http://edamontology.org] -is_a: EDAM_topic:0622 ! Genomics - -[Term] -id: EDAM_topic:0122 -name: Structural genomics -namespace: topic -subset: topics -def: "Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism." [http://edamontology.org] -xref: BioCatalogue:Structural Genomics -is_a: EDAM_topic:2226 ! Structure determination -is_a: EDAM_topic:0622 ! Genomics - -[Term] -id: EDAM_topic:3173 !{since=1.1} -name: Epigenomics -namespace: topic -subset: topics -def: "A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc." [http://edamontology.org] -comment: Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. -synonym: "Epigenetics" EXACT [http://edamontology.org] -is_a: EDAM_topic:0622 ! Genomics - - - -[Term] -id: EDAM_topic:3061 !{since=beta13} -name: Documentation and help -namespace: topic -subset: topics -def: "Topic concerning documentation and getting help." [http://edamontology.org] -is_a: EDAM_topic:3068 ! Literature and reference - - - -[Term] -id: EDAM_topic:3047 !{since=beta13} -name: Molecular biology reference -namespace: topic -subset: topics -def: "Topic concerning general molecular biology information extracted from the literature." [http://edamontology.org] -xref: BioCatalogue: Document Discovery -xref: BioCatalogue: Literature retrieval -is_a: EDAM_topic:0606 ! Literature data resources - - -[Term] -id: EDAM_topic:0089 -name: Ontology -namespace: topic -subset: topics -! alt_id: EDAM_topic:2255 -def: "Topic concerning ontologies, controlled vocabularies, structured glossary or other related resource." [http://edamontology.org] -comment: This includes the annotation of entities (typically biological database entries) with concepts from a controlled vocabulary. -synonym: "Ontologies" EXACT [http://edamontology.org] -synonym: "Applied ontology" NARROW [http://edamontology.org] -xref: BioCatalogue:Ontology -xref: BioCatalogue:Ontology Lookup -is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification - -[Term] -id: EDAM_topic:0090 -name: Data search and retrieval -namespace: topic -subset: topics -! alt_id: EDAM_topic:0155 -! alt_id: EDAM_topic:2274 -! alt_id: EDAM_topic:0165 -def: "Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [http://edamontology.org] -comment: This includes, for example, search, query and retrieval of molecular sequences and associated data. -synonym: "Data retrieval" EXACT [http://edamontology.org] -xref: BioCatalogue:Sequence Retrieval -xref: BioCatalogue:Data Retrieval -xref: BioCatalogue:Identifier Retrieval -xref: BioCatalogue:Image Retrieval -xref: BioCatalogue:Structure Retrieval -is_a: EDAM_topic:0091 ! Data handling - -[Term] -id: EDAM_topic:0091 -name: Data handling -namespace: topic -subset: topics -! alt_id: EDAM_topic:2282 -def: "Topic for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation." [http://edamontology.org] -synonym: "Data types, processing and visualisation" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - -[Term] -id: EDAM_topic:0092 -name: Data visualisation -namespace: topic -subset: topics -def: "Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [http://edamontology.org] -synonym: "Data rendering and visualisation" EXACT [http://edamontology.org] -synonym: "Data rendering" EXACT [http://edamontology.org] -synonym: "Data plotting" EXACT [http://edamontology.org] -is_a: EDAM_topic:0091 ! Data handling - - -[Term] -id: EDAM_topic:2258 -name: Chemoinformatics -namespace: topic -subset: topics -def: "Topic for the application of information technology to chemistry." [http://edamontology.org] -synonym: "Cheminformatics" EXACT [http://edamontology.org] -synonym: "Chemical informatics" EXACT [http://edamontology.org] -synonym: "Computational chemistry" EXACT [http://edamontology.org] -xref: BioCatalogue:Chemoinformatics -is_a: EDAM_topic:0003 ! Topic - -[Term] -id: EDAM_topic:2269 -name: Biostatistics -namespace: topic -subset: topics -def: "Topic for the application of statistical methods to biological problems." [http://edamontology.org] -synonym: "Biometry" EXACT [http://edamontology.org] -synonym: "Biometrics" EXACT [http://edamontology.org] -synonym: "Biostatistics" EXACT [http://en.wikipedia.org/wiki/Biostatistics] -xref: BioCatalogue:Biostatistics -is_a: EDAM_topic:0091 ! Data handling - -[Term] -id: EDAM_topic:3077 !{since=beta13} -! alt_id: EDAM_topic:1779 -name: Data acquisition and deposition -namespace: topic -subset: topics -def: "Topic concerning the acquisition and deposition of biological data." [http://edamontology.org] -synonym: "Database submission" EXACT [http://edamontology.org] -is_a: EDAM_topic:0091 ! Data handling - - -[Term] -id: EDAM_topic:0094 -name: Nucleic acid thermodynamics -namespace: topic -subset: topics -! alt_id: EDAM_topic:0614 -! alt_id: EDAM_topic:0104 -def: "Topic concerning the study of the thermodynamic properties of a nucleic acid." [http://edamontology.org] -comment: This includes the study of thermal and conformational properties including DNA or DNA/RNA denaturation (melting). -synonym: "Nucleic acid physicochemistry" EXACT [http://edamontology.org] -synonym: "Nucleic acid properties" EXACT [http://edamontology.org] -synonym: "Nucleic acid denaturation" EXACT [http://edamontology.org] -synonym: "DNA melting" EXACT [http://edamontology.org] -is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis - - - -[Term] -id: EDAM_topic:0097 -name: Nucleic acid structure analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:0699 -! alt_id: EDAM_topic:0106 -def: "The processing and analysis of nucleic acid (secondary or tertiary) structural data." [http://edamontology.org] -is_a: EDAM_topic:0081 ! Structure analysis -is_a: EDAM_topic:0077 ! Nucleic acid analysis - - -[Term] -id: EDAM_topic:3039 !{since=beta13} -name: Nucleic acid structure -namespace: topic -subset: topics -! alt_id: EDAM_topic:2833 -def: "Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." [http://edamontology.org] -is_a: EDAM_topic:3038 ! Structure databases - - -[Term] -id: EDAM_topic:0099 -name: RNA -namespace: topic -subset: topics -! alt_id: EDAM_topic:0653 -def: "Topic concerning RNA sequences and structures." [http://edamontology.org] -is_a: EDAM_topic:3042 ! Nucleic acid sequences - - -[Term] -id: EDAM_topic:0100 -name: Nucleic acid restriction -namespace: topic -subset: topics -def: "Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." [http://edamontology.org] -is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis -is_a: EDAM_topic:0821 ! Enzymes and reactions - - -[Term] -id: EDAM_topic:0107 -name: Codon usage analysis -namespace: topic -subset: topics -def: "Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on." [http://edamontology.org] -is_a: EDAM_topic:0110 ! Transcription - -[Term] -id: EDAM_topic:0109 -name: Gene finding -namespace: topic -subset: topics -def: "Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences." [http://edamontology.org] -comment: This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. -synonym: "Gene prediction" EXACT [http://edamontology.org] -synonym: "Gene discovery" EXACT [http://edamontology.org] -xref: BioCatalogue:Gene Prediction -is_a: EDAM_topic:3073 ! Nucleic acid feature detection - -[Term] -id: EDAM_topic:0110 -name: Transcription -namespace: topic -subset: topics -def: "Topic concerning the transcription of DNA into mRNA." [http://edamontology.org] -xref: BioCatalogue:Transcription Factors -is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis - -[Term] -id: EDAM_topic:0108 -name: Translation -namespace: topic -subset: topics -def: "Topic concerning the translation of mRNA into protein." [http://edamontology.org] -is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis - -[Term] -id: EDAM_topic:0111 -name: Promoters -namespace: topic -subset: topics -def: "Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins)." [http://edamontology.org] -xref: BioCatalogue:Promoter Prediction -is_obsolete: true !{since=beta13} -consider: EDAM_topic:0749 ! Transcription factors and regulatory sites - -[Term] -id: EDAM_topic:0112 -name: Nucleic acid folding -namespace: topic -subset: topics -def: "Topic concerning the folding (in 3D space) of nucleic acid molecules." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0173 ! Nucleic acid structure prediction - -[Term] -id: EDAM_topic:0114 -name: Gene structure and RNA splicing -namespace: topic -subset: topics -! alt_id: EDAM_topic:0750 -def: "Topic concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [http://edamontology.org] -comment: This includes splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. -synonym: "RNA splicing" EXACT [http://edamontology.org] -synonym: "Gene structure" EXACT [http://edamontology.org] -is_a: EDAM_topic:3062 ! Genetic organisation -is_a: EDAM_topic:0747 ! Nucleic acid sites and features - - - -[Term] -id: EDAM_topic:0123 -name: Protein properties -namespace: topic -subset: topics -! alt_id: EDAM_topic:0615 -def: "Topic for the study of the physical and biochemical properties of peptides and proteins." [http://edamontology.org] -synonym: "Protein physicochemistry" EXACT [http://edamontology.org] -is_a: EDAM_topic:0639 ! Protein sequence analysis - - -[Term] -id: EDAM_topic:1775 -name: Protein function analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:3057 -def: "Topic for the study of protein function." [http://edamontology.org] -is_a: EDAM_topic:0078 ! Protein analysis - - -[Term] -id: EDAM_topic:0128 -name: Protein interactions -namespace: topic -subset: topics -! alt_id: EDAM_topic:0587 -def: "Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." [http://edamontology.org] -comment: This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. -xref: BioCatalogue:Protein Interaction -is_a: EDAM_topic:1775 ! Protein function analysis -is_a: EDAM_topic:2225 ! Protein databases - - -[Term] -id: EDAM_topic:0130 -name: Protein folding and stability -namespace: topic -subset: topics -def: "Topic concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation." [http://edamontology.org] -is_a: EDAM_topic:2814 ! Protein structure analysis - -[Term] -id: EDAM_topic:2232 -name: Lipoproteins -namespace: topic -subset: topics -def: "Topic concerning lipoproteins (protein-lipid assemblies)." [http://edamontology.org] -is_a: EDAM_topic:0635 ! Specific protein resources - -[Term] -id: EDAM_topic:0137 -name: Protein hydropathy -namespace: topic -subset: topics -def: "Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein." [http://edamontology.org] -is_a: EDAM_topic:0123 ! Protein properties - -[Term] -id: EDAM_topic:0140 -name: Protein targeting and localization -namespace: topic -subset: topics -! alt_id: EDAM_topic:0588 -def: "Topic for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [http://edamontology.org] -is_a: EDAM_topic:2276 ! Protein function prediction -is_a: EDAM_topic:2225 ! Protein databases - - -[Term] -id: EDAM_topic:0143 -name: Protein structure comparison -namespace: topic -subset: topics -def: "Topic concerning the comparison of two or more protein structures." [http://edamontology.org] -comment: Use this concept for methods that are exclusively for protein structure. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0698 ! Protein tertiary structure -consider: EDAM_topic:1770 ! Structure comparison - -[Term] -id: EDAM_topic:2280 -name: Nucleic acid structure comparison -namespace: topic -subset: topics -def: "Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [http://edamontology.org] -comment: Use this concept for methods that are exclusively for nucleic acid structures. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0097 ! Nucleic acid structure analysis -consider: EDAM_topic:1770 ! Structure comparison - -[Term] -id: EDAM_topic:0144 -name: Protein residue interaction analysis -namespace: topic -subset: topics -def: "The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures." [http://edamontology.org] -synonym: "Protein residue interactions" EXACT [http://edamontology.org] -is_a: EDAM_topic:2814 ! Protein structure analysis - - - -[Term] -id: EDAM_topic:2276 -name: Protein function prediction -namespace: topic -subset: topics -def: "Topic concerning the prediction of functional properties of a protein." [http://edamontology.org] -xref: BioCatalogue:Function Prediction -is_a: EDAM_topic:1775 ! Protein function analysis - -[Term] -id: EDAM_topic:0147 -name: Protein-protein interactions -namespace: topic -subset: topics -! alt_id: EDAM_topic:0719 -def: "Topic concerning protein-protein interactions, protein complexes, protein functional coupling etc." [http://edamontology.org] -is_a: EDAM_topic:0128 ! Protein interactions - -[Term] -id: EDAM_topic:0148 -name: Protein-ligand interactions -namespace: topic -subset: topics -! alt_id: EDAM_topic:0717 -def: "Topic concerning protein-ligand (small molecule) interactions." [http://edamontology.org] -xref: BioCatalogue:Ligand Interaction -is_a: EDAM_topic:0128 ! Protein interactions - -[Term] -id: EDAM_topic:0149 -name: Protein-nucleic acid interactions -namespace: topic -subset: topics -! alt_id: EDAM_topic:0718 -def: "Topic concerning protein-DNA/RNA interactions." [http://edamontology.org] -is_a: EDAM_topic:0128 ! Protein interactions - -[Term] -id: EDAM_topic:0150 -name: Protein design -namespace: topic -subset: topics -def: "Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [http://edamontology.org] -is_a: EDAM_topic:0172 ! Protein structure prediction - - -[Term] -id: EDAM_topic:0151 -name: G protein-coupled receptors (GPCR) -namespace: topic -subset: topics -def: "Topic concerning G-protein coupled receptors (GPCRs)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0820 ! Membrane proteins - -[Term] -id: EDAM_topic:2278 -name: Transmembrane protein prediction -namespace: topic -subset: topics -def: "Predict transmembrane domains and topology in protein sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0820 ! Membrane proteins -consider: EDAM_topic:0178 ! Protein secondary structure prediction - -[Term] -id: EDAM_topic:0152 -name: Carbohydrates -namespace: topic -subset: topics -! alt_id: EDAM_topic:0695 -def: "Topic concerning carbohydrates, typically including structural information." [http://edamontology.org] -is_a: EDAM_topic:3038 ! Structure databases - -[Term] -id: EDAM_topic:0153 -name: Lipids -namespace: topic -subset: topics -! alt_id: EDAM_topic:2624 -def: "Topic concerning lipids and their structures." [http://edamontology.org] -is_a: EDAM_topic:3038 ! Structure databases - -[Term] -id: EDAM_topic:0154 -name: Small molecules -namespace: topic -subset: topics -! alt_id: EDAM_topic:0696 -def: "Topic concerning small molecules of biological significance, typically including structural information." [http://edamontology.org] -comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. -synonym: "molecular entity" RELATED [CHEBI:23367] -is_a: EDAM_topic:3038 ! Structure databases - - - -[Term] -id: EDAM_topic:0156 -name: Sequence editing -namespace: topic -subset: topics -def: "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0080 ! Sequence analysis -consider: EDAM_topic:0091 ! Data handling - -[Term] -id: EDAM_topic:0157 -name: Sequence composition analysis -namespace: topic -subset: topics -def: "Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [http://edamontology.org] -is_a: EDAM_topic:0080 ! Sequence analysis - - - - - -[Term] -id: EDAM_topic:0158 -name: Sequence motifs -namespace: topic -subset: topics -! alt_id: EDAM_topic:0161 -! alt_id: EDAM_topic:0162 -def: "Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." [http://edamontology.org] -synonym: "Motifs" EXACT [http://edamontology.org] -is_a: EDAM_topic:0594 ! Sequence classification - - -[Term] -id: EDAM_topic:0188 -name: Sequence profiles and HMMs -namespace: topic -subset: topics -! alt_id: EDAM_topic:0744 -! alt_id: EDAM_topic:0746 -! alt_id: EDAM_topic:1763 -def: "Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [http://edamontology.org] -comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. -is_a: EDAM_topic:0594 ! Sequence classification - -[Term] -id: EDAM_topic:0159 -! alt_id: EDAM_topic:2260 -! alt_id: EDAM_topic:2261 -name: Sequence comparison -namespace: topic -subset: topics -def: "Topic concerning the comparison of two or more molecular sequences." [http://edamontology.org] -comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. -xref: BioCatalogue:Protein Sequence Similarity -xref: BioCatalogue:Nucleotide Sequence Similarity -is_a: EDAM_topic:0080 ! Sequence analysis - - -[Term] -id: EDAM_topic:0160 -name: Sequence sites and features -namespace: topic -subset: topics -! alt_id: EDAM_topic:0600 -def: "Topic concerning the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org] -is_a: EDAM_topic:3041 ! Sequence databases - - -[Term] -id: EDAM_topic:3072 !{since=beta13} -name: Sequence feature detection -namespace: topic -subset: topics -def: "Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org] -is_a: EDAM_topic:0080 ! Sequence analysis - - -[Term] -id: EDAM_topic:0163 -name: Sequence database search -namespace: topic -subset: topics -def: "Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence)." [http://edamontology.org] -comment: The query is a sequence-based entity such as another sequence, a motif or profile. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0159 ! Sequence comparison - -[Term] -id: EDAM_topic:3052 !{since=beta13} -name: Sequence clusters and classification -namespace: topic -subset: topics -def: "Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity." [http://edamontology.org] -comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. -synonym: "Sequence clusters" EXACT [http://edamontology.org] -synonym: "Sequence families" EXACT [http://edamontology.org] -is_a: EDAM_topic:3041 ! Sequence databases - - -[Term] -id: EDAM_topic:0164 -name: Sequence clustering -namespace: topic -subset: topics -def: "Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities." [http://edamontology.org] -comment: This includes systems that generate, process and analyse sequence clusters. -is_a: EDAM_topic:0159 ! Sequence comparison - - -[Term] -id: EDAM_topic:0594 -name: Sequence classification -namespace: topic -subset: topics -def: "Topic concerning the classification of molecular sequences based on some measure of their similarity." [http://edamontology.org] -comment: Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. -is_a: EDAM_topic:0080 ! Sequence analysis - - - - -[Term] -id: EDAM_topic:0166 -name: Protein structural motifs and surfaces -namespace: topic -subset: topics -! alt_id: EDAM_topic:0139 -! alt_id: EDAM_topic:0170 -! alt_id: EDAM_topic:0146 -! alt_id: EDAM_topic:0589 -def: "Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules." [http://edamontology.org] -comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. -synonym: "Protein structural features" EXACT [http://edamontology.org] -synonym: "Protein surfaces" EXACT [http://edamontology.org] -synonym: "Protein structural motifs" EXACT [http://edamontology.org] -synonym: "Structural motifs" EXACT [http://edamontology.org] -is_a: EDAM_topic:0698 ! Protein tertiary structure - -[Term] -id: EDAM_topic:0167 -name: Structural (3D) profiles -namespace: topic -subset: topics -! alt_id: EDAM_topic:0599 -def: "The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment." [http://edamontology.org] -synonym: "Structural profiles" EXACT [http://edamontology.org] -is_a: EDAM_topic:1770 ! Structure comparison - -[Term] -id: EDAM_topic:1770 -! alt_id: EDAM_topic:0168 -! alt_id: EDAM_topic:0169 -name: Structure comparison -namespace: topic -subset: topics -def: "Topic concerning the comparison of two or more molecular structures." [http://edamontology.org] -comment: This might involve comparison of secondary or tertiary (3D) structural information. -is_a: EDAM_topic:0081 ! Structure analysis - -[Term] -id: EDAM_topic:2844 -name: Structural clustering -namespace: topic -subset: topics -def: "Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." [http://edamontology.org] -synonym: "Structure classification" EXACT [http://edamontology.org] -is_a: EDAM_topic:1770 ! Structure comparison - - - -[Term] -id: EDAM_topic:2271 -name: Structure database search -namespace: topic -subset: topics -def: "Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure)." [http://edamontology.org] -comment: The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:1770 ! Structure comparison - - -[Term] -id: EDAM_topic:0172 -name: Protein structure prediction -namespace: topic -subset: topics -def: "Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." [http://edamontology.org] -xref: BioCatalogue:Protein Structure Prediction -is_a: EDAM_topic:0082 ! Structure prediction -is_a: EDAM_topic:2814 ! Protein structure analysis - -[Term] -id: EDAM_topic:0173 -name: Nucleic acid structure prediction -namespace: topic -subset: topics -! alt_id: EDAM_topic:0181 -def: "Topic concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure." [http://edamontology.org] -synonym: "Nucleic acid folding" EXACT [http://edamontology.org] -synonym: "RNA/DNA structure prediction" EXACT [http://edamontology.org] -xref: BioCatalogue:Nucleotide Structure Prediction -xref: BioCatalogue:Nucleotide Secondary Structure -xref: BioCatalogue:Nucleotide Tertiary Structure -is_a: EDAM_topic:0082 ! Structure prediction -is_a: EDAM_topic:0097 ! Nucleic acid structure analysis - -[Term] -id: EDAM_topic:2953 -name: Nucleic acid design -namespace: topic -subset: topics -def: "Topic for the design of nucleic acid sequences with specific conformations." [http://edamontology.org] -is_a: EDAM_topic:0077 ! Nucleic acid analysis - -[Term] -id: EDAM_topic:0174 -name: Ab initio structure prediction -namespace: topic -subset: topics -def: "Topic for the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [http://edamontology.org] -synonym: "de novo protein structure prediction" EXACT [http://edamontology.org] -is_a: EDAM_topic:0082 ! Structure prediction - -[Term] -id: EDAM_topic:2275 -name: Molecular modelling -namespace: topic -subset: topics -def: "Topic for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. " [http://edamontology.org] -is_a: EDAM_topic:0082 ! Structure prediction -is_a: EDAM_topic:0172 ! Protein structure prediction - -[Term] -id: EDAM_topic:0175 -name: Homology modelling -namespace: topic -subset: topics -def: "Topic for the modelling of the three-dimensional structure of a protein using known sequence and structural data." [http://edamontology.org] -synonym: "Comparative modelling" EXACT [http://edamontology.org] -is_a: EDAM_topic:2275 ! Molecular modelling - -[Term] -id: EDAM_topic:0176 -! alt_id: EDAM_topic:0145 -name: Molecular dynamics -namespace: topic -subset: topics -def: "Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org] -comment: This includes resources concerning flexibility and motion in protein and other molecular structures. -synonym: "Molecular motions" EXACT [http://edamontology.org] -synonym: "Molecular flexibility" EXACT [http://edamontology.org] -is_a: EDAM_topic:2275 ! Molecular modelling - -[Term] -id: EDAM_topic:0177 -name: Molecular docking -namespace: topic -subset: topics -def: "Topic for modelling the structure of proteins in complex with small molecules or other macromolecules." [http://edamontology.org] -is_a: EDAM_topic:2275 ! Molecular modelling - -[Term] -id: EDAM_topic:0178 -name: Protein secondary structure prediction -namespace: topic -subset: topics -def: "Topic concerning the prediction of secondary or supersecondary structure of protein sequences." [http://edamontology.org] -xref: BioCatalogue:Protein Secondary Structure -is_a: EDAM_topic:0172 ! Protein structure prediction -is_a: EDAM_topic:0694 ! Protein secondary structure - -[Term] -id: EDAM_topic:0179 -name: Protein tertiary structure prediction -namespace: topic -subset: topics -def: "Topic concerning the prediction of tertiary structure of protein sequences." [http://edamontology.org] -xref: BioCatalogue:Protein Tertiary Structure -is_a: EDAM_topic:0172 ! Protein structure prediction -is_a: EDAM_topic:0698 ! Protein tertiary structure - -[Term] -id: EDAM_topic:0180 -name: Protein fold recognition -namespace: topic -subset: topics -def: "Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [http://edamontology.org] -is_a: EDAM_topic:0172 ! Protein structure prediction - - -[Term] -id: EDAM_topic:0182 -name: Sequence alignment -namespace: topic -subset: topics -! alt_id: EDAM_topic:2283 -! alt_id: EDAM_topic:0185 -! alt_id: EDAM_topic:0186 -! alt_id: EDAM_topic:0187 -! alt_id: EDAM_topic:0596 -! alt_id: EDAM_topic:0189 -def: "Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments)." [http://edamontology.org] -comment: This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. -xref: BioCatalogue:Protein Sequence Alignment -xref: BioCatalogue:Nucleotide Sequence Alignment -xref: BioCatalogue:Protein Pairwise Alignment -xref: BioCatalogue:Nucleotide Pairwise Alignment -xref: BioCatalogue:Protein Multiple Alignment -xref: BioCatalogue:Nucleotide Multiple Alignment -is_a: EDAM_topic:0159 ! Sequence comparison -is_a: EDAM_topic:3041 ! Sequence databases - - -[Term] -id: EDAM_topic:3178 -name: RNA-Seq alignment -namespace: topic -subset: topics -def: "Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing." [http://edamontology.org] -synonym: "RNA-seq alignment" EXACT [http://edamontology.org] -is_a: EDAM_topic:0182 ! Sequence alignment - - - - -[Term] -id: EDAM_topic:0183 -! alt_id: EDAM_topic:2272 -! alt_id: EDAM_topic:2273 -name: Structure alignment -namespace: topic -subset: topics -! alt_id: EDAM_topic:0597 -! alt_id: EDAM_topic:0190 -def: "Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [http://edamontology.org] -comment: This includes the generation, storage, analysis, rendering etc. of structure alignments. -synonym: "Structure alignment generation" EXACT [http://edamontology.org] -is_a: EDAM_topic:1770 ! Structure comparison -is_a: EDAM_topic:3038 ! Structure databases - - -[Term] -id: EDAM_topic:0184 -name: Threading -namespace: topic -subset: topics -def: "Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [http://edamontology.org] -synonym: "Sequence-structure alignment" EXACT [http://edamontology.org] -is_a: EDAM_topic:0180 ! Protein fold recognition - - - -[Term] -id: EDAM_topic:0191 -name: Phylogeny reconstruction -namespace: topic -subset: topics -def: "Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." [http://edamontology.org] -comment: Currently too specific for the topic sub-ontology (but might be unobsoleted). -xref: BioCatalogue:Tree Inference -xref: BioCatalogue:Evolutionary Distance Measurements -is_a: EDAM_topic:0084 ! Phylogenetics - - - -[Term] -id: EDAM_topic:2257 -name: Phylogeny visualisation -namespace: topic -subset: topics -def: "Visualise a phylogeny, for example, render a phylogenetic tree." [http://edamontology.org] -xref: BioCatalogue:Tree Display -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0084 ! Phylogenetics - - -[Term] -id: EDAM_topic:0194 -name: Phylogenomics -namespace: topic -subset: topics -def: "Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction." [http://edamontology.org] -is_a: EDAM_topic:0084 ! Phylogenetics -is_a: EDAM_topic:0622 ! Genomics - -[Term] -id: EDAM_topic:2842 -name: High-throughput sequencing -namespace: topic -subset: topics -def: "Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [http://edamontology.org] -synonym: "Next-generation sequencing" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:3168 ! Sequencing - -[Term] -id: EDAM_topic:0195 -name: Virtual PCR -namespace: topic -subset: topics -def: "Topic concerning simulated polymerase chain reaction (PCR)." [http://edamontology.org] -synonym: "PCR" EXACT [http://edamontology.org] -synonym: "Polymerase chain reaction" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:0077 ! Nucleic acid analysis - -[Term] -id: EDAM_topic:0196 -name: Sequence assembly -namespace: topic -subset: topics -def: "Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] -is_a: EDAM_topic:3168 ! Sequencing - - -[Term] -id: EDAM_topic:0133 -name: Two-dimensional gel electrophoresis -namespace: topic -subset: topics -! alt_id: EDAM_topic:0765 -def: "Topic concerning two-dimensional gel electrophoresis image and related data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:0121 ! Proteomics - - - - -[Term] -id: EDAM_topic:0134 -name: Mass spectrometry -namespace: topic -subset: topics -! alt_id: EDAM_topic:0766 -def: "Topic concerning mass spectrometry and related data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:0121 ! Proteomics - - -[Term] -id: EDAM_topic:0135 -name: Protein microarrays -namespace: topic -subset: topics -def: "Topic concerning protein microarray data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:0121 ! Proteomics -consider: EDAM_topic:0200 ! Microarrays - - -[Term] -id: EDAM_topic:0102 -name: Mapping -namespace: topic -subset: topics -def: "Topic concerning the mapping of complete (typically nucleotide) sequences." [http://edamontology.org] -is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis - -[Term] -id: EDAM_topic:3168 !{since=1.1} -name: Sequencing -namespace: topic -subset: topics -def: "Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes." [http://edamontology.org] -is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis - - -[Term] -id: EDAM_topic:3169 !{since=1.1} -name: ChIP-seq -namespace: topic -subset: topics -def: "Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins." [http://edamontology.org] -synonym: "Chip-sequencing" EXACT [http://edamontology.org] -synonym: "Chip sequencing" EXACT [http://edamontology.org] -synonym: "Chip seq" EXACT [http://edamontology.org] -is_a: EDAM_topic:3168 ! Sequencing -is_a: EDAM_topic:0128 ! Protein interactions - -[Term] -id: EDAM_topic:3179 !{since=1.1} -name: ChIP-on-chip -namespace: topic -subset: topics -def: "Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions." [http://edamontology.org] -synonym: "ChIP-chip" EXACT [http://edamontology.org] -is_a: EDAM_topic:3168 ! Sequencing -is_a: EDAM_topic:0128 ! Protein interactions - - - -[Term] -id: EDAM_topic:3170 !{since=1.1} -name: RNA-Seq -namespace: topic -subset: topics -def: "A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. " [http://edamontology.org] -comment: This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. -synonym: "RNA-seq" EXACT [http://edamontology.org] -synonym: "Small RNA-Seq" EXACT [http://edamontology.org] -synonym: "Small RNA-seq" EXACT [http://edamontology.org] -synonym: "Whole transcriptome shotgun sequencing" EXACT [http://edamontology.org] -synonym: "WTSS" EXACT [http://edamontology.org] -is_a: EDAM_topic:3168 ! Sequencing -is_a: EDAM_topic:0203 ! Transcriptomics - - - - - -[Term] -id: EDAM_topic:3177 !{since=1.1} -name: DNA-Seq -namespace: topic -subset: topics -def: "A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements." [http://edamontology.org] -synonym: "DNA-seq" EXACT [http://edamontology.org] -is_a: EDAM_topic:3168 ! Sequencing - - -[Term] -id: EDAM_topic:3062 !{since=beta13} -name: Genetic organisation -namespace: topic -subset: topics -def: "Topic concerning the structural and functional organisation of genes and other genetic elements." [http://edamontology.org] -is_a: EDAM_topic:2816 ! Gene resources - - - - -[Term] -id: EDAM_topic:0204 -name: Gene regulation -namespace: topic -subset: topics -! alt_id: EDAM_topic:3049 -! alt_id: EDAM_topic:0631 -def: "Topic concerning primarily the regulation of gene expression." [http://edamontology.org] -synonym: "Gene regulation resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:2816 ! Gene resources - - -[Term] -id: EDAM_topic:0199 -name: Genetic variation -namespace: topic -subset: topics -! alt_id: EDAM_topic:0626 -def: "Topic concerning DNA sequence variation (mutation and polymorphism) data." [http://edamontology.org] -synonym: "Mutation and polymorphism" EXACT [http://edamontology.org] -synonym: "DNA variation" EXACT [http://edamontology.org] -is_a: EDAM_topic:0625 ! Genotype and phenotype -is_a: EDAM_topic:3041 ! Sequence databases -is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis - -[Term] -id: EDAM_topic:0202 -name: Pharmacoinformatics -namespace: topic -subset: topics -def: "Topic for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on." [http://edamontology.org] -synonym: "Computational pharmacology" EXACT [http://edamontology.org] -is_a: EDAM_topic:2258 ! Chemoinformatics - -[Term] -id: EDAM_topic:0203 -name: Transcriptomics -namespace: topic -subset: topics -alt_id: EDAM_topic:0197 -def: "Topic concerning primarily raw or processed gene (mRNA) expression (typically microarray) data, including the analysis of gene expression levels, by identifying, quantifying or comparing mRNA transcripts and the interpretation (in functional terms) of gene expression data." [http://edamontology.org] -comment: This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein. -synonym: "Gene expression profiling" EXACT [http://edamontology.org] -synonym: "Expression profiling" EXACT [http://edamontology.org] -synonym: "Gene expression resources" EXACT [http://edamontology.org] -synonym: "Gene expression analysis" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic -is_a: EDAM_topic:2816 ! Gene resources - - -[Term] -id: EDAM_topic:2277 -name: SNPs -namespace: topic -subset: topics -def: "Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs." [http://edamontology.org] -comment: A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. -is_a: EDAM_topic:0199 ! Genetic variation - - -[Term] -id: EDAM_topic:0208 -name: Pharmacogenomics -namespace: topic -subset: topics -def: "Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [http://edamontology.org] -synonym: "Pharmacogenetics" EXACT [http://edamontology.org] -is_a: EDAM_topic:0202 ! Pharmacoinformatics -is_a: EDAM_topic:0622 ! Genomics - -[Term] -id: EDAM_topic:0209 -name: Drug design -namespace: topic -subset: topics -def: "Topic concerning the design of drugs or potential drug compounds." [http://edamontology.org] -comment: This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. -is_a: EDAM_topic:0202 ! Pharmacoinformatics - -[Term] -id: EDAM_topic:0210 -name: Fish -namespace: topic -subset: topics -def: "Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a fish, a group of fish or all fish. -is_a: EDAM_topic:2820 ! Vertebrates - -[Term] -id: EDAM_topic:0211 -name: Flies -namespace: topic -subset: topics -def: "Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a fly, a group of flies or all flies. -synonym: "Fly" EXACT [http://edamontology.org] -is_a: EDAM_topic:2819 ! Invertebrates - -[Term] -id: EDAM_topic:3048 !{since=beta13} -name: Mammals -namespace: topic -subset: topics -def: "Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." [http://edamontology.org] -is_a: EDAM_topic:2820 ! Vertebrates - - -[Term] -id: EDAM_topic:0213 -name: Mice or rats -namespace: topic -subset: topics -def: "Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a group of mice / rats or all mice / rats. -synonym: "Mouse or rat" EXACT [http://edamontology.org] -is_a: EDAM_topic:3048 ! Mammals - - - -[Term] -id: EDAM_topic:0215 -name: Worms -namespace: topic -subset: topics -def: "Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a worm, a group of worms or all worms. -synonym: "Worm" EXACT [http://edamontology.org] -is_a: EDAM_topic:2819 ! Invertebrates - - -[Term] -id: EDAM_topic:0217 -name: Literature analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:0088 -! alt_id: EDAM_topic:3058 -def: "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." [http://edamontology.org] -xref: BioCatalogue: Document Discovery -xref: BioCatalogue: Literature retrieval -synonym: "Literature search and analysis" EXACT [http://edamontology.org] -synonym: "Literature sources" EXACT [http://edamontology.org] -is_a: EDAM_topic:3068 ! Literature and reference - - - -[Term] -id: EDAM_topic:0606 -name: Literature data resources -namespace: topic -subset: topics -def: "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." [http://edamontology.org] -is_a: EDAM_topic:3068 ! Literature and reference -is_a: EDAM_topic:3071 ! Biological data resources - - -[Term] -id: EDAM_topic:3068 !{since=beta13} -name: Literature and reference -namespace: topic -subset: topics -def: "Topic concerning the scientific literature, reference information and documentation." [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:0218 -name: Text mining -namespace: topic -subset: topics -def: "Topic concerning the analysis of the biomedical and informatics literature." [http://edamontology.org] -synonym: "Text data mining" EXACT [http://edamontology.org] -xref: BioCatalogue:Text Mining -xref: BioCatalogue:Document Similarity -xref: BioCatalogue:Document Clustering -xref: BioCatalogue:Named Entity Recognition -is_a: EDAM_topic:0217 ! Literature analysis - - -[Term] -id: EDAM_topic:0219 -name: Annotation -namespace: topic -subset: topics -! alt_id: EDAM_topic:2256 -def: "Topic for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [http://edamontology.org] -synonym: "Ontology annotation" EXACT [http://edamontology.org] -xref: BioCatalogue:Genome Annotation -xref: BioCatalogue:Ontology Annotation -is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification - -[Term] -id: EDAM_topic:0221 -name: Sequence annotation -namespace: topic -subset: topics -def: "Annotate a molecular sequence." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0219 ! Annotation - - -[Term] -id: EDAM_topic:0222 -name: Genome annotation -namespace: topic -subset: topics -def: "Annotate a genome." [http://edamontology.org] -xref: BioCatalogue:Genome Annotation -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0219 ! Annotation -consider: EDAM_topic:0621 ! Genome, proteome and model organisms - - - -[Term] -id: EDAM_topic:2230 -name: Classification -namespace: topic -subset: topics -def: "Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:2829 ! Ontologies, nomenclature and classification - -[Term] -id: EDAM_topic:2829 -name: Ontologies, nomenclature and classification -namespace: topic -subset: topics -def: "Topic concerning conceptualisation, categorisation and naming, or that help to identify, group, or name things in a structured way according to some schema based on observable relationships." [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:2811 -name: Nomenclature -namespace: topic -subset: topics -! alt_id: EDAM_topic:0619 -def: "Topic concerning biological nomenclature (naming), symbols and terminology." [http://edamontology.org] -is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification - -[Term] -id: EDAM_topic:2229 -name: Cell biology resources -namespace: topic -subset: topics -def: "Topic concerning cells, such as key genes and proteins involved in the cell cycle." [http://edamontology.org] -is_a: EDAM_topic:3070 ! Biological science resources - - -[Term] -id: EDAM_topic:3064 !{since=beta13} -name: Developmental biology resources -namespace: topic -subset: topics -def: "Topic concerning how organisms grow and develop." [http://edamontology.org] -is_a: EDAM_topic:3070 ! Biological science resources - -[Term] -id: EDAM_topic:3067 !{since=beta13} -name: Anatomy resources -namespace: topic -subset: topics -def: "Topic concerning the structures of living organisms." [http://edamontology.org] -is_a: EDAM_topic:3070 ! Biological science resources - - - - -[Term] -id: EDAM_topic:3065 !{since=beta13} -name: Embryology resources -namespace: topic -subset: topics -def: "Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage." [http://edamontology.org] -is_a: EDAM_topic:3064 ! Developmental biology resources - - -[Term] -id: EDAM_topic:3053 !{since=beta13} -name: Genetics -namespace: topic -subset: topics -! alt_id: EDAM_topic:2227 -def: "Topic concerning the study of genes, genetic variation and heredity in living organisms." [http://edamontology.org] -synonym: "Genetics data resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:2226 -name: Structure determination -namespace: topic -subset: topics -! alt_id: EDAM_topic:0136 -def: "Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, including the assignment or modelling of molecular structure from such data." [http://edamontology.org] -synonym: "Structural determination" EXACT [http://edamontology.org] -synonym: "Structural assignment" EXACT [http://edamontology.org] -synonym: "Structure assignment" EXACT [http://edamontology.org] -synonym: "Raw structural data analysis" EXACT [http://edamontology.org] -is_a: EDAM_topic:0081 ! Structure analysis - - - -[Term] -id: EDAM_topic:0595 -name: Protein classification -namespace: topic -subset: topics -! alt_id: EDAM_topic:0129 -def: "Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." [http://edamontology.org] -is_a: EDAM_topic:0078 ! Protein analysis -is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification -is_a: EDAM_topic:0594 ! Sequence classification - -[Term] -id: EDAM_topic:0598 -name: Sequence motif or profile -namespace: topic -subset: topics -def: "Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [http://edamontology.org] -comment: This includes comparison, discovery, recognition etc. of sequence motifs. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0158 ! Sequence motifs -consider: EDAM_topic:0188 ! Sequence profiles and HMMs - - -[Term] -id: EDAM_topic:0601 -name: Protein modifications -namespace: topic -subset: topics -! alt_id: EDAM_topic:0142 -def: "Topic concerning protein chemical modifications, e.g. post-translational modifications." [http://edamontology.org] -comment: EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) -synonym: "Protein post-translation modification" EXACT [http:edamontology.souceforge.net] -synonym: "protein modification" RELATED [MOD:00000] -synonym: "protein modification process" RELATED [GO:0006464] -is_a: EDAM_topic:0123 ! Protein properties -is_a: EDAM_topic:2225 ! Protein databases - -[Term] -id: EDAM_topic:0602 -name: Pathways, networks and models -namespace: topic -subset: topics -alt_id: EDAM_topic:3076 !{since=beta13} -! alt_id: EDAM_topic:0198 -! alt_id: EDAM_topic:0755 -def: "Topic concerning biological pathways, networks and other models, including their construction and analysis." [http://edamontology.org] -synonym: "Network or pathway analysis" EXACT [http://edamontology.org] -xref: BioCatalogue:Pathways -xref: BioCatalogue:Pathway Retrieval -is_a: EDAM_topic:2259 ! Systems biology -is_a: EDAM_topic:3071 ! Biological data resources - - - -[Term] -id: EDAM_topic:3075 !{since=beta13} -name: Biological system modelling -namespace: topic -subset: topics -def: "Topic for modelling biological systems in mathematical terms." [http://edamontology.org] -xref: BioCatalogue:Model Analysis -xref: BioCatalogue:Model Execution -is_a: EDAM_topic:2259 ! Systems biology - - - -[Term] -id: EDAM_topic:2259 -name: Systems biology -namespace: topic -subset: topics -def: "Topic concerning the holistic modelling and analysis of biological systems and the interactions therein." [http://edamontology.org] -synonym: "Systems biology" EXACT [http://en.wikipedia.org/wiki/Systems_biology] -xref: BioCatalogue:Systems Biology -is_a: EDAM_topic:0003 ! Topic - - - -[Term] -id: EDAM_topic:0605 -name: Informatics -namespace: topic -subset: topics -! alt_id: EDAM_topic:2841 -def: "A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0091 ! Data handling - - - -[Term] -id: EDAM_topic:0607 -name: Laboratory resources -namespace: topic -subset: topics -def: "Topic concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." [http://edamontology.org] -is_a: EDAM_topic:3071 ! Biological data resources - -[Term] -id: EDAM_topic:0608 -name: Cell culture resources -namespace: topic -subset: topics -def: "Topic concerning general cell culture or data on a specific cell lines." [http://edamontology.org] -is_a: EDAM_topic:0607 ! Laboratory resources - - -[Term] -id: EDAM_topic:0610 -name: Ecoinformatics -namespace: topic -subset: topics -def: "Topic concerning the application of information technology to the ecological and environmental sciences." [http://edamontology.org] -synonym: "Computational ecology" EXACT [http://edamontology.org] -synonym: "Ecological informatics" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:3063 !{since=beta13} -name: Medical informatics resources -namespace: topic -subset: topics -! alt_id: EDAM_topic:0087 -def: "Topic for the application of information technology to health, disease and biomedicine." [http://edamontology.org] -synonym: "Health and disease" EXACT [http://edamontology.org] -synonym: "Healthcare informatics" EXACT [http://edamontology.org] -synonym: "Health informatics" EXACT [http://edamontology.org] -synonym: "Clinical informatics" EXACT [http://edamontology.org] -synonym: "Biomedical informatics" EXACT [http://edamontology.org] -is_a: EDAM_topic:0607 ! Laboratory resources - - -[Term] -id: EDAM_topic:3050 !{since=beta13} -name: Biodiversity -namespace: topic -subset: topics -def: "Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet." [http://edamontology.org] -synonym: "Biodiversity data resource" EXACT [http://edamontology.org] -synonym: "Biodiversity data resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:0610 ! Ecoinformatics - - -[Term] -id: EDAM_topic:2840 -name: Toxicoinformatics -namespace: topic -subset: topics -def: "Topic concerning the adverse effects of chemical substances on living organisms." [http://edamontology.org] -synonym: "Computational toxicology" EXACT [http://edamontology.org] -is_a: EDAM_topic:2258 ! Chemoinformatics - -[Term] -id: EDAM_topic:2661 -name: Toxins and targets -namespace: topic -subset: topics -def: "Topic concerning structural and associated data for toxic chemical substances." [http://edamontology.org] -is_a: EDAM_topic:2840 ! Toxicoinformatics -is_a: EDAM_topic:0154 ! Small molecules - -[Term] -id: EDAM_topic:0611 -name: Electron microscopy -namespace: topic -subset: topics -def: "Topic concerning electron microscopy data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:2226 ! Structure determination - -[Term] -id: EDAM_topic:2828 -name: X-ray crystallography -namespace: topic -subset: topics -def: "Topic concerning X-ray crystallography data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:2226 ! Structure determination - -[Term] -id: EDAM_topic:0593 -name: NMR -namespace: topic -subset: topics -def: "Topic concerning raw NMR data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:2226 ! Structure determination - - - -[Term] -id: EDAM_topic:0612 -name: Cell cycle -namespace: topic -subset: topics -! alt_id: EDAM_topic:0609 -def: "Topic concerning the cell cycle including key genes and proteins." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:2229 ! Cell biology resources - - -[Term] -id: EDAM_topic:0613 -name: Peptides and amino acids -namespace: topic -subset: topics -! alt_id: EDAM_topic:0604 -def: "Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides." [http://edamontology.org] -is_a: EDAM_topic:0154 ! Small molecules - - -[Term] -id: EDAM_topic:0616 -name: Organelle genes and proteins -namespace: topic -subset: topics -def: "Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." [http://edamontology.org] -is_a: EDAM_topic:3078 ! Gene and protein resources - -[Term] -id: EDAM_topic:0617 -name: Ribosomal genes and proteins -namespace: topic -subset: topics -def: "Topic concerning ribosomes, typically of ribosome-related genes and proteins." [http://edamontology.org] -synonym: "Ribosome genes and proteins" EXACT [http://edamontology.org] -is_a: EDAM_topic:0616 ! Organelle genes and proteins - - -[Term] -id: EDAM_topic:0621 -name: Genome, proteome and model organisms -namespace: topic -subset: topics -! alt_id: EDAM_topic:0086 -! alt_id: EDAM_topic:0591 -! alt_id: EDAM_topic:0643 -! alt_id: EDAM_topic:0800 -! alt_id: EDAM_topic:0795 -def: "Topic concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms." [http://edamontology.org] -comment: General information on or more organisms, genomes (including molecular sequences and map, genes and annotation) and proteomes may be included. -synonym: "Genome map" EXACT [http://edamontology.org] -is_a: EDAM_topic:0622 ! Genomics -is_a: EDAM_topic:0121 ! Proteomics -is_a: EDAM_topic:0625 ! Genotype and phenotype - -[Term] -id: EDAM_topic:0622 -name: Genomics -namespace: topic -subset: topics -! alt_id: EDAM_topic:0093 -! alt_id: EDAM_topic:0794 -def: "Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." [http://edamontology.org] -xref: BioCatalogue:Genomics -xref: BioCatalogue:Functional Genomics -is_a: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:2816 -name: Gene resources -namespace: topic -subset: topics -! alt_id: EDAM_topic:0630 -def: "Informatics resource (typically a database) primarily focussed on genes." [http://edamontology.org] -synonym: "Gene database" EXACT [http://edamontology.org] -synonym: "Gene resource" EXACT [http://edamontology.org] -is_a: EDAM_topic:3071 ! Biological data resources -is_a: EDAM_topic:3053 ! Genetics - - -! [Term] born obsolete -! id: EDAM_topic:3054 !{since=beta13} -! name: Molecular genetics -! namespace: topic -! subset: topics -! def: "Topic concerning the structure and function of genes at a molecular level." [http://edamontology.org] -! is_obsolete: true !{since=beta13} -! consider: EDAM_topic:3053 ! Genetics - - -[Term] -id: EDAM_topic:3055 !{since=beta13} -name: Quantitative genetics -namespace: topic -subset: topics -def: "Topic concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight)." [http://edamontology.org] -is_a: EDAM_topic:3053 ! Genetics - - -[Term] -id: EDAM_topic:3056 !{since=beta13} -name: Population genetics -namespace: topic -subset: topics -def: "Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow." [http://edamontology.org] -is_a: EDAM_topic:3053 ! Genetics - - - - -[Term] -id: EDAM_topic:0623 -name: Genes, gene family or system -namespace: topic -subset: topics -def: "Topic concerning particular gene(s), gene system or groups of genes." [http://edamontology.org] -is_a: EDAM_topic:3052 ! Sequence clusters and classification -is_a: EDAM_topic:2816 ! Gene resources - - - -[Term] -id: EDAM_topic:0624 -name: Chromosomes -namespace: topic -subset: topics -def: "Topic concerning chromosomes." [http://edamontology.org] -is_a: EDAM_topic:3062 ! Genetic organisation - -[Term] -id: EDAM_topic:3175 !{since=1.1} -name: Structural variation -namespace: topic -subset: topics -def: "Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations." [http://edamontology.org] -synonym: "Genomic structural variation" EXACT [http://edamontology.org] -is_a: EDAM_topic:0624 ! Chromosomes -is_a: EDAM_topic:0199 ! Genetic variation - - - - -[Term] -id: EDAM_topic:0625 -name: Genotype and phenotype -namespace: topic -subset: topics -! alt_id: EDAM_topic:2231 -def: "Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on." [http://edamontology.org] -synonym: "Genotyping" EXACT [http://edamontology.org] -synonym: "Genotype and phenotype resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:2816 ! Gene resources - -[Term] -id: EDAM_topic:3078 !{since=beta13} -name: Gene and protein resources -namespace: topic -subset: topics -def: "Topic concerning specific genes and their encoded proteins or a related group of such genes and proteins." [http://edamontology.org] -synonym: "Genes and proteins resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:0635 ! Specific protein resources -is_a: EDAM_topic:0623 ! Genes, gene family or system - - -[Term] -id: EDAM_topic:3070 !{since=beta13} -name: Biological science resources -namespace: topic -subset: topics -! alt_id: EDAM_topic:3066 -def: "Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." [http://edamontology.org] -synonym: "Phenotype resource" EXACT [http://edamontology.org] -is_a: EDAM_topic:3071 ! Biological data resources - - -[Term] -id: EDAM_topic:0629 -name: Gene expression and microarray -namespace: topic -subset: topics -def: "Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0203 ! Transcriptomics -consider: EDAM_topic:0200 ! Microarrays - - -[Term] -id: EDAM_topic:0634 -name: Disease resources -namespace: topic -subset: topics -def: "Topic concerning diseases." [http://edamontology.org] -is_a: EDAM_topic:0625 ! Genotype and phenotype - -[Term] -id: EDAM_topic:2813 -name: Disease genes and proteins -namespace: topic -subset: topics -! alt_id: EDAM_topic:0819 -def: "Topic concerning the genes, gene variations and proteins involved in one or more specific diseases." [http://edamontology.org] -is_a: EDAM_topic:0634 ! Disease resources -is_a: EDAM_topic:3078 ! Gene and protein resources - -[Term] -id: EDAM_topic:0635 -name: Specific protein resources -namespace: topic -subset: topics -def: "Topic concerning a particular protein, protein family or other group of proteins." [http://edamontology.org] -synonym: "Specific protein" EXACT [http://edamontology.org] -is_a: EDAM_topic:2225 ! Protein databases - - -[Term] -id: EDAM_topic:0637 -name: Taxonomy -namespace: topic -subset: topics -def: "Topic concerning organism classification, identification and naming." [http://edamontology.org] -is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification - - -[Term] -id: EDAM_topic:0639 -name: Protein sequence analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:0125 -def: "Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org] -xref: BioCatalogue:Protein Sequence Analysis -is_a: EDAM_topic:0080 ! Sequence analysis -is_a: EDAM_topic:0078 ! Protein analysis - -[Term] -id: EDAM_topic:3043 !{since=beta13} -name: Protein sequences -namespace: topic -subset: topics -def: "Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] -xref: BioCatalogue:Protein Sequence Analysis -is_a: EDAM_topic:3041 ! Sequence databases -is_a: EDAM_topic:2225 ! Protein databases - -[Term] -id: EDAM_topic:0640 -name: Nucleic acid sequence analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:0096 -def: "Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org] -xref: BioCatalogue:Nucleotide Sequence Analysis -is_a: EDAM_topic:0080 ! Sequence analysis -is_a: EDAM_topic:0077 ! Nucleic acid analysis - -[Term] -id: EDAM_topic:3042 !{since=beta13} -name: Nucleic acid sequences -namespace: topic -subset: topics -def: "Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] -is_a: EDAM_topic:3041 ! Sequence databases - - -[Term] -id: EDAM_topic:0641 -name: Repeat sequences -namespace: topic -subset: topics -! alt_id: EDAM_topic:2262 -def: "Topic concerning the repetitive nature of molecular sequences." [http://edamontology.org] -synonym: "Repeat sequence" EXACT [http://edamontology.org] -xref: BioCatalogue:Repeats -is_a: EDAM_topic:0157 ! Sequence composition analysis -is_a: EDAM_topic:3041 ! Sequence databases - -[Term] -id: EDAM_topic:0642 -name: Low complexity sequences -namespace: topic -subset: topics -! alt_id: EDAM_topic:2263 -def: "Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity." [http://edamontology.org] -is_a: EDAM_topic:0157 ! Sequence composition analysis -is_a: EDAM_topic:3041 ! Sequence databases - - -[Term] -id: EDAM_topic:0644 -name: Proteome -namespace: topic -subset: topics -def: "Topic concerning a specific proteome including protein sequences and annotation." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:0080 ! Sequence analysis - -! [Term] -! id: EDAM:0000646 -! name: BLAST -! namespace: resources -! def: "A BLAST-format database of sequences." [http://edamontology.org] -! is_obsolete: true !{since=beta12orEarlier} -! consider: EDAM_topic:3041 ! Sequence database - - - -[Term] -id: EDAM_topic:0654 -name: DNA -namespace: topic -subset: topics -! alt_id: EDAM_topic:0098 -! alt_id: EDAM_topic:0666 -! alt_id: EDAM_topic:0627 -! alt_id: EDAM_topic:0628 -def: "Topic concerning DNA sequences and structure, including processes such as methylation and replication." [http://edamontology.org] -comment: The DNA sequences might be coding or non-coding sequences. -synonym: "DNA analysis" EXACT [http://edamontology.org] -is_a: EDAM_topic:3042 ! Nucleic acid sequences -is_a: EDAM_topic:0077 ! Nucleic acid analysis - -[Term] -id: EDAM_topic:3176 -name: DNA packaging -namespace: topic -subset: topics -def: "Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures." [http://edamontology.org] -is_a: EDAM_topic:0654 ! DNA -is_a: EDAM_topic:0624 ! Chromosomes - - -[Term] -id: EDAM_topic:3171 !{since=1.1} -name: DNA methylation -namespace: topic -subset: topics -def: "Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc." [http://edamontology.org] -is_a: EDAM_topic:0654 ! DNA - - - - -[Term] -id: EDAM_topic:0655 -name: mRNA, EST or cDNA database -namespace: topic -subset: topics -! alt_id: EDAM_topic:0205 -def: "Topic concerning data resources for messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [http://edamontology.org] -synonym: "Transcriptome" EXACT [http://edamontology.org] -synonym: "Transcriptome database" EXACT [http://edamontology.org] -synonym: "mRNA, EST or cDNA" EXACT [http://edamontology.org] -is_a: EDAM_topic:0099 ! RNA - -[Term] -id: EDAM_topic:0659 -name: Functional and non-coding RNA -namespace: topic -subset: topics -! alt_id: EDAM_topic:0113 -! alt_id: EDAM_topic:0119 -! alt_id: EDAM_topic:0664 -! alt_id: EDAM_topic:0665 -! alt_id: EDAM_topic:0120 -def: "Topic concerning functional or non-coding RNA sequences." [http://edamontology.org] -comment: For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). -synonym: "Non-coding RNA" EXACT [http://edamontology.org] -synonym: "Functional RNA" EXACT [http://edamontology.org] -is_a: EDAM_topic:0099 ! RNA - - -[Term] -id: EDAM_topic:3060 !{since=beta13} -name: Regulatory RNA -namespace: topic -subset: topics -! alt_id: EDAM_topic:0661 -! alt_id: EDAM_topic:0662 -! alt_id: EDAM_topic:0117 -! alt_id: EDAM_topic:0118 -def: "Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA)." [http://edamontology.org] -comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. -is_a: EDAM_topic:0659 ! Functional and non-coding RNA - - -[Term] -id: EDAM_topic:0660 -name: rRNA -namespace: topic -subset: topics -! alt_id: EDAM_topic:0116 -def: "Topic concerning one or more ribosomal RNA (rRNA) sequences." [http://edamontology.org] -is_a: EDAM_topic:0659 ! Functional and non-coding RNA - - -[Term] -id: EDAM_topic:0663 -name: tRNA -namespace: topic -subset: topics -! alt_id: EDAM_topic:0115 -def: "Topic concerning one or more transfer RNA (tRNA) sequences." [http://edamontology.org] -is_a: EDAM_topic:0659 ! Functional and non-coding RNA - - -[Term] -id: EDAM_topic:2814 -name: Protein structure analysis -namespace: topic -subset: topics -! alt_id: EDAM_topic:0126 -! alt_id: EDAM_topic:0590 -alt_id: EDAM_topic:3040 !{since=beta13} -def: "Topic concerning protein secondary or tertiary structural data and/or associated annotation." [http://edamontology.org] -synonym: "Protein structure" EXACT [http://edamontology.org] -is_a: EDAM_topic:0078 ! Protein analysis -is_a: EDAM_topic:0081 ! Structure analysis -is_a: EDAM_topic:3038 ! Structure databases -is_a: EDAM_topic:2225 ! Protein databases - - -[Term] -id: EDAM_topic:0694 -name: Protein secondary structure -namespace: topic -subset: topics -! alt_id: EDAM_topic:2124 -def: "Topic concerning protein secondary structure or secondary structure alignments." [http://edamontology.org] -comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. -synonym: "Protein secondary structure analysis" EXACT [http://edamontology.org] -is_a: EDAM_topic:2814 ! Protein structure analysis - -[Term] -id: EDAM_topic:0698 -name: Protein tertiary structure -namespace: topic -subset: topics -! alt_id: EDAM_topic:2125 -def: "Topic concerning protein tertiary structures." [http://edamontology.org] -synonym: "Protein tertiary structure analysis" EXACT [http://edamontology.org] -is_a: EDAM_topic:2814 ! Protein structure analysis - - - - -[Term] -id: EDAM_topic:0697 -name: RNA structure and alignment -namespace: topic -subset: topics -def: "Topic concerning RNA secondary or tertiary structure and alignments." [http://edamontology.org] -synonym: "RNA structure" EXACT [http://edamontology.org] -synonym: "RNA structure alignment" EXACT [http://edamontology.org] -synonym: "RNA alignment" EXACT [http://edamontology.org] -is_a: EDAM_topic:0183 ! Structure alignment - -[Term] -id: EDAM_topic:2826 -name: Protein structure alignment -namespace: topic -subset: topics -def: "Topic concerning protein secondary or tertiary structure alignments." [http://edamontology.org] -is_a: EDAM_topic:0183 ! Structure alignment -is_a: EDAM_topic:2814 ! Protein structure analysis - - -[Term] -id: EDAM_topic:0620 -name: Drugs and targets -namespace: topic -subset: topics -def: "Topic concerning the structures of drugs, drug target, their interactions and binding affinities." [http://edamontology.org] -is_a: EDAM_topic:0154 ! Small molecules -is_a: EDAM_topic:0202 ! Pharmacoinformatics - -[Term] -id: EDAM_topic:0618 -name: Scents -namespace: topic -subset: topics -def: "A database about scents." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:0154 ! Small molecules - - - -[Term] -id: EDAM_topic:0722 -name: Nucleic acid classification -namespace: topic -subset: topics -def: "Topic concerning nucleic acid classification (typically sequence classification)." [http://edamontology.org] -is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification -is_a: EDAM_topic:0077 ! Nucleic acid analysis -is_a: EDAM_topic:0594 ! Sequence classification - -! [Term] -! id: EDAM:0000723 -! name: Protein structure classification -! namespace: resources -! def: "Topic concerning protein structural classifications." [http://edamontology.org] -! is_obsolete: true !{since=beta12orEarlier} -! consider: EDAM_topic:1770 ! Structure comparison -! consider: EDAM_topic:0736 ! Protein domains and folds - - -[Term] -id: EDAM_topic:0724 -name: Protein families -namespace: topic -subset: topics -def: "Topic concerning primarily proteins that have been classified as members of a protein family (or other grouping)." [http://edamontology.org] -comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. -synonym: "Protein sequence classification" EXACT [http://edamontology.org] -synonym: "Protein secondary" EXACT [http://edamontology.org] -is_a: EDAM_topic:3052 ! Sequence clusters and classification -is_a: EDAM_topic:2225 ! Protein databases - -[Term] -id: EDAM_topic:0736 -name: Protein domains and folds -namespace: topic -subset: topics -! alt_id: EDAM_topic:0703 -! alt_id: EDAM_topic:0700 -! alt_id: EDAM_topic:0127 -def: "Topic concerning protein tertiary structural domains and folds." [http://edamontology.org] -xref: BioCatalogue:Domains -is_a: EDAM_topic:0698 ! Protein tertiary structure -is_a: EDAM_topic:0724 ! Protein families - - -[Term] -id: EDAM_topic:0740 -name: Nucleic acid sequence alignment -namespace: topic -subset: topics -def: "Topic concerning nucleotide sequence alignments." [http://edamontology.org] -is_a: EDAM_topic:0182 ! Sequence alignment -is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis - -[Term] -id: EDAM_topic:0741 -name: Protein sequence alignment -namespace: topic -subset: topics -def: "Topic concerning protein sequence alignments." [http://edamontology.org] -comment: A sequence profile typically represents a sequence alignment. -is_a: EDAM_topic:0182 ! Sequence alignment -is_a: EDAM_topic:0639 ! Protein sequence analysis - -! [Term] -! id: EDAM:0000742 -! name: Sequence motif or profile (nucleotide) -! namespace: resources -! def: "Topic concerning nucleotide sequence motifs, or sequence profiles derived from an nucleic acid sequence alignment." [http://edamontology.org] -! is_obsolete: true !{since=beta12orEarlier} -! consider: EDAM_topic:0158 ! Sequence motifs - - -! [Term] -! id: EDAM:0000743 -! name: Sequence motif or profile (protein) -! namespace: resources -! def: "Topic concerning protein sequence motifs, or sequence profiles derived from an protein sequence alignment." [http://edamontology.org] -! is_obsolete: true !{since=beta12orEarlier} -! consider: EDAM_topic:0158 ! Sequence motifs - - - -[Term] -id: EDAM_topic:0747 -name: Nucleic acid sites and features -namespace: topic -subset: topics -! alt_id: EDAM_topic:0105 -! alt_id: EDAM_topic:0095 -def: "Topic concerning positional features such as functional sites in nucleotide sequences." [http://edamontology.org] -synonym: "Nucleic acid functional sites" EXACT [http://edamontology.org] -synonym: "Nucleic acid features" EXACT [http://edamontology.org] -is_a: EDAM_topic:0160 ! Sequence sites and features -is_a: EDAM_topic:3042 ! Nucleic acid sequences - - -[Term] -id: EDAM_topic:3073 !{since=beta13} -name: Nucleic acid feature detection -namespace: topic -subset: topics -def: "Topic concerning the detection of positional features such as functional sites in nucleotide sequences." [http://edamontology.org] -is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis -is_a: EDAM_topic:3072 ! Sequence feature detection - - -[Term] -id: EDAM_topic:0748 -name: Protein sites and features -namespace: topic -subset: topics -! alt_id: EDAM_topic:0124 -! alt_id: EDAM_topic:0138 -def: "Topic concerning positional features such as functional sites in protein sequences." [http://edamontology.org] -synonym: "Protein functional sites" EXACT [http://edamontology.org] -synonym: "Protein sequence features" EXACT [http://edamontology.org] -is_a: EDAM_topic:0160 ! Sequence sites and features -is_a: EDAM_topic:3043 ! Protein sequences - - -[Term] -id: EDAM_topic:3074 !{since=beta13} -name: Protein feature detection -namespace: topic -subset: topics -def: "Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites." [http://edamontology.org] -is_a: EDAM_topic:0639 ! Protein sequence analysis -is_a: EDAM_topic:3072 ! Sequence feature detection - - -[Term] -id: EDAM_topic:0749 -name: Transcription factors and regulatory sites -namespace: topic -subset: topics -! alt_id: EDAM_topic:0811 -def: "Topic concerning transcription factors; proteins that bind to DNA and control transcription of DNA to mRNA, either promoting (as an activator) or blocking (as a repressor) the binding to DNA of RNA polymerase, and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences." [http://edamontology.org] -comment: This includes promoters, enhancers, silencers and boundary elements / insulators. This includes sequence and structural information, binding profiles etc, and may also include the transcription factor binding site in DNA. -synonym: "Transcriptional regulatory sites" EXACT [http://edamontology.org] -synonym: "Transcription factors" EXACT [http://edamontology.org] -synonym: "Transcription factor and binding site" EXACT [http://edamontology.org] -is_a: EDAM_topic:0204 ! Gene regulation -is_a: EDAM_topic:0110 ! Transcription -is_a: EDAM_topic:0635 ! Specific protein resources -is_a: EDAM_topic:0747 ! Nucleic acid sites and features -is_a: EDAM_topic:3062 ! Genetic organisation -is_a: EDAM_topic:3073 ! Nucleic acid feature detection - - - -[Term] -id: EDAM_topic:0751 -name: Phosphorylation sites -namespace: topic -subset: topics -def: "Topic concerning protein phosphorylation and phosphorylation sites in protein sequences." [http://edamontology.org] -! is_a: EDAM_topic:0601 ! Protein modifications -! is_a: EDAM_topic:0748 ! Protein sites and features -is_obsolete: true !{since=1.0} -consider: EDAM_topic:0601 ! Protein modifications -consider: EDAM_topic:0748 ! Protein sites and features - -[Term] -id: EDAM_topic:0753 -name: Metabolic pathways -namespace: topic -subset: topics -def: "Topic concerning metabolic pathways." [http://edamontology.org] -is_a: EDAM_topic:0602 ! Pathways, networks and models -is_a: EDAM_topic:3172 ! Metabolomics - - -[Term] -id: EDAM_topic:0754 -name: Signaling pathways -namespace: topic -subset: topics -def: "Topic concerning signaling pathways." [http://edamontology.org] -is_a: EDAM_topic:0602 ! Pathways, networks and models - -[Term] -id: EDAM_topic:3044 !{since=beta13} -name: Protein interaction networks -namespace: topic -subset: topics -def: "Topic concerning protein-protein interaction networks." [http://edamontology.org] -is_a: EDAM_topic:0602 ! Pathways, networks and models -is_a: EDAM_topic:0147 ! Protein-protein interactions - -[Term] -id: EDAM_topic:0771 -name: Biological models -namespace: topic -subset: topics -! alt_id: EDAM_topic:2267 -! alt_id: EDAM_topic:2268 -def: "Topic concerning mathematical or other models of biological processes." [http://edamontology.org] -comment: This includes databases of models and methods to construct or analyse a model. -xref: BioCatalogue:Model Creation -is_a: EDAM_topic:0602 ! Pathways, networks and models - - -[Term] -id: EDAM_topic:2846 -name: Gene regulatory networks -namespace: topic -subset: topics -def: "Topic concerning gene regulatory networks." [http://edamontology.org] -is_a: EDAM_topic:0602 ! Pathways, networks and models -is_a: EDAM_topic:0204 ! Gene regulation - - -[Term] -id: EDAM_topic:0767 -name: Protein and peptide identification -namespace: topic -subset: topics -! alt_id: EDAM_topic:0603 -def: "Topic concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays." [http://edamontology.org] -comment: This includes the results of any methods that separate, characterize and identify expressed proteins. -synonym: "Peptide identification and proteolysis" EXACT [http://edamontology.org] -synonym: "Proteomics data" EXACT [http://edamontology.org] -synonym: "Proteomics data resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:0121 ! Proteomics -is_a: EDAM_topic:0639 ! Protein sequence analysis -is_a: EDAM_topic:2225 ! Protein databases - - -[Term] -id: EDAM_topic:0141 -name: Protein cleavage sites and proteolysis -namespace: topic -subset: topics -def: "Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence." [http://edamontology.org] -is_a: EDAM_topic:0639 ! Protein sequence analysis - - - - -[Term] -id: EDAM_topic:0769 -name: Workflows -namespace: topic -subset: topics -def: "Topic concerning biological or biomedical analytical workflows or pipelines." [http://edamontology.org] -! is_a: EDAM_topic:0091 ! Data handling -is_obsolete: true !{since=1.0} -! consider: EDAM_topic:0003 ! Topic - - -[Term] -id: EDAM_topic:0220 -name: Data processing and validation -namespace: topic -subset: topics -! alt_id: EDAM_topic:2286 -! alt_id: EDAM_topic:2270 -! alt_id: EDAM_topic:2834 -def: "Topic concerning basic manipulations of files or reports of generic biological data." [http://edamontology.org] -comment: This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. -synonym: "Report handling" EXACT [http://edamontology.org] -synonym: "File handling" EXACT [http://edamontology.org] -synonym: "Data file handling" EXACT [http://edamontology.org] -synonym: "Report processing" EXACT [http://edamontology.org] -is_a: EDAM_topic:0091 ! Data handling - -[Term] -id: EDAM_topic:0770 -name: Data types and objects -namespace: topic -subset: topics -def: "Topic concerning structuring data into basic types and (computational) objects." [http://edamontology.org] -! is_a: EDAM_topic:0091 ! Data handling -is_obsolete: true !{since=1.0} -consider: EDAM_topic:0091 ! Data handling - - -[Term] -id: EDAM_topic:0632 -name: Probes and primers -namespace: topic -subset: topics -! alt_id: EDAM_topic:0207 -def: "Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR)." [http://edamontology.org] -is_a: EDAM_topic:0607 ! Laboratory resources -is_a: EDAM_topic:3041 ! Sequence databases - - -[Term] -id: EDAM_topic:3032 !{since=beta13} -name: Primer or probe design -namespace: topic -subset: topics -def: "Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes." [http://edamontology.org] -is_a: EDAM_topic:0080 ! Sequence analysis - - - -[Term] -id: EDAM_topic:0779 -name: Mitochondrial genes and proteins -namespace: topic -subset: topics -def: "Topic concerning mitochondria, typically of mitochondrial genes and proteins." [http://edamontology.org] -synonym: "Mitochondria genes and proteins" EXACT [http://edamontology.org] -is_a: EDAM_topic:0616 ! Organelle genes and proteins - - -[Term] -id: EDAM_topic:2818 -name: Eukaryotes -namespace: topic -subset: topics -! alt_id: EDAM_topic:0669 -def: "Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. -synonym: "Eukaryote" EXACT [http://edamontology.org] -is_a: EDAM_topic:0621 ! Genome, proteome and model organisms - - -[Term] -id: EDAM_topic:2821 -name: Unicellular eukaryotes -namespace: topic -subset: topics -! alt_id: EDAM_topic:0675 -def: "Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. -synonym: "Unicellular eukaryote" EXACT [http://edamontology.org] -is_a: EDAM_topic:2818 ! Eukaryotes - - - -[Term] -id: EDAM_topic:2819 -name: Invertebrates -namespace: topic -subset: topics -! alt_id: EDAM_topic:0678 -def: "Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. -is_a: EDAM_topic:2818 ! Eukaryotes - -[Term] -id: EDAM_topic:2820 -name: Vertebrates -namespace: topic -subset: topics -! alt_id: EDAM_topic:0679 -def: "Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. -synonym: "Vertebrate" EXACT [http://edamontology.org] -is_a: EDAM_topic:2818 ! Eukaryotes - -[Term] -id: EDAM_topic:2815 -name: Humans -namespace: topic -subset: topics -! alt_id: EDAM_topic:0692 -! alt_id: EDAM_topic:0687 -def: "Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general." [http://edamontology.org] -comment: The resource may be specific to a human, a group of humans or all humans. -synonym: "Human" EXACT [http://edamontology.org] -is_a: EDAM_topic:3048 ! Mammals - - -[Term] -id: EDAM_topic:0780 -name: Plants -namespace: topic -subset: topics -! alt_id: EDAM_topic:0677 -! alt_id: EDAM_topic:0785 -! alt_id: EDAM_topic:0784 -! alt_id: EDAM_topic:0214 -def: "Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a plant, a group of plants or all plants. -synonym: "Plant" EXACT [http://edamontology.org] -is_a: EDAM_topic:2818 ! Eukaryotes - - -[Term] -id: EDAM_topic:0781 -name: Viruses -namespace: topic -subset: topics -! alt_id: EDAM_topic:0790 -! alt_id: EDAM_topic:0671 -! alt_id: EDAM_topic:0791 -def: "Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a virus, a group of viruses or all viruses. -synonym: "Virus" EXACT [http://edamontology.org] -is_a: EDAM_topic:0621 ! Genome, proteome and model organisms - - -[Term] -id: EDAM_topic:0782 -name: Fungi -namespace: topic -subset: topics -! alt_id: EDAM_topic:0792 -! alt_id: EDAM_topic:0793 -! alt_id: EDAM_topic:0676 -def: "Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a fungus, a group of fungi or all fungi. -synonym: "Fungal" EXACT [http://edamontology.org] -is_a: EDAM_topic:2818 ! Eukaryotes - - -[Term] -id: EDAM_topic:0783 -name: Pathogens -namespace: topic -subset: topics -def: "Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a pathogen, a group of pathogens or all pathogens. -synonym: "Pathogen" EXACT [http://edamontology.org] -is_a: EDAM_topic:0621 ! Genome, proteome and model organisms - - -[Term] -id: EDAM_topic:1811 -name: Prokaryotes and archae -namespace: topic -subset: topics -! alt_id: EDAM_topic:0691 -! alt_id: EDAM_topic:0670 -! alt_id: EDAM_topic:0212 -def: "Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] -comment: The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. -synonym: "Prokaryote and archae" EXACT [http://edamontology.org] -is_a: EDAM_topic:0621 ! Genome, proteome and model organisms - -[Term] -id: EDAM_topic:0786 -name: Arabidopsis -namespace: topic -subset: topics -def: "Topic concerning Arabidopsis-specific data." [http://edamontology.org] -is_a: EDAM_topic:0780 ! Plants - -[Term] -id: EDAM_topic:0787 -name: Rice -namespace: topic -subset: topics -def: "Topic concerning rice-specific data." [http://edamontology.org] -is_a: EDAM_topic:0780 ! Plants - - -[Term] -id: EDAM_topic:2817 -name: Yeast -namespace: topic -subset: topics -! alt_id: EDAM_topic:0682 -! alt_id: EDAM_topic:0216 -def: "Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." [http://edamontology.org] -is_a: EDAM_topic:0782 ! Fungi - - -[Term] -id: EDAM_topic:0796 -name: Genetic mapping and linkage -namespace: topic -subset: topics -! alt_id: EDAM_topic:0103 -def: "Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny." [http://edamontology.org] -synonym: "Genetic linkage" EXACT [http://edamontology.org] -synonym: "Linkage mapping" EXACT [http://edamontology.org] -is_a: EDAM_topic:0102 ! Mapping -relationship: has_topic EDAM_topic:3053 ! Genetics - - -[Term] -id: EDAM_topic:0797 -name: Comparative genomics -namespace: topic -subset: topics -! alt_id: EDAM_topic:0101 -def: "Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes." [http://edamontology.org] -xref: BioCatalogue:Comparative Genomics -is_a: EDAM_topic:0622 ! Genomics - - -[Term] -id: EDAM_topic:0798 -name: Mobile genetic elements -namespace: topic -subset: topics -def: "Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [http://edamontology.org] -is_a: EDAM_topic:3062 ! Genetic organisation - - -! [Term] -! id: EDAM_topic:0801 -! name: Human genes -! namespace: resources -! def: "Topic concerning human genes." [http://edamontology.org] -! is_obsolete: true !{since=beta12orEarlier} -! consider: EDAM_topic:0623 ! Genes, gene family or system - - -[Term] -id: EDAM_topic:0803 -name: Human disease -namespace: topic -subset: topics -def: "Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_topic:0634 ! Disease resources - -[Term] -id: EDAM_topic:0804 -name: Immunoinformatics -namespace: topic -subset: topics -! alt_id: EDAM_topic:0201 -! alt_id: EDAM_topic:0633 -def: "Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." [http://edamontology.org] -synonym: "Computational immunology" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topic - -[Term] -id: EDAM_topic:2830 -name: Immunity genes, immunoproteins and antigens -namespace: topic -subset: topics -def: "Topic concerning immunity-related genes, proteins and their ligands." [http://edamontology.org] -comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." -synonym: "Immunoproteins and immunopeptides" EXACT [http://edamontology.org] -is_a: EDAM_topic:0804 ! Immunoinformatics -is_a: EDAM_topic:3078 ! Gene and protein resources - - -[Term] -id: EDAM_topic:2847 -name: Disease (specific) -namespace: topic -subset: topics -def: "Informatics resources dedicated to one or more specific diseases (not diseases in general)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0634 ! Disease resources - -[Term] -id: EDAM_topic:2640 -name: Cancer -namespace: topic -subset: topics -! alt_id: EDAM_topic:0805 -def: "Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer." [http://edamontology.org] -synonym: "Cancer resources" EXACT [http://edamontology.org] -is_a: EDAM_topic:0634 ! Disease resources - - - -[Term] -id: EDAM_topic:0820 -name: Membrane proteins -namespace: topic -subset: topics -! alt_id: EDAM_topic:0131 -def: "Topic concerning a protein or region of a protein that spans a membrane." [http://edamontology.org] -synonym: "Transmembrane proteins" EXACT [http://edamontology.org] -is_a: EDAM_topic:0635 ! Specific protein resources - -[Term] -id: EDAM_topic:0821 -name: Enzymes and reactions -namespace: topic -subset: topics -! alt_id: EDAM_topic:0132 -def: "Topic concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." [http://edamontology.org] -is_a: EDAM_topic:0635 ! Specific protein resources - - - - - - - - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - - - - - - - - -! -! Operation -! - - -[Term] -id: EDAM_operation:2945 -name: Analysis -namespace: operation -subset: operations -def: "Apply analytical methods to existing data of a specific type." [http://edamontology.org] -comment: For non-analytical operations, see the 'Processing' branch. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2420 ! Analysis and processing - -[Term] -id: EDAM_operation:2420 -name: Analysis and processing -namespace: operation -subset: operations -def: "Process (read and / or write) data of a specific type, for example applying analytical methods." [http://edamontology.org] -synonym: "Calculation" EXACT [http://edamontology.org] -synonym: "Computation" EXACT [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation -relationship: has_input EDAM_data:0006 !{min_cardinality=0} ! Data -relationship: has_output EDAM_data:0006 !{min_cardinality=0} ! Data - -[Term] -id: EDAM_operation:2423 -name: Prediction, detection and recognition -namespace: operation -subset: operations -def: "Predict, recognise, detect or identify some properties of a biomolecule." [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation - -[Term] -id: EDAM_operation:3023 -name: Prediction, detection and recognition (protein) -namespace: operation -subset: operations -def: "Predict, recognise, detect or identify some properties of proteins." [http://edamontology.org] -is_a: EDAM_operation:2423 ! Prediction, detection and recognition - -[Term] -id: EDAM_operation:3024 -name: Prediction, detection and recognition (nucleic acid) -namespace: operation -subset: operations -def: "Predict, recognise, detect or identify some properties of nucleic acids." [http://edamontology.org] -is_a: EDAM_operation:2423 ! Prediction, detection and recognition - - -[Term] -id: EDAM_operation:2946 -name: Alignment analysis -namespace: operation -subset: operations -def: "Analyse an existing alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] -is_a: EDAM_operation:2951 ! Alignment processing -relationship: has_input EDAM_data:1916 !{min_cardinality=1} ! Alignment ! Extends cardinality constraint on parent. -relationship: has_output EDAM_data:2083 !{min_cardinality=1} ! Alignment report - -[Term] -id: EDAM_operation:2947 -name: Article analysis -namespace: operation -subset: operations -def: "Analyse a body of scientific text (typically a full text article from a scientific journal.)" [http://edamontology.org] -is_a: EDAM_operation:2505 ! Text processing -relationship: has_input EDAM_data:0971 !{min_cardinality=1} ! Article -relationship: has_output EDAM_data:2954 ! Article report -relationship: has_topic EDAM_topic:0217 ! Literature analysis - -[Term] -id: EDAM_operation:2993 -name: Molecular interaction data processing -namespace: operation -subset: operations -def: "Process (read and / or write) molecular interaction data." [http://edamontology.org] -is_obsolete: true !{since=beta13} - - -[Term] -id: EDAM_operation:2948 -name: Molecular interaction analysis -namespace: operation -subset: operations -def: "Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact." [http://edamontology.org] -is_obsolete: true !{since=beta13} - -[Term] -id: EDAM_operation:2949 -name: Protein interaction analysis -namespace: operation -subset: operations -def: "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." [http://edamontology.org] -is_a: EDAM_operation:2405 ! Protein interaction data processing -relationship: has_output EDAM_data:0906 !{min_cardinality=1} ! Protein interaction -relationship: has_topic EDAM_topic:0128 ! Protein interactions - - -[Term] -id: EDAM_operation:3096 !{since=beta13} -name: Editing -namespace: operation -subset: operations -def: "Edit, convert or otherwise change a data entity, either randomly or specifically." [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation - - - -[Term] -id: EDAM_operation:2928 -name: Alignment construction -namespace: operation -subset: operations -def: "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." [http://edamontology.org] -synonym: "Alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:2951 ! Alignment processing -relationship: has_output EDAM_data:1916 !{min_cardinality=1} ! Alignment - -[Term] -id: EDAM_operation:2424 -name: Comparison -namespace: operation -subset: operations -def: "Compare two or more things to identify similarities." [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation - -[Term] -id: EDAM_operation:2997 -name: Protein comparison -namespace: operation -subset: operations -def: "Compare two or more proteins (or some aspect) to identify similarities." [http://edamontology.org] -is_a: EDAM_operation:2424 ! Comparison - -[Term] -id: EDAM_operation:2998 -name: Nucleic acid comparison -namespace: operation -subset: operations -def: "Compare two or more nucleic acids to identify similarities." [http://edamontology.org] -is_a: EDAM_operation:2424 ! Comparison - -[Term] -id: EDAM_operation:2990 -name: Classification -namespace: operation -subset: operations -def: "Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category." [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation -relationship: has_output EDAM_data:2987 !{min_cardinality=1} ! Classification - -[Term] -id: EDAM_operation:2995 -name: Sequence classification -namespace: operation -subset: operations -def: "Assign molecular sequence(s) to a group or category." [http://edamontology.org] -is_a: EDAM_operation:2990 ! Classification -is_a: EDAM_operation:2403 ! Sequence analysis - - -[Term] -id: EDAM_operation:3093 !{since=beta13} -name: Sequence screening -namespace: operation -subset: operations -def: "Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries." [http://edamontology.org] -is_a: EDAM_operation:2995 ! Sequence classification - - - - - -[Term] -id: EDAM_operation:2996 -name: Structure classification -namespace: operation -subset: operations -def: "Assign molecular structure(s) to a group or category." [http://edamontology.org] -is_a: EDAM_operation:2990 ! Classification -is_a: EDAM_operation:2480 ! Structure analysis - - -[Term] -id: EDAM_operation:2425 -name: Optimisation and refinement -namespace: operation -subset: operations -def: "Refine or optimise some data model." [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation - -[Term] -id: EDAM_operation:2426 -name: Modelling and simulation -namespace: operation -subset: operations -def: "Model or simulate some biological entity or system." [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation -relationship: has_topic EDAM_topic:2275 ! Molecular modelling - - -[Term] -id: EDAM_operation:2427 -name: Data handling -namespace: operation -subset: operations -def: "Perform basic operations on some data or a database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2420 ! Analysis and processing - - -[Term] -id: EDAM_operation:2428 -name: Evaluation and validation -namespace: operation -subset: operations -def: "Validate or standardise some data." [http://edamontology.org] -synonym: "Validation and standardisation" EXACT [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation - - -[Term] -id: EDAM_operation:2429 -name: Mapping and assembly -namespace: operation -subset: operations -def: "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." [http://edamontology.org] -comment: This is a broad concept and is used a placeholder for other, more specific concepts. -is_a: EDAM_operation:0004 ! Operation -relationship: has_topic EDAM_topic:0102 ! Mapping -relationship: has_topic EDAM_topic:0196 ! Sequence assembly - -[Term] -id: EDAM_operation:2430 -name: Design -namespace: operation -subset: operations -def: "Design a biological entity (typically a molecular sequence or structure) with specific properties." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) - - -[Term] -id: EDAM_operation:2238 -name: Statistical calculation -namespace: operation -subset: operations -def: "Perform a statistical data operation of some type, e.g. calibration or validation." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0004 ! Operation - -[Term] -id: EDAM_operation:0224 -name: Search and retrieval -namespace: operation -subset: operations -def: "Search or query a data resource and retrieve entries and / or annotation." [http://edamontology.org] -synonym: "Database retrieval" EXACT [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation -relationship: has_output EDAM_data:0006 !{min_cardinality=0} ! Data -relationship: has_topic EDAM_topic:0090 ! Data search and retrieval - -[Term] -id: EDAM_operation:2501 -name: Nucleic acid data processing -namespace: operation -subset: operations -def: "Process (read and / or write) nucleic acid sequence or structural data." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2084 !{min_cardinality=0} ! Nucleic acid report -relationship: has_output EDAM_data:2084 !{min_cardinality=0} ! Nucleic acid report -relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis - - -[Term] -id: EDAM_operation:2502 -name: Protein data processing -namespace: operation -subset: operations -def: "Process (read and / or write) protein sequence or structural data." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0896 !{min_cardinality=0} ! Protein report -relationship: has_output EDAM_data:0896 !{min_cardinality=0} ! Protein report -relationship: has_topic EDAM_topic:0078 ! Protein analysis - - -[Term] -id: EDAM_operation:2407 -name: Annotation processing -namespace: operation -subset: operations -def: "Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2422 ! Data retrieval - - -[Term] -id: EDAM_operation:2951 -name: Alignment processing -namespace: operation -subset: operations -def: "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:1916 !{min_cardinality=0} ! Alignment -relationship: has_output EDAM_data:1916 !{min_cardinality=0} ! Alignment - - - -[Term] -id: EDAM_operation:2412 -name: Data index processing -namespace: operation -subset: operations -def: "Process (read and / or write) an index of (typically a file of) biological data." [http://edamontology.org] -synonym: "Database index processing" EXACT [http://edamontology.org] -is_a: EDAM_operation:2409 ! File processing -relationship: has_input EDAM_data:0955 !{min_cardinality=0} ! Data index -relationship: has_output EDAM_data:0955 !{min_cardinality=0} ! Data index -relationship: has_topic EDAM_topic:0220 ! Data processing and validation - -[Term] -id: EDAM_operation:2504 -name: Structural data processing -namespace: operation -subset: operations -def: "Process (read and / or write) molecular structural data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2465 ! Structure processing - - -[Term] -id: EDAM_operation:2403 -name: Sequence analysis -namespace: operation -subset: operations -! alt_id: EDAM_operation:2477 -def: "Analyse one or more known molecular sequences." [http://edamontology.org] -synonym: "Sequence analysis (general)" EXACT [http://edamontology.org] -is_a: EDAM_operation:2446 ! Sequence processing -relationship: has_input EDAM_data:2044 !{min_cardinality=1} ! Sequence -relationship: has_output EDAM_data:2955 !{min_cardinality=1} ! Sequence report -relationship: has_topic EDAM_topic:0080 ! Sequence analysis - -[Term] -id: EDAM_operation:2408 -name: Sequence feature analysis -namespace: operation -subset: operations -def: "Analyse features in molecular sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0253 ! Feature prediction - - -[Term] -id: EDAM_operation:2404 -name: Sequence motif processing -namespace: operation -subset: operations -def: "Process (read and / or write) molecular sequence motifs." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:1353 !{min_cardinality=0} ! Sequence motif -relationship: has_output EDAM_data:1353 !{min_cardinality=0} ! Sequence motif -relationship: has_topic EDAM_topic:0158 ! Sequence motifs - - -[Term] -id: EDAM_operation:2417 -name: Physicochemical property data processing -namespace: operation -subset: operations -def: "Process (read and / or write) data on the physicochemical property of a molecule." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2420 ! Analysis and processing - - -[Term] -id: EDAM_operation:2414 -name: Protein function analysis -namespace: operation -subset: operations -def: "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." [http://edamontology.org] -comment: This is a broad concept and is used a placeholder for other, more specific concepts. -is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_output EDAM_data:0896 ! Protein report - -[Term] -id: EDAM_operation:0258 -name: Sequence alignment analysis -namespace: operation -subset: operations -def: "Analyse a molecular sequence alignment." [http://edamontology.org] -is_a: EDAM_operation:2463 ! Sequence alignment processing -is_a: EDAM_operation:2946 ! Alignment analysis -relationship: has_input EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment ! Extends cardinality constraint on parent. -relationship: has_output EDAM_data:0867 !{min_cardinality=1} ! Sequence alignment report -relationship: has_topic EDAM_topic:0182 ! Sequence alignment - - -[Term] -id: EDAM_operation:2506 -name: Sequence alignment analysis (protein) -namespace: operation -subset: operations -def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org] -is_a: EDAM_operation:0258 ! Sequence alignment analysis -is_a: EDAM_operation:2502 ! Protein data processing -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_input EDAM_data:1384 !{min_cardinality=1} ! Sequence alignment (protein) -relationship: has_topic EDAM_topic:0741 ! Protein sequence alignment - -[Term] -id: EDAM_operation:2507 -name: Sequence alignment analysis (nucleic acid) -namespace: operation -subset: operations -def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org] -is_a: EDAM_operation:0258 ! Sequence alignment analysis -is_a: EDAM_operation:2501 ! Nucleic acid data processing -is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_input EDAM_data:1383 !{min_cardinality=1} ! Sequence alignment (nucleic acid) -relationship: has_topic EDAM_topic:0740 ! Nucleic acid sequence alignment - -[Term] -id: EDAM_operation:2416 -name: Protein secondary structure analysis -namespace: operation -subset: operations -def: "Analyse known protein secondary structure data." [http://edamontology.org] -is_a: EDAM_operation:2444 ! Protein secondary structure processing -synonym: "Secondary structure analysis (protein)" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:0876 !{min_cardinality=1} ! Protein features (secondary structure) -relationship: has_output EDAM_data:2956 ! Protein secondary structure report -relationship: has_topic EDAM_topic:0694 ! Protein secondary structure - - -[Term] -id: EDAM_operation:0270 -name: Transmembrane protein analysis -namespace: operation -subset: operations -def: "Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions." [http://edamontology.org] -comment: Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). -is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) -relationship: has_topic EDAM_topic:0820 ! Membrane proteins - - -[Term] -id: EDAM_operation:2476 -name: Molecular dynamics simulation -namespace: operation -subset: operations -def: "Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org] -is_a: EDAM_operation:2423 ! Prediction, detection and recognition -is_a: EDAM_operation:2480 ! Structure analysis -is_a: EDAM_operation:2426 ! Modelling and simulation -relationship: has_output EDAM_data:0883 ! Structure -relationship: has_topic EDAM_topic:0082 ! Structure prediction -relationship: has_topic EDAM_topic:0176 ! Molecular dynamics - - -[Term] -id: EDAM_operation:0271 -name: Structure prediction -namespace: operation -subset: operations -def: "Predict tertiary structure of a molecular (biopolymer) sequence." [http://edamontology.org] -is_a: EDAM_operation:2423 ! Prediction, detection and recognition -is_a: EDAM_operation:2465 ! Structure processing -relationship: has_output EDAM_data:0883 ! Structure -relationship: has_topic EDAM_topic:0082 ! Structure prediction - - -[Term] -id: EDAM_operation:2405 -name: Protein interaction data processing -namespace: operation -subset: operations -def: "Process (read and / or write) protein interaction data." [http://edamontology.org] -is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_input EDAM_data:0906 !{min_cardinality=0} ! Protein interaction -relationship: has_output EDAM_data:0906 !{min_cardinality=0} ! Protein interaction -relationship: has_topic EDAM_topic:0128 ! Protein interactions - -[Term] -id: EDAM_operation:2521 -name: Map data processing -namespace: operation -subset: operations -def: "Process (read and / or write) a DNA map of some type." [http://edamontology.org] -synonym: "DNA map data processing" EXACT [http://edamontology.org] -is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:1274 !{min_cardinality=0} ! Map -relationship: has_output EDAM_data:1274 !{min_cardinality=0} ! Map -relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage - - - -[Term] -id: EDAM_operation:3229 !{since=1.1} -name: Exome analysis -namespace: operation -subset: operations -def: "Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome." [http://edamontology.org] -comment: Exome sequencing is considered a cheap alternative to whole genome sequencing. -synonym: "Exome sequence analysis" EXACT [http://edamontology.org] -synonym: "Targeted exome capture" EXACT [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis - - -[Term] -id: EDAM_operation:3230 !{since=1.1} -name: Read depth analysis -namespace: operation -subset: operations -def: "Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications." [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis - - -[Term] -id: EDAM_operation:3225 !{since=1.1} -name: Variant classification -namespace: operation -subset: operations -def: "Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins." [http://edamontology.org] -comment: Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -is_a: EDAM_operation:2995 ! Sequence classification - -[Term] -id: EDAM_operation:3226 !{since=1.1} -name: Variant prioritization -namespace: operation -subset: operations -def: "Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes." [http://edamontology.org] -comment: Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis - -[Term] -id: EDAM_operation:3221 !{since=1.1} -name: Species frequency estimation -namespace: operation -subset: operations -def: "Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples." [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -relationship: has_topic EDAM_topic:3174 ! Metagenomics - - - -[Term] -id: EDAM_operation:3216 !{since=1.1} -name: Scaffolding -namespace: operation -subset: operations -def: "Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps." [http://edamontology.org] -comment: Scaffold may be positioned along a chromosome physical map to create a "golden path". -synonym: "Scaffold construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:2429 ! Mapping and assembly -is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis - -[Term] -id: EDAM_operation:3217 !{since=1.1} -name: Scaffold gap completion -namespace: operation -subset: operations -def: "Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences." [http://edamontology.org] -comment: Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. -is_a: EDAM_operation:2429 ! Mapping and assembly -is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis - - - -[Term] -id: EDAM_operation:3218 !{since=1.1} -name: Sequencing quality control -namespace: operation -subset: operations -def: "Raw sequence data quality control." [http://edamontology.org] -synonym: "Sequencing QC" EXACT [http://edamontology.org] -synonym: "Analyse raw sequence data from a sequencing pipeline and identify problems." EXACT [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -is_a: EDAM_operation:2428 ! Evaluation and validation - - -[Term] -id: EDAM_operation:2520 -name: DNA mapping -namespace: operation -subset: operations -def: "Generate a map of a DNA sequence annotated with positional or non-positional features of some type." [http://edamontology.org] -is_a: EDAM_operation:2521 ! Map data processing -is_a: EDAM_operation:2429 ! Mapping and assembly -relationship: has_output EDAM_data:1274 !{min_cardinality=1} ! Map -relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage - -[Term] -id: EDAM_operation:0282 -name: Genetic mapping -namespace: operation -subset: operations -def: "Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances." [http://edamontology.org] -comment: Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. -synonym: "Genetic map generation" EXACT [http://edamontology.org] -synonym: "Linkage mapping" EXACT [http://edamontology.org] -is_a: EDAM_operation:2520 ! DNA mapping -relationship: has_output EDAM_data:1278 !{min_cardinality=1} ! Genetic map -relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage - - -[Term] -id: EDAM_operation:2944 -name: Physical mapping -namespace: operation -subset: operations -def: "Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers." [http://edamontology.org] -is_a: EDAM_operation:2520 ! DNA mapping -relationship: has_output EDAM_data:1280 !{min_cardinality=1} ! Physical map -relationship: has_topic EDAM_topic:0102 ! Mapping - - -[Term] -id: EDAM_operation:2871 -name: Sequence tagged site (STS) mapping -namespace: operation -subset: operations -def: "Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS)." [http://edamontology.org] -comment: An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. -synonym: "Sequence mapping" EXACT [http://edamontology.org] -is_a: EDAM_operation:2944 ! Physical mapping -relationship: has_output EDAM_data:1279 !{min_cardinality=1} ! Sequence map - - - -[Term] -id: EDAM_operation:3233 !{since=1.1} -name: Copy number estimation -namespace: operation -subset: operations -def: "Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors." [http://edamontology.org] -comment: Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). -synonym: "Transcript copy number estimation" EXACT [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis - -[Term] -id: EDAM_operation:3219 !{since=1.1} -name: Read pre-processing -namespace: operation -subset: operations -def: "Pre-process sequence reads to ensure (or improve) quality and reliability." [http://edamontology.org] -comment: This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. -synonym: "Sequence read pre-processing" EXACT [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis - - -[Term] -id: EDAM_operation:0283 -name: Linkage analysis -namespace: operation -subset: operations -def: "Analyse genetic linkage." [http://edamontology.org] -comment: For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -relationship: has_output EDAM_data:0927 ! Gene annotation (linkage) -relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage - -[Term] -id: EDAM_operation:2493 -name: Codon usage data processing -namespace: operation -subset: operations -def: "Process (read and / or write) codon usage data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:0286 ! Codon usage analysis - - - -[Term] -id: EDAM_operation:2503 -name: Sequence data processing -namespace: operation -subset: operations -def: "Process (read and / or write) molecular sequence data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2446 ! Sequence processing - - -[Term] -id: EDAM_operation:2463 -name: Sequence alignment processing -namespace: operation -subset: operations -def: "Process (read and / or write) a molecular sequence alignment." [http://edamontology.org] -is_a: EDAM_operation:2951 ! Alignment processing -relationship: has_input EDAM_data:0863 !{min_cardinality=0} ! Sequence alignment -relationship: has_output EDAM_data:0863 !{min_cardinality=0} ! Sequence alignment -relationship: has_topic EDAM_topic:0182 ! Sequence alignment - -[Term] -id: EDAM_operation:2952 -name: Structure alignment processing -namespace: operation -subset: operations -def: "Process (read and / or write) a molecular tertiary (3D) structure alignment." [http://edamontology.org] -is_a: EDAM_operation:2951 ! Alignment processing -relationship: has_input EDAM_data:0886 !{min_cardinality=0} ! Structure alignment -relationship: has_output EDAM_data:0886 !{min_cardinality=0} ! Structure alignment -relationship: has_topic EDAM_topic:0183 ! Structure alignment - - -[Term] -id: EDAM_operation:0292 -name: Sequence alignment construction -namespace: operation -subset: operations -def: "Align (identify equivalent sites within) molecular sequences." [http://edamontology.org] -synonym: "Sequence alignment" EXACT [http://edamontology.org] -synonym: "Sequence alignment computation" EXACT [http://edamontology.org] -synonym: "Sequence alignment generation" EXACT [http://edamontology.org] -is_a: EDAM_operation:2463 ! Sequence alignment processing !(?) -is_a: EDAM_operation:2451 ! Sequence comparison -is_a: EDAM_operation:2928 ! Alignment construction -relationship: has_input EDAM_data:2044 !{minCardinality=2, note="Applies to both pure/raw sequences and sequence records. Indirectly also to sequence sets or IDs (?)"} ! Sequence -relationship: has_output EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment -relationship: has_topic EDAM_topic:0182 ! Sequence alignment - -[Term] -id: EDAM_operation:0293 -name: Hybrid sequence alignment construction -namespace: operation -subset: operations -def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [http://edamontology.org] -synonym: "Hybrid sequence alignment" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:0292 ! Sequence alignment construction - -[Term] -id: EDAM_operation:0294 -name: Structure-based sequence alignment construction -namespace: operation -subset: operations -def: "Align molecular sequences using sequence and structural information." [http://edamontology.org] -synonym: "Structure-based sequence alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:0292 ! Sequence alignment construction -relationship: has_topic EDAM_topic:0182 ! Sequence alignment - - - -[Term] -id: EDAM_operation:2480 -name: Structure analysis -namespace: operation -subset: operations -! alt_id: EDAM_operation:2431 -def: "Analyse known molecular tertiary structures." [http://edamontology.org] -is_a: EDAM_operation:2465 ! Structure processing -relationship: has_input EDAM_data:0883 !{min_cardinality=1} ! Structure -relationship: has_output EDAM_data:2085 !{min_cardinality=1} ! Structure report -relationship: has_topic EDAM_topic:0081 ! Structure analysis - -[Term] -id: EDAM_operation:2931 -name: Secondary structure comparison -namespace: operation -subset: operations -def: "Compare two or more molecular secondary structures." [http://edamontology.org] -is_a: EDAM_operation:2424 ! Comparison -relationship: has_input EDAM_data:2081 !{min_cardinality=2} ! Secondary structure -relationship: has_output EDAM_data:2881 !{min_cardinality=1} ! Secondary structure report -relationship: has_topic EDAM_topic:1770 ! Structure comparison - -[Term] -id: EDAM_operation:2483 -name: Structure comparison -namespace: operation -subset: operations -def: "Compare two or more molecular tertiary structures." [http://edamontology.org] -is_a: EDAM_operation:2424 ! Comparison -is_a: EDAM_operation:2480 ! Structure analysis -relationship: has_topic EDAM_topic:1770 ! Structure comparison - - -[Term] -id: EDAM_operation:0295 -name: Structure alignment construction -namespace: operation -subset: operations -def: "Align (superimpose) molecular tertiary structures." [http://edamontology.org] -synonym: "Structure alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:2928 ! Alignment construction -is_a: EDAM_operation:2483 ! Structure comparison -is_a: EDAM_operation:2952 ! Structure alignment processing -relationship: has_output EDAM_data:0886 !{min_cardinality=1} ! Structure alignment -relationship: has_topic EDAM_topic:0183 ! Structure alignment - -[Term] -id: EDAM_operation:2413 -name: Sequence profile processing -namespace: operation -subset: operations -def: "Process (read and / or write) some type of sequence profile." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:1354 !{min_cardinality=0} ! Sequence profile -relationship: has_output EDAM_data:1354 !{min_cardinality=0} ! Sequence profile -relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs - -[Term] -id: EDAM_operation:2411 -name: Structural (3D) profile processing -namespace: operation -subset: operations -def: "Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0889 !{min_cardinality=0} ! Structural (3D) profile -relationship: has_output EDAM_data:0889 !{min_cardinality=0} ! Structural (3D) profile -relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles - - -[Term] -id: EDAM_operation:0303 -name: Protein fold recognition -namespace: operation -subset: operations -def: "Recognize (predict and identify) known protein structural domains or folds in protein sequence(s)." [http://edamontology.org] -comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. -synonym: "Protein domain prediction" EXACT [http://edamontology.org] -synonym: "Protein fold prediction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) -is_a: EDAM_operation:0474 ! Protein structure prediction -is_a: EDAM_operation:2997 ! Protein comparison -relationship: has_output EDAM_data:0901 !{min_cardinality=1} ! Protein features (domains) -relationship: has_topic EDAM_topic:0184 ! Threading - -[Term] -id: EDAM_operation:2246 -name: Demonstration -namespace: operation -subset: operations -def: "An operation performing purely illustrative (pedagogical) purposes." [http://edamontology.org] -is_obsolete: true !{since=beta13} - -[Term] -id: EDAM_operation:2505 -name: Text processing -namespace: operation -subset: operations -def: "Process (read and / or write) text." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2048 !{min_cardinality=0} ! Report -relationship: has_output EDAM_data:2048 !{min_cardinality=0} ! Report - -[Term] -id: EDAM_operation:0306 -name: Text mining -namespace: operation -subset: operations -def: "Process and analyse text (typically the biomedical and informatics literature) to extract information from it." [http://edamontology.org] -synonym: "Text data mining" EXACT [http://edamontology.org] -is_a: EDAM_operation:2947 ! Article analysis -relationship: has_input EDAM_data:2048 !{min_cardinality=0} ! Report -relationship: has_output EDAM_data:0972 ! Text mining report -relationship: has_topic EDAM_topic:0218 ! Text mining - -[Term] -id: EDAM_operation:2419 -name: Primer and probe design -namespace: operation -subset: operations -def: "Predict oligonucleotide primers or probes." [http://edamontology.org] -is_a: EDAM_operation:3095 ! Nucleic acid design -is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) -synonym: "Primer and probe prediction" EXACT [http://edamontology.org] -relationship: has_topic EDAM_topic:3032 ! Primer or probe design - -[Term] -id: EDAM_operation:0310 -name: Sequence assembly -namespace: operation -subset: operations -def: "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] -comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. -is_a: EDAM_operation:2429 ! Mapping and assembly -is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -relationship: has_output EDAM_data:0925 ! Sequence assembly -relationship: has_topic EDAM_topic:0196 ! Sequence assembly - -[Term] -id: EDAM_operation:3180 !{since=1.1} -name: Sequence assembly evaluation -namespace: operation -subset: operations -def: "Evaluate a DNA sequence assembly, typically for purposes of quality control." [http://edamontology.org] -is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -is_a: EDAM_operation:2425 ! Optimisation and refinement -relationship: has_input EDAM_data:0925 ! Sequence assembly -relationship: has_output EDAM_data:3181 ! Sequence assembly report -relationship: has_topic EDAM_topic:0196 ! Sequence assembly - - -[Term] -id: EDAM_operation:2432 -name: Microarray data processing -namespace: operation -subset: operations -def: "Process (read and / or write) microarray data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2495 ! Gene expression data processing - -[Term] -id: EDAM_operation:2495 -name: Gene expression data processing -namespace: operation -subset: operations -def: "Process (read and / or write) gene expression (typically microarray) data." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -synonym: "Gene expression (microarray) data processing" EXACT [http://edamontology.org] -synonym: "Microarray data processing" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:3117 !{min_cardinality=0} ! Microarray hybridisation data -relationship: has_output EDAM_data:3117 !{min_cardinality=0} ! Microarray hybridisation data -relationship: has_topic EDAM_topic:0203 ! Transcriptomics -relationship: has_topic EDAM_topic:0200 ! Microarrays - - -[Term] -id: EDAM_operation:2500 -name: Microarray raw data analysis -namespace: operation -subset: operations -def: "Analyse raw microarray data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2495 ! Gene expression data processing - -[Term] -id: EDAM_operation:0311 -name: Microarray data standardization and normalization -namespace: operation -subset: operations -def: "Standardize or normalize microarray data." [http://edamontology.org] -comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. -is_a: EDAM_operation:2495 ! Gene expression data processing -is_a: EDAM_operation:2428 ! Evaluation and validation -relationship: has_input EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data -relationship: has_output EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data - -[Term] -id: EDAM_operation:0318 -name: Structural genomics target selection -namespace: operation -subset: operations -def: "Identify and select targets for protein structural determination." [http://edamontology.org] -comment: Methods will typically navigate a graph of protein families of known structure. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2406 ! Protein structure analysis - -[Term] -id: EDAM_operation:2406 -name: Protein structure analysis -namespace: operation -subset: operations -! alt_id: EDAM_operation:2458 -def: "Analyse protein tertiary structural data." [http://edamontology.org] -is_a: EDAM_operation:2480 ! Structure analysis -is_a: EDAM_operation:2459 ! Structure processing (protein) -synonym: "Structure analysis (protein)" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:1460 !{min_cardinality=1} ! Protein structure -relationship: has_output EDAM_data:0897 ! Protein property - - -[Term] -id: EDAM_operation:2481 -name: Nucleic acid structure analysis -namespace: operation -subset: operations -! alt_id: EDAM_operation:2418 -def: "Analyse nucleic acid tertiary structural data." [http://edamontology.org] -is_a: EDAM_operation:2480 ! Structure analysis -is_a: EDAM_operation:2519 ! Structure processing (nucleic acid) -relationship: has_input EDAM_data:1459 !{min_cardinality=1} ! Nucleic acid structure -relationship: has_output EDAM_data:0912 !{min_cardinality=1} ! Nucleic acid property - -[Term] -id: EDAM_operation:0324 -name: Phylogenetic tree analysis -namespace: operation -subset: operations -def: "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." [http://edamontology.org] -is_a: EDAM_operation:2443 ! Phylogenetic tree processing -relationship: has_input EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree -relationship: has_output EDAM_data:1438 !{min_cardinality=1} ! Phylogenetic tree report - -[Term] -id: EDAM_operation:2438 -name: Pathway or network processing -namespace: operation -subset: operations -def: "Generate, analyse or handle a biological pathway or network." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2600 !{min_cardinality=0} ! Pathway or network -relationship: has_output EDAM_data:2600 !{min_cardinality=0} ! Pathway or network -relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models - -[Term] -id: EDAM_operation:3083 !{since=beta13} -name: Pathway or network rendering -namespace: operation -subset: operations -def: "Render (visualise) a biological pathway or network." [http://edamontology.org] -is_a: EDAM_operation:2438 ! Pathway or network processing -is_a: EDAM_operation:0337 ! Plotting and rendering -relationship: has_input EDAM_data:2600 !{min_cardinality=1} ! Pathway or network -relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models - - -[Term] -id: EDAM_operation:3203 !{since=1.1} -name: Chromatogram visualisation -namespace: operation -subset: operations -def: "Visualise, format or render an image of a Chromatogram." [http://edamontology.org] -synonym: "Chromatogram viewing" EXACT [http://edamontology.org] -is_a: EDAM_operation:0337 ! Plotting and rendering - - - - -[Term] -id: EDAM_operation:2497 -name: Pathway or network analysis -namespace: operation -subset: operations -def: "Analyse a known biological pathway or network." [http://edamontology.org] -synonym: "Network analysis" EXACT [http://edamontology.org] -synonym: "Pathway analysis" EXACT [http://edamontology.org] -is_a: EDAM_operation:2438 ! Pathway or network processing -relationship: has_input EDAM_data:2600 !{min_cardinality=1} ! Pathway or network -relationship: has_output EDAM_data:2984 !{min_cardinality=1} ! Pathway or network report - -[Term] -id: EDAM_operation:2415 -name: Protein folding analysis -namespace: operation -subset: operations -def: "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." [http://edamontology.org] -comment: This is a broad concept and is used a placeholder for other, more specific concepts. -synonym: "Protein folding modelling" EXACT [http://edamontology.org] -is_a: EDAM_operation:2502 ! Protein data processing -is_a: EDAM_operation:2426 ! Modelling and simulation -relationship: has_output EDAM_data:0903 !{min_cardinality=1} ! Protein folding report -relationship: has_topic EDAM_topic:0130 ! Protein folding and stability - - -[Term] -id: EDAM_operation:0331 -name: Protein modelling (mutation) -namespace: operation -subset: operations -def: "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function." [http://edamontology.org] -comment: Methods might predict silent or pathological mutations. -is_a: EDAM_operation:0477 ! Protein modelling -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -synonym: "Protein mutation modelling" EXACT [http://edamontology.org] -relationship: has_topic EDAM_topic:0130 ! Protein folding and stability -relationship: has_topic EDAM_topic:0199 ! Genetic variation - -[Term] -id: EDAM_operation:0332 -name: Immunogen design -namespace: operation -subset: operations -def: "Design molecules that elicit an immune response (immunogens)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0559 ! Peptide immunogen prediction and optimisation - - -[Term] -id: EDAM_operation:2409 -name: File processing -namespace: operation -subset: operations -def: "Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations." [http://edamontology.org] -synonym: "Report handling" EXACT [http://edamontology.org] -synonym: "File handling" EXACT [http://edamontology.org] -synonym: "Data file processing" EXACT [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0006 !{min_cardinality=0} ! Data -relationship: has_output EDAM_data:0006 !{min_cardinality=0} ! Data -relationship: has_topic EDAM_topic:0220 ! Data processing and validation - - -[Term] -id: EDAM_operation:0337 -name: Plotting and rendering -namespace: operation -subset: operations -def: "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." [http://edamontology.org] -synonym: "Visualisation" EXACT [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation -relationship: has_input EDAM_data:0006 !{min_cardinality=1} ! Data -relationship: has_output EDAM_data:2968 !{min_cardinality=0} ! Image -relationship: has_topic EDAM_topic:0092 ! Data visualisation - - -[Term] -id: EDAM_operation:2121 -name: Sequence file processing -namespace: operation -subset: operations -def: "Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences." [http://edamontology.org] -is_a: EDAM_operation:2446 ! Sequence processing -is_a: EDAM_operation:2409 ! File processing - -[Term] -id: EDAM_operation:3081 !{since=beta13} -name: Sequence alignment editing -namespace: operation -subset: operations -def: "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." [http://edamontology.org] -is_a: EDAM_operation:2122 ! Sequence alignment file processing -is_a: EDAM_operation:3096 ! Editing - -[Term] -id: EDAM_operation:2122 -name: Sequence alignment file processing -namespace: operation -subset: operations -def: "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." [http://edamontology.org] -is_a: EDAM_operation:2409 ! File processing -is_a: EDAM_operation:2463 ! Sequence alignment processing -relationship: has_input EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment -relationship: has_output EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment - - - - - -[Term] -id: EDAM_operation:3080 !{since=beta13} -name: Structure editing -namespace: operation -subset: operations -def: "Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically." [http://edamontology.org] -is_a: EDAM_operation:2234 ! Structure file processing -is_a: EDAM_operation:3096 ! Editing -relationship: has_input EDAM_data:0883 !{min_cardinality=1} ! Structure - -[Term] -id: EDAM_operation:2234 -name: Structure file processing -namespace: operation -subset: operations -def: "Perform basic (non-analytical) operations on a file of molecular tertiary structural data." [http://edamontology.org] -is_a: EDAM_operation:2409 ! File processing -is_a: EDAM_operation:2465 ! Structure processing - - - -[Term] -id: EDAM_operation:2120 -name: Listfile processing -namespace: operation -subset: operations -def: "Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses)." [http://edamontology.org] -is_a: EDAM_operation:2409 ! File processing -relationship: has_input EDAM_data:1111 ! EMBOSS listfile -relationship: has_output EDAM_data:1111 ! EMBOSS listfile - - -[Term] -id: EDAM_operation:1812 -name: Data loading -namespace: operation -subset: operations -def: "Prepare or load a user-specified data file so that it is available for use." [http://edamontology.org] -synonym: "Database submission" EXACT [http://edamontology.org] -synonym: "Data submission" EXACT [http://edamontology.org] -xref: WHATIF:UploadPDB -is_a: EDAM_operation:2409 ! File processing -relationship: has_input EDAM_data:0842 !{min_cardinality=1} ! Identifier - -[Term] -id: EDAM_operation:0335 -name: File reformatting -namespace: operation -subset: operations -def: "Reformat a file of data (or equivalent entity in memory)." [http://edamontology.org] -is_a: EDAM_operation:2409 ! File processing - - -[Term] -id: EDAM_operation:0336 -name: File validation -namespace: operation -subset: operations -def: "Test and validate the format and content of a data file." [http://edamontology.org] -is_a: EDAM_operation:2409 ! File processing -is_a: EDAM_operation:2428 ! Evaluation and validation - - -[Term] -id: EDAM_operation:2421 -name: Database search -namespace: operation -subset: operations -def: "Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query." [http://edamontology.org] -comment: Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. -is_a: EDAM_operation:0224 ! Search and retrieval -is_a: EDAM_operation:2424 ! Comparison -relationship: has_output EDAM_data:2080 !{min_cardinality=0} ! Database hits - -[Term] -id: EDAM_operation:2422 -name: Data retrieval -namespace: operation -subset: operations -def: "Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords." [http://edamontology.org] -synonym: "Information retrieval" BROAD [http://edamontology.org] -is_a: EDAM_operation:0224 ! Search and retrieval -relationship: has_input EDAM_data:0842 !{min_cardinality=1} ! Identifier - -[Term] -id: EDAM_operation:0343 -name: Transmembrane protein database search -namespace: operation -subset: operations -def: "Search a database of transmembrane proteins, for example for sequence or structural similarities." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2421 ! Database search - -[Term] -id: EDAM_operation:0304 -name: Data retrieval (metadata and documentation) -namespace: operation -subset: operations -def: "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described." [http://edamontology.org] -comment: This includes documentation, general information and other metadata on entities such as databases, database entries and tools. -synonym: "Data retrieval (documentation)" EXACT [http://edamontology.org] -synonym: "Data retrieval (metadata)" EXACT [http://edamontology.org] -relationship: has_output EDAM_data:2337 !{min_cardinality=1} ! Metadata -is_a: EDAM_operation:2422 ! Data retrieval - - -[Term] -id: EDAM_operation:0225 -name: Data retrieval (database cross-reference) -namespace: operation -subset: operations -def: "Search database to retrieve all relevant references to a particular entity or entry." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:1813 -name: Sequence retrieval -namespace: operation -subset: operations -def: "Query a sequence data resource (typically a database) and retrieve sequences and / or annotation." [http://edamontology.org] -comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. -synonym: "Data retrieval (sequences)" EXACT [http://edamontology.org] -is_a: EDAM_operation:2422 ! Data retrieval -is_a: EDAM_operation:2446 ! Sequence processing -relationship: has_output EDAM_data:2044 !{min_cardinality=0} ! Sequence - -[Term] -id: EDAM_operation:1814 -name: Structure retrieval -namespace: operation -subset: operations -def: "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation." [http://edamontology.org] -comment: This includes direct retrieval methods but not those that perform calculations on the sequence or structure. -xref: WHATIF:DownloadPDB -xref: WHATIF:EchoPDB -is_a: EDAM_operation:2422 ! Data retrieval -is_a: EDAM_operation:2465 ! Structure processing -relationship: has_output EDAM_data:0883 !{min_cardinality=0} ! Structure - - -[Term] -id: EDAM_operation:2237 -name: Data retrieval (sequence profile) -namespace: operation -subset: operations -def: "Query a profile data resource and retrieve one or more profile(s) and / or associated annotation." [http://edamontology.org] -comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - - -[Term] -id: EDAM_operation:2434 -name: Data retrieval (codon usage table) -namespace: operation -subset: operations -def: "Retrieve a codon usage table and / or associated annotation." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:2264 -name: Data retrieval (pathway or network) -namespace: operation -subset: operations -def: "Query a biological pathways database and retrieve annotation on one or more pathways." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - - -[Term] -id: EDAM_operation:2265 -name: Data retrieval (identifier) -namespace: operation -subset: operations -def: "Query a database and retrieve one or more data identifiers." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:2224 -name: Data retrieval (ontology concept) -namespace: operation -subset: operations -def: "Query an ontology and retrieve concepts or relations." [http://edamontology.org] -synonym: "Ontology retrieval" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:2222 -name: Data retrieval (ontology annotation) -namespace: operation -subset: operations -def: "Search and retrieve documentation on a bioinformatics ontology." [http://edamontology.org] -synonym: "Ontology information retrieval" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:2468 -name: Data retrieval (phylogenetic tree) -namespace: operation -subset: operations -def: "Retrieve a phylogenetic tree from a data resource." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:0257 -name: Data retrieval (sequence alignment) -namespace: operation -subset: operations -def: "Display basic information about a sequence alignment." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:2473 -name: Data retrieval (genotype and phenotype annotation) -namespace: operation -subset: operations -def: "Retrieve information on a specific genotype or phenotype." [http://edamontology.org] -synonym: "Genotype and phenotype information retrieval" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:2472 -name: Data retrieval (gene annotation) -namespace: operation -subset: operations -def: "Retrieve information on a specific gene." [http://edamontology.org] -synonym: "Gene information retrieval" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:2471 -name: Data retrieval (RNA family annotation) -namespace: operation -subset: operations -def: "Retrieve information on an RNA family." [http://edamontology.org] -synonym: "RNA family information retrieval" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - - -[Term] -id: EDAM_operation:2470 -name: Data retrieval (protein family annotation) -namespace: operation -subset: operations -def: "Retrieve information on a protein family." [http://edamontology.org] -synonym: "Protein family information retrieval" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:2469 -name: Data retrieval (protein interaction annotation) -namespace: operation -subset: operations -def: "Retrieve information on a protein interaction." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:2467 -name: Data retrieval (protein annotation) -namespace: operation -subset: operations -def: "Retrieve information on a protein." [http://edamontology.org] -synonym: "Protein information retrieval" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - -[Term] -id: EDAM_operation:0280 -name: Data retrieval (restriction enzyme annotation) -namespace: operation -subset: operations -def: "Retrieve information on restriction enzymes or restriction enzyme sites." [http://edamontology.org] -synonym: "Restriction enzyme information retrieval" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - - -[Term] -id: EDAM_operation:0515 -name: Data retrieval (tool metadata) -namespace: operation -subset: operations -def: "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." [http://edamontology.org] -synonym: "Tool information retrieval" EXACT [http://edamontology.org] -synonym: "Data retrieval (tool annotation)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) -relationship: has_output EDAM_data:0958 !{min_cardinality=0} ! Tool metadata - - -[Term] -id: EDAM_operation:0516 -name: Data retrieval (database metadata) -namespace: operation -subset: operations -def: "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." [http://edamontology.org] -synonym: "Database information retrieval" EXACT [http://edamontology.org] -synonym: "Data retrieval (database annotation)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) -relationship: has_output EDAM_data:0957 !{min_cardinality=0} ! Database metadata - - -[Term] -id: EDAM_operation:0344 -name: Sequence retrieval (by code) -namespace: operation -subset: operations -def: "Query a database and retrieve sequences with a given entry code or accession number." [http://edamontology.org] -is_a: EDAM_operation:1813 ! Sequence retrieval - -[Term] -id: EDAM_operation:0345 -name: Sequence retrieval (by keyword) -namespace: operation -subset: operations -def: "Query a database and retrieve sequences containing a given keyword." [http://edamontology.org] -is_a: EDAM_operation:1813 ! Sequence retrieval - - -[Term] -id: EDAM_operation:1845 -name: PDB file sequence retrieval -namespace: operation -subset: operations -def: "Extract a molecular sequence from a PDB file." [http://edamontology.org, WHATIF] -xref: WHATIF: PDB_sequence -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0344 ! Sequence retrieval (by code) - -[Term] -id: EDAM_operation:0305 -name: Literature search -namespace: operation -subset: operations -def: "Query the biomedical and informatics literature." [http://edamontology.org] -is_a: EDAM_operation:2421 ! Database search -relationship: has_output EDAM_data:0970 !{min_cardinality=0} ! Bibliographic reference -relationship: has_topic EDAM_topic:0217 ! Literature analysis - -[Term] -id: EDAM_operation:0338 -name: Sequence database search -namespace: operation -subset: operations -def: "Search a sequence database by sequence comparison and retrieve similar sequences." [http://edamontology.org] -comment: This excludes direct retrieval methods (e.g. the dbfetch program). -is_a: EDAM_operation:2421 ! Database search -is_a: EDAM_operation:2403 ! Sequence analysis -relationship: has_output EDAM_data:0857 !{min_cardinality=0} ! Database hits (sequence) -relationship: has_topic EDAM_topic:0159 ! Sequence comparison - - -[Term] -id: EDAM_operation:0339 -name: Structure database search -namespace: operation -subset: operations -def: "Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data." [http://edamontology.org] -is_a: EDAM_operation:2421 ! Database search -is_a: EDAM_operation:2996 ! Structure classification -relationship: has_output EDAM_data:0885 !{min_cardinality=0} ! Database hits (structure) -relationship: has_topic EDAM_topic:0081 ! Structure analysis - -[Term] -id: EDAM_operation:0340 -name: Protein secondary database search -namespace: operation -subset: operations -def: "Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group." [http://edamontology.org] -comment: Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). -synonym: "Protein sequence classification" EXACT [http://edamontology.org] -is_a: EDAM_operation:2421 ! Database search -is_a: EDAM_operation:3093 ! Sequence screening -relationship: has_output EDAM_data:0858 !{min_cardinality=0} ! Database hits (secondary) -relationship: has_topic EDAM_topic:0595 ! Protein classification - -[Term] -id: EDAM_operation:0341 -name: Motif database search -namespace: operation -subset: operations -def: "Screen a sequence against a motif or pattern database." [http://edamontology.org] -is_a: EDAM_operation:2421 ! Database search -is_a: EDAM_operation:0239 ! Sequence motif recognition -is_a: EDAM_operation:3093 ! Sequence screening -relationship: has_output EDAM_data:1298 !{min_cardinality=0} ! Sequence features (motifs) -relationship: has_topic EDAM_topic:0158 ! Sequence motifs - -[Term] -id: EDAM_operation:0342 -name: Sequence profile database search -namespace: operation -subset: operations -def: "Search a database of sequence profiles with a query sequence." [http://edamontology.org] -is_a: EDAM_operation:2421 ! Database search -is_a: EDAM_operation:0300 ! Sequence-profile alignment construction -is_a: EDAM_operation:3093 ! Sequence screening -relationship: has_output EDAM_data:1298 ! Sequence features (motifs) - -[Term] -id: EDAM_operation:0346 -name: Sequence database search (by sequence) -namespace: operation -subset: operations -def: "Search a sequence database and retrieve sequences that are similar to a query sequence." [http://edamontology.org] -synonym: "Sequence similarity search" EXACT [http://edamontology.org] -is_a: EDAM_operation:0338 ! Sequence database search -is_a: EDAM_operation:3093 ! Sequence screening -is_a: EDAM_operation:2451 ! Sequence comparison - - - -[Term] -id: EDAM_operation:0347 -name: Sequence database search (by motif or pattern) -namespace: operation -subset: operations -def: "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." [http://edamontology.org] -is_a: EDAM_operation:0338 ! Sequence database search -is_a: EDAM_operation:0239 ! Sequence motif recognition -relationship: has_input EDAM_data:1353 !{min_cardinality=1} ! Sequence motif -relationship: has_topic EDAM_topic:0158 ! Sequence motifs - - -[Term] -id: EDAM_operation:0348 -name: Sequence database search (by amino acid composition) -namespace: operation -subset: operations -def: "Search a sequence database and retrieve sequences of a given amino acid composition." [http://edamontology.org] -is_a: EDAM_operation:0338 ! Sequence database search -relationship: has_input EDAM_data:1267 ! Amino acid frequencies -relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis - - -[Term] -id: EDAM_operation:0349 -name: Sequence database search (by physicochemical property) -namespace: operation -subset: operations -def: "Search a sequence database and retrieve sequences with a specified physicochemical property." [http://edamontology.org] -is_a: EDAM_operation:0338 ! Sequence database search - - -[Term] -id: EDAM_operation:0350 -name: Sequence database search (by sequence using word-based methods) -namespace: operation -subset: operations -def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method." [http://edamontology.org] -comment: Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. -synonym: "Sequence similarity search (word-based methods)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0346 ! Sequence database search (by sequence) -is_a: EDAM_operation:0288 ! Sequence word comparison - -[Term] -id: EDAM_operation:0351 -name: Sequence database search (by sequence using profile-based methods) -namespace: operation -subset: operations -def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query." [http://edamontology.org] -comment: This includes tools based on PSI-BLAST. -synonym: "Sequence similarity search (profile-based methods)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0346 ! Sequence database search (by sequence) -is_a: EDAM_operation:0300 ! Sequence-profile alignment construction - -[Term] -id: EDAM_operation:0352 -name: Sequence database search (by sequence using local alignment-based methods) -namespace: operation -subset: operations -def: "Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method." [http://edamontology.org] -comment: This includes tools based on the Smith-Waterman algorithm or FASTA. -synonym: "Sequence similarity search (local alignment-based methods) " EXACT [http://edamontology.org] -is_a: EDAM_operation:0346 ! Sequence database search (by sequence) -is_a: EDAM_operation:0493 ! Pairwise sequence alignment construction (local) -relationship: has_topic EDAM_topic:0182 ! Sequence alignment - -[Term] -id: EDAM_operation:0353 -name: Sequence database search (by sequence using global alignment-based methods) -namespace: operation -subset: operations -def: "Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method." [http://edamontology.org] -comment: This includes tools based on the Needleman and Wunsch algorithm. -synonym: "Sequence similarity search (global alignment-based methods)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0346 ! Sequence database search (by sequence) -is_a: EDAM_operation:0494 ! Pairwise sequence alignment construction (global) -relationship: has_topic EDAM_topic:0182 ! Sequence alignment - -[Term] -id: EDAM_operation:0354 -name: Sequence database search (by sequence for primer sequences) -namespace: operation -subset: operations -def: "Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences." [http://edamontology.org] -comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. -synonym: "Sequence similarity search (primer sequences)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0346 ! Sequence database search (by sequence) -relationship: has_topic EDAM_topic:3032 ! Primer or probe design - -[Term] -id: EDAM_operation:0355 -name: Sequence database search (by molecular weight) -namespace: operation -subset: operations -def: "Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry." [http://edamontology.org] -synonym: "Protein fingerprinting" EXACT [http://edamontology.org] -synonym: "Peptide mass fingerprinting" EXACT [http://edamontology.org] -is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property) -relationship: has_input EDAM_data:0944 ! Peptide mass fingerprint -relationship: has_topic EDAM_topic:0123 ! Protein properties -relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification - - -[Term] -id: EDAM_operation:0356 -name: Sequence database search (by isoelectric point) -namespace: operation -subset: operations -def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [http://edamontology.org] -is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property) -relationship: has_topic EDAM_topic:0123 ! Protein properties - -[Term] -id: EDAM_operation:0357 -name: Structure retrieval (by code) -namespace: operation -subset: operations -def: "Query a tertiary structure database and retrieve entries with a given entry code or accession number." [http://edamontology.org] -is_a: EDAM_operation:1814 ! Structure retrieval - -[Term] -id: EDAM_operation:0358 -name: Structure retrieval (by keyword) -namespace: operation -subset: operations -def: "Query a tertiary structure database and retrieve entries containing a given keyword." [http://edamontology.org] -is_a: EDAM_operation:1814 ! Structure retrieval - -[Term] -id: EDAM_operation:1914 -name: Structure retrieval (water) -namespace: operation -subset: operations -def: "Query a tertiary structure database and retrieve water molecules." [http://edamontology.org] -xref: WHATIF:MovedWaterPDB -is_a: EDAM_operation:1814 ! Structure retrieval - - -[Term] -id: EDAM_operation:0359 -name: Structure database search (by sequence) -namespace: operation -subset: operations -def: "Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence." [http://edamontology.org] -synonym: "Structure retrieval by sequence" EXACT [http://edamontology.org] -is_a: EDAM_operation:0339 ! Structure database search -is_a: EDAM_operation:2451 ! Sequence comparison -is_a: EDAM_operation:3093 ! Sequence screening - -[Term] -id: EDAM_operation:0360 -name: Structure database search (by structure) -namespace: operation -subset: operations -def: "Search a tertiary structure database and retrieve structures that are similar to a query structure." [http://edamontology.org] -synonym: "Structure retrieval by structure" EXACT [http://edamontology.org] -synonym: "Structural similarity search" EXACT [http://edamontology.org] -is_a: EDAM_operation:0339 ! Structure database search -relationship: has_topic EDAM_topic:1770 ! Structure comparison -relationship: has_topic EDAM_topic:1770 ! Structure comparison - -[Term] -id: EDAM_operation:0226 -name: Annotation -namespace: operation -subset: operations -def: "Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary." [http://edamontology.org] -comment: This is a broad concept and is used a placeholder for other, more specific concepts. -is_a: EDAM_operation:0004 ! Operation -relationship: has_input EDAM_data:0582 ! Ontology -relationship: has_topic EDAM_topic:0089 ! Ontology - - -[Term] -id: EDAM_operation:1774 -name: Annotation retrieval -namespace: operation -subset: operations -def: "Retrieve existing annotation (or documentation), typically annotation on a database entity." [http://edamontology.org] -comment: Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2422 ! Data retrieval - - -[Term] -id: EDAM_operation:0361 -name: Sequence annotation -namespace: operation -subset: operations -def: "Annotate a molecular sequence record with terms from a controlled vocabulary." [http://edamontology.org] -is_a: EDAM_operation:0226 ! Annotation -relationship: has_input EDAM_data:0849 !{min_cardinality=1} ! Sequence record -relationship: has_output EDAM_data:0849 !{min_cardinality=1} ! Sequence record - - -[Term] -id: EDAM_operation:0362 -name: Genome annotation -namespace: operation -subset: operations -def: "Annotate a genome sequence with terms from a controlled vocabulary." [http://edamontology.org] -is_a: EDAM_operation:0361 ! Sequence annotation - - -[Term] -id: EDAM_operation:2466 -name: Map annotation -namespace: operation -subset: operations -def: "Annotate a DNA map of some type with terms from a controlled vocabulary." [http://edamontology.org] -is_a: EDAM_operation:0226 ! Annotation -is_a: EDAM_operation:2521 ! Map data processing -relationship: has_input EDAM_data:1274 !{min_cardinality=1} ! Map -relationship: has_output EDAM_data:1274 !{min_cardinality=1} ! Map - - -[Term] -id: EDAM_operation:0227 -name: Data indexing -namespace: operation -subset: operations -def: "Generate an index of (typically a file of) biological data." [http://edamontology.org] -synonym: "Database indexing" EXACT [http://edamontology.org] -is_a: EDAM_operation:2412 ! Data index processing -relationship: has_output EDAM_data:0955 ! Data index - - -[Term] -id: EDAM_operation:3211 !{since=1.1} -name: Genome indexing -namespace: operation -subset: operations -def: "Generate an index of a genome sequence." [http://edamontology.org] -comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. -is_a: EDAM_operation:0227 ! Data indexing -relationship: has_output EDAM_data:3210 ! Genome index - -[Term] -id: EDAM_operation:3212 !{since=1.1} -name: Genome indexing (Burrows-Wheeler) -namespace: operation -subset: operations -def: "Generate an index of a genome sequence using the Burrows-Wheeler algorithm." [http://edamontology.org] -comment: The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. -synonym: "Burrows-Wheeler" EXACT [http://edamontology.org] -synonym: "Burrows Wheeler" EXACT [http://edamontology.org] -synonym: "Genome indexing (Burrows Wheeler)" EXACT [http://edamontology.org] -is_a: EDAM_operation:3211 ! Genome indexing - -[Term] -id: EDAM_operation:3213 !{since=1.1} -name: Genome indexing (suffix arrays) -namespace: operation -subset: operations -def: "Generate an index of a genome sequence using a suffix arrays algorithm." [http://edamontology.org] -comment: A suffix array consists of the lexicographically sorted list of suffixes of a genome. -synonym: "suffix arrays" EXACT [http://edamontology.org] -is_a: EDAM_operation:3211 ! Genome indexing - - - -[Term] -id: EDAM_operation:0228 -name: Data index analysis -namespace: operation -subset: operations -def: "Analyse an index of biological data." [http://edamontology.org] -is_a: EDAM_operation:2412 ! Data index processing -is_a: EDAM_operation:2412 ! Data index processing -synonym: "Database index analysis" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:0955 !{min_cardinality=1} ! Data index -relationship: has_output EDAM_data:0956 !{min_cardinality=1} ! Data index report - - -[Term] -id: EDAM_operation:2478 -name: Nucleic acid sequence analysis -namespace: operation -subset: operations -def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [http://edamontology.org] -synonym: "Sequence analysis (nucleic acid)" EXACT [http://edamontology.org] -is_a: EDAM_operation:2403 ! Sequence analysis -is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) -relationship: has_input EDAM_data:2977 !{min_cardinality=1} ! Nucleic acid sequence -relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis - - -[Term] -id: EDAM_operation:3095 !{since=beta13} -name: Nucleic acid design -namespace: operation -subset: operations -def: "Design (or predict) nucleic acid sequences with specific chemical or physical properties." [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis - - - - - -[Term] -id: EDAM_operation:2479 -name: Protein sequence analysis -namespace: operation -subset: operations -def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [http://edamontology.org] -synonym: "Sequence analysis (protein)" EXACT [http://edamontology.org] -is_a: EDAM_operation:2403 ! Sequence analysis -is_a: EDAM_operation:2447 ! Sequence processing (protein) -synonym: "Sequence analysis (protein)" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:2976 !{min_cardinality=1} ! Protein sequence -relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis - - - -[Term] -id: EDAM_operation:3214 !{since=1.1} -name: Spectrum analysis -namespace: operation -subset: operations -def: "Analyse a spectrum from a mass spectrometry (or other) experiment." [http://edamontology.org] -synonym: "Spectral analysis" EXACT [http://edamontology.org] -synonym: "Mass spectrum analysis" EXACT [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing - -[Term] -id: EDAM_operation:3215 !{since=1.1} -name: Peak detection -namespace: operation -subset: operations -def: "Identify peaks in a spectrum from a mass spectrometry experiment." [http://edamontology.org] -synonym: "Peak finding" EXACT [http://edamontology.org] -is_a: EDAM_operation:3214 ! Spectrum analysis -relationship: has_input EDAM_data:0943 !{min_cardinality=1} ! Mass spectrometry spectra - - -[Term] -id: EDAM_operation:2446 -name: Sequence processing -namespace: operation -subset: operations -! alt_id: EDAM_operation:2449 -def: "Process (read and / or write) one or more molecular sequences and associated annotation." [http://edamontology.org] -synonym: "Sequence processing (general)" EXACT [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2044 !{min_cardinality=0} ! Sequence -relationship: has_output EDAM_data:2044 !{min_cardinality=0} ! Sequence -relationship: has_topic EDAM_topic:0080 ! Sequence analysis - -[Term] -id: EDAM_operation:2447 -name: Sequence processing (protein) -namespace: operation -subset: operations -def: "Process (read and / or write) a protein sequence and associated annotation." [http://edamontology.org] -is_a: EDAM_operation:2446 ! Sequence processing -is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_input EDAM_data:2976 !{min_cardinality=0} ! Protein sequence -relationship: has_output EDAM_data:2976 !{min_cardinality=0} ! Protein sequence - -[Term] -id: EDAM_operation:2448 -name: Sequence processing (nucleic acid) -namespace: operation -subset: operations -def: "Process (read and / or write) a nucleotide sequence and associated annotation." [http://edamontology.org] -is_a: EDAM_operation:2446 ! Sequence processing -is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:2977 !{min_cardinality=0} ! Nucleic acid sequence -relationship: has_output EDAM_data:2977 !{min_cardinality=0} ! Nucleic acid sequence - -[Term] -id: EDAM_operation:0229 -name: Annotation retrieval (sequence) -namespace: operation -subset: operations -def: "Retrieve basic information about a molecular sequence." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:1813 ! Sequence retrieval - -[Term] -id: EDAM_operation:0230 -name: Sequence generation -namespace: operation -subset: operations -def: "Generate a molecular sequence by some means." [http://edamontology.org] -is_a: EDAM_operation:2121 ! Sequence file processing - -[Term] -id: EDAM_operation:2513 -name: Sequence generation (nucleic acid) -namespace: operation -subset: operations -def: "Generate a nucleic acid sequence by some means." [http://edamontology.org] -is_a: EDAM_operation:0230 ! Sequence generation -is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) -relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis - - -[Term] -id: EDAM_operation:2514 -name: Sequence generation (protein) -namespace: operation -subset: operations -def: "Generate a protein sequence by some means." [http://edamontology.org] -is_a: EDAM_operation:0230 ! Sequence generation -is_a: EDAM_operation:2447 ! Sequence processing (protein) -relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis - -[Term] -id: EDAM_operation:0231 -name: Sequence editing -namespace: operation -subset: operations -def: "Edit or change a molecular sequence, either randomly or specifically." [http://edamontology.org] -is_a: EDAM_operation:2121 ! Sequence file processing -is_a: EDAM_operation:3096 ! Editing - -[Term] -id: EDAM_operation:2511 -name: Sequence editing (nucleic acid) -namespace: operation -subset: operations -def: "Edit or change a nucleic acid sequence, either randomly or specifically." [http://edamontology.org] -is_a: EDAM_operation:0231 ! Sequence editing -is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) - -[Term] -id: EDAM_operation:2512 -name: Sequence editing (protein) -namespace: operation -subset: operations -def: "Edit or change a protein sequence, either randomly or specifically." [http://edamontology.org] -is_a: EDAM_operation:0231 ! Sequence editing -is_a: EDAM_operation:2447 ! Sequence processing (protein) - - -[Term] -id: EDAM_operation:0232 -name: Sequence merging -namespace: operation -subset: operations -def: "Merge two or more (typically overlapping) molecular sequences." [http://edamontology.org] -synonym: "Sequence splicing" EXACT [http://edamontology.org] -is_a: EDAM_operation:0231 ! Sequence editing - -[Term] -id: EDAM_operation:0233 -name: Sequence conversion -namespace: operation -subset: operations -def: "Convert a molecular sequence from one type to another." [http://edamontology.org] -is_a: EDAM_operation:0231 ! Sequence editing - -[Term] -id: EDAM_operation:1780 -name: Sequence submission -namespace: operation -subset: operations -def: "Submit a molecular sequence to a database." [http://edamontology.org] -is_a: EDAM_operation:2446 ! Sequence processing -relationship: has_input EDAM_data:2044 !{min_cardinality=1} ! Sequence -relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition - -[Term] -id: EDAM_operation:0234 -name: Sequence complexity calculation -namespace: operation -subset: operations -! alt_id: EDAM_operation:0373 -! alt_id: EDAM_operation:0374 -def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [http://edamontology.org] -is_a: EDAM_operation:0236 ! Sequence composition calculation -relationship: has_output EDAM_data:1259 !{min_cardinality=1} ! Sequence complexity -relationship: has_topic EDAM_topic:0642 ! Low complexity sequences - - -[Term] -id: EDAM_operation:0235 -name: Sequence ambiguity calculation -namespace: operation -subset: operations -! alt_id: EDAM_operation:0375 -! alt_id: EDAM_operation:0376 -def: "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." [http://edamontology.org] -is_a: EDAM_operation:0236 ! Sequence composition calculation -relationship: has_output EDAM_data:1260 !{min_cardinality=1} ! Sequence ambiguity -relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis - - -[Term] -id: EDAM_operation:0291 -name: Sequence clustering -namespace: operation -subset: operations -def: "Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org] -comment: The clusters may be output or used internally for some other purpose. -synonym: "Sequence cluster generation" EXACT [http://edamontology.org] -is_a: EDAM_operation:2451 ! Sequence comparison -is_a: EDAM_operation:2452 ! Sequence cluster processing -is_a: EDAM_operation:2995 ! Sequence classification -relationship: has_output EDAM_data:1235 !{min_cardinality=0} ! Sequence cluster - -[Term] -id: EDAM_operation:0236 -name: Sequence composition calculation -namespace: operation -subset: operations -def: "Calculate character or word composition or frequency of a molecular sequence." [http://edamontology.org] -is_a: EDAM_operation:2403 ! Sequence analysis -relationship: has_output EDAM_data:1261 ! Sequence composition -relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis -relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis - - -[Term] -id: EDAM_operation:0237 -name: Repeat sequence analysis -namespace: operation -subset: operations -def: "Find and/or analyse repeat sequences in (typically nucleotide) sequences." [http://edamontology.org] -comment: Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. -is_a: EDAM_operation:2403 ! Sequence analysis -relationship: has_topic EDAM_topic:0641 ! Repeat sequences - -[Term] -id: EDAM_operation:0290 -name: Sequence redundancy removal -namespace: operation -subset: operations -def: "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." [http://edamontology.org] -is_a: EDAM_operation:0291 ! Sequence clustering -relationship: has_output EDAM_data:2044 !{min_cardinality=0} ! Sequence -relationship: has_topic EDAM_topic:0164 ! Sequence clustering - - -[Term] -id: EDAM_operation:2451 -name: Sequence comparison -namespace: operation -subset: operations -def: "Compare two or more molecular sequences." [http://edamontology.org] -is_a: EDAM_operation:2403 ! Sequence analysis -is_a: EDAM_operation:2424 ! Comparison -relationship: has_input EDAM_data:2044 !{min_cardinality=2} ! Sequence -relationship: has_output EDAM_data:2955 ! Sequence report -relationship: has_topic EDAM_topic:0159 ! Sequence comparison - - -[Term] -id: EDAM_operation:2508 -name: Nucleic acid sequence comparison -namespace: operation -subset: operations -def: "Compare two or more nucleic acid sequences." [http://edamontology.org] -synonym: "Sequence comparison (nucleic acid)" EXACT [http://edamontology.org] -is_a: EDAM_operation:2451 ! Sequence comparison -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -is_a: EDAM_operation:2998 ! Nucleic acid comparison - -[Term] -id: EDAM_operation:2509 -name: Protein sequence comparison -namespace: operation -subset: operations -def: "Compare two or more protein sequences." [http://edamontology.org] -synonym: "Sequence comparison (protein)" EXACT [http://edamontology.org] -is_a: EDAM_operation:2451 ! Sequence comparison -is_a: EDAM_operation:2479 ! Protein sequence analysis -is_a: EDAM_operation:2997 ! Protein comparison - -[Term] -id: EDAM_operation:0288 -name: Sequence word comparison -namespace: operation -subset: operations -def: "Find exact character or word matches between molecular sequences without full sequence alignment." [http://edamontology.org] -is_a: EDAM_operation:2451 ! Sequence comparison -relationship: has_output EDAM_data:0861 !{min_cardinality=1} ! Sequence alignment (words) - -[Term] -id: EDAM_operation:0289 -name: Sequence distance matrix generation -namespace: operation -subset: operations -def: "Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences." [http://edamontology.org] -synonym: "Phylogenetic distance matrix generation" EXACT [http://edamontology.org] -is_a: EDAM_operation:2451 ! Sequence comparison -relationship: has_output EDAM_data:0870 ! Sequence distance matrix -relationship: has_topic EDAM_topic:0084 ! Phylogenetics - -[Term] -id: EDAM_operation:3200 !{since=1.1} -name: DNA barcoding -namespace: operation -subset: operations -def: "Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms." [http://edamontology.org] -synonym: "Sample barcoding" EXACT [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction - - - -[Term] -id: EDAM_operation:3204 !{since=1.1} -name: Methylation analysis -namespace: operation -subset: operations -def: "Determine cytosine methylation states in nucleic acid sequences." [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction - -[Term] -id: EDAM_operation:3205 !{since=1.1} -name: Methylation calling -namespace: operation -subset: operations -def: "Determine cytosine methylation status of specific positions in a nucleic acid sequences." [http://edamontology.org] -is_a: EDAM_operation:3204 ! Methylation analysis - -[Term] -id: EDAM_operation:3206 !{since=1.1} -name: Methylation level analysis (global) -namespace: operation -subset: operations -def: "Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay." [http://edamontology.org] -synonym: "Global methylation analysis" EXACT [http://edamontology.org] -is_a: EDAM_operation:3205 ! Methylation calling - -[Term] -id: EDAM_operation:3207 !{since=1.1} -name: Methylation level analysis (gene-specific) -namespace: operation -subset: operations -def: "Measure the level of methyl cytosines in specific genes." [http://edamontology.org] -comment: Many different techniques are available for this. -synonym: "Gene-specific methylation analysis" EXACT [http://edamontology.org] -is_a: EDAM_operation:3205 ! Methylation calling - - -[Term] -id: EDAM_operation:3209 !{since=1.1} -name: Genome comparison -namespace: operation -subset: operations -def: "Compare the sequence or features of two or more genomes, for example, to find matching regions." [http://edamontology.org] -synonym: "Genomic region matching" EXACT [http://edamontology.org] -is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison - - -[Term] -id: EDAM_operation:0266 -name: Vector sequence detection -namespace: operation -subset: operations -def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [http://edamontology.org] -is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction - -[Term] -id: EDAM_operation:2233 -name: Representative sequence identification -namespace: operation -subset: operations -def: "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org] -is_a: EDAM_operation:0291 ! Sequence clustering -relationship: has_topic EDAM_topic:0164 ! Sequence clustering - -[Term] -id: EDAM_operation:0317 -name: EST and cDNA sequence analysis -namespace: operation -subset: operations -def: "Analyse EST or cDNA sequences." [http://edamontology.org] -comment: For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2403 ! Sequence analysis - -[Term] -id: EDAM_operation:3185 !{since=1.1} -name: Base-calling -namespace: operation -subset: operations -def: "Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer." [http://edamontology.org] -synonym: "Base calling" EXACT [http://edamontology.org] -synonym: "Phred base calling" EXACT [http://edamontology.org] -synonym: "Phred base-calling" EXACT [http://edamontology.org] -is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) -relationship: has_topic EDAM_topic:3168 ! Sequencing - - -[Term] -id: EDAM_operation:3195 -name: Sequencing error detection -namespace: operation -subset: operations -def: "Detect errors in DNA sequences generated from sequencing projects)." [http://edamontology.org] -synonym: "Short-read error correction" EXACT [http://edamontology.org] -synonym: "Short read error correction" EXACT [http://edamontology.org] -is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison -relationship: has_topic EDAM_topic:3168 ! Sequencing - -[Term] -id: EDAM_operation:0265 -name: Frameshift error detection -namespace: operation -subset: operations -def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [http://edamontology.org] -comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. -is_a: EDAM_operation:3195 ! Sequencing error detection -is_a: EDAM_operation:3197 ! Genetic variation analysis -relationship: has_topic EDAM_topic:3168 ! Sequencing - - -[Term] -id: EDAM_operation:0241 -name: Transcription regulatory sequence analysis -namespace: operation -subset: operations -def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [http://edamontology.org] -comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. -is_obsolete: true !{since=beta13} -consider: EDAM_operation:0438 ! Transcription regulatory element prediction - - -[Term] -id: EDAM_operation:0281 -name: Genetic marker identification -namespace: operation -subset: operations -def: "Identify genetic markers in DNA sequences." [http://edamontology.org] -comment: A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. -is_obsolete: true !{since=beta13} -consider: EDAM_operation:0415 ! Nucleic acid feature prediction - - -[Term] -id: EDAM_operation:0363 -name: Nucleic acid sequence reverse and complement -namespace: operation -subset: operations -def: "Generate the reverse and / or complement of a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid) - -[Term] -id: EDAM_operation:0364 -name: Random sequence generation -namespace: operation -subset: operations -def: "Generate a random sequence, for example, with a specific character composition." [http://edamontology.org] -is_a: EDAM_operation:0230 ! Sequence generation - -[Term] -id: EDAM_operation:0365 -name: Nucleic acid restriction digest -namespace: operation -subset: operations -def: "Generate digest fragments for a nucleotide sequence containing restriction sites." [http://edamontology.org] -is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid) -is_a: EDAM_operation:0262 ! Nucleic acid property calculation -relationship: has_output EDAM_data:1239 ! Restriction digest -relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction - - -[Term] -id: EDAM_operation:0366 -name: Protein sequence cleavage -namespace: operation -subset: operations -def: "Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses." [http://edamontology.org] -is_a: EDAM_operation:2514 ! Sequence generation (protein) -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:1238 ! Proteolytic digest -relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification - -[Term] -id: EDAM_operation:0367 -name: Sequence mutation and randomization -namespace: operation -subset: operations -def: "Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition." [http://edamontology.org] -is_a: EDAM_operation:0231 ! Sequence editing - -[Term] -id: EDAM_operation:0368 -name: Sequence masking -namespace: operation -subset: operations -def: "Mask characters in a molecular sequence (replacing those characters with a mask character)." [http://edamontology.org] -comment: For example, SNPs or repeats in a DNA sequence might be masked. -is_a: EDAM_operation:0231 ! Sequence editing -relationship: has_input EDAM_data:0851 !{min_cardinality=1} ! Sequence mask character - -[Term] -id: EDAM_operation:0369 -name: Sequence cutting -namespace: operation -subset: operations -def: "Cut (remove) characters or a region from a molecular sequence." [http://edamontology.org] -is_a: EDAM_operation:0231 ! Sequence editing - -[Term] -id: EDAM_operation:3192 !{since=1.1} -name: Sequence trimming -namespace: operation -subset: operations -def: "Cut (remove) the end from a molecular sequence." [http://edamontology.org] -is_a: EDAM_operation:0369 ! Sequence cutting - - -[Term] -id: EDAM_operation:3212 !{since=1.1} -name: Primer removal -namespace: operation -subset: operations -def: "Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products)." [http://edamontology.org] -is_a: EDAM_operation:0369 ! Sequence cutting -is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid) - - -[Term] -id: EDAM_operation:3189 !{since=1.1} -name: Trim ends -namespace: operation -subset: operations -def: "Trim sequences (typically from an automated DNA sequencer) to remove misleading ends." [http://edamontology.org] -comment: For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. -is_a: EDAM_operation:3192 ! Sequence trimming - -[Term] -id: EDAM_operation:3190 !{since=1.1} -name: Trim vector -namespace: operation -subset: operations -def: "Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences." [http://edamontology.org] -is_a: EDAM_operation:3192 ! Sequence trimming - -[Term] -id: EDAM_operation:3191 !{since=1.1} -name: Trim to reference -namespace: operation -subset: operations -def: "Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence." [http://edamontology.org] -is_a: EDAM_operation:3192 ! Sequence trimming - - - -[Term] -id: EDAM_operation:0370 -name: Restriction site creation -namespace: operation -subset: operations -def: "Create (or remove) restriction sites in sequences, for example using silent mutations." [http://edamontology.org] -is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid) -relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction - -[Term] -id: EDAM_operation:0371 -name: DNA translation -namespace: operation -subset: operations -def: "Translate a DNA sequence into protein." [http://edamontology.org] -is_a: EDAM_operation:0233 ! Sequence conversion -relationship: has_topic EDAM_topic:0108 ! Translation - - -[Term] -id: EDAM_operation:0372 -name: DNA transcription -namespace: operation -subset: operations -def: "Transcribe a nucleotide sequence into mRNA sequence(s)." [http://edamontology.org] -is_a: EDAM_operation:0233 ! Sequence conversion -relationship: has_topic EDAM_topic:0110 ! Transcription - - -[Term] -id: EDAM_operation:2510 -name: DNA back-translation -namespace: operation -subset: operations -def: "Back-translate a protein sequence into DNA." [http://edamontology.org] -is_a: EDAM_operation:0233 ! Sequence conversion -relationship: has_topic EDAM_topic:0108 ! Translation - - -[Term] -id: EDAM_operation:0377 -name: Sequence composition calculation (nucleic acid) -namespace: operation -subset: operations -def: "Calculate base frequency or word composition of a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_operation:0236 ! Sequence composition calculation -is_a: EDAM_operation:0262 ! Nucleic acid property calculation - - -[Term] -id: EDAM_operation:0378 -name: Sequence composition calculation (protein) -namespace: operation -subset: operations -def: "Calculate amino acid frequency or word composition of a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:0236 ! Sequence composition calculation -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) - -[Term] -id: EDAM_operation:2284 -name: Nucleic acid density plotting -namespace: operation -subset: operations -def: "Calculate a density plot (of base composition) for a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_operation:0377 ! Sequence composition calculation (nucleic acid) - -[Term] -id: EDAM_operation:0379 -name: Repeat sequence detection -namespace: operation -subset: operations -! alt_id: EDAM_operation:2450 -def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] -is_a: EDAM_operation:0237 ! Repeat sequence analysis -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:1299 ! Sequence features (repeats) - - -[Term] -id: EDAM_operation:0380 -name: Repeat sequence organisation analysis -namespace: operation -subset: operations -def: "Analyse repeat sequence organization such as periodicity." [http://edamontology.org] -is_a: EDAM_operation:0237 ! Repeat sequence analysis -is_a: EDAM_operation:0236 ! Sequence composition calculation - - -[Term] -id: EDAM_operation:0490 -name: Dotplot plotting -namespace: operation -subset: operations -def: "Draw a dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] -is_a: EDAM_operation:0288 ! Sequence word comparison -is_a: EDAM_operation:0565 ! Sequence alignment rendering -relationship: has_output EDAM_data:0862 !{min_cardinality=1} ! Dotplot - -[Term] -id: EDAM_operation:0242 -name: Conserved transcription regulatory sequence identification -namespace: operation -subset: operations -def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." [http://edamontology.org] -comment: For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. -is_a: EDAM_operation:0438 ! Transcription regulatory element prediction -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:1315 ! Gene features (TFBS) - -[Term] -id: EDAM_operation:0238 -name: Sequence motif discovery -namespace: operation -subset: operations -def: "Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery)." [http://edamontology.org] -comment: Motifs and patterns might be conserved or over-represented (occur with improbable frequency). -synonym: "Motif discovery" EXACT [http://edamontology.org] -is_a: EDAM_operation:0253 ! Feature prediction -is_a: EDAM_operation:2404 ! Sequence motif processing -relationship: has_output EDAM_data:1298 ! Sequence features (motifs) - -[Term] -id: EDAM_operation:0239 -name: Sequence motif recognition -namespace: operation -subset: operations -def: "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." [http://edamontology.org] -synonym: "Sequence motif detection" EXACT [http://edamontology.org] -synonym: "Motif detection" EXACT [http://edamontology.org] -synonym: "Motif recognition" EXACT [http://edamontology.org] -is_a: EDAM_operation:2404 ! Sequence motif processing -is_a: EDAM_operation:0253 ! Feature prediction -relationship: has_output EDAM_data:1298 ! Sequence features (motifs) - - -[Term] -id: EDAM_operation:0240 -name: Sequence motif comparison -namespace: operation -subset: operations -def: "Find motifs shared by molecular sequences." [http://edamontology.org] -is_a: EDAM_operation:2451 ! Sequence comparison -is_a: EDAM_operation:2404 ! Sequence motif processing -relationship: has_output EDAM_data:1298 ! Sequence features (motifs) - - - -[Term] -id: EDAM_operation:2123 -name: Small molecule data processing -namespace: operation -subset: operations -def: "Process (read and / or write) physicochemical property data for small molecules." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2420 ! Analysis and processing - - -[Term] -id: EDAM_operation:0250 -name: Protein property calculation -namespace: operation -subset: operations -! alt_id: EDAM_operation:2933 -def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [http://edamontology.org] -comment: This includes methods to render and visualise the properties of a protein sequence. -synonym: "Protein property rendering" EXACT [http://edamontology.org] -is_a: EDAM_operation:2502 ! Protein data processing -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_input EDAM_data:0897 !{min_cardinality=0} ! Protein property -relationship: has_output EDAM_data:0897 !{min_cardinality=0} ! Protein property -relationship: has_topic EDAM_topic:0123 ! Protein properties - -[Term] -id: EDAM_operation:3088 !{since=beta13} -name: Protein property calculation (from sequence) -namespace: operation -subset: operations -def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:0250 ! Protein property calculation -is_a: EDAM_operation:2479 ! Protein sequence analysis - - - -[Term] -id: EDAM_operation:0261 -name: Nucleic acid property processing -namespace: operation -subset: operations -def: "Process (read and / or write) physicochemical property data of nucleic acids." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:0262 ! Nucleic acid property calculation - - -[Term] -id: EDAM_operation:0334 -name: Enzyme kinetics calculation -namespace: operation -subset: operations -def: "Calculate Km, Vmax and derived data for an enzyme reaction." [http://edamontology.org] -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:2024 !{min_cardinality=1} ! Enzyme kinetics data -relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions - -[Term] -id: EDAM_operation:0398 -name: Protein molecular weight calculation -namespace: operation -subset: operations -def: "Calculate the molecular weight of a protein sequence or fragments." [http://edamontology.org] -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:1519 !{min_cardinality=1} ! Peptide molecular weights -relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification - - -[Term] -id: EDAM_operation:2930 -name: Protein property comparison -namespace: operation -subset: operations -def: "Compare the physicochemical properties of two or more proteins (or reference data)." [http://edamontology.org] -is_a: EDAM_operation:2997 ! Protein comparison -relationship: has_output EDAM_data:0897 !{min_cardinality=1} ! Protein property - - -[Term] -id: EDAM_operation:2929 -name: Protein fragment weight comparison -namespace: operation -subset: operations -def: "Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data." [http://edamontology.org] -is_a: EDAM_operation:0398 ! Protein molecular weight calculation -is_a: EDAM_operation:2930 ! Protein property comparison - -[Term] -id: EDAM_operation:0399 -name: Protein extinction coefficient calculation -namespace: operation -subset: operations -def: "Predict extinction coefficients or optical density of a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:1531 !{min_cardinality=1} ! Protein extinction coefficient - - -[Term] -id: EDAM_operation:0400 -name: Protein pH-dependent property calculation -namespace: operation -subset: operations -def: "Calculate pH-dependent properties from pKa calculations of a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:0897 ! Protein property -relationship: has_topic EDAM_topic:0137 ! Protein hydropathy - -[Term] -id: EDAM_operation:0401 -name: Protein hydropathy calculation (from sequence) -namespace: operation -subset: operations -def: "Hydropathy calculation on a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:2574 ! Protein hydropathy calculation - -[Term] -id: EDAM_operation:0252 -name: Peptide immunogenicity prediction -namespace: operation -subset: operations -def: "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins." [http://edamontology.org] -comment: This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. -is_a: EDAM_operation:2492 ! Protein interaction prediction -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:1534 !{min_cardinality=1} ! Peptide immunogenicity data -relationship: has_topic EDAM_topic:0804 ! Immunoinformatics - - -[Term] -id: EDAM_operation:2932 -name: Hopp and Woods plotting -namespace: operation -subset: operations -def: "Generate a Hopp and Woods plot of antigenicity of a protein." [http://edamontology.org] -is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction - - -[Term] -id: EDAM_operation:0402 -name: Protein titration curve plotting -namespace: operation -subset: operations -def: "Plot a protein titration curve." [http://edamontology.org] -is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation -relationship: has_output EDAM_data:1527 !{min_cardinality=1} ! Protein titration curve - - -[Term] -id: EDAM_operation:0403 -name: Protein isoelectric point calculation -namespace: operation -subset: operations -def: "Calculate isoelectric point of a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation -relationship: has_output EDAM_data:1528 !{min_cardinality=1} ! Protein isoelectric point - - -[Term] -id: EDAM_operation:0404 -name: Protein hydrogen exchange rate calculation -namespace: operation -subset: operations -def: "Estimate hydrogen exchange rate of a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation -relationship: has_output EDAM_data:1530 !{min_cardinality=1} ! Protein hydrogen exchange rate - -[Term] -id: EDAM_operation:0405 -name: Protein hydrophobic region calculation -namespace: operation -subset: operations -def: "Calculate hydrophobic or hydrophilic / charged regions of a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) - -[Term] -id: EDAM_operation:0406 -name: Protein aliphatic index calculation -namespace: operation -subset: operations -def: "Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein." [http://edamontology.org] -is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM_data:1521 !{min_cardinality=1} ! Protein aliphatic index - -[Term] -id: EDAM_operation:0407 -name: Protein hydrophobic moment plotting -namespace: operation -subset: operations -def: "Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity." [http://edamontology.org] -comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. -is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM_data:1520 !{min_cardinality=1} ! Peptide hydrophobic moment - -[Term] -id: EDAM_operation:0408 -name: Protein globularity prediction -namespace: operation -subset: operations -def: "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." [http://edamontology.org] -is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM_data:1526 !{min_cardinality=1} ! Protein globularity - -[Term] -id: EDAM_operation:0409 -name: Protein solubility prediction -namespace: operation -subset: operations -def: "Predict the solubility or atomic solvation energy of a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM_data:1524 !{min_cardinality=1} ! Protein solubility - -[Term] -id: EDAM_operation:0410 -name: Protein crystallizability prediction -namespace: operation -subset: operations -def: "Predict crystallizability of a protein sequence." [http://edamontology.org] -is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM_data:1525 !{min_cardinality=1} ! Protein crystallizability - - -[Term] -id: EDAM_operation:0455 -name: Nucleic acid thermodynamic property calculation -namespace: operation -subset: operations -def: "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." [http://edamontology.org] -is_a: EDAM_operation:0262 ! Nucleic acid property calculation -relationship: has_output EDAM_data:2985 !{min_cardinality=1} ! Nucleic acid thermodynamic data - - - -[Term] -id: EDAM_operation:0456 -name: Nucleic acid melting profile plotting -namespace: operation -subset: operations -def: "Calculate and plot a DNA or DNA/RNA melting profile." [http://edamontology.org] -comment: A melting profile is used to visualise and analyse partly melted DNA conformations. -is_a: EDAM_operation:0262 ! Nucleic acid property calculation -relationship: has_output EDAM_data:1583 !{min_cardinality=1} ! Nucleic acid melting profile - - -[Term] -id: EDAM_operation:0262 -name: Nucleic acid property calculation -namespace: operation -subset: operations -def: "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -relationship: has_output EDAM_data:0912 !{min_cardinality=1} ! Nucleic acid property - - - -[Term] -id: EDAM_operation:2439 -name: RNA secondary structure processing -namespace: operation -subset: operations -def: "Process (read and / or write) RNA secondary structure data." [http://edamontology.org] -is_a: EDAM_operation:2482 ! Secondary structure processing -is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:0880 !{min_cardinality=0} ! RNA secondary structure record -relationship: has_output EDAM_data:0880 !{min_cardinality=0} ! RNA secondary structure record -relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis -relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment - - -[Term] -id: EDAM_operation:2519 -name: Structure processing (nucleic acid) -namespace: operation -subset: operations -def: "Process (read and / or write) nucleic acid tertiary structure data." [http://edamontology.org] -is_a: EDAM_operation:2465 ! Structure processing -is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:1459 !{min_cardinality=0} ! Nucleic acid structure -relationship: has_output EDAM_data:1459 !{min_cardinality=0} ! Nucleic acid structure -relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis - - -[Term] -id: EDAM_operation:2440 -name: Structure processing (RNA) -namespace: operation -subset: operations -def: "Process (read and / or write) RNA tertiary structure data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2519 ! Structure processing (nucleic acid) - - - -[Term] -id: EDAM_operation:0278 -name: RNA secondary structure prediction -namespace: operation -subset: operations -def: "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." [http://edamontology.org] -comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). -is_a: EDAM_operation:2439 ! RNA secondary structure processing -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:0880 !{min_cardinality=1} ! RNA secondary structure record -relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction - -[Term] -id: EDAM_operation:2441 -name: RNA structure prediction -namespace: operation -subset: operations -def: "Predict RNA tertiary structure." [http://edamontology.org] -is_a: EDAM_operation:0475 ! Nucleic acid structure prediction -relationship: has_output EDAM_data:1465 !{min_cardinality=1} ! RNA structure record - - -[Term] -id: EDAM_operation:2442 -name: DNA structure prediction -namespace: operation -subset: operations -def: "Predict DNA tertiary structure." [http://edamontology.org] -is_a: EDAM_operation:0475 ! Nucleic acid structure prediction -relationship: has_output EDAM_data:1464 !{min_cardinality=1} ! DNA structure - -[Term] -id: EDAM_operation:0279 -name: Nucleic acid folding analysis -namespace: operation -subset: operations -def: "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." [http://edamontology.org] -is_a: EDAM_operation:2426 ! Modelling and simulation -is_a: EDAM_operation:2501 ! Nucleic acid data processing -synonym: "Nucleic acid folding" EXACT [http://edamontology.org] -synonym: "Nucleic acid folding modelling" EXACT [http://edamontology.org] -relationship: has_output EDAM_data:1596 ! Nucleic acid folding report -relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction - - -[Term] -id: EDAM_operation:0461 -name: Nucleic acid curvature calculation -namespace: operation -subset: operations -def: "Calculate curvature and flexibility / stiffness of a nucleotide sequence." [http://edamontology.org] -comment: This includes properties such as. -is_a: EDAM_operation:0262 ! Nucleic acid property calculation -relationship: has_output EDAM_data:0912 !{min_cardinality=1} ! Nucleic acid property -relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis +remark: EDAM editors: Jon Ison and Matus Kalas. Co-authors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE (FP6, EU), EMBOSS (BBSRC, UK), eSysbio and FUGE Bioinformatics Platform (both Research Council of Norway). See http://edamontology.org for documentation and licence. +page: http://edamontology.org/page +definedBy: EDAM_1.2.owl +next_id: 3263 +saved-by: Jon Ison, Matus Kalas + +![Term] +!id: ObsoleteClass +!name: Obsolete concept (EDAM) +!comment: Needed for conversion to the OBO format. +!created_in: "1.2 / http://www.geneontology.org/formats/oboInOwl" +!def: "An obsolete concept (redefined in EDAM)." [http://edamontology.org] +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +!is_a: owl:DeprecatedClass +!is_obsolete: true [Term] -id: EDAM_operation:1768 -name: Nucleic acid folding family identification -namespace: operation -subset: operations -def: "Identify folding families of related RNAs." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0483 ! Structured RNA prediction and optimisation +id: EDAM_data:0005 +name: Resource type +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A type of computational resource used in bioinformatics." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_operation:1769 -name: Nucleic acid folding energy calculation -namespace: operation -subset: operations -def: "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." [http://edamontology.org] -is_a: EDAM_operation:0279 ! Nucleic acid folding analysis - +id: EDAM_data:0006 +name: Data +subset: bioinformatics +subset: data +subset: edam +synonym: "Continuant" BROAD [] +synonym: "Data record" EXACT [] +synonym: "Data set" NARROW [] +synonym: "WSIO_data:002" EXACT [] +synonym: "Datum" NARROW [] +synonym: "DigitalEntity" RELATED [] +synonym: "IAO:0000027" RELATED [] +synonym: "IAO:0000030" RELATED [] +synonym: "Perpetuant" RELATED [] +synonym: "SIO:000069" RELATED [] +synonym: "SIO:000088" RELATED [] +created_in: "beta12orEarlier" +def: "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output." [http://edamontology.org] +namespace: data +disjoint_from: EDAM_format:1915 ! Format +disjoint_from: EDAM_operation:0004 ! Operation +disjoint_from: EDAM_topic:0003 ! Topic [Term] -id: EDAM_operation:1777 -name: Protein function prediction -namespace: operation -subset: operations -def: "Predict general functional properties of a protein." [http://edamontology.org] -comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. -is_a: EDAM_operation:2414 ! Protein function analysis -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_topic EDAM_topic:2276 ! Protein function prediction - +id: EDAM_data:0007 +name: Tool +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A bioinformatics package or tool, e.g. a standalone application or web service." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_operation:3084 !{since=beta13} -name: Protein function prediction (from sequence) -namespace: operation -subset: operations -def: "Predict general (non-positional) functional properties of a protein from analysing its sequence." [http://edamontology.org] -comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. -is_a: EDAM_operation:1777 ! Protein function prediction -is_a: EDAM_operation:2479 ! Protein sequence analysis -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_topic EDAM_topic:2276 ! Protein function prediction - - +id: EDAM_data:0581 +name: Database +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_operation:1778 -name: Protein function comparison -namespace: operation -subset: operations -def: "Compare the functional properties of two or more proteins." [http://edamontology.org] -is_a: EDAM_operation:2414 ! Protein function analysis -is_a: EDAM_operation:2997 ! Protein comparison -relationship: has_topic EDAM_topic:1775 ! Protein function analysis +id: EDAM_data:0582 +name: Ontology +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] -id: EDAM_operation:0413 -name: MHC peptide immunogenicity prediction -namespace: operation -subset: operations -def: "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." [http://edamontology.org] -is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction +id: EDAM_data:0583 +name: Directory metadata +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A directory on disk from which files are read." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3106 ! System metadata [Term] -id: EDAM_operation:0253 -name: Feature prediction -namespace: operation -subset: operations -def: "Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions." [http://edamontology.org] -synonym: "Sequence feature detection" EXACT [http://edamontology.org] -synonym: "sequence_feature" RELATED [SO:0000110] -is_a: EDAM_operation:2403 ! Sequence analysis -is_a: EDAM_operation:2423 ! Prediction, detection and recognition -relationship: has_output EDAM_data:1255 !{min_cardinality=1} ! Feature record -relationship: has_topic EDAM_topic:3072 ! Sequence feature detection - +id: EDAM_data:0831 +name: MeSH vocabulary +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0582 ! Ontology [Term] -id: EDAM_operation:2453 -name: Feature table processing -namespace: operation -subset: operations -def: "Process (read and / or write) a sequence feature table." [http://edamontology.org] -is_a: EDAM_operation:2446 ! Sequence processing -relationship: has_input EDAM_data:1270 !{min_cardinality=0} ! Sequence feature table -relationship: has_input EDAM_data:2201 !{min_cardinality=0} ! Sequence record full -relationship: has_output EDAM_data:1255 !{min_cardinality=0} ! Feature record -relationship: has_topic EDAM_topic:0160 ! Sequence sites and features +id: EDAM_data:0832 +name: HGNC vocabulary +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0582 ! Ontology [Term] -id: EDAM_operation:0254 -name: Data retrieval (feature table) -namespace: operation -subset: operations -def: "Extract a sequence feature table from a sequence database entry." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:2422 ! Data retrieval - +id: EDAM_data:0835 +name: UMLS vocabulary +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0582 ! Ontology [Term] -id: EDAM_operation:0255 -name: Feature table query -namespace: operation -subset: operations -def: "Query the features (in a feature table) of molecular sequence(s)." [http://edamontology.org] -is_a: EDAM_operation:2453 ! Feature table processing -relationship: has_input EDAM_data:1270 !{min_cardinality=0} ! Sequence feature table -relationship: has_input EDAM_data:2201 !{min_cardinality=0} ! Sequence record full -relationship: has_output EDAM_data:1255 ! Feature record +id: EDAM_data:0842 +name: Identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "WSIO_data:005" EXACT [] +synonym: "http://purl.org/dc/elements/1.1/identifier" NARROW [] +synonym: "ID" EXACT [] +synonym: "SIO:000115" EXACT [] +created_in: "beta12orEarlier" +def: "A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0006 ! Data +disjoint_from: EDAM_data:2048 ! Report +disjoint_from: EDAM_data:2527 ! Parameter +disjoint_from: EDAM_data:3031 ! Core data +relationship: is_identifier_of EDAM_data:0006 ! Data [Term] -id: EDAM_operation:0256 -name: Feature comparison -namespace: operation -subset: operations -def: "Compare the feature tables of two or more molecular sequences." [http://edamontology.org] -synonym: "Feature table comparison" EXACT [http://edamontology.org] -synonym: "Sequence feature comparison" EXACT [http://edamontology.org] -is_a: EDAM_operation:2453 ! Feature table processing -is_a: EDAM_operation:2424 ! Comparison -relationship: has_input EDAM_data:1270 !{min_cardinality=0} ! Sequence feature table -relationship: has_input EDAM_data:2201 !{min_cardinality=0} ! Sequence record full - - +id: EDAM_data:0843 +name: Database entry +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An entry (retrievable via URL) from a biological database." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0006 ! Data [Term] -id: EDAM_operation:3092 !{since=beta13} -name: Protein feature prediction -namespace: operation -subset: operations -def: "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures." [http://edamontology.org] -is_a: EDAM_operation:2502 ! Protein data processing -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -is_a: EDAM_operation:0253 ! Feature prediction -relationship: has_output EDAM_data:1277 !{min_cardinality=1} ! Protein features -relationship: has_topic EDAM_topic:3074 ! Protein feature detection - - +id: EDAM_data:0844 +name: Molecular mass +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Mass of a molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2050 ! Molecular property (general) [Term] -id: EDAM_operation:0414 -name: Protein feature prediction (from sequence) -namespace: operation -subset: operations -def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." [http://edamontology.org] -comment: Methods typically involve scanning for known motifs, patterns and regular expressions. -synonym: "Sequence feature detection (protein)" EXACT [http://edamontology.org] -is_a: EDAM_operation:3092 ! Protein feature prediction -! is_a: EDAM_operation:0253 ! Feature prediction -is_a: EDAM_operation:2479 ! Protein sequence analysis - - +id: EDAM_data:0845 +name: Molecular charge +subset: bioinformatics +subset: data +subset: edam +xref: PDBML:pdbx_formal_charge +created_in: "beta12orEarlier" +def: "Net charge of a molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2050 ! Molecular property (general) [Term] -id: EDAM_operation:3090 !{since=beta13} -name: Protein feature prediction (from structure) -namespace: operation -subset: operations -def: "Predict, recognise and identify positional features in proteins from analysing protein structure." [http://edamontology.org] -is_a: EDAM_operation:3092 ! Protein feature prediction -is_a: EDAM_operation:2406 ! Protein structure analysis - - - +id: EDAM_data:0846 +name: Chemical formula +subset: bioinformatics +subset: data +subset: edam +synonym: "Chemical structure specification" EXACT [] +created_in: "beta12orEarlier" +def: "A specification of a chemical structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2050 ! Molecular property (general) [Term] -id: EDAM_operation:3087 !{since=beta13} -name: Protein site detection -namespace: operation -subset: operations -! alt_id: EDAM_operation:0382 -def: "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org] -synonym: "name: Sequence motif recognition (protein)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) -is_a: EDAM_operation:0239 ! Sequence motif recognition - - - +id: EDAM_data:0847 +name: QSAR descriptor +comment: QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A QSAR quantitative descriptor (name-value pair) of chemical structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2050 ! Molecular property (general) [Term] -id: EDAM_operation:0415 -name: Nucleic acid feature prediction -namespace: operation -subset: operations -! alt_id: EDAM_operation:0381 -def: "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org] -comment: Methods typically involve scanning for known motifs, patterns and regular expressions. -synonym: "Sequence feature detection (nucleic acid)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0239 ! Sequence motif recognition -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) -is_a: EDAM_operation:0253 ! Feature prediction -relationship: has_output EDAM_data:1276 !{min_cardinality=1} ! Nucleic acid features -relationship: has_topic EDAM_topic:3073 ! Nucleic acid feature detection - - - - +id: EDAM_data:0848 +name: Raw sequence +comment: Non-sequence characters may be used for example for gaps and translation stop. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2044 ! Sequence +[Term] +id: EDAM_data:0849 +name: Sequence record +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A molecular sequence and associated metadata." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2044 ! Sequence +[Term] +id: EDAM_data:0850 +name: Sequence set +comment: This concept may be used for arbitrary sequence sets and associated data arising from processing. +subset: bioinformatics +subset: data +subset: edam +synonym: "SO:0001260" RELATED [] +created_in: "beta12orEarlier" +def: "A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2955 ! Sequence report +[Term] +id: EDAM_data:0851 +name: Sequence mask character +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A character used to replace (mask) other characters in a molecular sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2023 ! Sequence mask parameter +[Term] +id: EDAM_data:0852 +name: Sequence mask type +comment: Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A label (text token) describing the type of sequence masking to perform." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2023 ! Sequence mask parameter +is_a: EDAM_data:2100 ! Type [Term] -id: EDAM_operation:0416 -name: Epitope mapping -namespace: operation -subset: operations -def: "Predict antigenic determinant sites (epitopes) in protein sequences." [http://edamontology.org] -comment: Epitope mapping is commonly done during vaccine design. -is_a: EDAM_operation:3087 ! Protein site detection -is_a: EDAM_operation:2429 ! Mapping and assembly -relationship: has_output EDAM_data:1326 ! Protein features (binding sites) -relationship: has_topic EDAM_topic:0804 ! Immunoinformatics +id: EDAM_data:0853 +name: DNA sense specification +comment: The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. +subset: bioinformatics +subset: data +subset: edam +synonym: "DNA strand specification" EXACT [] +synonym: "Strand" EXACT [] +created_in: "beta12orEarlier" +def: "The strand of a DNA sequence (forward or reverse)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2534 ! Sequence parameter +is_a: EDAM_data:2914 ! Sequence features metadata [Term] -id: EDAM_operation:0417 -name: Protein post-translation modification site prediction -namespace: operation -subset: operations -def: "Predict post-translation modification sites in protein sequences." [http://edamontology.org] -comment: Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. -is_a: EDAM_operation:3087 ! Protein site detection -relationship: has_output EDAM_data:1324 ! Protein features (post-translation modifications) -relationship: has_topic EDAM_topic:0601 ! Protein modifications +id: EDAM_data:0854 +name: Sequence length specification +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A specification of sequence length(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM_operation:2489 -name: Protein subcellular localization prediction -namespace: operation -subset: operations -def: "Predict the subcellular localization of a protein sequence." [http://edamontology.org] -comment: The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. -synonym: "Protein targeting prediction" EXACT [http://edamontology.org] -is_a: EDAM_operation:3084 ! Protein function prediction (from sequence) -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization +id: EDAM_data:0855 +name: Sequence metadata +comment: This is used for such things as a report including the sequence identifier, type and length. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Basic or general information concerning molecular sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1254 ! Sequence property +is_a: EDAM_data:2337 ! Metadata +is_a: EDAM_data:2955 ! Sequence report [Term] -id: EDAM_operation:0418 -name: Protein signal peptide detection -namespace: operation -subset: operations -def: "Detect or predict signal peptides and signal peptide cleavage sites in protein sequences." [http://edamontology.org] -comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. -is_a: EDAM_operation:3087 ! Protein site detection -is_a: EDAM_operation:2489 ! Protein subcellular localization prediction -relationship: has_output EDAM_data:1322 ! Protein features (signal peptides) -relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization +id: EDAM_data:0856 +name: Sequence feature source +comment: This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2042 ! Evidence +is_a: EDAM_data:2914 ! Sequence features metadata +[Term] +id: EDAM_data:0857 +name: Database hits (sequence) +comment: The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2080 ! Database hits [Term] -id: EDAM_operation:0419 -name: Binding site prediction (from sequence) -namespace: operation -subset: operations -def: "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." [http://edamontology.org] -synonym: "Ligand-binding and active site prediction (from sequence)" EXACT [http://edamontology.org] -is_a: EDAM_operation:3087 ! Protein site detection -is_a: EDAM_operation:2575 ! Binding site prediction +id: EDAM_data:0858 +name: Database hits (secondary) +comment: Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report of hits from a search of a protein secondary or domain database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2080 ! Database hits +[Term] +id: EDAM_data:0859 +name: Sequence signature model +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data files used by motif or profile methods." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0950 ! Biological model [Term] -id: EDAM_operation:0420 -name: Protein-nucleic acid binding prediction -namespace: operation -subset: operations -def: "Predict RNA and DNA-binding binding sites in protein sequences." [http://edamontology.org] -is_a: EDAM_operation:0419 ! Binding site prediction (from sequence) -relationship: has_output EDAM_data:1326 !{min_cardinality=0} ! Protein features (binding sites) +id: EDAM_data:0860 +name: Sequence signature +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A classifier of sequences such as a sequence motif, profile or other diagnostic element." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1353 ! Sequence motif +consider: EDAM_data:1354 ! Sequence profile [Term] -id: EDAM_operation:0421 -name: Protein folding site prediction -namespace: operation -subset: operations -def: "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization." [http://edamontology.org] -is_a: EDAM_operation:3087 ! Protein site detection -is_a: EDAM_operation:2415 ! Protein folding analysis -relationship: has_output EDAM_data:2989 !{min_cardinality=1} ! Protein features (key folding sites) +id: EDAM_data:0861 +name: Sequence alignment (words) +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence word alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Alignment of exact matches between subsequences (words) within two or more molecular sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM_operation:0422 -name: Protein cleavage site prediction -namespace: operation -subset: operations -def: "Detect or predict cleavage sites (enzymatic or chemical) in protein sequences." [http://edamontology.org] -is_a: EDAM_operation:3087 ! Protein site detection -relationship: has_output EDAM_data:1323 ! Protein features (cleavage sites) -relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification +id: EDAM_data:0862 +name: Dotplot +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2161 ! Sequence similarity plot [Term] -id: EDAM_operation:0423 -name: Epitope mapping (MHC Class I) -namespace: operation -subset: operations -def: "Predict epitopes that bind to MHC class I molecules." [http://edamontology.org] -is_a: EDAM_operation:0416 ! Epitope mapping +id: EDAM_data:0863 +name: Sequence alignment +subset: bioinformatics +subset: data +subset: edam +synonym: "http://purl.bioontology.org/ontology/MSH/D016415" EXACT [] +synonym: "Sequence:alignment" EXACT [] +synonym: "SIO:010066" EXACT [] +created_in: "beta12orEarlier" +def: "Alignment of multiple molecular sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1916 ! Alignment +relationship: has_topic EDAM_topic:0182 ! Sequence alignment +[Term] +id: EDAM_data:0864 +name: Sequence alignment parameter +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Some simple value controlling a sequence alignment (or similar 'match') operation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM_operation:0424 -name: Epitope mapping (MHC Class II) -namespace: operation -subset: operations -def: "Predict epitopes that bind to MHC class II molecules." [http://edamontology.org] -is_a: EDAM_operation:0416 ! Epitope mapping +id: EDAM_data:0865 +name: Sequence similarity score +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A value representing molecular sequence similarity." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1772 ! Score or penalty [Term] -id: EDAM_operation:0411 -name: Protein signal peptide detection (eukaryotes) -namespace: operation -subset: operations -def: "Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins." [http://edamontology.org] -is_a: EDAM_operation:0418 ! Protein signal peptide detection +id: EDAM_data:0866 +name: Sequence alignment metadata +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0867 ! Sequence alignment report +is_a: EDAM_data:2337 ! Metadata +[Term] +id: EDAM_data:0867 +name: Sequence alignment report +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report of molecular sequence alignment-derived data or metadata." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2083 ! Alignment report [Term] -id: EDAM_operation:0412 -name: Protein signal peptide detection (bacteria) -namespace: operation -subset: operations -def: "Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins." [http://edamontology.org] -is_a: EDAM_operation:0418 ! Protein signal peptide detection +id: EDAM_data:0868 +name: Sequence profile alignment +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A profile-profile alignment (each profile typically representing a sequence alignment)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1916 ! Alignment +[Term] +id: EDAM_data:0869 +name: Sequence-profile alignment +comment: Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1916 ! Alignment +[Term] +id: EDAM_data:0870 +name: Sequence distance matrix +comment: Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. +subset: bioinformatics +subset: data +subset: edam +synonym: "Phylogenetic distance matrix" EXACT [] +xref: Moby:phylogenetic_distance_matrix +created_in: "beta12orEarlier" +def: "A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2855 ! Distance matrix +[Term] +id: EDAM_data:0871 +name: Phylogenetic character data +comment: As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments +subset: bioinformatics +subset: data +subset: edam +synonym: "Character" RELATED [] +created_in: "beta12orEarlier" +def: "Basic character data from which a phylogenetic tree may be generated." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] -id: EDAM_operation:3222 !{since=1.1} -name: Peak calling -namespace: operation -subset: operations -def: "Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data." [http://edamontology.org] -comment: Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). -synonym: "Protein binding peak detection" EXACT [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction - +id: EDAM_data:0872 +name: Phylogenetic tree +comment: A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. +subset: bioinformatics +subset: data +subset: edam +synonym: "http://purl.bioontology.org/ontology/MSH/D010802" RELATED [] +synonym: "Phylogeny" EXACT [] +synonym: "Tree" RELATED [] +xref: Moby:myTree +xref: Moby:phylogenetic_tree +xref: Moby:Tree +created_in: "beta12orEarlier" +def: "The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0084 ! Phylogenetics +[Term] +id: EDAM_data:0874 +name: Comparison matrix +comment: The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). +subset: bioinformatics +subset: data +subset: edam +synonym: "Substitution matrix" EXACT [] +created_in: "beta12orEarlier" +def: "Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2082 ! Matrix [Term] -id: EDAM_operation:2454 -name: Gene and gene component prediction -namespace: operation -subset: operations -def: "Detect, predict and identify genes or components of genes in DNA sequences." [http://edamontology.org] -synonym: "Gene finding" EXACT [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) -relationship: has_topic EDAM_topic:0109 ! Gene finding +id: EDAM_data:0875 +name: Protein topology +comment: The location and size of the secondary structure elements and intervening loop regions is usually indicated. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Predicted or actual protein topology represented as a string of protein secondary structure elements." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0876 ! Protein features (secondary structure) +[Term] +id: EDAM_data:0876 +name: Protein features (secondary structure) +comment: The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein secondary structure" EXACT [] +created_in: "beta12orEarlier" +def: "Secondary structure assignment (predicted or real) of a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +is_a: EDAM_data:2081 ! Secondary structure +relationship: has_topic EDAM_topic:0694 ! Protein secondary structure +[Term] +id: EDAM_data:0877 +name: Protein features (super-secondary) +comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein structure report (super-secondary)" EXACT [] +created_in: "beta12orEarlier" +def: "A report of predicted or actual super-secondary structure of protein sequence(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +is_a: EDAM_data:1537 ! Protein structure report +[Term] +id: EDAM_data:0878 +name: Secondary structure alignment (protein) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of the (1D representations of) secondary structure of two or more proteins." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2366 ! Secondary structure alignment +is_a: EDAM_data:3154 ! Protein alignment [Term] -id: EDAM_operation:0425 -name: Whole gene prediction -namespace: operation -subset: operations -def: "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." [http://edamontology.org] -is_a: EDAM_operation:2454 ! Gene and gene component prediction +id: EDAM_data:0879 +name: Secondary structure alignment metadata (protein) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2083 ! Alignment report +[Term] +id: EDAM_data:0880 +name: RNA secondary structure record +comment: This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. +subset: bioinformatics +subset: data +subset: edam +xref: Moby:RNAStructML +created_in: "beta12orEarlier" +def: "An informative report of secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2081 ! Secondary structure +relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] -id: EDAM_operation:0426 -name: Gene component prediction -namespace: operation -subset: operations -def: "Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences." [http://edamontology.org] -comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. -is_a: EDAM_operation:2454 ! Gene and gene component prediction +id: EDAM_data:0881 +name: Secondary structure alignment (RNA) +subset: bioinformatics +subset: data +subset: edam +xref: Moby:RNAStructAlignmentML +created_in: "beta12orEarlier" +def: "Alignment of the (1D representations of) secondary structure of two or more RNA molecules." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2366 ! Secondary structure alignment +[Term] +id: EDAM_data:0882 +name: Secondary structure alignment metadata (RNA) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report of RNA secondary structure alignment-derived data or metadata." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2083 ! Alignment report [Term] -id: EDAM_operation:0427 -name: Transposon prediction -namespace: operation -subset: operations -def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:1301 ! Nucleic acid features (mobile genetic elements) +id: EDAM_data:0883 +name: Structure +comment: The coordinate data may be predicted or real. +subset: bioinformatics +subset: data +subset: edam +synonym: "http://purl.bioontology.org/ontology/MSH/D015394" RELATED [] +synonym: "Structure data" EXACT [] +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM_operation:0428 -name: PolyA signal detection -namespace: operation -subset: operations -def: "Detect polyA signals in nucleotide sequences." [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:1302 ! Nucleic acid features (PolyA signal or site) +id: EDAM_data:0884 +name: Tertiary structure record +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An entry from a molecular tertiary (3D) structure database." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0883 ! Structure [Term] -id: EDAM_operation:0429 -name: Quadruplex formation site detection -namespace: operation -subset: operations -! alt_id: EDAM_operation:2455 -def: "Detect quadruplex-forming motifs in nucleotide sequences." [http://edamontology.org] -comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -synonym: "Quadruplex structure prediction" EXACT [http://edamontology.org] -relationship: has_output EDAM_data:1303 ! Nucleic acid features (quadruplexes) -relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction +id: EDAM_data:0885 +name: Database hits (structure) +comment: This includes alignment and score data. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Results (hits) from searching a database of tertiary structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2080 ! Database hits [Term] -id: EDAM_operation:0430 -name: CpG island and isochore detection -namespace: operation -subset: operations -! alt_id: EDAM_operation:0576 -def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences." [http://edamontology.org] -comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. -synonym: "CpG island and isochores detection" EXACT [http://edamontology.org] -synonym: "CpG island and isochores rendering" EXACT [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:1304 ! Nucleic acid features (CpG island and isochore) -relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis +id: EDAM_data:0886 +name: Structure alignment +comment: A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of molecular tertiary (3D) structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0883 ! Structure +is_a: EDAM_data:1916 ! Alignment +relationship: has_topic EDAM_topic:0183 ! Structure alignment +[Term] +id: EDAM_data:0887 +name: Structure alignment report +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on molecular tertiary structure alignment-derived data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2083 ! Alignment report [Term] -id: EDAM_operation:0431 -name: Restriction site recognition -namespace: operation -subset: operations -def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:1305 ! Nucleic acid features (restriction sites) -relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction +id: EDAM_data:0888 +name: Structure similarity score +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1772 ! Score or penalty [Term] -id: EDAM_operation:0433 -name: Splice site prediction -namespace: operation -subset: operations -def: "Identify, predict or analyse splice sites in nucleotide sequences." [http://edamontology.org] -comment: Methods might require a pre-mRNA or genomic DNA sequence. -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:1307 ! Nucleic acid features (splice sites) -relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing +id: EDAM_data:0889 +name: Structural (3D) profile +subset: bioinformatics +subset: data +subset: edam +synonym: "3D profile" EXACT [] +created_in: "beta12orEarlier" +def: "Some type of structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] -id: EDAM_operation:0453 -name: Nucleosome formation potential prediction -namespace: operation -subset: operations -def: "Predict nucleosome formation potential of DNA sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0432 ! Nucleosome formation or exclusion sequence prediction +id: EDAM_data:0890 +name: Structural (3D) profile alignment +subset: bioinformatics +subset: data +subset: edam +synonym: "Structural profile alignment" EXACT [] +created_in: "beta12orEarlier" +def: "A 3D profile-3D profile alignment (each profile representing structures or a structure alignment)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1916 ! Alignment [Term] -id: EDAM_operation:0432 -name: Nucleosome formation or exclusion sequence prediction -namespace: operation -subset: operations -def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:1306 ! Nucleic acid features (nucleosome exclusion sequences) +id: EDAM_data:0891 +name: Sequence-3D profile alignment +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence-structural profile alignment" EXACT [] +created_in: "beta12orEarlier" +def: "An alignment of a sequence to a 3D profile (representing structures or a structure alignment)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0893 ! Sequence-structure alignment +[Term] +id: EDAM_data:0892 +name: Protein sequence-structure scoring matrix +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Matrix of values used for scoring sequence-structure compatibility." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2082 ! Matrix [Term] -id: EDAM_operation:0434 -name: Integrated gene prediction -namespace: operation -subset: operations -def: "Predict whole gene structure using a combination of multiple methods to achieve better predictions." [http://edamontology.org] -is_a: EDAM_operation:0425 ! Whole gene prediction +id: EDAM_data:0893 +name: Sequence-structure alignment +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s))." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1916 ! Alignment +[Term] +id: EDAM_data:0894 +name: Amino acid annotation +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report about a specific amino acid." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0962 ! Small molecule annotation +is_a: EDAM_data:2016 ! Amino acid property [Term] -id: EDAM_operation:0435 -name: Operon prediction -namespace: operation -subset: operations -def: "Find operons (operators, promoters and genes) in bacteria genes." [http://edamontology.org] -is_a: EDAM_operation:0425 ! Whole gene prediction +id: EDAM_data:0895 +name: Peptide annotation +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report about a specific peptide." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0962 ! Small molecule annotation +is_a: EDAM_data:2979 ! Peptide property +relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids +[Term] +id: EDAM_data:0896 +name: Protein report +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene product annotation" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2529 ! Molecule report +relationship: has_topic EDAM_topic:0078 ! Protein analysis [Term] -id: EDAM_operation:0464 -name: tRNA gene prediction -namespace: operation -subset: operations -def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [http://edamontology.org] -is_a: EDAM_operation:0425 ! Whole gene prediction -relationship: has_topic EDAM_topic:0663 ! tRNA +id: EDAM_data:0897 +name: Protein property +comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein physicochemical property" EXACT [] +created_in: "beta12orEarlier" +def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0896 ! Protein report +is_a: EDAM_data:2087 ! Molecular property [Term] -id: EDAM_operation:0436 -name: Coding region prediction -namespace: operation -subset: operations -def: "Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences." [http://edamontology.org] -is_a: EDAM_operation:0426 ! Gene component prediction -relationship: has_output EDAM_data:1313 ! Nucleic acid features (coding sequence) +id: EDAM_data:0899 +name: Protein features (3D motif) +comment: This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein structure report (3D motif)" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on the 3D structural motifs in a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +is_a: EDAM_data:1537 ! Protein structure report +relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces +[Term] +id: EDAM_data:0900 +name: Protein domain classification +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2980 ! Protein classification +relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] -id: EDAM_operation:0437 -name: Selenocysteine insertion sequence (SECIS) prediction -namespace: operation -subset: operations -def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [http://edamontology.org] -comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. -is_a: EDAM_operation:0426 ! Gene component prediction -relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) +id: EDAM_data:0901 +name: Protein features (domains) +comment: The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein domain assignment" EXACT [] +synonym: "Protein structural domains" EXACT [] +created_in: "beta12orEarlier" +def: "Summary of structural domains or 3D folds in a protein or polypeptide chain." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] -id: EDAM_operation:0438 -name: Transcription regulatory element prediction -namespace: operation -subset: operations -def: "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences." [http://edamontology.org] -comment: This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. -is_a: EDAM_operation:0426 ! Gene component prediction -relationship: has_topic EDAM_topic:0110 ! Transcription -relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites +id: EDAM_data:0902 +name: Protein architecture report +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein property (architecture)" EXACT [] +synonym: "Protein structure report (architecture)" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on architecture (spatial arrangement of secondary structure) of a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property +is_a: EDAM_data:1537 ! Protein structure report +[Term] +id: EDAM_data:0903 +name: Protein folding report +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein property (folding)" EXACT [] +synonym: "Protein report (folding)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_operation:0439 -name: Translation initiation site prediction -namespace: operation -subset: operations -def: "Predict translation initiation sites, possibly by searching a database of sites." [http://edamontology.org] -is_a: EDAM_operation:0436 ! Coding region prediction -relationship: has_topic EDAM_topic:0108 ! Translation +id: EDAM_data:0904 +name: Protein features (mutation) +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein property (mutation)" EXACT [] +synonym: "Protein report (mutation)" EXACT [] +synonym: "Protein structure report (mutation)" EXACT [] +created_in: "beta12orEarlier" +def: "Data on the effect of (typically point) mutation on protein folding, stability, structure and function." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0896 ! Protein report [Term] -id: EDAM_operation:0440 -name: Promoter prediction -namespace: operation -subset: operations -def: "Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences." [http://edamontology.org] -comment: Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. -is_a: EDAM_operation:0438 ! Transcription regulatory element prediction -relationship: has_output EDAM_data:1312 ! Gene features (promoter) +id: EDAM_data:0905 +name: Protein interaction raw data +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3108 ! Experimental measurement [Term] -id: EDAM_operation:0441 -name: Transcription regulatory element prediction (DNA-cis) -namespace: operation -subset: operations -def: "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." [http://edamontology.org] -comment: Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. -is_a: EDAM_operation:0438 ! Transcription regulatory element prediction +id: EDAM_data:0906 +name: Protein interaction +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein report (interaction)" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0896 ! Protein report +is_a: EDAM_data:2599 ! Molecular interaction +relationship: has_topic EDAM_topic:0128 ! Protein interactions +[Term] +id: EDAM_data:0907 +name: Protein family +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein family annotation" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on a specific protein family or other group of classified proteins." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2980 ! Protein classification +relationship: has_topic EDAM_topic:0724 ! Protein families [Term] -id: EDAM_operation:0442 -name: Transcription regulatory element prediction (RNA-cis) -namespace: operation -subset: operations -def: "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." [http://edamontology.org] -comment: Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. -is_a: EDAM_operation:0438 ! Transcription regulatory element prediction +id: EDAM_data:0909 +name: Vmax +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2024 ! Enzyme kinetics data +[Term] +id: EDAM_data:0910 +name: Km +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] -id: EDAM_operation:0443 -name: Transcription regulatory element prediction (trans) -namespace: operation -subset: operations -def: "Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets." [http://edamontology.org] -comment: Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. -synonym: "Functional RNA identification" EXACT [http://edamontology.org] -is_a: EDAM_operation:0438 ! Transcription regulatory element prediction -relationship: has_topic EDAM_topic:3060 ! Regulatory RNA +id: EDAM_data:0911 +name: Nucleotide base annotation +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report about a specific nucleotide base." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0962 ! Small molecule annotation +[Term] +id: EDAM_data:0912 +name: Nucleic acid property +comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics +subset: data +subset: edam +synonym: "Nucleic acid physicochemical property" EXACT [] +created_in: "beta12orEarlier" +def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2084 ! Nucleic acid report +is_a: EDAM_data:2087 ! Molecular property [Term] -id: EDAM_operation:0444 -name: Matrix/scaffold attachment site prediction -namespace: operation -subset: operations -def: "Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences." [http://edamontology.org] -comment: MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. -is_a: EDAM_operation:0438 ! Transcription regulatory element prediction -relationship: has_output EDAM_data:1308 ! Nucleic acid features (matrix/scaffold attachment sites) +id: EDAM_data:0914 +name: Codon usage report +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report +relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] -id: EDAM_operation:0445 -name: Transcription factor binding site prediction -namespace: operation -subset: operations -def: "Identify or predict transcription factor binding sites in DNA sequences." [http://edamontology.org] -is_a: EDAM_operation:0440 ! Promoter prediction -relationship: has_output EDAM_data:1315 ! Gene features (TFBS) +id: EDAM_data:0916 +name: Gene annotation +comment: This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene annotation (functional)" EXACT [] +synonym: "Gene report" EXACT [] +xref: Moby:gene +xref: Moby:GeneInfo +xref: Moby_namespace:Human_Readable_Description +created_in: "beta12orEarlier" +def: "An informative report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features +relationship: has_topic EDAM_topic:0623 ! Genes, gene family or system +[Term] +id: EDAM_data:0917 +name: Gene classification +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0916 ! Gene annotation [Term] -id: EDAM_operation:0446 -name: Exonic splicing enhancer prediction -namespace: operation -subset: operations -def: "Identify or predict exonic splicing enhancers (ESE) in exons." [http://edamontology.org] -comment: An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. -is_a: EDAM_operation:0440 ! Promoter prediction -relationship: has_output EDAM_data:2397 ! Nucleic acid features (exon) -relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing +id: EDAM_data:0918 +name: Nucleic acid features (variation) +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence variation annotation" EXACT [] +synonym: "SO:0001059" RELATED [] +created_in: "beta12orEarlier" +def: "A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3122 ! Nucleic acid features (difference and change) +relationship: has_topic EDAM_topic:0199 ! Genetic variation [Term] -id: EDAM_operation:2008 -name: siRNA duplex prediction -namespace: operation -subset: operations -def: "Identify or predict siRNA duplexes in RNA." [http://edamontology.org] -is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) -relationship: has_output EDAM_data:2169 ! Nucleic acid features (siRNA) -relationship: has_topic EDAM_topic:3060 ! Regulatory RNA - +id: EDAM_data:0919 +name: Gene annotation (chromosome) +comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific chromosome." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0916 ! Gene annotation +relationship: has_topic EDAM_topic:0624 ! Chromosomes [Term] -id: EDAM_operation:0465 -name: siRNA binding specificity prediction -namespace: operation -subset: operations -def: "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." [http://edamontology.org] -is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) -relationship: has_topic EDAM_topic:3060 ! Regulatory RNA +id: EDAM_data:0920 +name: Genotype/phenotype annotation +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report +[Term] +id: EDAM_data:0922 +name: Nucleic acid features (primers) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination) +relationship: has_topic EDAM_topic:0632 ! Probes and primers [Term] -id: EDAM_operation:0463 -name: microRNA detection -namespace: operation -subset: operations -def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence." [http://edamontology.org] -is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) -relationship: has_output EDAM_data:1310 ! Nucleic acid features (microRNA) +id: EDAM_data:0923 +name: Experiment annotation (PCR assay data) +subset: bioinformatics +subset: data +subset: edam +synonym: "PCR assay data" EXACT [] +created_in: "beta12orEarlier" +def: "Data on a PCR assay or electronic / virtual PCR." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2531 ! Experiment annotation +relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis +[Term] +id: EDAM_data:0924 +name: Sequence trace +comment: This is the raw data produced by a DNA sequencing machine. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2887 ! Sequence record (nucleic acid) +is_a: EDAM_data:3108 ! Experimental measurement +[Term] +id: EDAM_data:0925 +name: Sequence assembly +comment: Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence:assembly" EXACT [] +synonym: "SO:0000353" EXACT [] +synonym: "SO:0001248" NARROW [] +created_in: "beta12orEarlier" +def: "An assembly of fragments of a (typically genomic) DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] -id: EDAM_operation:0259 -name: Sequence alignment comparison -namespace: operation -subset: operations -def: "Compare (typically by aligning) two molecular sequence alignments." [http://edamontology.org] -comment: See also 'Sequence profile alignment'. -is_a: EDAM_operation:0258 ! Sequence alignment analysis -is_a: EDAM_operation:2424 ! Comparison +id: EDAM_data:0926 +name: Radiation Hybrid (RH) scores +comment: Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Radiation hybrid scores (RH) scores for one or more markers." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3108 ! Experimental measurement [Term] -id: EDAM_operation:0260 -name: Sequence alignment conversion -namespace: operation -subset: operations -def: "Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence)." [http://edamontology.org] -is_a: EDAM_operation:3081 ! Sequence alignment editing +id: EDAM_data:0927 +name: Gene annotation (linkage) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on the linkage of alleles." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0916 ! Gene annotation +[Term] +id: EDAM_data:0928 +name: Gene expression profile +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene expression pattern" EXACT [] +created_in: "beta12orEarlier" +def: "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_operation:0447 -name: Sequence alignment quality evaluation -namespace: operation -subset: operations -def: "Evaluate molecular sequence alignment accuracy." [http://edamontology.org] -comment: Evaluation might be purely sequence-based or use structural information. -is_a: EDAM_operation:2428 ! Evaluation and validation -is_a: EDAM_operation:0258 ! Sequence alignment analysis +id: EDAM_data:0931 +name: Experiment annotation (microarray) +comment: This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. +subset: bioinformatics +subset: data +subset: edam +synonym: "Experimental design annotation" EXACT [] +created_in: "beta12orEarlier" +def: "Information on a microarray experiment such as conditions, protocol, sample:data relationships etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2531 ! Experiment annotation +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] -id: EDAM_operation:0448 -name: Sequence alignment analysis (conservation) -namespace: operation -subset: operations -def: "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." [http://edamontology.org] -comment: Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. -is_a: EDAM_operation:0258 ! Sequence alignment analysis -relationship: has_output EDAM_data:1415 ! Sequence alignment report (site conservation) +id: EDAM_data:0932 +name: Oligonucleotide probe data +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data on oligonucleotide probes (typically for use with DNA microarrays)." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2717 ! Oligonucleotide probe annotation [Term] -id: EDAM_operation:0449 -name: Sequence alignment analysis (site correlation) -namespace: operation -subset: operations -def: "Analyse correlations between sites in a molecular sequence alignment." [http://edamontology.org] -comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. -is_a: EDAM_operation:0258 ! Sequence alignment analysis -relationship: has_output EDAM_data:1416 ! Sequence alignment report (site correlation) +id: EDAM_data:0933 +name: SAGE experimental data +subset: bioinformatics +subset: data +subset: edam +synonym: "Serial analysis of gene expression (SAGE) experimental data" EXACT [] +created_in: "beta12orEarlier" +def: "Output from a serial analysis of gene expression (SAGE) experiment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2535 ! Sequence tag profile [Term] -id: EDAM_operation:0450 -name: Sequence alignment analysis (chimeric sequence detection) -namespace: operation -subset: operations -def: "Detects chimeric sequences (chimeras) from a sequence alignment." [http://edamontology.org] -comment: A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. -is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) -relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis +id: EDAM_data:0934 +name: MPSS experimental data +subset: bioinformatics +subset: data +subset: edam +synonym: "Massively parallel signature sequencing (MPSS) experimental data" EXACT [] +created_in: "beta12orEarlier" +def: "Massively parallel signature sequencing (MPSS) data." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2535 ! Sequence tag profile +[Term] +id: EDAM_data:0935 +name: SBS experimental data +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequencing by synthesis (SBS) experimental data" EXACT [] +created_in: "beta12orEarlier" +def: "Sequencing by synthesis (SBS) data." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2535 ! Sequence tag profile [Term] -id: EDAM_operation:0451 -name: Sequence alignment analysis (recombination detection) -namespace: operation -subset: operations -def: "Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment." [http://edamontology.org] -comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. -is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) +id: EDAM_data:0936 +name: Sequence tag profile (with gene assignment) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2535 ! Sequence tag profile +[Term] +id: EDAM_data:0937 +name: Protein X-ray crystallographic data +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "X-ray crystallography data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2537 ! Protein structure raw data [Term] -id: EDAM_operation:0452 -name: Sequence alignment analysis (indel detection) -namespace: operation -subset: operations -def: "Identify insertion, deletion and duplication events from a sequence alignment." [http://edamontology.org] -comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. -is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) +id: EDAM_data:0938 +name: Protein NMR data +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Protein nuclear magnetic resonance (NMR) raw data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2537 ! Protein structure raw data +[Term] +id: EDAM_data:0939 +name: Protein circular dichroism (CD) spectroscopic data +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2537 ! Protein structure raw data [Term] -id: EDAM_operation:0457 -name: Nucleic acid stitch profile plotting -namespace: operation -subset: operations -def: "Calculate and plot a DNA or DNA/RNA stitch profile." [http://edamontology.org] -comment: A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. -is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting -relationship: has_output EDAM_data:1587 ! Nucleic acid stitch profile +id: EDAM_data:0940 +name: Electron microscopy volume map +subset: bioinformatics +subset: data +subset: edam +synonym: "EM volume map" EXACT [] +created_in: "beta12orEarlier" +def: "Volume map data from electron microscopy." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3108 ! Experimental measurement +relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] -id: EDAM_operation:0458 -name: Nucleic acid melting curve plotting -namespace: operation -subset: operations -def: "Calculate and plot a DNA or DNA/RNA melting curve." [http://edamontology.org] -is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting -relationship: has_output EDAM_data:2958 ! Nucleic acid melting curve +id: EDAM_data:0941 +name: Electron microscopy model +comment: This might include the location in the model of the known features of a particular macromolecule. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Annotation on a structural 3D model (volume map) from electron microscopy." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0940 ! Electron microscopy volume map +relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] -id: EDAM_operation:0459 -name: Nucleic acid probability profile plotting -namespace: operation -subset: operations -def: "Calculate and plot a DNA or DNA/RNA probability profile." [http://edamontology.org] -is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting -relationship: has_output EDAM_data:2959 ! Nucleic acid probability profile +id: EDAM_data:0942 +name: 2D PAGE image +subset: bioinformatics +subset: data +subset: edam +synonym: "Two-dimensional gel electrophoresis image" EXACT [] +created_in: "beta12orEarlier" +def: "Two-dimensional gel electrophoresis image." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2968 ! Image +is_a: EDAM_data:3108 ! Experimental measurement +relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] -id: EDAM_operation:0460 -name: Nucleic acid temperature profile plotting -namespace: operation -subset: operations -def: "Calculate and plot a DNA or DNA/RNA temperature profile." [http://edamontology.org] -is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting -relationship: has_output EDAM_data:2960 ! Nucleic acid temperature profile - +id: EDAM_data:0943 +name: Mass spectrometry spectra +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Spectra from mass spectrometry." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2536 ! Mass spectrometry data +relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] -id: EDAM_operation:2444 -name: Protein secondary structure processing -namespace: operation -subset: operations -def: "Process (read and / or write) protein secondary structure data." [http://edamontology.org] -is_a: EDAM_operation:2482 ! Secondary structure processing -is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_input EDAM_data:0876 !{min_cardinality=0} ! Protein features (secondary structure) -relationship: has_output EDAM_data:0876 !{min_cardinality=0} ! Protein features (secondary structure) -relationship: has_topic EDAM_topic:0694 ! Protein secondary structure +id: EDAM_data:0944 +name: Peptide mass fingerprint +subset: bioinformatics +subset: data +subset: edam +synonym: "Peak list" EXACT [] +synonym: "Protein fingerprint" EXACT [] +created_in: "beta12orEarlier" +def: "A set of peptide masses (peptide mass fingerprint) from mass spectrometry." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2536 ! Mass spectrometry data +is_a: EDAM_data:2979 ! Peptide property +relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] -id: EDAM_operation:0319 -name: Protein secondary structure assignment -namespace: operation -subset: operations -def: "Assign secondary structure from protein coordinate or experimental data." [http://edamontology.org] -is_a: EDAM_operation:2444 ! Protein secondary structure processing -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM_data:0876 !{min_cardinality=1} ! Protein features (secondary structure) -relationship: has_topic EDAM_topic:2226 ! Structure determination +id: EDAM_data:0945 +name: Peptide identification +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2979 ! Peptide property +relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] -id: EDAM_operation:0267 -name: Protein secondary structure prediction -namespace: operation -subset: operations -def: "Predict secondary structure of protein sequences." [http://edamontology.org] -comment: Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. -synonym: "Secondary structure prediction (protein)" EXACT [http://edamontology.org] -is_a: EDAM_operation:2444 ! Protein secondary structure processing -is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM_data:0876 !{min_cardinality=1} ! Protein features (secondary structure) -relationship: has_topic EDAM_topic:0178 ! Protein secondary structure prediction +id: EDAM_data:0946 +name: Pathway or network annotation +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2984 ! Pathway or network report [Term] -id: EDAM_operation:0268 -name: Protein super-secondary structure prediction -namespace: operation -subset: operations -def: "Predict super-secondary structure of protein sequence(s)." [http://edamontology.org] -comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. -is_a: EDAM_operation:0267 ! Protein secondary structure prediction -relationship: has_output EDAM_data:0877 ! Protein features (super-secondary) +id: EDAM_data:0947 +name: Biological pathway map +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A map (typically a diagram) of a biological pathway." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM_operation:0534 -name: Protein secondary structure assignment (from coordinate data) -namespace: operation -subset: operations -def: "Assign secondary structure from protein coordinate data." [http://edamontology.org] -is_a: EDAM_operation:0319 ! Protein secondary structure assignment -is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) +id: EDAM_data:0948 +name: Data resource definition +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1883 ! Annotated URI [Term] -id: EDAM_operation:0535 -name: Protein secondary structure assignment (from CD data) -namespace: operation -subset: operations -def: "Assign secondary structure from circular dichroism (CD) spectroscopic data." [http://edamontology.org] -is_a: EDAM_operation:0319 ! Protein secondary structure assignment -relationship: has_input EDAM_data:0939 ! Protein circular dichroism (CD) spectroscopic data +id: EDAM_data:0949 +name: Workflow metadata +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata [Term] -id: EDAM_operation:1847 -name: DSSP secondary structure assignment -namespace: operation -subset: operations -def: "Determine for residue the DSSP determined secondary structure in three-state (HSC)." [http://edamontology.org, WHATIF] -xref: WHATIF: ResidueDSSP -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data) - +id: EDAM_data:0950 +name: Biological model +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A biological model which can be represented in mathematical terms." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0771 ! Biological models [Term] -id: EDAM_operation:0467 -name: Protein secondary structure prediction (integrated) -namespace: operation -subset: operations -def: "Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions." [http://edamontology.org] -is_a: EDAM_operation:0267 ! Protein secondary structure prediction +id: EDAM_data:0951 +name: Statistical estimate score +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A value representing estimated statistical significance of some observed data; typically sequence database hits." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1772 ! Score or penalty +is_a: EDAM_data:2914 ! Sequence features metadata [Term] -id: EDAM_operation:0468 -name: Protein secondary structure prediction (helices) -namespace: operation -subset: operations -def: "Predict helical secondary structure of protein sequences." [http://edamontology.org] -is_a: EDAM_operation:0267 ! Protein secondary structure prediction +id: EDAM_data:0952 +name: EMBOSS database resource definition +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Resource definition for an EMBOSS database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0957 ! Database metadata +[Term] +id: EDAM_data:0953 +name: Version information +comment: Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. +subset: bioinformatics +subset: data +subset: edam +synonym: "IAO:0000129" NARROW [] +synonym: "SIO:000653" NARROW [] +synonym: "SWO:9000061" NARROW [] +synonym: "Version" EXACT [] +created_in: "beta12orEarlier" +def: "Information on a version of software or data, for example name, version number and release date." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata [Term] -id: EDAM_operation:0469 -name: Protein secondary structure prediction (turns) -namespace: operation -subset: operations -def: "Predict turn structure (for example beta hairpin turns) of protein sequences." [http://edamontology.org] -is_a: EDAM_operation:0267 ! Protein secondary structure prediction +id: EDAM_data:0954 +name: Database cross-mapping +comment: The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2093 ! Data reference [Term] -id: EDAM_operation:0470 -name: Protein secondary structure prediction (coils) -namespace: operation -subset: operations -def: "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." [http://edamontology.org] -is_a: EDAM_operation:0267 ! Protein secondary structure prediction +id: EDAM_data:0955 +name: Data index +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An index of data of biological relevance." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] -id: EDAM_operation:0471 -name: Protein secondary structure prediction (disulfide bonds) -namespace: operation -subset: operations -def: "Predict cysteine bonding state and disulfide bond partners in protein sequences." [http://edamontology.org] -is_a: EDAM_operation:0267 ! Protein secondary structure prediction +id: EDAM_data:0956 +name: Data index report +subset: bioinformatics +subset: data +subset: edam +synonym: "Database index annotation" EXACT [] +created_in: "beta12orEarlier" +def: "A report of an analysis of an index of biological data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report +relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] -id: EDAM_operation:0269 -name: Transmembrane protein prediction -namespace: operation -subset: operations -def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [http://edamontology.org] -is_a: EDAM_operation:0270 ! Transmembrane protein analysis -is_a: EDAM_operation:0267 ! Protein secondary structure prediction -relationship: has_output EDAM_data:1456 !{min_cardinality=1} ! Protein features (membrane regions) +id: EDAM_data:0957 +name: Database metadata +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3106 ! System metadata [Term] -id: EDAM_operation:2456 -name: GPCR classification -namespace: operation -subset: operations -def: "Classify G-protein coupled receptors (GPCRs) into families and subfamilies." [http://edamontology.org] -synonym: "G protein-coupled receptor (GPCR) classification" EXACT [http://edamontology.org] -is_a: EDAM_operation:0473 ! GPCR analysis -is_a: EDAM_operation:2995 ! Sequence classification -relationship: has_output EDAM_data:0907 !{min_cardinality=1} ! Protein family +id: EDAM_data:0958 +name: Tool metadata +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3106 ! System metadata +[Term] +id: EDAM_data:0959 +name: Job metadata +subset: bioinformatics +subset: data +subset: edam +xref: Moby:PDGJOB +created_in: "beta12orEarlier" +def: "Textual metadata on a submitted or completed job." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3106 ! System metadata [Term] -id: EDAM_operation:2457 -name: GPCR coupling selectivity prediction -namespace: operation -subset: operations -def: "Predict G-protein coupled receptor (GPCR) coupling selectivity." [http://edamontology.org] -is_a: EDAM_operation:0473 ! GPCR analysis -is_a: EDAM_operation:2492 ! Protein interaction prediction -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:0896 !{min_cardinality=1} ! Protein report +id: EDAM_data:0960 +name: User metadata +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Textual metadata on a software author or end-user, for example a person or other software." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3106 ! System metadata +[Term] +id: EDAM_data:0962 +name: Small molecule annotation +subset: bioinformatics +subset: data +subset: edam +synonym: "Chemical compound annotation" EXACT [] +synonym: "Small molecule report" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on a specific chemical compound." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2085 ! Structure report +is_a: EDAM_data:2529 ! Molecule report +relationship: has_topic EDAM_topic:0154 ! Small molecules [Term] -id: EDAM_operation:0473 -name: GPCR analysis -namespace: operation -subset: operations -def: "Analyse G-protein coupled receptor proteins (GPCRs)." [http://edamontology.org] -synonym: "G protein-coupled receptor (GPCR) analysis" EXACT [http://edamontology.org] -is_a: EDAM_operation:0270 ! Transmembrane protein analysis -relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) -relationship: has_topic EDAM_topic:0820 ! Membrane proteins +id: EDAM_data:0963 +name: Cell line annotation +subset: bioinformatics +subset: data +subset: edam +synonym: "Organism strain data" EXACT [] +created_in: "beta12orEarlier" +def: "Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2530 ! Organism annotation +[Term] +id: EDAM_data:0964 +name: Scent annotation +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report about a specific scent." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0962 ! Small molecule annotation [Term] -id: EDAM_operation:0472 -name: GPCR prediction -namespace: operation -subset: operations -def: "Predict G protein-coupled receptors (GPCR)." [http://edamontology.org] -synonym: "G protein-coupled receptor (GPCR) prediction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0269 ! Transmembrane protein prediction -is_a: EDAM_operation:0473 ! GPCR analysis +id: EDAM_data:0966 +name: Ontology term +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A term (name) from an ontology." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0967 ! Ontology concept metadata [Term] -id: EDAM_operation:0474 -name: Protein structure prediction -namespace: operation -subset: operations -def: "Predict tertiary structure (backbone and side-chain conformation) of protein sequences." [http://edamontology.org] -is_a: EDAM_operation:0271 ! Structure prediction -is_a: EDAM_operation:2459 ! Structure processing (protein) -is_a: EDAM_operation:2479 ! Protein sequence analysis -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM_data:1460 !{min_cardinality=1} ! Protein structure -relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction +id: EDAM_data:0967 +name: Ontology concept metadata +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning or derived from a concept from a biological ontology." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] -id: EDAM_operation:0475 -name: Nucleic acid structure prediction -namespace: operation -subset: operations -def: "Predict tertiary structure of DNA or RNA." [http://edamontology.org] -comment: Methods might identify thermodynamically stable or evolutionarily conserved structures. -is_a: EDAM_operation:0271 ! Structure prediction -is_a: EDAM_operation:2519 ! Structure processing (nucleic acid) -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM_data:1459 !{min_cardinality=1} ! Nucleic acid structure -relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction +id: EDAM_data:0968 +name: Keyword +comment: Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. +subset: bioinformatics +subset: data +subset: edam +xref: Moby:BooleanQueryString +xref: Moby:Global_Keyword +xref: Moby:QueryString +xref: Moby:Wildcard_Query +created_in: "beta12orEarlier" +def: "Keyword(s) or phrase(s) used (typically) for text-searching purposes." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM_operation:0476 -name: Ab initio structure prediction -namespace: operation -subset: operations -def: "Predict tertiary structure of protein sequence(s) without homologs of known structure." [http://edamontology.org] -is_a: EDAM_operation:0474 ! Protein structure prediction -relationship: has_topic EDAM_topic:0174 ! Ab initio structure prediction +id: EDAM_data:0970 +name: Bibliographic reference +comment: A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. +subset: bioinformatics +subset: data +subset: edam +synonym: "Citation" EXACT [] +synonym: "Reference" EXACT [] +xref: Moby:GCP_SimpleCitation +xref: Moby:Publication +created_in: "beta12orEarlier" +def: "Bibliographic data that uniquely identifies a scientific article, book or other published material." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2093 ! Data reference +is_a: EDAM_data:2857 ! Article metadata +[Term] +id: EDAM_data:0971 +name: Article +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A body of scientific text, typically a full text article from a scientific journal." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:3068 ! Literature and reference [Term] -id: EDAM_operation:0477 -name: Protein modelling -namespace: operation -subset: operations -def: "Build a three-dimensional protein model based on known (for example homologs) structures." [http://edamontology.org] -comment: The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. -synonym: "Comparative modelling" EXACT [http://edamontology.org] -synonym: "Homology modelling" EXACT [http://edamontology.org] -synonym: "Homology structure modelling" EXACT [http://edamontology.org] -synonym: "Protein structure comparative modelling" EXACT [http://edamontology.org] -is_a: EDAM_operation:2406 ! Protein structure analysis -is_a: EDAM_operation:0474 ! Protein structure prediction -is_a: EDAM_operation:2426 ! Modelling and simulation -relationship: has_topic EDAM_topic:0175 ! Homology modelling +id: EDAM_data:0972 +name: Text mining report +comment: A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An abstract of the results of text mining." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2954 ! Article report +[Term] +id: EDAM_data:0974 +name: Entity identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a biological entity or phenomenon." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0842 ! Identifier [Term] -id: EDAM_operation:0478 -name: Protein docking -namespace: operation -subset: operations -def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [http://edamontology.org] -comment: This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. -is_a: EDAM_operation:0477 ! Protein modelling -is_a: EDAM_operation:2492 ! Protein interaction prediction -relationship: has_output EDAM_data:1461 !{min_cardinality=0} ! Protein-ligand complex -relationship: has_output EDAM_data:2877 !{min_cardinality=0} ! Protein complex -relationship: has_topic EDAM_topic:0177 ! Molecular docking +id: EDAM_data:0975 +name: Data resource identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a data resource." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0842 ! Identifier +[Term] +id: EDAM_data:0976 +name: Identifier (typed) +comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier that identifies a particular type of data." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0842 ! Identifier [Term] -id: EDAM_operation:0302 -name: Protein threading -namespace: operation -subset: operations -def: "Align molecular sequence to structure in 3D space (threading)." [http://edamontology.org] -comment: Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. -synonym: "Sequence-structure alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:0303 ! Protein fold recognition -is_a: EDAM_operation:2928 ! Alignment construction -relationship: has_input EDAM_data:1460 !{min_cardinality=1} ! Protein structure -relationship: has_output EDAM_data:0893 !{min_cardinality=1} ! Sequence-structure alignment -relationship: has_topic EDAM_topic:0175 ! Homology modelling -relationship: has_topic EDAM_topic:0184 ! Threading +id: EDAM_data:0977 +name: Tool identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a bioinformatics tool, e.g. an application or web service." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +[Term] +id: EDAM_data:0978 +name: Discrete entity identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence)." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0842 ! Identifier [Term] -id: EDAM_operation:0479 -name: Protein modelling (backbone) -namespace: operation -subset: operations -def: "Model protein backbone conformation." [http://edamontology.org] -comment: Methods might require a preliminary C(alpha) trace. -is_a: EDAM_operation:0477 ! Protein modelling +id: EDAM_data:0979 +name: Entity feature identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing)." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0842 ! Identifier [Term] -id: EDAM_operation:0480 -name: Protein modelling (side chains) -namespace: operation -subset: operations -def: "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc." [http://edamontology.org] -comment: Methods might use a residue rotamer library. -is_a: EDAM_operation:0477 ! Protein modelling +id: EDAM_data:0980 +name: Entity collection identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of a collection of discrete biological entities." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0842 ! Identifier [Term] -id: EDAM_operation:0481 -name: Protein modelling (loops) -namespace: operation -subset: operations -def: "Model loop conformation in protein structures." [http://edamontology.org] -is_a: EDAM_operation:0477 ! Protein modelling +id: EDAM_data:0981 +name: Phenomenon identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of a physical, observable biological occurrence or event." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0842 ! Identifier [Term] -id: EDAM_operation:1841 -name: Rotamer likelihood prediction -namespace: operation -subset: operations -def: "Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure." [http://edamontology.org, WHATIF] -comment: Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. -xref: WHATIF:ShowLikelyRotamers -xref: WHATIF:ShowLikelyRotamers100 -xref: WHATIF:ShowLikelyRotamers200 -xref: WHATIF:ShowLikelyRotamers300 -xref: WHATIF:ShowLikelyRotamers400 -xref: WHATIF:ShowLikelyRotamers500 -xref: WHATIF:ShowLikelyRotamers600 -xref: WHATIF:ShowLikelyRotamers700 -xref: WHATIF:ShowLikelyRotamers800 -xref: WHATIF:ShowLikelyRotamers900 -is_a: EDAM_operation:0480 ! Protein modelling (side chains) +id: EDAM_data:0982 +name: Molecule identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of a molecule." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:2529 ! Molecule report +[Term] +id: EDAM_data:0983 +name: Atom identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier (e.g. character symbol) of a specific atom." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_operation:0482 -name: Protein-ligand docking -namespace: operation -subset: operations -def: "Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques." [http://edamontology.org] -comment: Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. -synonym: "Virtual ligand screening" EXACT [http://edamontology.org] -is_a: EDAM_operation:0478 ! Protein docking -relationship: has_output EDAM_data:1461 !{min_cardinality=1} ! Protein-ligand complex -relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions +id: EDAM_data:0984 +name: Molecule name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a specific molecule." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0982 ! Molecule identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_operation:0483 -name: Structured RNA prediction and optimisation -namespace: operation -subset: operations -def: "Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection." [http://edamontology.org] -synonym: "RNA inverse folding" EXACT [http://edamontology.org] -synonym: "Nucleic acid folding family identification" EXACT [http://edamontology.org] -is_a: EDAM_operation:3095 ! Nucleic acid design -is_a: EDAM_operation:2425 ! Optimisation and refinement -relationship: has_output EDAM_data:1234 ! Sequence set (nucleic acid) -relationship: has_topic EDAM_topic:2953 ! Nucleic acid design +id: EDAM_data:0985 +name: Molecule type +comment: For example, 'Protein', 'DNA', 'RNA' etc. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A label (text token) describing the type a molecule." [http://edamontology.org] +example: "Protein|DNA|RNA" +namespace: data +is_a: EDAM_data:2100 ! Type [Term] -id: EDAM_operation:0273 -name: Protein interaction raw data analysis -namespace: operation -subset: operations -def: "Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [http://edamontology.org] -is_a: EDAM_operation:2949 ! Protein interaction analysis -relationship: has_input EDAM_data:0905 ! Protein interaction raw data -relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions +id: EDAM_data:0986 +name: Chemical identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a chemical compound." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1086 ! Compound identifier [Term] -id: EDAM_operation:2492 -name: Protein interaction prediction -namespace: operation -subset: operations -def: "Predict the interactions of proteins with other molecules." [http://edamontology.org] -is_a: EDAM_operation:2405 ! Protein interaction data processing -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM_data:0906 !{min_cardinality=1} ! Protein interaction +id: EDAM_data:0987 +name: Chromosome name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a chromosome." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0984 ! Molecule name +is_a: EDAM_data:2119 ! Nucleic acid identifier +relationship: is_identifier_of EDAM_data:0919 ! Gene annotation (chromosome) [Term] -id: EDAM_operation:2464 -name: Protein-protein interaction prediction -namespace: operation -subset: operations -def: "Identify or predict protein-protein interactions, interfaces, binding sites etc." [http://edamontology.org] -is_a: EDAM_operation:2492 ! Protein interaction prediction -relationship: has_output EDAM_data:1565 !{min_cardinality=1} ! Protein-protein interaction -relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions +id: EDAM_data:0988 +name: Peptide identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a peptide chain." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0982 ! Molecule identifier +[Term] +id: EDAM_data:0989 +name: Protein identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a protein." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0982 ! Molecule identifier +relationship: is_identifier_of EDAM_data:0896 ! Protein report [Term] -id: EDAM_operation:0274 -name: Protein-protein interaction prediction (from protein sequence) -namespace: operation -subset: operations -def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." [http://edamontology.org] -is_a: EDAM_operation:2464 ! Protein-protein interaction prediction -is_a: EDAM_operation:3084 ! Protein function prediction (from sequence) +id: EDAM_data:0990 +name: Compound name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Chemical name" EXACT [] +created_in: "beta12orEarlier" +def: "Unique name of a chemical compound." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0984 ! Molecule name +is_a: EDAM_data:1086 ! Compound identifier [Term] -id: EDAM_operation:0275 -name: Protein-protein interaction prediction (from protein structure) -namespace: operation -subset: operations -def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [http://edamontology.org] -is_a: EDAM_operation:2464 ! Protein-protein interaction prediction -is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) +id: EDAM_data:0991 +name: Chemical registry number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique registry number of a chemical compound." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2894 ! Compound accession +[Term] +id: EDAM_data:0992 +name: Ligand identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Code word for a ligand, for example from a PDB file." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1086 ! Compound identifier +[Term] +id: EDAM_data:0993 +name: Drug identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a drug." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1086 ! Compound identifier +relationship: is_identifier_of EDAM_data:2851 ! Drug structure [Term] -id: EDAM_operation:2445 -name: Protein interaction network processing -namespace: operation -subset: operations -def: "Process (read and / or write) a network of protein interactions." [http://edamontology.org] -is_a: EDAM_operation:2405 ! Protein interaction data processing -is_a: EDAM_operation:2438 ! Pathway or network processing -relationship: has_input EDAM_data:1663 !{min_cardinality=0} ! Pathway or network (protein-protein interaction) -relationship: has_output EDAM_data:1663 !{min_cardinality=0} ! Pathway or network (protein-protein interaction) -relationship: has_topic EDAM_topic:3044 ! Protein interaction networks +id: EDAM_data:0994 +name: Amino acid identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Residue identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an amino acid." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1086 ! Compound identifier +relationship: is_identifier_of EDAM_data:2016 ! Amino acid property [Term] -id: EDAM_operation:0333 -name: Zinc finger protein domain prediction and optimisation -namespace: operation -subset: operations -def: "Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases)." [http://edamontology.org] -is_a: EDAM_operation:0420 ! Protein-nucleic acid binding prediction -is_a: EDAM_operation:2425 ! Optimisation and refinement -relationship: has_output EDAM_data:1567 ! Protein-nucleic acid interaction -relationship: has_topic EDAM_topic:0150 ! Protein design +id: EDAM_data:0995 +name: Nucleotide identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of a nucleotide." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1086 ! Compound identifier +[Term] +id: EDAM_data:0996 +name: Monosaccharide identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a monosaccharide." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1086 ! Compound identifier [Term] -id: EDAM_operation:0276 -name: Protein interaction network analysis -namespace: operation -subset: operations -def: "Analyse a network of protein interactions." [http://edamontology.org] -is_a: EDAM_operation:2445 ! Protein interaction network processing -is_a: EDAM_operation:2949 ! Protein interaction analysis -is_a: EDAM_operation:2497 ! Pathway or network analysis -relationship: has_input EDAM_data:1663 !{min_cardinality=1} ! Pathway or network (protein-protein interaction) -relationship: has_output EDAM_data:2984 ! Pathway or network report +id: EDAM_data:0997 +name: Chemical name (ChEBI) +comment: This is the recommended chemical name for use for example in database annotation. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "ChEBI chemical name" EXACT [] +created_in: "beta12orEarlier" +def: "Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0990 ! Compound name [Term] -id: EDAM_operation:0277 -name: Protein interaction network comparison -namespace: operation -subset: operations -def: "Compare two or more networks of protein interactions." [http://edamontology.org] -is_a: EDAM_operation:0276 ! Protein interaction network analysis -is_a: EDAM_operation:1778 ! Protein function comparison -relationship: has_input EDAM_data:1663 !{min_cardinality=2} ! Pathway or network (protein-protein interaction) +id: EDAM_data:0998 +name: Chemical name (IUPAC) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "IUPAC chemical name" EXACT [] +created_in: "beta12orEarlier" +def: "IUPAC recommended name of a chemical compound." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0990 ! Compound name +[Term] +id: EDAM_data:0999 +name: Chemical name (INN) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "INN chemical name" EXACT [] +created_in: "beta12orEarlier" +def: "International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0990 ! Compound name +[Term] +id: EDAM_data:1000 +name: Chemical name (brand) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Brand chemical name" EXACT [] +created_in: "beta12orEarlier" +def: "Brand name of a chemical compound." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0990 ! Compound name [Term] -id: EDAM_operation:3197 !{since=1.1} -name: Genetic variation analysis -namespace: operation -subset: operations -def: "Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model." [http://edamontology.org] -comment: Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. -synonym: "Sequence variation analysis" EXACT [http://edamontology.org] -synonym: "Genetic variation annotation" EXACT [http://edamontology.org] -is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison -relationship: has_output EDAM_data:0918 ! Nucleic acid features (variation) +id: EDAM_data:1001 +name: Chemical name (synonymous) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Synonymous chemical name" EXACT [] +created_in: "beta12orEarlier" +def: "Synonymous name of a chemical compound." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0990 ! Compound name +[Term] +id: EDAM_data:1002 +name: Chemical registry number (CAS) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "CAS chemical registry number" EXACT [] +created_in: "beta12orEarlier" +def: "CAS registry number of a chemical compound." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0991 ! Chemical registry number [Term] -id: EDAM_operation:3227 !{since=1.1} -name: Variant mapping -namespace: operation -subset: operations -def: "Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence." [http://edamontology.org] -comment: Methods often utilise a database of aligned reads. -synonym: "Variant calling" EXACT [http://edamontology.org] -is_a: EDAM_operation:3197 ! Genetic variation analysis +id: EDAM_data:1003 +name: Chemical registry number (Beilstein) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Beilstein chemical registry number" EXACT [] +created_in: "beta12orEarlier" +def: "Beilstein registry number of a chemical compound." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0991 ! Chemical registry number +[Term] +id: EDAM_data:1004 +name: Chemical registry number (Gmelin) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Gmelin chemical registry number" EXACT [] +created_in: "beta12orEarlier" +def: "Gmelin registry number of a chemical compound." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0991 ! Chemical registry number [Term] -id: EDAM_operation:3228 !{since=1.1} -name: Structural variation discovery -namespace: operation -subset: operations -def: "Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s)." [http://edamontology.org] -comment: Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. -is_a: EDAM_operation:3197 ! Genetic variation analysis +id: EDAM_data:1005 +name: HET group name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Component identifier code" EXACT [] +synonym: "Short ligand name" EXACT [] +created_in: "beta12orEarlier" +def: "3-letter code word for a ligand (HET group) from a PDB file, for example ATP." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0990 ! Compound name +[Term] +id: EDAM_data:1006 +name: Amino acid name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "String of one or more ASCII characters representing an amino acid." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0994 ! Amino acid identifier [Term] -id: EDAM_operation:3196 !{since=1.1} -name: Genotyping -namespace: operation -subset: operations -def: "Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence." [http://edamontology.org] -comment: Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. -is_a: EDAM_operation:3197 ! Genetic variation analysis +id: EDAM_data:1007 +name: Nucleotide code +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "String of one or more ASCII characters representing a nucleotide." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0990 ! Compound name +is_a: EDAM_data:0995 ! Nucleotide identifier +[Term] +id: EDAM_data:1008 +name: Polypeptide chain ID +comment: This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Chain identifier" EXACT [] +synonym: "PDB chain identifier" EXACT [] +synonym: "PDB strand id" EXACT [] +synonym: "Polypeptide chain identifier" EXACT [] +synonym: "Protein chain identifier" EXACT [] +xref: PDBML:pdbx_PDB_strand_id +xref: WHATIF: chain +created_in: "beta12orEarlier" +def: "Identifier of a polypeptide chain from a protein." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0988 ! Peptide identifier +relationship: is_identifier_of EDAM_data:1467 ! Protein chain -! Link frameshift error detection and SNP detection to this one [Term] -id: EDAM_operation:3202 !{since=1.1} -name: Mutation detection -namespace: operation -subset: operations -def: "Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware." [http://edamontology.org] -synonym: "Polymorphism detection" EXACT [http://edamontology.org] -is_a: EDAM_operation:3197 ! Genetic variation analysis +id: EDAM_data:1009 +name: Protein name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a protein." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0984 ! Molecule name +is_a: EDAM_data:0989 ! Protein identifier +[Term] +id: EDAM_data:1010 +name: Enzyme identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of an enzyme or record from a database of enzymes." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0989 ! Protein identifier +relationship: is_identifier_of EDAM_data:1509 ! Enzyme property [Term] -id: EDAM_operation:0484 -name: SNP detection -namespace: operation -subset: operations -def: "Find single nucleotide polymorphisms (SNPs) between sequences." [http://edamontology.org] -comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. -synonym: "Single nucleotide polymorphism detection" EXACT [http://edamontology.org] -is_a: EDAM_operation:3202 ! Mutation detection -is_a: EDAM_operation:0415 ! Nucleic acid feature prediction -relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) +id: EDAM_data:1011 +name: EC number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "EC" EXACT [] +synonym: "EC code" EXACT [] +synonym: "Enzyme Commission number" EXACT [] +xref: Moby:Annotated_EC_Number +xref: Moby:EC_Number +created_in: "beta12orEarlier" +def: "An Enzyme Commission (EC) number of an enzyme." [http://edamontology.org] +regex: "[0-9]+\\.-\\.-\\.-|[0-9]+\\.[0-9]+\\.-\\.-|[0-9]+\\.[0-9]+\\.[0-9]+\\.-|[0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+" +namespace: identifier +is_a: EDAM_data:2321 ! Enzyme ID +[Term] +id: EDAM_data:1012 +name: Enzyme name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of an enzyme." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1009 ! Protein name +is_a: EDAM_data:1010 ! Enzyme identifier [Term] -id: EDAM_operation:3201 !{since=1.1} -name: SNP calling -namespace: operation -subset: operations -def: "Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism." [http://edamontology.org] -comment: Operations usually score confidence in the prediction or some other statistical measure of evidence. -is_a: EDAM_operation:0484 ! SNP detection +id: EDAM_data:1013 +name: Restriction enzyme name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a restriction enzyme." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1012 ! Enzyme name +relationship: is_identifier_of EDAM_data:1517 ! Restriction enzyme property +[Term] +id: EDAM_data:1014 +name: Sequence position specification +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A specification (partial or complete) of one or more positions or regions of a molecular sequence or map." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM_operation:0485 -name: Radiation Hybrid Mapping -namespace: operation -subset: operations -def: "Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers." [http://edamontology.org] -is_a: EDAM_operation:2944 ! Physical mapping -relationship: has_output EDAM_data:2870 !{min_cardinality=1} ! Radiation hybrid map +id: EDAM_data:1015 +name: Sequence feature ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:3034 ! Sequence feature identifier +[Term] +id: EDAM_data:1016 +name: Sequence position +subset: bioinformatics +subset: data +subset: edam +synonym: "SO:0000735" RELATED [] +xref: PDBML:_atom_site.id +xref: WHATIF: number +xref: WHATIF: PDBx_atom_site +created_in: "beta12orEarlier" +def: "A position of a single point (base or residue) in a sequence, or part of such a specification." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1014 ! Sequence position specification [Term] -id: EDAM_operation:3186 !{since=1.1} -name: Bisulfite mapping -namespace: operation -subset: operations -def: "The mapping of methylation sites in a DNA (genome) sequence." [http://edamontology.org] -comment: Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. -synonym: "Bisulfite sequence mapping" EXACT [http://edamontology.org] -synonym: "Bisulfite sequence alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:2944 ! Physical mapping +id: EDAM_data:1017 +name: Sequence range +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Specification of range(s) of sequence positions." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1014 ! Sequence position specification +[Term] +id: EDAM_data:1018 +name: Nucleic acid feature identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of an nucleic acid feature." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1015 ! Sequence feature ID [Term] -id: EDAM_operation:0486 -name: Functional mapping -namespace: operation -subset: operations -def: "Map the genetic architecture of dynamic complex traits." [http://edamontology.org] -comment: This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0282 ! Genetic mapping +id: EDAM_data:1019 +name: Protein feature identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of a protein feature." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1015 ! Sequence feature ID +[Term] +id: EDAM_data:1020 +name: Sequence feature key +comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence feature method" EXACT [] +synonym: "Sequence feature type" EXACT [] +created_in: "beta12orEarlier" +def: "The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2914 ! Sequence features metadata [Term] -id: EDAM_operation:0487 -name: Haplotype inference -namespace: operation -subset: operations -def: "Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated." [http://edamontology.org] -comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). -synonym: "Haplotype mapping" EXACT [http://edamontology.org] -synonym: "Haplotype reconstruction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0283 ! Linkage analysis -relationship: has_output EDAM_data:1863 !{min_cardinality=1} ! Haplotype map +id: EDAM_data:1021 +name: Sequence feature qualifier +comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Typically one of the EMBL or Swiss-Prot feature qualifiers." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2914 ! Sequence features metadata [Term] -id: EDAM_operation:0488 -name: Linkage disequilibrium calculation -namespace: operation -subset: operations -def: "Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [http://edamontology.org] -comment: Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. -is_a: EDAM_operation:0283 ! Linkage analysis -relationship: has_output EDAM_data:1634 !{min_cardinality=1} ! Gene annotation (linkage disequilibrium) +id: EDAM_data:1022 +name: Sequence feature label +comment: A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence feature name" EXACT [] +created_in: "beta12orEarlier" +def: "Typically an EMBL or Swiss-Prot feature label." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2914 ! Sequence features metadata +[Term] +id: EDAM_data:1023 +name: EMBOSS Uniform Feature Object +subset: bioinformatics +subset: data +subset: edam +synonym: "UFO" EXACT [] +created_in: "beta12orEarlier" +def: "The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:3034 ! Sequence feature identifier [Term] -id: EDAM_operation:0286 -name: Codon usage analysis -namespace: operation -subset: operations -! alt_id: EDAM_operation:2494 -def: "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." [http://edamontology.org] -synonym: "synon: Codon usage table analysis" EXACT [http://edamontology.org] -synonym: "synon: Codon usage data analysis" EXACT [http://edamontology.org] -is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:2977 !{min_cardinality=0} ! Nucleic acid sequence -relationship: has_input EDAM_data:1597 !{min_cardinality=0} ! Codon usage table -relationship: has_output EDAM_data:1597 !{min_cardinality=0} ! Codon usage table -relationship: has_output EDAM_data:0914 !{min_cardinality=0} ! Codon usage report -relationship: has_topic EDAM_topic:0107 ! Codon usage analysis +id: EDAM_data:1024 +name: Codon name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "String of one or more ASCII characters representing a codon." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1276 ! Nucleic acid features +[Term] +id: EDAM_data:1025 +name: Gene identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +xref: Moby:GeneAccessionList +created_in: "beta12orEarlier" +def: "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:0916 ! Gene annotation [Term] -id: EDAM_operation:2433 -name: Codon usage table processing -namespace: operation -subset: operations -def: "Process (read and / or write) a codon usage table." [http://edamontology.org] -is_a: EDAM_operation:0286 ! Codon usage analysis -relationship: has_input EDAM_data:1597 !{min_cardinality=0} ! Codon usage table -relationship: has_output EDAM_data:1597 !{min_cardinality=0} ! Codon usage table +id: EDAM_data:1026 +name: Gene symbol +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +xref: Moby_namespace:Global_GeneCommonName +xref: Moby_namespace:Global_GeneSymbol +created_in: "beta12orEarlier" +def: "The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2299 ! Gene name [Term] -id: EDAM_operation:0287 -name: Base position variability plotting -namespace: operation -subset: operations -def: "Identify and plot third base position variability in a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_operation:0286 ! Codon usage analysis -relationship: has_output EDAM_data:1263 !{min_cardinality=1} ! Sequence composition (base position variability) -relationship: has_topic EDAM_topic:0109 ! Gene finding +id: EDAM_data:1027 +name: Gene ID (NCBI) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Entrez gene ID" EXACT [] +synonym: "Gene identifier (Entrez)" EXACT [] +synonym: "Gene identifier (NCBI)" EXACT [] +synonym: "NCBI gene ID" EXACT [] +synonym: "NCBI geneid" EXACT [] +xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID +xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene +created_in: "beta12orEarlier" +def: "An NCBI unique identifier of a gene." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1098 ! RefSeq accession +is_a: EDAM_data:2295 ! Gene ID +[Term] +id: EDAM_data:1028 +name: Gene identifier (NCBI RefSeq) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An NCBI RefSeq unique identifier of a gene." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1027 ! Gene ID (NCBI) [Term] -id: EDAM_operation:0489 -name: Genetic code prediction -namespace: operation -subset: operations -def: "Predict genetic code from analysis of codon usage data." [http://edamontology.org] -is_a: EDAM_operation:0286 ! Codon usage analysis -is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM_data:1598 !{min_cardinality=1} ! Genetic code +id: EDAM_data:1029 +name: Gene identifier (NCBI UniGene) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An NCBI UniGene unique identifier of a gene." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1104 ! Sequence cluster ID (UniGene) [Term] -id: EDAM_operation:2962 -name: Codon usage bias calculation -namespace: operation -subset: operations -def: "Calculate codon usage bias." [http://edamontology.org] -is_a: EDAM_operation:0286 ! Codon usage analysis -relationship: has_output EDAM_data:2865 !{min_cardinality=1} ! Codon usage bias +id: EDAM_data:1030 +name: Gene identifier (Entrez) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An Entrez unique identifier of a gene." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1027 ! Gene ID (NCBI) [Term] -id: EDAM_operation:2963 -name: Codon usage bias plotting -namespace: operation -subset: operations -def: "Generate a codon usage bias plot." [http://edamontology.org] -is_a: EDAM_operation:2962 ! Codon usage bias calculation -relationship: has_output EDAM_data:1600 !{min_cardinality=1} ! Codon usage bias plot +id: EDAM_data:1031 +name: Gene ID (CGD) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "CGD ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a gene or feature from the CGD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_operation:2964 -name: Codon usage fraction calculation -namespace: operation -subset: operations -def: "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." [http://edamontology.org] -is_a: EDAM_operation:0286 ! Codon usage analysis -relationship: has_output EDAM_data:1602 !{min_cardinality=1} ! Codon usage fraction difference +id: EDAM_data:1032 +name: Gene ID (DictyBase) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a gene from DictyBase." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID +[Term] +id: EDAM_data:1033 +name: Gene ID (Ensembl) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Ensembl Gene ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier for a gene (or other feature) from the Ensembl database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID +is_a: EDAM_data:2610 ! Ensembl ID +[Term] +id: EDAM_data:1034 +name: Gene ID (SGD) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "SGD identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry from the SGD database." [http://edamontology.org] +regex: "S[0-9]+" +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID +is_a: EDAM_data:2632 ! SGD ID [Term] -id: EDAM_operation:0284 -name: Codon usage table generation -namespace: operation -subset: operations -def: "Calculate codon usage statistics and create a codon usage table." [http://edamontology.org] -is_a: EDAM_operation:2433 ! Codon usage table processing -relationship: has_output EDAM_data:1597 !{min_cardinality=1} ! Codon usage table +id: EDAM_data:1035 +name: Gene ID (GeneDB) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "GeneDB identifier" EXACT [] +xref: Moby_namespace:GeneDB +created_in: "beta12orEarlier" +def: "Identifier of a gene from the GeneDB database." [http://edamontology.org] +regex: "[a-zA-Z_0-9\\.-]*" +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_operation:0285 -name: Codon usage table comparison -namespace: operation -subset: operations -def: "Compare two or more codon usage tables." [http://edamontology.org] -is_a: EDAM_operation:2433 ! Codon usage table processing -is_a: EDAM_operation:2998 ! Nucleic acid comparison +id: EDAM_data:1036 +name: TIGR identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the TIGR database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2109 ! Identifier (hybrid) +is_a: EDAM_data:2295 ! Gene ID +[Term] +id: EDAM_data:1037 +name: TAIR accession (gene) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an gene from the TAIR database." [http://edamontology.org] +regex: "Gene:[0-9]{7}" +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID +is_a: EDAM_data:2387 ! TAIR accession [Term] -id: EDAM_operation:3193 !{since=1.1} -name: Genome comparison -namespace: operation -subset: operations -def: "Compare two (tpyically huge) molecular sequences that represent genomes." [http://edamontology.org] -is_a: EDAM_operation:2451 ! Sequence comparison +id: EDAM_data:1038 +name: Protein domain ID +comment: This is typically a character or string concatenated with a PDB identifier and a chain identifier. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a protein structural domain." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:1468 ! Protein domain [Term] -id: EDAM_operation:3194 !{since=1.1} -name: Genome feature comparison -namespace: operation -subset: operations -def: "Compare the features of two genome sequences." [http://edamontology.org] -comment: Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. -is_a: EDAM_operation:0256 ! Feature comparison +id: EDAM_data:1039 +name: SCOP domain identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a protein domain (or other node) from the SCOP database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1038 ! Protein domain ID +relationship: is_identifier_of EDAM_data:1554 ! SCOP node +[Term] +id: EDAM_data:1040 +name: CATH domain ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "CATH domain identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a protein domain from CATH." [http://edamontology.org] +example: "1nr3A00" +namespace: identifier +is_a: EDAM_data:2700 ! CATH identifier [Term] -id: EDAM_operation:3182 !{since=1.1} -name: Genome alignment construction -namespace: operation -subset: operations -def: "Align two or more (tpyically huge) molecular sequences that represent genomes." [http://edamontology.org] -synonym: "Genome alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:0292 ! Sequence alignment construction +id: EDAM_data:1041 +name: SCOP concise classification string (sccs) +comment: An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1039 ! SCOP domain identifier +[Term] +id: EDAM_data:1042 +name: SCOP sunid +comment: A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "SCOP unique identifier" EXACT [] +synonym: "sunid" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229." [http://edamontology.org] +example: "33229" +namespace: identifier +is_a: EDAM_data:1039 ! SCOP domain identifier [Term] -id: EDAM_operation:3198 !{since=1.1} -name: Oligonucleotide alignment construction -namespace: operation -subset: operations -def: "Align short oligonucleotide sequences (reads) to a larger (genomic) sequence." [http://edamontology.org] -comment: The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. -synonym: "Short sequence read mapping" EXACT [http://edamontology.org] -synonym: "Short read mapping" EXACT [http://edamontology.org] -synonym: "Read mapping" EXACT [http://edamontology.org] -synonym: "Short oligonucleotide alignment" EXACT [http://edamontology.org] -synonym: "Oligonucleotide mapping" EXACT [http://edamontology.org] -synonym: "Oligonucleotide alignment" EXACT [http://edamontology.org] -synonym: "Short read alignment" EXACT [http://edamontology.org] -synonym: "Read alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:0292 ! Sequence alignment construction +id: EDAM_data:1043 +name: CATH node ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "CATH code" EXACT [] +synonym: "CATH node identifier" EXACT [] +created_in: "beta12orEarlier" +def: "A code number identifying a node from the CATH database." [http://edamontology.org] +example: "3.30.1190.10.1.1.1.1.1" +namespace: identifier +is_a: EDAM_data:2700 ! CATH identifier +[Term] +id: EDAM_data:1044 +name: Kingdom name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM_operation:3199 !{since=1.1} -name: Split read mapping -namespace: operation -subset: operations -def: "A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation." [http://edamontology.org] -is_a: EDAM_operation:3198 ! Oligonucleotide alignment construction +id: EDAM_data:1045 +name: Species name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Organism species" EXACT [] +created_in: "beta12orEarlier" +def: "The name of a species (typically a taxonomic group) of organism." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1868 ! Taxon +[Term] +id: EDAM_data:1046 +name: Strain name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2379 ! Strain identifier +is_a: EDAM_data:2909 ! Organism name +[Term] +id: EDAM_data:1047 +name: URI +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A string of characters that name or otherwise identify a resource on the Internet." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0842 ! Identifier [Term] -id: EDAM_operation:0491 -name: Pairwise sequence alignment construction -namespace: operation -subset: operations -def: "Align exactly two molecular sequences." [http://edamontology.org] -synonym: "Pairwise sequence alignment" EXACT [http://edamontology.org] -comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. -is_a: EDAM_operation:0292 ! Sequence alignment construction -relationship: has_output EDAM_data:1381 !{min_cardinality=1} ! Sequence alignment (pair) +id: EDAM_data:1048 +name: Database identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a biological or bioinformatics database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:0957 ! Database metadata [Term] -id: EDAM_operation:0492 -name: Multiple sequence alignment construction -namespace: operation -subset: operations -def: "Align two or more molecular sequences." [http://edamontology.org] -synonym: "Multiple sequence alignment" EXACT [http://edamontology.org] -comment: This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. -is_a: EDAM_operation:0292 ! Sequence alignment construction +id: EDAM_data:1049 +name: Directory name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a directory." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_operation:2089 -name: Sequence alignment refinement -namespace: operation -subset: operations -def: "Refine an existing sequence alignment." [http://edamontology.org] -is_a: EDAM_operation:0258 ! Sequence alignment analysis -is_a: EDAM_operation:2425 ! Optimisation and refinement +id: EDAM_data:1050 +name: File name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name (or part of a name) of a file (of any type)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +[Term] +id: EDAM_data:1051 +name: Ontology name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2338 ! Ontology identifier +relationship: is_identifier_of EDAM_data:0582 ! Ontology [Term] -id: EDAM_operation:0493 -name: Pairwise sequence alignment construction (local) -namespace: operation -subset: operations -def: "Locally align exactly two molecular sequences." [http://edamontology.org] -synonym: "Pairwise sequence alignment (local)" EXACT [http://edamontology.org] -comment: Local alignment methods identify regions of local similarity. -synonym: "Local pairwise sequence alignment construction" EXACT [http.//edamontology.org] -is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction +id: EDAM_data:1052 +name: URL +subset: bioinformatics +subset: data +subset: edam +xref: Moby:Link +xref: Moby:URL +created_in: "beta12orEarlier" +def: "A Uniform Resource Locator (URL)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1047 ! URI [Term] -id: EDAM_operation:0494 -name: Pairwise sequence alignment construction (global) -namespace: operation -subset: operations -def: "Globally align exactly two molecular sequences." [http://edamontology.org] -synonym: "Pairwise sequence alignment (global)" EXACT [http://edamontology.org] -comment: Global alignment methods identify similarity across the entire length of the sequences. -synonym: "Global pairwise sequence alignment construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction +id: EDAM_data:1053 +name: URN +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A Uniform Resource Name (URN)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1047 ! URI [Term] -id: EDAM_operation:0495 -name: Multiple sequence alignment construction (local) -namespace: operation -subset: operations -def: "Locally align two or more molecular sequences." [http://edamontology.org] -synonym: "Multiple sequence alignment (local)" EXACT [http://edamontology.org] -comment: Local alignment methods identify regions of local similarity. -synonym: "Local multiple sequence alignment construction" EXACT [http.//edamontology.org] -is_a: EDAM_operation:0492 ! Multiple sequence alignment construction +id: EDAM_data:1055 +name: LSID +comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following EDAM_format: URN:LSID:::[:] +subset: bioinformatics +subset: data +subset: edam +synonym: "Life Science Identifier" EXACT [] +created_in: "beta12orEarlier" +def: "A Life Science Identifier (LSID) - a unique identifier of some data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1053 ! URN [Term] -id: EDAM_operation:0496 -name: Multiple sequence alignment construction (global) -namespace: operation -subset: operations -def: "Globally align two or more molecular sequences." [http://edamontology.org] -synonym: "Multiple sequence alignment (global)" EXACT [http://edamontology.org] -comment: Global alignment methods identify similarity across the entire length of the sequences. -synonym: "Global multiple sequence alignment construction" EXACT [http.//edamontology.org] -is_a: EDAM_operation:0492 ! Multiple sequence alignment construction +id: EDAM_data:1056 +name: Database name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a biological or bioinformatics database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1048 ! Database identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_operation:0497 -name: Multiple sequence alignment construction (constrained) -namespace: operation -subset: operations -def: "Align two or more molecular sequences with user-defined constraints." [http://edamontology.org] -synonym: "Multiple sequence alignment (constrained)" EXACT [http://edamontology.org] -synonym: "Constrained multiple sequence alignment construction" EXACT [http.//edamontology.org] -is_a: EDAM_operation:0492 ! Multiple sequence alignment construction +id: EDAM_data:1057 +name: Sequence database name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a molecular sequence database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1056 ! Database name [Term] -id: EDAM_operation:0498 -name: Multiple sequence alignment construction (consensus) -namespace: operation -subset: operations -def: "Align two or more molecular sequences using multiple methods to achieve higher quality." [http://edamontology.org] -synonym: "Multiple sequence alignment (consensus)" EXACT [http://edamontology.org] -synonym: "Consensus multiple sequence alignment construction" EXACT [http.//edamontology.org] -is_a: EDAM_operation:0492 ! Multiple sequence alignment construction +id: EDAM_data:1058 +name: Enumerated file name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a file (of any type) with restricted possible values." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1050 ! File name [Term] -id: EDAM_operation:0499 -name: Multiple sequence alignment construction (phylogenetic tree-based) -namespace: operation -subset: operations -def: "Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree." [http://edamontology.org] -synonym: "Multiple sequence alignment (phylogenetic tree-based)" EXACT [http://edamontology.org] -comment: This is supposed to give a more biologically meaningful alignment than standard alignments. -synonym: "Phylogenetic tree-based multiple sequence alignment construction" EXACT [http.//edamontology.org] -is_a: EDAM_operation:0492 ! Multiple sequence alignment construction -relationship: has_topic EDAM_topic:0084 ! Phylogenetics +id: EDAM_data:1059 +name: File name extension +comment: A file extension is the characters appearing after the final '.' in the file name. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The extension of a file name." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1050 ! File name +[Term] +id: EDAM_data:1060 +name: File base name +comment: A file base name is the file name stripped of its directory specification and extension. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The base name of a file." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1050 ! File name [Term] -id: EDAM_operation:0500 -name: Secondary structure alignment construction -namespace: operation -subset: operations -def: "Align molecular secondary structure (represented as a 1D string)." [http://edamontology.org] -synonym: "Secondary structure alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:2482 ! Secondary structure processing -is_a: EDAM_operation:2931 ! Secondary structure comparison -is_a: EDAM_operation:0294 ! Structure-based sequence alignment construction -relationship: has_output EDAM_data:2366 !{min_cardinality=1} ! Secondary structure alignment -relationship: has_topic EDAM_topic:0182 ! Sequence alignment +id: EDAM_data:1061 +name: QSAR descriptor name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a QSAR descriptor." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2110 ! Molecular property identifier +relationship: is_identifier_of EDAM_data:0847 ! QSAR descriptor +[Term] +id: EDAM_data:1062 +name: Database entry identifier +comment: This concept is required for completeness. It should never have child concepts. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0842 ! Identifier [Term] -id: EDAM_operation:0501 -name: Protein secondary structure alignment construction -namespace: operation -subset: operations -def: "Align protein secondary structures." [http://edamontology.org] -synonym: "Protein secondary structure alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:0500 ! Secondary structure alignment construction -is_a: EDAM_operation:2488 ! Protein secondary structure comparison -synonym: "Secondary structure alignment (protein)" EXACT [http://edamontology.org] -relationship: has_output EDAM_data:0878 !{min_cardinality=1} ! Secondary structure alignment (protein) +id: EDAM_data:1063 +name: Sequence identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of molecular sequence(s) or entries from a molecular sequence database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:2044 ! Sequence [Term] -id: EDAM_operation:0502 -name: RNA secondary structure alignment construction -namespace: operation -subset: operations -def: "Align RNA secondary structures." [http://edamontology.org] -synonym: "RNA secondary structure alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:2439 ! RNA secondary structure processing -is_a: EDAM_operation:0500 ! Secondary structure alignment construction -synonym: "Secondary structure alignment (RNA)" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:0880 !{min_cardinality=2} ! RNA secondary structure record -relationship: has_output EDAM_data:0881 !{min_cardinality=1} ! Secondary structure alignment (RNA) +id: EDAM_data:1064 +name: Sequence set ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a set of molecular sequence(s)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:0850 ! Sequence set [Term] -id: EDAM_operation:0503 -name: Pairwise structure alignment construction -namespace: operation -subset: operations -def: "Align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] -synonym: "Pairwise structure alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:0295 ! Structure alignment construction +id: EDAM_data:1065 +name: Sequence signature identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1114 ! Sequence motif identifier +consider: EDAM_data:1115 ! Sequence profile ID [Term] -id: EDAM_operation:0504 -name: Multiple structure alignment construction -namespace: operation -subset: operations -def: "Align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] -synonym: "Multiple structure alignment" EXACT [http://edamontology.org] -comment: This includes methods that use an existing alignment. -is_a: EDAM_operation:0295 ! Structure alignment construction +id: EDAM_data:1066 +name: Sequence alignment ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a molecular sequence alignment, for example a record from an alignment database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM_operation:2488 -name: Protein secondary structure comparison -namespace: operation -subset: operations -def: "Compare protein secondary structures." [http://edamontology.org] -synonym: "Protein secondary structure" EXACT [http://edamontology.org] -is_a: EDAM_operation:2416 ! Protein secondary structure analysis -is_a: EDAM_operation:2931 ! Secondary structure comparison -is_a: EDAM_operation:2997 ! Protein comparison -synonym: "Secondary structure comparison (protein)" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:0876 !{min_cardinality=2} ! Protein features (secondary structure) +id: EDAM_data:1067 +name: Phylogenetic distance matrix identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a phylogenetic distance matrix." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_operation:2487 -name: Protein structure comparison -namespace: operation -subset: operations -def: "Compare protein tertiary structures." [http://edamontology.org] -comment: Methods might identify structural neighbors, find structural similarities or define a structural core. -is_a: EDAM_operation:2459 ! Structure processing (protein) -is_a: EDAM_operation:2483 ! Structure comparison -is_a: EDAM_operation:2997 ! Protein comparison -synonym: "Structure comparison (protein)" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:1460 !{min_cardinality=2} ! Protein structure -relationship: has_output EDAM_data:0897 ! Protein property +id: EDAM_data:1068 +name: Phylogenetic tree ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a phylogenetic tree for example from a phylogenetic tree database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:0872 ! Phylogenetic tree +[Term] +id: EDAM_data:1069 +name: Comparison matrix identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Substitution matrix identifier" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier of a comparison matrix." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:3036 ! Matrix identifier +relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix +[Term] +id: EDAM_data:1070 +name: Structure ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:3035 ! Structure identifier [Term] -id: EDAM_operation:2518 -name: Nucleic acid structure comparison -namespace: operation -subset: operations -def: "Compare nucleic acid tertiary structures." [http://edamontology.org] -synonym: "Structure comparison (nucleic acid)" EXACT [http://edamontology.org] -is_a: EDAM_operation:2483 ! Structure comparison -is_a: EDAM_operation:2481 ! Nucleic acid structure analysis -is_a: EDAM_operation:2998 ! Nucleic acid comparison +id: EDAM_data:1071 +name: Structural (3D) profile ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Structural profile identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:0889 ! Structural (3D) profile [Term] -id: EDAM_operation:0505 -name: Structure alignment (protein) -namespace: operation -subset: operations -def: "Align protein tertiary structures." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:0295 ! Structure alignment construction +id: EDAM_data:1072 +name: Structure alignment ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from a database of tertiary structure alignments." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:0886 ! Structure alignment [Term] -id: EDAM_operation:0506 -name: Structure alignment (RNA) -namespace: operation -subset: operations -def: "Align RNA tertiary structures." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_operation:0295 ! Structure alignment construction +id: EDAM_data:1073 +name: Amino acid index ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an index of amino acid physicochemical and biochemical property data." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:3036 ! Matrix identifier +relationship: is_identifier_of EDAM_data:1501 ! Amino acid index [Term] -id: EDAM_operation:0507 -name: Pairwise structure alignment construction (local) -namespace: operation -subset: operations -def: "Locally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] -synonym: "Pairwise structure alignment (local)" EXACT [http://edamontology.org] -comment: Local alignment methods identify regions of local similarity, common substructures etc. -synonym: "Local pairwise structure alignment construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0503 ! Pairwise structure alignment construction +id: EDAM_data:1074 +name: Protein interaction ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a report of protein interactions from a protein interaction database (typically)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2627 ! Molecular interaction ID [Term] -id: EDAM_operation:0508 -name: Pairwise structure alignment construction (global) -namespace: operation -subset: operations -def: "Globally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] -synonym: "Pairwise structure alignment (global)" EXACT [http://edamontology.org] -comment: Global alignment methods identify similarity across the entire structures. -synonym: "Global pairwise structure alignment construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0503 ! Pairwise structure alignment construction +id: EDAM_data:1075 +name: Protein family identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Protein secondary database record identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a protein family." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:0907 ! Protein family [Term] -id: EDAM_operation:0509 -name: Multiple structure alignment construction (local) -namespace: operation -subset: operations -def: "Locally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] -synonym: "Multiple structure alignment (local)" EXACT [http://edamontology.org] -comment: Local alignment methods identify regions of local similarity, common substructures etc. -synonym: "Local multiple structure alignment construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0504 ! Multiple structure alignment construction +id: EDAM_data:1076 +name: Codon usage table name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique name of a codon usage table." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2111 ! Codon usage table identifier +relationship: is_identifier_of EDAM_data:1597 ! Codon usage table +relationship: is_identifier_of EDAM_data:1598 ! Genetic code [Term] -id: EDAM_operation:0510 -name: Multiple structure alignment construction (global) -namespace: operation -subset: operations -def: "Globally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] -synonym: "Multiple structure alignment (global)" EXACT [http://edamontology.org] -comment: Global alignment methods identify similarity across the entire structures. -synonym: "Global multiple structure alignment construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0504 ! Multiple structure alignment construction +id: EDAM_data:1077 +name: Transcription factor identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a transcription factor (or a TF binding site)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:0989 ! Protein identifier +relationship: is_identifier_of EDAM_data:1315 ! Gene features (TFBS) [Term] -id: EDAM_operation:0296 -name: Sequence profile generation -namespace: operation -subset: operations -def: "Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment." [http://edamontology.org] -is_a: EDAM_operation:2413 ! Sequence profile processing -is_a: EDAM_operation:2463 ! Sequence alignment processing -relationship: has_input EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment -relationship: has_output EDAM_data:1354 !{min_cardinality=1} ! Sequence profile +id: EDAM_data:1078 +name: Microarray experiment annotation ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from a database of microarray data." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:0931 ! Experiment annotation (microarray) [Term] -id: EDAM_operation:0298 -name: Sequence profile alignment construction -namespace: operation -subset: operations -def: "Align sequence profiles (representing sequence alignments)." [http://edamontology.org] -synonym: "Sequence profile alignment" EXACT [http://edamontology.org] -comment: See also 'Sequence alignment comparison'. -is_a: EDAM_operation:2413 ! Sequence profile processing -is_a: EDAM_operation:2928 ! Alignment construction -relationship: has_input EDAM_data:1354 !{min_cardinality=2} ! Sequence profile -relationship: has_output EDAM_data:0868 !{min_cardinality=1} ! Sequence profile alignment +id: EDAM_data:1079 +name: Electron microscopy model ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from a database of electron microscopy data." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:0941 ! Electron microscopy model +[Term] +id: EDAM_data:1080 +name: Gene expression report ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Gene expression profile identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Accession of a report of gene expression (e.g. a gene expression profile) from a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:3111 ! Processed microarray data [Term] -id: EDAM_operation:0300 -name: Sequence-profile alignment construction -namespace: operation -subset: operations -def: "Align molecular sequence(s) to sequence profile(s)." [http://edamontology.org] -synonym: "Sequence-profile alignment" EXACT [http://edamontology.org] -comment: A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. -is_a: EDAM_operation:2413 ! Sequence profile processing -is_a: EDAM_operation:2403 ! Sequence analysis -is_a: EDAM_operation:2928 ! Alignment construction -relationship: has_input EDAM_data:1354 !{min_cardinality=1} ! Sequence profile -relationship: has_output EDAM_data:0869 !{min_cardinality=1} ! Sequence-profile alignment +id: EDAM_data:1081 +name: Genotype and phenotype annotation ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from a database of genotypes and phenotypes." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:0920 ! Genotype/phenotype annotation [Term] -id: EDAM_operation:0511 -name: Sequence profile alignment construction (pairwise) -namespace: operation -subset: operations -def: "Align exactly two molecular profiles." [http://edamontology.org] -synonym: "Sequence profile alignment (pairwise)" EXACT [http://edamontology.org] -comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. -synonym: "Pairwise sequence profile alignment construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0298 ! Sequence profile alignment construction +id: EDAM_data:1082 +name: Pathway or network identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from a database of biological pathways or networks." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:2600 ! Pathway or network +[Term] +id: EDAM_data:1083 +name: Workflow ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a biological or biomedical workflow, typically from a database of workflows." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:2972 ! Workflow [Term] -id: EDAM_operation:0512 -name: Sequence profile alignment construction (multiple) -namespace: operation -subset: operations -def: "Align two or more molecular profiles." [http://edamontology.org] -synonym: "Sequence profile alignment (multiple)" EXACT [http://edamontology.org] -synonym: "Multiple sequence profile alignment construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0298 ! Sequence profile alignment construction +id: EDAM_data:1084 +name: Data resource definition identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a data type definition from some provider." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_operation:0297 -name: Structural (3D) profile generation -namespace: operation -subset: operations -def: "Generate some type of structural (3D) profile or template from a structure or structure alignment." [http://edamontology.org] -synonym: "Structural profile generation" EXACT [http://edamontology.org] -is_a: EDAM_operation:2411 ! Structural (3D) profile processing -is_a: EDAM_operation:2952 ! Structure alignment processing -is_a: EDAM_operation:2465 ! Structure processing -relationship: has_input EDAM_data:0886 !{min_cardinality=1} ! Structure alignment -relationship: has_input EDAM_data:0883 !{min_cardinality=1} ! Structure -relationship: has_output EDAM_data:0889 !{min_cardinality=1} ! Structural (3D) profile +id: EDAM_data:1085 +name: Biological model identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a mathematical model, typically an entry from a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:0950 ! Biological model [Term] -id: EDAM_operation:0299 -name: Structural (3D) profile alignment construction -namespace: operation -subset: operations -def: "Align structural (3D) profiles or templates (representing structures or structure alignments)." [http://edamontology.org] -synonym: "Structural (3D) profile alignment" EXACT [http://edamontology.org] -synonym: "Structural profile alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:2411 ! Structural (3D) profile processing -is_a: EDAM_operation:2928 ! Alignment construction -relationship: has_input EDAM_data:0889 !{min_cardinality=2} ! Structural (3D) profile -relationship: has_output EDAM_data:0890 !{min_cardinality=1} ! Structural (3D) profile alignment -relationship: has_topic EDAM_topic:0183 ! Structure alignment +id: EDAM_data:1086 +name: Compound identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Chemical compound identifier" EXACT [] +synonym: "Small molecule identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry from a database of chemicals." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0982 ! Molecule identifier +relationship: is_identifier_of EDAM_data:0846 ! Chemical formula +relationship: is_identifier_of EDAM_data:0962 ! Small molecule annotation +relationship: is_identifier_of EDAM_data:1712 ! Structure image (small molecule) [Term] -id: EDAM_operation:0513 -name: Structural (3D) profile alignment construction (pairwise) -namespace: operation -subset: operations -def: "Align exactly two molecular Structural (3D) profiles." [http://edamontology.org] -synonym: "Structural (3D) profile alignment (pairwise)" EXACT [http://edamontology.org] -comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. -synonym: "Pairwise structural (3D) profile alignment construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction - +id: EDAM_data:1087 +name: Ontology concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Ontology concept ID" EXACT [] +created_in: "beta12orEarlier" +def: "A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:3025 ! Ontology concept identifier [Term] -id: EDAM_operation:0514 -name: Structural (3D) profile alignment construction (multiple) -namespace: operation -subset: operations -def: "Align two or more molecular 3D profiles." [http://edamontology.org] -synonym: "Structural (3D) profile alignment (multiple)" EXACT [http://edamontology.org] -synonym: "Multiple structural (3D) profile alignment construction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction +id: EDAM_data:1088 +name: Article ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a scientific article." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:0971 ! Article [Term] -id: EDAM_operation:0301 -name: Sequence-3D profile alignment construction -namespace: operation -subset: operations -def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment)." [http://edamontology.org] -synonym: "Sequence-3D profile alignment" EXACT [http://edamontology.org] -comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. -is_a: EDAM_operation:0303 ! Protein fold recognition -is_a: EDAM_operation:2928 ! Alignment construction -is_a: EDAM_operation:2403 ! Sequence analysis -relationship: has_input EDAM_data:0889 !{min_cardinality=2} ! Structural (3D) profile -relationship: has_output EDAM_data:0891 !{min_cardinality=1} ! Sequence-3D profile alignment -relationship: has_topic EDAM_topic:0184 ! Threading - +id: EDAM_data:1089 +name: FlyBase ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an object from the FlyBase database." [http://edamontology.org] +regex: "FB[a-zA-Z_0-9]{2}[0-9]{7}" +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_operation:0308 -name: PCR primer design -namespace: operation -subset: operations -def: "Design or predict oligonucleotide primers for PCR and DNA amplification etc." [http://edamontology.org] -comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. -synonym: "PCR primer prediction" EXACT [http://edamontology.org] -is_a: EDAM_operation:2419 ! Primer and probe design -relationship: has_input EDAM_data:2977 ! Nucleic acid sequence -relationship: has_output EDAM_data:1240 !{min_cardinality=0} ! PCR primers -relationship: has_topic EDAM_topic:3032 ! Primer or probe design +id: EDAM_data:1091 +name: WormBase name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of an object from the WormBase database, usually a human-readable name." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2113 ! WormBase identifier [Term] -id: EDAM_operation:0309 -name: Microarray probe design -namespace: operation -subset: operations -def: "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [http://edamontology.org] -synonym: "Microarray probe prediction" EXACT [http://edamontology.org] -is_a: EDAM_operation:2419 ! Primer and probe design -is_a: EDAM_operation:2425 ! Optimisation and refinement -relationship: has_input EDAM_data:2977 ! Nucleic acid sequence -relationship: has_output EDAM_data:2717 !{min_cardinality=1} ! Oligonucleotide probe annotation -relationship: has_topic EDAM_topic:0200 ! Microarrays -relationship: has_topic EDAM_topic:3032 ! Primer or probe design - +id: EDAM_data:1092 +name: WormBase class +comment: A WormBase class describes the type of object such as 'sequence' or 'protein'. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Class of an object from the WormBase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2113 ! WormBase identifier [Term] -id: EDAM_operation:0307 -name: Virtual PCR -namespace: operation -subset: operations -def: "Perform in-silico (virtual) PCR." [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis - +id: EDAM_data:1093 +name: Sequence accession +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Sequence accession number" EXACT [] +created_in: "beta12orEarlier" +def: "A persistent, unique identifier of a molecular sequence database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1063 ! Sequence identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_operation:3187 -name: Sequence contamination filtering -namespace: operation -subset: operations -def: "Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced." [http://edamontology.org] -is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis -relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis - +id: EDAM_data:1094 +name: Sequence type +comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A label (text token) describing a type of molecular sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2100 ! Type +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM_operation:0517 -name: PCR primer design (for large scale sequencing) -namespace: operation -subset: operations -def: "Predict primers for large scale sequencing." [http://edamontology.org] -is_a: EDAM_operation:0308 ! PCR primer design -relationship: has_topic EDAM_topic:3168 ! Sequencing +id: EDAM_data:1095 +name: EMBOSS Uniform Sequence Address +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "EMBOSS USA" EXACT [] +created_in: "beta12orEarlier" +def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1063 ! Sequence identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_operation:0518 -name: PCR primer design (for genotyping polymorphisms) -namespace: operation -subset: operations -def: "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [http://edamontology.org] -is_a: EDAM_operation:0308 ! PCR primer design +id: EDAM_data:1096 +name: Sequence accession (protein) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Protein sequence accession number" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of a protein sequence database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1093 ! Sequence accession +relationship: is_identifier_of EDAM_data:2976 ! Protein sequence [Term] -id: EDAM_operation:0519 -name: PCR primer design (for gene transcription profiling) -namespace: operation -subset: operations -def: "Predict primers for gene transcription profiling." [http://edamontology.org] -is_a: EDAM_operation:0308 ! PCR primer design -relationship: has_topic EDAM_topic:0203 ! Transcriptomics +id: EDAM_data:1097 +name: Sequence accession (nucleic acid) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Nucleotide sequence accession number" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of a nucleotide sequence database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1093 ! Sequence accession +relationship: is_identifier_of EDAM_data:2977 ! Nucleic acid sequence +[Term] +id: EDAM_data:1098 +name: RefSeq accession +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "RefSeq ID" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of a RefSeq database entry." [http://edamontology.org] +regex: "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+" +namespace: identifier +is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] -id: EDAM_operation:0520 -name: PCR primer design (for conserved primers) -namespace: operation -subset: operations -def: "Predict primers that are conserved across multiple genomes or species." [http://edamontology.org] -is_a: EDAM_operation:0308 ! PCR primer design +id: EDAM_data:1099 +name: UniProt accession (extended) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number." [http://edamontology.org] +example: "Q7M1G0|P43353-2|P01012.107" +regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+" +namespace: identifier +obsolete_since: "1.0" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:3021 ! UniProt accession [Term] -id: EDAM_operation:0521 -name: PCR primer design (based on gene structure) -namespace: operation -subset: operations -def: "Predict primers based on gene structure, promoters, exon-exon junctions etc." [http://edamontology.org] -is_a: EDAM_operation:0308 ! PCR primer design -relationship: has_topic EDAM_topic:0109 ! Gene finding +id: EDAM_data:1100 +name: PIR identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "PIR accession number" EXACT [] +synonym: "PIR ID" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier of PIR sequence database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1096 ! Sequence accession (protein) +relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] -id: EDAM_operation:0522 -name: PCR primer design (for methylation PCRs) -namespace: operation -subset: operations -def: "Predict primers for methylation PCRs." [http://edamontology.org] -is_a: EDAM_operation:0308 ! PCR primer design +id: EDAM_data:1101 +name: TREMBL accession +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a TREMBL sequence database entry." [http://edamontology.org] +namespace: identifier +obsolete_since: "1.2" +replaced_by: EDAM_data:3021 +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +[Term] +id: EDAM_data:1102 +name: Gramene primary identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Gramene primary ID" EXACT [] +created_in: "beta12orEarlier" +def: "Primary identifier of a Gramene database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2915 ! Gramene identifier [Term] -id: EDAM_operation:3183 !{since=1.1} -name: Localized reassembly -namespace: operation -subset: operations -def: "Reconstruction of a sequence assembly in a localised area." [http://edamontology.org] -is_a: EDAM_operation:0310 ! Sequence assembly +id: EDAM_data:1103 +name: EMBL/GenBank/DDBJ ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) +[Term] +id: EDAM_data:1104 +name: Sequence cluster ID (UniGene) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "UniGene cluster ID" EXACT [] +synonym: "UniGene cluster id" EXACT [] +synonym: "UniGene ID" EXACT [] +synonym: "UniGene identifier" EXACT [] +created_in: "beta12orEarlier" +def: "A unique identifier of an entry (gene cluster) from the NCBI UniGene database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1112 ! Sequence cluster ID [Term] -id: EDAM_operation:0523 -name: Sequence assembly (mapping assembly) -namespace: operation -subset: operations -def: "Sequence assembly by combining fragments using an existing backbone sequence." [http://edamontology.org] -comment: The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. -is_a: EDAM_operation:0310 ! Sequence assembly +id: EDAM_data:1105 +name: dbEST accession +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "dbEST ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a dbEST database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2292 ! GenBank accession +is_a: EDAM_data:2728 ! EST accession [Term] -id: EDAM_operation:0524 -name: Sequence assembly (de-novo assembly) -namespace: operation -subset: operations -def: "Sequence assembly by combining fragments into a new, previously unknown sequence." [http://edamontology.org] -comment: De-novo assemblers are much slower and more memory intensive than mapping assemblers. -is_a: EDAM_operation:0310 ! Sequence assembly +id: EDAM_data:1106 +name: dbSNP ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "dbSNP identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a dbSNP database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2294 ! Sequence variation ID [Term] -id: EDAM_operation:0525 -name: Sequence assembly (genome assembly) -namespace: operation -subset: operations -def: "Sequence assembly capable on a very large scale such as assembly of whole genomes." [http://edamontology.org] -is_a: EDAM_operation:0310 ! Sequence assembly +id: EDAM_data:1110 +name: EMBOSS sequence type +comment: See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The EMBOSS type of a molecular sequence." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1094 ! Sequence type [Term] -id: EDAM_operation:0526 -name: Sequence assembly (EST assembly) -namespace: operation -subset: operations -def: "Sequence assembly for EST sequences (transcribed mRNA)." [http://edamontology.org] -comment: Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. -is_a: EDAM_operation:0310 ! Sequence assembly +id: EDAM_data:1111 +name: EMBOSS listfile +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2872 ! ID list [Term] -id: EDAM_operation:2410 -name: Gene expression analysis -namespace: operation -subset: operations -def: "Analyse gene expression and regulation data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2495 ! Gene expression data processing - +id: EDAM_data:1112 +name: Sequence cluster ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a cluster of molecular sequence(s)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1064 ! Sequence set ID +relationship: is_identifier_of EDAM_data:1235 ! Sequence cluster [Term] -id: EDAM_operation:2435 -name: Gene expression profile processing -namespace: operation -subset: operations -def: "Process (read and / or write) a gene expression profile." [http://edamontology.org] -is_a: EDAM_operation:2495 ! Gene expression data processing -relationship: has_input EDAM_data:0928 !{min_cardinality=0} ! Gene expression profile -relationship: has_output EDAM_data:0928 !{min_cardinality=0} ! Gene expression profile -relationship: has_topic EDAM_topic:0203 ! Transcriptomics - - +id: EDAM_data:1113 +name: Sequence cluster ID (COG) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "COG ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the COG database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1112 ! Sequence cluster ID [Term] -id: EDAM_operation:0312 -name: Sequencing-based expression profile data processing -namespace: operation -subset: operations -def: "Process (read and / or write) SAGE, MPSS or SBS experimental data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2495 ! Gene expression data processing - +id: EDAM_data:1114 +name: Sequence motif identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a sequence motif, for example an entry from a motif database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:1353 ! Sequence motif [Term] -id: EDAM_operation:2498 -name: Sequencing-based expression profile data analysis -namespace: operation -subset: operations -def: "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2495 ! Gene expression data processing - +id: EDAM_data:1115 +name: Sequence profile ID +comment: A sequence profile typically represents a sequence alignment. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a sequence profile." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:1354 ! Sequence profile [Term] -id: EDAM_operation:2496 -name: Gene regulatory network processing -namespace: operation -subset: operations -def: "Process (read and / or write) a network of gene regulation." [http://edamontology.org] -is_a: EDAM_operation:2438 ! Pathway or network processing -relationship: has_input EDAM_data:2961 !{min_cardinality=0} ! Pathway or network (gene regulation) -relationship: has_output EDAM_data:2961 !{min_cardinality=0} ! Pathway or network (gene regulation) -relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks - +id: EDAM_data:1116 +name: ELM ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the ELMdb database of protein functional sites." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1114 ! Sequence motif identifier [Term] -id: EDAM_operation:1781 -name: Gene regulatory network analysis -namespace: operation -subset: operations -def: "Analyse a known network of gene regulation." [http://edamontology.org] -is_a: EDAM_operation:2496 ! Gene regulatory network processing -is_a: EDAM_operation:2497 ! Pathway or network analysis -relationship: has_input EDAM_data:2961 !{min_cardinality=1} ! Pathway or network (gene regulation) - +id: EDAM_data:1117 +name: Prosite accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Prosite ID" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of an entry from the Prosite database." [http://edamontology.org] +regex: "PS[0-9]{5}" +namespace: identifier +is_a: EDAM_data:1114 ! Sequence motif identifier [Term] -id: EDAM_operation:2437 -name: Gene regulatory network prediction -namespace: operation -subset: operations -def: "Predict a network of gene regulation." [http://edamontology.org] -is_a: EDAM_operation:2496 ! Gene regulatory network processing -is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM_data:2961 !{min_cardinality=1} ! Pathway or network (gene regulation) - +id: EDAM_data:1118 +name: HMMER hidden Markov model ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier or name of a HMMER hidden Markov model." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1115 ! Sequence profile ID +relationship: is_identifier_of EDAM_data:1364 ! Hidden Markov model [Term] -id: EDAM_operation:3094 !{since=beta13} -name: Protein interaction network prediction -namespace: operation -subset: operations -def: "Predict a network of protein interactions." [http://edamontology.org] -is_a: EDAM_operation:2445 ! Protein interaction network processing -relationship: has_output EDAM_data:1663 !{min_cardinality=1} ! Pathway or network (protein-protein interaction) - - - +id: EDAM_data:1119 +name: JASPAR profile ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier or name of a profile from the JASPAR database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1115 ! Sequence profile ID [Term] -id: EDAM_operation:0316 -name: Functional profiling -namespace: operation -subset: operations -def: "Interpret (in functional terms) and annotate gene expression data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0532 ! Gene expression profile analysis +id: EDAM_data:1120 +name: Sequence alignment type +comment: Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A label (text token) describing the type of a sequence alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0864 ! Sequence alignment parameter +is_a: EDAM_data:2100 ! Type +[Term] +id: EDAM_data:1121 +name: BLAST sequence alignment type +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The type of a BLAST sequence alignment." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1120 ! Sequence alignment type [Term] -id: EDAM_operation:0264 -name: Splice transcript prediction -namespace: operation -subset: operations -def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [http://edamontology.org] -is_a: EDAM_operation:2499 ! Splicing analysis -relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing +id: EDAM_data:1122 +name: Phylogenetic tree type +comment: For example 'nj', 'upgmp' etc. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A label (text token) describing the type of a phylogenetic tree." [http://edamontology.org] +example: "nj|upgmp" +namespace: data +is_a: EDAM_data:2100 ! Type [Term] -id: EDAM_operation:2499 -name: Splicing analysis -namespace: operation -subset: operations -def: "Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences." [http://edamontology.org] -synonym: "Splicing modelling" EXACT [http://edamontology.org] -is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison -is_a: EDAM_operation:2426 ! Modelling and simulation -is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM_data:1307 !{min_cardinality=1} ! Nucleic acid features (splice sites) -relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing +id: EDAM_data:1123 +name: TreeBASE study accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of an entry from the TreeBASE database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1068 ! Phylogenetic tree ID [Term] -id: EDAM_operation:0313 -name: Gene expression profile clustering -namespace: operation -subset: operations -def: "Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles." [http://edamontology.org] -is_a: EDAM_operation:0315 ! Gene expression profile comparison -relationship: has_output EDAM_data:3111 ! Processed microarray data +id: EDAM_data:1124 +name: TreeFam accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of an entry from the TreeFam database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1068 ! Phylogenetic tree ID [Term] -id: EDAM_operation:3223 !{since=1.1} -name: Differential expression analysis -namespace: operation -subset: operations -def: "Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups." [http://edamontology.org] -comment: Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. -synonym: "Differentially expressed gene identification" EXACT [http://edamontology.org] -is_a: EDAM_operation:0315 ! Gene expression profile comparison +id: EDAM_data:1125 +name: Comparison matrix type +comment: For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. +subset: bioinformatics +subset: data +subset: edam +synonym: "Substitution matrix type" EXACT [] +created_in: "beta12orEarlier" +def: "A label (text token) describing the type of a comparison matrix." [http://edamontology.org] +example: "blosum|pam|gonnet|id" +namespace: data +is_a: EDAM_data:0864 ! Sequence alignment parameter +is_a: EDAM_data:2100 ! Type +[Term] +id: EDAM_data:1126 +name: Comparison matrix name +comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Substitution matrix name" EXACT [] +created_in: "beta12orEarlier" +def: "Unique name or identifier of a comparison matrix." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1069 ! Comparison matrix identifier +is_a: EDAM_data:2099 ! Name +relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix [Term] -id: EDAM_operation:3224 !{since=1.1} -name: Gene set testing -namespace: operation -subset: operations -def: "Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc." [http://edamontology.org] -comment: Gene sets can be defined beforehand by biological function, chromosome locations and so on. -is_a: EDAM_operation:2435 ! Gene expression profile processing - +id: EDAM_data:1127 +name: PDB ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "PDB identifier" EXACT [] +synonym: "PDBID" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier of an entry from the PDB database." [http://edamontology.org] +regex: "[a-zA-Z_0-9]{4}" +namespace: identifier +is_a: EDAM_data:1070 ! Structure ID [Term] -id: EDAM_operation:0314 -name: Gene expression profile generation -namespace: operation -subset: operations -def: "Generate a gene expression profile or pattern, for example from microarray data." [http://edamontology.org] -synonym: "Expression profiling" EXACT [http://edamontology.org] -synonym: "Gene expression profiling" EXACT [http://edamontology.org] -is_a: EDAM_operation:2435 ! Gene expression profile processing -relationship: has_output EDAM_data:0928 !{min_cardinality=1} ! Gene expression profile - +id: EDAM_data:1128 +name: AAindex ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the AAindex database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1073 ! Amino acid index ID [Term] -id: EDAM_operation:0315 -name: Gene expression profile comparison -namespace: operation -subset: operations -def: "Compare gene expression profiles or patterns." [http://edamontology.org] -is_a: EDAM_operation:0532 ! Gene expression profile analysis -is_a: EDAM_operation:2998 ! Nucleic acid comparison -relationship: has_output EDAM_data:3111 ! Processed microarray data +id: EDAM_data:1129 +name: BIND accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of an entry from the BIND database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM_operation:2436 -name: Gene expression profile annotation -namespace: operation -subset: operations -def: "Annotate a gene expression profile with concepts from an ontology of gene functions." [http://edamontology.org] -is_a: EDAM_operation:0532 ! Gene expression profile analysis -is_a: EDAM_operation:0226 ! Annotation -relationship: has_output EDAM_data:0928 !{min_cardinality=1} ! Gene expression profile +id: EDAM_data:1130 +name: IntAct accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of an entry from the IntAct database." [http://edamontology.org] +regex: "EBI\\-[0-9]+" +namespace: identifier +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM_operation:0532 -name: Gene expression profile analysis -namespace: operation -subset: operations -def: "Analyse one or more gene expression profiles, typically to interpret them in functional terms." [http://edamontology.org] -synonym: "Functional profiling" EXACT [http://edamontology.org] -is_a: EDAM_operation:2435 ! Gene expression profile processing -relationship: has_input EDAM_data:0928 !{min_cardinality=1} ! Gene expression profile - +id: EDAM_data:1131 +name: Protein family name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a protein family." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1075 ! Protein family identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_operation:0533 -name: Gene expression profile pathway mapping -namespace: operation -subset: operations -def: "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." [http://edamontology.org] -is_a: EDAM_operation:0532 ! Gene expression profile analysis -is_a: EDAM_operation:2497 ! Pathway or network analysis -relationship: has_output EDAM_data:2984 ! Pathway or network report - +id: EDAM_data:1132 +name: InterPro entry name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of an InterPro entry, usually indicating the type of protein matches for that entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1131 ! Protein family name +relationship: is_identifier_of EDAM_data:1355 ! Protein signature [Term] -id: EDAM_operation:3232 !{since=1.1} -name: Gene expression QTL analysis -namespace: operation -subset: operations -def: "Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes." [http://edamontology.org] -synonym: "eQTL profiling" EXACT [http://edamontology.org] -synonym: "expression QTL profiling" EXACT [http://edamontology.org] -synonym: "expression quantitative trait loci profiling" EXACT [http://edamontology.org] -is_a: EDAM_operation:0532 ! Gene expression profile analysis -relationship: has_output EDAM_data:2984 ! Pathway or network report +id: EDAM_data:1133 +name: InterPro accession +comment: Every InterPro entry has a unique accession number to provide a persistent citation of database records. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "InterPro primary accession" EXACT [] +synonym: "InterPro primary accession number" EXACT [] +created_in: "beta12orEarlier" +def: "Primary accession number of an InterPro entry." [http://edamontology.org] +example: "IPR015590" +regex: "IPR[0-9]{6}" +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession +relationship: is_identifier_of EDAM_data:1355 ! Protein signature +[Term] +id: EDAM_data:1134 +name: InterPro secondary accession +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "InterPro secondary accession number" EXACT [] +created_in: "beta12orEarlier" +def: "Secondary accession number of an InterPro entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1133 ! InterPro accession +relationship: is_identifier_of EDAM_data:1355 ! Protein signature [Term] -id: EDAM_operation:0527 -name: Tag mapping -namespace: operation -subset: operations -def: "Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts." [http://edamontology.org] -comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. -synonym: "Tag to gene assignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:2436 ! Gene expression profile annotation -relationship: has_output EDAM_data:0936 !{min_cardinality=0} ! Sequence tag profile (with gene assignment) +id: EDAM_data:1135 +name: Gene3D ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the Gene3D database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM_operation:0528 -name: SAGE data processing -namespace: operation -subset: operations -def: "Process (read and / or write) serial analysis of gene expression (SAGE) data." [http://edamontology.org] -synonym: "Serial analysis of gene expression data processing" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2495 ! Gene expression data processing +id: EDAM_data:1136 +name: PIRSF ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the PIRSF database." [http://edamontology.org] +regex: "PIRSF[0-9]{6}" +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession +[Term] +id: EDAM_data:1137 +name: PRINTS code +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The unique identifier of an entry in the PRINTS database." [http://edamontology.org] +regex: "PR[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM_operation:0529 -name: MPSS data processing -namespace: operation -subset: operations -def: "Process (read and / or write) massively parallel signature sequencing (MPSS) data." [http://edamontology.org] -synonym: "Massively parallel signature sequencing data processing" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2495 ! Gene expression data processing +id: EDAM_data:1138 +name: Pfam accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of a Pfam entry." [http://edamontology.org] +regex: "PF[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession +[Term] +id: EDAM_data:1139 +name: SMART accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of an entry from the SMART database." [http://edamontology.org] +regex: "SM[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM_operation:0530 -name: SBS data processing -namespace: operation -subset: operations -def: "Process (read and / or write) sequencing by synthesis (SBS) data." [http://edamontology.org] -synonym: "Sequencing by synthesis data processing" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:2495 ! Gene expression data processing +id: EDAM_data:1140 +name: Superfamily hidden Markov model number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier (number) of a hidden Markov model from the Superfamily database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession +[Term] +id: EDAM_data:1141 +name: TIGRFam ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "TIGRFam accession number" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM_operation:0531 -name: Heat map generation -namespace: operation -subset: operations -def: "Generate a heat map of gene expression from microarray data." [http://edamontology.org] -comment: The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. -is_a: EDAM_operation:0571 ! Microarray data rendering -relationship: has_output EDAM_data:1636 !{min_cardinality=1} ! Heat map +id: EDAM_data:1142 +name: ProDom accession number +comment: ProDom is a protein domain family database. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A ProDom domain family accession number." [http://edamontology.org] +regex: "PD[0-9]+" +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession +[Term] +id: EDAM_data:1143 +name: TRANSFAC accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the TRANSFAC database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2911 ! Transcription factor accession [Term] -id: EDAM_operation:2934 -name: Microarray cluster textual view rendering -namespace: operation -subset: operations -def: "Visualise gene clusters with gene names." [http://edamontology.org] -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1144 +name: ArrayExpress accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "ArrayExpress experiment ID" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of an entry from the ArrayExpress database." [http://edamontology.org] +regex: "[AEP]-[a-zA-Z_0-9]{4}-[0-9]+" +namespace: identifier +is_a: EDAM_data:1078 ! Microarray experiment annotation ID +[Term] +id: EDAM_data:1145 +name: PRIDE experiment accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "PRIDE experiment accession number." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] -id: EDAM_operation:2935 -name: Microarray wave graph rendering -namespace: operation -subset: operations -synonym: "Microarray cluster temporal graph rendering" EXACT [http://edamontology.org] -def: "Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis." [http://edamontology.org] -comment: This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1146 +name: EMDB ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the EMDB electron microscopy database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1079 ! Electron microscopy model ID +[Term] +id: EDAM_data:1147 +name: GEO accession number +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of an entry from the GEO database." [http://edamontology.org] +regex: "o^GDS[0-9]+" +namespace: identifier +is_a: EDAM_data:1080 ! Gene expression report ID [Term] -id: EDAM_operation:2936 -name: Microarray dendrograph rendering -namespace: operation -subset: operations -synonym: "Microarray checks view rendering" EXACT [http://edamontology.org] -synonym: "Microarray view rendering" EXACT [http://edamontology.org] -def: "Generate a dendrograph of raw, preprocessed or clustered microarray data." [http://edamontology.org] -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1148 +name: GermOnline ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the GermOnline database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1080 ! Gene expression report ID +[Term] +id: EDAM_data:1149 +name: EMAGE ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the EMAGE database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1080 ! Gene expression report ID [Term] -id: EDAM_operation:2937 -name: Microarray proximity map rendering -namespace: operation -subset: operations -synonym: "Microarray distance map rendering" EXACT [http://edamontology.org] -def: "Generate a plot of distances (distance matrix) between genes." [http://edamontology.org] -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1150 +name: Disease ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from a database of disease." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:1622 ! Disease annotation +[Term] +id: EDAM_data:1151 +name: HGVbase ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the HGVbase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID [Term] -id: EDAM_operation:2938 -name: Microarray tree or dendrogram view rendering -namespace: operation -subset: operations -synonym: "Microarray matrix tree plot rendering" EXACT [http://edamontology.org] -synonym: "Microarray 2-way dendrogram rendering" EXACT [http://edamontology.org] -def: "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." [http://edamontology.org] -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1152 +name: HIVDB identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the HIVDB database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0842 ! Identifier +[Term] +id: EDAM_data:1153 +name: OMIM ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the OMIM database." [http://edamontology.org] +regex: "[*#+%^]?[0-9]{6}" +namespace: identifier +is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID [Term] -id: EDAM_operation:2939 -name: Microarray principal component rendering -namespace: operation -subset: operations -def: "Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values." [http://edamontology.org] -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1154 +name: KEGG object identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an object from one of the KEGG databases (excluding the GENES division)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) +[Term] +id: EDAM_data:1155 +name: Pathway ID (reactome) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Reactome ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry from the Reactome database." [http://edamontology.org] +regex: "REACT_[0-9]+(\\.[0-9]+)?" +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_operation:2940 -name: Microarray scatter plot rendering -namespace: operation -subset: operations -def: "Generate a scatter plot of microarray data, typically after principal component analysis." [http://edamontology.org] -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1156 +name: Pathway ID (aMAZE) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "aMAZE ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry from the aMAZE database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1082 ! Pathway or network identifier +[Term] +id: EDAM_data:1157 +name: Pathway ID (BioCyc) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "BioCyc pathway ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an pathway from the BioCyc biological pathways database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2104 ! BioCyc ID +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_operation:2941 -name: Whole microarray graph view rendering -namespace: operation -subset: operations -def: "Visualise gene expression data where each band (or line graph) corresponds to a sample." [http://edamontology.org] -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1158 +name: Pathway ID (INOH) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "INOH identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry from the INOH database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession +[Term] +id: EDAM_data:1159 +name: Pathway ID (PATIKA) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "PATIKA ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry from the PATIKA database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_operation:2942 -name: Microarray tree-map rendering -namespace: operation -subset: operations -def: "Visualise gene expression data after hierarchical clustering for representing hierarchical relationships." [http://edamontology.org] -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1160 +name: Pathway ID (CPDB) +comment: This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "CPDB ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession +[Term] +id: EDAM_data:1161 +name: Pathway ID (Panther) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Panther Pathways ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a biological pathway from the Panther Pathways database." [http://edamontology.org] +regex: "PTHR[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_operation:2943 -name: Microarray Box-Whisker plot rendering -namespace: operation -subset: operations -def: "Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles." [http://edamontology.org] -is_a: EDAM_operation:0571 ! Microarray data rendering +id: EDAM_data:1162 +name: MIRIAM identifier +comment: This is the identifier used internally by MIRIAM for a data type. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a MIRIAM data resource." [http://edamontology.org] +example: MIR:00100005 +regex: "MIR:[0-9]{8}" +namespace: identifier +is_a: EDAM_data:2902 ! Data resource definition accession +relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype +[Term] +id: EDAM_data:1163 +name: MIRIAM data type name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a data type from the MIRIAM database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2253 ! Data resource definition name +relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype [Term] -id: EDAM_operation:2459 -name: Structure processing (protein) -namespace: operation -subset: operations -def: "Process (read and / or write) a protein tertiary structure." [http://edamontology.org] -is_a: EDAM_operation:2465 ! Structure processing -is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_input EDAM_data:1460 !{min_cardinality=0} ! Protein structure -relationship: has_output EDAM_data:1460 !{min_cardinality=0} ! Protein structure -relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure +id: EDAM_data:1164 +name: MIRIAM URI +comment: A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The URI (URL or URN) of a data entity from the MIRIAM database." [http://edamontology.org] +example: urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 +namespace: identifier +is_a: EDAM_data:1047 ! URI +is_a: EDAM_data:2902 ! Data resource definition accession +relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype +[Term] +id: EDAM_data:1165 +name: MIRIAM data type primary name +comment: The primary name of a MIRIAM data type is taken from a controlled vocabulary. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The primary name of a data type from the MIRIAM database." [http://edamontology.org] +example: "UniProt|Enzyme Nomenclature" +namespace: identifier +is_a: EDAM_data:1163 ! MIRIAM data type name [Term] -id: EDAM_operation:0243 -name: Protein property calculation (from structure) -namespace: operation -subset: operations -! alt_id: EDAM_operation:3089 !{since=beta13} ! Not released -def: "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." [http://edamontology.org] -comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. -is_a: EDAM_operation:2406 ! Protein structure analysis -is_a: EDAM_operation:0250 ! Protein property calculation -synonym: "Protein structural property calculation" EXACT [http://edamontology.org] -relationship: has_output EDAM_data:0897 !{min_cardinality=0} ! Protein property -relationship: has_topic EDAM_topic:0123 ! Protein properties -relationship: has_topic EDAM_topic:2814 ! Protein structure analysis +id: EDAM_data:1166 +name: MIRIAM data type synonymous name +comment: A synonymous name for a MIRIAM data type taken from a controlled vocabulary. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A synonymous name of a data type from the MIRIAM database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1163 ! MIRIAM data type name [Term] -id: EDAM_operation:0244 -name: Protein flexibility and motion analysis -namespace: operation -subset: operations -def: "Analyse flexibility and motion in protein structure." [http://edamontology.org] -comment: Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. -is_a: EDAM_operation:0243 ! Protein property calculation (from structure) -is_a: EDAM_operation:2476 ! Molecular dynamics simulation -relationship: has_output EDAM_data:1541 !{min_cardinality=1} ! Protein flexibility or motion report +id: EDAM_data:1167 +name: Taverna workflow ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a Taverna workflow." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1083 ! Workflow ID +[Term] +id: EDAM_data:1170 +name: Biological model name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a biological (mathematical) model." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1085 ! Biological model identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_operation:0245 -name: Protein structural motif recognition -namespace: operation -subset: operations -def: "Identify or screen for 3D structural motifs in protein structure(s)." [http://edamontology.org] -comment: This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. -synonym: "Protein structural feature identification" EXACT [http://edamontology.org] -is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) -relationship: has_output EDAM_data:0899 !{min_cardinality=1} ! Protein features (3D motif) -relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces +id: EDAM_data:1171 +name: BioModel ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the BioModel database." [http://edamontology.org] +regex: "(BIOMD|MODEL)[0-9]{10}" +namespace: identifier +is_a: EDAM_data:2891 ! Biological model accession [Term] -id: EDAM_operation:0246 -name: Protein domain recognition -namespace: operation -subset: operations -def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [http://edamontology.org] -is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) -relationship: has_output EDAM_data:0901 !{min_cardinality=1} ! Protein features (domains) -relationship: has_topic EDAM_topic:0736 ! Protein domains and folds +id: EDAM_data:1172 +name: PubChem CID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "PubChem compound accession identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2639 ! PubChem identifier +is_a: EDAM_data:2894 ! Compound accession +[Term] +id: EDAM_data:1173 +name: ChemSpider ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the ChemSpider database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM_operation:0247 -name: Protein architecture analysis -namespace: operation -subset: operations -def: "Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s)." [http://edamontology.org] -is_a: EDAM_operation:2406 ! Protein structure analysis -relationship: has_output EDAM_data:0902 !{min_cardinality=1} ! Protein architecture report +id: EDAM_data:1174 +name: ChEBI ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "ChEBI identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry from the ChEBI database." [http://edamontology.org] +regex: "CHEBI:[0-9]+" +namespace: identifier +is_a: EDAM_data:2894 ! Compound accession +[Term] +id: EDAM_data:1175 +name: BioPax concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from the BioPax ontology." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID [Term] -id: EDAM_operation:2474 -name: Protein architecture comparison -namespace: operation -subset: operations -def: "Compare the architecture of two or more protein structures." [http://edamontology.org] -is_a: EDAM_operation:0247 ! Protein architecture analysis -is_a: EDAM_operation:2488 ! Protein secondary structure comparison -relationship: has_output EDAM_data:0902 !{min_cardinality=1} ! Protein architecture report +id: EDAM_data:1176 +name: GO concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "GO concept identifier" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier of a concept from The Gene Ontology." [http://edamontology.org] +regex: "[0-9]{7}|GO:[0-9]{7}" +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID [Term] -id: EDAM_operation:2475 -name: Protein architecture recognition -namespace: operation -subset: operations -def: "Identify the architecture of a protein structure." [http://edamontology.org] -is_a: EDAM_operation:0247 ! Protein architecture analysis -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -is_a: EDAM_operation:2996 ! Structure classification -relationship: has_output EDAM_data:0902 !{min_cardinality=1} ! Protein architecture report +id: EDAM_data:1177 +name: MeSH concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from the MeSH vocabulary." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID [Term] -id: EDAM_operation:0248 -name: Residue interaction calculation -namespace: operation -subset: operations -def: "Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s)." [http://edamontology.org] -xref: WHATIF:ListContactsNormal -xref: WHATIF:ListContactsRelaxed -xref: WHATIF:ListSideChainContactsNormal -xref: WHATIF:ListSideChainContactsRelaxed -xref: WHATIF: SymShellOneXML -xref: WHATIF: SymShellTwoXML -xref: WHATIF: SymShellFiveXML -xref: WHATIF: SymShellTenXML -is_a: EDAM_operation:0243 ! Protein property calculation (from structure) -relationship: has_output EDAM_data:1540 !{min_cardinality=1} ! Protein residue interactions -relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis +id: EDAM_data:1178 +name: HGNC concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from the HGNC controlled vocabulary." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID +[Term] +id: EDAM_data:1179 +name: NCBI taxonomy ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "NCBI tax ID" EXACT [] +synonym: "NCBI taxonomy identifier" EXACT [] +created_in: "beta12orEarlier" +def: "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." [http://edamontology.org] +example: "9662|3483|182682" +regex: "[1-9][0-9]{0,8}" +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID [Term] -id: EDAM_operation:0272 -name: Residue interaction prediction -namespace: operation -subset: operations -def: "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences." [http://edamontology.org] -comment: Methods usually involve multiple sequence alignment analysis. -is_a: EDAM_operation:0243 ! Protein property calculation (from structure) -is_a: EDAM_operation:2506 ! Sequence alignment analysis (protein) -relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis +id: EDAM_data:1180 +name: Plant Ontology concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from the Plant Ontology (PO)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID +[Term] +id: EDAM_data:1181 +name: UMLS concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from the UMLS vocabulary." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID [Term] -id: EDAM_operation:0249 -name: Torsion angle calculation -namespace: operation -subset: operations -def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [http://edamontology.org] -is_a: EDAM_operation:0243 ! Protein property calculation (from structure) -relationship: has_output EDAM_data:2991 ! Protein torsion angle data +id: EDAM_data:1182 +name: FMA concept ID +comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from Foundational Model of Anatomy." [http://edamontology.org] +regex: "FMA:[0-9]+" +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID [Term] -id: EDAM_operation:0320 -name: Protein structure assignment -namespace: operation -subset: operations -def: "Assign a protein tertiary structure (3D coordinates) from raw experimental data." [http://edamontology.org] -is_a: EDAM_operation:2459 ! Structure processing (protein) -relationship: has_output EDAM_data:1460 !{min_cardinality=1} ! Protein structure -relationship: has_topic EDAM_topic:2226 ! Structure determination +id: EDAM_data:1183 +name: EMAP concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from the EMAP mouse ontology." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID +[Term] +id: EDAM_data:1184 +name: ChEBI concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from the ChEBI ontology." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID [Term] -id: EDAM_operation:0321 -name: Protein model evaluation -namespace: operation -subset: operations -def: "Evaluate the quality or correctness a protein three-dimensional model." [http://edamontology.org] -comment: Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. -xref: WHATIF: UseFileDB -is_a: EDAM_operation:0477 ! Protein modelling -is_a: EDAM_operation:2428 ! Evaluation and validation -relationship: has_output EDAM_data:1539 !{min_cardinality=1} ! Protein structural quality report -relationship: has_topic EDAM_topic:2275 ! Molecular modelling -relationship: has_topic EDAM_topic:0175 ! Homology modelling -relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction +id: EDAM_data:1185 +name: MGED concept ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from the MGED ontology." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID [Term] -id: EDAM_operation:0322 -name: Protein model refinement -namespace: operation -subset: operations -def: "Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc." [http://edamontology.org] -comment: The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. -xref: WHATIF: CorrectedPDBasXML -is_a: EDAM_operation:0321 ! Protein model evaluation -is_a: EDAM_operation:2425 ! Optimisation and refinement +id: EDAM_data:1186 +name: myGrid concept ID +comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a concept from the myGrid ontology." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID +[Term] +id: EDAM_data:1187 +name: PubMed ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "PMID" EXACT [] +created_in: "beta12orEarlier" +def: "PubMed unique identifier of an article." [http://edamontology.org] +example: "4963447" +regex: "[1-9][0-9]{0,8}" +namespace: identifier +is_a: EDAM_data:1088 ! Article ID [Term] -id: EDAM_operation:2239 -name: 3D-1D scoring matrix generation -namespace: operation -subset: operations -def: "Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data." [http://edamontology.org] -comment: A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. -is_a: EDAM_operation:0243 ! Protein property calculation (from structure) -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:1499 !{min_cardinality=1} ! 3D-1D scoring matrix -relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles +id: EDAM_data:1188 +name: Digital Object Identifier +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Digital Object Identifier (DOI) of a published article." [http://edamontology.org] +regex: "(doi\\:)?[0-9]{2}\\.[0-9]{4}/.*" +namespace: identifier +is_a: EDAM_data:1088 ! Article ID +[Term] +id: EDAM_data:1189 +name: Medline UI +comment: The use of Medline UI has been replaced by the PubMed unique identifier. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Medline unique identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Medline UI (unique identifier) of an article." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1088 ! Article ID [Term] -id: EDAM_operation:2574 -name: Protein hydropathy calculation -namespace: operation -subset: operations -def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." [http://edamontology.org] -is_a: EDAM_operation:0250 ! Protein property calculation -relationship: has_output EDAM_data:2970 !{min_cardinality=1} ! Protein hydropathy data -relationship: has_topic EDAM_topic:0137 ! Protein hydropathy +id: EDAM_data:1190 +name: Tool name +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a computer package, application, method or function." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0977 ! Tool identifier +[Term] +id: EDAM_data:1191 +name: Tool name (signature) +comment: Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The unique name of a signature (sequence classifier) method." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1190 ! Tool name [Term] -id: EDAM_operation:0383 -name: Protein hydropathy calculation (from structure) -namespace: operation -subset: operations -def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." [http://edamontology.org] -is_a: EDAM_operation:2574 ! Protein hydropathy calculation -is_a: EDAM_operation:0243 ! Protein property calculation (from structure) +id: EDAM_data:1192 +name: Tool name (BLAST) +comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "BLAST name" EXACT [] +created_in: "beta12orEarlier" +def: "The name of a BLAST tool." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1190 ! Tool name +[Term] +id: EDAM_data:1193 +name: Tool name (FASTA) +comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a FASTA tool." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1190 ! Tool name [Term] -id: EDAM_operation:0384 -name: Protein solvent accessibility calculation -namespace: operation -subset: operations -def: "Calculate solvent accessible or buried surface areas in protein structures." [http://edamontology.org] -is_a: EDAM_operation:0243 ! Protein property calculation (from structure) -relationship: has_output EDAM_data:1542 ! Protein solvent accessibility -relationship: has_topic EDAM_topic:0137 ! Protein hydropathy +id: EDAM_data:1194 +name: Tool name (EMBOSS) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of an EMBOSS application." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1190 ! Tool name [Term] -id: EDAM_operation:1850 -name: Protein cysteine and disulfide bond assignment -namespace: operation -subset: operations -def: "Assign cysteine bonding state and disulfide bond partners in protein structures." [http://edamontology.org] -is_a: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data) -relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis +id: EDAM_data:1195 +name: Tool name (EMBASSY package) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of an EMBASSY package." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1190 ! Tool name [Term] -id: EDAM_operation:0385 -name: Protein hydropathy cluster calculation -namespace: operation -subset: operations -def: "Identify clusters of hydrophobic or charged residues in a protein structure." [http://edamontology.org] -is_a: EDAM_operation:0383 ! Protein hydropathy calculation (from structure) -is_a: EDAM_operation:0393 ! Protein residue cluster calculation +id: EDAM_data:1201 +name: QSAR descriptor (constitutional) +subset: bioinformatics +subset: data +subset: edam +synonym: "QSAR constitutional descriptor" EXACT [] +created_in: "beta12orEarlier" +def: "A QSAR constitutional descriptor." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0847 ! QSAR descriptor [Term] -id: EDAM_operation:0386 -name: Protein dipole moment calculation -namespace: operation -subset: operations -def: "Calculate whether a protein structure has an unusually large net charge (dipole moment)." [http://edamontology.org] -is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:1545 !{min_cardinality=1} ! Protein dipole moment +id: EDAM_data:1202 +name: QSAR descriptor (electronic) +subset: bioinformatics +subset: data +subset: edam +synonym: "QSAR electronic descriptor" EXACT [] +created_in: "beta12orEarlier" +def: "A QSAR electronic descriptor." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0847 ! QSAR descriptor [Term] -id: EDAM_operation:0387 -name: Protein surface and interior calculation -namespace: operation -subset: operations -def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [http://edamontology.org] -is_a: EDAM_operation:0384 ! Protein solvent accessibility calculation -relationship: has_output EDAM_data:1543 !{min_cardinality=1} ! Protein surface report -relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces +id: EDAM_data:1203 +name: QSAR descriptor (geometrical) +subset: bioinformatics +subset: data +subset: edam +synonym: "QSAR geometrical descriptor" EXACT [] +created_in: "beta12orEarlier" +def: "A QSAR geometrical descriptor." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0847 ! QSAR descriptor +[Term] +id: EDAM_data:1204 +name: QSAR descriptor (topological) +subset: bioinformatics +subset: data +subset: edam +synonym: "QSAR topological descriptor" EXACT [] +created_in: "beta12orEarlier" +def: "A QSAR topological descriptor." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0847 ! QSAR descriptor [Term] -id: EDAM_operation:1816 -name: Surface rendering -namespace: operation -subset: operations -def: "Calculate the positions of dots that are homogeneously distributed over the surface of a molecule." [http://edamontology.org, WHATIF] -comment: A dot has three coordinates (x,y,z) and (typically) a color. -xref: WHATIF:GetSurfaceDots -is_a: EDAM_operation:2462 ! Protein surface calculation -is_a: EDAM_operation:0570 ! Structure rendering +id: EDAM_data:1205 +name: QSAR descriptor (molecular) +subset: bioinformatics +subset: data +subset: edam +synonym: "QSAR molecular descriptor" EXACT [] +created_in: "beta12orEarlier" +def: "A QSAR molecular descriptor." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0847 ! QSAR descriptor +[Term] +id: EDAM_data:1233 +name: Sequence set (protein) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0850 ! Sequence set +[Term] +id: EDAM_data:1234 +name: Sequence set (nucleic acid) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0850 ! Sequence set +is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] -id: EDAM_operation:2460 -name: Protein atom surface calculation -namespace: operation -subset: operations -def: "Calculate the solvent accessibility for each atom in a structure." [http://edamontology.org, WHATIF] -comment: Waters are not considered. -is_a: EDAM_operation:0387 ! Protein surface and interior calculation +id: EDAM_data:1235 +name: Sequence cluster +comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0850 ! Sequence set +relationship: has_topic EDAM_topic:0724 ! Protein families +relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification +[Term] +id: EDAM_data:1236 +name: Psiblast checkpoint file +comment: A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0850 ! Sequence set [Term] -id: EDAM_operation:1817 -name: Protein atom surface calculation (accessible) -namespace: operation -subset: operations -def: "Calculate the solvent accessibility ('accessible surface') for each atom in a structure." [http://edamontology.org, WHATIF] -comment: Waters are not considered. -xref: WHATIF:AtomAccessibilitySolvent -xref: WHATIF:AtomAccessibilitySolventPlus -is_a: EDAM_operation:2460 ! Protein atom surface calculation +id: EDAM_data:1237 +name: HMMER synthetic sequences set +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Sequences generated by HMMER package in FASTA-style format." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0850 ! Sequence set +[Term] +id: EDAM_data:1238 +name: Proteolytic digest +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1233 ! Sequence set (protein) +relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] -id: EDAM_operation:1818 -name: Protein atom surface calculation (accessible molecular) -namespace: operation -subset: operations -def: "Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure." [http://edamontology.org, WHATIF] -comment: Waters are not considered. -xref: WHATIF:AtomAccessibilityMolecular -xref: WHATIF:AtomAccessibilityMolecularPlus -is_a: EDAM_operation:2460 ! Protein atom surface calculation +id: EDAM_data:1239 +name: Restriction digest +subset: bioinformatics +subset: data +subset: edam +xref: SO:0000412 +created_in: "beta12orEarlier" +def: "Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1234 ! Sequence set (nucleic acid) +[Term] +id: EDAM_data:1240 +name: PCR primers +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] -id: EDAM_operation:2461 -name: Protein residue surface calculation -namespace: operation -subset: operations -def: "Calculate the solvent accessibility for each residue in a structure." [http://edamontology.org, WHATIF] -is_a: EDAM_operation:0387 ! Protein surface and interior calculation +id: EDAM_data:1241 +name: vectorstrip cloning vector definition file +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0850 ! Sequence set +[Term] +id: EDAM_data:1242 +name: Primer3 internal oligo mishybridizing library +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0850 ! Sequence set [Term] -id: EDAM_operation:1819 -name: Protein residue surface calculation (accessible) -namespace: operation -subset: operations -def: "Calculate the solvent accessibility ('accessible surface') for each residue in a structure." [http://edamontology.org, WHATIF] -comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). -xref: WHATIF:ResidueAccessibilitySolvent -is_a: EDAM_operation:2461 ! Protein residue surface calculation +id: EDAM_data:1243 +name: Primer3 mispriming library file +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0850 ! Sequence set +[Term] +id: EDAM_data:1244 +name: primersearch primer pairs sequence record +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0850 ! Sequence set [Term] -id: EDAM_operation:1820 -name: Protein residue surface calculation (vacuum accessible) -namespace: operation -subset: operations -def: "Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [http://edamontology.org, WHATIF] -comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). -xref: WHATIF:ResidueAccessibilityVacuum -is_a: EDAM_operation:2461 ! Protein residue surface calculation - +id: EDAM_data:1245 +name: Sequence cluster (protein) +comment: The sequences are typically related, for example a family of sequences. +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein sequence cluster" EXACT [] +created_in: "beta12orEarlier" +def: "A cluster of protein sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1233 ! Sequence set (protein) +is_a: EDAM_data:1235 ! Sequence cluster [Term] -id: EDAM_operation:1821 -name: Protein residue surface calculation (accessible molecular) -namespace: operation -subset: operations -def: "Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure." [http://edamontology.org, WHATIF] -comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). -xref: WHATIF:ResidueAccessibilityMolecular -is_a: EDAM_operation:2461 ! Protein residue surface calculation +id: EDAM_data:1246 +name: Sequence cluster (nucleic acid) +comment: The sequences are typically related, for example a family of sequences. +subset: bioinformatics +subset: data +subset: edam +synonym: "Nucleotide sequence cluster" EXACT [] +created_in: "beta12orEarlier" +def: "A cluster of nucleotide sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1234 ! Sequence set (nucleic acid) +is_a: EDAM_data:1235 ! Sequence cluster [Term] -id: EDAM_operation:1822 -name: Protein residue surface calculation (vacuum molecular) -namespace: operation -subset: operations -def: "Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [http://edamontology.org, WHATIF] -comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). -xref: WHATIF:ResidueAccessibilityVacuumMolecular -is_a: EDAM_operation:2461 ! Protein residue surface calculation +id: EDAM_data:1249 +name: Sequence length +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "The size (length) of a sequence, subsequence or region in a sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0854 ! Sequence length specification +[Term] +id: EDAM_data:1250 +name: Word size +comment: Word size is used for example in word-based sequence database search methods. +subset: bioinformatics +subset: data +subset: edam +synonym: "Word length" EXACT [] +created_in: "beta12orEarlier" +def: "Size of a sequence word." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1249 ! Sequence length [Term] -id: EDAM_operation:2462 -name: Protein surface calculation -namespace: operation -subset: operations -def: "Calculate the solvent accessibility of a structure as a whole." [http://edamontology.org, WHATIF] -is_a: EDAM_operation:0387 ! Protein surface and interior calculation +id: EDAM_data:1251 +name: Window size +comment: A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Size of a sequence window." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1249 ! Sequence length +[Term] +id: EDAM_data:1252 +name: Sequence length range +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Specification of range(s) of length of sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0854 ! Sequence length specification [Term] -id: EDAM_operation:1823 -name: Protein surface calculation (accessible molecular) -namespace: operation -subset: operations -def: "Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole." [http://edamontology.org, WHATIF] -xref: WHATIF:TotAccessibilityMolecular -is_a: EDAM_operation:2462 ! Protein surface calculation +id: EDAM_data:1253 +name: Sequence information report +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0855 ! Sequence metadata +consider: EDAM_data:2043 ! Sequence record lite +[Term] +id: EDAM_data:1254 +name: Sequence property +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence properties report" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2955 ! Sequence report [Term] -id: EDAM_operation:1824 -name: Protein surface calculation (accessible) -namespace: operation -subset: operations -def: "Calculate the solvent accessibility ('accessible surface') for a structure as a whole." [http://edamontology.org, WHATIF] -xref: WHATIF:TotAccessibilitySolvent -is_a: EDAM_operation:2462 ! Protein surface calculation +id: EDAM_data:1255 +name: Feature record +comment: This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. +subset: bioinformatics +subset: data +subset: edam +synonym: "Features" EXACT [] +synonym: "General sequence features" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D058977" RELATED [] +synonym: "Sequence features" EXACT [] +synonym: "Sequence features report" EXACT [] +synonym: "SO:0000110" RELATED [] +created_in: "beta12orEarlier" +def: "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2955 ! Sequence report [Term] -id: EDAM_operation:1829 -name: Cysteine bridge detection -namespace: operation -subset: operations -def: "Detect cysteine bridges (from coordinate data) in a protein structure." [http://edamontology.org, WHATIF] -xref: WHATIF:ShowCysteineBridge -is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment +id: EDAM_data:1256 +name: Sequence features (comparative) +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1255 ! Feature record +[Term] +id: EDAM_data:1257 +name: Sequence property (protein) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report of general sequence properties derived from protein sequence data." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0897 ! Protein property [Term] -id: EDAM_operation:1830 -name: Free cysteine detection -namespace: operation -subset: operations -def: "Detect free cysteines in a protein structure." [http://edamontology.org, WHATIF] -comment: A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. -xref: WHATIF:ShowCysteineFree -is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment +id: EDAM_data:1258 +name: Sequence property (nucleic acid) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report of general sequence properties derived from nucleotide sequence data." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0912 ! Nucleic acid property +[Term] +id: EDAM_data:1259 +name: Sequence complexity +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence property (complexity)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on sequence complexity, for example low-complexity or repeat regions in sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1254 ! Sequence property [Term] -id: EDAM_operation:1831 -name: Metal-bound cysteine detection -namespace: operation -subset: operations -def: "Detect cysteines that are bound to metal in a protein structure." [http://edamontology.org, WHATIF] -xref: WHATIF:ShowCysteineMetal -is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment +id: EDAM_data:1260 +name: Sequence ambiguity +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence property (ambiguity)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on ambiguity in molecular sequence(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1254 ! Sequence property [Term] -id: EDAM_operation:2575 -name: Binding site prediction -namespace: operation -subset: operations -def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [http://edamontology.org] -synonym: "Ligand-binding and active site prediction" EXACT [http://edamontology.org] -is_a: EDAM_operation:2492 ! Protein interaction prediction -relationship: has_output EDAM_data:1325 !{min_cardinality=0} ! Protein features (active sites) -relationship: has_output EDAM_data:1326 !{min_cardinality=0} ! Protein features (binding sites) -relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions +id: EDAM_data:1261 +name: Sequence composition +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence property (composition)" EXACT [] +created_in: "beta12orEarlier" +def: "A report (typically a table) on character or word composition / frequency of a molecular sequence(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1254 ! Sequence property [Term] -id: EDAM_operation:0388 -name: Binding site prediction (from structure) -namespace: operation -subset: operations -def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." [http://edamontology.org] -synonym: "Ligand-binding and active site prediction (from structure)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0245 ! Protein structural motif recognition -is_a: EDAM_operation:2575 ! Binding site prediction +id: EDAM_data:1262 +name: Peptide molecular weight hits +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on peptide fragments of certain molecular weight(s) in one or more protein sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1233 ! Sequence set (protein) +[Term] +id: EDAM_data:1263 +name: Sequence composition (base position variability) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Report on or plot of third base position variability in a nucleotide sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] -id: EDAM_operation:0389 -name: Protein-nucleic acid binding site analysis -namespace: operation -subset: operations -def: "Analyse RNA or DNA-binding sites in protein structure." [http://edamontology.org] -is_a: EDAM_operation:2949 ! Protein interaction analysis -relationship: has_input EDAM_data:1567 ! Protein-nucleic acid interaction -relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions +id: EDAM_data:1264 +name: Sequence composition table +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A table of character or word composition / frequency of a molecular sequence." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1261 ! Sequence composition [Term] -id: EDAM_operation:0390 -name: Protein peeling -namespace: operation -subset: operations -def: "Decompose a structure into compact or globular fragments (protein peeling)." [http://edamontology.org] -is_a: EDAM_operation:0246 ! Protein domain recognition -relationship: has_output EDAM_data:0901 !{min_cardinality=1} ! Protein features (domains) +id: EDAM_data:1265 +name: Sequence composition (base frequencies) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A table of base frequencies of a nucleotide sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3086 ! Nucleic acid sequence composition +[Term] +id: EDAM_data:1266 +name: Sequence composition (base words) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A table of word composition of a nucleotide sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] -id: EDAM_operation:0391 -name: Protein distance matrix calculation -namespace: operation -subset: operations -def: "Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org] -is_a: EDAM_operation:0248 ! Residue interaction calculation -relationship: has_output EDAM_data:1546 !{min_cardinality=1} ! Protein distance matrix +id: EDAM_data:1267 +name: Amino acid frequencies +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence composition (amino acid frequencies)" EXACT [] +created_in: "beta12orEarlier" +def: "A table of amino acid frequencies of a protein sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3085 ! Protein sequence composition [Term] -id: EDAM_operation:0394 -name: Hydrogen bond calculation -namespace: operation -subset: operations -def: "Identify potential hydrogen bonds between amino acids and other groups." [http://edamontology.org, WHATIF] -comment: The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. -xref: WHATIF:ShowHydrogenBondsM -xref: WHATIF:ShowHydrogenBonds -xref: WHATIF:ShowHydrogenBonds -xref: WHATIF:HasHydrogenBonds -is_a: EDAM_operation:0248 ! Residue interaction calculation -relationship: has_output EDAM_data:1549 !{min_cardinality=1} ! Protein hydrogen bonds +id: EDAM_data:1268 +name: Amino acid word frequencies +subset: bioinformatics +subset: data +subset: edam +synonym: "Sequence composition (amino acid words)" EXACT [] +created_in: "beta12orEarlier" +def: "A table of amino acid word composition of a protein sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3085 ! Protein sequence composition +[Term] +id: EDAM_data:1269 +name: DAS sequence feature annotation +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Annotation of a molecular sequence in DAS format." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1978 ! DASGFF [Term] -id: EDAM_operation:2491 -name: Hydrogen bond calculation (inter-residue) -namespace: operation -subset: operations -def: "Identify potential hydrogen bonds between amino acid residues." [http://edamontology.org, WHATIF] -is_a: EDAM_operation:0394 ! Hydrogen bond calculation -is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) +id: EDAM_data:1270 +name: Sequence feature table +subset: bioinformatics +subset: data +subset: edam +synonym: "Feature table" EXACT [] +created_in: "beta12orEarlier" +def: "Annotation of positional sequence features, organized into a standard feature table." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1255 ! Feature record [Term] -id: EDAM_operation:1839 -name: Salt bridge calculation -namespace: operation -subset: operations -def: "Calculate (and possibly score) salt bridges in a protein structure." [http://edamontology.org, WHATIF] -comment: Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. -xref: WHATIF:HasSaltBridge -xref: WHATIF:HasSaltBridgePlus -xref: WHATIF:ShowSaltBridges -xref: WHATIF:ShowSaltBridgesH -is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) +id: EDAM_data:1274 +name: Map +subset: bioinformatics +subset: data +subset: edam +synonym: "DNA map" EXACT [] +created_in: "beta12orEarlier" +def: "A map of (typically one) DNA sequence annotated with positional or non-positional features." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0102 ! Mapping [Term] -id: EDAM_operation:1846 -name: HET group detection -namespace: operation -subset: operations -def: "Identify HET groups in PDB files." [http://edamontology.org, WHATIF] -comment: A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. -xref: WHATIF: HETGroupNames -is_a: EDAM_operation:1838 ! Residue contact calculation (residue-ligand) - +id: EDAM_data:1276 +name: Nucleic acid features +comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. +subset: bioinformatics +subset: data +subset: edam +synonym: "Feature table (nucleic acid)" EXACT [] +synonym: "Nucleic acid feature table" EXACT [] +created_in: "beta12orEarlier" +def: "Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1255 ! Feature record +is_a: EDAM_data:2084 ! Nucleic acid report [Term] -id: EDAM_operation:2950 -! alt_id: EDAM_operation:1833 -name: Residue contact calculation -namespace: operation -subset: operations -def: "Calculate contacts between residues and some other group in a protein structure." [http://edamontology.org, WHATIF] -is_a: EDAM_operation:0248 ! Residue interaction calculation +id: EDAM_data:1277 +name: Protein features +comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. +subset: bioinformatics +subset: data +subset: edam +synonym: "Feature table (protein)" EXACT [] +synonym: "Protein feature table" EXACT [] +created_in: "beta12orEarlier" +def: "Protein sequence-specific feature annotation (positional features of a protein sequence)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0896 ! Protein report +is_a: EDAM_data:1255 ! Feature record +[Term] +id: EDAM_data:1278 +name: Genetic map +comment: A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. +subset: bioinformatics +subset: data +subset: edam +synonym: "Linkage map" EXACT [] +xref: Moby:GeneticMap +created_in: "beta12orEarlier" +def: "A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1274 ! Map +relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] -id: EDAM_operation:1838 -name: Residue contact calculation (residue-ligand) -namespace: operation -subset: operations -def: "Calculate contacts between residues and ligands in a protein structure." [http://edamontology.org, WHATIF] -xref: WHATIF:ShowLigandContacts -xref: WHATIF:ShowDrugContacts -xref: WHATIF:ShowDrugContactsShort -is_a: EDAM_operation:2950 ! Residue contact calculation -is_a: EDAM_operation:0388 ! Binding site prediction (from structure) +id: EDAM_data:1279 +name: Sequence map +comment: A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1280 ! Physical map +[Term] +id: EDAM_data:1280 +name: Physical map +comment: Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1274 ! Map [Term] -id: EDAM_operation:2490 -name: Residue contact calculation (residue-residue) -namespace: operation -subset: operations -def: "Calculate contacts between residues in a protein structure." [http://edamontology.org, WHATIF] -is_a: EDAM_operation:2950 ! Residue contact calculation +id: EDAM_data:1281 +name: Sequence signature map +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Image of a sequence with matches to signatures, motifs or profiles." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1298 ! Sequence features (motifs) +[Term] +id: EDAM_data:1283 +name: Cytogenetic map +comment: This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. +subset: bioinformatics +subset: data +subset: edam +synonym: "Chromosome map" EXACT [] +synonym: "Cytogenic map" EXACT [] +synonym: "Cytologic map" EXACT [] +created_in: "beta12orEarlier" +def: "A map showing banding patterns derived from direct observation of a stained chromosome." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1280 ! Physical map [Term] -id: EDAM_operation:0392 -name: Protein contact map calculation -namespace: operation -subset: operations -def: "Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure." [http://edamontology.org] -is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) -relationship: has_output EDAM_data:1547 !{min_cardinality=1} ! Protein contact map +id: EDAM_data:1284 +name: DNA transduction map +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A gene map showing distances between loci based on relative cotransduction frequencies." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1278 ! Genetic map +[Term] +id: EDAM_data:1285 +name: Gene map +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1279 ! Sequence map [Term] -id: EDAM_operation:0393 -name: Protein residue cluster calculation -namespace: operation -subset: operations -def: "Calculate clusters of contacting residues in protein structures." [http://edamontology.org] -comment: Cluster of contacting residues might be key structural residues. -is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) -relationship: has_output EDAM_data:1548 !{min_cardinality=1} ! Protein residue 3D cluster +id: EDAM_data:1286 +name: Plasmid map +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Sequence map of a plasmid (circular DNA)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1279 ! Sequence map +[Term] +id: EDAM_data:1288 +name: Genome map +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Sequence map of a whole genome." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1279 ! Sequence map [Term] -id: EDAM_operation:1832 -name: Residue contact calculation (residue-nucleic acid) -namespace: operation -subset: operations -def: "Calculate protein residue contacts with nucleic acids in a structure." [http://edamontology.org, WHATIF] -xref: WHATIF:HasNucleicContacts -xref: WHATIF:ShowProteiNucleicContacts -is_a: EDAM_operation:2950 ! Residue contact calculation -is_a: EDAM_operation:0389 ! Protein-nucleic acid binding site analysis -is_a: EDAM_operation:0245 ! Protein structural motif recognition +id: EDAM_data:1289 +name: Restriction map +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1279 ! Sequence map +is_a: EDAM_data:1305 ! Nucleic acid features (restriction sites) +is_a: EDAM_data:2969 ! Sequence image +[Term] +id: EDAM_data:1290 +name: InterPro compact match image +comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Image showing matches between protein sequence(s) and InterPro Entries." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_operation:1834 -name: Residue contact calculation (residue-metal) -namespace: operation -subset: operations -def: "Calculate protein residue contacts with metal in a structure." [http://edamontology.org, WHATIF] -xref: WHATIF:HasMetalContacts -xref: WHATIF:HasMetalContactsPlus -is_a: EDAM_operation:2950 ! Residue contact calculation -is_a: EDAM_operation:0388 ! Binding site prediction (from structure) +id: EDAM_data:1291 +name: InterPro detailed match image +comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Image showing detailed information on matches between protein sequence(s) and InterPro Entries." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1298 ! Sequence features (motifs) +[Term] +id: EDAM_data:1292 +name: InterPro architecture image +comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Image showing the architecture of InterPro domains in a protein sequence." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_operation:1835 -name: Residue contact calculation (residue-negative ion) -namespace: operation -subset: operations -def: "Calculate ion contacts in a structure (all ions for all side chain atoms)." [http://edamontology.org, WHATIF] -xref: WHATIF:HasNegativeIonContacts -xref: WHATIF:HasNegativeIonContactsPlus -is_a: EDAM_operation:2950 ! Residue contact calculation +id: EDAM_data:1293 +name: SMART protein schematic +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "SMART protein schematic in PNG format." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_operation:1837 -name: Residue symmetry contact calculation -namespace: operation -subset: operations -def: "Calculate the number of symmetry contacts made by residues in a protein structure." [http://edamontology.org, WHATIF] -comment: A symmetry contact is a contact between two atoms in different asymmetric unit. -xref: WHATIF:SymmetryContact -is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) +id: EDAM_data:1294 +name: GlobPlot domain image +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_operation:0396 -name: Ramachandran plot calculation -namespace: operation -subset: operations -def: "Calculate a Ramachandran plot of a protein structure." [http://edamontology.org] -is_a: EDAM_operation:0249 ! Torsion angle calculation -relationship: has_output EDAM_data:1544 !{min_cardinality=1} ! Ramachandran plot +id: EDAM_data:1298 +name: Sequence features (motifs) +comment: Use this concept if another, more specific concept is not available. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1255 ! Feature record +[Term] +id: EDAM_data:1299 +name: Sequence features (repeats) +comment: The report might include derived data map such as classification, annotation, organization, periodicity etc. +subset: bioinformatics +subset: data +subset: edam +synonym: "Repeat sequence map" EXACT [] +created_in: "beta12orEarlier" +def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1255 ! Feature record [Term] -id: EDAM_operation:0397 -name: Ramachandran plot evaluation -namespace: operation -subset: operations -def: "Analyse (typically to validate) a Ramachandran plot of a protein structure." [http://edamontology.org] -is_a: EDAM_operation:1844 ! Dihedral angle validation -relationship: has_input EDAM_data:1544 !{min_cardinality=1} ! Ramachandran plot -relationship: has_output EDAM_data:1539 ! Protein structural quality report +id: EDAM_data:1300 +name: Nucleic acid features (gene and transcript structure) +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene annotation (structure)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0916 ! Gene annotation +is_a: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_operation:1825 -name: Backbone torsion angle calculation -namespace: operation -subset: operations -def: "Calculate for each residue in a protein structure all its backbone torsion angles." [http://edamontology.org, WHATIF] -xref: WHATIF:ResidueTorsionsBB -is_a: EDAM_operation:0249 ! Torsion angle calculation - +id: EDAM_data:1301 +name: Nucleic acid features (mobile genetic elements) +comment: This includes transposons, Plasmids, Bacteriophage elements and Group II introns. +subset: bioinformatics +subset: data +subset: edam +synonym: "Nucleic acid features (transposons)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on a region of a nucleic acid sequence containin mobile genetic elements." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_operation:1826 -name: Full torsion angle calculation -namespace: operation -subset: operations -def: "Calculate for each residue in a protein structure all its torsion angles." [http://edamontology.org, WHATIF] -xref: WHATIF:ResidueTorsions -is_a: EDAM_operation:0249 ! Torsion angle calculation +id: EDAM_data:1302 +name: Nucleic acid features (PolyA signal or site) +comment: A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. +subset: bioinformatics +subset: data +subset: edam +synonym: "PolyA signal" EXACT [] +synonym: "PolyA site" EXACT [] +created_in: "beta12orEarlier" +def: "A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) +[Term] +id: EDAM_data:1303 +name: Nucleic acid features (quadruplexes) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on quadruplex-forming motifs in a nucleotide sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] -id: EDAM_operation:1827 -name: Cysteine torsion angle calculation -namespace: operation -subset: operations -def: "Calculate for each cysteine (bridge) all its torsion angles." [http://edamontology.org, WHATIF] -xref: WHATIF:CysteineTorsions -is_a: EDAM_operation:0249 ! Torsion angle calculation +id: EDAM_data:1304 +name: Nucleic acid features (CpG island and isochore) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report or plot of CpG rich regions (isochores) in a nucleotide sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) +[Term] +id: EDAM_data:1305 +name: Nucleic acid features (restriction sites) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3125 ! Nucleic acid features (binding) [Term] -id: EDAM_operation:1828 -name: Tau angle calculation -namespace: operation -subset: operations -def: "For each amino acid in a protein structure calculate the backbone angle tau." [http://edamontology.org, WHATIF] -comment: Tau is the backbone angle N-Calpha-C (angle over the C-alpha). -xref: WHATIF:ShowTauAngle -is_a: EDAM_operation:0249 ! Torsion angle calculation +id: EDAM_data:1306 +name: Nucleic acid features (nucleosome exclusion sequences) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on nucleosome formation potential or exclusion sequence(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination) +[Term] +id: EDAM_data:1307 +name: Nucleic acid features (splice sites) +subset: bioinformatics +subset: data +subset: edam +synonym: "Nucleic acid report (RNA splice model)" EXACT [] +synonym: "Nucleic acid report (RNA splicing)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on splice sites in a nucleotide sequence or alternative RNA splicing events." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] -id: EDAM_operation:0536 -name: Protein structure assignment (from X-ray crystallographic data) -namespace: operation -subset: operations -def: "Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data." [http://edamontology.org] -is_a: EDAM_operation:0320 ! Protein structure assignment -relationship: has_input EDAM_data:0937 !{min_cardinality=1} ! Protein X-ray crystallographic data +id: EDAM_data:1308 +name: Nucleic acid features (matrix/scaffold attachment sites) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) [Term] -id: EDAM_operation:0537 -name: Protein structure assignment (from NMR data) -namespace: operation -subset: operations -def: "Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data." [http://edamontology.org] -is_a: EDAM_operation:0320 ! Protein structure assignment -relationship: has_input EDAM_data:0938 !{min_cardinality=1} ! Protein NMR data +id: EDAM_data:1309 +name: Gene features (exonic splicing enhancer) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on exonic splicing enhancers (ESE) in an exon." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2397 ! Nucleic acid features (exon) [Term] -id: EDAM_operation:0395 -name: Residue non-canonical interaction detection -namespace: operation -subset: operations -def: "Calculate non-canonical atomic interactions in protein structures." [http://edamontology.org] -is_a: EDAM_operation:0248 ! Residue interaction calculation -is_a: EDAM_operation:0321 ! Protein model evaluation -relationship: has_output EDAM_data:1550 !{min_cardinality=1} ! Protein non-canonical interactions +id: EDAM_data:1310 +name: Nucleic acid features (microRNA) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA) +relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] -id: EDAM_operation:1913 -name: Residue validation -namespace: operation -subset: operations -def: "Identify poor quality amino acid positions in protein structures." [http://edamontology.org, WHATIF] -comment: The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). -xref: WHATIF: UseResidueDB -is_a: EDAM_operation:0321 ! Protein model evaluation +id: EDAM_data:1311 +name: Nucleic acid features (operon) +comment: The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene features (operon)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on operons (operators, promoters and genes) from a bacterial genome." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] -id: EDAM_operation:1843 -name: Residue packing validation -namespace: operation -subset: operations -def: "Identify poorly packed residues in protein structures." [http://edamontology.org, WHATIF] -xref: WHATIF: PackingQuality -is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection +id: EDAM_data:1312 +name: Gene features (promoter) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) [Term] -id: EDAM_operation:1844 -name: Dihedral angle validation -namespace: operation -subset: operations -def: "Identify for each residue in a protein structure any improper dihedral (phi/psi) angles." [http://edamontology.org, WHATIF] -xref: WHATIF: ImproperQualitySum -xref: WHATIF: ImproperQualityMax -is_a: EDAM_operation:0321 ! Protein model evaluation +id: EDAM_data:1313 +name: Nucleic acid features (coding sequence) +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene annotation (translation)" EXACT [] +synonym: "Gene features (coding region)" EXACT [] +synonym: "Gene features (coding sequence)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] -id: EDAM_operation:1836 -name: Residue bump detection -namespace: operation -subset: operations -def: "Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance." [http://edamontology.org, WHATIF] -xref: WHATIF:ShowBumps -is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection +id: EDAM_data:1314 +name: Gene features (SECIS element) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) +[Term] +id: EDAM_data:1315 +name: Gene features (TFBS) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on the transcription factor binding sites (TFBS) in a DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1312 ! Gene features (promoter) +is_a: EDAM_data:3125 ! Nucleic acid features (binding) +relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites +[Term] +id: EDAM_data:1321 +name: Protein features (sites) +comment: Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1277 ! Protein features +[Term] +id: EDAM_data:1322 +name: Protein features (signal peptides) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on the location of signal peptides or signal peptide cleavage sites in protein sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features [Term] -id: EDAM_operation:2443 -name: Phylogenetic tree processing -namespace: operation -subset: operations -def: "Process (read and / or write) a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0872 !{min_cardinality=0} ! Phylogenetic tree -relationship: has_output EDAM_data:0872 !{min_cardinality=0} ! Phylogenetic tree -relationship: has_topic EDAM_topic:0084 ! Phylogenetics +id: EDAM_data:1323 +name: Protein features (cleavage sites) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification +[Term] +id: EDAM_data:1324 +name: Protein features (post-translation modifications) +subset: bioinformatics +subset: data +subset: edam +synonym: "Post-translation modification" EXACT [] +synonym: "Protein features (post-translation modification sites)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on post-translation modifications in a protein sequence, typically describing the specific sites involved." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2191 ! Protein features (chemical modification) [Term] -id: EDAM_operation:0550 -name: Sequence alignment analysis (phylogenetic modelling) -namespace: operation -subset: operations -def: "Identify a plausible model of DNA substitution that explains a DNA sequence alignment." [http://edamontology.org] -is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) -is_a: EDAM_operation:2426 ! Modelling and simulation -relationship: has_output EDAM_data:1439 ! DNA substitution model -relationship: has_topic EDAM_topic:0084 ! Phylogenetics +id: EDAM_data:1325 +name: Protein features (active sites) +subset: bioinformatics +subset: data +subset: edam +synonym: "Enzyme active site" EXACT [] +created_in: "beta12orEarlier" +def: "A report on catalytic residues (active site) of an enzyme." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +[Term] +id: EDAM_data:1326 +name: Protein features (binding sites) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features [Term] -id: EDAM_operation:0554 -name: Phylogenetic tree analysis (natural selection) -namespace: operation -subset: operations -def: "Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive)." [http://edamontology.org] -comment: Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. -is_a: EDAM_operation:0324 ! Phylogenetic tree analysis +id: EDAM_data:1327 +name: Protein features (epitopes) +comment: Epitope mapping is commonly done during vaccine design. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1326 ! Protein features (binding sites) +[Term] +id: EDAM_data:1328 +name: Protein features (nucleic acid binding sites) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on RNA and DNA-binding proteins and binding sites in protein sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features [Term] -id: EDAM_operation:0323 -name: Phylogenetic tree construction -namespace: operation -subset: operations -def: "Construct a phylogenetic tree." [http://edamontology.org] -synonym: "Phylogenetic tree construction" EXACT [http://edamontology.org] -comment: Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. -synonym: "Phylogenetic tree generation" EXACT [http://edamontology.org] -is_a: EDAM_operation:2443 ! Phylogenetic tree processing -is_a: EDAM_operation:2995 ! Sequence classification -relationship: has_output EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree -relationship: has_topic EDAM_topic:0080 ! Sequence analysis -relationship: has_topic EDAM_topic:0084 ! Phylogenetics - +id: EDAM_data:1329 +name: MHC Class I epitopes report +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on epitopes that bind to MHC class I molecules." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1326 ! Protein features (binding sites) [Term] -id: EDAM_operation:0325 -name: Phylogenetic tree comparison -namespace: operation -subset: operations -def: "Compare two or more phylogenetic trees." [http://edamontology.org] -comment: For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. -is_a: EDAM_operation:0324 ! Phylogenetic tree analysis -is_a: EDAM_operation:2424 ! Comparison +id: EDAM_data:1330 +name: MHC Class II epitopes report +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on predicted epitopes that bind to MHC class II molecules." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1326 ! Protein features (binding sites) [Term] -id: EDAM_operation:0326 -name: Phylogenetic tree editing -namespace: operation -subset: operations -def: "Edit a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_operation:2443 ! Phylogenetic tree processing -is_a: EDAM_operation:3096 ! Editing -relationship: has_input EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree -relationship: has_output EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree +id: EDAM_data:1331 +name: Protein features (PEST sites) +comment: 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report or plot of PEST sites in a protein sequence." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1323 ! Protein features (cleavage sites) +[Term] +id: EDAM_data:1338 +name: Sequence database hits scores list +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Scores from a sequence database search (for example a BLAST search)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0857 ! Database hits (sequence) [Term] -id: EDAM_operation:0551 -name: Phylogenetic tree analysis (shape) -namespace: operation -subset: operations -def: "Analyse the shape (topology) of a phylogenetic tree." [http://edamontology.org] -synonym: "Phylogenetic tree topology analysis" EXACT [http://edamontology.org] -is_a: EDAM_operation:0324 ! Phylogenetic tree analysis -relationship: has_output EDAM_data:1440 !{min_cardinality=1} ! Phylogenetic tree report (tree shape) +id: EDAM_data:1339 +name: Sequence database hits alignments list +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignments from a sequence database search (for example a BLAST search)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0857 ! Database hits (sequence) [Term] -id: EDAM_operation:0552 -name: Phylogenetic tree bootstrapping -namespace: operation -subset: operations -def: "Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_operation:0324 ! Phylogenetic tree analysis -is_a: EDAM_operation:2428 ! Evaluation and validation -relationship: has_output EDAM_data:1441 !{min_cardinality=1} ! Phylogenetic tree report (tree evaluation) +id: EDAM_data:1340 +name: Sequence database hits evaluation data +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0857 ! Database hits (sequence) +[Term] +id: EDAM_data:1344 +name: MEME motif alphabet +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alphabet for the motifs (patterns) that MEME will search for." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0950 ! Biological model [Term] -id: EDAM_operation:0553 -name: Phylogenetic tree analysis (gene family prediction) -namespace: operation -subset: operations -def: "Predict families of genes and gene function based on their position in a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_operation:0324 ! Phylogenetic tree analysis -relationship: has_output EDAM_data:0916 ! Gene annotation -relationship: has_topic EDAM_topic:0194 ! Phylogenomics +id: EDAM_data:1345 +name: MEME background frequencies file +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "MEME background frequencies file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0950 ! Biological model [Term] -id: EDAM_operation:0538 -name: Phylogenetic tree construction (data centric) -namespace: operation -subset: operations -def: "Construct a phylogenetic tree from a specific type of data." [http://edamontology.org] -is_a: EDAM_operation:0323 ! Phylogenetic tree construction +id: EDAM_data:1346 +name: MEME motifs directive file +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "File of directives for ordering and spacing of MEME motifs." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0950 ! Biological model [Term] -id: EDAM_operation:0539 -name: Phylogenetic tree construction (method centric) -namespace: operation -subset: operations -def: "Construct a phylogenetic tree using a specific method." [http://edamontology.org] -is_a: EDAM_operation:0323 ! Phylogenetic tree construction +id: EDAM_data:1347 +name: Dirichlet distribution +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Dirichlet distribution used by hidden Markov model analysis programs." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0950 ! Biological model [Term] -id: EDAM_operation:0540 -name: Phylogenetic tree construction (from molecular sequences) -namespace: operation -subset: operations -def: "Phylogenetic tree construction from molecular sequences." [http://edamontology.org] -comment: Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. -is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) -is_a: EDAM_operation:2403 ! Sequence analysis +id: EDAM_data:1348 +name: HMM emission and transition counts +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0950 ! Biological model +[Term] +id: EDAM_data:1352 +name: Regular expression +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Regular expression pattern." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM_operation:0541 -name: Phylogenetic tree construction (from continuous quantitative characters) -namespace: operation -subset: operations -def: "Phylogenetic tree construction from continuous quantitative character data." [http://edamontology.org] -is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) -relationship: has_input EDAM_data:1426 !{min_cardinality=1} ! Phylogenetic continuous quantitative data +id: EDAM_data:1353 +name: Sequence motif +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0158 ! Sequence motifs +[Term] +id: EDAM_data:1354 +name: Sequence profile +subset: bioinformatics +subset: data +subset: edam +synonym: "SIO:010531" EXACT [] +created_in: "beta12orEarlier" +def: "Some type of statistical model representing a (typically multiple) sequence alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] -id: EDAM_operation:0542 -name: Phylogenetic tree construction (from gene frequencies) -namespace: operation -subset: operations -def: "Phylogenetic tree construction from gene frequency data." [http://edamontology.org] -is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) -relationship: has_input EDAM_data:2873 !{min_cardinality=1} ! Phylogenetic gene frequencies data -relationship: has_topic EDAM_topic:0203 ! Transcriptomics +id: EDAM_data:1355 +name: Protein signature +subset: bioinformatics +subset: data +subset: edam +synonym: "InterPro entry" EXACT [] +created_in: "beta12orEarlier" +def: "An entry (sequence classifier and associated data) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0907 ! Protein family +[Term] +id: EDAM_data:1358 +name: Prosite nucleotide pattern +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A nucleotide regular expression pattern from the Prosite database." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1353 ! Sequence motif [Term] -id: EDAM_operation:0543 -name: Phylogenetic tree construction (from polymorphism data) -namespace: operation -subset: operations -def: "Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data." [http://edamontology.org] -is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) -relationship: has_topic EDAM_topic:0199 ! Genetic variation +id: EDAM_data:1359 +name: Prosite protein pattern +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein regular expression pattern from the Prosite database." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1353 ! Sequence motif [Term] -id: EDAM_operation:0544 -name: Phylogenetic species tree construction -namespace: operation -subset: operations -def: "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." [http://edamontology.org] -is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences) +id: EDAM_data:1361 +name: Position frequency matrix +subset: bioinformatics +subset: data +subset: edam +synonym: "PFM" EXACT [] +created_in: "beta12orEarlier" +def: "A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2854 ! Position-specific scoring matrix +[Term] +id: EDAM_data:1362 +name: Position weight matrix +comment: Contributions of individual sequences to the matrix might be uneven (weighted). +subset: bioinformatics +subset: data +subset: edam +synonym: "PWM" EXACT [] +created_in: "beta12orEarlier" +def: "A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] -id: EDAM_operation:0327 -name: Phylogenetic footprinting / shadowing -namespace: operation -subset: operations -def: "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing)." [http://edamontology.org] -comment: A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. -is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences) -relationship: has_topic EDAM_topic:0194 ! Phylogenomics +id: EDAM_data:1363 +name: Information content matrix +subset: bioinformatics +subset: data +subset: edam +synonym: "ICM" EXACT [] +created_in: "beta12orEarlier" +def: "A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] -id: EDAM_operation:0545 -name: Phylogenetic tree construction (parsimony methods) -namespace: operation -subset: operations -def: "Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment." [http://edamontology.org] -comment: This includes evolutionary parsimony (invariants) methods. -is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) +id: EDAM_data:1364 +name: Hidden Markov model +subset: bioinformatics +subset: data +subset: edam +synonym: "HMM" EXACT [] +created_in: "beta12orEarlier" +def: "A hidden Markov model representation of a set or alignment of sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1354 ! Sequence profile [Term] -id: EDAM_operation:0546 -name: Phylogenetic tree construction (minimum distance methods) -namespace: operation -subset: operations -def: "Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances." [http://edamontology.org] -comment: This includes neighbor joining (NJ) clustering method. -is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) +id: EDAM_data:1365 +name: Fingerprint +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "One or more fingerprints (sequence classifiers) as used in the PRINTS database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] -id: EDAM_operation:0547 -name: Phylogenetic tree construction (maximum likelihood and Bayesian methods) -namespace: operation -subset: operations -def: "Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution." [http://edamontology.org] -comment: Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. -is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) +id: EDAM_data:1368 +name: Domainatrix signature +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein signature of the type used in the EMBASSY Signature package." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1354 ! Sequence profile [Term] -id: EDAM_operation:0548 -name: Phylogenetic tree construction (quartet methods) -namespace: operation -subset: operations -def: "Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely." [http://edamontology.org] -is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) +id: EDAM_data:1371 +name: HMMER NULL hidden Markov model +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "NULL hidden Markov model representation used by the HMMER package." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1364 ! Hidden Markov model [Term] -id: EDAM_operation:0549 -name: Phylogenetic tree construction (AI methods) -namespace: operation -subset: operations -def: "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." [http://edamontology.org] -is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) - +id: EDAM_data:1372 +name: Protein family signature +comment: Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1355 ! Protein signature [Term] -id: EDAM_operation:0555 -name: Phylogenetic tree construction (consensus) -namespace: operation -subset: operations -def: "Compare two or more phylogenetic trees to produce a consensus tree." [http://edamontology.org] -comment: Methods typically test for topological similarity between trees using for example a congruence index. -is_a: EDAM_operation:0325 ! Phylogenetic tree comparison -is_a: EDAM_operation:0323 ! Phylogenetic tree construction +id: EDAM_data:1373 +name: Protein domain signature +comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein domain signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1355 ! Protein signature +[Term] +id: EDAM_data:1374 +name: Protein region signature +comment: A protein region signature defines a region which cannot be described as a protein family or domain signature. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein region signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1355 ! Protein signature [Term] -id: EDAM_operation:0556 -name: Phylogenetic sub/super tree detection -namespace: operation -subset: operations -def: "Compare two or more phylogenetic trees to detect subtrees or supertrees." [http://edamontology.org] -is_a: EDAM_operation:0325 ! Phylogenetic tree comparison +id: EDAM_data:1375 +name: Protein repeat signature +comment: A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein repeat signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1355 ! Protein signature +[Term] +id: EDAM_data:1376 +name: Protein site signature +comment: A protein site signature is a classifier for a specific site in a protein. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein site signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1355 ! Protein signature [Term] -id: EDAM_operation:0557 -name: Phylogenetic tree distances calculation -namespace: operation -subset: operations -def: "Compare two or more phylogenetic trees to calculate distances between trees." [http://edamontology.org] -is_a: EDAM_operation:0325 ! Phylogenetic tree comparison -relationship: has_output EDAM_data:1442 !{min_cardinality=1} ! Phylogenetic tree report (tree distances) +id: EDAM_data:1377 +name: Protein conserved site signature +comment: A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein conserved site signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1376 ! Protein site signature [Term] -id: EDAM_operation:0558 -name: Phylogenetic tree annotation -namespace: operation -subset: operations -def: "Annotate a phylogenetic tree with terms from a controlled vocabulary." [http://edamontology.org] -synonym: "CDAOAnnotattion" RELATED [http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation] -is_a: EDAM_operation:0326 ! Phylogenetic tree editing -is_a: EDAM_operation:0226 ! Annotation +id: EDAM_data:1378 +name: Protein active site signature +comment: A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein active site signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1376 ! Protein site signature [Term] -id: EDAM_operation:0328 -name: Protein folding simulation -namespace: operation -subset: operations -def: "Simulate the folding of a protein." [http://edamontology.org] -is_a: EDAM_operation:2415 ! Protein folding analysis +id: EDAM_data:1379 +name: Protein binding site signature +comment: A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein binding site signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1376 ! Protein site signature +[Term] +id: EDAM_data:1380 +name: Protein post-translational modification signature +comment: A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A protein post-translational modification signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1376 ! Protein site signature [Term] -id: EDAM_operation:0329 -name: Protein folding pathway prediction -namespace: operation -subset: operations -def: "Predict the folding pathway(s) or non-native structural intermediates of a protein." [http://edamontology.org] -is_a: EDAM_operation:2415 ! Protein folding analysis -is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +id: EDAM_data:1381 +name: Sequence alignment (pair) +subset: bioinformatics +subset: data +subset: edam +synonym: "SIO:010068" RELATED [] +created_in: "beta12orEarlier" +def: "Alignment of exactly two molecular sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0863 ! Sequence alignment +[Term] +id: EDAM_data:1382 +name: Sequence alignment (multiple) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of more than two molecular sequences." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM_operation:1842 -name: Proline mutation value calculation -namespace: operation -subset: operations -def: "Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein." [http://edamontology.org, WHATIF] -xref: WHATIF:ProlineMutationValue -is_a: EDAM_operation:0331 ! Protein modelling (mutation) +id: EDAM_data:1383 +name: Sequence alignment (nucleic acid) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of multiple nucleotide sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0863 ! Sequence alignment +is_a: EDAM_data:2084 ! Nucleic acid report +[Term] +id: EDAM_data:1384 +name: Sequence alignment (protein) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of multiple protein sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0863 ! Sequence alignment +is_a: EDAM_data:3154 ! Protein alignment [Term] -id: EDAM_operation:0330 -name: Protein SNP mapping -namespace: operation -subset: operations -def: "Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s)." [http://edamontology.org] -is_a: EDAM_operation:0331 ! Protein modelling (mutation) -relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) -relationship: has_topic EDAM_topic:2277 ! SNPs +id: EDAM_data:1385 +name: Sequence alignment (hybrid) +comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of multiple molecular sequences of different types." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM_operation:0559 -name: Peptide immunogen prediction and optimisation -namespace: operation -subset: operations -def: "Predict and optimise peptide ligands that elicit an immunological response." [http://edamontology.org] -is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction -is_a: EDAM_operation:2425 ! Optimisation and refinement -relationship: has_output EDAM_data:1460 ! Protein structure -relationship: has_topic EDAM_topic:0150 ! Protein design -relationship: has_topic EDAM_topic:0804 ! Immunoinformatics +id: EDAM_data:1386 +name: Sequence alignment (nucleic acid pair) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of exactly two nucleotide sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1381 ! Sequence alignment (pair) +is_a: EDAM_data:1383 ! Sequence alignment (nucleic acid) +[Term] +id: EDAM_data:1387 +name: Sequence alignment (protein pair) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of exactly two protein sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1381 ! Sequence alignment (pair) +is_a: EDAM_data:1384 ! Sequence alignment (protein) +[Term] +id: EDAM_data:1388 +name: Hybrid sequence alignment (pair) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of exactly two molecular sequences of different types." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1385 ! Sequence alignment (hybrid) [Term] -id: EDAM_operation:0560 -name: DNA vaccine prediction and optimisation -namespace: operation -subset: operations -def: "Predict or optimise DNA to elicit (via DNA vaccination) an immunological response." [http://edamontology.org] -is_a: EDAM_operation:3095 ! Nucleic acid design -is_a: EDAM_operation:2425 ! Optimisation and refinement -relationship: has_topic EDAM_topic:0804 ! Immunoinformatics -relationship: has_topic EDAM_topic:2953 ! Nucleic acid design +id: EDAM_data:1389 +name: Multiple nucleotide sequence alignment +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of more than two nucleotide sequences." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM_operation:0561 -name: Sequence reformatting -namespace: operation -subset: operations -def: "Reformat (a file or other report of) molecular sequence(s)." [http://edamontology.org] -is_a: EDAM_operation:0335 ! File reformatting -is_a: EDAM_operation:2121 ! Sequence file processing +id: EDAM_data:1390 +name: Multiple protein sequence alignment +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of more than two protein sequences." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM_operation:0562 -name: Sequence alignment reformatting -namespace: operation -subset: operations -def: "Reformat (a file or other report of) molecular sequence alignment(s)." [http://edamontology.org] -is_a: EDAM_operation:0335 ! File reformatting -is_a: EDAM_operation:2122 ! Sequence alignment file processing +id: EDAM_data:1394 +name: Alignment score or penalty +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A simple floating point number defining the penalty for opening or extending a gap in an alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0864 ! Sequence alignment parameter +is_a: EDAM_data:1772 ! Score or penalty [Term] -id: EDAM_operation:0563 -name: Codon usage table reformatting -namespace: operation -subset: operations -def: "Reformat a codon usage table." [http://edamontology.org] -is_a: EDAM_operation:0335 ! File reformatting -is_a: EDAM_operation:2433 ! Codon usage table processing -relationship: has_input EDAM_data:1597 !{min_cardinality=1} ! Codon usage table -relationship: has_output EDAM_data:1597 !{min_cardinality=1} ! Codon usage table +id: EDAM_data:1395 +name: Score end gaps control +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Whether end gaps are scored or not." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2527 ! Parameter +[Term] +id: EDAM_data:1396 +name: Aligned sequence order +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Controls the order of sequences in an output sequence alignment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2134 ! Results sort order [Term] -id: EDAM_operation:1848 -name: Structure reformatting -namespace: operation -subset: operations -def: "Reformat (a file or other report of) tertiary structure data." [http://edamontology.org, WHATIF] -xref: WHATIF: PDBasXML -is_a: EDAM_operation:2234 ! Structure file processing -is_a: EDAM_operation:0335 ! File reformatting +id: EDAM_data:1397 +name: Gap opening penalty +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A penalty for opening a gap in an alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2137 ! Gap penalty +[Term] +id: EDAM_data:1398 +name: Gap extension penalty +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A penalty for extending a gap in an alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2137 ! Gap penalty [Term] -id: EDAM_operation:0564 -name: Sequence rendering -namespace: operation -subset: operations -def: "Visualise, format or render a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org] -is_a: EDAM_operation:0337 ! Plotting and rendering -is_a: EDAM_operation:2446 ! Sequence processing -relationship: has_input EDAM_data:2044 !{min_cardinality=1} ! Sequence -relationship: has_output EDAM_data:2969 !{min_cardinality=1} ! Sequence image +id: EDAM_data:1399 +name: Gap separation penalty +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A penalty for gaps that are close together in an alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2137 ! Gap penalty [Term] -id: EDAM_operation:2515 -name: Sequence rendering (nucleic acid) -namespace: operation -subset: operations -def: "Visualise, format or render a nucleic acid sequence." [http://edamontology.org] -comment: Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. -is_a: EDAM_operation:0564 ! Sequence rendering -is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) -relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis +id: EDAM_data:1400 +name: Terminal gap penalty +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1410 ! Terminal gap opening penalty +consider: EDAM_data:1411 ! Terminal gap extension penalty +[Term] +id: EDAM_data:1401 +name: Match reward score +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "The score for a 'match' used in various sequence database search applications with simple scoring schemes." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1394 ! Alignment score or penalty [Term] -id: EDAM_operation:3208 !{since=1.1} -name: Genome rendering -namespace: operation -subset: operations -def: "Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence." [http://edamontology.org] -synonym: "Genome browsing" EXACT [http://edamontology.org] -synonym: "Genome viewing" EXACT [http://edamontology.org] -synonym: "Genome visualisation" EXACT [http://edamontology.org] -synonym: "Genome visualization" EXACT [http://edamontology.org] -is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) +id: EDAM_data:1402 +name: Mismatch penalty score +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1394 ! Alignment score or penalty +[Term] +id: EDAM_data:1403 +name: Drop off score +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "This is the threshold drop in score at which extension of word alignment is halted." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1394 ! Alignment score or penalty [Term] -id: EDAM_operation:2516 -name: Sequence rendering (protein) -namespace: operation -subset: operations -def: "Visualise, format or render a protein sequence." [http://edamontology.org] -comment: Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. -is_a: EDAM_operation:0564 ! Sequence rendering -is_a: EDAM_operation:2447 ! Sequence processing (protein) +id: EDAM_data:1404 +name: Gap opening penalty (integer) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1397 ! Gap opening penalty [Term] -id: EDAM_operation:0565 -name: Sequence alignment rendering -namespace: operation -subset: operations -def: "Visualise, format or print a molecular sequence alignment." [http://edamontology.org] -is_a: EDAM_operation:0337 ! Plotting and rendering -is_a: EDAM_operation:2463 ! Sequence alignment processing -relationship: has_input EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment -relationship: has_output EDAM_data:1711 !{min_cardinality=1} ! Sequence alignment image +id: EDAM_data:1405 +name: Gap opening penalty (float) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1397 ! Gap opening penalty +[Term] +id: EDAM_data:1406 +name: Gap extension penalty (integer) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1398 ! Gap extension penalty +[Term] +id: EDAM_data:1407 +name: Gap extension penalty (float) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1398 ! Gap extension penalty [Term] -id: EDAM_operation:2452 -name: Sequence cluster processing -namespace: operation -subset: operations -def: "Process (read and / or write) a sequence cluster." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:1235 !{min_cardinality=0} ! Sequence cluster -relationship: has_output EDAM_data:1235 !{min_cardinality=0} ! Sequence cluster -relationship: has_topic EDAM_topic:0164 ! Sequence clustering +id: EDAM_data:1408 +name: Gap separation penalty (integer) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1399 ! Gap separation penalty +[Term] +id: EDAM_data:1409 +name: Gap separation penalty (float) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1399 ! Gap separation penalty [Term] -id: EDAM_operation:0566 -name: Sequence cluster rendering -namespace: operation -subset: operations -def: "Visualise, format or render sequence clusters." [http://edamontology.org] -is_a: EDAM_operation:0337 ! Plotting and rendering -is_a: EDAM_operation:2452 ! Sequence cluster processing -relationship: has_input EDAM_data:1235 !{min_cardinality=1} ! Sequence cluster +id: EDAM_data:1410 +name: Terminal gap opening penalty +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1397 ! Gap opening penalty [Term] -id: EDAM_operation:0567 -name: Phylogenetic tree rendering -namespace: operation -subset: operations -def: "Visualise or plot a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_operation:2443 ! Phylogenetic tree processing -is_a: EDAM_operation:0337 ! Plotting and rendering -relationship: has_output EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree +id: EDAM_data:1411 +name: Terminal gap extension penalty +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1398 ! Gap extension penalty +[Term] +id: EDAM_data:1412 +name: Sequence identity +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0865 ! Sequence similarity score [Term] -id: EDAM_operation:0568 -name: RNA secondary structure rendering -namespace: operation -subset: operations -def: "Visualise RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] -is_a: EDAM_operation:0337 ! Plotting and rendering -is_a: EDAM_operation:2439 ! RNA secondary structure processing -relationship: has_input EDAM_data:0880 !{min_cardinality=1} ! RNA secondary structure record +id: EDAM_data:1413 +name: Sequence similarity +comment: Data Type is float probably. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0865 ! Sequence similarity score [Term] -id: EDAM_operation:0569 -name: Protein secondary structure rendering -namespace: operation -subset: operations -def: "Render and visualise protein secondary structure." [http://edamontology.org] -is_a: EDAM_operation:0337 ! Plotting and rendering -is_a: EDAM_operation:2444 ! Protein secondary structure processing -relationship: has_input EDAM_data:0876 !{min_cardinality=1} ! Protein features (secondary structure) +id: EDAM_data:1414 +name: Sequence alignment metadata (quality report) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data on molecular sequence alignment quality (estimated accuracy)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0867 ! Sequence alignment report [Term] -id: EDAM_operation:2485 -name: Helical wheel rendering -namespace: operation -subset: operations -def: "Render a helical wheel representation of protein secondary structure." [http://edamontology.org] -is_a: EDAM_operation:0569 ! Protein secondary structure rendering -relationship: has_output EDAM_data:2162 !{min_cardinality=1} ! Helical wheel +id: EDAM_data:1415 +name: Sequence alignment report (site conservation) +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data on character conservation in a molecular sequence alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0867 ! Sequence alignment report [Term] -id: EDAM_operation:2486 -name: Topology diagram rendering -namespace: operation -subset: operations -def: "Render a topology diagram of protein secondary structure." [http://edamontology.org] -is_a: EDAM_operation:0569 ! Protein secondary structure rendering -relationship: has_output EDAM_data:2992 ! Protein structure image +id: EDAM_data:1416 +name: Sequence alignment report (site correlation) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0867 ! Sequence alignment report [Term] -id: EDAM_operation:2241 -name: Transmembrane protein rendering -namespace: operation -subset: operations -def: "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." [http://edamontology.org] -is_a: EDAM_operation:0569 ! Protein secondary structure rendering -is_a: EDAM_operation:0270 ! Transmembrane protein analysis -relationship: has_input EDAM_data:1456 !{min_cardinality=1} ! Protein features (membrane regions) -relationship: has_output EDAM_data:2992 ! Protein structure image +id: EDAM_data:1417 +name: Sequence-profile alignment (Domainatrix signature) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0869 ! Sequence-profile alignment [Term] -id: EDAM_operation:2482 -name: Secondary structure processing -namespace: operation -subset: operations -def: "Process (read and / or write) a molecular secondary structure." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2081 !{min_cardinality=0} ! Secondary structure -relationship: has_output EDAM_data:2081 !{min_cardinality=0} ! Secondary structure -relationship: has_topic EDAM_topic:0081 ! Structure analysis +id: EDAM_data:1418 +name: Sequence-profile alignment (HMM) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of molecular sequence(s) to a hidden Markov model(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0869 ! Sequence-profile alignment +[Term] +id: EDAM_data:1420 +name: Sequence-profile alignment (fingerprint) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of molecular sequences to a protein fingerprint from the PRINTS database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0869 ! Sequence-profile alignment [Term] -id: EDAM_operation:2465 -name: Structure processing -namespace: operation -subset: operations -! alt_id: EDAM_operation:2484 -def: "Process (read and / or write) a molecular tertiary structure." [http://edamontology.org] -is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0883 !{min_cardinality=0} ! Structure -relationship: has_output EDAM_data:0883 !{min_cardinality=0} ! Structure -relationship: has_topic EDAM_topic:0081 ! Structure analysis +id: EDAM_data:1426 +name: Phylogenetic continuous quantitative data +subset: bioinformatics +subset: data +subset: edam +synonym: "Phylogenetic continuous quantitative characters" EXACT [] +synonym: "Quantitative traits" EXACT [] +created_in: "beta12orEarlier" +def: "Continuous quantitative data that may be read during phylogenetic tree calculation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0871 ! Phylogenetic character data [Term] -id: EDAM_operation:0570 -name: Structure rendering -namespace: operation -subset: operations -def: "Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation." [http://edamontology.org] -is_a: EDAM_operation:0337 ! Plotting and rendering -is_a: EDAM_operation:2465 ! Structure processing -relationship: has_input EDAM_data:0883 !{min_cardinality=1} ! Structure -relationship: has_output EDAM_data:1710 ! Structure image +id: EDAM_data:1427 +name: Phylogenetic discrete data +subset: bioinformatics +subset: data +subset: edam +synonym: "Discrete characters" EXACT [] +synonym: "Discretely coded characters" EXACT [] +synonym: "Phylogenetic discrete states" EXACT [] +created_in: "beta12orEarlier" +def: "Character data with discrete states that may be read during phylogenetic tree calculation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0871 ! Phylogenetic character data +[Term] +id: EDAM_data:1428 +name: Phylogenetic character cliques +subset: bioinformatics +subset: data +subset: edam +synonym: "Phylogenetic report (cliques)" EXACT [] +created_in: "beta12orEarlier" +def: "One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] -id: EDAM_operation:0571 -name: Microarray data rendering -namespace: operation -subset: operations -def: "Visualise microarray data." [http://edamontology.org] -is_a: EDAM_operation:0337 ! Plotting and rendering -is_a: EDAM_operation:2435 ! Gene expression profile processing -relationship: has_input EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data -relationship: has_output EDAM_data:2967 !{min_cardinality=1} ! Microarray image +id: EDAM_data:1429 +name: Phylogenetic invariants +subset: bioinformatics +subset: data +subset: edam +synonym: "Phylogenetic report (invariants)" EXACT [] +created_in: "beta12orEarlier" +def: "Phylogenetic invariants data for testing alternative tree topologies." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] -id: EDAM_operation:0572 -name: Protein interaction network rendering -namespace: operation -subset: operations -def: "Identify and analyse networks of protein interactions." [http://edamontology.org] -is_a: EDAM_operation:3083 ! Pathway or network rendering -is_a: EDAM_operation:2445 ! Protein interaction network processing -relationship: has_input EDAM_data:1663 !{min_cardinality=1} ! Pathway or network (protein-protein interaction) +id: EDAM_data:1438 +name: Phylogenetic tree report +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics +subset: data +subset: edam +synonym: "Phylogenetic tree-derived report" EXACT [] +created_in: "beta12orEarlier" +def: "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_operation:0573 -name: Map rendering -namespace: operation -subset: operations -def: "Render and visualise a DNA map." [http://edamontology.org] -synonym: "DNA map rendering" EXACT [http://edamontology.org] -is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) -is_a: EDAM_operation:2521 ! Map data processing -relationship: has_input EDAM_data:1274 !{min_cardinality=1} ! Map +id: EDAM_data:1439 +name: DNA substitution model +subset: bioinformatics +subset: data +subset: edam +synonym: "Phylogenetic tree report (DNA substitution model)" EXACT [] +synonym: "Sequence alignment report (DNA substitution model)" EXACT [] +created_in: "beta12orEarlier" +def: "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0867 ! Sequence alignment report +is_a: EDAM_data:0950 ! Biological model +is_a: EDAM_data:1438 ! Phylogenetic tree report +[Term] +id: EDAM_data:1440 +name: Phylogenetic tree report (tree shape) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data about the shape of a phylogenetic tree." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] -id: EDAM_operation:3184 !{since=1.1} -name: Sequence assembly rendering -namespace: operation -subset: operations -def: "Render and visualise a DNA sequence assembly." [http://edamontology.org] -synonym: "Assembly rendering" EXACT [http://edamontology.org] -synonym: "Assembly visualisation" EXACT [http://edamontology.org] -synonym: "Sequence assembly visualisation" EXACT [http://edamontology.org] -is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) +id: EDAM_data:1441 +name: Phylogenetic tree report (tree evaluation) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data on the confidence of a phylogenetic tree." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1438 ! Phylogenetic tree report +[Term] +id: EDAM_data:1442 +name: Phylogenetic tree report (tree distances) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Distances, such as Branch Score distance, between two or more phylogenetic trees." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] -id: EDAM_operation:0574 -name: Sequence motif rendering -namespace: operation -subset: operations -def: "Render a sequence with motifs." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0564 ! Sequence rendering +id: EDAM_data:1443 +name: Phylogenetic tree report (tree stratigraphic) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1438 ! Phylogenetic tree report +[Term] +id: EDAM_data:1444 +name: Phylogenetic character contrasts +subset: bioinformatics +subset: data +subset: edam +synonym: "Phylogenetic report (character contrasts)" EXACT [] +created_in: "beta12orEarlier" +def: "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] -id: EDAM_operation:0577 -name: DNA linear map rendering -namespace: operation -subset: operations -def: "Draw a linear maps of DNA." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_operation:0573 ! Map rendering +id: EDAM_data:1446 +name: Comparison matrix (integers) +subset: bioinformatics +subset: data +subset: edam +synonym: "Substitution matrix (integers)" EXACT [] +created_in: "beta12orEarlier" +def: "Matrix of integer numbers for sequence comparison." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0874 ! Comparison matrix [Term] -id: EDAM_operation:0578 -name: DNA circular map rendering -namespace: operation -subset: operations -def: "Draw a circular maps of DNA, for example a plasmid map." [http://edamontology.org] -is_a: EDAM_operation:0573 ! Map rendering +id: EDAM_data:1447 +name: Comparison matrix (floats) +subset: bioinformatics +subset: data +subset: edam +synonym: "Substitution matrix (floats)" EXACT [] +created_in: "beta12orEarlier" +def: "Matrix of floating point numbers for sequence comparison." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0874 ! Comparison matrix [Term] -id: EDAM_operation:0579 -name: Operon rendering -namespace: operation -subset: operations -def: "Visualise operon structure etc." [http://edamontology.org] -is_a: EDAM_operation:0573 ! Map rendering -relationship: has_topic EDAM_topic:0109 ! Gene finding +id: EDAM_data:1448 +name: Comparison matrix (nucleotide) +subset: bioinformatics +subset: data +subset: edam +synonym: "Nucleotide substitution matrix" EXACT [] +created_in: "beta12orEarlier" +def: "Matrix of integer or floating point numbers for nucleotide comparison." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0874 ! Comparison matrix +[Term] +id: EDAM_data:1449 +name: Comparison matrix (amino acid) +subset: bioinformatics +subset: data +subset: edam +synonym: "Amino acid substitution matrix" EXACT [] +created_in: "beta12orEarlier" +def: "Matrix of integer or floating point numbers for amino acid comparison." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0874 ! Comparison matrix +is_a: EDAM_data:2016 ! Amino acid property [Term] -id: EDAM_operation:0575 -name: Restriction map rendering -namespace: operation -subset: operations -def: "Visualise restriction maps in DNA sequences." [http://edamontology.org] -is_a: EDAM_operation:0573 ! Map rendering -is_a: EDAM_operation:0431 ! Restriction site recognition -relationship: has_output EDAM_data:1289 ! Restriction map +id: EDAM_data:1450 +name: Nucleotide comparison matrix (integers) +subset: bioinformatics +subset: data +subset: edam +synonym: "Nucleotide substitution matrix (integers)" EXACT [] +created_in: "beta12orEarlier" +def: "Matrix of integer numbers for nucleotide comparison." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1448 ! Comparison matrix (nucleotide) +[Term] +id: EDAM_data:1451 +name: Nucleotide comparison matrix (floats) +subset: bioinformatics +subset: data +subset: edam +synonym: "Nucleotide substitution matrix (floats)" EXACT [] +created_in: "beta12orEarlier" +def: "Matrix of floating point numbers for nucleotide comparison." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1448 ! Comparison matrix (nucleotide) +[Term] +id: EDAM_data:1452 +name: Amino acid comparison matrix (integers) +subset: bioinformatics +subset: data +subset: edam +synonym: "Amino acid substitution matrix (integers)" EXACT [] +created_in: "beta12orEarlier" +def: "Matrix of integer numbers for amino acid comparison." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1449 ! Comparison matrix (amino acid) +[Term] +id: EDAM_data:1453 +name: Amino acid comparison matrix (floats) +subset: bioinformatics +subset: data +subset: edam +synonym: "Amino acid substitution matrix (floats)" EXACT [] +created_in: "beta12orEarlier" +def: "Matrix of floating point numbers for amino acid comparison." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1449 ! Comparison matrix (amino acid) +[Term] +id: EDAM_data:1456 +name: Protein features (membrane regions) +comment: This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. +subset: bioinformatics +subset: data +subset: edam +synonym: "Intramembrane region report" EXACT [] +synonym: "Protein report (membrane protein)" EXACT [] +synonym: "Transmembrane region report" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +[Term] +id: EDAM_data:1459 +name: Nucleic acid structure +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a nucleic acid tertiary (3D) structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0883 ! Structure +relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis +[Term] +id: EDAM_data:1460 +name: Protein structure +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a protein tertiary (3D) structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0883 ! Structure +relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure +relationship: has_topic EDAM_topic:2814 ! Protein structure analysis +[Term] +id: EDAM_data:1461 +name: Protein-ligand complex +comment: This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1460 ! Protein structure -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +[Term] +id: EDAM_data:1462 +name: Carbohydrate structure +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a carbohydrate (3D) structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0883 ! Structure +relationship: has_topic EDAM_topic:0152 ! Carbohydrates +relationship: has_topic EDAM_topic:0153 ! Lipids +[Term] +id: EDAM_data:1463 +name: Small molecule structure +subset: bioinformatics +subset: data +subset: edam +synonym: "CHEBI:23367" RELATED [] +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0883 ! Structure +relationship: has_topic EDAM_topic:0154 ! Small molecules +[Term] +id: EDAM_data:1464 +name: DNA structure +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a DNA tertiary (3D) structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1459 ! Nucleic acid structure +[Term] +id: EDAM_data:1465 +name: RNA structure record +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for an RNA tertiary (3D) structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1459 ! Nucleic acid structure +relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment +[Term] +id: EDAM_data:1466 +name: tRNA structure record +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1465 ! RNA structure record +[Term] +id: EDAM_data:1467 +name: Protein chain +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1460 ! Protein structure +[Term] +id: EDAM_data:1468 +name: Protein domain +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for the tertiary (3D) structure of a protein domain." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1460 ! Protein structure +relationship: has_topic EDAM_topic:0736 ! Protein domains and folds +[Term] +id: EDAM_data:1469 +name: Protein structure (all atoms) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a protein tertiary (3D) structure (all atoms)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1460 ! Protein structure -! -! Data -! +[Term] +id: EDAM_data:1470 +name: Protein structure (C-alpha atoms) +comment: C-beta atoms from amino acid side-chains may be included. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1460 ! Protein structure +[Term] +id: EDAM_data:1471 +name: Protein chain (all atoms) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1467 ! Protein chain +consider: EDAM_data:1469 ! Protein structure (all atoms) [Term] -id: EDAM_data:0005 -name: Resource type +id: EDAM_data:1472 +name: Protein chain (C-alpha atoms) +comment: C-beta atoms from amino acid side-chains may be included. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1467 ! Protein chain +consider: EDAM_data:1470 ! Protein structure (C-alpha atoms) + +[Term] +id: EDAM_data:1473 +name: Protein domain (all atoms) +subset: bioinformatics subset: data -def: "A type of computational resource used in bioinformatics." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1468 ! Protein domain +consider: EDAM_data:1469 ! Protein structure (all atoms) [Term] -id: EDAM_data:2831 -name: Databank +id: EDAM_data:1474 +name: Protein domain (C-alpha atoms) +comment: C-beta atoms from amino acid side-chains may be included. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1468 ! Protein domain +consider: EDAM_data:1470 ! Protein structure (C-alpha atoms) + +[Term] +id: EDAM_data:1479 +name: Structure alignment (pair) +subset: bioinformatics subset: data -def: "A flat-file (textual) data archive." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of exactly two molecular tertiary (3D) structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0886 ! Structure alignment [Term] -id: EDAM_data:2832 -name: Web portal +id: EDAM_data:1480 +name: Structure alignment (multiple) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of more than two molecular tertiary (3D) structures." [http://edamontology.org] namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0886 ! Structure alignment + +[Term] +id: EDAM_data:1481 +name: Structure alignment (protein) +subset: bioinformatics subset: data -def: "A web site providing data (web pages) on a common theme to a HTTP client." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of protein tertiary (3D) structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0886 ! Structure alignment +is_a: EDAM_data:3154 ! Protein alignment +[Term] +id: EDAM_data:1482 +name: Structure alignment (nucleic acid) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of nucleic acid tertiary (3D) structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0886 ! Structure alignment +is_a: EDAM_data:2084 ! Nucleic acid report [Term] -id: EDAM_data:0581 -name: Database +id: EDAM_data:1483 +name: Structure alignment (protein pair) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures." [http://edamontology.org] namespace: data +is_a: EDAM_data:1479 ! Structure alignment (pair) +is_a: EDAM_data:1481 ! Structure alignment (protein) + +[Term] +id: EDAM_data:1484 +name: Multiple protein tertiary structure alignment +subset: bioinformatics subset: data -def: "A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of more than two protein tertiary (3D) structures." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1481 ! Structure alignment (protein) +[Term] +id: EDAM_data:1485 +name: Structure alignment (protein all atoms) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1481 ! Structure alignment (protein) [Term] -id: EDAM_data:0007 -name: Tool +id: EDAM_data:1486 +name: Structure alignment (protein C-alpha atoms) +comment: C-beta atoms from amino acid side-chains may be considered. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] namespace: data +is_a: EDAM_data:1481 ! Structure alignment (protein) + +[Term] +id: EDAM_data:1487 +name: Pairwise protein tertiary structure alignment (all atoms) +subset: bioinformatics subset: data -def: "A bioinformatics package or tool, e.g. a standalone application or web service." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1485 ! Structure alignment (protein all atoms) [Term] -id: EDAM_data:1884 -name: UniProt keywords +id: EDAM_data:1488 +name: Pairwise protein tertiary structure alignment (C-alpha atoms) +comment: C-beta atoms from amino acid side-chains may be included. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms) + +[Term] +id: EDAM_data:1489 +name: Multiple protein tertiary structure alignment (all atoms) +subset: bioinformatics subset: data -def: "A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0582 ! Ontology +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1485 ! Structure alignment (protein all atoms) +[Term] +id: EDAM_data:1490 +name: Multiple protein tertiary structure alignment (C-alpha atoms) +comment: C-beta atoms from amino acid side-chains may be included. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms) [Term] -id: EDAM_data:0831 -name: MeSH vocabulary +id: EDAM_data:1491 +name: Structure alignment (nucleic acid pair) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures." [http://edamontology.org] namespace: data +is_a: EDAM_data:1479 ! Structure alignment (pair) +is_a: EDAM_data:1482 ! Structure alignment (nucleic acid) + +[Term] +id: EDAM_data:1492 +name: Multiple nucleic acid tertiary structure alignment +subset: bioinformatics subset: data -def: "Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0582 ! Ontology +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1482 ! Structure alignment (nucleic acid) +[Term] +id: EDAM_data:1493 +name: Structure alignment (RNA) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Alignment (superimposition) of RNA tertiary (3D) structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1482 ! Structure alignment (nucleic acid) [Term] -id: EDAM_data:0832 -name: HGNC vocabulary +id: EDAM_data:1494 +name: Structural transformation matrix +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures." [http://edamontology.org] namespace: data +is_a: EDAM_data:2082 ! Matrix + +[Term] +id: EDAM_data:1495 +name: DaliLite hit table +comment: The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. +subset: bioinformatics subset: data -def: "Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0582 ! Ontology +subset: edam +created_in: "beta12orEarlier" +def: "DaliLite hit table of protein chain tertiary structure alignment data." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0887 ! Structure alignment report +[Term] +id: EDAM_data:1496 +name: Molecular similarity score +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A score reflecting structural similarities of two molecules." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0888 ! Structure similarity score [Term] -id: EDAM_data:0835 -name: UMLS vocabulary +id: EDAM_data:1497 +name: Root-mean-square deviation +subset: bioinformatics +subset: data +subset: edam +synonym: "RMSD" EXACT [] +created_in: "beta12orEarlier" +def: "Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates." [http://edamontology.org] namespace: data -subset: data -def: "Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0582 ! Ontology - +is_a: EDAM_data:0888 ! Structure similarity score [Term] -id: EDAM_data:2100 -name: Type -namespace: data +id: EDAM_data:1498 +name: Tanimoto similarity score +comment: A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. +subset: bioinformatics subset: data -! alt_id: EDAM_data:2864 -def: "A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values)." [http://edamontology.org] -synonym: "Type" EXACT [http://purl.org/dc/elements/1.1/type] -is_a: EDAM_data:2527 ! Parameter +subset: edam +created_in: "beta12orEarlier" +def: "A measure of the similarity between two ligand fingerprints." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0888 ! Structure similarity score [Term] -id: EDAM_data:1866 -name: Map type -namespace: data +id: EDAM_data:1499 +name: 3D-1D scoring matrix +subset: bioinformatics subset: data -def: "A designation of the type of map (genetic map, physical map, sequence map etc) or map set." [http://edamontology.org] -comment: Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. -is_a: EDAM_data:2100 ! Type -is_a: EDAM_data:2019 ! Map attribute +subset: edam +created_in: "beta12orEarlier" +def: "A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0892 ! Protein sequence-structure scoring matrix [Term] -id: EDAM_data:1094 -name: Sequence type -namespace: data +id: EDAM_data:1501 +name: Amino acid index +subset: bioinformatics subset: data -def: "A label (text token) describing a type of molecular sequence." [http://edamontology.org] -comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). -is_a: EDAM_data:2100 ! Type -is_a: EDAM_data:2534 ! Sequence parameter -relationship: is_identifier_of EDAM_data:2044 ! Sequence -relationship: is_identifier_of EDAM_data:0849 ! Sequence record - +subset: edam +created_in: "beta12orEarlier" +def: "A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2016 ! Amino acid property +is_a: EDAM_data:2082 ! Matrix [Term] -id: EDAM_data:2132 -name: Mutation type -namespace: data +id: EDAM_data:1502 +name: Amino acid index (chemical classes) +subset: bioinformatics subset: data -def: "A type of point or block mutation, including insertion, deletion, change, duplication and moves." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2100 ! Type +subset: edam +created_in: "beta12orEarlier" +def: "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1501 ! Amino acid index [Term] -id: EDAM_data:0985 -name: Molecule type -namespace: data +id: EDAM_data:1503 +name: Amino acid pair-wise contact potentials +subset: bioinformatics subset: data -def: "A label (text token) describing the type a molecule." [http://edamontology.org] -comment: For example, 'Protein', 'DNA', 'RNA' etc. -example: "Protein" "DNA" "RNA" -is_a: EDAM_data:2100 ! Type +subset: edam +created_in: "beta12orEarlier" +def: "Statistical protein contact potentials." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2016 ! Amino acid property [Term] -id: EDAM_data:1122 -name: Phylogenetic tree type -namespace: data +id: EDAM_data:1505 +name: Amino acid index (molecular weight) +subset: bioinformatics subset: data -def: "A label (text token) describing the type of a phylogenetic tree." [http://edamontology.org] -comment: For example 'nj', 'upgmp' etc. -example: "nj" "upgmp" -is_a: EDAM_data:2100 ! Type -relationship: is_identifier_of EDAM_data:0872 ! Phylogenetic tree +subset: edam +created_in: "beta12orEarlier" +def: "Molecular weights of amino acids." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1501 ! Amino acid index [Term] -id: EDAM_data:2592 -name: Cancer type -namespace: data +id: EDAM_data:1506 +name: Amino acid index (hydropathy) +subset: bioinformatics subset: data -def: "A type (represented as a string) of cancer." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2100 ! Type +subset: edam +created_in: "beta12orEarlier" +def: "Hydrophobic, hydrophilic or charge properties of amino acids." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1501 ! Amino acid index [Term] -id: EDAM_data:2524 -name: Protein data -namespace: data +id: EDAM_data:1507 +name: Amino acid index (White-Wimley data) +subset: bioinformatics subset: data -def: "Data concerning one or more protein molecules." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0896 ! Protein report +subset: edam +created_in: "beta12orEarlier" +def: "Experimental free energy values for the water-interface and water-octanol transitions for the amino acids." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1501 ! Amino acid index [Term] -id: EDAM_data:2525 -name: Nucleic acid data -namespace: data +id: EDAM_data:1508 +name: Amino acid index (van der Waals radii) +subset: bioinformatics subset: data -def: "Data concerning one or more nucleic acid molecules." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:2084 ! Nucleic acid report +subset: edam +created_in: "beta12orEarlier" +def: "Van der Waals radii of atoms for different amino acid residues." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1501 ! Amino acid index [Term] -id: EDAM_data:2248 -name: Schema -namespace: data +id: EDAM_data:1509 +name: Enzyme property +subset: bioinformatics subset: data -def: "A data schema for organising or transforming data of some type." [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data - +subset: edam +synonym: "Enzyme report" EXACT [] +synonym: "Protein report (enzyme)" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on a specific enzyme." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property +relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions [Term] -id: EDAM_data:0843 -name: Database entry +id: EDAM_data:1517 +name: Restriction enzyme property +comment: This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein report (restriction enzyme)" EXACT [] +synonym: "Restriction enzyme pattern data" EXACT [] +synonym: "Restriction enzyme report" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on a specific restriction enzyme such as enzyme reference data." [http://edamontology.org] namespace: data -subset: data -def: "An entry (retrievable via URL) from a biological database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0006 ! Data - +is_a: EDAM_data:1509 ! Enzyme property [Term] -id: EDAM_data:2767 -name: Identifier with metadata -namespace: data +id: EDAM_data:1519 +name: Peptide molecular weights +comment: The report might include associated data such as frequency of peptide fragment molecular weights. +subset: bioinformatics subset: data -def: "Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance." [http://edamontology.org] -is_a: EDAM_data:0842 ! Identifier +subset: edam +created_in: "beta12orEarlier" +def: "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:2768 -name: Gene symbol annotation -namespace: data +id: EDAM_data:1520 +name: Peptide hydrophobic moment +comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. +subset: bioinformatics subset: data -def: "Annotation about a gene symbol." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2767 ! Identifier with metadata - +subset: edam +created_in: "beta12orEarlier" +def: "Report on the hydrophobic moment of a polypeptide sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2970 ! Protein hydropathy data [Term] -id: EDAM_data:2087 -name: Molecular property -namespace: data +id: EDAM_data:1521 +name: Protein aliphatic index +comment: The aliphatic index is the relative protein volume occupied by aliphatic side chains. +subset: bioinformatics subset: data -def: "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." [http://edamontology.org] -synonym: "Physicochemical property" EXACT [http://edamontology.org] -synonym: "sequence_attribute" RELATED [SO:0000400] -is_a: EDAM_data:3031 ! Core data - +subset: edam +created_in: "beta12orEarlier" +def: "The aliphatic index of a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2970 ! Protein hydropathy data [Term] -id: EDAM_data:1917 -name: Atomic property -namespace: data +id: EDAM_data:1522 +name: Protein sequence hydropathy plot +comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. +subset: bioinformatics subset: data -def: "Data for an atom (in a molecular structure)." [http://edamontology.org] -synonym: "General atomic property" EXACT [http://edamontology.org] -is_a: EDAM_data:2087 ! Molecular property +subset: edam +created_in: "beta12orEarlier" +def: "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2970 ! Protein hydropathy data [Term] -id: EDAM_data:2050 -name: Molecular property (general) -namespace: data +id: EDAM_data:1523 +name: Protein charge plot +subset: bioinformatics subset: data -def: "General data for a molecule." [http://edamontology.org] -synonym: "General molecular property" EXACT [http://edamontology.org] -is_a: EDAM_data:2087 ! Molecular property - +subset: edam +created_in: "beta12orEarlier" +def: "A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:2925 -name: Sequence data -namespace: data +id: EDAM_data:1524 +name: Protein solubility +subset: bioinformatics subset: data -def: "Data concerning molecular sequence(s)." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:2044 ! Sequence -consider: EDAM_data:2955 ! Sequence report - +subset: edam +synonym: "Protein solubility data" EXACT [] +created_in: "beta12orEarlier" +def: "The solubility or atomic solvation energy of a protein sequence or structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2970 ! Protein hydropathy data [Term] -id: EDAM_data:2044 -name: Sequence -namespace: data +id: EDAM_data:1525 +name: Protein crystallizability +subset: bioinformatics subset: data -def: "One or more molecular sequences, possibly with associated annotation." [http://edamontology.org] -comment: This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. -synonym: "bio molecular sequence information" RELATED [http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation] -relationship: has_topic EDAM_topic:0080 ! Sequence analysis -is_a: EDAM_data:3031 ! Core data - +subset: edam +synonym: "Protein crystallizability data" EXACT [] +created_in: "beta12orEarlier" +def: "Data on the crystallizability of a protein sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2970 ! Protein hydropathy data [Term] -id: EDAM_data:2976 -name: Protein sequence -namespace: data +id: EDAM_data:1526 +name: Protein globularity +subset: bioinformatics subset: data -def: "One or more protein sequences, possibly with associated annotation." [http://edamontology.org] -synonym: "amino acid sequence information" RELATED [http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation] -is_a: EDAM_data:2044 ! Sequence +subset: edam +synonym: "Protein globularity data" EXACT [] +created_in: "beta12orEarlier" +def: "Data on the stability, intrinsic disorder or globularity of a protein sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2970 ! Protein hydropathy data [Term] -id: EDAM_data:2977 -name: Nucleic acid sequence -namespace: data +id: EDAM_data:1527 +name: Protein titration curve +subset: bioinformatics subset: data -def: "One or more nucleic acid sequences, possibly with associated annotation." [http://edamontology.org] -synonym: "nucleotide sequence information" RELATED [http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation] -is_a: EDAM_data:2044 ! Sequence +subset: edam +created_in: "beta12orEarlier" +def: "The titration curve of a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:2955 -name: Sequence report -namespace: data +id: EDAM_data:1528 +name: Protein isoelectric point +subset: bioinformatics subset: data -def: "An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata)." [http://edamontology.org] -synonym: "Sequence-derived report" EXACT [http://edamontology.org] -is_a: EDAM_data:2048 ! Report - +subset: edam +created_in: "beta12orEarlier" +def: "The isoelectric point of one proteins." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:0855 -name: Sequence metadata -namespace: data +id: EDAM_data:1529 +name: Protein pKa value +subset: bioinformatics subset: data -def: "Basic or general information concerning molecular sequences." [http://edamontology.org] -comment: This is used for such things as a report including the sequence identifier, type and length. -is_a: EDAM_data:1254 ! Sequence property -is_a: EDAM_data:2955 ! Sequence report -is_a: EDAM_data:2337 ! Metadata +subset: edam +created_in: "beta12orEarlier" +def: "The pKa value of a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:2522 -name: Map data -namespace: data +id: EDAM_data:1530 +name: Protein hydrogen exchange rate +subset: bioinformatics subset: data -def: "Data concerning a map of molecular sequence(s)." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:1274 ! Map -consider: EDAM_data:2019 ! Map attribute - +subset: edam +created_in: "beta12orEarlier" +def: "The hydrogen exchange rate of a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:1274 -name: Map -namespace: data +id: EDAM_data:1531 +name: Protein extinction coefficient +subset: bioinformatics subset: data -def: "A map of (typically one) DNA sequence annotated with positional or non-positional features." [http://edamontology.org] -synonym: "DNA map" EXACT [http://edamontology.org] -relationship: has_topic EDAM_topic:0102 ! Mapping -is_a: EDAM_data:3031 ! Core data +subset: edam +created_in: "beta12orEarlier" +def: "The extinction coefficient of a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:1864 -name: Map set -namespace: data +id: EDAM_data:1532 +name: Protein optical density +subset: bioinformatics subset: data -def: "Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped." [http://edamontology.org] -xref: Moby:GCP_CorrelatedMapSet -xref: Moby:GCP_CorrelatedLinkageMapSet -is_a: EDAM_data:2019 ! Map attribute - +subset: edam +created_in: "beta12orEarlier" +def: "The optical density of a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:2019 -name: Map attribute -namespace: data +id: EDAM_data:1533 +name: Protein subcellular localization +subset: bioinformatics subset: data -def: "An attribute of a molecular map (genetic or physical)." [http://edamontology.org] -is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:0102 ! Mapping - +subset: edam +synonym: "Protein report (subcellular localization)" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0896 ! Protein report [Term] -id: EDAM_data:2080 -name: Database hits -namespace: data +id: EDAM_data:1534 +name: Peptide immunogenicity data +comment: This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. +subset: bioinformatics subset: data -def: "A report of hits from searching a database of some type." [http://edamontology.org] -is_a: EDAM_data:2093 ! Data reference +subset: edam +synonym: "Peptide immunogenicity" EXACT [] +synonym: "Peptide immunogenicity report" EXACT [] +created_in: "beta12orEarlier" +def: "An report on allergenicity / immunogenicity of peptides and proteins." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:0860 -name: Sequence signature -namespace: data +id: EDAM_data:1536 +name: MHC peptide immunogenicity report +subset: bioinformatics subset: data -def: "A classifier of sequences such as a sequence motif, profile or other diagnostic element." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1353 ! Sequence motif -consider: EDAM_data:1354 ! Sequence profile +subset: edam +created_in: "beta12orEarlier" +def: "A report on the immunogenicity of MHC class I or class II binding peptides." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1534 ! Peptide immunogenicity data [Term] -id: EDAM_data:2981 -name: Sequence motif data +id: EDAM_data:1537 +name: Protein structure report +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein property (structural)" EXACT [] +synonym: "Protein report (structure)" EXACT [] +synonym: "Protein structural property" EXACT [] +synonym: "Protein structure report (domain)" EXACT [] +synonym: "Protein structure-derived report" EXACT [] +created_in: "beta12orEarlier" +def: "Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains." [http://edamontology.org] namespace: data -subset: data -def: "Data concerning specific or conserved pattern in molecular sequences." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:1353 ! Sequence motif +is_a: EDAM_data:0896 ! Protein report +is_a: EDAM_data:2085 ! Structure report [Term] -id: EDAM_data:1353 -name: Sequence motif -namespace: data +id: EDAM_data:1539 +name: Protein structural quality report +comment: Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. +subset: bioinformatics subset: data -def: "Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence." [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0158 ! Sequence motifs +subset: edam +synonym: "Protein property (structural quality)" EXACT [] +synonym: "Protein report (structural quality)" EXACT [] +synonym: "Protein structure report (quality evaluation)" EXACT [] +created_in: "beta12orEarlier" +def: "Report on the quality of a protein three-dimensional model." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property +is_a: EDAM_data:1537 ! Protein structure report [Term] -id: EDAM_data:2762 -name: Sequence motif metadata -namespace: data +id: EDAM_data:1540 +name: Protein residue interactions +subset: bioinformatics subset: data -def: "Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc." [http://edamontology.org] -is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:0158 ! Sequence motifs +subset: edam +synonym: "Atom interaction data" EXACT [] +synonym: "Residue interaction data" EXACT [] +created_in: "beta12orEarlier" +def: "Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0906 ! Protein interaction +is_a: EDAM_data:2599 ! Molecular interaction +relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] -id: EDAM_data:2982 -name: Sequence profile data -namespace: data +id: EDAM_data:1541 +name: Protein flexibility or motion report +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics subset: data -def: "Data concerning models representing a (typically multiple) sequence alignment." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:1354 ! Sequence profile +subset: edam +synonym: "Protein flexibility or motion" EXACT [] +synonym: "Protein property (flexibility or motion)" EXACT [] +synonym: "Protein structure report (flexibility or motion)" EXACT [] +created_in: "beta12orEarlier" +def: "Informative report on flexibility or motion of a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property +is_a: EDAM_data:1537 ! Protein structure report [Term] -id: EDAM_data:1354 -name: Sequence profile -namespace: data +id: EDAM_data:1542 +name: Protein solvent accessibility +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. +subset: bioinformatics subset: data -def: "Some type of statistical model representing a (typically multiple) sequence alignment." [http://edamontology.org] -synonym: "sequence profile" EXACT [http://semanticscience.org/resource/SIO_010531] -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs +subset: edam +created_in: "beta12orEarlier" +def: "Data on the solvent accessible or buried surface area of a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1540 ! Protein residue interactions [Term] -id: EDAM_data:2788 -name: Sequence profile metadata -namespace: data +id: EDAM_data:1543 +name: Protein surface report +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics subset: data -def: "Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on." [http://edamontology.org] -is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs +subset: edam +synonym: "Protein structure report (surface)" EXACT [] +created_in: "beta12orEarlier" +def: "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1537 ! Protein structure report +is_a: EDAM_data:1542 ! Protein solvent accessibility [Term] -id: EDAM_data:1355 -name: Protein signature -namespace: data +id: EDAM_data:1544 +name: Ramachandran plot +subset: bioinformatics subset: data -def: "An entry (sequence classifier and associated data) from the InterPro database." [http://edamontology.org] -synonym: "InterPro entry" EXACT [http://edamontology.org] -is_a: EDAM_data:0907 ! Protein family +subset: edam +created_in: "beta12orEarlier" +def: "Phi/psi angle data or a Ramachandran plot of a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2991 ! Protein torsion angle data [Term] -id: EDAM_data:2161 -name: Sequence similarity plot -namespace: data +id: EDAM_data:1545 +name: Protein dipole moment +subset: bioinformatics subset: data -def: "A plot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] -is_a: EDAM_data:0867 ! Sequence alignment report +subset: edam +created_in: "beta12orEarlier" +def: "Data on the net charge distribution (dipole moment) of a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:0862 -name: Dotplot -namespace: data +id: EDAM_data:1546 +name: Protein distance matrix +subset: bioinformatics subset: data -def: "A dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] -is_a: EDAM_data:2161 ! Sequence similarity plot +subset: edam +created_in: "beta12orEarlier" +def: "A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1540 ! Protein residue interactions [Term] -id: EDAM_data:2539 -name: Alignment data -namespace: data +id: EDAM_data:1547 +name: Protein contact map +subset: bioinformatics subset: data -def: "Data concerning an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. -is_obsolete: true !{since=beta13} -consider: EDAM_data:1916 ! Alignment -consider: EDAM_data:2083 ! Alignment report - +subset: edam +created_in: "beta12orEarlier" +def: "An amino acid residue contact map for a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1540 ! Protein residue interactions [Term] -id: EDAM_data:1916 -name: Alignment -namespace: data +id: EDAM_data:1548 +name: Protein residue 3D cluster +subset: bioinformatics subset: data -def: "An alignment of molecular sequences, structures or profiles derived from them." [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data +subset: edam +created_in: "beta12orEarlier" +def: "Report on clusters of contacting residues in protein structures such as a key structural residue network." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1540 ! Protein residue interactions [Term] -id: EDAM_data:2083 -name: Alignment report -namespace: data +id: EDAM_data:1549 +name: Protein hydrogen bonds +subset: bioinformatics subset: data -def: "An informative report about a molecular alignment of some type, including alignment-derived data or metadata." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_a: EDAM_data:2048 ! Report +subset: edam +created_in: "beta12orEarlier" +def: "Patterns of hydrogen bonding in protein structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1540 ! Protein residue interactions [Term] -id: EDAM_data:2711 -name: Genome metadata -namespace: data +id: EDAM_data:1550 +name: Protein non-canonical interactions +subset: bioinformatics subset: data -def: "Provenance metadata or other general information concerning a genome as a whole." [http://edamontology.org] -is_a: EDAM_data:0855 ! Sequence metadata - +subset: edam +synonym: "Protein non-canonical interactions report" EXACT [] +created_in: "beta12orEarlier" +def: "Non-canonical atomic interactions in protein structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1539 ! Protein structural quality report +is_a: EDAM_data:1540 ! Protein residue interactions [Term] -id: EDAM_data:0867 -name: Sequence alignment report -namespace: data +id: EDAM_data:1553 +name: CATH node +comment: The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. +subset: bioinformatics subset: data -def: "An informative report of molecular sequence alignment-derived data or metadata." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_a: EDAM_data:2083 ! Alignment report - - +subset: edam +synonym: "CATH classification node report" EXACT [] +created_in: "beta12orEarlier" +def: "Information on a node from the CATH database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3101 ! Protein domain classification node [Term] -id: EDAM_data:3181 !{since=1.1} -name: Sequence assembly report -namespace: data +id: EDAM_data:1554 +name: SCOP node +subset: bioinformatics subset: data -def: "An informative report about a DNA sequence assembly." [http://edamontology.org] -is_a: EDAM_data:2955 ! Sequence report - +subset: edam +synonym: "SCOP classification node" EXACT [] +created_in: "beta12orEarlier" +def: "Information on a node from the SCOP database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3101 ! Protein domain classification node [Term] -id: EDAM_data:2598 -name: Secondary structure alignment metadata -namespace: data +id: EDAM_data:1555 +name: EMBASSY domain classification +subset: bioinformatics subset: data -def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2083 ! Alignment report +subset: edam +created_in: "beta12orEarlier" +def: "An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0900 ! Protein domain classification [Term] -id: EDAM_data:0879 -name: Secondary structure alignment metadata (protein) -namespace: data +id: EDAM_data:1556 +name: CATH class +subset: bioinformatics subset: data -def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2083 ! Alignment report - +subset: edam +created_in: "beta12orEarlier" +def: "Information on a protein 'class' node from the CATH database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM_data:0882 -name: Secondary structure alignment metadata (RNA) -namespace: data +id: EDAM_data:1557 +name: CATH architecture +subset: bioinformatics subset: data -def: "An informative report of RNA secondary structure alignment-derived data or metadata." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2083 ! Alignment report - +subset: edam +created_in: "beta12orEarlier" +def: "Information on a protein 'architecture' node from the CATH database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM_data:2082 -name: Matrix -namespace: data +id: EDAM_data:1558 +name: CATH topology +subset: bioinformatics subset: data -def: "An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_a: EDAM_data:3031 ! Core data +subset: edam +created_in: "beta12orEarlier" +def: "Information on a protein 'topology' node from the CATH database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM_data:2855 -name: Distance matrix -namespace: data +id: EDAM_data:1559 +name: CATH homologous superfamily +subset: bioinformatics subset: data -def: "A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity." [http://edamontology.org] -is_a: EDAM_data:2082 ! Matrix +subset: edam +created_in: "beta12orEarlier" +def: "Information on a protein 'homologous superfamily' node from the CATH database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM_data:0870 -name: Sequence distance matrix -namespace: data +id: EDAM_data:1560 +name: CATH structurally similar group +subset: bioinformatics subset: data -def: "A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation." [http://edamontology.org] -comment: Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. -synonym: "Phylogenetic distance matrix" EXACT [http://edamontology.org] -xref: Moby:phylogenetic_distance_matrix -is_a: EDAM_data:2855 ! Distance matrix +subset: edam +created_in: "beta12orEarlier" +def: "Information on a protein 'structurally similar group' node from the CATH database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM_data:2856 -name: Structural distance matrix -namespace: data +id: EDAM_data:1561 +name: CATH functional category +subset: bioinformatics subset: data -def: "Distances (values representing similarity) between a group of molecular structures." [http://edamontology.org] -is_a: EDAM_data:2855 ! Distance matrix - +subset: edam +created_in: "beta12orEarlier" +def: "Information on a protein 'functional category' node from the CATH database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM_data:2523 -name: Phylogenetic raw data -namespace: data +id: EDAM_data:1564 +name: Protein fold recognition report +comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. +subset: bioinformatics subset: data -def: "Data concerning phylogeny, typically of molecular sequences." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Phylogenetic data" EXACT [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data - +subset: edam +created_in: "beta12orEarlier" +def: "A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0901 ! Protein features (domains) [Term] -id: EDAM_data:0871 -name: Phylogenetic character data -namespace: data +id: EDAM_data:1565 +name: Protein-protein interaction +comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains). +subset: bioinformatics subset: data -def: "Data from which a phylogenetic tree may be generated." [http://edamontology.org] -is_a: EDAM_data:2523 ! Phylogenetic raw data -synonym: "Character" RELATED [http://www.evolutionaryontology.org/cdao.owl#Character] -! Phylogenetic character data! Also molecular sequences, microsatellites), polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments +subset: edam +synonym: "Protein structure report (protein complex)" EXACT [] +created_in: "beta12orEarlier" +def: "Data on protein-protein interaction(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0906 ! Protein interaction +relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] -id: EDAM_data:0872 -name: Phylogenetic tree -namespace: data +id: EDAM_data:1566 +name: Protein-ligand interaction +subset: bioinformatics subset: data -def: "The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length." [http://edamontology.org] -comment: A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. -synonym: "Tree" RELATED [http://www.evolutionaryontology.org/cdao.owl#Tree] -xref: Moby:Tree -xref: Moby:phylogenetic_tree -xref: Moby:myTree -relationship: has_topic EDAM_topic:0084 ! Phylogenetics -is_a: EDAM_data:3031 ! Core data - +subset: edam +created_in: "beta12orEarlier" +def: "Data on protein-ligand (small molecule) interaction(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0906 ! Protein interaction +relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] -id: EDAM_data:1438 -name: Phylogenetic tree report -namespace: data +id: EDAM_data:1567 +name: Protein-nucleic acid interaction +subset: bioinformatics subset: data -! alt_id: EDAM_data:0873 -def: "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Phylogenetic tree-derived report" EXACT [http://edamontology.org] -is_a: EDAM_data:2048 ! Report - +subset: edam +created_in: "beta12orEarlier" +def: "Data on protein-DNA/RNA interaction(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0906 ! Protein interaction +relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions [Term] -id: EDAM_data:0874 -name: Comparison matrix -namespace: data +id: EDAM_data:1583 +name: Nucleic acid melting profile +comment: A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. +subset: bioinformatics subset: data -def: "Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison." [http://edamontology.org] -comment: The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). -synonym: "Substitution matrix" EXACT [http://edamontology.org] -is_a: EDAM_data:2082 ! Matrix - +subset: edam +synonym: "Nucleic acid stability profile" EXACT [] +created_in: "beta12orEarlier" +def: "Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] -id: EDAM_data:2053 -name: Structural data -namespace: data +id: EDAM_data:1584 +name: Nucleic acid enthalpy +subset: bioinformatics subset: data -def: "Data concerning molecular structural data." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0883 ! Structure -consider: EDAM_data:2085 ! Structure report - +subset: edam +created_in: "beta12orEarlier" +def: "Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] -id: EDAM_data:2085 -name: Structure report -namespace: data +id: EDAM_data:1585 +name: Nucleic acid entropy +subset: bioinformatics subset: data -def: "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." [http://edamontology.org] -synonym: "Structure-derived report" EXACT [http://edamontology.org] -is_a: EDAM_data:2048 ! Report +subset: edam +created_in: "beta12orEarlier" +def: "Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] -id: EDAM_data:2973 -name: Secondary structure data -namespace: data +id: EDAM_data:1586 +name: Nucleic acid melting temperature +subset: bioinformatics subset: data -def: "Data concerning molecular secondary structure data." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:2081 ! Secondary structure -consider: EDAM_data:2881 ! Secondary structure report - +subset: edam +created_in: "beta12orEarlier" +def: "Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2139 ! Nucleic acid melting temperature [Term] -id: EDAM_data:2881 -name: Secondary structure report -namespace: data +id: EDAM_data:1587 +name: Nucleic acid stitch profile +comment: A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. +subset: bioinformatics subset: data -def: "An informative report on general information, properties or features of one or more molecular secondary structures." [http://edamontology.org] -synonym: "Secondary structure-derived report" EXACT [http://edamontology.org] -is_a: EDAM_data:2048 ! Report - +subset: edam +created_in: "beta12orEarlier" +def: "Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] -id: EDAM_data:2956 -name: Protein secondary structure report -namespace: data +id: EDAM_data:1588 +name: DNA base pair stacking energies data +subset: bioinformatics subset: data -def: "An informative report about the properties or features of one or more protein secondary structures." [http://edamontology.org] -is_a: EDAM_data:2881 ! Secondary structure report +subset: edam +created_in: "beta12orEarlier" +def: "DNA base pair stacking energies data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2088 ! DNA base structural data [Term] -id: EDAM_data:1494 -name: Structural transformation matrix -namespace: data +id: EDAM_data:1589 +name: DNA base pair twist angle data +subset: bioinformatics subset: data -def: "Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures." [http://edamontology.org] -is_a: EDAM_data:2082 ! Matrix +subset: edam +created_in: "beta12orEarlier" +def: "DNA base pair twist angle data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2088 ! DNA base structural data [Term] -id: EDAM_data:0887 -name: Structure alignment report -namespace: data +id: EDAM_data:1590 +name: DNA base trimer roll angles data +subset: bioinformatics subset: data -def: "An informative report on molecular tertiary structure alignment-derived data." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_a: EDAM_data:2083 ! Alignment report +subset: edam +created_in: "beta12orEarlier" +def: "DNA base trimer roll angles data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2088 ! DNA base structural data [Term] -id: EDAM_data:0889 -name: Structural (3D) profile -namespace: data +id: EDAM_data:1591 +name: Vienna RNA parameters +subset: bioinformatics subset: data -def: "Some type of structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org] -synonym: "3D profile" EXACT [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles +subset: edam +created_in: "beta12orEarlier" +def: "RNA parameters used by the Vienna package." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:0892 -name: Protein sequence-structure scoring matrix -namespace: data +id: EDAM_data:1592 +name: Vienna RNA structure constraints +subset: bioinformatics subset: data -def: "Matrix of values used for scoring sequence-structure compatibility." [http://edamontology.org] -is_a: EDAM_data:2082 ! Matrix +subset: edam +created_in: "beta12orEarlier" +def: "Structure constraints used by the Vienna package." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:2528 -name: Molecular data -namespace: data +id: EDAM_data:1593 +name: Vienna RNA concentration data +subset: bioinformatics subset: data -def: "Data concerning a specific type of molecule." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Molecule-specific data" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:2529 ! Molecule report - +subset: edam +created_in: "beta12orEarlier" +def: "RNA concentration data used by the Vienna package." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:2599 -name: Molecular interaction -namespace: data +id: EDAM_data:1594 +name: Vienna RNA calculated energy +subset: bioinformatics subset: data -def: "Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." [http://edamontology.org] -synonym: "Molecular interaction data" EXACT [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data - +subset: edam +created_in: "beta12orEarlier" +def: "RNA calculated energy data generated by the Vienna package." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1584 ! Nucleic acid enthalpy [Term] -id: EDAM_data:2601 -name: Small molecule data -namespace: data +id: EDAM_data:1595 +name: Base pairing probability matrix dotplot +comment: Such as generated by the Vienna package. +subset: bioinformatics subset: data -def: "Data concerning one or more small molecules." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0962 ! Small molecule annotation +subset: edam +created_in: "beta12orEarlier" +def: "Dotplot of RNA base pairing probability matrix." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2088 ! DNA base structural data [Term] -id: EDAM_data:2016 -name: Amino acid property -namespace: data +id: EDAM_data:1596 +name: Nucleic acid folding report +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics subset: data -def: "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." [http://edamontology.org] -synonym: "Amino acid data" EXACT [http://edamontology.org] -is_a: EDAM_data:2087 ! Molecular property +subset: edam +synonym: "Nucleic acid report (folding model)" EXACT [] +synonym: "Nucleic acid report (folding)" EXACT [] +created_in: "beta12orEarlier" +def: "A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0912 ! Nucleic acid property [Term] -id: EDAM_data:2979 -name: Peptide property -namespace: data +id: EDAM_data:1597 +name: Codon usage table +comment: A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. +subset: bioinformatics subset: data -def: "Data concerning small peptides." [http://edamontology.org] -synonym: "Peptide data" EXACT [http://edamontology.org] -is_a: EDAM_data:2087 ! Molecular property - +subset: edam +created_in: "beta12orEarlier" +def: "Table of codon usage data calculated from one or more nucleic acid sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] -id: EDAM_data:0895 -name: Peptide annotation -namespace: data +id: EDAM_data:1598 +name: Genetic code +comment: A genetic code need not include detailed codon usage information. +subset: bioinformatics subset: data -def: "An informative report about a specific peptide." [http://edamontology.org] -is_a: EDAM_data:0962 ! Small molecule annotation -is_a: EDAM_data:2979 ! Peptide property -relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids - +subset: edam +created_in: "beta12orEarlier" +def: "A genetic code for an organism." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1597 ! Codon usage table [Term] -id: EDAM_data:2399 -name: Gene annotation (transcript) -namespace: data +id: EDAM_data:1599 +name: Codon adaptation index +subset: bioinformatics subset: data -! alt_id: EDAM_data:2703 -def: "An informative report on a specific gene transcript, clone or EST." [http://edamontology.org] -synonym: "Gene transcript annotation" EXACT [http://edamontology.org] -synonym: "Gene annotation (clone or EST)" EXACT [http://edamontology.org] -is_a: EDAM_data:0916 ! Gene annotation - +subset: edam +synonym: "CAI" EXACT [] +created_in: "beta12orEarlier" +def: "A simple measure of synonymous codon usage bias often used to predict gene expression levels." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2865 ! Codon usage bias [Term] -id: EDAM_data:0896 -name: Protein report -namespace: data +id: EDAM_data:1600 +name: Codon usage bias plot +subset: bioinformatics subset: data -def: "An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data." [http://edamontology.org] -synonym: "Gene product annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2529 ! Molecule report -relationship: has_topic EDAM_topic:0078 ! Protein analysis - +subset: edam +synonym: "Synonymous codon usage statistic plot" EXACT [] +created_in: "beta12orEarlier" +def: "A plot of the synonymous codon usage calculated for windows over a nucleotide sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2865 ! Codon usage bias [Term] -id: EDAM_data:0897 -name: Protein property -namespace: data +id: EDAM_data:1601 +name: Nc statistic +subset: bioinformatics subset: data -def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model." [http://edamontology.org] -comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Protein physicochemical property" EXACT [http://edamontology.org] -is_a: EDAM_data:0896 ! Protein report -is_a: EDAM_data:2087 ! Molecular property - +subset: edam +created_in: "beta12orEarlier" +def: "The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2865 ! Codon usage bias [Term] -id: EDAM_data:1537 -name: Protein structure report -namespace: data +id: EDAM_data:1602 +name: Codon usage fraction difference +subset: bioinformatics subset: data -def: "Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains." [http://edamontology.org] -! alt_id: EDAM_data:0898 -! alt_id: EDAM_data:1538 -! alt_id: EDAM_data:2377 -synonym: "Protein structure report (domain)" EXACT [http://edamontology.org] -synonym: "Protein structure-derived report" EXACT [http://edamontology.org] -synonym: "Protein structural property" EXACT [http://edamontology.org] -synonym: "Protein report (structure)" EXACT [http://edamontology.org] -synonym: "Protein property (structural)" EXACT [http://edamontology.org] -is_a: EDAM_data:0896 ! Protein report -is_a: EDAM_data:2085 ! Structure report - - -! [Term] born obsolete -! id: EDAM_data:3151 !{since=beta13} -! name: Protein property (physicochemical) -! namespace: data -! subset: data -! def: "A report of primarily non-positional data describing intrinsic physicochemical properties of a protein molecule." [http://edamontology.org] -! synonym: "Protein physicochemical property" EXACT [http://edamontology.org] -! is_obsolete: true !{since=beta13} -! consider: EDAM_data:0897 ! Protein property - - -! [Term] born obsolete -! id: EDAM_data:3152 !{since=beta13} -! name: Protein property (sequence) -! namespace: data -! subset: data -! def: "A non-positional property of a protein sequence." [http://edamontology.org] -! synonym: "Protein sequence property" EXACT [http://edamontology.org] -! is_obsolete: true !{since=beta13} -! consider: EDAM_data:0897 ! Protein property - +subset: edam +created_in: "beta12orEarlier" +def: "The differences in codon usage fractions between two codon usage tables." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0914 ! Codon usage report [Term] -id: EDAM_data:2313 -name: Carbohydrate structure report -namespace: data +id: EDAM_data:1621 +name: Pharmacogenomic annotation +comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. +subset: bioinformatics subset: data -def: "Annotation on or information derived from one or more specific carbohydrate 3D structure(s)." [http://edamontology.org] -is_a: EDAM_data:2085 ! Structure report +subset: edam +created_in: "beta12orEarlier" +def: "Data on the influence of genotype on drug response." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0920 ! Genotype/phenotype annotation [Term] -id: EDAM_data:2879 -name: Lipid structure report -namespace: data +id: EDAM_data:1622 +name: Disease annotation +subset: bioinformatics subset: data -def: "Annotation on or information derived from one or more specific lipid 3D structure(s)." [http://edamontology.org] -is_a: EDAM_data:2085 ! Structure report - - +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific disease." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0920 ! Genotype/phenotype annotation +relationship: has_topic EDAM_topic:0634 ! Disease resources [Term] -id: EDAM_data:2987 -name: Classification -namespace: data +id: EDAM_data:1634 +name: Gene annotation (linkage disequilibrium) +subset: bioinformatics subset: data -def: "Data concerning a classification of molecular sequences, structures or other entities." [http://edamontology.org] -comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. -synonym: "Classification data" EXACT [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:2829 ! Ontologies, nomenclature and classification +subset: edam +created_in: "beta12orEarlier" +def: "A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0927 ! Gene annotation (linkage) [Term] -id: EDAM_data:3028 -name: Taxonomy -namespace: data +id: EDAM_data:1636 +name: Heat map +comment: A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. +subset: bioinformatics subset: data -def: "Data concerning the classification, identification and naming of organisms." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Taxonomic data" EXACT [http://edamontology.org] -is_a: EDAM_data:2987 ! Classification -relationship: has_topic EDAM_topic:0637 ! Taxonomy - - +subset: edam +created_in: "beta12orEarlier" +def: "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2967 ! Microarray image [Term] -id: EDAM_data:2986 -name: Nucleic acid classification -namespace: data +id: EDAM_data:1642 +name: Affymetrix probe sets library file +subset: bioinformatics subset: data -def: "Data concerning the classification of nucleic acid sequences or structures." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Nucleic acid classification data" EXACT [http://edamontology.org] -is_a: EDAM_data:2084 ! Nucleic acid report -is_a: EDAM_data:2987 ! Classification -relationship: has_topic EDAM_topic:0722 ! Nucleic acid classification +subset: edam +synonym: "CDF file" RELATED [] +created_in: "beta12orEarlier" +def: "Affymetrix library file of information about which probes belong to which probe set." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation [Term] -id: EDAM_data:2980 -name: Protein classification -namespace: data +id: EDAM_data:1643 +name: Affymetrix probe sets information library file +subset: bioinformatics subset: data -def: "Data concerning the classification of protein sequences or structures." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Protein classification data" EXACT [http://edamontology.org] -is_a: EDAM_data:0896 ! Protein report -is_a: EDAM_data:2987 ! Classification -relationship: has_topic EDAM_topic:0595 ! Protein classification +subset: edam +synonym: "GIN file" RELATED [] +created_in: "beta12orEarlier" +def: "Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation [Term] -id: EDAM_data:0900 -name: Protein domain classification -namespace: data +id: EDAM_data:1646 +name: Molecular weights standard fingerprint +subset: bioinformatics subset: data -def: "Data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org] -is_a: EDAM_data:2980 ! Protein classification -relationship: has_topic EDAM_topic:0736 ! Protein domains and folds +subset: edam +created_in: "beta12orEarlier" +def: "Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0944 ! Peptide mass fingerprint [Term] -id: EDAM_data:3101 !{since=beta13} -name: Protein domain classification node -namespace: data +id: EDAM_data:1656 +name: Pathway or network (metabolic) +comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. +subset: bioinformatics subset: data -def: "A node from a classification of protein structural domain(s)." [http://edamontology.org] -is_a: EDAM_data:0900 ! Protein domain classification - +subset: edam +created_in: "beta12orEarlier" +def: "A report typically including a map (diagram) of a metabolic pathway." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM_data:0906 -name: Protein interaction -namespace: data +id: EDAM_data:1657 +name: Pathway or network (genetic information processing) +subset: bioinformatics subset: data -def: "An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand." [http://edamontology.org] -synonym: "Protein report (interaction)" EXACT [http://edamontology.org] -is_a: EDAM_data:2599 ! Molecular interaction -is_a: EDAM_data:0896 ! Protein report -relationship: has_topic EDAM_topic:0128 ! Protein interactions +subset: edam +created_in: "beta12orEarlier" +def: "A report typically including a map (diagram) of a genetic information processing pathway." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM_data:0907 -name: Protein family -namespace: data +id: EDAM_data:1658 +name: Pathway or network (environmental information processing) +subset: bioinformatics subset: data -def: "An informative report on a specific protein family or other group of classified proteins." [http://edamontology.org] -synonym: "Protein family annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2980 ! Protein classification -relationship: has_topic EDAM_topic:0724 ! Protein families - +subset: edam +created_in: "beta12orEarlier" +def: "A report typically including a map (diagram) of an environmental information processing pathway." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM_data:2354 -name: RNA family annotation -namespace: data +id: EDAM_data:1659 +name: Pathway or network (signal transduction) +subset: bioinformatics subset: data -def: "An informative report on a specific RNA family or other group of classified RNA sequences." [http://edamontology.org] -is_a: EDAM_data:2986 ! Nucleic acid classification +subset: edam +created_in: "beta12orEarlier" +def: "A report typically including a map (diagram) of a signal transduction pathway." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM_data:2978 -name: Reaction data -namespace: data +id: EDAM_data:1660 +name: Pathway or network (cellular process) +subset: bioinformatics subset: data -! alt_id: EDAM_data:0908 -def: "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Reaction annotation" EXACT [http://edamontology.org] -synonym: "Enzyme kinetics annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data +subset: edam +created_in: "beta12orEarlier" +def: "A report typically including a map (diagram) of a cellular process pathway." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network +[Term] +id: EDAM_data:1661 +name: Pathway or network (disease) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network +[Term] +id: EDAM_data:1662 +name: Pathway or network (drug structure relationship) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report typically including a map (diagram) of drug structure relationships." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM_data:2024 -name: Enzyme kinetics data -namespace: data +id: EDAM_data:1663 +name: Pathway or network (protein-protein interaction) +subset: bioinformatics subset: data -def: "Data concerning chemical reaction(s) catalysed by enzyme(s)." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_a: EDAM_data:2978 ! Reaction data +subset: edam +created_in: "beta12orEarlier" +def: "A report typically including a map (diagram) of a network of protein interactions." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM_data:0911 -name: Nucleotide base annotation -namespace: data +id: EDAM_data:1664 +name: MIRIAM datatype +comment: A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. +subset: bioinformatics subset: data -def: "An informative report about a specific nucleotide base." [http://edamontology.org] -is_a: EDAM_data:0962 ! Small molecule annotation +subset: edam +created_in: "beta12orEarlier" +def: "An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0948 ! Data resource definition [Term] -id: EDAM_data:2116 -name: Nucleic acid features (codon) -namespace: data +id: EDAM_data:1667 +name: E-value +comment: An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. +subset: bioinformatics subset: data -def: "An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1276 ! Nucleic acid features +subset: edam +synonym: "Expectation value" EXACT [] +created_in: "beta12orEarlier" +def: "A simple floating point number defining the lower or upper limit of an expectation value (E-value)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0951 ! Statistical estimate score [Term] -id: EDAM_data:2084 -name: Nucleic acid report -namespace: data +id: EDAM_data:1668 +name: Z-value +comment: A z-value might be specified as a threshold for reporting hits from database searches. +subset: bioinformatics subset: data -def: "An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." [http://edamontology.org] -is_a: EDAM_data:2529 ! Molecule report +subset: edam +created_in: "beta12orEarlier" +def: "The z-value is the number of standard deviations a data value is above or below a mean value." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0951 ! Statistical estimate score [Term] -id: EDAM_data:0912 -name: Nucleic acid property -namespace: data +id: EDAM_data:1669 +name: P-value +comment: A z-value might be specified as a threshold for reporting hits from database searches. +subset: bioinformatics subset: data -def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule." [http://edamontology.org] -comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Nucleic acid physicochemical property" EXACT [http://edamontology.org] -is_a: EDAM_data:2084 ! Nucleic acid report -is_a: EDAM_data:2087 ! Molecular property - +subset: edam +created_in: "beta12orEarlier" +def: "The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0951 ! Statistical estimate score [Term] -id: EDAM_data:2086 -name: Nucleic acid structure report -namespace: data +id: EDAM_data:1670 +name: Database version information +subset: bioinformatics subset: data -! alt_id: EDAM_data:0913 -def: "A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s)." [http://edamontology.org] -comment: This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. -synonym: "Nucleic acid structural property" EXACT [http://edamontology.org] -synonym: "Nucleic acid property (structural)" EXACT [http://edamontology.org] -is_a: EDAM_data:0912 ! Nucleic acid property -is_a: EDAM_data:2085 ! Structure report - - +subset: edam +synonym: "Ontology version information" EXACT [] +created_in: "beta12orEarlier" +def: "Information on a database (or ontology) version, for example name, version number and release date." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0953 ! Version information +is_a: EDAM_data:0957 ! Database metadata [Term] -id: EDAM_data:2927 -name: Codon usage data -namespace: data +id: EDAM_data:1671 +name: Tool version information +subset: bioinformatics subset: data -def: "Data concerning codon usage." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:1597 ! Codon usage table -consider: EDAM_data:0914 ! Codon usage report - +subset: edam +created_in: "beta12orEarlier" +def: "Information on an application version, for example name, version number and release date." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0953 ! Version information +is_a: EDAM_data:0958 ! Tool metadata [Term] -id: EDAM_data:1597 -name: Codon usage table -namespace: data +id: EDAM_data:1672 +name: CATH version information +subset: bioinformatics subset: data -def: "Table of codon usage data calculated from one or more nucleic acid sequences." [http://edamontology.org] -comment: A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0107 ! Codon usage analysis +subset: edam +created_in: "beta12orEarlier" +def: "Information on a version of the CATH database." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1670 ! Database version information [Term] -id: EDAM_data:0914 -name: Codon usage report -namespace: data +id: EDAM_data:1673 +name: Swiss-Prot to PDB mapping +subset: bioinformatics subset: data -def: "Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_a: EDAM_data:2048 ! Report -relationship: has_topic EDAM_topic:0107 ! Codon usage analysis +subset: edam +created_in: "beta12orEarlier" +def: "Cross-mapping of Swiss-Prot codes to PDB identifiers." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0954 ! Database cross-mapping [Term] -id: EDAM_data:2603 -name: Microarray data -namespace: data +id: EDAM_data:1674 +name: Sequence database cross-references +subset: bioinformatics subset: data -! alt_id: EDAM_data:2541 -def: "Image or hybridisation data for a microarray, typically a study of gene expression." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. See also EDAM_data:0931 ! Experiment annotation (microarray) -synonym: "Gene expression data" EXACT [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data - - +subset: edam +created_in: "beta12orEarlier" +def: "Cross-references from a sequence record to other databases." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2093 ! Data reference [Term] -id: EDAM_data:3110 !{since=beta13} -name: Raw microarray data -namespace: data +id: EDAM_data:1675 +name: Job status +comment: Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). +subset: bioinformatics subset: data -def: "Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment." [http://edamontology.org] -comment: Such data as found in Affymetrix CEL or GPR files. -is_a: EDAM_data:3117 ! Microarray hybridisation data -is_a: EDAM_data:3108 ! Experimental measurement - +subset: edam +created_in: "beta12orEarlier" +def: "Metadata on the status of a submitted job." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0959 ! Job metadata [Term] -id: EDAM_data:3111 !{since=beta13} -name: Processed microarray data -namespace: data +id: EDAM_data:1676 +name: Job ID +subset: bioinformatics subset: data -! alt_id: EDAM_data:0929 -def: "Data generated from processing and analysis of probe set data from a microarray experiment." [http://edamontology.org] -comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. -synonym: "Microarray probe set data" EXACT [http://edamontology.org] -synonym: "Gene expression report" EXACT [http://edamontology.org] -synonym: "Gene annotation (expression)" EXACT [http://edamontology.org] -is_a: EDAM_data:3117 ! Microarray hybridisation data -is_a: EDAM_data:0928 ! Gene expression profile -relationship: has_topic EDAM_topic:0200 ! Microarrays - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The (typically numeric) unique identifier of a submitted job." [http://edamontology.org] +namespace: identifier +obsolete_since: "1.0" +replaced_by: EDAM_data:2098 +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:3117 !{since=beta13} -name: Microarray hybridisation data -namespace: data +id: EDAM_data:1677 +name: Job type +subset: bioinformatics subset: data -def: "Data concerning the hybridisations measured during a microarray experiment." [http://edamontology.org] -is_a: EDAM_data:2603 ! Microarray data -relationship: has_topic EDAM_topic:0200 ! Microarrays +subset: edam +created_in: "beta12orEarlier" +def: "A label (text token) describing the type of job, for example interactive or non-interactive." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2100 ! Type [Term] -id: EDAM_data:3112 !{since=beta13} -name: Normalised microarray data -namespace: data +id: EDAM_data:1678 +name: Tool log +subset: bioinformatics subset: data -def: "The final processed (normalised) data for a set of hybridisations in a microarray experiment." [http://edamontology.org] -comment: This combines data from all hybridisations. -synonym: "Gene expression matrix" EXACT [http://edamontology.org] -synonym: "Gene expression data matrix" EXACT [http://edamontology.org] -is_a: EDAM_data:3117 ! Microarray hybridisation data +subset: edam +created_in: "beta12orEarlier" +def: "A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0959 ! Job metadata [Term] -id: EDAM_data:3113 !{since=beta13} -name: Sample annotation -namespace: data +id: EDAM_data:1679 +name: DaliLite log file +subset: bioinformatics subset: data -def: "Annotation on a biological sample, for example experimental factors and their values." [http://edamontology.org] -comment: This might include compound and dose in a dose response experiment. -is_a: EDAM_data:0931 ! Experiment annotation (microarray) - - - - - +subset: edam +created_in: "beta12orEarlier" +def: "DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:3115 !{since=beta13} -name: Microarray annotation -namespace: data +id: EDAM_data:1680 +name: STRIDE log file +subset: bioinformatics subset: data -def: "Annotation on the array itself used in a microarray experiment." [http://edamontology.org] -comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. -is_a: EDAM_data:0931 ! Experiment annotation (microarray) - +subset: edam +created_in: "beta12orEarlier" +def: "STRIDE log file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:3116 !{since=beta13} -name: Microarray protocol annotation -namespace: data +id: EDAM_data:1681 +name: NACCESS log file +subset: bioinformatics subset: data -def: "Annotation on laboratory and/or data processing protocols used in an microarray experiment." [http://edamontology.org] -comment: This might describe e.g. the normalisation methods used to process the raw data. -is_a: EDAM_data:0931 ! Experiment annotation (microarray) - +subset: edam +created_in: "beta12orEarlier" +def: "NACCESS log file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:2763 -name: Locus annotation -namespace: data +id: EDAM_data:1682 +name: EMBOSS wordfinder log file +subset: bioinformatics subset: data -def: "An informative report on a particular locus." [http://edamontology.org] -synonym: "Locus report" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0916 ! Gene annotation +subset: edam +created_in: "beta12orEarlier" +def: "EMBOSS wordfinder log file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:0916 -name: Gene annotation -namespace: data +id: EDAM_data:1683 +name: EMBOSS domainatrix log file +subset: bioinformatics subset: data -! alt_id: EDAM_data:2394 -! alt_id: EDAM_data:2361 -def: "An informative report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org] -comment: This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). -synonym: "Gene report" EXACT [http://edamontology.org] -synonym: "Gene annotation (functional)" EXACT [http://edamontology.org] -xref: Moby:gene -xref: Moby:GeneInfo -xref: Moby_namespace:Human_Readable_Description -is_a: EDAM_data:1276 ! Nucleic acid features -relationship: has_topic EDAM_topic:0623 ! Genes, gene family or system +subset: edam +created_in: "beta12orEarlier" +def: "EMBOSS (EMBASSY) domainatrix application log file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:3148 !{since=beta13} -name: Gene family annotation -namespace: data +id: EDAM_data:1684 +name: EMBOSS sites log file +subset: bioinformatics subset: data -def: "An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene." [http://edamontology.org] -is_a: EDAM_data:2986 ! Nucleic acid classification -is_a: EDAM_data:0916 ! Gene annotation - +subset: edam +created_in: "beta12orEarlier" +def: "EMBOSS (EMBASSY) sites application log file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:0918 -name: Nucleic acid features (variation) -namespace: data +id: EDAM_data:1685 +name: EMBOSS supermatcher error file +subset: bioinformatics subset: data -def: "A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms." [http://edamontology.org] -synonym: "Sequence variation annotation" EXACT [http://edamontology.org] -synonym: "sequence_alteration" RELATED [SO:0001059] -is_a: EDAM_data:3122 ! Nucleic acid features (difference and change) -relationship: has_topic EDAM_topic:0199 ! Genetic variation - +subset: edam +created_in: "beta12orEarlier" +def: "EMBOSS (EMBASSY) supermatcher error file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:0919 -name: Gene annotation (chromosome) -namespace: data +id: EDAM_data:1686 +name: EMBOSS megamerger log file +subset: bioinformatics subset: data -def: "An informative report on a specific chromosome." [http://edamontology.org] -comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. -is_a: EDAM_data:0916 ! Gene annotation -relationship: has_topic EDAM_topic:0624 ! Chromosomes +subset: edam +created_in: "beta12orEarlier" +def: "EMBOSS megamerger log file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:2602 -name: Genotype and phenotype data -namespace: data +id: EDAM_data:1687 +name: EMBOSS whichdb log file +subset: bioinformatics subset: data -def: "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:0920 ! Genotype/phenotype annotation - +subset: edam +created_in: "beta12orEarlier" +def: "EMBOSS megamerger log file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:0920 -name: Genotype/phenotype annotation -namespace: data +id: EDAM_data:1688 +name: EMBOSS vectorstrip log file +subset: bioinformatics subset: data -! alt_id: EDAM_data:2890 -def: "An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes." [http://edamontology.org] -is_a: EDAM_data:2048 ! Report - +subset: edam +created_in: "beta12orEarlier" +def: "EMBOSS vectorstrip log file." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM_data:2531 -name: Experiment annotation -namespace: data +id: EDAM_data:1689 +name: Username +subset: bioinformatics subset: data -def: "Annotation on a wet lab experiment, such as experimental conditions." [http://edamontology.org] -is_a: EDAM_data:2048 ! Report - -! [Term] born obsolete -! id: EDAM_data:3109 !{since=beta13} -! name: Experimental measurement annotation -! namespace: data -! subset: data -! def: "Annotation on the result of a wet lab experiment." [http://edamontology.org] -! is_obsolete: true !{since=beta13} -! consider: EDAM_data:3108 ! Experimental measurement -! consider: EDAM_data:2531 ! Experiment annotation - - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A username on a computer system." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2101 ! User ID [Term] -id: EDAM_data:2381 -name: Experiment annotation (genotype) -namespace: data +id: EDAM_data:1690 +name: Password +subset: bioinformatics subset: data -def: "Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." [http://edamontology.org] -is_a: EDAM_data:2531 ! Experiment annotation - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A password on a computer system." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2101 ! User ID [Term] -id: EDAM_data:3231 !{since=1.1} -name: Experiment annotation (GWAS) -namespace: data +id: EDAM_data:1691 +name: Email address +subset: bioinformatics subset: data -def: "Metadata on a genome-wide association study (GWAS)." [http://edamontology.org] -synonym: "Experiment annotation (genome-wide association study)" EXACT [http://edamontology.org] -is_a: EDAM_data:2531 ! Experiment annotation - - - +subset: edam +subset: identifiers +xref: Moby:Email +xref: Moby:EmailAddress +created_in: "beta12orEarlier" +def: "A valid email address of an end-user." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2101 ! User ID [Term] -id: EDAM_data:0925 -name: Sequence assembly -namespace: data +id: EDAM_data:1692 +name: Person name +subset: bioinformatics subset: data -def: "An assembly of fragments of a (typically genomic) DNA sequence." [http://edamontology.org] -comment: Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. -synonym: "Sequence assembly" EXACT [http://en.wikipedia.org/wiki/Sequence_assembly] -synonym: "sequence_assembly" EXACT [SO:0000353] -synonym: "assembly" NARROW [SO:0001248] !{note="Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'."} -is_a: EDAM_data:1234 ! Sequence set (nucleic acid) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a person." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2118 ! Person identifier [Term] -id: EDAM_data:2028 -name: Experimental data -namespace: data +id: EDAM_data:1693 +name: Number of iterations +subset: bioinformatics subset: data -def: "Raw data from or annotation on laboratory experiments." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -synonym: "Experimental measurement data" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:3108 ! Experimental measurement -consider: EDAM_data:2531 ! Experiment annotation +subset: edam +created_in: "beta12orEarlier" +def: "Number of iterations of an algorithm." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2079 ! Search parameter [Term] -id: EDAM_data:3108 !{since=beta13} -name: Experimental measurement -namespace: data +id: EDAM_data:1694 +name: Number of output entities +subset: bioinformatics subset: data -def: "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -synonym: "Raw experimental data" EXACT [http://edamontology.org] -synonym: "Experimental measurement data" EXACT [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data - - - +subset: edam +created_in: "beta12orEarlier" +def: "Number of entities (for example database hits, sequences, alignments etc) to write to an output file." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2079 ! Search parameter [Term] -id: EDAM_data:2042 -name: Evidence -namespace: data +id: EDAM_data:1695 +name: Hit sort order +subset: bioinformatics subset: data -def: "Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc." [http://edamontology.org] -is_a: EDAM_data:2527 ! Parameter +subset: edam +created_in: "beta12orEarlier" +def: "Controls the order of hits (reported matches) in an output file from a database search." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2134 ! Results sort order [Term] -id: EDAM_data:0941 -name: Electron microscopy model -namespace: data +id: EDAM_data:1696 +name: Drug annotation +subset: bioinformatics subset: data -def: "Annotation on a structural 3D model (volume map) from electron microscopy." [http://edamontology.org] -comment: This might include the location in the model of the known features of a particular macromolecule. -is_a: EDAM_data:0940 ! Electron microscopy volume map -relationship: has_topic EDAM_topic:2226 ! Structure determination +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific drug." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0962 ! Small molecule annotation +relationship: has_topic EDAM_topic:0620 ! Drugs and targets [Term] -id: EDAM_data:2971 -name: Workflow data -namespace: data +id: EDAM_data:1707 +name: Phylogenetic tree image +comment: See also 'Phylogenetic tree' +subset: bioinformatics subset: data -def: "Data concerning a computational workflow." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:0949 ! Workflow metadata -consider: EDAM_data:2972 ! Workflow - +subset: edam +created_in: "beta12orEarlier" +def: "An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1438 ! Phylogenetic tree report +is_a: EDAM_data:2968 ! Image [Term] -id: EDAM_data:0949 -name: Workflow metadata -namespace: data +id: EDAM_data:1708 +name: RNA secondary structure image +subset: bioinformatics subset: data -def: "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." [http://edamontology.org] -is_a: EDAM_data:2337 ! Metadata -! relationship: has_topic EDAM_topic:0769 ! Workflows - +subset: edam +created_in: "beta12orEarlier" +def: "Image of RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2880 ! Secondary structure image [Term] -id: EDAM_data:2972 -name: Workflow -namespace: data +id: EDAM_data:1709 +name: Protein secondary structure image +subset: bioinformatics subset: data -def: "A computational workflow." [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data -! relationship: has_topic EDAM_topic:0769 ! Workflows - +subset: edam +created_in: "beta12orEarlier" +def: "Image of protein secondary structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2880 ! Secondary structure image +is_a: EDAM_data:2956 ! Protein secondary structure report [Term] -id: EDAM_data:0950 -name: Biological model -namespace: data +id: EDAM_data:1710 +name: Structure image +subset: bioinformatics subset: data -def: "A biological model which can be represented in mathematical terms." [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0771 ! Biological models +subset: edam +created_in: "beta12orEarlier" +def: "Image of one or more molecular tertiary (3D) structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2085 ! Structure report +is_a: EDAM_data:2968 ! Image [Term] -id: EDAM_data:2983 -name: Pathway or network data -namespace: data +id: EDAM_data:1711 +name: Sequence alignment image +subset: bioinformatics subset: data -def: "Data concerning a specific biological pathway or network." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:2600 ! Pathway or network -consider: EDAM_data:2984 ! Pathway or network report - +subset: edam +created_in: "beta12orEarlier" +def: "Image of two or more aligned molecular sequences possibly annotated with alignment features." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0867 ! Sequence alignment report +is_a: EDAM_data:2968 ! Image [Term] -id: EDAM_data:2984 -name: Pathway or network report -namespace: data +id: EDAM_data:1712 +name: Structure image (small molecule) +comment: The molecular identifier and formula are typically included. +subset: bioinformatics subset: data -def: "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." [http://edamontology.org] -is_a: EDAM_data:2048 ! Report -relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models +subset: edam +synonym: "Chemical structure image" EXACT [] +synonym: "Small molecule structure image" EXACT [] +created_in: "beta12orEarlier" +def: "An image of the structure of a small chemical compound." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0962 ! Small molecule annotation +is_a: EDAM_data:1710 ! Structure image [Term] -id: EDAM_data:2600 -name: Pathway or network -namespace: data +id: EDAM_data:1713 +name: Fate map +subset: bioinformatics subset: data -def: "Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network)." [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models - +subset: edam +created_in: "beta12orEarlier" +def: " A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2724 ! Embryo annotation [Term] -id: EDAM_data:1883 -name: Annotated URI -namespace: data +id: EDAM_data:1714 +name: Microarray spots image +subset: bioinformatics subset: data -def: "A URI along with annotation describing the data found at the address." [http://edamontology.org] -xref: Moby:DescribedLink -is_a: EDAM_data:2337 ! Metadata -is_a: EDAM_data:2093 ! Data reference - +subset: edam +created_in: "beta12orEarlier" +def: "An image of spots from a microarray experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2967 ! Microarray image +is_a: EDAM_data:3108 ! Experimental measurement [Term] -id: EDAM_data:0954 -name: Database cross-mapping -namespace: data +id: EDAM_data:1715 +name: BioPax +subset: bioinformatics subset: data -def: "A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases." [http://edamontology.org] -comment: The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. -is_a: EDAM_data:2093 ! Data reference - +subset: edam +created_in: "beta12orEarlier" +def: "A term from the BioPax ontology." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:2872 -name: ID list +id: EDAM_data:1716 +name: GO +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene Ontology term" EXACT [] +xref: Moby:Annotated_GO_Term +xref: Moby:Annotated_GO_Term_With_Probability +xref: Moby:GO_Term +xref: Moby:GOTerm +created_in: "beta12orEarlier" +def: "A term definition from The Gene Ontology (GO)." [http://edamontology.org] namespace: data -subset: data -def: "A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data." [http://edamontology.org] -is_a: EDAM_data:2093 ! Data reference +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:2765 -name: Term ID list -namespace: data +id: EDAM_data:1717 +name: MeSH +subset: bioinformatics subset: data -def: "One or more terms from one or more controlled vocabularies which are annotations on an entity." [http://edamontology.org] -comment: The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. -is_a: EDAM_data:2872 ! ID list +subset: edam +created_in: "beta12orEarlier" +def: "A term from the MeSH vocabulary." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:1111 -name: EMBOSS listfile -namespace: data +id: EDAM_data:1718 +name: HGNC +subset: bioinformatics subset: data -def: "List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile)." [http://edamontology.org] -is_a: EDAM_data:2872 ! ID list - +subset: edam +created_in: "beta12orEarlier" +def: "A term from the HGNC controlled vocabulary." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:2093 -name: Data reference -namespace: data +id: EDAM_data:1719 +name: NCBI taxonomy vocabulary +subset: bioinformatics subset: data -def: "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology." [http://edamontology.org] -comment: A list of database accessions or identifiers are usually included. -is_a: EDAM_data:3031 ! Core data +subset: edam +created_in: "beta12orEarlier" +def: "A term from the NCBI taxonomy vocabulary." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:2540 -name: Data index data -namespace: data +id: EDAM_data:1720 +name: Plant ontology term +subset: bioinformatics subset: data -def: "Data concerning an index of data." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Database index" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:0955 ! Data index -consider: EDAM_data:0956 ! Data index report +subset: edam +created_in: "beta12orEarlier" +def: "A term from the Plant Ontology (PO)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:0955 -name: Data index -namespace: data +id: EDAM_data:1721 +name: UMLS +subset: bioinformatics subset: data -def: "An index of data of biological relevance." [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0220 ! Data processing and validation - +subset: edam +created_in: "beta12orEarlier" +def: "A term from the UMLS vocabulary." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:3210 !{since=1.1} -name: Genome index -namespace: data +id: EDAM_data:1722 +name: FMA +comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. +subset: bioinformatics subset: data -def: "An index of a genome sequence." [http://edamontology.org] -comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. -is_a: EDAM_data:0955 ! Data index - - +subset: edam +created_in: "beta12orEarlier" +def: "A term from Foundational Model of Anatomy." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:0956 -name: Data index report -namespace: data +id: EDAM_data:1723 +name: EMAP +subset: bioinformatics subset: data -def: "A report of an analysis of an index of biological data." [http://edamontology.org] -synonym: "Database index annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2048 ! Report -relationship: has_topic EDAM_topic:0220 ! Data processing and validation - +subset: edam +created_in: "beta12orEarlier" +def: "A term from the EMAP mouse ontology." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:2048 -name: Report -namespace: data +id: EDAM_data:1724 +name: ChEBI +subset: bioinformatics subset: data -! alt_id: EDAM_data:0969 -! alt_id: EDAM_data:3037 !{since=beta13} ! Not released -def: "A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing. -synonym: "Document" EXACT [http://edamontology.org] -synonym: "Text" EXACT [http://edamontology.org] -synonym: "document" RELATED [http://semanticscience.org/resource/SIO_000148] ! Related external synonym in EDAM without a note is usually almost exact. -is_a: EDAM_data:0006 ! Data - +subset: edam +created_in: "beta12orEarlier" +def: "A term from the ChEBI ontology." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:1772 -name: Score or penalty -namespace: data +id: EDAM_data:1725 +name: MGED +subset: bioinformatics subset: data -! alt_id: EDAM_data:2138 -def: "A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty)." [http://edamontology.org] -is_a: EDAM_data:2527 ! Parameter - +subset: edam +created_in: "beta12orEarlier" +def: "A term from the MGED ontology." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:2529 -name: Molecule report -namespace: data +id: EDAM_data:1726 +name: myGrid +comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. +subset: bioinformatics subset: data -def: "An informative report on a specific molecule." [http://edamontology.org] -synonym: "Molecular report" EXACT [http://edamontology.org] -is_a: EDAM_data:2048 ! Report +subset: edam +created_in: "beta12orEarlier" +def: "A term from the myGrid ontology." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM_data:0962 -name: Small molecule annotation -namespace: data +id: EDAM_data:1727 +name: GO (biological process) +comment: Data Type is an enumerated string. +subset: bioinformatics subset: data -def: "An informative report on a specific chemical compound." [http://edamontology.org] -synonym: "Chemical compound annotation" EXACT [http://edamontology.org] -synonym: "Small molecule report" EXACT [http://edamontology.org] -is_a: EDAM_data:2085 ! Structure report -is_a: EDAM_data:2529 ! Molecule report -relationship: has_topic EDAM_topic:0154 ! Small molecules - +subset: edam +created_in: "beta12orEarlier" +def: "A term definition for a biological process from the Gene Ontology (GO)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2858 ! Ontology concept [Term] -id: EDAM_data:0963 -name: Cell line annotation -namespace: data +id: EDAM_data:1728 +name: GO (molecular function) +comment: Data Type is an enumerated string. +subset: bioinformatics subset: data -def: "Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on." [http://edamontology.org] -synonym: "Organism strain data" EXACT [http://edamontology.org] -is_a: EDAM_data:2530 ! Organism annotation +subset: edam +created_in: "beta12orEarlier" +def: "A term definition for a molecular function from the Gene Ontology (GO)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2858 ! Ontology concept [Term] -id: EDAM_data:2530 -name: Organism annotation -namespace: data +id: EDAM_data:1729 +name: GO (cellular component) +comment: Data Type is an enumerated string. +subset: bioinformatics subset: data -def: "An informative report on a specific organism." [http://edamontology.org] -is_a: EDAM_data:2048 ! Report +subset: edam +created_in: "beta12orEarlier" +def: "A term definition for a cellular component from the Gene Ontology (GO)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2858 ! Ontology concept [Term] -id: EDAM_data:2307 -name: Virus annotation -namespace: data +id: EDAM_data:1730 +name: Ontology relation type +subset: bioinformatics subset: data -def: "An informative report on a specific virus." [http://edamontology.org] -is_a: EDAM_data:2530 ! Organism annotation +subset: edam +created_in: "beta12orEarlier" +def: "A relation type defined in an ontology." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0967 ! Ontology concept metadata [Term] -id: EDAM_data:2395 -name: Fungi annotation -namespace: data +id: EDAM_data:1731 +name: Ontology concept definition +subset: bioinformatics subset: data -def: "An informative report on a specific fungus." [http://edamontology.org] -is_a: EDAM_data:2530 ! Organism annotation +subset: edam +created_in: "beta12orEarlier" +def: "The definition of a concept from an ontology." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0967 ! Ontology concept metadata [Term] -id: EDAM_data:0964 -name: Scent annotation -namespace: data +id: EDAM_data:1732 +name: Ontology concept comment +subset: bioinformatics subset: data -def: "An informative report about a specific scent." [http://edamontology.org] -is_a: EDAM_data:0962 ! Small molecule annotation - - +subset: edam +created_in: "beta12orEarlier" +def: "A comment on a concept from an ontology." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0967 ! Ontology concept metadata [Term] -id: EDAM_data:2968 -name: Image -namespace: data +id: EDAM_data:1733 +name: Ontology concept reference +subset: bioinformatics subset: data -! alt_id: EDAM_data:0965 -def: "Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type." [http://edamontology.org] -synonym: "visual entity" BROAD [http://semanticscience.org/resource/SIO_000079] -synonym: "image" NARROW [http://semanticscience.org/resource/SIO_000081] -is_a: EDAM_data:3031 ! Core data - +subset: edam +created_in: "beta12orEarlier" +def: "Reference for a concept from an ontology." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2093 ! Data reference [Term] -id: EDAM_data:2884 -name: Plot -namespace: data +id: EDAM_data:1738 +name: doc2loc document information +comment: The doc2loc output includes the url, format, type and availability code of a document for every service provider. +subset: bioinformatics subset: data -def: "Biological data that is plotted as a graph of some type." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2968 ! Image +subset: edam +created_in: "beta12orEarlier" +def: "Information on a published article provided by the doc2loc program." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0970 ! Bibliographic reference [Term] -id: EDAM_data:2353 -name: Ontological data -namespace: data +id: EDAM_data:1742 +name: PDB residue number +subset: bioinformatics subset: data -def: "Data concerning an ontology." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:2223 ! Ontology metadata -consider: EDAM_data:0582 ! Ontology - +subset: edam +xref: PDBML:PDB_residue_no +xref: WHATIF: pdb_number +created_in: "beta12orEarlier" +def: "A residue identifier (a string) from a PDB file." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1016 ! Sequence position [Term] -id: EDAM_data:2849 -name: Abstract -namespace: data +id: EDAM_data:1743 +name: Atomic coordinate +subset: bioinformatics subset: data -def: "An abstract of a scientific article." [http://edamontology.org] -is_a: EDAM_data:2857 ! Article metadata - +subset: edam +synonym: "Cartesian coordinate" EXACT [] +created_in: "beta12orEarlier" +def: "Cartesian coordinate of an atom (in a molecular structure)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1917 ! Atomic property [Term] -id: EDAM_data:0970 -name: Bibliographic reference -namespace: data +id: EDAM_data:1744 +name: Atomic x coordinate +subset: bioinformatics subset: data -def: "Bibliographic data that uniquely identifies a scientific article, book or other published material." [http://edamontology.org] -comment: A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. -synonym: "Reference" EXACT [http://edamontology.org] -synonym: "Citation" EXACT [http://edamontology.org] -xref: Moby:GCP_SimpleCitation -xref: Moby:Publication -is_a: EDAM_data:2857 ! Article metadata -is_a: EDAM_data:2093 ! Data reference +subset: edam +synonym: "Cartesian x coordinate" EXACT [] +xref: PDBML:_atom_site.Cartn_x in PDBML +xref: WHATIF: PDBx_Cartn_x +created_in: "beta12orEarlier" +def: "Cartesian x coordinate of an atom (in a molecular structure)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1743 ! Atomic coordinate +[Term] +id: EDAM_data:1745 +name: Atomic y coordinate +subset: bioinformatics +subset: data +subset: edam +synonym: "Cartesian y coordinate" EXACT [] +xref: PDBML:_atom_site.Cartn_y in PDBML +xref: WHATIF: PDBx_Cartn_y +created_in: "beta12orEarlier" +def: "Cartesian y coordinate of an atom (in a molecular structure)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1743 ! Atomic coordinate [Term] -id: EDAM_data:2526 -name: Article data -namespace: data +id: EDAM_data:1746 +name: Atomic z coordinate +subset: bioinformatics subset: data -def: "Data concerning the scientific literature." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0971 ! Article +subset: edam +synonym: "Cartesian z coordinate" EXACT [] +xref: PDBML:_atom_site.Cartn_z +xref: WHATIF: PDBx_Cartn_z +created_in: "beta12orEarlier" +def: "Cartesian z coordinate of an atom (in a molecular structure)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1743 ! Atomic coordinate [Term] -id: EDAM_data:0971 -name: Article -namespace: data +id: EDAM_data:1748 +name: PDB atom name +subset: bioinformatics subset: data -def: "A body of scientific text, typically a full text article from a scientific journal." [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:3068 ! Literature and reference +subset: edam +subset: identifiers +xref: PDBML:pdbx_PDB_atom_name +xref: WHATIF: alternate_atom +xref: WHATIF: atom_type +xref: WHATIF: PDBx_auth_atom_id +xref: WHATIF: PDBx_type_symbol +created_in: "beta12orEarlier" +def: "Identifier (a string) of a specific atom from a PDB file for a molecular structure." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1757 ! Atom name [Term] -id: EDAM_data:2857 -name: Article metadata -namespace: data +id: EDAM_data:1755 +name: Protein atom +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics subset: data -def: "Bibliographic data concerning scientific article(s)." [http://edamontology.org] -is_a: EDAM_data:2954 ! Article report -is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:3068 ! Literature and reference - +subset: edam +synonym: "Atom data" EXACT [] +synonym: "CHEBI:33250" RELATED [] +created_in: "beta12orEarlier" +def: "Data on a single atom from a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1460 ! Protein structure [Term] -id: EDAM_data:2954 -name: Article report -namespace: data +id: EDAM_data:1756 +name: Protein residue +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics subset: data -def: "Data concerning or derived from the analysis of a scientific article." [http://edamontology.org] -is_a: EDAM_data:2048 ! Report - +subset: edam +synonym: "Residue" EXACT [] +created_in: "beta12orEarlier" +def: "Data on a single amino acid residue position in a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1460 ! Protein structure [Term] -id: EDAM_data:0972 -name: Text mining report -namespace: data +id: EDAM_data:1757 +name: Atom name +subset: bioinformatics subset: data -def: "An abstract of the results of text mining." [http://edamontology.org] -comment: A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. -is_a: EDAM_data:2954 ! Article report - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of an atom." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0983 ! Atom identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:2143 -name: EMBOSS report -namespace: data +id: EDAM_data:1758 +name: PDB residue name +subset: bioinformatics subset: data -def: "An application report generated by the EMBOSS suite." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2048 ! Report +subset: edam +subset: identifiers +xref: WHATIF: type +created_in: "beta12orEarlier" +def: "Three-letter amino acid residue names as used in PDB files." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2564 ! Amino acid name (three letter) [Term] -id: EDAM_data:2176 -name: Cardinality -namespace: data +id: EDAM_data:1759 +name: PDB model number +subset: bioinformatics subset: data -def: "The number of a certain thing." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} - +subset: edam +subset: identifiers +synonym: "Model number" EXACT [] +xref: PDBML:pdbx_PDB_model_num +xref: WHATIF: model_number +created_in: "beta12orEarlier" +def: "Identifier of a model structure from a PDB file." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:3035 ! Structure identifier [Term] -id: EDAM_data:2527 -name: Parameter -namespace: data +id: EDAM_data:1762 +name: CATH domain report +comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. +subset: bioinformatics subset: data -! alt_id: EDAM_data:2029 -! alt_id: EDAM_data:1773 -! alt_id: EDAM_data:0961 -def: "Typically a simple numerical or string value that controls the operation of a tool." [http://edamontology.org] -synonym: "Parameter or primitive" EXACT [http://edamontology.org] -synonym: "Tool parameter" EXACT [http://edamontology.org] -synonym: "Tool-specific parameter" EXACT [http://edamontology.org] -synonym: "Parameter" EXACT [http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter] -synonym: "parameter" EXACT [http://semanticscience.org/resource/SIO_000144] !{note="Slightly narrower in the sense of changing the characteristics of a system/function."} -is_a: EDAM_data:0006 ! Data - +subset: edam +created_in: "beta12orEarlier" +def: "Summary of domain classification information for a CATH domain." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0900 ! Protein domain classification [Term] -id: EDAM_data:2190 -name: Sequence checksum -namespace: data +id: EDAM_data:1764 +name: CATH representative domain sequences (ATOM) +subset: bioinformatics subset: data -def: "A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing." [http://edamontology.org] -synonym: "Hash code" EXACT [http://edamontology.org] -synonym: "Hash sum" EXACT [http://edamontology.org] -synonym: "Hash" EXACT [http://edamontology.org] -synonym: "Hash value" EXACT [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter -is_a: EDAM_data:0855 ! Sequence metadata - +subset: edam +created_in: "beta12orEarlier" +def: "FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1235 ! Sequence cluster [Term] -id: EDAM_data:2192 -name: Error -namespace: data +id: EDAM_data:1765 +name: CATH representative domain sequences (COMBS) +subset: bioinformatics subset: data -def: "Data on an error generated by computer system or tool." [http://edamontology.org] -is_a: EDAM_data:0959 ! Job metadata +subset: edam +created_in: "beta12orEarlier" +def: "FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1235 ! Sequence cluster [Term] -id: EDAM_data:2249 -name: DTD -namespace: data +id: EDAM_data:1766 +name: CATH domain sequences (ATOM) +subset: bioinformatics subset: data -def: "A DTD (document type definition)." [http://edamontology.org] -is_a: EDAM_data:2248 ! Schema - +subset: edam +created_in: "beta12orEarlier" +def: "FASTA sequence database for all CATH domains (based on PDB ATOM records)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0850 ! Sequence set [Term] -id: EDAM_data:2250 -name: XML Schema -namespace: data +id: EDAM_data:1767 +name: CATH domain sequences (COMBS) +subset: bioinformatics subset: data -def: "An XML Schema." [http://edamontology.org] -synonym: "XSD" EXACT [http://edamontology.org] -is_a: EDAM_data:2248 ! Schema - +subset: edam +created_in: "beta12orEarlier" +def: "FASTA sequence database for all CATH domains (based on COMBS sequence data)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0850 ! Sequence set [Term] -id: EDAM_data:2251 -name: Relax-NG schema -namespace: data +id: EDAM_data:1771 +name: Sequence version information +subset: bioinformatics subset: data -def: "A relax-NG schema." [http://edamontology.org] -is_a: EDAM_data:2248 ! Schema - +subset: edam +created_in: "beta12orEarlier" +def: "Information on an molecular sequence version." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0855 ! Sequence metadata +is_a: EDAM_data:0953 ! Version information [Term] -id: EDAM_data:2252 -name: XSLT stylesheet -namespace: data +id: EDAM_data:1772 +name: Score or penalty +subset: bioinformatics subset: data -def: "An XSLT stylesheet." [http://edamontology.org] -is_a: EDAM_data:2248 ! Schema - +subset: edam +created_in: "beta12orEarlier" +def: "A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:1743 -name: Atomic coordinate -namespace: data +id: EDAM_data:1776 +name: Protein report (function) +comment: For properties that can be mapped to a sequence, use 'Sequence report' instead. +subset: bioinformatics subset: data -def: "Cartesian coordinate of an atom (in a molecular structure)." [http://edamontology.org] -synonym: "Cartesian coordinate" EXACT [http://edamontology.org] -is_a: EDAM_data:1917 ! Atomic property - +subset: edam +created_in: "beta12orEarlier" +def: "Report on general functional properties of specific protein(s)." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0896 ! Protein report [Term] -id: EDAM_data:1857 -name: Atomic occupancy -namespace: data +id: EDAM_data:1783 +name: Gene name (ASPGD) +subset: bioinformatics subset: data -def: "The fraction of an atom type present at a site in a molecular structure." [http://edamontology.org] -comment: The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. -xref: WHATIF: PDBx_occupancy -is_a: EDAM_data:1917 ! Atomic property - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS +created_in: "beta12orEarlier" +def: "Name of a gene from Aspergillus Genome Database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1858 -name: Isotropic B factor -namespace: data +id: EDAM_data:1784 +name: Gene name (CGD) +subset: bioinformatics subset: data -def: "Isotropic B factor (atomic displacement parameter) for an atom from a PDB file." [http://edamontology.org] -xref: WHATIF: PDBx_B_iso_or_equiv -is_a: EDAM_data:1917 ! Atomic property +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS +created_in: "beta12orEarlier" +def: "Name of a gene from Candida Genome Database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1744 -name: Atomic x coordinate -namespace: data +id: EDAM_data:1785 +name: Gene name (dictyBase) +subset: bioinformatics subset: data -def: "Cartesian x coordinate of an atom (in a molecular structure)." [http://edamontology.org] -synonym: "Cartesian x coordinate" EXACT [http://edamontology.org] -xref: WHATIF: PDBx_Cartn_x -is_a: EDAM_data:1743 ! Atomic coordinate -! _atom_site.Cartn_x in PDBML +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase +created_in: "beta12orEarlier" +def: "Name of a gene from dictyBase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1745 -name: Atomic y coordinate -namespace: data +id: EDAM_data:1786 +name: Gene name (EcoGene primary) +subset: bioinformatics subset: data -def: "Cartesian y coordinate of an atom (in a molecular structure)." [http://edamontology.org] -synonym: "Cartesian y coordinate" EXACT [http://edamontology.org] -xref: WHATIF: PDBx_Cartn_y -is_a: EDAM_data:1743 ! Atomic coordinate -! _atom_site.Cartn_y in PDBML +subset: edam +subset: identifiers +synonym: "EcoGene primary gene name" EXACT [] +xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G +created_in: "beta12orEarlier" +def: "Primary name of a gene from EcoGene Database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1746 -name: Atomic z coordinate -namespace: data +id: EDAM_data:1787 +name: Gene name (MaizeGDB) +subset: bioinformatics subset: data -def: "Cartesian z coordinate of an atom (in a molecular structure)." [http://edamontology.org] -synonym: "Cartesian z coordinate" EXACT [http://edamontology.org] -xref: WHATIF: PDBx_Cartn_z -is_a: EDAM_data:1743 ! Atomic coordinate -! _atom_site.Cartn_z in PDBML +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus +created_in: "beta12orEarlier" +def: "Name of a gene from MaizeGDB (maize genes) database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:0844 -name: Molecular mass -namespace: data +id: EDAM_data:1788 +name: Gene name (SGD) +subset: bioinformatics subset: data -def: "Mass of a molecule." [http://edamontology.org] -is_a: EDAM_data:2050 ! Molecular property (general) +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS +created_in: "beta12orEarlier" +def: "Name of a gene from Saccharomyces Genome Database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol +is_a: EDAM_data:2632 ! SGD ID [Term] -id: EDAM_data:0845 -name: Molecular charge -namespace: data +id: EDAM_data:1789 +name: Gene name (TGD) +subset: bioinformatics subset: data -def: "Net charge of a molecule." [http://edamontology.org] -is_a: EDAM_data:2050 ! Molecular property (general) -! pdbx_formal_charge in PDBML - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS +created_in: "beta12orEarlier" +def: "Name of a gene from Tetrahymena Genome Database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:0846 -name: Chemical formula -namespace: data +id: EDAM_data:1790 +name: Gene name (CGSC) +subset: bioinformatics subset: data -def: "A specification of a chemical structure." [http://edamontology.org] -synonym: "Chemical structure specification" EXACT [http://edamontology.org] -is_a: EDAM_data:2050 ! Molecular property (general) - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC +created_in: "beta12orEarlier" +def: "Symbol of a gene from E.coli Genetic Stock Center." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:0847 -name: QSAR descriptor -namespace: data -subset: data -def: "A QSAR quantitative descriptor (name-value pair) of chemical structure." [http://edamontology.org] -comment: QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. -is_a: EDAM_data:2050 ! Molecular property (general) +id: EDAM_data:1791 +name: Gene name (HGNC) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "Gene name (HUGO)" EXACT [] +synonym: "HGNC gene name" EXACT [] +synonym: "HGNC gene symbol" EXACT [] +synonym: "HGNC symbol" EXACT [] +synonym: "HUGO gene name" EXACT [] +synonym: "HUGO gene symbol" EXACT [] +synonym: "HUGO symbol" EXACT [] +synonym: "Official gene name" EXACT [] +xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene +created_in: "beta12orEarlier" +def: "Symbol of a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org] +regex: "HGNC:[0-9]{1,5}" +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:2301 -name: SMILES string -namespace: data +id: EDAM_data:1792 +name: Gene name (MGD) +subset: bioinformatics subset: data -def: "A specification of a chemical structure in SMILES format." [http://edamontology.org] -is_a: EDAM_data:0846 ! Chemical formula - -! Many subtypes of the individual descriptors below (not included here) cover all types of protein properties. +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD +created_in: "beta12orEarlier" +def: "Symbol of a gene from the Mouse Genome Database." [http://edamontology.org] +regex: "MGI:[0-9]+" +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1201 -name: QSAR descriptor (constitutional) -namespace: data +id: EDAM_data:1793 +name: Gene name (Bacillus subtilis) +subset: bioinformatics subset: data -def: "A QSAR constitutional descriptor." [http://edamontology.org] -synonym: "QSAR constitutional descriptor" EXACT [http://edamontology.org] -is_a: EDAM_data:0847 ! QSAR descriptor - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG +created_in: "beta12orEarlier" +def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1202 -name: QSAR descriptor (electronic) -namespace: data +id: EDAM_data:1794 +name: Gene ID (PlasmoDB) +subset: bioinformatics subset: data -def: "A QSAR electronic descriptor." [http://edamontology.org] -synonym: "QSAR electronic descriptor" EXACT [http://edamontology.org] -is_a: EDAM_data:0847 ! QSAR descriptor - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB +created_in: "beta12orEarlier" +def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1203 -name: QSAR descriptor (geometrical) -namespace: data +id: EDAM_data:1795 +name: Gene ID (EcoGene) +subset: bioinformatics subset: data -def: "A QSAR geometrical descriptor." [http://edamontology.org] -synonym: "QSAR geometrical descriptor" EXACT [http://edamontology.org] -is_a: EDAM_data:0847 ! QSAR descriptor - +subset: edam +subset: identifiers +synonym: "EcoGene Accession" EXACT [] +synonym: "EcoGene ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a gene from EcoGene Database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1204 -name: QSAR descriptor (topological) -namespace: data +id: EDAM_data:1796 +name: Gene ID (FlyBase) +subset: bioinformatics subset: data -def: "A QSAR topological descriptor." [http://edamontology.org] -synonym: "QSAR topological descriptor" EXACT [http://edamontology.org] -is_a: EDAM_data:0847 ! QSAR descriptor - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB +xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase +created_in: "beta12orEarlier" +def: "Gene identifier from FlyBase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1205 -name: QSAR descriptor (molecular) -namespace: data +id: EDAM_data:1797 +name: Gene ID (GeneDB Glossina morsitans) +subset: bioinformatics subset: data -def: "A QSAR molecular descriptor." [http://edamontology.org] -synonym: "QSAR molecular descriptor" EXACT [http://edamontology.org] -is_a: EDAM_data:0847 ! QSAR descriptor +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans +created_in: "beta12orEarlier" +def: "Gene identifier from Glossina morsitans GeneDB database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM_data:0848 -name: Raw sequence -namespace: data +id: EDAM_data:1798 +name: Gene ID (GeneDB Leishmania major) +subset: bioinformatics subset: data -def: "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] -comment: Non-sequence characters may be used for example for gaps and translation stop. -is_a: EDAM_data:2044 ! Sequence - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor +created_in: "beta12orEarlier" +def: "Gene identifier from Leishmania major GeneDB database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM_data:2201 -name: Sequence record full -namespace: data +id: EDAM_data:1799 +name: Gene ID (GeneDB Plasmodium falciparum) +subset: bioinformatics subset: data -def: "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] -xref: SO:2000061 -is_a: EDAM_data:0849 ! Sequence record - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum +created_in: "beta12orEarlier" +def: "Gene identifier from Plasmodium falciparum GeneDB database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM_data:2888 -name: Sequence record full (protein) -namespace: data +id: EDAM_data:1800 +name: Gene ID (GeneDB Schizosaccharomyces pombe) +subset: bioinformatics subset: data -def: "A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] -xref: SO:2000061 -is_a: EDAM_data:2201 ! Sequence record full -is_a: EDAM_data:2886 ! Sequence record (protein) +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe +created_in: "beta12orEarlier" +def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM_data:2889 -name: Sequence record full (nucleic acid) -namespace: data +id: EDAM_data:1801 +name: Gene ID (GeneDB Trypanosoma brucei) +subset: bioinformatics subset: data -def: "A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] -xref: SO:2000061 -is_a: EDAM_data:2201 ! Sequence record full -is_a: EDAM_data:2887 ! Sequence record (nucleic acid) +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei +created_in: "beta12orEarlier" +def: "Gene identifier from Trypanosoma brucei GeneDB database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM_data:0849 -name: Sequence record -namespace: data +id: EDAM_data:1802 +name: Gene ID (Gramene) +subset: bioinformatics subset: data -! alt_id: EDAM_data:1220 -! alt_id: EDAM_data:1224 -! alt_id: EDAM_data:1225 -! alt_id: EDAM_data:1226 -! alt_id: EDAM_data:1227 -! alt_id: EDAM_data:1229 -! alt_id: EDAM_data:1230 -! alt_id: EDAM_data:1231 -! alt_id: EDAM_data:1232 -def: "A molecular sequence and associated metadata." [http://edamontology.org] -is_a: EDAM_data:2044 ! Sequence - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE +xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene +created_in: "beta12orEarlier" +def: "Gene identifier from Gramene database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:2886 -name: Sequence record (protein) -namespace: data +id: EDAM_data:1803 +name: Gene ID (Virginia microbial) +subset: bioinformatics subset: data -! alt_id: EDAM_data:1222 -def: "A protein sequence and associated metadata." [http://edamontology.org] -synonym: "Protein sequence record" EXACT [http://edamontology.org] -is_a: EDAM_data:0849 ! Sequence record -is_a: EDAM_data:2976 ! Protein sequence +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD +xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD +created_in: "beta12orEarlier" +def: "Gene identifier from Virginia Bioinformatics Institute microbial database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:2887 -name: Sequence record (nucleic acid) -namespace: data +id: EDAM_data:1804 +name: Gene ID (SGN) +subset: bioinformatics subset: data -! alt_id: EDAM_data:1221 -def: "A nucleic acid sequence and associated metadata." [http://edamontology.org] -synonym: "Nucleic acid sequence record" EXACT [http://edamontology.org] -synonym: "Nucleotide sequence record" EXACT [http://edamontology.org] -is_a: EDAM_data:0849 ! Sequence record -is_a: EDAM_data:2977 ! Nucleic acid sequence - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN +created_in: "beta12orEarlier" +def: "Gene identifier from Sol Genomics Network." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:0850 -name: Sequence set -namespace: data +id: EDAM_data:1805 +name: Gene ID (WormBase) +subset: bioinformatics subset: data -def: "A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method." [http://edamontology.org] -comment: This concept may be used for arbitrary sequence sets and associated data arising from processing. -synonym: "sequence_collection" EXACT [SO:0001260] -is_a: EDAM_data:2955 ! Sequence report - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB +xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase +created_in: "beta12orEarlier" +def: "Gene identifier used by WormBase database." [http://edamontology.org] +regex: "WBGene[0-9]{8}" +namespace: identifier +is_a: EDAM_data:2113 ! WormBase identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:2974 -name: Raw sequence (protein) -namespace: data +id: EDAM_data:1806 +name: Gene synonym +subset: bioinformatics subset: data -def: "A raw protein sequence (string of characters)." [http://edamontology.org] -is_a: EDAM_data:0848 ! Raw sequence -is_a: EDAM_data:2976 ! Protein sequence +subset: edam +subset: identifiers +synonym: "Gene name synonym" EXACT [] +created_in: "beta12orEarlier" +def: "Any name (other than the recommended one) for a gene." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:2975 -name: Raw sequence (nucleic acid) -namespace: data +id: EDAM_data:1807 +name: ORF name +subset: bioinformatics subset: data -def: "A raw nucleic acid sequence." [http://edamontology.org] -is_a: EDAM_data:0848 ! Raw sequence -is_a: EDAM_data:2977 ! Nucleic acid sequence - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of an open reading frame attributed by a sequencing project." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2795 ! ORF identifier [Term] -id: EDAM_data:2046 -name: Sequence record lite (nucleic acid) -namespace: data +id: EDAM_data:1852 +name: Sequence assembly component +subset: bioinformatics subset: data -def: "A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] -is_a: EDAM_data:2043 ! Sequence record lite -is_a: EDAM_data:2887 ! Sequence record (nucleic acid) +subset: edam +created_in: "beta12orEarlier" +def: "A component of a larger sequence assembly." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0925 ! Sequence assembly [Term] -id: EDAM_data:2047 -name: Sequence record lite (protein) -namespace: data +id: EDAM_data:1853 +name: Chromosome annotation (aberration) +subset: bioinformatics subset: data -def: "A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] -is_a: EDAM_data:2043 ! Sequence record lite -is_a: EDAM_data:2886 ! Sequence record (protein) +subset: edam +created_in: "beta12orEarlier" +def: "A report on a chromosome aberration such as abnormalities in chromosome structure." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0919 ! Gene annotation (chromosome) [Term] -id: EDAM_data:2043 -name: Sequence record lite -namespace: data +id: EDAM_data:1855 +name: Clone ID +subset: bioinformatics subset: data -! alt_id: EDAM_data:1223 -def: "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] -is_a: EDAM_data:0849 ! Sequence record - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a clone (cloned molecular sequence) from a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2769 ! Transcript ID [Term] -id: EDAM_data:2173 -name: Sequence set (stream) -namespace: data +id: EDAM_data:1856 +name: PDB insertion code +subset: bioinformatics subset: data -def: "A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing." [http://edamontology.org] -comment: This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0850 ! Sequence set +subset: edam +xref: PDBML:pdbx_PDB_ins_code +xref: WHATIF: insertion_code +created_in: "beta12orEarlier" +def: "An insertion code (part of the residue number) for an amino acid residue from a PDB file." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1016 ! Sequence position [Term] -id: EDAM_data:2245 -name: Sequence set (bootstrapped) -namespace: data +id: EDAM_data:1857 +name: Atomic occupancy +comment: The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. +subset: bioinformatics subset: data -def: "A collection of sequences output from a bootstrapping (resampling) procedure." [http://edamontology.org] -comment: Bootstrapping is often performed in phylogenetic analysis. -is_a: EDAM_data:0850 ! Sequence set - +subset: edam +xref: WHATIF: PDBx_occupancy +created_in: "beta12orEarlier" +def: "The fraction of an atom type present at a site in a molecular structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1917 ! Atomic property [Term] -id: EDAM_data:1233 -name: Sequence set (protein) -namespace: data +id: EDAM_data:1858 +name: Isotropic B factor +subset: bioinformatics subset: data -def: "Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] -is_a: EDAM_data:0850 ! Sequence set - +subset: edam +xref: WHATIF: PDBx_B_iso_or_equiv +created_in: "beta12orEarlier" +def: "Isotropic B factor (atomic displacement parameter) for an atom from a PDB file." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1917 ! Atomic property [Term] -id: EDAM_data:1234 -name: Sequence set (nucleic acid) -namespace: data +id: EDAM_data:1859 +name: Deletion map +comment: A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. +subset: bioinformatics subset: data -def: "Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] -is_a: EDAM_data:0850 ! Sequence set -is_a: EDAM_data:2977 ! Nucleic acid sequence - +subset: edam +synonym: "Deletion-based cytogenetic map" EXACT [] +created_in: "beta12orEarlier" +def: "A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1283 ! Cytogenetic map [Term] -id: EDAM_data:1235 -name: Sequence cluster -namespace: data +id: EDAM_data:1860 +name: QTL map +subset: bioinformatics subset: data -def: "A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information." [http://edamontology.org] -comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information. -is_a: EDAM_data:0850 ! Sequence set -relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification -relationship: has_topic EDAM_topic:0724 ! Protein families - +subset: edam +synonym: "Quantitative trait locus map" EXACT [] +created_in: "beta12orEarlier" +def: "A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1278 ! Genetic map [Term] -id: EDAM_data:1236 -name: Psiblast checkpoint file -namespace: data +id: EDAM_data:1863 +name: Haplotype map +subset: bioinformatics subset: data -def: "A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration." [http://edamontology.org] -comment: A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0850 ! Sequence set +subset: edam +xref: Moby:Haplotyping_Study_obj +created_in: "beta12orEarlier" +def: "A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1278 ! Genetic map [Term] -id: EDAM_data:1237 -name: HMMER synthetic sequences set -namespace: data +id: EDAM_data:1864 +name: Map set +subset: bioinformatics subset: data -def: "Sequences generated by HMMER package in FASTA-style format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0850 ! Sequence set - +subset: edam +xref: Moby:GCP_CorrelatedLinkageMapSet +xref: Moby:GCP_CorrelatedMapSet +created_in: "beta12orEarlier" +def: "Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2019 ! Map attribute [Term] -id: EDAM_data:1238 -name: Proteolytic digest -namespace: data +id: EDAM_data:1865 +name: Map feature +comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. +subset: bioinformatics subset: data -def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses." [http://edamontology.org] -is_a: EDAM_data:1233 ! Sequence set (protein) -relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification +subset: edam +xref: Moby:MapFeature +created_in: "beta12orEarlier" +def: "A feature which may mapped (positioned) on a genetic or other type of map." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1255 ! Feature record +consider: EDAM_data:1276 ! Nucleic acid features +consider: EDAM_data:2019 ! Map attribute [Term] -id: EDAM_data:1766 -name: CATH domain sequences (ATOM) -namespace: data +id: EDAM_data:1866 +name: Map type +comment: Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. +subset: bioinformatics subset: data -def: "FASTA sequence database for all CATH domains (based on PDB ATOM records)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0850 ! Sequence set - +subset: edam +created_in: "beta12orEarlier" +def: "A designation of the type of map (genetic map, physical map, sequence map etc) or map set." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2019 ! Map attribute +is_a: EDAM_data:2100 ! Type [Term] -id: EDAM_data:1767 -name: CATH domain sequences (COMBS) -namespace: data +id: EDAM_data:1867 +name: Protein fold name +subset: bioinformatics subset: data -def: "FASTA sequence database for all CATH domains (based on COMBS sequence data)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0850 ! Sequence set +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a protein fold." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:1239 -name: Restriction digest -namespace: data +id: EDAM_data:1868 +name: Taxon +comment: For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. +subset: bioinformatics subset: data -def: "Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease." [http://edamontology.org] -xref: SO:0000412 -is_a: EDAM_data:1234 ! Sequence set (nucleic acid) - +subset: edam +subset: identifiers +synonym: "Taxonomic rank" EXACT [] +synonym: "Taxonomy rank" EXACT [] +xref: Moby:BriefTaxonConcept +xref: Moby:PotentialTaxon +created_in: "beta12orEarlier" +def: "The name of a group of organisms belonging to the same taxonomic rank." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2909 ! Organism name [Term] -id: EDAM_data:2874 -name: Sequence set (polymorphic) -namespace: data +id: EDAM_data:1869 +name: Organism identifier +subset: bioinformatics subset: data -def: "A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1234 ! Sequence set (nucleic acid) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of a (group of) organisms." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:2530 ! Organism annotation [Term] -id: EDAM_data:1240 -name: PCR primers -namespace: data +id: EDAM_data:1870 +name: Genus name +subset: bioinformatics subset: data -def: "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." [http://edamontology.org] -is_a: EDAM_data:1234 ! Sequence set (nucleic acid) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a genus of organism." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM_data:1241 -name: vectorstrip cloning vector definition file -namespace: data +id: EDAM_data:1872 +name: Taxonomic classification +comment: Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. +subset: bioinformatics subset: data -def: "File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0850 ! Sequence set +subset: edam +subset: identifiers +synonym: "Taxonomic information" EXACT [] +synonym: "Taxonomic name" EXACT [] +xref: Moby:GCP_Taxon +xref: Moby:iANT_organism-xml +xref: Moby:TaxonName +xref: Moby:TaxonScientificName +xref: Moby:TaxonTCS +created_in: "beta12orEarlier" +def: "The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2909 ! Organism name [Term] -id: EDAM_data:1242 -name: Primer3 internal oligo mishybridizing library -namespace: data +id: EDAM_data:1873 +name: iHOP organism ID +subset: bioinformatics subset: data -def: "A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0850 ! Sequence set - +subset: edam +subset: identifiers +xref: Moby_namespace:iHOPorganism +created_in: "beta12orEarlier" +def: "A unique identifier for an organism used in the iHOP database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2908 ! Organism accession [Term] -id: EDAM_data:1243 -name: Primer3 mispriming library file -namespace: data +id: EDAM_data:1874 +name: Genbank common name +subset: bioinformatics subset: data -def: "A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0850 ! Sequence set +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Common name for an organism as used in the GenBank database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2909 ! Organism name [Term] -id: EDAM_data:1244 -name: primersearch primer pairs sequence record -namespace: data +id: EDAM_data:1875 +name: NCBI taxon +subset: bioinformatics subset: data -def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0850 ! Sequence set +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a taxon from the NCBI taxonomy database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM_data:1245 -name: Sequence cluster (protein) -namespace: data +id: EDAM_data:1877 +name: Synonym +subset: bioinformatics subset: data -def: "A cluster of protein sequences." [http://edamontology.org] -comment: The sequences are typically related, for example a family of sequences. -synonym: "Protein sequence cluster" EXACT [http://edamontology.org] -is_a: EDAM_data:1233 ! Sequence set (protein) -is_a: EDAM_data:1235 ! Sequence cluster - +subset: edam +synonym: "Alternative name" EXACT [] +created_in: "beta12orEarlier" +def: "An alternative for a word." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0968 ! Keyword [Term] -id: EDAM_data:1246 -name: Sequence cluster (nucleic acid) -namespace: data +id: EDAM_data:1878 +name: Misspelling +subset: bioinformatics subset: data -def: "A cluster of nucleotide sequences." [http://edamontology.org] -comment: The sequences are typically related, for example a family of sequences. -synonym: "Nucleotide sequence cluster" EXACT [http://edamontology.org] -is_a: EDAM_data:1234 ! Sequence set (nucleic acid) -is_a: EDAM_data:1235 ! Sequence cluster - +subset: edam +created_in: "beta12orEarlier" +def: "A common misspelling of a word." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0968 ! Keyword [Term] -id: EDAM_data:1764 -name: CATH representative domain sequences (ATOM) -namespace: data +id: EDAM_data:1879 +name: Acronym +subset: bioinformatics subset: data -def: "FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1235 ! Sequence cluster - +subset: edam +created_in: "beta12orEarlier" +def: "An abbreviation of a phrase or word." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0968 ! Keyword [Term] -id: EDAM_data:1765 -name: CATH representative domain sequences (COMBS) -namespace: data +id: EDAM_data:1880 +name: Misnomer +subset: bioinformatics subset: data -def: "FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1235 ! Sequence cluster - +subset: edam +created_in: "beta12orEarlier" +def: "A term which is likely to be misleading of its meaning." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0968 ! Keyword [Term] -id: EDAM_data:2198 -name: Gene cluster -namespace: data +id: EDAM_data:1881 +name: Author ID +subset: bioinformatics subset: data -def: "A cluster of similar genes." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1246 ! Sequence cluster (nucleic acid) +subset: edam +subset: identifiers +xref: Moby:Author +created_in: "beta12orEarlier" +def: "Information on the authors of a published work." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2118 ! Person identifier [Term] -id: EDAM_data:1253 -name: Sequence information report -namespace: data +id: EDAM_data:1882 +name: DragonDB author identifier +subset: bioinformatics subset: data -def: "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2043 ! Sequence record lite -consider: EDAM_data:0855 ! Sequence metadata +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier representing an author in the DragonDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1881 ! Author ID [Term] -id: EDAM_data:1254 -name: Sequence property -namespace: data +id: EDAM_data:1883 +name: Annotated URI +subset: bioinformatics subset: data -def: "An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." [http://edamontology.org] -synonym: "Sequence properties report" EXACT [http://edamontology.org] -is_a: EDAM_data:2955 ! Sequence report - +subset: edam +xref: Moby:DescribedLink +created_in: "beta12orEarlier" +def: "A URI along with annotation describing the data found at the address." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2093 ! Data reference +is_a: EDAM_data:2337 ! Metadata [Term] -id: EDAM_data:1255 -name: Feature record -namespace: data +id: EDAM_data:1884 +name: UniProt keywords +subset: bioinformatics subset: data -! alt_id: EDAM_data:1271 -! alt_id: EDAM_data:1275 -def: "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence." [http://edamontology.org] -comment: This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. -synonym: "Sequence features" EXACT [http://edamontology.org] -synonym: "Sequence features report" EXACT [http://edamontology.org] -synonym: "General sequence features" EXACT [http://edamontology.org] -synonym: "sequence_feature" RELATED [SO:0000110] -is_a: EDAM_data:2955 ! Sequence report - +subset: edam +created_in: "beta12orEarlier" +def: "A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0582 ! Ontology [Term] -id: EDAM_data:2914 -name: Sequence features metadata -namespace: data +id: EDAM_data:1885 +name: Gene ID (GeneFarm) +subset: bioinformatics subset: data -def: "Metadata on sequence features." [http://edamontology.org] -is_a: EDAM_data:0855 ! Sequence metadata - +subset: edam +subset: identifiers +xref: Moby_namespace:GENEFARM_GeneID +created_in: "beta12orEarlier" +def: "Identifier of a gene from the GeneFarm database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1020 -name: Sequence feature key -namespace: data +id: EDAM_data:1886 +name: Blattner number +subset: bioinformatics subset: data -def: "The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key." [http://edamontology.org] -comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. -synonym: "Sequence feature type" EXACT [http://edamontology.org] -synonym: "Sequence feature method" EXACT [http://edamontology.org] -is_a: EDAM_data:2914 ! Sequence features metadata - +subset: edam +subset: identifiers +xref: Moby_namespace:Blattner_number +created_in: "beta12orEarlier" +def: "The blattner identifier for a gene." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1021 -name: Sequence feature qualifier -namespace: data +id: EDAM_data:1887 +name: Gene ID (MIPS Maize) +subset: bioinformatics subset: data -def: "Typically one of the EMBL or Swiss-Prot feature qualifiers." [http://edamontology.org] -comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location. -is_a: EDAM_data:2914 ! Sequence features metadata +subset: edam +subset: identifiers +synonym: "MIPS genetic element identifier (Maize)" EXACT [] +xref: Moby_namespace:MIPS_GE_Maize +created_in: "beta12orEarlier" +def: "Identifier for genetic elements in MIPS Maize database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2285 ! Gene ID (MIPS) [Term] -id: EDAM_data:1022 -name: Sequence feature label -namespace: data +id: EDAM_data:1888 +name: Gene ID (MIPS Medicago) +subset: bioinformatics subset: data -def: "Typically an EMBL or Swiss-Prot feature label." [http://edamontology.org] -comment: A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. -synonym: "Sequence feature name" EXACT [http://edamontology.org] -is_a: EDAM_data:2914 ! Sequence features metadata +subset: edam +subset: identifiers +synonym: "MIPS genetic element identifier (Medicago)" EXACT [] +xref: Moby_namespace:MIPS_GE_Medicago +created_in: "beta12orEarlier" +def: "Identifier for genetic elements in MIPS Medicago database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2285 ! Gene ID (MIPS) [Term] -id: EDAM_data:1278 -name: Genetic map -namespace: data +id: EDAM_data:1889 +name: Gene name (DragonDB) +subset: bioinformatics subset: data -def: "A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies." [http://edamontology.org] -comment: A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. -synonym: "Linkage map" EXACT [http://edamontology.org] -xref: Moby:GeneticMap -is_a: EDAM_data:1274 ! Map -relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage +subset: edam +subset: identifiers +xref: Moby_namespace:DragonDB_Gene +created_in: "beta12orEarlier" +def: "The name of an Antirrhinum Gene from the DragonDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1283 -name: Cytogenetic map -namespace: data +id: EDAM_data:1890 +name: Gene name (Arabidopsis) +subset: bioinformatics subset: data -! alt_id: EDAM_data:1287 -def: "A map showing banding patterns derived from direct observation of a stained chromosome." [http://edamontology.org] -comment: This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. -synonym: "Cytologic map" EXACT [http://edamontology.org] -synonym: "Cytogenic map" EXACT [http://edamontology.org] -synonym: "Chromosome map" EXACT [http://edamontology.org] -is_a: EDAM_data:1280 ! Physical map - +subset: edam +subset: identifiers +xref: Moby_namespace:ArabidopsisGeneSymbol +created_in: "beta12orEarlier" +def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:2870 -name: Radiation hybrid map -namespace: data +id: EDAM_data:1891 +name: iHOP symbol +subset: bioinformatics subset: data -def: "A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome." [http://edamontology.org] -comment: The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. -synonym: "RH map" EXACT [http://edamontology.org] -is_a: EDAM_data:1280 ! Physical map +subset: edam +subset: identifiers +xref: Moby_namespace:iHOPsymbol +created_in: "beta12orEarlier" +def: "A unique identifier of a protein or gene used in the iHOP database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2109 ! Identifier (hybrid) +is_a: EDAM_data:2295 ! Gene ID +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1279 -name: Sequence map -namespace: data +id: EDAM_data:1892 +name: Gene name (GeneFarm) +subset: bioinformatics subset: data -def: "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs." [http://edamontology.org] -comment: A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. -is_a: EDAM_data:1280 ! Physical map +subset: edam +subset: identifiers +synonym: "GeneFarm gene ID" EXACT [] +xref: Moby_namespace:GENEFARM_GeneName +created_in: "beta12orEarlier" +def: "Name of a gene from the GeneFarm database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1280 -name: Physical map -namespace: data +id: EDAM_data:1893 +name: Locus ID +subset: bioinformatics subset: data -def: "A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them." [http://edamontology.org] -comment: Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. -is_a: EDAM_data:1274 ! Map - +subset: edam +subset: identifiers +synonym: "Locus identifier" EXACT [] +synonym: "Locus name" EXACT [] +created_in: "beta12orEarlier" +def: "A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:2012 ! Map position [Term] -id: EDAM_data:1284 -name: DNA transduction map -namespace: data +id: EDAM_data:1895 +name: Locus ID (AGI) +subset: bioinformatics subset: data -def: "A gene map showing distances between loci based on relative cotransduction frequencies." [http://edamontology.org] -is_a: EDAM_data:1278 ! Genetic map +subset: edam +subset: identifiers +synonym: "AGI ID" EXACT [] +synonym: "AGI identifier" EXACT [] +synonym: "AGI locus code" EXACT [] +synonym: "Arabidopsis gene loci number" EXACT [] +xref: http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode +created_in: "beta12orEarlier" +def: "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" [http://edamontology.org] +regex: "AT[1-5]G[0-9]{5}" +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID +[Term] +id: EDAM_data:1896 +name: Locus ID (ASPGD) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD +xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID +created_in: "beta12orEarlier" +def: "Identifier for loci from ASPGD (Aspergillus Genome Database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1860 -name: QTL map -namespace: data +id: EDAM_data:1897 +name: Locus ID (MGG) +subset: bioinformatics subset: data -def: "A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers." [http://edamontology.org] -synonym: "Quantitative trait locus map" EXACT [http://edamontology.org] -is_a: EDAM_data:1278 ! Genetic map +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG +created_in: "beta12orEarlier" +def: "Identifier for loci from Magnaporthe grisea Database at the Broad Institute." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1859 -name: Deletion map -namespace: data +id: EDAM_data:1898 +name: Locus ID (CGD) +subset: bioinformatics subset: data -def: "A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type." [http://edamontology.org] -comment: A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. -synonym: "Deletion-based cytogenetic map" EXACT [http://edamontology.org] -is_a: EDAM_data:1283 ! Cytogenetic map +subset: edam +subset: identifiers +synonym: "CGD locus identifier" EXACT [] +synonym: "CGDID" EXACT [] +xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGD +xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGDID +created_in: "beta12orEarlier" +def: "Identifier for loci from CGD (Candida Genome Database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1863 -name: Haplotype map -namespace: data +id: EDAM_data:1899 +name: Locus ID (CMR) +subset: bioinformatics subset: data -def: "A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation." [http://edamontology.org] -xref: Moby:Haplotyping_Study_obj -is_a: EDAM_data:1278 ! Genetic map - +subset: edam +subset: identifiers +xref: http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR +xref: http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR +created_in: "beta12orEarlier" +def: "Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1285 -name: Gene map -namespace: data +id: EDAM_data:1900 +name: NCBI locus tag +subset: bioinformatics subset: data -def: "Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene." [http://edamontology.org] -is_a: EDAM_data:1279 ! Sequence map - +subset: edam +subset: identifiers +synonym: "Locus ID (NCBI)" EXACT [] +xref: http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag +xref: Moby_namespace:LocusID +created_in: "beta12orEarlier" +def: "Identifier for loci from NCBI database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1286 -name: Plasmid map -namespace: data +id: EDAM_data:1901 +name: Locus ID (SGD) +subset: bioinformatics subset: data -def: "Sequence map of a plasmid (circular DNA)." [http://edamontology.org] -is_a: EDAM_data:1279 ! Sequence map +subset: edam +subset: identifiers +synonym: "SGDID" EXACT [] +xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGD +xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGDID +created_in: "beta12orEarlier" +def: "Identifier for loci from SGD (Saccharomyces Genome Database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID +is_a: EDAM_data:2632 ! SGD ID [Term] -id: EDAM_data:1288 -name: Genome map -namespace: data +id: EDAM_data:1902 +name: Locus ID (MMP) +subset: bioinformatics subset: data -def: "Sequence map of a whole genome." [http://edamontology.org] -is_a: EDAM_data:1279 ! Sequence map - +subset: edam +subset: identifiers +xref: Moby_namespace:MMP_Locus +created_in: "beta12orEarlier" +def: "Identifier of loci from Maize Mapping Project." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1865 -name: Map feature -namespace: data +id: EDAM_data:1903 +name: Locus ID (DictyBase) +subset: bioinformatics subset: data -def: "A feature which may mapped (positioned) on a genetic or other type of map." [http://edamontology.org] -comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. -xref: Moby:MapFeature -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1255 ! Feature record -consider: EDAM_data:2019 ! Map attribute -consider: EDAM_data:1276 ! Nucleic acid features +subset: edam +subset: identifiers +xref: Moby_namespace:DDB_gene +created_in: "beta12orEarlier" +def: "Identifier of locus from DictyBase (Dictyostelium discoideum)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1257 -name: Sequence property (protein) -namespace: data +id: EDAM_data:1904 +name: Locus ID (EntrezGene) +subset: bioinformatics subset: data -def: "A report of general sequence properties derived from protein sequence data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0897 ! Protein property +subset: edam +subset: identifiers +xref: Moby_namespace:EntrezGene_EntrezGeneID +xref: Moby_namespace:EntrezGene_ID +created_in: "beta12orEarlier" +def: "Identifier of a locus from EntrezGene database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1258 -name: Sequence property (nucleic acid) -namespace: data +id: EDAM_data:1905 +name: Locus ID (MaizeGDB) +subset: bioinformatics subset: data -def: "A report of general sequence properties derived from nucleotide sequence data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0912 ! Nucleic acid property - +subset: edam +subset: identifiers +xref: Moby_namespace:MaizeGDB_Locus +created_in: "beta12orEarlier" +def: "Identifier of locus from MaizeGDB (Maize genome database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1259 -name: Sequence complexity -namespace: data +id: EDAM_data:1906 +name: Quantitative trait locus +comment: A QTL sometimes but does not necessarily correspond to a gene. +subset: bioinformatics subset: data -def: "A report on sequence complexity, for example low-complexity or repeat regions in sequences." [http://edamontology.org] -synonym: "Sequence property (complexity)" EXACT [http://edamontology.org] -is_a: EDAM_data:1254 ! Sequence property - +subset: edam +synonym: "QTL" EXACT [] +xref: Moby:SO_QTL +created_in: "beta12orEarlier" +def: "A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2012 ! Map position [Term] -id: EDAM_data:1260 -name: Sequence ambiguity -namespace: data +id: EDAM_data:1907 +name: Gene ID (KOME) +subset: bioinformatics subset: data -def: "A report on ambiguity in molecular sequence(s)." [http://edamontology.org] -synonym: "Sequence property (ambiguity)" EXACT [http://edamontology.org] -is_a: EDAM_data:1254 ! Sequence property - +subset: edam +subset: identifiers +xref: Moby_namespace:GeneId +created_in: "beta12orEarlier" +def: "Identifier of a gene from the KOME database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1261 -name: Sequence composition -namespace: data +id: EDAM_data:1908 +name: Locus ID (Tropgene) +subset: bioinformatics subset: data -def: "A report (typically a table) on character or word composition / frequency of a molecular sequence(s)." [http://edamontology.org] -synonym: "Sequence property (composition)" EXACT [http://edamontology.org] -is_a: EDAM_data:1254 ! Sequence property - +subset: edam +subset: identifiers +xref: Moby:Tropgene_locus +created_in: "beta12orEarlier" +def: "Identifier of a locus from the Tropgene database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:3119 !{since=beta13} -name: Sequence features (compositionally-biased regions) -namespace: data +id: EDAM_data:1916 +name: Alignment +subset: bioinformatics subset: data -def: "A report of regions in a molecular sequence that are biased to certain characters." [http://edamontology.org] -is_a: EDAM_data:1261 ! Sequence composition - - - +subset: edam +created_in: "beta12orEarlier" +def: "An alignment of molecular sequences, structures or profiles derived from them." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:3085 !{since=beta13} -name: Protein sequence composition -namespace: data +id: EDAM_data:1917 +name: Atomic property +subset: bioinformatics subset: data -def: "A report (typically a table) on character or word composition / frequency of protein sequence(s)." [http://edamontology.org] -synonym: "Sequence property (protein composition)" EXACT [http://edamontology.org] -is_a: EDAM_data:1261 ! Sequence composition +subset: edam +synonym: "General atomic property" EXACT [] +created_in: "beta12orEarlier" +def: "Data for an atom (in a molecular structure)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2087 ! Molecular property [Term] -id: EDAM_data:3086 !{since=beta13} -name: Nucleic acid sequence composition -namespace: data +id: EDAM_data:2007 +name: UniProt keyword +subset: bioinformatics subset: data -def: "A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s)." [http://edamontology.org] -synonym: "Sequence property (nucleic acid composition)" EXACT [http://edamontology.org] -is_a: EDAM_data:1261 ! Sequence composition -is_a: EDAM_data:0912 ! Nucleic acid property - - +subset: edam +xref: http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW +xref: Moby_namespace:SP_KW +created_in: "beta12orEarlier" +def: "A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0968 ! Keyword [Term] -id: EDAM_data:1262 -name: Peptide molecular weight hits -namespace: data +id: EDAM_data:2009 +name: Ordered locus name +subset: bioinformatics subset: data -def: "A report on peptide fragments of certain molecular weight(s) in one or more protein sequences." [http://edamontology.org] -is_a: EDAM_data:1233 ! Sequence set (protein) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1263 -name: Sequence composition (base position variability) -namespace: data +id: EDAM_data:2012 +name: Map position +comment: This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. +subset: bioinformatics subset: data -def: "Report on or plot of third base position variability in a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_data:3086 ! Nucleic acid sequence composition - +subset: edam +synonym: "Locus" EXACT [] +xref: Moby:GCP_MapInterval +xref: Moby:GCP_MapPoint +xref: Moby:GCP_MapPosition +xref: Moby:GenePosition +xref: Moby:HitPosition +xref: Moby:Locus +xref: Moby:MapPosition +xref: Moby:Position +xref: PDBML:_atom_site.id +created_in: "beta12orEarlier" +def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1016 ! Sequence position +is_a: EDAM_data:1017 ! Sequence range +is_a: EDAM_data:2019 ! Map attribute [Term] -id: EDAM_data:2157 -name: Word composition -namespace: data +id: EDAM_data:2016 +name: Amino acid property +subset: bioinformatics subset: data -def: "Word composition data for a molecular sequence." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1268 ! Amino acid word frequencies -consider: EDAM_data:1266 ! Sequence composition (base words) +subset: edam +synonym: "Amino acid data" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2087 ! Molecular property [Term] -id: EDAM_data:1264 -name: Sequence composition table -namespace: data +id: EDAM_data:2018 +name: Annotation +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "A table of character or word composition / frequency of a molecular sequence." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1261 ! Sequence composition +subset: edam +created_in: "beta12orEarlier" +def: "A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2048 ! Report [Term] -id: EDAM_data:2166 -name: Sequence composition plot -namespace: data +id: EDAM_data:2019 +name: Map attribute +subset: bioinformatics subset: data -def: "A plot of character or word composition / frequency of a molecular sequence." [http://edamontology.org] -is_a: EDAM_data:1261 ! Sequence composition +subset: edam +created_in: "beta12orEarlier" +def: "An attribute of a molecular map (genetic or physical)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata +relationship: has_topic EDAM_topic:0102 ! Mapping [Term] -id: EDAM_data:1265 -name: Sequence composition (base frequencies) -namespace: data +id: EDAM_data:2022 +name: Vienna RNA structural data +subset: bioinformatics subset: data -def: "A table of base frequencies of a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_data:3086 ! Nucleic acid sequence composition - +subset: edam +created_in: "beta12orEarlier" +def: "Data used by the Vienna RNA analysis package." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:1267 -name: Amino acid frequencies -namespace: data +id: EDAM_data:2023 +name: Sequence mask parameter +subset: bioinformatics subset: data -def: "A table of amino acid frequencies of a protein sequence." [http://edamontology.org] -synonym: "Sequence composition (amino acid frequencies)" EXACT [http://edamontology.org] -is_a: EDAM_data:3085 ! Protein sequence composition - +subset: edam +created_in: "beta12orEarlier" +def: "Data used to replace (mask) characters in a molecular sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM_data:1266 -name: Sequence composition (base words) -namespace: data +id: EDAM_data:2024 +name: Enzyme kinetics data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "A table of word composition of a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_data:3086 ! Nucleic acid sequence composition - +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning chemical reaction(s) catalysed by enzyme(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2978 ! Reaction data [Term] -id: EDAM_data:1268 -name: Amino acid word frequencies -namespace: data +id: EDAM_data:2025 +name: Michaelis Menten plot +subset: bioinformatics subset: data -def: "A table of amino acid word composition of a protein sequence." [http://edamontology.org] -synonym: "Sequence composition (amino acid words)" EXACT [http://edamontology.org] -is_a: EDAM_data:3085 ! Protein sequence composition - - +subset: edam +created_in: "beta12orEarlier" +def: "A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] -id: EDAM_data:1269 -name: DAS sequence feature annotation -namespace: data +id: EDAM_data:2026 +name: Hanes Woolf plot +subset: bioinformatics subset: data -def: "Annotation of a molecular sequence in DAS format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1978 ! DASGFF - +subset: edam +created_in: "beta12orEarlier" +def: "A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] -id: EDAM_data:3002 -name: Sequence annotation track -namespace: data +id: EDAM_data:2028 +name: Experimental data +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics subset: data -def: "Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser." [http://edamontology.org] -synonym: "Annotation track" EXACT [http://edamontology.org] -synonym: "Genome track" EXACT [http://edamontology.org] -synonym: "Genomic track" EXACT [http://edamontology.org] -synonym: "Genome-browser track" EXACT [http://edamontology.org] -synonym: "Genome annotation track" EXACT [http://edamontology.org] -is_a: EDAM_data:1255 ! Feature record - +subset: edam +synonym: "Experimental measurement data" EXACT [] +created_in: "beta12orEarlier" +def: "Raw data from or annotation on laboratory experiments." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2531 ! Experiment annotation +consider: EDAM_data:3108 ! Experimental measurement [Term] -id: EDAM_data:1270 -name: Sequence feature table -namespace: data +id: EDAM_data:2041 +name: Genome version information +subset: bioinformatics subset: data -def: "Annotation of positional sequence features, organized into a standard feature table." [http://edamontology.org] -synonym: "Feature table" EXACT [http://edamontology.org] -is_a: EDAM_data:1255 ! Feature record - +subset: edam +created_in: "beta12orEarlier" +def: "Information on a genome version." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0953 ! Version information +is_a: EDAM_data:2711 ! Genome metadata [Term] -id: EDAM_data:1276 -name: Nucleic acid features -namespace: data +id: EDAM_data:2042 +name: Evidence +subset: bioinformatics subset: data -! alt_id: EDAM_data:1273 -def: "Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence)." [http://edamontology.org] -comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. -synonym: "Nucleic acid feature table" EXACT [http://edamontology.org] -synonym: "Feature table (nucleic acid)" EXACT [http://edamontology.org] -is_a: EDAM_data:2084 ! Nucleic acid report -is_a: EDAM_data:1255 ! Feature record - +subset: edam +created_in: "beta12orEarlier" +def: "Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:3139 !{since=beta13} -name: Nucleic acid features (STS) -namespace: data +id: EDAM_data:2043 +name: Sequence record lite +subset: bioinformatics subset: data -def: "A report on sequence tagged sites (STS) in nucleic acid sequences." [http://edamontology.org] -comment: Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. -is_a: EDAM_data:1276 ! Nucleic acid features - +subset: edam +created_in: "beta12orEarlier" +def: "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0849 ! Sequence record [Term] -id: EDAM_data:3122 !{since=beta13} -name: Nucleic acid features (difference and change) -namespace: data +id: EDAM_data:2044 +name: Sequence +comment: This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. +subset: bioinformatics subset: data -def: "A report on features in a nucleic acid sequence that indicate changes to or differences between sequences." [http://edamontology.org] -is_a: EDAM_data:1276 ! Nucleic acid features +subset: edam +synonym: "BioMolecularSequenceInformation" RELATED [] +synonym: "http://purl.bioontology.org/ontology/MSH/D008969" NARROW [] +created_in: "beta12orEarlier" +def: "One or more molecular sequences, possibly with associated annotation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM_data:3123 !{since=beta13} -name: Nucleic acid features (expression signal) -namespace: data +id: EDAM_data:2046 +name: Sequence record lite (nucleic acid) +subset: bioinformatics subset: data -def: "A report on regions within a nucleic acid sequence containing a signal that alters a biological function." [http://edamontology.org] -is_a: EDAM_data:1276 ! Nucleic acid features - +subset: edam +created_in: "beta12orEarlier" +def: "A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2043 ! Sequence record lite +is_a: EDAM_data:2887 ! Sequence record (nucleic acid) [Term] -id: EDAM_data:3125 !{since=beta13} -name: Nucleic acid features (binding) -namespace: data +id: EDAM_data:2047 +name: Sequence record lite (protein) +subset: bioinformatics subset: data -def: "A report on regions of a nucleic acid sequence that bind some other molecule." [http://edamontology.org] -comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). -is_a: EDAM_data:1276 ! Nucleic acid features - +subset: edam +created_in: "beta12orEarlier" +def: "A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2043 ! Sequence record lite +is_a: EDAM_data:2886 ! Sequence record (protein) [Term] -id: EDAM_data:3126 !{since=beta13} -name: Nucleic acid features (repeats) +id: EDAM_data:2048 +name: Report +comment: This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing. +subset: bioinformatics +subset: data +subset: edam +synonym: "Document" EXACT [] +synonym: "document" EXACT [] +synonym: "SIO:000148" RELATED [] +synonym: "Text" EXACT [] +created_in: "beta12orEarlier" +def: "A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself." [http://edamontology.org] namespace: data -subset: data -def: "A report on repetitive elements within a nucleic acid sequence." [http://edamontology.org] -comment: This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. -is_a: EDAM_data:1299 ! Sequence features (repeats) -is_a: EDAM_data:1276 ! Nucleic acid features - +is_a: EDAM_data:0006 ! Data [Term] -id: EDAM_data:3127 !{since=beta13} -name: Nucleic acid features (replication and recombination) -namespace: data +id: EDAM_data:2050 +name: Molecular property (general) +subset: bioinformatics subset: data -def: "A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination." [http://edamontology.org] -comment: This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. -is_a: EDAM_data:1276 ! Nucleic acid features +subset: edam +synonym: "General molecular property" EXACT [] +created_in: "beta12orEarlier" +def: "General data for a molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2087 ! Molecular property [Term] -id: EDAM_data:3128 !{since=beta13} -name: Nucleic acid features (structure) -namespace: data +id: EDAM_data:2053 +name: Structural data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures." [http://edamontology.org] -is_a: EDAM_data:1276 ! Nucleic acid features +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning molecular structural data." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0883 ! Structure +consider: EDAM_data:2085 ! Structure report [Term] -id: EDAM_data:3132 !{since=beta13} -name: Nucleic acid features (d-loop) -namespace: data +id: EDAM_data:2070 +name: Sequence motif (nucleic acid) +subset: bioinformatics subset: data -def: "A report on displacement loops in a mitochondrial DNA sequence." [http://edamontology.org] -comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. -is_a: EDAM_data:3128 ! Nucleic acid features (structure) +subset: edam +created_in: "beta12orEarlier" +def: "A nucleotide sequence motif." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1353 ! Sequence motif [Term] -id: EDAM_data:3133 !{since=beta13} -name: Nucleic acid features (stem loop) -namespace: data +id: EDAM_data:2071 +name: Sequence motif (protein) +subset: bioinformatics subset: data -def: "A report on stem loops in a DNA sequence." [http://edamontology.org] -comment: A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. -is_a: EDAM_data:3128 ! Nucleic acid features (structure) - +subset: edam +created_in: "beta12orEarlier" +def: "An amino acid sequence motif." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1353 ! Sequence motif [Term] -id: EDAM_data:2882 -name: DNA features -namespace: data +id: EDAM_data:2079 +name: Search parameter +subset: bioinformatics subset: data -def: "DNA sequence-specific feature annotation (not in a feature table)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1276 ! Nucleic acid features +subset: edam +created_in: "beta12orEarlier" +def: "Some simple value controlling a search operation, typically a search of a database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:2883 -name: Nucleic acid features (RNA features) -namespace: data +id: EDAM_data:2080 +name: Database hits +subset: bioinformatics subset: data -def: "Features concerning RNA or regions of DNA that encode an RNA molecule." [http://edamontology.org] -synonym: "RNA features" EXACT [http://edamontology.org] -is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) +subset: edam +created_in: "beta12orEarlier" +def: "A report of hits from searching a database of some type." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2093 ! Data reference [Term] -id: EDAM_data:3134 !{since=beta13} -name: Nucleic acid features (mRNA features) -namespace: data +id: EDAM_data:2081 +name: Secondary structure +subset: bioinformatics subset: data -def: "Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules." [http://edamontology.org] -comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). -synonym: "mRNA features" EXACT [http://edamontology.org] -is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) - +subset: edam +created_in: "beta12orEarlier" +def: "The secondary structure assignment (predicted or real) of a nucleic acid or protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:3137 !{since=beta13} -name: Nucleic acid features (non-coding RNA) -namespace: data +id: EDAM_data:2082 +name: Matrix +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "Features concerning non-coding or functional RNA molecules, including tRNA and rRNA." [http://edamontology.org] -synonym: "ncRNA features" EXACT [http://edamontology.org] -synonym: "Non-coding RNA features" EXACT [http://edamontology.org] -is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) +subset: edam +created_in: "beta12orEarlier" +def: "An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:3138 !{since=beta13} -name: Nucleic acid features (transcriptional) -namespace: data +id: EDAM_data:2083 +name: Alignment report +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "Features concerning transcription of DNA into RNA including the regulation of transcription." [http://edamontology.org] -comment: This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. -is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) - +subset: edam +created_in: "beta12orEarlier" +def: "An informative report about a molecular alignment of some type, including alignment-derived data or metadata." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_data:1277 -name: Protein features -namespace: data +id: EDAM_data:2084 +name: Nucleic acid report +subset: bioinformatics subset: data -! alt_id: EDAM_data:1272 -def: "Protein sequence-specific feature annotation (positional features of a protein sequence)." [http://edamontology.org] -comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. -synonym: "Feature table (protein)" EXACT [http://edamontology.org] -synonym: "Protein feature table" EXACT [http://edamontology.org] -is_a: EDAM_data:1255 ! Feature record -is_a: EDAM_data:0896 ! Protein report - +subset: edam +created_in: "beta12orEarlier" +def: "An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2529 ! Molecule report [Term] -id: EDAM_data:1256 -name: Sequence features (comparative) -namespace: data +id: EDAM_data:2085 +name: Structure report +subset: bioinformatics subset: data -def: "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -is_obsolete: true !{since=beta13} -consider: EDAM_data:1255 ! Feature record - +subset: edam +synonym: "Structure-derived report" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_data:1298 -name: Sequence features (motifs) -namespace: data +id: EDAM_data:2086 +name: Nucleic acid structure report +comment: This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. +subset: bioinformatics subset: data -def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." [http://edamontology.org] -comment: Use this concept if another, more specific concept is not available. -is_a: EDAM_data:1255 ! Feature record +subset: edam +synonym: "Nucleic acid property (structural)" EXACT [] +synonym: "Nucleic acid structural property" EXACT [] +created_in: "beta12orEarlier" +def: "A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0912 ! Nucleic acid property +is_a: EDAM_data:2085 ! Structure report [Term] -id: EDAM_data:3130 !{since=beta13} -name: Protein features (motifs) -namespace: data +id: EDAM_data:2087 +name: Molecular property +subset: bioinformatics subset: data -def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." [http://edamontology.org] -comment: Use this concept if another, more specific concept is not available. -is_a: EDAM_data:1277 ! Protein features -is_a: EDAM_data:1298 ! Sequence features (motifs) +subset: edam +synonym: "Physicochemical property" EXACT [] +synonym: "SO:0000400" RELATED [] +created_in: "beta12orEarlier" +def: "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:3131 !{since=beta13} -name: Nucleic acid features (motifs) -namespace: data +id: EDAM_data:2088 +name: DNA base structural data +subset: bioinformatics subset: data -def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences." [http://edamontology.org] -comment: Use this concept if another, more specific concept is not available. -is_a: EDAM_data:1276 ! Nucleic acid features -is_a: EDAM_data:1298 ! Sequence features (motifs) - +subset: edam +created_in: "beta12orEarlier" +def: "Structural data for DNA base pairs or runs of bases, such as energy or angle data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0912 ! Nucleic acid property +is_a: EDAM_data:2086 ! Nucleic acid structure report [Term] -id: EDAM_data:0858 -name: Database hits (secondary) -namespace: data +id: EDAM_data:2090 +name: Database entry version information +subset: bioinformatics subset: data -def: "A report of hits from a search of a protein secondary or domain database." [http://edamontology.org] -comment: Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'. -is_a: EDAM_data:2080 ! Database hits - +subset: edam +created_in: "beta12orEarlier" +def: "Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0953 ! Version information +is_a: EDAM_data:2193 ! Database entry metadata [Term] -id: EDAM_data:0901 -name: Protein features (domains) -namespace: data +id: EDAM_data:2091 +name: Accession +subset: bioinformatics subset: data -def: "Summary of structural domains or 3D folds in a protein or polypeptide chain." [http://edamontology.org] -comment: The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. -synonym: "Protein domain assignment" EXACT [http://edamontology.org] -synonym: "Protein structural domains" EXACT [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features -relationship: has_topic EDAM_topic:0736 ! Protein domains and folds +subset: edam +subset: identifiers +synonym: "SIO:000675" BROAD [] +synonym: "SIO:000731" BROAD [] +created_in: "beta12orEarlier" +def: "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0842 ! Identifier [Term] -id: EDAM_data:3118 !{since=beta13} -name: Protein features (topological domains) -namespace: data +id: EDAM_data:2092 +name: Nucleic acid features (SNP) +comment: An SNP is an individual point mutation or substitution of a single nucleotide. +subset: bioinformatics subset: data -def: "Summary of topological domains such as cytoplasmic regions in a protein." [http://edamontology.org] -synonym: "Protein topological domains" EXACT [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features -relationship: has_topic EDAM_topic:0736 ! Protein domains and folds - - - - - +subset: edam +synonym: "Single nucleotide polymorphism" EXACT [] +synonym: "SNP annotation" EXACT [] +created_in: "beta12orEarlier" +def: "Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] -id: EDAM_data:1299 -name: Sequence features (repeats) -namespace: data +id: EDAM_data:2093 +name: Data reference +comment: A list of database accessions or identifiers are usually included. +subset: bioinformatics subset: data -! alt_id: EDAM_data:1282 -def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] -comment: The report might include derived data map such as classification, annotation, organization, periodicity etc. -synonym: "Repeat sequence map" EXACT [http://edamontology.org] -is_a: EDAM_data:1255 ! Feature record - +subset: edam +created_in: "beta12orEarlier" +def: "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:3129 !{since=beta13} -name: Protein features (repeats) -namespace: data +id: EDAM_data:2098 +name: Job identifier +subset: bioinformatics subset: data -def: "Location of short repetitive subsequences (repeat sequences) in a protein sequence." [http://edamontology.org] -is_a: EDAM_data:1299 ! Sequence features (repeats) -is_a: EDAM_data:1277 ! Protein features - - +subset: edam +subset: identifiers +synonym: "WSIO_data:009" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier of a submitted job." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_data:1281 -name: Sequence signature map -namespace: data +id: EDAM_data:2099 +name: Name +subset: bioinformatics subset: data -def: "Image of a sequence with matches to signatures, motifs or profiles." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1298 ! Sequence features (motifs) - +subset: edam +subset: identifiers +synonym: "label" BROAD [] +synonym: "name" EXACT [] +synonym: "SIO:000116" EXACT [] +synonym: "Symbolic name" EXACT [] +created_in: "beta12orEarlier" +def: "A name of a thing, which need not necessarily uniquely identify it." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0842 ! Identifier [Term] -id: EDAM_data:1290 -name: InterPro compact match image -namespace: data +id: EDAM_data:2100 +name: Type +subset: bioinformatics subset: data -def: "Image showing matches between protein sequence(s) and InterPro Entries." [http://edamontology.org] -comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1298 ! Sequence features (motifs) +subset: edam +synonym: "http://purl.org/dc/elements/1.1/type" EXACT [] +created_in: "beta12orEarlier" +def: "A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:1291 -name: InterPro detailed match image -namespace: data +id: EDAM_data:2101 +name: User ID +subset: bioinformatics subset: data -def: "Image showing detailed information on matches between protein sequence(s) and InterPro Entries." [http://edamontology.org] -comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1298 ! Sequence features (motifs) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2118 ! Person identifier [Term] -id: EDAM_data:1292 -name: InterPro architecture image -namespace: data +id: EDAM_data:2102 +name: KEGG organism code +subset: bioinformatics subset: data -def: "Image showing the architecture of InterPro domains in a protein sequence." [http://edamontology.org] -comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1298 ! Sequence features (motifs) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A three-letter code used in the KEGG databases to uniquely identify organisms." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1154 ! KEGG object identifier +is_a: EDAM_data:2909 ! Organism name [Term] -id: EDAM_data:1293 -name: SMART protein schematic -namespace: data +id: EDAM_data:2103 +name: Gene name (KEGG GENES) +subset: bioinformatics subset: data -def: "SMART protein schematic in PNG format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1298 ! Sequence features (motifs) - +subset: edam +subset: identifiers +synonym: "KEGG GENES entry name" EXACT [] +xref: Moby_namespace:GeneId +created_in: "beta12orEarlier" +def: "Name of an entry (gene) from the KEGG GENES database." [http://edamontology.org] +regex: "[a-zA-Z_0-9]+:[a-zA-Z_0-9\\.-]*" +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol +is_a: EDAM_data:1154 ! KEGG object identifier [Term] -id: EDAM_data:1294 -name: GlobPlot domain image -namespace: data +id: EDAM_data:2104 +name: BioCyc ID +subset: bioinformatics subset: data -def: "Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1298 ! Sequence features (motifs) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an object from one of the BioCyc databases." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:1564 -name: Protein fold recognition report -namespace: data +id: EDAM_data:2105 +name: Compound ID (BioCyc) +subset: bioinformatics subset: data -def: "A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s)." [http://edamontology.org] -comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0901 ! Protein features (domains) +subset: edam +subset: identifiers +synonym: "BioCyc compound ID" EXACT [] +synonym: "BioCyc compound identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a compound from the BioCyc chemical compounds database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2104 ! BioCyc ID +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM_data:1300 -name: Nucleic acid features (gene and transcript structure) -namespace: data +id: EDAM_data:2106 +name: Reaction ID (BioCyc) +subset: bioinformatics subset: data -def: "A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc." [http://edamontology.org] -synonym: "Gene annotation (structure)" EXACT [http://edamontology.org] -is_a: EDAM_data:0916 ! Gene annotation -is_a: EDAM_data:1276 ! Nucleic acid features +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a biological reaction from the BioCyc reactions database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2104 ! BioCyc ID +is_a: EDAM_data:2108 ! Reaction ID +relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids [Term] -id: EDAM_data:3140 !{since=beta13} -name: Nucleic acid features (immunoglobulin gene structure) -namespace: data +id: EDAM_data:2107 +name: Enzyme ID (BioCyc) +subset: bioinformatics subset: data -def: "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." [http://edamontology.org] -is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) - - +subset: edam +subset: identifiers +synonym: "BioCyc enzyme ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an enzyme from the BioCyc enzymes database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2104 ! BioCyc ID +is_a: EDAM_data:2321 ! Enzyme ID +[Term] +id: EDAM_data:2108 +name: Reaction ID +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a biological reaction from a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:2978 ! Reaction data [Term] -id: EDAM_data:1301 -name: Nucleic acid features (mobile genetic elements) -namespace: data +id: EDAM_data:2109 +name: Identifier (hybrid) +comment: This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. +subset: bioinformatics subset: data -def: "A report on a region of a nucleic acid sequence containin mobile genetic elements." [http://edamontology.org] -comment: This includes transposons, Plasmids, Bacteriophage elements and Group II introns. -synonym: "Nucleic acid features (transposons)" EXACT [http://edamontology.org] -is_a: EDAM_data:1276 ! Nucleic acid features - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier that is re-used for data objects of fundamentally different types (typically served from a single database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0842 ! Identifier [Term] -id: EDAM_data:1302 -name: Nucleic acid features (PolyA signal or site) -namespace: data +id: EDAM_data:2110 +name: Molecular property identifier +subset: bioinformatics subset: data -def: "A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript." [http://edamontology.org] -comment: A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. -synonym: "PolyA signal" EXACT [http://edamontology.org] -synonym: "PolyA site" EXACT [http://edamontology.org] -is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) - - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a molecular property." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:2087 ! Molecular property [Term] -id: EDAM_data:3135 !{since=beta13} -name: Nucleic acid features (signal or transit peptide) -namespace: data +id: EDAM_data:2111 +name: Codon usage table identifier +subset: bioinformatics subset: data -def: "A report on a coding sequence for a signal or transit peptide." [http://edamontology.org] -comment: A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. -is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) - - - - - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a codon usage table, for example a genetic code." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:1597 ! Codon usage table +relationship: is_identifier_of EDAM_data:1598 ! Genetic code [Term] -id: EDAM_data:1303 -name: Nucleic acid features (quadruplexes) -namespace: data +id: EDAM_data:2112 +name: FlyBase primary identifier +subset: bioinformatics subset: data -def: "A report on quadruplex-forming motifs in a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_data:3128 ! Nucleic acid features (structure) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Primary identifier of an object from the FlyBase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1089 ! FlyBase ID [Term] -id: EDAM_data:1304 -name: Nucleic acid features (CpG island and isochore) -namespace: data +id: EDAM_data:2113 +name: WormBase identifier +subset: bioinformatics subset: data -def: "A report or plot of CpG rich regions (isochores) in a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an object from the WormBase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:1305 -name: Nucleic acid features (restriction sites) -namespace: data +id: EDAM_data:2114 +name: WormBase wormpep ID +subset: bioinformatics subset: data -def: "Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org] -is_a: EDAM_data:3125 ! Nucleic acid features (binding) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Protein identifier used by WormBase database." [http://edamontology.org] +regex: "CE[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2113 ! WormBase identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1306 -name: Nucleic acid features (nucleosome exclusion sequences) -namespace: data +id: EDAM_data:2116 +name: Nucleic acid features (codon) +subset: bioinformatics subset: data -def: "A report on nucleosome formation potential or exclusion sequence(s)." [http://edamontology.org] -is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination) +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_data:1307 -name: Nucleic acid features (splice sites) -namespace: data +id: EDAM_data:2117 +name: Map identifier +subset: bioinformatics subset: data -! alt_id: EDAM_data:0915 -def: "A report on splice sites in a nucleotide sequence or alternative RNA splicing events." [http://edamontology.org] -synonym: "Nucleic acid report (RNA splice model)" EXACT [http://edamontology.org] -synonym: "Nucleic acid report (RNA splicing)" EXACT [http://edamontology.org] -is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a map of a molecular sequence." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:1274 ! Map [Term] -id: EDAM_data:1308 -name: Nucleic acid features (matrix/scaffold attachment sites) -namespace: data +id: EDAM_data:2118 +name: Person identifier +subset: bioinformatics subset: data -def: "A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence." [http://edamontology.org] -is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_data:1309 -name: Gene features (exonic splicing enhancer) -namespace: data +id: EDAM_data:2119 +name: Nucleic acid identifier +subset: bioinformatics subset: data -def: "A report on exonic splicing enhancers (ESE) in an exon." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:2397 ! Nucleic acid features (exon) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name or other identifier of a nucleic acid molecule." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0982 ! Molecule identifier +relationship: is_identifier_of EDAM_data:2084 ! Nucleic acid report [Term] -id: EDAM_data:1310 -name: Nucleic acid features (microRNA) -namespace: data +id: EDAM_data:2126 +name: Translation frame specification +subset: bioinformatics subset: data -def: "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." [http://edamontology.org] -is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA) -relationship: has_topic EDAM_topic:3060 ! Regulatory RNA +subset: edam +created_in: "beta12orEarlier" +def: "Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM_data:2169 -name: Nucleic acid features (siRNA) -namespace: data +id: EDAM_data:2127 +name: Genetic code identifier +subset: bioinformatics subset: data -def: "A report on siRNA duplexes in mRNA." [http://edamontology.org] -is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA) -relationship: has_topic EDAM_topic:3060 ! Regulatory RNA +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a genetic code." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:1598 ! Genetic code [Term] -id: EDAM_data:0922 -name: Nucleic acid features (primers) -namespace: data +id: EDAM_data:2128 +name: Genetic code name +subset: bioinformatics subset: data -def: "Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence." [http://edamontology.org] -is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination) -relationship: has_topic EDAM_topic:0632 ! Probes and primers +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Informal name for a genetic code, typically an organism name." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2127 ! Genetic code identifier [Term] -id: EDAM_data:1311 -name: Nucleic acid features (operon) -namespace: data +id: EDAM_data:2129 +name: File format name +subset: bioinformatics subset: data -def: "A report on operons (operators, promoters and genes) from a bacterial genome." [http://edamontology.org] -comment: The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. -synonym: "Gene features (operon)" EXACT [http://edamontology.org] -is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:1312 -name: Gene features (promoter) -namespace: data +id: EDAM_data:2130 +name: Sequence profile type +subset: bioinformatics subset: data -def: "A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." [http://edamontology.org] -is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) - +subset: edam +created_in: "beta12orEarlier" +def: "A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2100 ! Type +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM_data:1313 -name: Nucleic acid features (coding sequence) -namespace: data +id: EDAM_data:2131 +name: Operating system name +subset: bioinformatics subset: data -! alt_id: EDAM_data:1317 -def: "A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." [http://edamontology.org] -synonym: "Gene features (coding sequence)" EXACT [http://edamontology.org] -synonym: "Gene features (coding region)" EXACT [http://edamontology.org] -synonym: "Gene annotation (translation)" EXACT [http://edamontology.org] -is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a computer operating system such as Linux, PC or Mac." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:1314 -name: Gene features (SECIS element) -namespace: data +id: EDAM_data:2132 +name: Mutation type +subset: bioinformatics subset: data -def: "A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) - +subset: edam +created_in: "beta12orEarlier" +def: "A type of point or block mutation, including insertion, deletion, change, duplication and moves." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2100 ! Type [Term] -id: EDAM_data:1315 -name: Gene features (TFBS) -namespace: data +id: EDAM_data:2133 +name: Logical operator +subset: bioinformatics subset: data -def: "A report on the transcription factor binding sites (TFBS) in a DNA sequence." [http://edamontology.org] -is_a: EDAM_data:1312 ! Gene features (promoter) -is_a: EDAM_data:3125 ! Nucleic acid features (binding) -relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A logical operator such as OR, AND, XOR, and NOT." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:2397 -name: Nucleic acid features (exon) -namespace: data +id: EDAM_data:2134 +name: Results sort order +comment: Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. +subset: bioinformatics subset: data -def: "An informative report on an exon in a nucleotide sequences." [http://edamontology.org] -synonym: "Gene features (exon)" EXACT [http://edamontology.org] -is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence) +subset: edam +created_in: "beta12orEarlier" +def: "A control of the order of data that is output, for example the order of sequences in an alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2079 ! Search parameter [Term] -id: EDAM_data:2754 -name: Nucleic acid features (intron) -namespace: data +id: EDAM_data:2135 +name: Toggle +subset: bioinformatics subset: data -def: "An informative report on an intron in a nucleotide sequences." [http://edamontology.org] -synonym: "Gene features (intron)" EXACT [http://edamontology.org] -is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) +subset: edam +created_in: "beta12orEarlier" +def: "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2527 ! Parameter +[Term] +id: EDAM_data:2136 +name: Sequence width +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "The width of an output sequence or alignment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1249 ! Sequence length [Term] -id: EDAM_data:2160 -name: Fickett testcode plot -namespace: data +id: EDAM_data:2137 +name: Gap penalty +subset: bioinformatics subset: data -def: "A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences." [http://edamontology.org] -is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence) - +subset: edam +created_in: "beta12orEarlier" +def: "A penalty for introducing or extending a gap in an alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1394 ! Alignment score or penalty [Term] -id: EDAM_data:1289 -name: Restriction map -namespace: data +id: EDAM_data:2139 +name: Nucleic acid melting temperature +subset: bioinformatics subset: data -def: "Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org] -is_a: EDAM_data:1305 ! Nucleic acid features (restriction sites) -is_a: EDAM_data:1279 ! Sequence map -is_a: EDAM_data:2969 ! Sequence image +subset: edam +synonym: "Melting temperature" EXACT [] +created_in: "beta12orEarlier" +def: "A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] -id: EDAM_data:1321 -name: Protein features (sites) -namespace: data +id: EDAM_data:2140 +name: Concentration +subset: bioinformatics subset: data -def: "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites." [http://edamontology.org] -comment: Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1277 ! Protein features +subset: edam +created_in: "beta12orEarlier" +def: "The concentration of a chemical compound." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2050 ! Molecular property (general) [Term] -id: EDAM_data:1322 -name: Protein features (signal peptides) -namespace: data +id: EDAM_data:2141 +name: Window step size +subset: bioinformatics subset: data -def: "A report on the location of signal peptides or signal peptide cleavage sites in protein sequences." [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features +subset: edam +created_in: "beta12orEarlier" +def: "Size of the incremental 'step' a sequence window is moved over a sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1249 ! Sequence length [Term] -id: EDAM_data:3120 !{since=beta13} -name: Protein features (sequence variants) -namespace: data +id: EDAM_data:2142 +name: EMBOSS graph +subset: bioinformatics subset: data -def: "A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features - - +subset: edam +created_in: "beta12orEarlier" +def: "An image of a graph generated by the EMBOSS suite." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2968 ! Image [Term] -id: EDAM_data:1323 -name: Protein features (cleavage sites) -namespace: data +id: EDAM_data:2143 +name: EMBOSS report +subset: bioinformatics subset: data -def: "A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence." [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features -relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification - +subset: edam +created_in: "beta12orEarlier" +def: "An application report generated by the EMBOSS suite." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2048 ! Report [Term] -id: EDAM_data:1324 -name: Protein features (post-translation modifications) -namespace: data +id: EDAM_data:2145 +name: Sequence offset +subset: bioinformatics subset: data -def: "A report on post-translation modifications in a protein sequence, typically describing the specific sites involved." [http://edamontology.org] -synonym: "Protein features (post-translation modification sites)" EXACT [http://edamontology.org] -synonym: "Post-translation modification" EXACT [http://edamontology.org] -is_a: EDAM_data:2191 ! Protein features (chemical modification) +subset: edam +created_in: "beta12orEarlier" +def: "An offset for a single-point sequence position." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1016 ! Sequence position +is_a: EDAM_data:2914 ! Sequence features metadata [Term] -id: EDAM_data:1325 -name: Protein features (active sites) -namespace: data +id: EDAM_data:2146 +name: Threshold +subset: bioinformatics subset: data -def: "A report on catalytic residues (active site) of an enzyme." [http://edamontology.org] -synonym: "Enzyme active site" EXACT [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features +subset: edam +created_in: "beta12orEarlier" +def: "A value that serves as a threshold for a tool (usually to control scoring or output)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1772 ! Score or penalty [Term] -id: EDAM_data:1326 -name: Protein features (binding sites) -namespace: data +id: EDAM_data:2147 +name: Protein report (transcription factor) +comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. +subset: bioinformatics subset: data -def: "A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features - +subset: edam +synonym: "Transcription factor binding site data" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on a transcription factor protein." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0896 ! Protein report [Term] -id: EDAM_data:2989 -name: Protein features (key folding sites) -namespace: data +id: EDAM_data:2149 +name: Database category name +subset: bioinformatics subset: data -def: "A report on key residues involved in protein folding." [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a category of biological or bioinformatics database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1056 ! Database name [Term] -id: EDAM_data:1327 -name: Protein features (epitopes) -namespace: data +id: EDAM_data:2150 +name: Sequence profile name +subset: bioinformatics subset: data -def: "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data." [http://edamontology.org] -comment: Epitope mapping is commonly done during vaccine design. -is_obsolete: true !{since=beta13} -consider: EDAM_data:1326 ! Protein features (binding sites) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a sequence profile." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1115 ! Sequence profile ID [Term] -id: EDAM_data:1328 -name: Protein features (nucleic acid binding sites) -namespace: data +id: EDAM_data:2151 +name: Color +subset: bioinformatics subset: data -def: "A report on RNA and DNA-binding proteins and binding sites in protein sequences." [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features - +subset: edam +created_in: "beta12orEarlier" +def: "Specification of one or more colors." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2152 ! Rendering parameter [Term] -id: EDAM_data:1329 -name: MHC Class I epitopes report -namespace: data +id: EDAM_data:2152 +name: Rendering parameter +subset: bioinformatics subset: data -def: "A report on epitopes that bind to MHC class I molecules." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1326 ! Protein features (binding sites) - +subset: edam +synonym: "Graphical parameter" EXACT [] +synonym: "Graphics parameter" EXACT [] +created_in: "beta12orEarlier" +def: "A parameter that is used to control rendering (drawing) to a device or image." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:1330 -name: MHC Class II epitopes report -namespace: data +id: EDAM_data:2154 +name: Sequence name +subset: bioinformatics subset: data -def: "A report on predicted epitopes that bind to MHC class II molecules." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1326 ! Protein features (binding sites) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Any arbitrary name of a molecular sequence." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1063 ! Sequence identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:1331 -name: Protein features (PEST sites) -namespace: data +id: EDAM_data:2156 +name: Date +subset: bioinformatics subset: data -def: "A report or plot of PEST sites in a protein sequence." [http://edamontology.org] -comment: 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. -is_obsolete: true !{since=beta13} -consider: EDAM_data:1323 ! Protein features (cleavage sites) +subset: edam +created_in: "beta12orEarlier" +def: "A temporal date." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3105 ! Geotemporal metadata [Term] -id: EDAM_data:0857 -name: Database hits (sequence) -namespace: data +id: EDAM_data:2157 +name: Word composition +subset: bioinformatics subset: data -def: "A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits." [http://edamontology.org] -comment: The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. -is_a: EDAM_data:2080 ! Database hits +subset: edam +created_in: "beta12orEarlier" +def: "Word composition data for a molecular sequence." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1266 ! Sequence composition (base words) +consider: EDAM_data:1268 ! Amino acid word frequencies [Term] -id: EDAM_data:0885 -name: Database hits (structure) -namespace: data +id: EDAM_data:2160 +name: Fickett testcode plot +subset: bioinformatics subset: data -def: "Results (hits) from searching a database of tertiary structure." [http://edamontology.org] -comment: This includes alignment and score data. -is_a: EDAM_data:2080 ! Database hits - +subset: edam +created_in: "beta12orEarlier" +def: "A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] -id: EDAM_data:1338 -name: Sequence database hits scores list -namespace: data +id: EDAM_data:2161 +name: Sequence similarity plot +subset: bioinformatics subset: data -def: "Scores from a sequence database search (for example a BLAST search)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0857 ! Database hits (sequence) - +subset: edam +created_in: "beta12orEarlier" +def: "A plot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0867 ! Sequence alignment report [Term] -id: EDAM_data:1339 -name: Sequence database hits alignments list -namespace: data +id: EDAM_data:2162 +name: Helical wheel +subset: bioinformatics subset: data -def: "Alignments from a sequence database search (for example a BLAST search)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0857 ! Database hits (sequence) +subset: edam +created_in: "beta12orEarlier" +def: "An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1709 ! Protein secondary structure image [Term] -id: EDAM_data:1340 -name: Sequence database hits evaluation data -namespace: data +id: EDAM_data:2163 +name: Helical net +comment: Useful for highlighting amphipathicity and other properties. +subset: bioinformatics subset: data -def: "A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0857 ! Database hits (sequence) +subset: edam +created_in: "beta12orEarlier" +def: "An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1709 ! Protein secondary structure image [Term] -id: EDAM_data:1358 -name: Prosite nucleotide pattern -namespace: data +id: EDAM_data:2164 +name: Protein sequence properties plot +subset: bioinformatics subset: data -def: "A nucleotide regular expression pattern from the Prosite database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1353 ! Sequence motif - +subset: edam +created_in: "beta12orEarlier" +def: "A plot of general physicochemical properties of a protein sequence." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:1359 -name: Prosite protein pattern -namespace: data +id: EDAM_data:2165 +name: Protein ionization curve +subset: bioinformatics subset: data -def: "A protein regular expression pattern from the Prosite database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1353 ! Sequence motif +subset: edam +created_in: "beta12orEarlier" +def: "A plot of pK versus pH for a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:1352 -name: Regular expression -namespace: data +id: EDAM_data:2166 +name: Sequence composition plot +subset: bioinformatics subset: data -def: "Regular expression pattern." [http://edamontology.org] -is_a: EDAM_data:2527 ! Parameter +subset: edam +created_in: "beta12orEarlier" +def: "A plot of character or word composition / frequency of a molecular sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1261 ! Sequence composition [Term] -id: EDAM_data:2070 -name: Sequence motif (nucleic acid) -namespace: data +id: EDAM_data:2167 +name: Nucleic acid density plot +subset: bioinformatics subset: data -def: "A nucleotide sequence motif." [http://edamontology.org] -is_a: EDAM_data:1353 ! Sequence motif - +subset: edam +created_in: "beta12orEarlier" +def: "Density plot (of base composition) for a nucleotide sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0912 ! Nucleic acid property [Term] -id: EDAM_data:2071 -name: Sequence motif (protein) -namespace: data +id: EDAM_data:2168 +name: Sequence trace image +subset: bioinformatics subset: data -def: "An amino acid sequence motif." [http://edamontology.org] -is_a: EDAM_data:1353 ! Sequence motif +subset: edam +created_in: "beta12orEarlier" +def: "Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2969 ! Sequence image [Term] -id: EDAM_data:2854 -name: Position-specific scoring matrix -namespace: data +id: EDAM_data:2169 +name: Nucleic acid features (siRNA) +subset: bioinformatics subset: data -def: "A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment." [http://edamontology.org] -is_a: EDAM_data:1354 ! Sequence profile -is_a: EDAM_data:2082 ! Matrix - +subset: edam +created_in: "beta12orEarlier" +def: "A report on siRNA duplexes in mRNA." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA) +relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] -id: EDAM_data:1361 -name: Position frequency matrix -namespace: data +id: EDAM_data:2173 +name: Sequence set (stream) +comment: This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. +subset: bioinformatics subset: data -def: "A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org] -synonym: "PFM" EXACT [http://edamontology.org] -is_a: EDAM_data:2854 ! Position-specific scoring matrix - +subset: edam +created_in: "beta12orEarlier" +def: "A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0850 ! Sequence set [Term] -id: EDAM_data:1362 -name: Position weight matrix -namespace: data +id: EDAM_data:2174 +name: FlyBase secondary identifier +comment: Secondary identifier are used to handle entries that were merged with or split from other entries in the database. +subset: bioinformatics subset: data -def: "A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org] -comment: Contributions of individual sequences to the matrix might be uneven (weighted). -synonym: "PWM" EXACT [http://edamontology.org] -is_a: EDAM_data:2854 ! Position-specific scoring matrix - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Secondary identifier of an object from the FlyBase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1089 ! FlyBase ID [Term] -id: EDAM_data:1363 -name: Information content matrix -namespace: data +id: EDAM_data:2176 +name: Cardinality +subset: bioinformatics subset: data -def: "A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position." [http://edamontology.org] -synonym: "ICM" EXACT [http://edamontology.org] -is_a: EDAM_data:2854 ! Position-specific scoring matrix - +subset: edam +created_in: "beta12orEarlier" +def: "The number of a certain thing." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:1364 -name: Hidden Markov model -namespace: data +id: EDAM_data:2177 +name: Exactly 1 +subset: bioinformatics subset: data -def: "A hidden Markov model representation of a set or alignment of sequences." [http://edamontology.org] -synonym: "HMM" EXACT [http://edamontology.org] -is_a: EDAM_data:1354 ! Sequence profile +subset: edam +created_in: "beta12orEarlier" +def: "A single thing." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:1365 -name: Fingerprint -namespace: data +id: EDAM_data:2178 +name: 1 or more +subset: bioinformatics subset: data -def: "One or more fingerprints (sequence classifiers) as used in the PRINTS database." [http://edamontology.org] -is_a: EDAM_data:2854 ! Position-specific scoring matrix - +subset: edam +created_in: "beta12orEarlier" +def: "One or more things." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:1368 -name: Domainatrix signature -namespace: data +id: EDAM_data:2179 +name: Exactly 2 +subset: bioinformatics subset: data -def: "A protein signature of the type used in the EMBASSY Signature package." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1354 ! Sequence profile +subset: edam +created_in: "beta12orEarlier" +def: "Exactly two things." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:1371 -name: HMMER NULL hidden Markov model -namespace: data +id: EDAM_data:2180 +name: 2 or more +subset: bioinformatics subset: data -def: "NULL hidden Markov model representation used by the HMMER package." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1364 ! Hidden Markov model +subset: edam +created_in: "beta12orEarlier" +def: "Two or more things." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:1372 -name: Protein family signature +id: EDAM_data:2190 +name: Sequence checksum +subset: bioinformatics +subset: data +subset: edam +synonym: "Hash" EXACT [] +synonym: "Hash code" EXACT [] +synonym: "Hash sum" EXACT [] +synonym: "Hash value" EXACT [] +created_in: "beta12orEarlier" +def: "A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing." [http://edamontology.org] namespace: data -subset: data -def: "A protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org] -comment: Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. -is_a: EDAM_data:1355 ! Protein signature +is_a: EDAM_data:0855 ! Sequence metadata +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM_data:1373 -name: Protein domain signature -namespace: data +id: EDAM_data:2191 +name: Protein features (chemical modification) +subset: bioinformatics subset: data -def: "A protein domain signature (sequence classifier) from the InterPro database." [http://edamontology.org] -comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries. -is_a: EDAM_data:1355 ! Protein signature +subset: edam +synonym: "GO:0006464" RELATED [] +synonym: "MOD:00000" RELATED [] +synonym: "Protein modification annotation" EXACT [] +created_in: "beta12orEarlier" +def: "Data on a chemical modification of a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features [Term] -id: EDAM_data:1374 -name: Protein region signature -namespace: data +id: EDAM_data:2192 +name: Error +subset: bioinformatics subset: data -def: "A protein region signature (sequence classifier) from the InterPro database." [http://edamontology.org] -comment: A protein region signature defines a region which cannot be described as a protein family or domain signature. -is_a: EDAM_data:1355 ! Protein signature +subset: edam +created_in: "beta12orEarlier" +def: "Data on an error generated by computer system or tool." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0959 ! Job metadata [Term] -id: EDAM_data:1375 -name: Protein repeat signature -namespace: data +id: EDAM_data:2193 +name: Database entry metadata +subset: bioinformatics subset: data -def: "A protein repeat signature (sequence classifier) from the InterPro database." [http://edamontology.org] -comment: A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. -is_a: EDAM_data:1355 ! Protein signature +subset: edam +created_in: "beta12orEarlier" +def: "Basic information on any arbitrary database entry." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0957 ! Database metadata [Term] -id: EDAM_data:1376 -name: Protein site signature -namespace: data +id: EDAM_data:2198 +name: Gene cluster +subset: bioinformatics subset: data -def: "A protein site signature (sequence classifier) from the InterPro database." [http://edamontology.org] -comment: A protein site signature is a classifier for a specific site in a protein. -is_a: EDAM_data:1355 ! Protein signature +subset: edam +created_in: "beta12orEarlier" +def: "A cluster of similar genes." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1246 ! Sequence cluster (nucleic acid) [Term] -id: EDAM_data:1377 -name: Protein conserved site signature -namespace: data +id: EDAM_data:2201 +name: Sequence record full +subset: bioinformatics subset: data -def: "A protein conserved site signature (sequence classifier) from the InterPro database." [http://edamontology.org] -comment: A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. -is_a: EDAM_data:1376 ! Protein site signature +subset: edam +synonym: "http://purl.bioontology.org/ontology/MSH/D058977" RELATED [] +xref: SO:2000061 +created_in: "beta12orEarlier" +def: "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0849 ! Sequence record [Term] -id: EDAM_data:1378 -name: Protein active site signature -namespace: data +id: EDAM_data:2208 +name: Plasmid identifier +subset: bioinformatics subset: data -def: "A protein active site signature (sequence classifier) from the InterPro database." [http://edamontology.org] -comment: A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. -is_a: EDAM_data:1376 ! Protein site signature +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a plasmid in a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2119 ! Nucleic acid identifier [Term] -id: EDAM_data:1379 -name: Protein binding site signature -namespace: data +id: EDAM_data:2209 +name: Mutation ID +subset: bioinformatics subset: data -def: "A protein binding site signature (sequence classifier) from the InterPro database." [http://edamontology.org] -comment: A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. -is_a: EDAM_data:1376 ! Protein site signature +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of a specific mutation catalogued in a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2538 ! Mutation identifier [Term] -id: EDAM_data:1380 -name: Protein post-translational modification signature -namespace: data +id: EDAM_data:2212 +name: Mutation annotation (basic) +subset: bioinformatics subset: data -def: "A protein post-translational modification signature (sequence classifier) from the InterPro database." [http://edamontology.org] -comment: A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. -is_a: EDAM_data:1376 ! Protein site signature +subset: edam +created_in: "beta12orEarlier" +def: "Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] -id: EDAM_data:0861 -name: Sequence alignment (words) -namespace: data +id: EDAM_data:2213 +name: Mutation annotation (prevalence) +subset: bioinformatics subset: data -def: "Alignment of exact matches between subsequences (words) within two or more molecular sequences." [http://edamontology.org] -synonym: "Sequence word alignment" EXACT [http://edamontology.org] -is_a: EDAM_data:0863 ! Sequence alignment +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] -id: EDAM_data:0863 -name: Sequence alignment -namespace: data +id: EDAM_data:2214 +name: Mutation annotation (prognostic) +subset: bioinformatics subset: data -def: "Alignment of multiple molecular sequences." [http://edamontology.org] -synonym: "Sequence alignment" EXACT [http://en.wikipedia.org/wiki/Sequence_alignment] -synonym: "sequence alignment" EXACT [http://semanticscience.org/resource/SIO_010066] -is_a: EDAM_data:1916 ! Alignment -relationship: has_topic EDAM_topic:0182 ! Sequence alignment +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] -id: EDAM_data:0868 -name: Sequence profile alignment -namespace: data +id: EDAM_data:2215 +name: Mutation annotation (functional) +subset: bioinformatics subset: data -def: "A profile-profile alignment (each profile typically representing a sequence alignment)." [http://edamontology.org] -is_a: EDAM_data:1916 ! Alignment - +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] -id: EDAM_data:0869 -name: Sequence-profile alignment -namespace: data +id: EDAM_data:2216 +name: Codon number +subset: bioinformatics subset: data -def: "Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment)." [http://edamontology.org] -comment: Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. -is_a: EDAM_data:1916 ! Alignment +subset: edam +created_in: "beta12orEarlier" +def: "The number of a codon, for instance, at which a mutation is located." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1016 ! Sequence position +[Term] +id: EDAM_data:2217 +name: Tumor annotation +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1622 ! Disease annotation [Term] -id: EDAM_data:2366 -name: Secondary structure alignment -namespace: data +id: EDAM_data:2218 +name: Server metadata +subset: bioinformatics subset: data -def: "Alignment of the (1D representations of) secondary structure of two or more molecules." [http://edamontology.org] -is_a: EDAM_data:1916 ! Alignment - +subset: edam +created_in: "beta12orEarlier" +def: "Basic information about a server on the web, such as an SRS server." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3106 ! System metadata [Term] -id: EDAM_data:0878 -name: Secondary structure alignment (protein) -namespace: data +id: EDAM_data:2219 +name: Database field name +subset: bioinformatics subset: data -def: "Alignment of the (1D representations of) secondary structure of two or more proteins." [http://edamontology.org] -is_a: EDAM_data:2366 ! Secondary structure alignment -is_a: EDAM_data:3154 ! Protein alignment +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a field in a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:0881 -name: Secondary structure alignment (RNA) -namespace: data +id: EDAM_data:2220 +name: Sequence cluster ID (SYSTERS) +subset: bioinformatics subset: data -def: "Alignment of the (1D representations of) secondary structure of two or more RNA molecules." [http://edamontology.org] -xref: Moby:RNAStructAlignmentML -is_a: EDAM_data:2366 ! Secondary structure alignment - +subset: edam +subset: identifiers +synonym: "SYSTERS cluster ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier of a sequence cluster from the SYSTERS database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1112 ! Sequence cluster ID [Term] -id: EDAM_data:0886 -name: Structure alignment -namespace: data +id: EDAM_data:2223 +name: Ontology metadata +subset: bioinformatics subset: data -def: "Alignment (superimposition) of molecular tertiary (3D) structures." [http://edamontology.org] -comment: A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. -is_a: EDAM_data:1916 ! Alignment -is_a: EDAM_data:0883 ! Structure -relationship: has_topic EDAM_topic:0183 ! Structure alignment +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning a biological ontology." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] -id: EDAM_data:0890 -name: Structural (3D) profile alignment -namespace: data +id: EDAM_data:2235 +name: Raw SCOP domain classification +comment: These are the parsable data files provided by SCOP. +subset: bioinformatics subset: data -def: "A 3D profile-3D profile alignment (each profile representing structures or a structure alignment)." [http://edamontology.org] -synonym: "Structural profile alignment" EXACT [http://edamontology.org] -is_a: EDAM_data:1916 ! Alignment +subset: edam +created_in: "beta12orEarlier" +def: "Raw SCOP domain classification data files." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0900 ! Protein domain classification [Term] -id: EDAM_data:0891 -name: Sequence-3D profile alignment -namespace: data +id: EDAM_data:2236 +name: Raw CATH domain classification +comment: These are the parsable data files provided by CATH. +subset: bioinformatics subset: data -def: "An alignment of a sequence to a 3D profile (representing structures or a structure alignment)." [http://edamontology.org] -synonym: "Sequence-structural profile alignment" EXACT [http://edamontology.org] -is_a: EDAM_data:0893 ! Sequence-structure alignment +subset: edam +created_in: "beta12orEarlier" +def: "Raw CATH domain classification data files." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0900 ! Protein domain classification [Term] -id: EDAM_data:0893 -name: Sequence-structure alignment -namespace: data +id: EDAM_data:2240 +name: Heterogen annotation +subset: bioinformatics subset: data -def: "An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s))." [http://edamontology.org] -is_a: EDAM_data:1916 ! Alignment +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0962 ! Small molecule annotation [Term] -id: EDAM_data:1381 -name: Sequence alignment (pair) -namespace: data +id: EDAM_data:2242 +name: Phylogenetic property values +subset: bioinformatics subset: data -def: "Alignment of exactly two molecular sequences." [http://edamontology.org] -synonym: "pairwise sequence alignment" RELATED [http://semanticscience.org/resource/SIO_010068] ! Related external synonym in EDAM without a note is usually almost exact. -is_a: EDAM_data:0863 ! Sequence alignment - +subset: edam +created_in: "beta12orEarlier" +def: "Phylogenetic property values data." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0871 ! Phylogenetic character data [Term] -id: EDAM_data:1382 -name: Sequence alignment (multiple) -namespace: data +id: EDAM_data:2245 +name: Sequence set (bootstrapped) +comment: Bootstrapping is often performed in phylogenetic analysis. +subset: bioinformatics subset: data -def: "Alignment of more than two molecular sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0863 ! Sequence alignment +subset: edam +created_in: "beta12orEarlier" +def: "A collection of sequences output from a bootstrapping (resampling) procedure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0850 ! Sequence set [Term] -id: EDAM_data:1383 -name: Sequence alignment (nucleic acid) -namespace: data +id: EDAM_data:2247 +name: Phylogenetic consensus tree +subset: bioinformatics subset: data -def: "Alignment of multiple nucleotide sequences." [http://edamontology.org] -is_a: EDAM_data:0863 ! Sequence alignment -is_a: EDAM_data:2084 ! Nucleic acid report - +subset: edam +created_in: "beta12orEarlier" +def: "A consensus phylogenetic tree derived from comparison of multiple trees." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0872 ! Phylogenetic tree [Term] -id: EDAM_data:1384 -name: Sequence alignment (protein) -namespace: data +id: EDAM_data:2248 +name: Schema +subset: bioinformatics subset: data -def: "Alignment of multiple protein sequences." [http://edamontology.org] -is_a: EDAM_data:0863 ! Sequence alignment -is_a: EDAM_data:3154 ! Protein alignment - +subset: edam +created_in: "beta12orEarlier" +def: "A data schema for organising or transforming data of some type." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:1385 -name: Sequence alignment (hybrid) -namespace: data +id: EDAM_data:2249 +name: DTD +subset: bioinformatics subset: data -def: "Alignment of multiple molecular sequences of different types." [http://edamontology.org] -comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. -is_a: EDAM_data:0863 ! Sequence alignment +subset: edam +created_in: "beta12orEarlier" +def: "A DTD (document type definition)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2248 ! Schema [Term] -id: EDAM_data:1386 -name: Sequence alignment (nucleic acid pair) -namespace: data +id: EDAM_data:2250 +name: XML Schema +subset: bioinformatics subset: data -def: "Alignment of exactly two nucleotide sequences." [http://edamontology.org] -is_a: EDAM_data:1381 ! Sequence alignment (pair) -is_a: EDAM_data:1383 ! Sequence alignment (nucleic acid) +subset: edam +synonym: "XSD" EXACT [] +created_in: "beta12orEarlier" +def: "An XML Schema." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2248 ! Schema [Term] -id: EDAM_data:1387 -name: Sequence alignment (protein pair) -namespace: data +id: EDAM_data:2251 +name: Relax-NG schema +subset: bioinformatics subset: data -def: "Alignment of exactly two protein sequences." [http://edamontology.org] -is_a: EDAM_data:1381 ! Sequence alignment (pair) -is_a: EDAM_data:1384 ! Sequence alignment (protein) - +subset: edam +created_in: "beta12orEarlier" +def: "A relax-NG schema." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2248 ! Schema [Term] -id: EDAM_data:1389 -name: Multiple nucleotide sequence alignment -namespace: data +id: EDAM_data:2252 +name: XSLT stylesheet +subset: bioinformatics subset: data -def: "Alignment of more than two nucleotide sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0863 ! Sequence alignment +subset: edam +created_in: "beta12orEarlier" +def: "An XSLT stylesheet." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2248 ! Schema [Term] -id: EDAM_data:1390 -name: Multiple protein sequence alignment -namespace: data +id: EDAM_data:2253 +name: Data resource definition name +subset: bioinformatics subset: data -def: "Alignment of more than two protein sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0863 ! Sequence alignment +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a data type." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1084 ! Data resource definition identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:1388 -name: Hybrid sequence alignment (pair) -namespace: data +id: EDAM_data:2254 +name: OBO file format name +subset: bioinformatics subset: data -def: "Alignment of exactly two molecular sequences of different types." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1385 ! Sequence alignment (hybrid) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of an OBO file format such as OBO-XML, plain and so on." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2129 ! File format name [Term] -id: EDAM_data:1417 -name: Sequence-profile alignment (Domainatrix signature) -namespace: data +id: EDAM_data:2285 +name: Gene ID (MIPS) +subset: bioinformatics subset: data -def: "Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0869 ! Sequence-profile alignment - +subset: edam +subset: identifiers +synonym: "MIPS genetic element identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier for genetic elements in MIPS database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1418 -name: Sequence-profile alignment (HMM) -namespace: data +id: EDAM_data:2288 +name: Sequence identifier (protein) +subset: bioinformatics subset: data -def: "Alignment of molecular sequence(s) to a hidden Markov model(s)." [http://edamontology.org] -is_a: EDAM_data:0869 ! Sequence-profile alignment +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of protein sequence(s) or protein sequence database entries." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1096 ! Sequence accession (protein) [Term] -id: EDAM_data:1420 -name: Sequence-profile alignment (fingerprint) -namespace: data +id: EDAM_data:2289 +name: Sequence identifier (nucleic acid) +subset: bioinformatics subset: data -def: "Alignment of molecular sequences to a protein fingerprint from the PRINTS database." [http://edamontology.org] -is_a: EDAM_data:0869 ! Sequence-profile alignment - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of nucleotide sequence(s) or nucleotide sequence database entries." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] -id: EDAM_data:1479 -name: Structure alignment (pair) -namespace: data +id: EDAM_data:2290 +name: EMBL accession +subset: bioinformatics subset: data -def: "Alignment (superimposition) of exactly two molecular tertiary (3D) structures." [http://edamontology.org] -is_a: EDAM_data:0886 ! Structure alignment - +subset: edam +subset: identifiers +synonym: "EMBL accession number" EXACT [] +synonym: "EMBL ID" EXACT [] +synonym: "EMBL identifier" EXACT [] +created_in: "beta12orEarlier" +def: "An accession number of an entry from the EMBL sequence database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID [Term] -id: EDAM_data:1480 -name: Structure alignment (multiple) -namespace: data +id: EDAM_data:2291 +name: UniProt ID +subset: bioinformatics subset: data -def: "Alignment (superimposition) of more than two molecular tertiary (3D) structures." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0886 ! Structure alignment - +subset: edam +subset: identifiers +synonym: "UniProt entry name" EXACT [] +synonym: "UniProt identifier" EXACT [] +synonym: "UniProtKB entry name" EXACT [] +synonym: "UniProtKB identifier" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier of a polypeptide in the UniProt database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2154 ! Sequence name +relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] -id: EDAM_data:1481 -name: Structure alignment (protein) -namespace: data +id: EDAM_data:2292 +name: GenBank accession +subset: bioinformatics subset: data -def: "Alignment (superimposition) of protein tertiary (3D) structures." [http://edamontology.org] -is_a: EDAM_data:0886 ! Structure alignment -is_a: EDAM_data:3154 ! Protein alignment +subset: edam +subset: identifiers +synonym: "GenBank accession number" EXACT [] +synonym: "GenBank ID" EXACT [] +synonym: "GenBank identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of an entry from the GenBank sequence database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID [Term] -id: EDAM_data:1482 -name: Structure alignment (nucleic acid) -namespace: data +id: EDAM_data:2293 +name: Gramene secondary identifier +subset: bioinformatics subset: data -def: "Alignment (superimposition) of nucleic acid tertiary (3D) structures." [http://edamontology.org] -is_a: EDAM_data:0886 ! Structure alignment -is_a: EDAM_data:2084 ! Nucleic acid report +subset: edam +subset: identifiers +synonym: "Gramene internal ID" EXACT [] +synonym: "Gramene internal identifier" EXACT [] +synonym: "Gramene secondary ID" EXACT [] +created_in: "beta12orEarlier" +def: "Secondary (internal) identifier of a Gramene database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2915 ! Gramene identifier [Term] -id: EDAM_data:1483 -name: Structure alignment (protein pair) -namespace: data +id: EDAM_data:2294 +name: Sequence variation ID +subset: bioinformatics subset: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures." [http://edamontology.org] -is_a: EDAM_data:1481 ! Structure alignment (protein) -is_a: EDAM_data:1479 ! Structure alignment (pair) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of an entry from a database of molecular sequence variation." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1484 -name: Multiple protein tertiary structure alignment -namespace: data +id: EDAM_data:2295 +name: Gene ID +subset: bioinformatics subset: data -def: "Alignment (superimposition) of more than two protein tertiary (3D) structures." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1481 ! Structure alignment (protein) +subset: edam +subset: identifiers +synonym: "Gene accession" EXACT [] +synonym: "Gene code" EXACT [] +created_in: "beta12orEarlier" +def: "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1025 ! Gene identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:1485 -name: Structure alignment (protein all atoms) -namespace: data +id: EDAM_data:2296 +name: Gene name (AceView) +subset: bioinformatics subset: data -def: "Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] -is_a: EDAM_data:1481 ! Structure alignment (protein) - +subset: edam +subset: identifiers +synonym: "AceView gene name" EXACT [] +created_in: "beta12orEarlier" +def: "Name of an entry (gene) from the AceView genes database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1486 -name: Structure alignment (protein C-alpha atoms) -namespace: data +id: EDAM_data:2297 +name: Gene ID (ECK) +subset: bioinformatics subset: data -def: "Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] -comment: C-beta atoms from amino acid side-chains may be considered. -is_a: EDAM_data:1481 ! Structure alignment (protein) - +subset: edam +subset: identifiers +synonym: "E. coli K-12 gene identifier" EXACT [] +synonym: "ECK accession" EXACT [] +xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK +created_in: "beta12orEarlier" +def: "Identifier of an E. coli K-12 gene from EcoGene Database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1795 ! Gene ID (EcoGene) [Term] -id: EDAM_data:1487 -name: Pairwise protein tertiary structure alignment (all atoms) -namespace: data +id: EDAM_data:2298 +name: Gene ID (HGNC) +subset: bioinformatics subset: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1485 ! Structure alignment (protein all atoms) - +subset: edam +subset: identifiers +synonym: "HGNC ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier for a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1488 -name: Pairwise protein tertiary structure alignment (C-alpha atoms) -namespace: data +id: EDAM_data:2299 +name: Gene name +subset: bioinformatics subset: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] -comment: C-beta atoms from amino acid side-chains may be included. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1025 ! Gene identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:1489 -name: Multiple protein tertiary structure alignment (all atoms) -namespace: data +id: EDAM_data:2300 +name: Gene name (NCBI) +subset: bioinformatics subset: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1485 ! Structure alignment (protein all atoms) +subset: edam +subset: identifiers +synonym: "NCBI gene name" EXACT [] +created_in: "beta12orEarlier" +def: "Name of an entry (gene) from the NCBI genes database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1490 -name: Multiple protein tertiary structure alignment (C-alpha atoms) -namespace: data +id: EDAM_data:2301 +name: SMILES string +subset: bioinformatics subset: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] -comment: C-beta atoms from amino acid side-chains may be included. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms) +subset: edam +created_in: "beta12orEarlier" +def: "A specification of a chemical structure in SMILES format." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0846 ! Chemical formula [Term] -id: EDAM_data:1491 -name: Structure alignment (nucleic acid pair) -namespace: data +id: EDAM_data:2302 +name: STRING ID +subset: bioinformatics subset: data -def: "Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures." [http://edamontology.org] -is_a: EDAM_data:1482 ! Structure alignment (nucleic acid) -is_a: EDAM_data:1479 ! Structure alignment (pair) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the STRING database of protein-protein interactions." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM_data:1492 -name: Multiple nucleic acid tertiary structure alignment -namespace: data +id: EDAM_data:2307 +name: Virus annotation +subset: bioinformatics subset: data -def: "Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1482 ! Structure alignment (nucleic acid) - +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific virus." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2530 ! Organism annotation [Term] -id: EDAM_data:1493 -name: Structure alignment (RNA) -namespace: data +id: EDAM_data:2308 +name: Virus annotation (taxonomy) +subset: bioinformatics subset: data -def: "Alignment (superimposition) of RNA tertiary (3D) structures." [http://edamontology.org] -is_a: EDAM_data:1482 ! Structure alignment (nucleic acid) +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on the taxonomy of a specific virus." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2307 ! Virus annotation [Term] -id: EDAM_data:0866 -name: Sequence alignment metadata -namespace: data +id: EDAM_data:2309 +name: Reaction ID (SABIO-RK) +subset: bioinformatics subset: data -def: "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." [http://edamontology.org] -is_a: EDAM_data:0867 ! Sequence alignment report -is_a: EDAM_data:2337 ! Metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a biological reaction from the SABIO-RK reactions database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2108 ! Reaction ID [Term] -id: EDAM_data:1414 -name: Sequence alignment metadata (quality report) -namespace: data +id: EDAM_data:2313 +name: Carbohydrate structure report +subset: bioinformatics subset: data -def: "Data on molecular sequence alignment quality (estimated accuracy)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0867 ! Sequence alignment report - +subset: edam +created_in: "beta12orEarlier" +def: "Annotation on or information derived from one or more specific carbohydrate 3D structure(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2085 ! Structure report [Term] -id: EDAM_data:1415 -name: Sequence alignment report (site conservation) -namespace: data +id: EDAM_data:2314 +name: GI number +comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. +subset: bioinformatics subset: data -def: "Data on character conservation in a molecular sequence alignment." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. -is_a: EDAM_data:0867 ! Sequence alignment report - +subset: edam +subset: identifiers +synonym: "gi number" EXACT [] +synonym: "NCBI GI number" EXACT [] +created_in: "beta12orEarlier" +def: "A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] -id: EDAM_data:1416 -name: Sequence alignment report (site correlation) -namespace: data +id: EDAM_data:2315 +name: NCBI version +comment: Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. +subset: bioinformatics subset: data -def: "Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures." [http://edamontology.org] -is_a: EDAM_data:0867 ! Sequence alignment report +subset: edam +subset: identifiers +synonym: "accession.version" EXACT [] +synonym: "NCBI accession.version" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] -id: EDAM_data:2242 -name: Phylogenetic property values -namespace: data +id: EDAM_data:2316 +name: Cell line name +subset: bioinformatics subset: data -def: "Phylogenetic property values data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0871 ! Phylogenetic character data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a cell line." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1046 ! Strain name [Term] -id: EDAM_data:1444 -name: Phylogenetic character contrasts -namespace: data +id: EDAM_data:2317 +name: Cell line name (exact) +subset: bioinformatics subset: data -def: "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." [http://edamontology.org] -synonym: "Phylogenetic report (character contrasts)" EXACT [http://edamontology.org] -is_a: EDAM_data:2523 ! Phylogenetic raw data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a cell line." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2316 ! Cell line name [Term] -id: EDAM_data:1426 -name: Phylogenetic continuous quantitative data -namespace: data +id: EDAM_data:2318 +name: Cell line name (truncated) +subset: bioinformatics subset: data -def: "Continuous quantitative data that may be read during phylogenetic tree calculation." [http://edamontology.org] -synonym: "Quantitative traits" EXACT [http://edamontology.org] -synonym: "Phylogenetic continuous quantitative characters" EXACT [http://edamontology.org] -is_a: EDAM_data:0871 ! Phylogenetic character data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a cell line." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2316 ! Cell line name [Term] -id: EDAM_data:2873 -name: Phylogenetic gene frequencies data -namespace: data +id: EDAM_data:2319 +name: Cell line name (no punctuation) +subset: bioinformatics subset: data -def: "Gene frequencies data that may be read during phylogenetic tree calculation." [http://edamontology.org] -is_a: EDAM_data:1426 ! Phylogenetic continuous quantitative data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a cell line." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2316 ! Cell line name [Term] -id: EDAM_data:1427 -name: Phylogenetic discrete data -namespace: data +id: EDAM_data:2320 +name: Cell line name (assonant) +subset: bioinformatics subset: data -def: "Character data with discrete states that may be read during phylogenetic tree calculation." [http://edamontology.org] -synonym: "Discretely coded characters" EXACT [http://edamontology.org] -synonym: "Discrete characters" EXACT [http://edamontology.org] -synonym: "Phylogenetic discrete states" EXACT [http://edamontology.org] -is_a: EDAM_data:0871 ! Phylogenetic character data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a cell line." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2316 ! Cell line name [Term] -id: EDAM_data:2994 -name: Phylogenetic character weights -namespace: data +id: EDAM_data:2321 +name: Enzyme ID +subset: bioinformatics subset: data -def: "Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted." [http://edamontology.org] -is_a: EDAM_data:2523 ! Phylogenetic raw data +subset: edam +subset: identifiers +synonym: "Enzyme accession" EXACT [] +created_in: "beta12orEarlier" +def: "A unique, persistent identifier of an enzyme." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1010 ! Enzyme identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1428 -name: Phylogenetic character cliques -namespace: data +id: EDAM_data:2325 +name: REBASE enzyme number +subset: bioinformatics subset: data -def: "One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny." [http://edamontology.org] -synonym: "Phylogenetic report (cliques)" EXACT [http://edamontology.org] -is_a: EDAM_data:2523 ! Phylogenetic raw data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an enzyme from the REBASE enzymes database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2321 ! Enzyme ID [Term] -id: EDAM_data:1429 -name: Phylogenetic invariants -namespace: data +id: EDAM_data:2326 +name: DrugBank ID +subset: bioinformatics subset: data -def: "Phylogenetic invariants data for testing alternative tree topologies." [http://edamontology.org] -synonym: "Phylogenetic report (invariants)" EXACT [http://edamontology.org] -is_a: EDAM_data:2523 ! Phylogenetic raw data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a drug from the DrugBank database." [http://edamontology.org] +regex: "DB[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2895 ! Drug accession [Term] -id: EDAM_data:2247 -name: Phylogenetic consensus tree -namespace: data +id: EDAM_data:2327 +name: GI number (protein) +comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. +subset: bioinformatics subset: data -def: "A consensus phylogenetic tree derived from comparison of multiple trees." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0872 ! Phylogenetic tree +subset: edam +subset: identifiers +synonym: "protein gi" EXACT [] +synonym: "protein gi number" EXACT [] +created_in: "beta12orEarlier" +def: "A unique identifier assigned to NCBI protein sequence records." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2314 ! GI number [Term] -id: EDAM_data:1439 -name: DNA substitution model -namespace: data +id: EDAM_data:2335 +name: Bit score +comment: Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. +subset: bioinformatics subset: data -def: "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." [http://edamontology.org] -synonym: "Sequence alignment report (DNA substitution model)" EXACT [http://edamontology.org] -synonym: "Phylogenetic tree report (DNA substitution model)" EXACT [http://edamontology.org] -is_a: EDAM_data:1438 ! Phylogenetic tree report -is_a: EDAM_data:0950 ! Biological model -is_a: EDAM_data:0867 ! Sequence alignment report - +subset: edam +created_in: "beta12orEarlier" +def: "A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1413 ! Sequence similarity [Term] -id: EDAM_data:1440 -name: Phylogenetic tree report (tree shape) -namespace: data +id: EDAM_data:2336 +name: Translation phase specification +subset: bioinformatics subset: data -def: "Data about the shape of a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_data:1438 ! Phylogenetic tree report +subset: edam +synonym: "Phase" EXACT [] +created_in: "beta12orEarlier" +def: "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2534 ! Sequence parameter +is_a: EDAM_data:2914 ! Sequence features metadata [Term] -id: EDAM_data:1441 -name: Phylogenetic tree report (tree evaluation) -namespace: data +id: EDAM_data:2337 +name: Metadata +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "Data on the confidence of a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_data:1438 ! Phylogenetic tree report - +subset: edam +synonym: "Provenance metadata" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_data:1442 -name: Phylogenetic tree report (tree distances) -namespace: data +id: EDAM_data:2338 +name: Ontology identifier +subset: bioinformatics subset: data -def: "Distances, such as Branch Score distance, between two or more phylogenetic trees." [http://edamontology.org] -is_a: EDAM_data:1438 ! Phylogenetic tree report +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Any arbitrary identifier of an ontology." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:0582 ! Ontology [Term] -id: EDAM_data:1443 -name: Phylogenetic tree report (tree stratigraphic) -namespace: data +id: EDAM_data:2339 +name: Ontology concept name +subset: bioinformatics subset: data -def: "Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis." [http://edamontology.org] -is_a: EDAM_data:1438 ! Phylogenetic tree report +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a concept in an ontology." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:3025 ! Ontology concept identifier [Term] -id: EDAM_data:1446 -name: Comparison matrix (integers) -namespace: data +id: EDAM_data:2340 +name: Genome build identifier +subset: bioinformatics subset: data -def: "Matrix of integer numbers for sequence comparison." [http://edamontology.org] -synonym: "Substitution matrix (integers)" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0874 ! Comparison matrix +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a build of a particular genome." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2749 ! Genome identifier [Term] -id: EDAM_data:1447 -name: Comparison matrix (floats) -namespace: data +id: EDAM_data:2342 +name: Pathway or network name +subset: bioinformatics subset: data -def: "Matrix of floating point numbers for sequence comparison." [http://edamontology.org] -synonym: "Substitution matrix (floats)" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0874 ! Comparison matrix +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a biological pathway or network." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1082 ! Pathway or network identifier [Term] -id: EDAM_data:1448 -name: Comparison matrix (nucleotide) -namespace: data +id: EDAM_data:2343 +name: Pathway ID (KEGG) +subset: bioinformatics subset: data -def: "Matrix of integer or floating point numbers for nucleotide comparison." [http://edamontology.org] -synonym: "Nucleotide substitution matrix" EXACT [http://edamontology.org] -is_a: EDAM_data:0874 ! Comparison matrix +subset: edam +subset: identifiers +synonym: "KEGG pathway ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a pathway from the KEGG pathway database." [http://edamontology.org] +regex: "[a-zA-Z_0-9]{2,3}[0-9]{5}" +namespace: identifier +is_a: EDAM_data:1154 ! KEGG object identifier +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_data:1449 -name: Comparison matrix (amino acid) -namespace: data +id: EDAM_data:2344 +name: Pathway ID (NCI-Nature) +subset: bioinformatics subset: data -def: "Matrix of integer or floating point numbers for amino acid comparison." [http://edamontology.org] -synonym: "Amino acid substitution matrix" EXACT [http://edamontology.org] -is_a: EDAM_data:2016 ! Amino acid property -is_a: EDAM_data:0874 ! Comparison matrix +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a pathway from the NCI-Nature pathway database." [http://edamontology.org] +regex: "[a-zA-Z_0-9]+" +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_data:1450 -name: Nucleotide comparison matrix (integers) -namespace: data +id: EDAM_data:2345 +name: Pathway ID (ConsensusPathDB) +subset: bioinformatics subset: data -def: "Matrix of integer numbers for nucleotide comparison." [http://edamontology.org] -synonym: "Nucleotide substitution matrix (integers)" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1448 ! Comparison matrix (nucleotide) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a pathway from the ConsensusPathDB pathway database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession +is_a: EDAM_data:2917 ! ConsensusPathDB identifier [Term] -id: EDAM_data:1451 -name: Nucleotide comparison matrix (floats) -namespace: data +id: EDAM_data:2346 +name: Sequence cluster ID (UniRef) +subset: bioinformatics subset: data -def: "Matrix of floating point numbers for nucleotide comparison." [http://edamontology.org] -synonym: "Nucleotide substitution matrix (floats)" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1448 ! Comparison matrix (nucleotide) - +subset: edam +subset: identifiers +synonym: "UniRef cluster id" EXACT [] +synonym: "UniRef entry accession" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the UniRef database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1112 ! Sequence cluster ID [Term] -id: EDAM_data:1452 -name: Amino acid comparison matrix (integers) -namespace: data +id: EDAM_data:2347 +name: Sequence cluster ID (UniRef100) +subset: bioinformatics subset: data -def: "Matrix of integer numbers for amino acid comparison." [http://edamontology.org] -synonym: "Amino acid substitution matrix (integers)" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1449 ! Comparison matrix (amino acid) - +subset: edam +subset: identifiers +synonym: "UniRef100 cluster id" EXACT [] +synonym: "UniRef100 entry accession" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the UniRef100 database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) [Term] -id: EDAM_data:1453 -name: Amino acid comparison matrix (floats) -namespace: data +id: EDAM_data:2348 +name: Sequence cluster ID (UniRef90) +subset: bioinformatics subset: data -def: "Matrix of floating point numbers for amino acid comparison." [http://edamontology.org] -synonym: "Amino acid substitution matrix (floats)" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1449 ! Comparison matrix (amino acid) - +subset: edam +subset: identifiers +synonym: "UniRef90 cluster id" EXACT [] +synonym: "UniRef90 entry accession" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the UniRef90 database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) [Term] -id: EDAM_data:1540 -name: Protein residue interactions -namespace: data +id: EDAM_data:2349 +name: Sequence cluster ID (UniRef50) +subset: bioinformatics subset: data -def: "Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups." [http://edamontology.org] -synonym: "Residue interaction data" EXACT [http://edamontology.org] -synonym: "Atom interaction data" EXACT [http://edamontology.org] -is_a: EDAM_data:2599 ! Molecular interaction -is_a: EDAM_data:0906 ! Protein interaction -relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis +subset: edam +subset: identifiers +synonym: "UniRef50 cluster id" EXACT [] +synonym: "UniRef50 entry accession" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the UniRef50 database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) [Term] -id: EDAM_data:1543 -name: Protein surface report -namespace: data +id: EDAM_data:2353 +name: Ontological data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -synonym: "Protein structure report (surface)" EXACT [http://edamontology.org] -is_a: EDAM_data:1542 ! Protein solvent accessibility -is_a: EDAM_data:1537 ! Protein structure report - +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning an ontology." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0582 ! Ontology +consider: EDAM_data:2223 ! Ontology metadata [Term] -id: EDAM_data:0875 -name: Protein topology -namespace: data +id: EDAM_data:2354 +name: RNA family annotation +subset: bioinformatics subset: data -def: "Predicted or actual protein topology represented as a string of protein secondary structure elements." [http://edamontology.org] -comment: The location and size of the secondary structure elements and intervening loop regions is usually indicated. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0876 ! Protein features (secondary structure) +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific RNA family or other group of classified RNA sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2986 ! Nucleic acid classification [Term] -id: EDAM_data:2081 -name: Secondary structure -namespace: data +id: EDAM_data:2355 +name: RNA family identifier +subset: bioinformatics subset: data -def: "The secondary structure assignment (predicted or real) of a nucleic acid or protein." [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an RNA family, typically an entry from a RNA sequence classification database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:2354 ! RNA family annotation [Term] -id: EDAM_data:0877 -name: Protein features (super-secondary) -namespace: data +id: EDAM_data:2356 +name: RFAM accession +subset: bioinformatics subset: data -def: "A report of predicted or actual super-secondary structure of protein sequence(s)." [http://edamontology.org] -comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. -synonym: "Protein structure report (super-secondary)" EXACT [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features -is_a: EDAM_data:1537 ! Protein structure report +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Stable accession number of an entry (RNA family) from the RFAM database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2355 ! RNA family identifier [Term] -id: EDAM_data:0902 -name: Protein architecture report -namespace: data +id: EDAM_data:2357 +name: Protein signature type +subset: bioinformatics subset: data -def: "An informative report on architecture (spatial arrangement of secondary structure) of a protein structure." [http://edamontology.org] -synonym: "Protein structure report (architecture)" EXACT [http://edamontology.org] -synonym: "Protein property (architecture)" EXACT [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property -is_a: EDAM_data:1537 ! Protein structure report +subset: edam +created_in: "beta12orEarlier" +def: "A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2100 ! Type +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM_data:0883 -name: Structure -namespace: data +id: EDAM_data:2358 +name: Domain-nucleic acid interaction +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [http://edamontology.org] -synonym: "Structure data" EXACT [http://edamontology.org] -comment: The coordinate data may be predicted or real. -relationship: has_topic EDAM_topic:0081 ! Structure analysis -is_a: EDAM_data:3031 ! Core data - +subset: edam +created_in: "beta12orEarlier" +def: "Data on protein domain-DNA/RNA interaction(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1567 ! Protein-nucleic acid interaction [Term] -id: EDAM_data:0884 -name: Tertiary structure record -namespace: data +id: EDAM_data:2359 +name: Domain-domain interaction +subset: bioinformatics subset: data -def: "An entry from a molecular tertiary (3D) structure database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0883 ! Structure - +subset: edam +created_in: "beta12orEarlier" +def: "Data on protein domain-protein domain interaction(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1565 ! Protein-protein interaction [Term] -id: EDAM_data:1546 -name: Protein distance matrix -namespace: data +id: EDAM_data:2360 +name: Domain-domain interaction (indirect) +subset: bioinformatics subset: data -def: "A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org] -is_a: EDAM_data:1540 ! Protein residue interactions - +subset: edam +created_in: "beta12orEarlier" +def: "Data on indirect protein domain-protein domain interaction(s)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2359 ! Domain-domain interaction [Term] -id: EDAM_data:1547 -name: Protein contact map -namespace: data +id: EDAM_data:2362 +name: Sequence accession (hybrid) +subset: bioinformatics subset: data -def: "An amino acid residue contact map for a protein structure." [http://edamontology.org] -is_a: EDAM_data:1540 ! Protein residue interactions +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of a nucleotide or protein sequence database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1093 ! Sequence accession +relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] -id: EDAM_data:1548 -name: Protein residue 3D cluster -namespace: data +id: EDAM_data:2363 +name: 2D PAGE data +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics subset: data -def: "Report on clusters of contacting residues in protein structures such as a key structural residue network." [http://edamontology.org] -is_a: EDAM_data:1540 ! Protein residue interactions +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning two-dimensional polygel electrophoresis." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0942 ! 2D PAGE image +consider: EDAM_data:2364 ! Experiment annotation (2D PAGE) [Term] -id: EDAM_data:1549 -name: Protein hydrogen bonds -namespace: data +id: EDAM_data:2364 +name: Experiment annotation (2D PAGE) +subset: bioinformatics subset: data -def: "Patterns of hydrogen bonding in protein structures." [http://edamontology.org] -is_a: EDAM_data:1540 ! Protein residue interactions +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2531 ! Experiment annotation +relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] -id: EDAM_data:1550 -name: Protein non-canonical interactions -namespace: data +id: EDAM_data:2365 +name: Pathway or network accession +subset: bioinformatics subset: data -def: "Non-canonical atomic interactions in protein structures." [http://edamontology.org] -synonym: "Protein non-canonical interactions report" EXACT [http://edamontology.org] -is_a: EDAM_data:1540 ! Protein residue interactions -is_a: EDAM_data:1539 ! Protein structural quality report +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A persistent, unique identifier of a biological pathway or network (typically a database entry)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1082 ! Pathway or network identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1542 -name: Protein solvent accessibility -namespace: data +id: EDAM_data:2366 +name: Secondary structure alignment +subset: bioinformatics subset: data -def: "Data on the solvent accessible or buried surface area of a protein structure." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. -is_a: EDAM_data:1540 ! Protein residue interactions +subset: edam +created_in: "beta12orEarlier" +def: "Alignment of the (1D representations of) secondary structure of two or more molecules." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1916 ! Alignment [Term] -id: EDAM_data:0876 -name: Protein features (secondary structure) -namespace: data +id: EDAM_data:2367 +name: ASTD ID +subset: bioinformatics subset: data -def: "Secondary structure assignment (predicted or real) of a protein." [http://edamontology.org] -comment: The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). -synonym: "Protein secondary structure" EXACT [http://edamontology.org] -is_a: EDAM_data:2081 ! Secondary structure -is_a: EDAM_data:1277 ! Protein features -relationship: has_topic EDAM_topic:0694 ! Protein secondary structure - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an object from the ASTD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:0880 -name: RNA secondary structure record -namespace: data +id: EDAM_data:2368 +name: ASTD ID (exon) +subset: bioinformatics subset: data -def: "An informative report of secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] -comment: This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. -xref: Moby:RNAStructML -is_a: EDAM_data:2081 ! Secondary structure -relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an exon from the ASTD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2367 ! ASTD ID [Term] -id: EDAM_data:1456 -name: Protein features (membrane regions) -namespace: data +id: EDAM_data:2369 +name: ASTD ID (intron) +subset: bioinformatics subset: data -def: "An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." [http://edamontology.org] -comment: This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. -synonym: "Transmembrane region report" EXACT [http://edamontology.org] -synonym: "Intramembrane region report" EXACT [http://edamontology.org] -synonym: "Protein report (membrane protein)" EXACT [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an intron from the ASTD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2367 ! ASTD ID [Term] -id: EDAM_data:1755 -name: Protein atom -namespace: data +id: EDAM_data:2370 +name: ASTD ID (polya) +subset: bioinformatics subset: data -def: "Data on a single atom from a protein structure." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -synonym: "Atom data" EXACT [http://edamontology.org] -synonym: "atom" RELATED [CHEBI:33250] -is_a: EDAM_data:1460 ! Protein structure +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a polyA signal from the ASTD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2367 ! ASTD ID [Term] -id: EDAM_data:1756 -name: Protein residue -namespace: data +id: EDAM_data:2371 +name: ASTD ID (tss) +subset: bioinformatics subset: data -def: "Data on a single amino acid residue position in a protein structure." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -synonym: "Residue" EXACT [http://edamontology.org] -is_a: EDAM_data:1460 ! Protein structure +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a transcription start site from the ASTD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2367 ! ASTD ID [Term] -id: EDAM_data:1459 -name: Nucleic acid structure -namespace: data +id: EDAM_data:2372 +name: 2D PAGE spot (annotated) +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a nucleic acid tertiary (3D) structure." [http://edamontology.org] -is_a: EDAM_data:0883 ! Structure -relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis - +subset: edam +synonym: "2D PAGE spot annotation" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2965 ! 2D PAGE image (annotated) [Term] -id: EDAM_data:1460 -name: Protein structure -namespace: data +id: EDAM_data:2373 +name: Spot ID +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a protein tertiary (3D) structure." [http://edamontology.org] -is_a: EDAM_data:0883 ! Structure -relationship: has_topic EDAM_topic:2814 ! Protein structure analysis -relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a spot from a two-dimensional (protein) gel." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1461 -name: Protein-ligand complex -namespace: data +id: EDAM_data:2374 +name: Spot serial number +subset: bioinformatics subset: data -def: "The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule." [http://edamontology.org] -comment: This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. -is_a: EDAM_data:1460 ! Protein structure - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2373 ! Spot ID [Term] -id: EDAM_data:1462 -name: Carbohydrate structure -namespace: data +id: EDAM_data:2375 +name: Spot ID (HSC-2DPAGE) +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a carbohydrate (3D) structure." [http://edamontology.org] -is_a: EDAM_data:0883 ! Structure -relationship: has_topic EDAM_topic:0152 ! Carbohydrates -relationship: has_topic EDAM_topic:0153 ! Lipids +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2373 ! Spot ID + +[Term] +id: EDAM_data:2378 +name: Protein-motif interaction +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1565 ! Protein-protein interaction [Term] -id: EDAM_data:2850 -name: Lipid structure -namespace: data +id: EDAM_data:2379 +name: Strain identifier +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a lipid structure." [http://edamontology.org] -is_a: EDAM_data:0883 ! Structure +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1869 ! Organism identifier [Term] -id: EDAM_data:1463 -name: Small molecule structure -namespace: data +id: EDAM_data:2380 +name: CABRI accession +subset: bioinformatics subset: data -def: "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." [http://edamontology.org] -synonym: "molecular entity" RELATED [CHEBI:23367] -is_a: EDAM_data:0883 ! Structure -relationship: has_topic EDAM_topic:0154 ! Small molecules +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of an item from the CABRI database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:2851 -name: Drug structure -namespace: data +id: EDAM_data:2381 +name: Experiment annotation (genotype) +subset: bioinformatics subset: data -def: "3D coordinate and associated data for the (3D) structure of a drug." [http://edamontology.org] -is_a: EDAM_data:1463 ! Small molecule structure +subset: edam +created_in: "beta12orEarlier" +def: "Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2531 ! Experiment annotation [Term] -id: EDAM_data:2852 -name: Toxin structure -namespace: data +id: EDAM_data:2382 +name: Genotype experiment ID +subset: bioinformatics subset: data -def: "3D coordinate and associated data for the (3D) structure of a toxin." [http://edamontology.org] -is_a: EDAM_data:1463 ! Small molecule structure - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from a database of genotype experiment metadata." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:2381 ! Experiment annotation (genotype) [Term] -id: EDAM_data:1464 -name: DNA structure -namespace: data +id: EDAM_data:2383 +name: EGA accession +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a DNA tertiary (3D) structure." [http://edamontology.org] -is_a: EDAM_data:1459 ! Nucleic acid structure +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the EGA database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2382 ! Genotype experiment ID [Term] -id: EDAM_data:1465 -name: RNA structure record -namespace: data +id: EDAM_data:2384 +name: IPI protein ID +subset: bioinformatics subset: data -def: "3D coordinate and associated data for an RNA tertiary (3D) structure." [http://edamontology.org] -is_a: EDAM_data:1459 ! Nucleic acid structure -relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a protein entry catalogued in the International Protein Index (IPI) database." [http://edamontology.org] +regex: "IPI[0-9]{8}" +namespace: identifier +is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] -id: EDAM_data:1466 -name: tRNA structure record -namespace: data +id: EDAM_data:2385 +name: RefSeq accession (protein) +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." [http://edamontology.org] -is_a: EDAM_data:1465 ! RNA structure record +subset: edam +subset: identifiers +synonym: "RefSeq protein ID" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of a protein from the RefSeq database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1098 ! RefSeq accession [Term] -id: EDAM_data:1467 -name: Protein chain -namespace: data +id: EDAM_data:2386 +name: EPD ID +subset: bioinformatics subset: data -def: "3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain." [http://edamontology.org] -is_a: EDAM_data:1460 ! Protein structure +subset: edam +subset: identifiers +synonym: "EPD identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry (promoter) from the EPD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2727 ! Promoter ID [Term] -id: EDAM_data:1468 -name: Protein domain -namespace: data +id: EDAM_data:2387 +name: TAIR accession +subset: bioinformatics subset: data -def: "3D coordinate and associated data for the tertiary (3D) structure of a protein domain." [http://edamontology.org] -is_a: EDAM_data:1460 ! Protein structure -relationship: has_topic EDAM_topic:0736 ! Protein domains and folds +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the TAIR database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:2877 -name: Protein complex -namespace: data +id: EDAM_data:2388 +name: TAIR accession (At gene) +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another." [http://edamontology.org] -is_a: EDAM_data:1460 ! Protein structure +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an Arabidopsis thaliana gene from the TAIR database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1037 ! TAIR accession (gene) [Term] -id: EDAM_data:2878 -name: Protein structural motif -namespace: data +id: EDAM_data:2389 +name: UniSTS accession +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role." [http://edamontology.org] -is_a: EDAM_data:1460 ! Protein structure +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the UniSTS database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] -id: EDAM_data:1469 -name: Protein structure (all atoms) -namespace: data +id: EDAM_data:2390 +name: UNITE accession +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a protein tertiary (3D) structure (all atoms)." [http://edamontology.org] -is_a: EDAM_data:1460 ! Protein structure +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the UNITE database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] -id: EDAM_data:1470 -name: Protein structure (C-alpha atoms) -namespace: data +id: EDAM_data:2391 +name: UTR accession +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] -comment: C-beta atoms from amino acid side-chains may be included. -is_a: EDAM_data:1460 ! Protein structure +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the UTR database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] -id: EDAM_data:1471 -name: Protein chain (all atoms) -namespace: data +id: EDAM_data:2392 +name: UniParc accession +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1467 ! Protein chain -consider: EDAM_data:1469 ! Protein structure (all atoms) +subset: edam +subset: identifiers +synonym: "UniParc ID" EXACT [] +synonym: "UPI" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of a UniParc (protein sequence) database entry." [http://edamontology.org] +regex: "UPI[A-F0-9]{10}" +namespace: identifier +is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] -id: EDAM_data:1472 -name: Protein chain (C-alpha atoms) -namespace: data +id: EDAM_data:2393 +name: mFLJ/mKIAA number +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] -comment: C-beta atoms from amino acid side-chains may be included. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1467 ! Protein chain -consider: EDAM_data:1470 ! Protein structure (C-alpha atoms) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the Rouge or HUGE databases." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1473 -name: Protein domain (all atoms) -namespace: data +id: EDAM_data:2395 +name: Fungi annotation +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1468 ! Protein domain -consider: EDAM_data:1469 ! Protein structure (all atoms) +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific fungus." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2530 ! Organism annotation [Term] -id: EDAM_data:1474 -name: Protein domain (C-alpha atoms) -namespace: data +id: EDAM_data:2396 +name: Fungi annotation (anamorph) +subset: bioinformatics subset: data -def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] -comment: C-beta atoms from amino acid side-chains may be included. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1468 ! Protein domain -consider: EDAM_data:1470 ! Protein structure (C-alpha atoms) - +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific fungus anamorph." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2395 ! Fungi annotation [Term] -id: EDAM_data:1495 -name: DaliLite hit table -namespace: data +id: EDAM_data:2397 +name: Nucleic acid features (exon) +subset: bioinformatics subset: data -def: "DaliLite hit table of protein chain tertiary structure alignment data." [http://edamontology.org] -comment: The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0887 ! Structure alignment report - +subset: edam +synonym: "Gene features (exon)" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on an exon in a nucleotide sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] -id: EDAM_data:1499 -name: 3D-1D scoring matrix -namespace: data +id: EDAM_data:2398 +name: Protein ID (Ensembl) +subset: bioinformatics subset: data -def: "A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments." [http://edamontology.org] -is_a: EDAM_data:0892 ! Protein sequence-structure scoring matrix - +subset: edam +subset: identifiers +synonym: "Ensembl protein ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier for a protein from the Ensembl database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2610 ! Ensembl ID +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:0894 -name: Amino acid annotation +id: EDAM_data:2399 +name: Gene annotation (transcript) +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene annotation (clone or EST)" EXACT [] +synonym: "Gene transcript annotation" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on a specific gene transcript, clone or EST." [http://edamontology.org] namespace: data +is_a: EDAM_data:0916 ! Gene annotation + +[Term] +id: EDAM_data:2400 +name: Toxin annotation +subset: bioinformatics subset: data -def: "An informative report about a specific amino acid." [http://edamontology.org] -is_a: EDAM_data:2016 ! Amino acid property +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific toxin." [http://edamontology.org] +namespace: data is_a: EDAM_data:0962 ! Small molecule annotation - +[Term] +id: EDAM_data:2401 +name: Protein report (membrane protein) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a membrane protein." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1456 ! Protein features (membrane regions) [Term] -id: EDAM_data:1501 -name: Amino acid index -namespace: data +id: EDAM_data:2402 +name: Protein-drug interaction +subset: bioinformatics subset: data -def: "A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids." [http://edamontology.org] -is_a: EDAM_data:2016 ! Amino acid property -is_a: EDAM_data:2082 ! Matrix +subset: edam +created_in: "beta12orEarlier" +def: "Informative report on protein-drug interaction(s) including binding affinity data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1566 ! Protein-ligand interaction [Term] -id: EDAM_data:1503 -name: Amino acid pair-wise contact potentials -namespace: data +id: EDAM_data:2522 +name: Map data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "Statistical protein contact potentials." [http://edamontology.org] -is_a: EDAM_data:2016 ! Amino acid property +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning a map of molecular sequence(s)." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1274 ! Map +consider: EDAM_data:2019 ! Map attribute [Term] -id: EDAM_data:1502 -name: Amino acid index (chemical classes) -namespace: data +id: EDAM_data:2523 +name: Phylogenetic raw data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." [http://edamontology.org] -is_a: EDAM_data:1501 ! Amino acid index - +subset: edam +synonym: "Phylogenetic data" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning phylogeny, typically of molecular sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:1505 -name: Amino acid index (molecular weight) -namespace: data +id: EDAM_data:2524 +name: Protein data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "Molecular weights of amino acids." [http://edamontology.org] -is_a: EDAM_data:1501 ! Amino acid index +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning one or more protein molecules." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0896 ! Protein report [Term] -id: EDAM_data:1506 -name: Amino acid index (hydropathy) -namespace: data +id: EDAM_data:2525 +name: Nucleic acid data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "Hydrophobic, hydrophilic or charge properties of amino acids." [http://edamontology.org] -is_a: EDAM_data:1501 ! Amino acid index - +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning one or more nucleic acid molecules." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2084 ! Nucleic acid report [Term] -id: EDAM_data:1507 -name: Amino acid index (White-Wimley data) -namespace: data +id: EDAM_data:2526 +name: Article data +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. +subset: bioinformatics subset: data -def: "Experimental free energy values for the water-interface and water-octanol transitions for the amino acids." [http://edamontology.org] -is_a: EDAM_data:1501 ! Amino acid index +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning the scientific literature." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0971 ! Article [Term] -id: EDAM_data:1508 -name: Amino acid index (van der Waals radii) +id: EDAM_data:2527 +name: Parameter +subset: bioinformatics +subset: data +subset: edam +synonym: "Parameter" EXACT [] +synonym: "Parameter or primitive" EXACT [] +synonym: "SIO:000144" EXACT [] +synonym: "Tool parameter" EXACT [] +synonym: "Tool-specific parameter" EXACT [] +created_in: "beta12orEarlier" +def: "Typically a simple numerical or string value that controls the operation of a tool." [http://edamontology.org] namespace: data -subset: data -def: "Van der Waals radii of atoms for different amino acid residues." [http://edamontology.org] -is_a: EDAM_data:1501 ! Amino acid index +is_a: EDAM_data:0006 ! Data +disjoint_from: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:1509 -name: Enzyme property -namespace: data +id: EDAM_data:2528 +name: Molecular data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "An informative report on a specific enzyme." [http://edamontology.org] -synonym: "Enzyme report" EXACT [http://edamontology.org] -synonym: "Protein report (enzyme)" EXACT [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property -relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions +subset: edam +synonym: "Molecule-specific data" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning a specific type of molecule." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2529 ! Molecule report [Term] -id: EDAM_data:1776 -name: Protein report (function) -namespace: data +id: EDAM_data:2529 +name: Molecule report +subset: bioinformatics subset: data -def: "Report on general functional properties of specific protein(s)." [http://edamontology.org] -comment: For properties that can be mapped to a sequence, use 'Sequence report' instead. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0896 ! Protein report - - +subset: edam +synonym: "Molecular report" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on a specific molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_data:2722 -name: Protein features (disordered structure) -namespace: data +id: EDAM_data:2530 +name: Organism annotation +subset: bioinformatics subset: data -def: "An informative report about disordered structure in a protein." [http://edamontology.org] -synonym: "Protein structure report (disordered structure)" EXACT [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features -is_a: EDAM_data:1537 ! Protein structure report - +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on a specific organism." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_data:2147 -name: Protein report (transcription factor) -namespace: data +id: EDAM_data:2531 +name: Experiment annotation +subset: bioinformatics subset: data -def: "An informative report on a transcription factor protein." [http://edamontology.org] -comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. -synonym: "Transcription factor binding site data" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:0896 ! Protein report - +subset: edam +created_in: "beta12orEarlier" +def: "Annotation on a wet lab experiment, such as experimental conditions." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_data:2401 -name: Protein report (membrane protein) -namespace: data +id: EDAM_data:2533 +name: Nucleic acid features (mutation) +subset: bioinformatics subset: data -def: "An informative report on a membrane protein." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1456 ! Protein features (membrane regions) - +subset: edam +synonym: "Mutation annotation" EXACT [] +created_in: "beta12orEarlier" +def: "Annotation on a mutation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0918 ! Nucleic acid features (variation) [Term] -id: EDAM_data:1517 -name: Restriction enzyme property -namespace: data +id: EDAM_data:2534 +name: Sequence parameter +subset: bioinformatics subset: data -! alt_id: EDAM_data:1510 -! alt_id: EDAM_data:1518 -def: "An informative report on a specific restriction enzyme such as enzyme reference data." [http://edamontology.org] -comment: This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. -synonym: "Restriction enzyme report" EXACT [http://edamontology.org] -synonym: "Restriction enzyme pattern data" EXACT [http://edamontology.org] -synonym: "Protein report (restriction enzyme)" EXACT [http://edamontology.org] -is_a: EDAM_data:1509 ! Enzyme property - +subset: edam +created_in: "beta12orEarlier" +def: "A parameter concerning calculations on molecular sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM_data:1533 -name: Protein subcellular localization -namespace: data +id: EDAM_data:2535 +name: Sequence tag profile +comment: SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. +subset: bioinformatics subset: data -def: "An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." [http://edamontology.org] -synonym: "Protein report (subcellular localization)" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:0896 ! Protein report +subset: edam +synonym: "Sequencing-based expression profile" EXACT [] +created_in: "beta12orEarlier" +def: "Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0928 ! Gene expression profile [Term] -id: EDAM_data:2191 -name: Protein features (chemical modification) -namespace: data +id: EDAM_data:2536 +name: Mass spectrometry data +subset: bioinformatics subset: data -def: "Data on a chemical modification of a protein." [http://edamontology.org] -synonym: "Protein modification annotation" EXACT [http://edamontology.org] -synonym: "protein modification" RELATED [MOD:00000] -synonym: "protein modification process" RELATED [GO:0006464] -is_a: EDAM_data:1277 ! Protein features - +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning a mass spectrometry measurement." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3108 ! Experimental measurement [Term] -id: EDAM_data:2991 -name: Protein torsion angle data -namespace: data +id: EDAM_data:2537 +name: Protein structure raw data +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics subset: data -def: "Torsion angle data for a protein structure." [http://edamontology.org] -synonym: "Torsion angle data" EXACT [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property - +subset: edam +created_in: "beta12orEarlier" +def: "Raw data from experimental methods for determining protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3108 ! Experimental measurement [Term] -id: EDAM_data:1544 -name: Ramachandran plot -namespace: data +id: EDAM_data:2538 +name: Mutation identifier +subset: bioinformatics subset: data -def: "Phi/psi angle data or a Ramachandran plot of a protein structure." [http://edamontology.org] -is_a: EDAM_data:2991 ! Protein torsion angle data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a mutation." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_data:1545 -name: Protein dipole moment -namespace: data +id: EDAM_data:2539 +name: Alignment data +comment: This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. +subset: bioinformatics subset: data -def: "Data on the net charge distribution (dipole moment) of a protein structure." [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property - +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1916 ! Alignment +consider: EDAM_data:2083 ! Alignment report [Term] -id: EDAM_data:1519 -name: Peptide molecular weights +id: EDAM_data:2540 +name: Data index data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics +subset: data +subset: edam +synonym: "Database index" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning an index of data." [http://edamontology.org] namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0955 ! Data index +consider: EDAM_data:0956 ! Data index report + +[Term] +id: EDAM_data:2563 +name: Amino acid name (single letter) +subset: bioinformatics subset: data -! alt_id: EDAM_data:1535 -def: "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents." [http://edamontology.org] -comment: The report might include associated data such as frequency of peptide fragment molecular weights. -is_a: EDAM_data:0897 ! Protein property +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Single letter amino acid identifier, e.g. G." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1006 ! Amino acid name +[Term] +id: EDAM_data:2564 +name: Amino acid name (three letter) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Three letter amino acid identifier, e.g. GLY." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1006 ! Amino acid name [Term] -id: EDAM_data:1520 -name: Peptide hydrophobic moment -namespace: data +id: EDAM_data:2565 +name: Amino acid name (full name) +subset: bioinformatics subset: data -def: "Report on the hydrophobic moment of a polypeptide sequence." [http://edamontology.org] -comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. -is_a: EDAM_data:2970 ! Protein hydropathy data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Full name of an amino acid, e.g. Glycine." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1006 ! Amino acid name [Term] -id: EDAM_data:2970 -name: Protein hydropathy data -namespace: data +id: EDAM_data:2576 +name: Toxin identifier +subset: bioinformatics subset: data -def: "A report on protein properties concerning hydropathy." [http://edamontology.org] -synonym: "Protein hydropathy report" EXACT [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a toxin." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1086 ! Compound identifier +relationship: is_identifier_of EDAM_data:2852 ! Toxin structure [Term] -id: EDAM_data:1521 -name: Protein aliphatic index -namespace: data +id: EDAM_data:2578 +name: ArachnoServer ID +subset: bioinformatics subset: data -def: "The aliphatic index of a protein." [http://edamontology.org] -comment: The aliphatic index is the relative protein volume occupied by aliphatic side chains. -is_a: EDAM_data:2970 ! Protein hydropathy data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a toxin from the ArachnoServer database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2897 ! Toxin accession [Term] -id: EDAM_data:2164 -name: Protein sequence properties plot -namespace: data +id: EDAM_data:2579 +name: Expressed gene list +subset: bioinformatics subset: data -def: "A plot of general physicochemical properties of a protein sequence." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0897 ! Protein property +subset: edam +synonym: "Gene annotation (expressed gene list)" EXACT [] +created_in: "beta12orEarlier" +def: "A simple summary of expressed genes." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2872 ! ID list [Term] -id: EDAM_data:2165 -name: Protein ionization curve -namespace: data +id: EDAM_data:2580 +name: BindingDB Monomer ID +subset: bioinformatics subset: data -def: "A plot of pK versus pH for a protein." [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a monomer from the BindingDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM_data:1522 -name: Protein sequence hydropathy plot -namespace: data +id: EDAM_data:2581 +name: GO concept name +subset: bioinformatics subset: data -def: "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc." [http://edamontology.org] -comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. -is_a: EDAM_data:2970 ! Protein hydropathy data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a concept from the GO ontology." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2339 ! Ontology concept name [Term] -id: EDAM_data:1523 -name: Protein charge plot -namespace: data +id: EDAM_data:2582 +name: GO concept ID (biological process) +subset: bioinformatics subset: data -def: "A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence." [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a 'biological process' concept from the the Gene Ontology." [http://edamontology.org] +regex: "[0-9]{7}|GO:[0-9]{7}" +namespace: identifier +is_a: EDAM_data:1176 ! GO concept ID [Term] -id: EDAM_data:1524 -name: Protein solubility -namespace: data +id: EDAM_data:2583 +name: GO concept ID (molecular function) +subset: bioinformatics subset: data -def: "The solubility or atomic solvation energy of a protein sequence or structure." [http://edamontology.org] -synonym: "Protein solubility data" EXACT [http://edamontology.org] -is_a: EDAM_data:2970 ! Protein hydropathy data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a 'molecular function' concept from the the Gene Ontology." [http://edamontology.org] +regex: "[0-9]{7}|GO:[0-9]{7}" +namespace: identifier +is_a: EDAM_data:1176 ! GO concept ID [Term] -id: EDAM_data:1525 -name: Protein crystallizability -namespace: data +id: EDAM_data:2584 +name: GO concept name (cellular component) +subset: bioinformatics subset: data -def: "Data on the crystallizability of a protein sequence." [http://edamontology.org] -synonym: "Protein crystallizability data" EXACT [http://edamontology.org] -is_a: EDAM_data:2970 ! Protein hydropathy data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a concept for a cellular component from the GO ontology." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2339 ! Ontology concept name [Term] -id: EDAM_data:1526 -name: Protein globularity -namespace: data +id: EDAM_data:2586 +name: Northern blot image +subset: bioinformatics subset: data -def: "Data on the stability, intrinsic disorder or globularity of a protein sequence." [http://edamontology.org] -synonym: "Protein globularity data" EXACT [http://edamontology.org] -is_a: EDAM_data:2970 ! Protein hydropathy data +subset: edam +created_in: "beta12orEarlier" +def: "An image arising from a Northern Blot experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3108 ! Experimental measurement [Term] -id: EDAM_data:1527 -name: Protein titration curve -namespace: data +id: EDAM_data:2587 +name: Blot ID +subset: bioinformatics subset: data -def: "The titration curve of a protein." [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a blot from a Northern Blot." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1528 -name: Protein isoelectric point -namespace: data +id: EDAM_data:2588 +name: BlotBase blot ID +subset: bioinformatics subset: data -def: "The isoelectric point of one proteins." [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a blot from a Northern Blot from the BlotBase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2587 ! Blot ID [Term] -id: EDAM_data:1529 -name: Protein pKa value -namespace: data +id: EDAM_data:2589 +name: Hierarchy +subset: bioinformatics subset: data -def: "The pKa value of a protein." [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property - +subset: edam +synonym: "Hierarchy annotation" EXACT [] +created_in: "beta12orEarlier" +def: "A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2987 ! Classification [Term] -id: EDAM_data:1530 -name: Protein hydrogen exchange rate -namespace: data +id: EDAM_data:2590 +name: Hierarchy identifier +subset: bioinformatics subset: data -def: "The hydrogen exchange rate of a protein." [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from a database of biological hierarchies." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2891 ! Biological model accession [Term] -id: EDAM_data:1531 -name: Protein extinction coefficient -namespace: data +id: EDAM_data:2591 +name: Brite hierarchy ID +subset: bioinformatics subset: data -def: "The extinction coefficient of a protein." [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the Brite database of biological hierarchies." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2891 ! Biological model accession [Term] -id: EDAM_data:1532 -name: Protein optical density -namespace: data +id: EDAM_data:2592 +name: Cancer type +subset: bioinformatics subset: data -def: "The optical density of a protein." [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property +subset: edam +created_in: "beta12orEarlier" +def: "A type (represented as a string) of cancer." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2100 ! Type [Term] -id: EDAM_data:1534 -name: Peptide immunogenicity data -namespace: data +id: EDAM_data:2593 +name: BRENDA organism ID +subset: bioinformatics subset: data -def: "An report on allergenicity / immunogenicity of peptides and proteins." [http://edamontology.org] -comment: This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. -synonym: "Peptide immunogenicity report" EXACT [http://edamontology.org] -synonym: "Peptide immunogenicity" EXACT [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier for an organism used in the BRENDA database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2908 ! Organism accession [Term] -id: EDAM_data:2957 -name: Hopp and Woods plot -namespace: data +id: EDAM_data:2594 +name: UniGene taxon +subset: bioinformatics subset: data -def: "A Hopp and Woods plot of predicted antigenicity of a peptide or protein." [http://edamontology.org] -is_a: EDAM_data:1534 ! Peptide immunogenicity data +subset: edam +subset: identifiers +synonym: "UniGene organism abbreviation" EXACT [] +created_in: "beta12orEarlier" +def: "The name of a taxon using the controlled vocabulary of the UniGene database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM_data:1536 -name: MHC peptide immunogenicity report -namespace: data +id: EDAM_data:2595 +name: UTRdb taxon +subset: bioinformatics subset: data -def: "A report on the immunogenicity of MHC class I or class II binding peptides." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1534 ! Peptide immunogenicity data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a taxon using the controlled vocabulary of the UTRdb database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM_data:2753 -name: Carbohydrate conformational map -namespace: data +id: EDAM_data:2596 +name: Catalogue identifier +subset: bioinformatics subset: data -def: "A conformational energy map of the glycosidic linkages in a carbohydrate molecule." [http://edamontology.org] -is_a: EDAM_data:2313 ! Carbohydrate structure report +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a catalogue of biological resources." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_data:0899 -name: Protein features (3D motif) -namespace: data +id: EDAM_data:2597 +name: CABRI catalogue name +subset: bioinformatics subset: data -def: "An informative report on the 3D structural motifs in a protein." [http://edamontology.org] -comment: This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. -synonym: "Protein structure report (3D motif)" EXACT [http://edamontology.org] -is_a: EDAM_data:1277 ! Protein features -is_a: EDAM_data:1537 ! Protein structure report -relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a catalogue of biological resources from the CABRI database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2596 ! Catalogue identifier [Term] -id: EDAM_data:1539 -name: Protein structural quality report -namespace: data +id: EDAM_data:2598 +name: Secondary structure alignment metadata +subset: bioinformatics subset: data -def: "Report on the quality of a protein three-dimensional model." [http://edamontology.org] -comment: Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. -synonym: "Protein structure report (quality evaluation)" EXACT [http://edamontology.org] -synonym: "Protein report (structural quality)" EXACT [http://edamontology.org] -synonym: "Protein property (structural quality)" EXACT [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property -is_a: EDAM_data:1537 ! Protein structure report +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2083 ! Alignment report [Term] -id: EDAM_data:1541 -name: Protein flexibility or motion report -namespace: data +id: EDAM_data:2599 +name: Molecular interaction +subset: bioinformatics subset: data -def: "Informative report on flexibility or motion of a protein structure." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -synonym: "Protein structure report (flexibility or motion)" EXACT [http://edamontology.org] -synonym: "Protein property (flexibility or motion)" EXACT [http://edamontology.org] -synonym: "Protein flexibility or motion" EXACT [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property -is_a: EDAM_data:1537 ! Protein structure report +subset: edam +synonym: "Molecular interaction data" EXACT [] +created_in: "beta12orEarlier" +def: "Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:2235 -name: Raw SCOP domain classification -namespace: data +id: EDAM_data:2600 +name: Pathway or network +subset: bioinformatics subset: data -def: "Raw SCOP domain classification data files." [http://edamontology.org] -comment: These are the parsable data files provided by SCOP. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0900 ! Protein domain classification - +subset: edam +synonym: "Network" EXACT [] +created_in: "beta12orEarlier" +def: "Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM_data:2236 -name: Raw CATH domain classification -namespace: data +id: EDAM_data:2601 +name: Small molecule data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "Raw CATH domain classification data files." [http://edamontology.org] -comment: These are the parsable data files provided by CATH. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0900 ! Protein domain classification - +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning one or more small molecules." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0962 ! Small molecule annotation [Term] -id: EDAM_data:1762 -name: CATH domain report -namespace: data +id: EDAM_data:2602 +name: Genotype and phenotype data +subset: bioinformatics subset: data -def: "Summary of domain classification information for a CATH domain." [http://edamontology.org] -comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0900 ! Protein domain classification - +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0920 ! Genotype/phenotype annotation [Term] -id: EDAM_data:1553 -name: CATH node -namespace: data +id: EDAM_data:2603 +name: Microarray data +comment: This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 +subset: bioinformatics subset: data -def: "Information on a node from the CATH database." [http://edamontology.org] -comment: The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. -synonym: "CATH classification node report" EXACT [http://edamontology.org] -is_a: EDAM_data:3101 ! Protein domain classification node - +subset: edam +synonym: "Gene expression data" EXACT [] +created_in: "beta12orEarlier" +def: "Image or hybridisation data for a microarray, typically a study of gene expression." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:1554 -name: SCOP node -namespace: data +id: EDAM_data:2605 +name: Compound ID (KEGG) +subset: bioinformatics subset: data -def: "Information on a node from the SCOP database." [http://edamontology.org] -synonym: "SCOP classification node" EXACT [http://edamontology.org] -is_a: EDAM_data:3101 ! Protein domain classification node - +subset: edam +subset: identifiers +synonym: "KEGG compound ID" EXACT [] +synonym: "KEGG compound identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier of a chemical compound from the KEGG database." [http://edamontology.org] +regex: "C[0-9]+" +namespace: identifier +is_a: EDAM_data:1154 ! KEGG object identifier +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM_data:3141 !{since=beta13} -name: SCOP class -namespace: data +id: EDAM_data:2606 +name: RFAM name +subset: bioinformatics subset: data -def: "Information on a 'class' node from the SCOP database." [http://edamontology.org] -is_a: EDAM_data:1554 ! SCOP node +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name (not necessarily stable) an entry (RNA family) from the RFAM database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2355 ! RNA family identifier [Term] -id: EDAM_data:3142 !{since=beta13} -name: SCOP fold -namespace: data +id: EDAM_data:2608 +name: Reaction ID (KEGG) +subset: bioinformatics subset: data -def: "Information on a 'fold' node from the SCOP database." [http://edamontology.org] -is_a: EDAM_data:1554 ! SCOP node +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a biological reaction from the KEGG reactions database." [http://edamontology.org] +regex: "R[0-9]+" +namespace: identifier +is_a: EDAM_data:1154 ! KEGG object identifier +is_a: EDAM_data:2108 ! Reaction ID [Term] -id: EDAM_data:3143 !{since=beta13} -name: SCOP superfamily -namespace: data +id: EDAM_data:2609 +name: Drug ID (KEGG) +subset: bioinformatics subset: data -def: "Information on a 'superfamily' node from the SCOP database." [http://edamontology.org] -is_a: EDAM_data:1554 ! SCOP node +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a drug from the KEGG Drug database." [http://edamontology.org] +regex: "D[0-9]+" +namespace: identifier +is_a: EDAM_data:1154 ! KEGG object identifier +is_a: EDAM_data:2895 ! Drug accession [Term] -id: EDAM_data:3144 !{since=beta13} -name: SCOP family -namespace: data +id: EDAM_data:2610 +name: Ensembl ID +subset: bioinformatics subset: data -def: "Information on a 'family' node from the SCOP database." [http://edamontology.org] -is_a: EDAM_data:1554 ! SCOP node +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database." [http://edamontology.org] +regex: "ENS[A-Z]*[FPTG][0-9]{11}" +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:3145 !{since=beta13} -name: SCOP protein -namespace: data +id: EDAM_data:2611 +name: ICD identifier +subset: bioinformatics subset: data -def: "Information on a 'protein' node from the SCOP database." [http://edamontology.org] -is_a: EDAM_data:1554 ! SCOP node +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a disease from the International Classification of Diseases (ICD) database." [http://edamontology.org] +regex: "[A-Z][0-9]+(\\.[-[0-9]+])?" +namespace: identifier +is_a: EDAM_data:1150 ! Disease ID +relationship: is_identifier_of EDAM_data:1622 ! Disease annotation [Term] -id: EDAM_data:3146 !{since=beta13} -name: SCOP species -namespace: data +id: EDAM_data:2612 +name: Sequence cluster ID (CluSTr) +subset: bioinformatics subset: data -def: "Information on a 'species' node from the SCOP database." [http://edamontology.org] -is_a: EDAM_data:1554 ! SCOP node - - - - +subset: edam +subset: identifiers +synonym: "CluSTr cluster ID" EXACT [] +synonym: "CluSTr ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier of a sequence cluster from the CluSTr database." [http://edamontology.org] +regex: "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\\.[0-9])?" +namespace: identifier +is_a: EDAM_data:1112 ! Sequence cluster ID [Term] -id: EDAM_data:1555 -name: EMBASSY domain classification -namespace: data +id: EDAM_data:2613 +name: KEGG Glycan ID +subset: bioinformatics subset: data -def: "An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0900 ! Protein domain classification - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND)." [http://edamontology.org] +regex: "G[0-9]+" +namespace: identifier +is_a: EDAM_data:1154 ! KEGG object identifier +is_a: EDAM_data:2900 ! Carbohydrate accession [Term] -id: EDAM_data:1556 -name: CATH class -namespace: data +id: EDAM_data:2614 +name: TCDB ID +comment: OBO file for regular expression. +subset: bioinformatics subset: data -def: "Information on a protein 'class' node from the CATH database." [http://edamontology.org] -is_a: EDAM_data:1553 ! CATH node +subset: edam +subset: identifiers +synonym: "TC number" EXACT [] +created_in: "beta12orEarlier" +def: "A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins." [http://edamontology.org] +regex: "[0-9]+\\.[A-Z]\\.[0-9]+\\.[0-9]+\\.[0-9]+" +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM_data:1557 -name: CATH architecture -namespace: data +id: EDAM_data:2615 +name: MINT ID +subset: bioinformatics subset: data -def: "Information on a protein 'architecture' node from the CATH database." [http://edamontology.org] -is_a: EDAM_data:1553 ! CATH node +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the MINT database of protein-protein interactions." [http://edamontology.org] +regex: "MINT\\-[0-9]{1,5}" +namespace: identifier +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM_data:1558 -name: CATH topology -namespace: data +id: EDAM_data:2616 +name: DIP ID +subset: bioinformatics subset: data -def: "Information on a protein 'topology' node from the CATH database." [http://edamontology.org] -is_a: EDAM_data:1553 ! CATH node +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the DIP database of protein-protein interactions." [http://edamontology.org] +regex: "DIP[\\:\\-][0-9]{3}[EN]" +namespace: identifier +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM_data:1559 -name: CATH homologous superfamily -namespace: data +id: EDAM_data:2617 +name: Signaling Gateway protein ID +subset: bioinformatics subset: data -def: "Information on a protein 'homologous superfamily' node from the CATH database." [http://edamontology.org] -is_a: EDAM_data:1553 ! CATH node +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database." [http://edamontology.org] +regex: "A[0-9]{6}" +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1560 -name: CATH structurally similar group -namespace: data +id: EDAM_data:2618 +name: Protein modification ID +subset: bioinformatics subset: data -def: "Information on a protein 'structurally similar group' node from the CATH database." [http://edamontology.org] -is_a: EDAM_data:1553 ! CATH node +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a protein modification catalogued in a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1561 -name: CATH functional category -namespace: data +id: EDAM_data:2619 +name: RESID ID +subset: bioinformatics subset: data -def: "Information on a protein 'functional category' node from the CATH database." [http://edamontology.org] -is_a: EDAM_data:1553 ! CATH node - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a protein modification catalogued in the RESID database." [http://edamontology.org] +regex: "AA[0-9]{4}" +namespace: identifier +is_a: EDAM_data:2618 ! Protein modification ID [Term] -id: EDAM_data:1565 -name: Protein-protein interaction -namespace: data +id: EDAM_data:2620 +name: RGD ID +subset: bioinformatics subset: data -! alt_id: EDAM_data:2712 -def: "Data on protein-protein interaction(s)." [http://edamontology.org] -comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains). -synonym: "Protein structure report (protein complex)" EXACT [http://edamontology.org] -is_a: EDAM_data:0906 ! Protein interaction -relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the RGD database." [http://edamontology.org] +regex: "[0-9]{4,7}" +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:1566 -name: Protein-ligand interaction -namespace: data +id: EDAM_data:2621 +name: TAIR accession (protein) +subset: bioinformatics subset: data -def: "Data on protein-ligand (small molecule) interaction(s)." [http://edamontology.org] -is_a: EDAM_data:0906 ! Protein interaction -relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a protein sequence from the TAIR database." [http://edamontology.org] +regex: "AASequence:[0-9]{10}" +namespace: identifier +is_a: EDAM_data:1096 ! Sequence accession (protein) +is_a: EDAM_data:2387 ! TAIR accession +relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] -id: EDAM_data:1567 -name: Protein-nucleic acid interaction -namespace: data +id: EDAM_data:2622 +name: Compound ID (HMDB) +subset: bioinformatics subset: data -def: "Data on protein-DNA/RNA interaction(s)." [http://edamontology.org] -is_a: EDAM_data:0906 ! Protein interaction -relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions - +subset: edam +subset: identifiers +synonym: "HMDB ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB)." [http://edamontology.org] +regex: "HMDB[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM_data:2359 -name: Domain-domain interaction -namespace: data +id: EDAM_data:2625 +name: LIPID MAPS ID +subset: bioinformatics subset: data -def: "Data on protein domain-protein domain interaction(s)." [http://edamontology.org] -is_a: EDAM_data:1565 ! Protein-protein interaction +subset: edam +subset: identifiers +synonym: "LM ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry from the LIPID MAPS database." [http://edamontology.org] +regex: "LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?" +namespace: identifier +is_a: EDAM_data:2905 ! Lipid accession [Term] -id: EDAM_data:2378 -name: Protein-motif interaction -namespace: data +id: EDAM_data:2626 +name: PeptideAtlas ID +subset: bioinformatics subset: data -def: "Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1565 ! Protein-protein interaction +subset: edam +subset: identifiers +xref: PDBML:pdbx_PDB_strand_id +created_in: "beta12orEarlier" +def: "Identifier of a peptide from the PeptideAtlas peptide databases." [http://edamontology.org] +regex: "PAp[0-9]{8}" +namespace: identifier +is_a: EDAM_data:2906 ! Peptide ID [Term] -id: EDAM_data:2360 -name: Domain-domain interaction (indirect) -namespace: data +id: EDAM_data:2627 +name: Molecular interaction ID +subset: bioinformatics subset: data -def: "Data on indirect protein domain-protein domain interaction(s)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2359 ! Domain-domain interaction - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a report of molecular interactions from a database (typically)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession +relationship: is_identifier_of EDAM_data:2599 ! Molecular interaction [Term] -id: EDAM_data:2402 -name: Protein-drug interaction -namespace: data +id: EDAM_data:2628 +name: BioGRID interaction ID +subset: bioinformatics subset: data -def: "Informative report on protein-drug interaction(s) including binding affinity data." [http://edamontology.org] -is_a: EDAM_data:1566 ! Protein-ligand interaction +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of an interaction from the BioGRID database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2627 ! Molecular interaction ID [Term] -id: EDAM_data:2358 -name: Domain-nucleic acid interaction -namespace: data +id: EDAM_data:2629 +name: Enzyme ID (MEROPS) +subset: bioinformatics subset: data -def: "Data on protein domain-DNA/RNA interaction(s)." [http://edamontology.org] -is_a: EDAM_data:1567 ! Protein-nucleic acid interaction - +subset: edam +subset: identifiers +synonym: "MEROPS ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier of a peptidase enzyme from the MEROPS database." [http://edamontology.org] +regex: "S[0-9]{2}\\.[0-9]{3}" +namespace: identifier +is_a: EDAM_data:2321 ! Enzyme ID [Term] -id: EDAM_data:2025 -name: Michaelis Menten plot -namespace: data +id: EDAM_data:2630 +name: Mobile genetic element ID +subset: bioinformatics subset: data -def: "A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent." [http://edamontology.org] -is_a: EDAM_data:2024 ! Enzyme kinetics data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a mobile genetic element." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:2026 -name: Hanes Woolf plot -namespace: data +id: EDAM_data:2631 +name: ACLAME ID +subset: bioinformatics subset: data -def: "A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v)." [http://edamontology.org] -is_a: EDAM_data:2024 ! Enzyme kinetics data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a mobile genetic element from the Aclame database." [http://edamontology.org] +regex: "mge:[0-9]+" +namespace: identifier +is_a: EDAM_data:2630 ! Mobile genetic element ID [Term] -id: EDAM_data:0909 -name: Vmax -namespace: data +id: EDAM_data:2632 +name: SGD ID +subset: bioinformatics subset: data -def: "The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large." [http://edamontology.org] -is_a: EDAM_data:2024 ! Enzyme kinetics data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the Saccharomyces genome database (SGD)." [http://edamontology.org] +regex: "PWY[a-zA-Z_0-9]{2}\\-[0-9]{3}" +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:0910 -name: Km -namespace: data +id: EDAM_data:2633 +name: Book ID +subset: bioinformatics subset: data -def: "Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction." [http://edamontology.org] -is_a: EDAM_data:2024 ! Enzyme kinetics data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a book." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:2720 -name: Dinucleotide property -namespace: data +id: EDAM_data:2634 +name: ISBN +subset: bioinformatics subset: data -def: "Physicochemical property data for one or more dinucleotides." [http://edamontology.org] -is_a: EDAM_data:2088 ! DNA base structural data - - - -! [Term] born obsolete -! id: EDAM_data:3149 !{since=beta13} -! name: Nucleic acid property (sequence) -! namespace: data -! subset: data -! def: "A non-positional property of a nucleic acid sequence." [http://edamontology.org] -! synonym: "Nucleic acid sequence property" EXACT [http://edamontology.org] -! is_obsolete: true !{since=beta13} -! consider: EDAM_data:0912 ! Nucleic acid property +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The International Standard Book Number (ISBN) is for identifying printed books." [http://edamontology.org] +regex: "(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)" +namespace: identifier +is_a: EDAM_data:2633 ! Book ID [Term] -id: EDAM_data:2985 -name: Nucleic acid thermodynamic data -namespace: data +id: EDAM_data:2635 +name: Compound ID (3DMET) +subset: bioinformatics subset: data -def: "A thermodynamic or kinetic property of a nucleic acid molecule." [http://edamontology.org] -synonym: "Nucleic acid property (thermodynamic or kinetic)" EXACT [http://edamontology.org] -synonym: "Nucleic acid thermodynamic property" EXACT [http://edamontology.org] -is_a: EDAM_data:0912 ! Nucleic acid property - - +subset: edam +subset: identifiers +synonym: "3DMET ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a metabolite from the 3DMET database." [http://edamontology.org] +regex: "B[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM_data:1583 -name: Nucleic acid melting profile -namespace: data +id: EDAM_data:2636 +name: MatrixDB interaction ID +subset: bioinformatics subset: data -def: "Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating." [http://edamontology.org] -comment: A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. -synonym: "Nucleic acid stability profile" EXACT [http://edamontology.org] -is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of an interaction from the MatrixDB database." [http://edamontology.org] +regex: "([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)" +namespace: identifier +is_a: EDAM_data:2627 ! Molecular interaction ID [Term] -id: EDAM_data:1584 -name: Nucleic acid enthalpy -namespace: data +id: EDAM_data:2637 +name: cPath ID +comment: These identifiers are unique within the cPath database, however, they are not stable between releases. +subset: bioinformatics subset: data -def: "Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] -is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2109 ! Identifier (hybrid) +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_data:1585 -name: Nucleic acid entropy -namespace: data +id: EDAM_data:2638 +name: PubChem bioassay ID +subset: bioinformatics subset: data -def: "Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] -is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an assay from the PubChem database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2639 ! PubChem identifier [Term] -id: EDAM_data:1586 -name: Nucleic acid melting temperature -namespace: data +id: EDAM_data:2639 +name: PubChem identifier +subset: bioinformatics subset: data -def: "Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2139 ! Nucleic acid melting temperature - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the PubChem database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:2088 -name: DNA base structural data -namespace: data +id: EDAM_data:2641 +name: Reaction ID (MACie) +subset: bioinformatics subset: data -def: "Structural data for DNA base pairs or runs of bases, such as energy or angle data." [http://edamontology.org] -is_a: EDAM_data:0912 ! Nucleic acid property -is_a: EDAM_data:2086 ! Nucleic acid structure report - +subset: edam +subset: identifiers +synonym: "MACie entry number" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an enzyme reaction mechanism from the MACie database." [http://edamontology.org] +regex: "M[0-9]{4}" +namespace: identifier +is_a: EDAM_data:2108 ! Reaction ID [Term] -id: EDAM_data:2167 -name: Nucleic acid density plot -namespace: data +id: EDAM_data:2642 +name: Gene ID (miRBase) +subset: bioinformatics subset: data -def: "Density plot (of base composition) for a nucleotide sequence." [http://edamontology.org] -is_a: EDAM_data:0912 ! Nucleic acid property - +subset: edam +subset: identifiers +synonym: "miRNA ID" EXACT [] +synonym: "miRNA identifier" EXACT [] +synonym: "miRNA name" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier for a gene from the miRBase database." [http://edamontology.org] +regex: "MI[0-9]{7}" +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1587 -name: Nucleic acid stitch profile -namespace: data +id: EDAM_data:2643 +name: Gene ID (ZFIN) +subset: bioinformatics subset: data -def: "Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] -comment: A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. -is_a: EDAM_data:1583 ! Nucleic acid melting profile +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier for a gene from the Zebrafish information network genome (ZFIN) database." [http://edamontology.org] +regex: "ZDB\\-GENE\\-[0-9]+\\-[0-9]+" +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:2958 -name: Nucleic acid melting curve -namespace: data +id: EDAM_data:2644 +name: Reaction ID (Rhea) +subset: bioinformatics subset: data -def: "A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] -comment: Shows the proportion of nucleic acid which are double-stranded versus temperature. -is_a: EDAM_data:1583 ! Nucleic acid melting profile +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an enzyme-catalysed reaction from the Rhea database." [http://edamontology.org] +regex: "[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2108 ! Reaction ID [Term] -id: EDAM_data:2959 -name: Nucleic acid probability profile -namespace: data -subset: data -def: "A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] -comment: Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature -is_a: EDAM_data:1583 ! Nucleic acid melting profile +id: EDAM_data:2645 +name: Pathway ID (Unipathway) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +synonym: "upaid" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a biological pathway from the Unipathway database." [http://edamontology.org] +regex: "UPA[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_data:2960 -name: Nucleic acid temperature profile -namespace: data +id: EDAM_data:2646 +name: Compound ID (ChEMBL) +subset: bioinformatics subset: data -def: "A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] -comment: Plots melting temperature versus base position. -synonym: "Melting map" EXACT [http://edamontology.org] -is_a: EDAM_data:1583 ! Nucleic acid melting profile +subset: edam +subset: identifiers +synonym: "ChEMBL ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a small molecular from the ChEMBL database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM_data:1594 -name: Vienna RNA calculated energy -namespace: data +id: EDAM_data:2647 +name: LGICdb identifier +subset: bioinformatics subset: data -def: "RNA calculated energy data generated by the Vienna package." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1584 ! Nucleic acid enthalpy +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database." [http://edamontology.org] +regex: "[a-zA-Z_0-9]+" +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1588 -name: DNA base pair stacking energies data -namespace: data +id: EDAM_data:2648 +name: Reaction kinetics ID (SABIO-RK) +subset: bioinformatics subset: data -def: "DNA base pair stacking energies data." [http://edamontology.org] -is_a: EDAM_data:2088 ! DNA base structural data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2309 ! Reaction ID (SABIO-RK) [Term] -id: EDAM_data:1589 -name: DNA base pair twist angle data -namespace: data +id: EDAM_data:2649 +name: PharmGKB ID +subset: bioinformatics subset: data -def: "DNA base pair twist angle data." [http://edamontology.org] -is_a: EDAM_data:2088 ! DNA base structural data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] +regex: "PA[0-9]+" +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:1590 -name: DNA base trimer roll angles data -namespace: data +id: EDAM_data:2650 +name: Pathway ID (PharmGKB) +subset: bioinformatics subset: data -def: "DNA base trimer roll angles data." [http://edamontology.org] -is_a: EDAM_data:2088 ! DNA base structural data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] +regex: "PA[0-9]+" +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession +is_a: EDAM_data:2649 ! PharmGKB ID [Term] -id: EDAM_data:1595 -name: Base pairing probability matrix dotplot -namespace: data +id: EDAM_data:2651 +name: Disease ID (PharmGKB) +subset: bioinformatics subset: data -def: "Dotplot of RNA base pairing probability matrix." [http://edamontology.org] -comment: Such as generated by the Vienna package. -is_a: EDAM_data:2088 ! DNA base structural data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] +regex: "PA[0-9]+" +namespace: identifier +is_a: EDAM_data:1150 ! Disease ID +is_a: EDAM_data:2649 ! PharmGKB ID [Term] -id: EDAM_data:1598 -name: Genetic code -namespace: data +id: EDAM_data:2652 +name: Drug ID (PharmGKB) +subset: bioinformatics subset: data -def: "A genetic code for an organism." [http://edamontology.org] -comment: A genetic code need not include detailed codon usage information. -is_a: EDAM_data:1597 ! Codon usage table - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] +regex: "PA[0-9]+" +namespace: identifier +is_a: EDAM_data:2649 ! PharmGKB ID +is_a: EDAM_data:2895 ! Drug accession [Term] -id: EDAM_data:2865 -name: Codon usage bias -namespace: data +id: EDAM_data:2653 +name: Drug ID (TTD) +subset: bioinformatics subset: data -def: "A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences." [http://edamontology.org] -is_a: EDAM_data:0914 ! Codon usage report - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a drug from the Therapeutic Target Database (TTD)." [http://edamontology.org] +regex: "DAP[0-9]+" +namespace: identifier +is_a: EDAM_data:2895 ! Drug accession [Term] -id: EDAM_data:1599 -name: Codon adaptation index -namespace: data +id: EDAM_data:2654 +name: Target ID (TTD) +subset: bioinformatics subset: data -def: "A simple measure of synonymous codon usage bias often used to predict gene expression levels." [http://edamontology.org] -synonym: "CAI" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2865 ! Codon usage bias - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a target protein from the Therapeutic Target Database (TTD)." [http://edamontology.org] +regex: "TTDS[0-9]+" +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1600 -name: Codon usage bias plot -namespace: data +id: EDAM_data:2655 +name: Cell type identifier +subset: bioinformatics subset: data -def: "A plot of the synonymous codon usage calculated for windows over a nucleotide sequence." [http://edamontology.org] -synonym: "Synonymous codon usage statistic plot" EXACT [http://edamontology.org] -is_a: EDAM_data:2865 ! Codon usage bias - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of a type or group of cells." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_data:1601 -name: Nc statistic -namespace: data +id: EDAM_data:2656 +name: NeuronDB ID +subset: bioinformatics subset: data -def: "The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2865 ! Codon usage bias - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of a neuron from the NeuronDB database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2893 ! Cell type accession [Term] -id: EDAM_data:1602 -name: Codon usage fraction difference -namespace: data +id: EDAM_data:2657 +name: NeuroMorpho ID +subset: bioinformatics subset: data -def: "The differences in codon usage fractions between two codon usage tables." [http://edamontology.org] -is_a: EDAM_data:0914 ! Codon usage report +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of a neuron from the NeuroMorpho database." [http://edamontology.org] +regex: "[a-zA-Z_0-9]+" +namespace: identifier +is_a: EDAM_data:2893 ! Cell type accession [Term] -id: EDAM_data:0917 -name: Gene classification -namespace: data +id: EDAM_data:2658 +name: Compound ID (ChemIDplus) +subset: bioinformatics subset: data -def: "A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0916 ! Gene annotation +subset: edam +subset: identifiers +synonym: "ChemIDplus ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of a chemical from the ChemIDplus database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM_data:0927 -name: Gene annotation (linkage) -namespace: data +id: EDAM_data:2659 +name: Pathway ID (SMPDB) +subset: bioinformatics subset: data -def: "An informative report on the linkage of alleles." [http://edamontology.org] -is_a: EDAM_data:0916 ! Gene annotation - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a pathway from the Small Molecule Pathway Database (SMPDB)." [http://edamontology.org] +regex: "SMP[0-9]{5}" +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_data:1634 -name: Gene annotation (linkage disequilibrium) -namespace: data +id: EDAM_data:2660 +name: BioNumbers ID +subset: bioinformatics subset: data -def: "A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [http://edamontology.org] -is_a: EDAM_data:0927 ! Gene annotation (linkage) - - - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:0928 -name: Gene expression profile -namespace: data +id: EDAM_data:2662 +name: T3DB ID +subset: bioinformatics subset: data -def: "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." [http://edamontology.org] -synonym: "Gene expression pattern" EXACT [http://edamontology.org] -is_a: EDAM_data:3031 ! Core data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database." [http://edamontology.org] +regex: "T3D[0-9]+" +namespace: identifier +is_a: EDAM_data:2897 ! Toxin accession [Term] -id: EDAM_data:2579 -name: Expressed gene list -namespace: data +id: EDAM_data:2663 +name: Carbohydrate identifier +subset: bioinformatics subset: data -def: "A simple summary of expressed genes." [http://edamontology.org] -synonym: "Gene annotation (expressed gene list)" EXACT [http://edamontology.org] -is_a: EDAM_data:2872 ! ID list +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a carbohydrate." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1086 ! Compound identifier +relationship: is_identifier_of EDAM_data:1462 ! Carbohydrate structure +relationship: is_identifier_of EDAM_data:2313 ! Carbohydrate structure report [Term] -id: EDAM_data:2586 -name: Northern blot image -namespace: data +id: EDAM_data:2664 +name: GlycomeDB ID +subset: bioinformatics subset: data -def: "An image arising from a Northern Blot experiment." [http://edamontology.org] -is_a: EDAM_data:3108 ! Experimental measurement - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the GlycomeDB database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2900 ! Carbohydrate accession [Term] -id: EDAM_data:1636 -name: Heat map -namespace: data +id: EDAM_data:2665 +name: LipidBank ID +subset: bioinformatics subset: data -def: "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." [http://edamontology.org] -comment: A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. -is_a: EDAM_data:2967 ! Microarray image +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the LipidBank database." [http://edamontology.org] +regex: "[a-zA-Z_0-9]+[0-9]+" +namespace: identifier +is_a: EDAM_data:2905 ! Lipid accession [Term] -id: EDAM_data:2092 -name: Nucleic acid features (SNP) -namespace: data +id: EDAM_data:2666 +name: CDD ID +subset: bioinformatics subset: data -def: "Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence." [http://edamontology.org] -comment: An SNP is an individual point mutation or substitution of a single nucleotide. -synonym: "Single nucleotide polymorphism" EXACT [http://edamontology.org] -synonym: "SNP annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a conserved domain from the Conserved Domain Database." [http://edamontology.org] +regex: "cd[0-9]{5}" +namespace: identifier +is_a: EDAM_data:1038 ! Protein domain ID [Term] -id: EDAM_data:2867 -name: Nucleic acid features (VNTR) -namespace: data +id: EDAM_data:2667 +name: MMDB ID +subset: bioinformatics subset: data -def: "Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence." [http://edamontology.org] -comment: VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. -synonym: "Variable number of tandem repeat polymorphism" EXACT [http://edamontology.org] -synonym: "VNTR annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) - +subset: edam +subset: identifiers +synonym: "MMDB accession" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier of an entry from the MMDB database." [http://edamontology.org] +regex: "[0-9]{1,5}" +namespace: identifier +is_a: EDAM_data:1070 ! Structure ID [Term] -id: EDAM_data:2868 -name: Nucleic acid features (microsatellite) -namespace: data +id: EDAM_data:2668 +name: iRefIndex ID +subset: bioinformatics subset: data -def: "Annotation on a microsatellite polymorphism in a DNA sequence." [http://edamontology.org] -comment: A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. -synonym: "Microsatellite annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the iRefIndex database of protein-protein interactions." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM_data:2869 -name: Nucleic acid features (RFLP) -namespace: data +id: EDAM_data:2669 +name: ModelDB ID +subset: bioinformatics subset: data -def: "Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence." [http://edamontology.org] -comment: An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. -synonym: "RFLP annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of an entry from the ModelDB database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2891 ! Biological model accession [Term] -id: EDAM_data:1853 -name: Chromosome annotation (aberration) -namespace: data +id: EDAM_data:2670 +name: Pathway ID (DQCS) +subset: bioinformatics subset: data -def: "A report on a chromosome aberration such as abnormalities in chromosome structure." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0919 ! Gene annotation (chromosome) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS)." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_data:1621 -name: Pharmacogenomic annotation -namespace: data +id: EDAM_data:2671 +name: Ensembl ID (Homo sapiens) +subset: bioinformatics subset: data -def: "Data on the influence of genotype on drug response." [http://edamontology.org] -comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. -is_a: EDAM_data:0920 ! Genotype/phenotype annotation - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division)." [http://edamontology.org] +regex: "ENS([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:1622 -name: Disease annotation -namespace: data +id: EDAM_data:2672 +name: Ensembl ID ('Bos taurus') +subset: bioinformatics subset: data -def: "An informative report on a specific disease." [http://edamontology.org] -is_a: EDAM_data:0920 ! Genotype/phenotype annotation -relationship: has_topic EDAM_topic:0634 ! Disease resources - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division)." [http://edamontology.org] +regex: "ENSBTA([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2533 -name: Nucleic acid features (mutation) -namespace: data +id: EDAM_data:2673 +name: Ensembl ID ('Canis familiaris') +subset: bioinformatics subset: data -def: "Annotation on a mutation." [http://edamontology.org] -synonym: "Mutation annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:0918 ! Nucleic acid features (variation) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division)." [http://edamontology.org] +regex: "ENSCAF([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2885 -name: Nucleic acid features (polymorphism annotation) -namespace: data +id: EDAM_data:2674 +name: Ensembl ID ('Cavia porcellus') +subset: bioinformatics subset: data -def: "Annotation on a polymorphism." [http://edamontology.org] -synonym: "Polymorphism annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:0918 ! Nucleic acid features (variation) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division)." [http://edamontology.org] +regex: "ENSCPO([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2212 -name: Mutation annotation (basic) -namespace: data +id: EDAM_data:2675 +name: Ensembl ID ('Ciona intestinalis') +subset: bioinformatics subset: data -def: "Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2533 ! Nucleic acid features (mutation) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division)." [http://edamontology.org] +regex: "ENSCIN([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2213 -name: Mutation annotation (prevalence) -namespace: data +id: EDAM_data:2676 +name: Ensembl ID ('Ciona savignyi') +subset: bioinformatics subset: data -def: "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2533 ! Nucleic acid features (mutation) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division)." [http://edamontology.org] +regex: "ENSCSAV([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2214 -name: Mutation annotation (prognostic) -namespace: data +id: EDAM_data:2677 +name: Ensembl ID ('Danio rerio') +subset: bioinformatics subset: data -def: "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2533 ! Nucleic acid features (mutation) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division)." [http://edamontology.org] +regex: "ENSDAR([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2215 -name: Mutation annotation (functional) -namespace: data +id: EDAM_data:2678 +name: Ensembl ID ('Dasypus novemcinctus') +subset: bioinformatics subset: data -def: "An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2533 ! Nucleic acid features (mutation) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division)." [http://edamontology.org] +regex: "ENSDNO([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2217 -name: Tumor annotation -namespace: data +id: EDAM_data:2679 +name: Ensembl ID ('Echinops telfairi') +subset: bioinformatics subset: data -def: "An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on." [http://edamontology.org] -is_a: EDAM_data:1622 ! Disease annotation +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division)." [http://edamontology.org] +regex: "ENSETE([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:1852 -name: Sequence assembly component -namespace: data +id: EDAM_data:2680 +name: Ensembl ID ('Erinaceus europaeus') +subset: bioinformatics subset: data -def: "A component of a larger sequence assembly." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0925 ! Sequence assembly +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division)." [http://edamontology.org] +regex: "ENSEEU([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID +[Term] +id: EDAM_data:2681 +name: Ensembl ID ('Felis catus') +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division)." [http://edamontology.org] +regex: "ENSFCA([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0923 -name: Experiment annotation (PCR assay data) -namespace: data +id: EDAM_data:2682 +name: Ensembl ID ('Gallus gallus') +subset: bioinformatics subset: data -def: "Data on a PCR assay or electronic / virtual PCR." [http://edamontology.org] -synonym: "PCR assay data" EXACT [http://edamontology.org] -is_a: EDAM_data:2531 ! Experiment annotation -relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division)." [http://edamontology.org] +regex: "ENSGAL([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:3165 !{since=1.0} -name: Experiment annotation (sequencing) -namespace: data +id: EDAM_data:2683 +name: Ensembl ID ('Gasterosteus aculeatus') +subset: bioinformatics subset: data -def: "Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis." [http://edamontology.org] -is_a: EDAM_data:2531 ! Experiment annotation -relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division)." [http://edamontology.org] +regex: "ENSGAC([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0924 -name: Sequence trace -namespace: data +id: EDAM_data:2684 +name: Ensembl ID ('Homo sapiens') +subset: bioinformatics subset: data -def: "Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores." [http://edamontology.org] -comment: This is the raw data produced by a DNA sequencing machine. -is_a: EDAM_data:3108 ! Experimental measurement -is_a: EDAM_data:2887 ! Sequence record (nucleic acid) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division)." [http://edamontology.org] +regex: "ENSHUM([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0926 -name: Radiation Hybrid (RH) scores -namespace: data +id: EDAM_data:2685 +name: Ensembl ID ('Loxodonta africana') +subset: bioinformatics subset: data -def: "Radiation hybrid scores (RH) scores for one or more markers." [http://edamontology.org] -comment: Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. -is_a: EDAM_data:3108 ! Experimental measurement +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division)." [http://edamontology.org] +regex: "ENSLAF([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2363 -name: 2D PAGE data -namespace: data +id: EDAM_data:2686 +name: Ensembl ID ('Macaca mulatta') +subset: bioinformatics subset: data -def: "Data concerning two-dimensional polygel electrophoresis." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0942 ! 2D PAGE image -consider: EDAM_data:2364 ! Experiment annotation (2D PAGE) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division)." [http://edamontology.org] +regex: "ENSMMU([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2838 -name: Experimental data (proteomics) -namespace: data +id: EDAM_data:2687 +name: Ensembl ID ('Monodelphis domestica') +subset: bioinformatics subset: data -def: "Data concerning a proteomics experiment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:3147 ! Experiment annotation (mass spectrometry) - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division)." [http://edamontology.org] +regex: "ENSMOD([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2536 -name: Mass spectrometry data -namespace: data +id: EDAM_data:2688 +name: Ensembl ID ('Mus musculus') +subset: bioinformatics subset: data -def: "Data concerning a mass spectrometry experiment." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -is_obsolete: true !{since=beta13} -consider: EDAM_data:0943 ! Mass spectrometry spectra -consider: EDAM_data:0944 ! Peptide mass fingerprint -consider: EDAM_data:3147 ! Experiment annotation (mass spectrometry) +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division)." [http://edamontology.org] +regex: "ENSMUS([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0943 -name: Mass spectrometry spectra -namespace: data +id: EDAM_data:2689 +name: Ensembl ID ('Myotis lucifugus') +subset: bioinformatics subset: data -def: "Spectra from mass spectrometry." [http://edamontology.org] -is_a: EDAM_data:3108 ! Experimental measurement -relationship: has_topic EDAM_topic:0121 ! Proteomics - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division)." [http://edamontology.org] +regex: "ENSMLU([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0944 -name: Peptide mass fingerprint -namespace: data +id: EDAM_data:2690 +name: Ensembl ID ("Ornithorhynchus anatinus") +subset: bioinformatics subset: data -def: "A set of peptide masses (peptide mass fingerprint) from mass spectrometry." [http://edamontology.org] -synonym: "Protein fingerprint" EXACT [http://edamontology.org] -synonym: "Peak list" EXACT [http://edamontology.org] -is_a: EDAM_data:2979 ! Peptide property -is_a: EDAM_data:3108 ! Experimental measurement -relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division)." [http://edamontology.org] +regex: "ENSOAN([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0945 -name: Peptide identification -namespace: data +id: EDAM_data:2691 +name: Ensembl ID ('Oryctolagus cuniculus') +subset: bioinformatics subset: data -def: "Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database." [http://edamontology.org] -is_a: EDAM_data:2979 ! Peptide property -relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division)." [http://edamontology.org] +regex: "ENSOCU([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2537 -name: Protein structure raw data -namespace: data +id: EDAM_data:2692 +name: Ensembl ID ('Oryzias latipes') +subset: bioinformatics subset: data -def: "Raw data from experimental methods for determining protein structure." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -is_a: EDAM_data:3108 ! Experimental measurement +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division)." [http://edamontology.org] +regex: "ENSORL([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0937 -name: Protein X-ray crystallographic data -namespace: data +id: EDAM_data:2693 +name: Ensembl ID ('Otolemur garnettii') +subset: bioinformatics subset: data -def: "X-ray crystallography data." [http://edamontology.org] -is_a: EDAM_data:2537 ! Protein structure raw data - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division)." [http://edamontology.org] +regex: "ENSSAR([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0938 -name: Protein NMR data -namespace: data +id: EDAM_data:2694 +name: Ensembl ID ('Pan troglodytes') +subset: bioinformatics subset: data -def: "Protein nuclear magnetic resonance (NMR) raw data." [http://edamontology.org] -is_a: EDAM_data:2537 ! Protein structure raw data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division)." [http://edamontology.org] +regex: "ENSPTR([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0939 -name: Protein circular dichroism (CD) spectroscopic data -namespace: data +id: EDAM_data:2695 +name: Ensembl ID ('Rattus norvegicus') +subset: bioinformatics subset: data -def: "Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data." [http://edamontology.org] -is_a: EDAM_data:2537 ! Protein structure raw data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division)." [http://edamontology.org] +regex: "ENSRNO([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0940 -name: Electron microscopy volume map -namespace: data +id: EDAM_data:2696 +name: Ensembl ID ('Spermophilus tridecemlineatus') +subset: bioinformatics subset: data -def: "Volume map data from electron microscopy." [http://edamontology.org] -synonym: "EM volume map" EXACT [http://edamontology.org] -is_a: EDAM_data:3108 ! Experimental measurement -relationship: has_topic EDAM_topic:2226 ! Structure determination - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division)." [http://edamontology.org] +regex: "ENSSTO([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0905 -name: Protein interaction raw data -namespace: data +id: EDAM_data:2697 +name: Ensembl ID ('Takifugu rubripes') +subset: bioinformatics subset: data -def: "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -is_a: EDAM_data:3108 ! Experimental measurement +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division)." [http://edamontology.org] +regex: "ENSFRU([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:0931 -name: Experiment annotation (microarray) -namespace: data +id: EDAM_data:2698 +name: Ensembl ID ('Tupaia belangeri') +subset: bioinformatics subset: data -! alt_id: EDAM_data:3114 !{since=beta13} ! Not released -def: "Information on a microarray experiment such as conditions, protocol, sample:data relationships etc." [http://edamontology.org] -comment: This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. -synonym: "Experimental design annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2531 ! Experiment annotation -relationship: has_topic EDAM_topic:0200 ! Microarrays +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division)." [http://edamontology.org] +regex: "ENSTBE([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:2866 -name: Experiment annotation (Northern blot) -namespace: data +id: EDAM_data:2699 +name: Ensembl ID ('Xenopus tropicalis') +subset: bioinformatics subset: data -def: "General annotation on a Northern Blot experiment." [http://edamontology.org] -is_a: EDAM_data:2531 ! Experiment annotation +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division)." [http://edamontology.org] +regex: "ENSXET([EGTP])[0-9]{11}" +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM_data:3147 !{since=beta13} -name: Experiment annotation (mass spectrometry) -namespace: data +id: EDAM_data:2700 +name: CATH identifier +subset: bioinformatics subset: data -def: "General annotation on a mass spectrometry experiment." [http://edamontology.org] -is_a: EDAM_data:2531 ! Experiment annotation - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a protein domain (or other node) from the CATH database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1038 ! Protein domain ID +relationship: is_identifier_of EDAM_data:1553 ! CATH node [Term] -id: EDAM_data:0932 -name: Oligonucleotide probe data -namespace: data +id: EDAM_data:2701 +name: CATH node ID (family) +subset: bioinformatics subset: data -def: "Data on oligonucleotide probes (typically for use with DNA microarrays)." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:2717 ! Oligonucleotide probe annotation - - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A code number identifying a family from the CATH database." [http://edamontology.org] +example: "2.10.10.10" +namespace: identifier +is_a: EDAM_data:1043 ! CATH node ID +relationship: is_identifier_of EDAM_data:1553 ! CATH node [Term] -id: EDAM_data:2535 -name: Sequence tag profile -namespace: data +id: EDAM_data:2702 +name: Enzyme ID (CAZy) +subset: bioinformatics subset: data -def: "Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed." [http://edamontology.org] -comment: SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. -synonym: "Sequencing-based expression profile" EXACT [http://edamontology.org] -is_a: EDAM_data:0928 ! Gene expression profile - +subset: edam +subset: identifiers +synonym: "CAZy ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an enzyme from the CAZy enzymes database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2321 ! Enzyme ID [Term] -id: EDAM_data:0933 -name: SAGE experimental data -namespace: data +id: EDAM_data:2704 +name: Clone ID (IMAGE) +subset: bioinformatics subset: data -def: "Output from a serial analysis of gene expression (SAGE) experiment." [http://edamontology.org] -synonym: "Serial analysis of gene expression (SAGE) experimental data" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2535 ! Sequence tag profile +subset: edam +subset: identifiers +synonym: "I.M.A.G.E. cloneID" EXACT [] +synonym: "IMAGE cloneID" EXACT [] +created_in: "beta12orEarlier" +def: "A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1855 ! Clone ID [Term] -id: EDAM_data:0934 -name: MPSS experimental data -namespace: data +id: EDAM_data:2705 +name: GO concept ID (cellular compartment) +subset: bioinformatics subset: data -def: "Massively parallel signature sequencing (MPSS) data." [http://edamontology.org] -synonym: "Massively parallel signature sequencing (MPSS) experimental data" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2535 ! Sequence tag profile +subset: edam +subset: identifiers +synonym: "GO concept identifier (cellular compartment)" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier of a 'cellular compartment' concept from the Gene Ontology." [http://edamontology.org] +regex: "[0-9]{7}|GO:[0-9]{7}" +namespace: identifier +is_a: EDAM_data:1176 ! GO concept ID +[Term] +id: EDAM_data:2706 +name: Chromosome name (BioCyc) +subset: bioinformatics +subset: data +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a chromosome as used in the BioCyc database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0987 ! Chromosome name [Term] -id: EDAM_data:0935 -name: SBS experimental data -namespace: data +id: EDAM_data:2709 +name: CleanEx entry name +subset: bioinformatics subset: data -def: "Sequencing by synthesis (SBS) data." [http://edamontology.org] -synonym: "Sequencing by synthesis (SBS) experimental data" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2535 ! Sequence tag profile +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a gene expression profile from the CleanEx database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1080 ! Gene expression report ID [Term] -id: EDAM_data:0936 -name: Sequence tag profile (with gene assignment) -namespace: data +id: EDAM_data:2710 +name: CleanEx dataset code +subset: bioinformatics subset: data -def: "Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers." [http://edamontology.org] -is_a: EDAM_data:2535 ! Sequence tag profile - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] -id: EDAM_data:0942 -name: 2D PAGE image -namespace: data +id: EDAM_data:2711 +name: Genome metadata +subset: bioinformatics subset: data -def: "Two-dimensional gel electrophoresis image." [http://edamontology.org] -synonym: "Two-dimensional gel electrophoresis image" EXACT [http://edamontology.org] -is_a: EDAM_data:2968 ! Image -is_a: EDAM_data:3108 ! Experimental measurement -relationship: has_topic EDAM_topic:0121 ! Proteomics +subset: edam +created_in: "beta12orEarlier" +def: "Provenance metadata or other general information concerning a genome as a whole." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0855 ! Sequence metadata [Term] -id: EDAM_data:2364 -name: Experiment annotation (2D PAGE) -namespace: data +id: EDAM_data:2713 +name: Protein ID (CORUM) +subset: bioinformatics subset: data -def: "An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel." [http://edamontology.org] -is_a: EDAM_data:2531 ! Experiment annotation -relationship: has_topic EDAM_topic:0121 ! Proteomics +subset: edam +subset: identifiers +synonym: "CORUM complex ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier for a protein complex from the CORUM database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:2965 -name: 2D PAGE image (annotated) -namespace: data +id: EDAM_data:2714 +name: CDD PSSM-ID +subset: bioinformatics subset: data -def: "An informative report on a two-dimensional (2D PAGE) gel." [http://edamontology.org] -synonym: "2D PAGE image annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:0942 ! 2D PAGE image - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a position-specific scoring matrix from the CDD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1115 ! Sequence profile ID [Term] -id: EDAM_data:2372 -name: 2D PAGE spot (annotated) -namespace: data +id: EDAM_data:2715 +name: Protein ID (CuticleDB) +subset: bioinformatics subset: data -def: "An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel." [http://edamontology.org] -synonym: "2D PAGE spot annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2965 ! 2D PAGE image (annotated) +subset: edam +subset: identifiers +synonym: "CuticleDB ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier for a protein from the CuticleDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1646 -name: Molecular weights standard fingerprint -namespace: data +id: EDAM_data:2716 +name: DBD ID +subset: bioinformatics subset: data -def: "Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS." [http://edamontology.org] -is_a: EDAM_data:0944 ! Peptide mass fingerprint +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a predicted transcription factor from the DBD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2911 ! Transcription factor accession [Term] id: EDAM_data:2717 name: Oligonucleotide probe annotation -namespace: data +subset: bioinformatics subset: data +subset: edam +created_in: "beta12orEarlier" def: "General annotation on an oligonucleotide probe." [http://edamontology.org] +namespace: data is_a: EDAM_data:3115 ! Microarray annotation relationship: has_topic EDAM_topic:0632 ! Probes and primers - - [Term] -id: EDAM_data:2966 -name: Oligonucleotide probe sets annotation -namespace: data +id: EDAM_data:2718 +name: Oligonucleotide ID +subset: bioinformatics subset: data -def: "General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set." [http://edamontology.org] -is_a: EDAM_data:2717 ! Oligonucleotide probe annotation - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an oligonucleotide from a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2119 ! Nucleic acid identifier +is_a: EDAM_data:2901 ! Molecule accession [Term] -id: EDAM_data:1642 -name: Affymetrix probe sets library file -namespace: data +id: EDAM_data:2719 +name: dbProbe ID +subset: bioinformatics subset: data -def: "Affymetrix library file of information about which probes belong to which probe set." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation -! synonym: "CDF file" EXACT [http://edamontology.org] - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an oligonucleotide probe from the dbProbe database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2718 ! Oligonucleotide ID [Term] -id: EDAM_data:1643 -name: Affymetrix probe sets information library file -namespace: data +id: EDAM_data:2720 +name: Dinucleotide property +subset: bioinformatics subset: data -def: "Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation -! synonym: "GIN file" EXACT [http://edamontology.org] +subset: edam +created_in: "beta12orEarlier" +def: "Physicochemical property data for one or more dinucleotides." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2088 ! DNA base structural data [Term] -id: EDAM_data:0856 -name: Sequence feature source -namespace: data +id: EDAM_data:2721 +name: DiProDB ID +subset: bioinformatics subset: data -def: "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived." [http://edamontology.org] -comment: This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). -is_a: EDAM_data:2042 ! Evidence -is_a: EDAM_data:2914 ! Sequence features metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an dinucleotide property from the DiProDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2718 ! Oligonucleotide ID [Term] -id: EDAM_data:0859 -name: Sequence signature model -namespace: data +id: EDAM_data:2722 +name: Protein features (disordered structure) +subset: bioinformatics subset: data -def: "Data files used by motif or profile methods." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0950 ! Biological model - +subset: edam +synonym: "Protein structure report (disordered structure)" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report about disordered structure in a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +is_a: EDAM_data:1537 ! Protein structure report [Term] -id: EDAM_data:0946 -name: Pathway or network annotation -namespace: data +id: EDAM_data:2723 +name: Protein ID (DisProt) +subset: bioinformatics subset: data -def: "An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2984 ! Pathway or network report +subset: edam +subset: identifiers +synonym: "DisProt ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier for a protein from the DisProt database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:2589 -name: Hierarchy -namespace: data +id: EDAM_data:2724 +name: Embryo annotation +subset: bioinformatics subset: data -def: "A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation." [http://edamontology.org] -synonym: "Hierarchy annotation" EXACT [http://edamontology.org] -is_a: EDAM_data:2987 ! Classification - +subset: edam +created_in: "beta12orEarlier" +def: "Annotation on an embryo or concerning embryological development." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2530 ! Organism annotation +relationship: has_topic EDAM_topic:3065 ! Embryology resources [Term] -id: EDAM_data:0904 -name: Protein features (mutation) -namespace: data +id: EDAM_data:2725 +name: Transcript ID (Ensembl) +subset: bioinformatics subset: data -def: "Data on the effect of (typically point) mutation on protein folding, stability, structure and function." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -synonym: "Protein property (mutation)" EXACT [http://edamontology.org] -synonym: "Protein report (mutation)" EXACT [http://edamontology.org] -synonym: "Protein structure report (mutation)" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:0896 ! Protein report +subset: edam +subset: identifiers +synonym: "Ensembl Transcript ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier for a gene transcript from the Ensembl database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2610 ! Ensembl ID +is_a: EDAM_data:2769 ! Transcript ID [Term] -id: EDAM_data:0903 -name: Protein folding report -namespace: data +id: EDAM_data:2726 +name: Inhibitor annotation +subset: bioinformatics subset: data -def: "A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -synonym: "Protein report (folding)" EXACT [http://edamontology.org] -synonym: "Protein property (folding)" EXACT [http://edamontology.org] -is_a: EDAM_data:0897 ! Protein property - +subset: edam +created_in: "beta12orEarlier" +def: "An informative report on one or more small molecules that are enzyme inhibitors." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0962 ! Small molecule annotation [Term] -id: EDAM_data:1596 -name: Nucleic acid folding report -namespace: data +id: EDAM_data:2727 +name: Promoter ID +subset: bioinformatics subset: data -def: "A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -synonym: "Nucleic acid report (folding model)" EXACT [http://edamontology.org] -synonym: "Nucleic acid report (folding)" EXACT [http://edamontology.org] -is_a: EDAM_data:0912 ! Nucleic acid property - +subset: edam +subset: identifiers +xref: Moby:GeneAccessionList +created_in: "beta12orEarlier" +def: "An identifier of a promoter of a gene that is catalogued in a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1344 -name: MEME motif alphabet -namespace: data +id: EDAM_data:2728 +name: EST accession +subset: bioinformatics subset: data -def: "Alphabet for the motifs (patterns) that MEME will search for." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0950 ! Biological model +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an EST sequence." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1855 ! Clone ID [Term] -id: EDAM_data:1345 -name: MEME background frequencies file -namespace: data +id: EDAM_data:2729 +name: COGEME EST ID +subset: bioinformatics subset: data -def: "MEME background frequencies file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0950 ! Biological model +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an EST sequence from the COGEME database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2728 ! EST accession [Term] -id: EDAM_data:1346 -name: MEME motifs directive file -namespace: data +id: EDAM_data:2730 +name: COGEME unisequence ID +comment: A unisequence is a single sequence assembled from ESTs. +subset: bioinformatics subset: data -def: "File of directives for ordering and spacing of MEME motifs." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0950 ! Biological model +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a unisequence from the COGEME database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2728 ! EST accession [Term] -id: EDAM_data:1347 -name: Dirichlet distribution -namespace: data +id: EDAM_data:2731 +name: Protein family ID (GeneFarm) +subset: bioinformatics subset: data -def: "Dirichlet distribution used by hidden Markov model analysis programs." [http://edamontology.org] -is_a: EDAM_data:0950 ! Biological model +subset: edam +subset: identifiers +synonym: "GeneFarm family ID" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM_data:1348 -name: HMM emission and transition counts -namespace: data +id: EDAM_data:2732 +name: Family name +subset: bioinformatics subset: data -def: "Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states." [http://edamontology.org] -is_a: EDAM_data:0950 ! Biological model +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a family of organism." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM_data:0947 -name: Biological pathway map -namespace: data +id: EDAM_data:2733 +name: Genus name (virus) +subset: bioinformatics subset: data -def: "A map (typically a diagram) of a biological pathway." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2600 ! Pathway or network - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a genus of viruses." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1870 ! Genus name [Term] -id: EDAM_data:1656 -name: Pathway or network (metabolic) -namespace: data +id: EDAM_data:2734 +name: Family name (virus) +subset: bioinformatics subset: data -def: "A report typically including a map (diagram) of a metabolic pathway." [http://edamontology.org] -comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. -is_a: EDAM_data:2600 ! Pathway or network +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a family of viruses." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2732 ! Family name [Term] -id: EDAM_data:1657 -name: Pathway or network (genetic information processing) -namespace: data +id: EDAM_data:2735 +name: Database name (SwissRegulon) +subset: bioinformatics subset: data -def: "A report typically including a map (diagram) of a genetic information processing pathway." [http://edamontology.org] -is_a: EDAM_data:2600 ! Pathway or network +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a SwissRegulon database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1056 ! Database name [Term] -id: EDAM_data:2961 -name: Pathway or network (gene regulation) -namespace: data +id: EDAM_data:2736 +name: Sequence feature ID (SwissRegulon) +comment: This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". +subset: bioinformatics subset: data -def: "A report typically including a map (diagram) of a gene regulatory network." [http://edamontology.org] -is_a: EDAM_data:2600 ! Pathway or network -relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A feature identifier as used in the SwissRegulon database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1015 ! Sequence feature ID [Term] -id: EDAM_data:1658 -name: Pathway or network (environmental information processing) -namespace: data +id: EDAM_data:2737 +name: FIG ID +comment: A FIG ID consists of four parts: a prefix, genome id, locus type and id number. +subset: bioinformatics subset: data -def: "A report typically including a map (diagram) of an environmental information processing pathway." [http://edamontology.org] -is_a: EDAM_data:2600 ! Pathway or network - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of gene in the NMPDR database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1659 -name: Pathway or network (signal transduction) -namespace: data +id: EDAM_data:2738 +name: Gene ID (Xenbase) +subset: bioinformatics subset: data -def: "A report typically including a map (diagram) of a signal transduction pathway." [http://edamontology.org] -is_a: EDAM_data:2600 ! Pathway or network - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of gene in the Xenbase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1660 -name: Pathway or network (cellular process) -namespace: data +id: EDAM_data:2739 +name: Gene ID (Genolist) +subset: bioinformatics subset: data -def: "A report typically including a map (diagram) of a cellular process pathway." [http://edamontology.org] -is_a: EDAM_data:2600 ! Pathway or network +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of gene in the Genolist database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1661 -name: Pathway or network (disease) -namespace: data +id: EDAM_data:2740 +name: Gene name (Genolist) +subset: bioinformatics subset: data -def: "A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease." [http://edamontology.org] -is_a: EDAM_data:2600 ! Pathway or network +subset: edam +subset: identifiers +synonym: "Genolist gene name" EXACT [] +created_in: "beta12orEarlier" +def: "Name of an entry (gene) from the Genolist genes database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM_data:1662 -name: Pathway or network (drug structure relationship) -namespace: data +id: EDAM_data:2741 +name: ABS ID +subset: bioinformatics subset: data -def: "A report typically including a map (diagram) of drug structure relationships." [http://edamontology.org] -is_a: EDAM_data:2600 ! Pathway or network - +subset: edam +subset: identifiers +synonym: "ABS identifier" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier of an entry (promoter) from the ABS database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2727 ! Promoter ID [Term] -id: EDAM_data:1663 -name: Pathway or network (protein-protein interaction) -namespace: data +id: EDAM_data:2742 +name: AraC-XylS ID +subset: bioinformatics subset: data -def: "A report typically including a map (diagram) of a network of protein interactions." [http://edamontology.org] -is_a: EDAM_data:2600 ! Pathway or network +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a transcription factor from the AraC-XylS database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2911 ! Transcription factor accession [Term] -id: EDAM_data:0951 -name: Statistical estimate score -namespace: data +id: EDAM_data:2743 +name: Gene name (HUGO) +subset: bioinformatics subset: data -def: "A value representing estimated statistical significance of some observed data; typically sequence database hits." [http://edamontology.org] -is_a: EDAM_data:1772 ! Score or penalty -is_a: EDAM_data:2914 ! Sequence features metadata +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of an entry (gene) from the HUGO database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1791 ! Gene name (HGNC) [Term] -id: EDAM_data:0865 -name: Sequence similarity score -namespace: data +id: EDAM_data:2744 +name: Locus ID (PseudoCAP) +subset: bioinformatics subset: data -def: "A value representing molecular sequence similarity." [http://edamontology.org] -is_a: EDAM_data:1772 ! Score or penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a locus from the PseudoCAP database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:0888 -name: Structure similarity score -namespace: data +id: EDAM_data:2745 +name: Locus ID (UTR) +subset: bioinformatics subset: data -def: "A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison." [http://edamontology.org] -is_a: EDAM_data:1772 ! Score or penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a locus from the UTR database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM_data:2146 -name: Threshold -namespace: data +id: EDAM_data:2746 +name: MonosaccharideDB ID +subset: bioinformatics subset: data -def: "A value that serves as a threshold for a tool (usually to control scoring or output)." [http://edamontology.org] -is_a: EDAM_data:1772 ! Score or penalty +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier of a monosaccharide from the MonosaccharideDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2898 ! Monosaccharide accession [Term] -id: EDAM_data:1667 -name: E-value -namespace: data +id: EDAM_data:2747 +name: Database name (CMD) +subset: bioinformatics subset: data -def: "A simple floating point number defining the lower or upper limit of an expectation value (E-value)." [http://edamontology.org] -comment: An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. -synonym: "Expectation value" EXACT [http://edamontology.org] -is_a: EDAM_data:0951 ! Statistical estimate score +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a subdivision of the Collagen Mutation Database (CMD) database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1056 ! Database name [Term] -id: EDAM_data:1668 -name: Z-value -namespace: data +id: EDAM_data:2748 +name: Database name (Osteogenesis) +subset: bioinformatics subset: data -def: "The z-value is the number of standard deviations a data value is above or below a mean value." [http://edamontology.org] -comment: A z-value might be specified as a threshold for reporting hits from database searches. -is_a: EDAM_data:0951 ! Statistical estimate score - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a subdivision of the Osteogenesis database." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1056 ! Database name [Term] -id: EDAM_data:1669 -name: P-value -namespace: data +id: EDAM_data:2749 +name: Genome identifier +subset: bioinformatics subset: data -def: "The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true." [http://edamontology.org] -comment: A z-value might be specified as a threshold for reporting hits from database searches. -is_a: EDAM_data:0951 ! Statistical estimate score +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a particular genome." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_data:1412 -name: Sequence identity -namespace: data +id: EDAM_data:2751 +name: GenomeReviews ID +subset: bioinformatics subset: data -def: "Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences." [http://edamontology.org] -is_a: EDAM_data:0865 ! Sequence similarity score - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a particular genome." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2903 ! Genome accession [Term] -id: EDAM_data:1413 -name: Sequence similarity -namespace: data +id: EDAM_data:2752 +name: GlycoMap ID +subset: bioinformatics subset: data -def: "Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension." [http://edamontology.org] -comment: Data Type is float probably. -is_a: EDAM_data:0865 ! Sequence similarity score - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2900 ! Carbohydrate accession [Term] -id: EDAM_data:2335 -name: Bit score -namespace: data +id: EDAM_data:2753 +name: Carbohydrate conformational map +subset: bioinformatics subset: data -def: "A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system." [http://edamontology.org] -comment: Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. -is_a: EDAM_data:1413 ! Sequence similarity +subset: edam +created_in: "beta12orEarlier" +def: "A conformational energy map of the glycosidic linkages in a carbohydrate molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2313 ! Carbohydrate structure report + +[Term] +id: EDAM_data:2754 +name: Nucleic acid features (intron) +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene features (intron)" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on an intron in a nucleotide sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] -id: EDAM_data:1496 -name: Molecular similarity score -namespace: data +id: EDAM_data:2755 +name: Transcription factor name +subset: bioinformatics subset: data -def: "A score reflecting structural similarities of two molecules." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0888 ! Structure similarity score - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a transcription factor." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1009 ! Protein name +is_a: EDAM_data:1077 ! Transcription factor identifier [Term] -id: EDAM_data:1497 -name: Root-mean-square deviation -namespace: data +id: EDAM_data:2756 +name: TCID +subset: bioinformatics subset: data -def: "Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates." [http://edamontology.org] -synonym: "RMSD" EXACT [http://edamontology.org] -is_a: EDAM_data:0888 ! Structure similarity score +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a membrane transport proteins from the transport classification database (TCDB)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1498 -name: Tanimoto similarity score -namespace: data +id: EDAM_data:2757 +name: Pfam domain name +subset: bioinformatics subset: data -def: "A measure of the similarity between two ligand fingerprints." [http://edamontology.org] -comment: A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. -is_a: EDAM_data:0888 ! Structure similarity score +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a domain from the Pfam database." [http://edamontology.org] +regex: "PF[0-9]{5}" +namespace: identifier +is_a: EDAM_data:1131 ! Protein family name [Term] -id: EDAM_data:1673 -name: Swiss-Prot to PDB mapping -namespace: data +id: EDAM_data:2758 +name: Pfam clan ID +subset: bioinformatics subset: data -def: "Cross-mapping of Swiss-Prot codes to PDB identifiers." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0954 ! Database cross-mapping - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession number of a Pfam clan." [http://edamontology.org] +regex: "CL[0-9]{4}" +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM_data:1674 -name: Sequence database cross-references -namespace: data +id: EDAM_data:2759 +name: Gene ID (VectorBase) +subset: bioinformatics subset: data -def: "Cross-references from a sequence record to other databases." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2093 ! Data reference - +subset: edam +subset: identifiers +synonym: "VectorBase ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier for a gene from the VectorBase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:2337 -name: Metadata -namespace: data +id: EDAM_data:2761 +name: UTRSite ID +subset: bioinformatics subset: data -! alt_id: EDAM_data:2853 -def: "Data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Provenance metadata" EXACT [http://edamontology.org] -is_a: EDAM_data:2048 ! Report - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1114 ! Sequence motif identifier [Term] -id: EDAM_data:2018 -name: Annotation -namespace: data +id: EDAM_data:2762 +name: Sequence motif metadata +subset: bioinformatics subset: data -def: "A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it." [http://edamontology.org] -comment: This is a broad data type and is used a placeholder for other, more specific types. -is_obsolete: true !{since=beta13} -consider: EDAM_data:2048 ! Report - - +subset: edam +created_in: "beta12orEarlier" +def: "Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata +relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] -id: EDAM_data:0948 -name: Data resource definition -namespace: data +id: EDAM_data:2763 +name: Locus annotation +subset: bioinformatics subset: data -def: "A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper." [http://edamontology.org] -is_a: EDAM_data:1883 ! Annotated URI +subset: edam +synonym: "Locus report" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on a particular locus." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0916 ! Gene annotation [Term] -id: EDAM_data:0957 -name: Database metadata -namespace: data +id: EDAM_data:2764 +name: Protein name (UniProt) +subset: bioinformatics subset: data -def: "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." [http://edamontology.org] -is_a: EDAM_data:3106 ! System metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Official name of a protein as used in the UniProt database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1009 ! Protein name [Term] -id: EDAM_data:2223 -name: Ontology metadata -namespace: data +id: EDAM_data:2765 +name: Term ID list +comment: The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. +subset: bioinformatics subset: data -def: "Data concerning a biological ontology." [http://edamontology.org] -is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:0089 ! Ontology +subset: edam +created_in: "beta12orEarlier" +def: "One or more terms from one or more controlled vocabularies which are annotations on an entity." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2872 ! ID list [Term] -id: EDAM_data:2193 -name: Database entry metadata -namespace: data +id: EDAM_data:2766 +name: HAMAP ID +subset: bioinformatics subset: data -def: "Basic information on any arbitrary database entry." [http://edamontology.org] -is_a: EDAM_data:0957 ! Database metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a protein family from the HAMAP database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM_data:0958 -name: Tool metadata -namespace: data +id: EDAM_data:2767 +name: Identifier with metadata +subset: bioinformatics subset: data -def: "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." [http://edamontology.org] -is_a: EDAM_data:3106 ! System metadata - +subset: edam +created_in: "beta12orEarlier" +def: "Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0842 ! Identifier [Term] -id: EDAM_data:2218 -name: Server metadata -namespace: data +id: EDAM_data:2768 +name: Gene symbol annotation +subset: bioinformatics subset: data -def: "Basic information about a server on the web, such as an SRS server." [http://edamontology.org] -is_a: EDAM_data:3106 ! System metadata - +subset: edam +created_in: "beta12orEarlier" +def: "Annotation about a gene symbol." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2767 ! Identifier with metadata [Term] -id: EDAM_data:0959 -name: Job metadata -namespace: data +id: EDAM_data:2769 +name: Transcript ID +subset: bioinformatics subset: data -def: "Textual metadata on a submitted or completed job." [http://edamontology.org] -xref: Moby:PDGJOB -is_a: EDAM_data:3106 ! System metadata +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a RNA transcript." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2119 ! Nucleic acid identifier +is_a: EDAM_data:2901 ! Molecule accession +relationship: is_identifier_of EDAM_data:2399 ! Gene annotation (transcript) [Term] -id: EDAM_data:0960 -name: User metadata -namespace: data +id: EDAM_data:2770 +name: HIT ID +subset: bioinformatics subset: data -def: "Textual metadata on a software author or end-user, for example a person or other software." [http://edamontology.org] -is_a: EDAM_data:3106 ! System metadata +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an RNA transcript from the H-InvDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2769 ! Transcript ID [Term] -id: EDAM_data:3106 !{since=beta13} -name: System metadata -namespace: data +id: EDAM_data:2771 +name: HIX ID +subset: bioinformatics subset: data -def: "Metadata concerning the software, hardware or other aspects of a computer system." [http://edamontology.org] -is_a: EDAM_data:2337 ! Metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of gene cluster in the H-InvDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:0583 -name: Directory metadata -namespace: data +id: EDAM_data:2772 +name: HPA antibody id +subset: bioinformatics subset: data -def: "A directory on disk from which files are read." [http://edamontology.org] -is_a: EDAM_data:3106 ! System metadata +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a antibody from the HPA database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:0953 -name: Version information -namespace: data +id: EDAM_data:2773 +name: IMGT/HLA ID +subset: bioinformatics subset: data -def: "Information on a version of software or data, for example name, version number and release date." [http://edamontology.org] -synonym: "Version" EXACT [http://usefulinc.com/ns/doap#Version] -synonym: "version identifier" NARROW [http://semanticscience.org/resource/SIO_000653] -synonym: "version name or number" NARROW [http://purl.obolibrary.org/obo/IAO_0000129] -synonym: "development status" NARROW [http://www.ebi.ac.uk/swo/maturity/SWO_9000061] !{note="Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records."} -is_a: EDAM_data:2337 ! Metadata +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:2724 -name: Embryo annotation -namespace: data +id: EDAM_data:2774 +name: Gene ID (JCVI) +subset: bioinformatics subset: data -def: "Annotation on an embryo or concerning embryological development." [http://edamontology.org] -is_a: EDAM_data:2530 ! Organism annotation -relationship: has_topic EDAM_topic:3065 ! Embryology resources +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1664 -name: MIRIAM datatype -namespace: data +id: EDAM_data:2775 +name: Kinase name +subset: bioinformatics subset: data -def: "An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources." [http://edamontology.org] -comment: A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. -is_a: EDAM_data:0948 ! Data resource definition - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a kinase protein." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1009 ! Protein name [Term] -id: EDAM_data:2875 -name: DRCAT resource -namespace: data +id: EDAM_data:2776 +name: ConsensusPathDB entity ID +subset: bioinformatics subset: data -def: "An entry (resource) from the DRCAT bioinformatics resource catalogue." [http://edamontology.org] -is_a: EDAM_data:0948 ! Data resource definition - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a physical entity from the ConsensusPathDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2917 ! ConsensusPathDB identifier [Term] -id: EDAM_data:0952 -name: EMBOSS database resource definition -namespace: data +id: EDAM_data:2777 +name: ConsensusPathDB entity name +subset: bioinformatics subset: data -def: "Resource definition for an EMBOSS database." [http://edamontology.org] -is_a: EDAM_data:0957 ! Database metadata - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a physical entity from the ConsensusPathDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2917 ! ConsensusPathDB identifier [Term] -id: EDAM_data:1675 -name: Job status -namespace: data +id: EDAM_data:2778 +name: CCAP strain number +subset: bioinformatics subset: data -def: "Metadata on the status of a submitted job." [http://edamontology.org] -comment: Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). -is_a: EDAM_data:0959 ! Job metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The number of a strain of algae and protozoa from the CCAP database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2912 ! Strain accession [Term] -id: EDAM_data:1678 -name: Tool log -namespace: data +id: EDAM_data:2779 +name: Stock number +subset: bioinformatics subset: data -def: "A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages." [http://edamontology.org] -is_a: EDAM_data:0959 ! Job metadata +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of stock from a catalogue of biological resources." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1677 -name: Job type -namespace: data +id: EDAM_data:2780 +name: Stock number (TAIR) +subset: bioinformatics subset: data -def: "A label (text token) describing the type of job, for example interactive or non-interactive." [http://edamontology.org] -is_a: EDAM_data:2100 ! Type - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A stock number from The Arabidopsis information resource (TAIR)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2779 ! Stock number [Term] -id: EDAM_data:1679 -name: DaliLite log file -namespace: data +id: EDAM_data:2781 +name: REDIdb ID +subset: bioinformatics subset: data -def: "DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the RNA editing database (REDIdb)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] -id: EDAM_data:1680 -name: STRIDE log file -namespace: data +id: EDAM_data:2782 +name: SMART domain name +subset: bioinformatics subset: data -def: "STRIDE log file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a domain from the SMART database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1131 ! Protein family name [Term] -id: EDAM_data:1681 -name: NACCESS log file -namespace: data +id: EDAM_data:2783 +name: Protein family ID (PANTHER) +subset: bioinformatics subset: data -def: "NACCESS log file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log +subset: edam +subset: identifiers +synonym: "Panther family ID" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of an entry (family) from the PANTHER database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM_data:1682 -name: EMBOSS wordfinder log file -namespace: data +id: EDAM_data:2784 +name: RNAVirusDB ID +comment: Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. +subset: bioinformatics subset: data -def: "EMBOSS wordfinder log file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier for a virus from the RNAVirusDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2785 ! Virus ID [Term] -id: EDAM_data:1683 -name: EMBOSS domainatrix log file -namespace: data +id: EDAM_data:2785 +name: Virus ID +subset: bioinformatics subset: data -def: "EMBOSS (EMBASSY) domainatrix application log file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2908 ! Organism accession +is_a: EDAM_data:2913 ! Virus identifier [Term] -id: EDAM_data:1684 -name: EMBOSS sites log file -namespace: data +id: EDAM_data:2786 +name: NCBI Genome Project ID +subset: bioinformatics subset: data -def: "EMBOSS (EMBASSY) sites application log file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a genome project assigned by NCBI." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2903 ! Genome accession [Term] -id: EDAM_data:1685 -name: EMBOSS supermatcher error file -namespace: data +id: EDAM_data:2787 +name: NCBI genome accession +subset: bioinformatics subset: data -def: "EMBOSS (EMBASSY) supermatcher error file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of a whole genome assigned by the NCBI." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2903 ! Genome accession [Term] -id: EDAM_data:1686 -name: EMBOSS megamerger log file -namespace: data +id: EDAM_data:2788 +name: Sequence profile metadata +subset: bioinformatics subset: data -def: "EMBOSS megamerger log file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log +subset: edam +created_in: "beta12orEarlier" +def: "Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata +relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] -id: EDAM_data:1687 -name: EMBOSS whichdb log file -namespace: data +id: EDAM_data:2789 +name: Protein ID (TopDB) +subset: bioinformatics subset: data -def: "EMBOSS megamerger log file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log +subset: edam +subset: identifiers +synonym: "TopDB ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier for a membrane protein from the TopDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1688 -name: EMBOSS vectorstrip log file -namespace: data +id: EDAM_data:2790 +name: Gel identifier +subset: bioinformatics subset: data -def: "EMBOSS vectorstrip log file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1678 ! Tool log - - - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a two-dimensional (protein) gel." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_data:1670 -name: Database version information -namespace: data +id: EDAM_data:2791 +name: Reference map name (SWISS-2DPAGE) +subset: bioinformatics subset: data -def: "Information on a database (or ontology) version, for example name, version number and release date." [http://edamontology.org] -synonym: "Ontology version information" EXACT [http://edamontology.org] -is_a: EDAM_data:0953 ! Version information -is_a: EDAM_data:0957 ! Database metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a reference map gel from the SWISS-2DPAGE database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2790 ! Gel identifier [Term] -id: EDAM_data:2090 -name: Database entry version information -namespace: data +id: EDAM_data:2792 +name: Protein ID (PeroxiBase) +subset: bioinformatics subset: data -def: "Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on." [http://edamontology.org] -is_a: EDAM_data:0953 ! Version information -is_a: EDAM_data:2193 ! Database entry metadata - +subset: edam +subset: identifiers +synonym: "PeroxiBase ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier for a peroxidase protein from the PeroxiBase database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1671 -name: Tool version information -namespace: data +id: EDAM_data:2793 +name: SISYPHUS ID +subset: bioinformatics subset: data -def: "Information on an application version, for example name, version number and release date." [http://edamontology.org] -is_a: EDAM_data:0953 ! Version information -is_a: EDAM_data:0958 ! Tool metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the SISYPHUS database of tertiary structure alignments." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1072 ! Structure alignment ID [Term] -id: EDAM_data:1771 -name: Sequence version information -namespace: data +id: EDAM_data:2794 +name: ORF ID +subset: bioinformatics subset: data -def: "Information on an molecular sequence version." [http://edamontology.org] -is_a: EDAM_data:0953 ! Version information -is_a: EDAM_data:0855 ! Sequence metadata +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of an open reading frame (catalogued in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1893 ! Locus ID +is_a: EDAM_data:2795 ! ORF identifier [Term] -id: EDAM_data:2041 -name: Genome version information -namespace: data +id: EDAM_data:2795 +name: ORF identifier +subset: bioinformatics subset: data -def: "Information on a genome version." [http://edamontology.org] -is_a: EDAM_data:0953 ! Version information -is_a: EDAM_data:2711 ! Genome metadata +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of an open reading frame." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM_data:1672 -name: CATH version information -namespace: data +id: EDAM_data:2796 +name: Linucs ID +subset: bioinformatics subset: data -def: "Information on a version of the CATH database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1670 ! Database version information - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2900 ! Carbohydrate accession [Term] -id: EDAM_data:1047 -name: URI -namespace: data +id: EDAM_data:2797 +name: Protein ID (LGICdb) +subset: bioinformatics subset: data -def: "A string of characters that name or otherwise identify a resource on the Internet." [http://edamontology.org] -is_a: EDAM_data:2527 ! Parameter - - +subset: edam +subset: identifiers +synonym: "LGICdb ID" EXACT [] +created_in: "beta12orEarlier" +def: "Unique identifier for a ligand-gated ion channel protein from the LGICdb database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:2079 -name: Search parameter -namespace: data +id: EDAM_data:2798 +name: MaizeDB ID +subset: bioinformatics subset: data -def: "Some simple value controlling a search operation, typically a search of a database." [http://edamontology.org] -is_a: EDAM_data:2527 ! Parameter - - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of an EST sequence from the MaizeDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2728 ! EST accession [Term] -id: EDAM_data:2534 -name: Sequence parameter -namespace: data +id: EDAM_data:2799 +name: Gene ID (MfunGD) +subset: bioinformatics subset: data -def: "A parameter concerning calculations on molecular sequences." [http://edamontology.org] -is_a: EDAM_data:2527 ! Parameter +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of gene in the MfunGD database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:2130 -name: Sequence profile type -namespace: data +id: EDAM_data:2800 +name: Orpha number +subset: bioinformatics subset: data -def: "A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc." [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter -is_a: EDAM_data:2100 ! Type - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of a disease from the Orpha database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1150 ! Disease ID +relationship: is_identifier_of EDAM_data:1622 ! Disease annotation [Term] -id: EDAM_data:2023 -name: Sequence mask parameter -namespace: data +id: EDAM_data:2802 +name: Protein ID (EcID) +subset: bioinformatics subset: data -def: "Data used to replace (mask) characters in a molecular sequence." [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier for a protein from the EcID database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:0853 -name: DNA sense specification -namespace: data +id: EDAM_data:2803 +name: Clone ID (RefSeq) +subset: bioinformatics subset: data -def: "The strand of a DNA sequence (forward or reverse)." [http://edamontology.org] -comment: The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. -synonym: "DNA strand specification" EXACT [http://edamontology.org] -synonym: "Strand" EXACT [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter -is_a: EDAM_data:2914 ! Sequence features metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "A unique identifier of a cDNA molecule catalogued in the RefSeq database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1098 ! RefSeq accession +is_a: EDAM_data:1855 ! Clone ID [Term] -id: EDAM_data:2126 -name: Translation frame specification -namespace: data +id: EDAM_data:2804 +name: Protein ID (ConoServer) +subset: bioinformatics subset: data -def: "Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome)." [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Unique identifier for a cone snail toxin protein from the ConoServer database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:2336 -name: Translation phase specification -namespace: data +id: EDAM_data:2805 +name: GeneSNP ID +subset: bioinformatics subset: data -def: "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." [http://edamontology.org] -synonym: "Phase" EXACT [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter -is_a: EDAM_data:2914 ! Sequence features metadata - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a GeneSNP database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2294 ! Sequence variation ID [Term] -id: EDAM_data:1014 -name: Sequence position specification -namespace: data +id: EDAM_data:2812 +name: Lipid identifier +subset: bioinformatics subset: data -def: "A specification (partial or complete) of one or more positions or regions of a molecular sequence or map." [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a lipid." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0982 ! Molecule identifier +relationship: is_identifier_of EDAM_data:2850 ! Lipid structure +relationship: is_identifier_of EDAM_data:2879 ! Lipid structure report [Term] -id: EDAM_data:0854 -name: Sequence length specification -namespace: data +id: EDAM_data:2831 +name: Databank +subset: bioinformatics subset: data -def: "A specification of sequence length(s)." [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter - +subset: edam +created_in: "beta12orEarlier" +def: "A flat-file (textual) data archive." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:2357 -name: Protein signature type -namespace: data +id: EDAM_data:2832 +name: Web portal +subset: bioinformatics subset: data -def: "A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter -is_a: EDAM_data:2100 ! Type +subset: edam +created_in: "beta12orEarlier" +def: "A web site providing data (web pages) on a common theme to a HTTP client." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:0864 -name: Sequence alignment parameter -namespace: data +id: EDAM_data:2835 +name: Gene ID (VBASE2) +subset: bioinformatics subset: data -def: "Some simple value controlling a sequence alignment (or similar 'match') operation." [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter +subset: edam +subset: identifiers +synonym: "VBASE2 ID" EXACT [] +created_in: "beta12orEarlier" +def: "Identifier for a gene from the VBASE2 database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM_data:1120 -name: Sequence alignment type -namespace: data +id: EDAM_data:2836 +name: DPVweb ID +subset: bioinformatics subset: data -def: "A label (text token) describing the type of a sequence alignment." [http://edamontology.org] -comment: Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. -is_a: EDAM_data:0864 ! Sequence alignment parameter -is_a: EDAM_data:2100 ! Type - - +subset: edam +subset: identifiers +synonym: "DPVweb virus ID" EXACT [] +created_in: "beta12orEarlier" +def: "A unique identifier for a virus from the DPVweb database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2785 ! Virus ID [Term] -id: EDAM_data:1052 -name: URL -namespace: data +id: EDAM_data:2837 +name: Pathway ID (BioSystems) +subset: bioinformatics subset: data -! alt_id: EDAM_data:1054 -! alt_id: EDAM_data:1168 -! alt_id: EDAM_data:1169 -def: "A Uniform Resource Locator (URL)." [http://edamontology.org] -xref: Moby:URL -xref: Moby:Link -is_a: EDAM_data:1047 ! URI - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a pathway from the BioSystems pathway database." [http://edamontology.org] +regex: "[0-9]+" +namespace: identifier +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM_data:1053 -name: URN -namespace: data +id: EDAM_data:2838 +name: Experimental data (proteomics) +subset: bioinformatics subset: data -def: "A Uniform Resource Name (URN)." [http://edamontology.org] -is_a: EDAM_data:1047 ! URI - +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning a proteomics experiment." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:3147 ! Experiment annotation (mass spectrometry) [Term] -id: EDAM_data:1055 -name: LSID -namespace: data +id: EDAM_data:2849 +name: Abstract +subset: bioinformatics subset: data -def: "A Life Science Identifier (LSID) - a unique identifier of some data." [http://edamontology.org] -comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:::[:] -synonym: "Life Science Identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:1053 ! URN +subset: edam +created_in: "beta12orEarlier" +def: "An abstract of a scientific article." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2857 ! Article metadata [Term] -id: EDAM_data:0968 -name: Keyword -namespace: data +id: EDAM_data:2850 +name: Lipid structure +subset: bioinformatics subset: data -def: "Keyword(s) or phrase(s) used (typically) for text-searching purposes." [http://edamontology.org] -comment: Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. -xref: Moby:Global_Keyword -xref: Moby:QueryString -xref: Moby:Wildcard_Query -xref: Moby:BooleanQueryString -is_a: EDAM_data:2527 ! Parameter - +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a lipid structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0883 ! Structure [Term] -id: EDAM_data:2022 -name: Vienna RNA structural data -namespace: data +id: EDAM_data:2851 +name: Drug structure +subset: bioinformatics subset: data -def: "Data used by the Vienna RNA analysis package." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2527 ! Parameter - +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for the (3D) structure of a drug." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1463 ! Small molecule structure [Term] -id: EDAM_data:2134 -name: Results sort order -namespace: data +id: EDAM_data:2852 +name: Toxin structure +subset: bioinformatics subset: data -def: "A control of the order of data that is output, for example the order of sequences in an alignment." [http://edamontology.org] -is_a: EDAM_data:2079 ! Search parameter +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for the (3D) structure of a toxin." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1463 ! Small molecule structure [Term] -id: EDAM_data:2135 -name: Toggle -namespace: data +id: EDAM_data:2854 +name: Position-specific scoring matrix +subset: bioinformatics subset: data -def: "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2527 ! Parameter - +subset: edam +created_in: "beta12orEarlier" +def: "A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1354 ! Sequence profile +is_a: EDAM_data:2082 ! Matrix [Term] -id: EDAM_data:2139 -name: Nucleic acid melting temperature -namespace: data +id: EDAM_data:2855 +name: Distance matrix +subset: bioinformatics subset: data -def: "A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate." [http://edamontology.org] -synonym: "Melting temperature" EXACT [http://edamontology.org] -is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data +subset: edam +created_in: "beta12orEarlier" +def: "A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2082 ! Matrix +[Term] +id: EDAM_data:2856 +name: Structural distance matrix +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Distances (values representing similarity) between a group of molecular structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2855 ! Distance matrix [Term] -id: EDAM_data:2140 -name: Concentration -namespace: data +id: EDAM_data:2857 +name: Article metadata +subset: bioinformatics subset: data -def: "The concentration of a chemical compound." [http://edamontology.org] -is_a: EDAM_data:2050 ! Molecular property (general) +subset: edam +created_in: "beta12orEarlier" +def: "Bibliographic data concerning scientific article(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata +is_a: EDAM_data:2954 ! Article report +relationship: has_topic EDAM_topic:3068 ! Literature and reference [Term] -id: EDAM_data:2151 -name: Color -namespace: data +id: EDAM_data:2858 +name: Ontology concept +comment: This includes any fields from the concept definition such as concept name, definition, comments and so on. +subset: bioinformatics subset: data -def: "Specification of one or more colors." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2152 ! Rendering parameter - +subset: edam +created_in: "beta12orEarlier" +def: "A concept from a biological ontology." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] -id: EDAM_data:2152 -name: Rendering parameter -namespace: data +id: EDAM_data:2865 +name: Codon usage bias +subset: bioinformatics subset: data -def: "A parameter that is used to control rendering (drawing) to a device or image." [http://edamontology.org] -synonym: "Graphics parameter" EXACT [http://edamontology.org] -synonym: "Graphical parameter" EXACT [http://edamontology.org] -is_a: EDAM_data:2527 ! Parameter - +subset: edam +created_in: "beta12orEarlier" +def: "A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0914 ! Codon usage report [Term] -id: EDAM_data:3105 !{since=beta13} -name: Geotemporal metadata -namespace: data +id: EDAM_data:2866 +name: Experiment annotation (Northern blot) +subset: bioinformatics subset: data -def: "Basic information concerning geographical location or time." [http://edamontology.org] -is_a: EDAM_data:2337 ! Metadata +subset: edam +created_in: "beta12orEarlier" +def: "General annotation on a Northern Blot experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2531 ! Experiment annotation [Term] -id: EDAM_data:2156 -name: Date -namespace: data +id: EDAM_data:2867 +name: Nucleic acid features (VNTR) +comment: VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. +subset: bioinformatics subset: data -def: "A temporal date." [http://edamontology.org] -is_a: EDAM_data:3105 ! Geotemporal metadata - +subset: edam +synonym: "Variable number of tandem repeat polymorphism" EXACT [] +synonym: "VNTR annotation" EXACT [] +created_in: "beta12orEarlier" +def: "Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] -id: EDAM_data:1693 -name: Number of iterations -namespace: data +id: EDAM_data:2868 +name: Nucleic acid features (microsatellite) +comment: A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. +subset: bioinformatics subset: data -def: "Number of iterations of an algorithm." [http://edamontology.org] -is_a: EDAM_data:2079 ! Search parameter +subset: edam +synonym: "Microsatellite annotation" EXACT [] +created_in: "beta12orEarlier" +def: "Annotation on a microsatellite polymorphism in a DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] -id: EDAM_data:1694 -name: Number of output entities -namespace: data +id: EDAM_data:2869 +name: Nucleic acid features (RFLP) +comment: An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. +subset: bioinformatics subset: data -def: "Number of entities (for example database hits, sequences, alignments etc) to write to an output file." [http://edamontology.org] -is_a: EDAM_data:2079 ! Search parameter - - - -! Possible values include: 'SC' (score) or 'RF' (rank), pvalue (sort by increasing P-value (probability). i.e. most statistically significant hits given first), count (sort hits by increasing number of submatches (for example HSP) in each hit, score (sort hits in order of increasing score - - +subset: edam +synonym: "RFLP annotation" EXACT [] +created_in: "beta12orEarlier" +def: "Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] -id: EDAM_data:1695 -name: Hit sort order -namespace: data +id: EDAM_data:2870 +name: Radiation hybrid map +comment: The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. +subset: bioinformatics subset: data -def: "Controls the order of hits (reported matches) in an output file from a database search." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2134 ! Results sort order +subset: edam +synonym: "RH map" EXACT [] +created_in: "beta12orEarlier" +def: "A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1280 ! Physical map [Term] -id: EDAM_data:0851 -name: Sequence mask character -namespace: data +id: EDAM_data:2872 +name: ID list +subset: bioinformatics subset: data -def: "A character used to replace (mask) other characters in a molecular sequence." [http://edamontology.org] -is_a: EDAM_data:2023 ! Sequence mask parameter +subset: edam +created_in: "beta12orEarlier" +def: "A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2093 ! Data reference [Term] -id: EDAM_data:0852 -name: Sequence mask type -namespace: data +id: EDAM_data:2873 +name: Phylogenetic gene frequencies data +subset: bioinformatics subset: data -def: "A label (text token) describing the type of sequence masking to perform." [http://edamontology.org] -comment: Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. -is_a: EDAM_data:2023 ! Sequence mask parameter -is_a: EDAM_data:2100 ! Type - +subset: edam +created_in: "beta12orEarlier" +def: "Gene frequencies data that may be read during phylogenetic tree calculation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1426 ! Phylogenetic continuous quantitative data [Term] -id: EDAM_data:1016 -name: Sequence position -namespace: data +id: EDAM_data:2874 +name: Sequence set (polymorphic) +subset: bioinformatics subset: data -def: "A position of a single point (base or residue) in a sequence, or part of such a specification." [http://edamontology.org] -synonym: "sequence_location" RELATED [SO:0000735] -xref: WHATIF: number -xref: WHATIF: PDBx_atom_site -is_a: EDAM_data:1014 ! Sequence position specification -! _atom_site.id in PDBML +subset: edam +created_in: "beta12orEarlier" +def: "A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] -id: EDAM_data:2145 -name: Sequence offset -namespace: data +id: EDAM_data:2875 +name: DRCAT resource +subset: bioinformatics subset: data -def: "An offset for a single-point sequence position." [http://edamontology.org] -is_a: EDAM_data:1016 ! Sequence position -is_a: EDAM_data:2914 ! Sequence features metadata +subset: edam +created_in: "beta12orEarlier" +def: "An entry (resource) from the DRCAT bioinformatics resource catalogue." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0948 ! Data resource definition [Term] -id: EDAM_data:1017 -name: Sequence range -namespace: data +id: EDAM_data:2877 +name: Protein complex +subset: bioinformatics subset: data -def: "Specification of range(s) of sequence positions." [http://edamontology.org] -is_a: EDAM_data:1014 ! Sequence position specification +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1460 ! Protein structure [Term] -id: EDAM_data:2012 -name: Map position -namespace: data +id: EDAM_data:2878 +name: Protein structural motif +subset: bioinformatics subset: data -! alt_id: EDAM_data:1894 -def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval." [http://edamontology.org] -comment: This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. -synonym: "Locus" EXACT [http://edamontology.org] -! synonym: An ontology concept covering the different types of position/locus RELATED [...] -xref: Moby:GCP_MapPoint -xref: Moby:GCP_MapPosition -xref: Moby:HitPosition -xref: Moby:GenePosition -xref: Moby:MapPosition -xref: Moby:Position -xref: Moby:GCP_MapInterval -xref: Moby:Locus -is_a: EDAM_data:1016 ! Sequence position -is_a: EDAM_data:1017 ! Sequence range -is_a: EDAM_data:2019 ! Map attribute -! _atom_site.id in PDBML +subset: edam +created_in: "beta12orEarlier" +def: "3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1460 ! Protein structure [Term] -id: EDAM_data:2216 -name: Codon number -namespace: data +id: EDAM_data:2879 +name: Lipid structure report +subset: bioinformatics subset: data -def: "The number of a codon, for instance, at which a mutation is located." [http://edamontology.org] -is_a: EDAM_data:1016 ! Sequence position +subset: edam +created_in: "beta12orEarlier" +def: "Annotation on or information derived from one or more specific lipid 3D structure(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2085 ! Structure report [Term] -id: EDAM_data:1742 -name: PDB residue number -namespace: data +id: EDAM_data:2880 +name: Secondary structure image +subset: bioinformatics subset: data -def: "A residue identifier (a string) from a PDB file." [http://edamontology.org] -xref: WHATIF: pdb_number -is_a: EDAM_data:1016 ! Sequence position -! PDB_residue_no in PDBML +subset: edam +created_in: "beta12orEarlier" +def: "Image of one or more molecular secondary structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2881 ! Secondary structure report [Term] -id: EDAM_data:1856 -name: PDB insertion code -namespace: data +id: EDAM_data:2881 +name: Secondary structure report +subset: bioinformatics subset: data -def: "An insertion code (part of the residue number) for an amino acid residue from a PDB file." [http://edamontology.org] -xref: WHATIF: insertion_code -is_a: EDAM_data:1016 ! Sequence position -! pdbx_PDB_ins_code in PDBML - +subset: edam +synonym: "Secondary structure-derived report" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on general information, properties or features of one or more molecular secondary structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_data:1906 -name: Quantitative trait locus -namespace: data +id: EDAM_data:2882 +name: DNA features +subset: bioinformatics subset: data -def: "A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment)." [http://edamontology.org] -comment: A QTL sometimes but does not necessarily correspond to a gene. -synonym: "QTL" EXACT [http://edamontology.org] -xref: Moby:SO_QTL -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2012 ! Map position +subset: edam +created_in: "beta12orEarlier" +def: "DNA sequence-specific feature annotation (not in a feature table)." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_data:1249 -name: Sequence length -namespace: data +id: EDAM_data:2883 +name: Nucleic acid features (RNA features) +subset: bioinformatics subset: data -def: "The size (length) of a sequence, subsequence or region in a sequence." [http://edamontology.org] -is_a: EDAM_data:0854 ! Sequence length specification +subset: edam +synonym: "RNA features" EXACT [] +created_in: "beta12orEarlier" +def: "Features concerning RNA or regions of DNA that encode an RNA molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] -id: EDAM_data:1252 -name: Sequence length range -namespace: data +id: EDAM_data:2884 +name: Plot +subset: bioinformatics subset: data -def: "Specification of range(s) of length of sequences." [http://edamontology.org] -is_a: EDAM_data:0854 ! Sequence length specification +subset: edam +created_in: "beta12orEarlier" +def: "Biological data that is plotted as a graph of some type." [http://edamontology.org] +namespace: data +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2968 ! Image [Term] -id: EDAM_data:1250 -name: Word size -namespace: data +id: EDAM_data:2885 +name: Nucleic acid features (polymorphism annotation) +subset: bioinformatics subset: data -def: "Size of a sequence word." [http://edamontology.org] -comment: Word size is used for example in word-based sequence database search methods. -synonym: "Word length" EXACT [http://edamontology.org] -is_a: EDAM_data:1249 ! Sequence length +subset: edam +synonym: "Polymorphism annotation" EXACT [] +created_in: "beta12orEarlier" +def: "Annotation on a polymorphism." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0918 ! Nucleic acid features (variation) +[Term] +id: EDAM_data:2886 +name: Sequence record (protein) +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein sequence record" EXACT [] +created_in: "beta12orEarlier" +def: "A protein sequence and associated metadata." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0849 ! Sequence record +is_a: EDAM_data:2976 ! Protein sequence [Term] -id: EDAM_data:1251 -name: Window size -namespace: data +id: EDAM_data:2887 +name: Sequence record (nucleic acid) +subset: bioinformatics subset: data -def: "Size of a sequence window." [http://edamontology.org] -comment: A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. -is_a: EDAM_data:1249 ! Sequence length - +subset: edam +synonym: "Nucleic acid sequence record" EXACT [] +synonym: "Nucleotide sequence record" EXACT [] +created_in: "beta12orEarlier" +def: "A nucleic acid sequence and associated metadata." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0849 ! Sequence record +is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] -id: EDAM_data:2141 -name: Window step size -namespace: data +id: EDAM_data:2888 +name: Sequence record full (protein) +subset: bioinformatics subset: data -def: "Size of the incremental 'step' a sequence window is moved over a sequence." [http://edamontology.org] -is_a: EDAM_data:1249 ! Sequence length +subset: edam +xref: SO:2000061 +created_in: "beta12orEarlier" +def: "A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2201 ! Sequence record full +is_a: EDAM_data:2886 ! Sequence record (protein) [Term] -id: EDAM_data:1125 -name: Comparison matrix type -namespace: data +id: EDAM_data:2889 +name: Sequence record full (nucleic acid) +subset: bioinformatics subset: data -def: "A label (text token) describing the type of a comparison matrix." [http://edamontology.org] -comment: For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. -example: "blosum" "pam" "gonnet" "id" -synonym: "Substitution matrix type" EXACT [http://edamontology.org] -is_a: EDAM_data:0864 ! Sequence alignment parameter -is_a: EDAM_data:2100 ! Type - +subset: edam +xref: SO:2000061 +created_in: "beta12orEarlier" +def: "A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2201 ! Sequence record full +is_a: EDAM_data:2887 ! Sequence record (nucleic acid) [Term] -id: EDAM_data:1394 -name: Alignment score or penalty -namespace: data +id: EDAM_data:2891 +name: Biological model accession +subset: bioinformatics subset: data -def: "A simple floating point number defining the penalty for opening or extending a gap in an alignment." [http://edamontology.org] -is_a: EDAM_data:0864 ! Sequence alignment parameter -is_a: EDAM_data:1772 ! Score or penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a mathematical model, typically an entry from a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1085 ! Biological model identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1395 -name: Score end gaps control -namespace: data +id: EDAM_data:2892 +name: Cell type name +subset: bioinformatics subset: data -def: "Whether end gaps are scored or not." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2527 ! Parameter - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a type or group of cells." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2655 ! Cell type identifier [Term] -id: EDAM_data:1396 -name: Aligned sequence order -namespace: data +id: EDAM_data:2893 +name: Cell type accession +subset: bioinformatics subset: data -def: "Controls the order of sequences in an output sequence alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2134 ! Results sort order +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a type or group of cells (catalogued in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2655 ! Cell type identifier [Term] -id: EDAM_data:2136 -name: Sequence width -namespace: data +id: EDAM_data:2894 +name: Compound accession +subset: bioinformatics subset: data -def: "The width of an output sequence or alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1249 ! Sequence length +subset: edam +subset: identifiers +synonym: "Chemical compound accession" EXACT [] +synonym: "Small molecule accession" EXACT [] +created_in: "beta12orEarlier" +def: "Accession of an entry from a database of chemicals." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1086 ! Compound identifier +is_a: EDAM_data:2901 ! Molecule accession [Term] -id: EDAM_data:2137 -name: Gap penalty -namespace: data +id: EDAM_data:2895 +name: Drug accession +subset: bioinformatics subset: data -def: "A penalty for introducing or extending a gap in an alignment." [http://edamontology.org] -is_a: EDAM_data:1394 ! Alignment score or penalty +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a drug." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0993 ! Drug identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1401 -name: Match reward score -namespace: data +id: EDAM_data:2896 +name: Toxin name +subset: bioinformatics subset: data -def: "The score for a 'match' used in various sequence database search applications with simple scoring schemes." [http://edamontology.org] -is_a: EDAM_data:1394 ! Alignment score or penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Name of a toxin." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:2576 ! Toxin identifier [Term] -id: EDAM_data:1402 -name: Mismatch penalty score -namespace: data +id: EDAM_data:2897 +name: Toxin accession +subset: bioinformatics subset: data -def: "The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes." [http://edamontology.org] -is_a: EDAM_data:1394 ! Alignment score or penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a toxin (catalogued in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2576 ! Toxin identifier [Term] -id: EDAM_data:1403 -name: Drop off score -namespace: data +id: EDAM_data:2898 +name: Monosaccharide accession +subset: bioinformatics subset: data -def: "This is the threshold drop in score at which extension of word alignment is halted." [http://edamontology.org] -is_a: EDAM_data:1394 ! Alignment score or penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a monosaccharide (catalogued in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0996 ! Monosaccharide identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1397 -name: Gap opening penalty -namespace: data +id: EDAM_data:2899 +name: Drug name +subset: bioinformatics subset: data -def: "A penalty for opening a gap in an alignment." [http://edamontology.org] -is_a: EDAM_data:2137 ! Gap penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Common name of a drug." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0990 ! Compound name +is_a: EDAM_data:0993 ! Drug identifier [Term] -id: EDAM_data:1398 -name: Gap extension penalty -namespace: data +id: EDAM_data:2900 +name: Carbohydrate accession +subset: bioinformatics subset: data -def: "A penalty for extending a gap in an alignment." [http://edamontology.org] -is_a: EDAM_data:2137 ! Gap penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of an entry from a database of carbohydrates." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2663 ! Carbohydrate identifier +is_a: EDAM_data:2901 ! Molecule accession [Term] -id: EDAM_data:1399 -name: Gap separation penalty -namespace: data +id: EDAM_data:2901 +name: Molecule accession +subset: bioinformatics subset: data -def: "A penalty for gaps that are close together in an alignment." [http://edamontology.org] -is_a: EDAM_data:2137 ! Gap penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a specific molecule (catalogued in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0982 ! Molecule identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1400 -name: Terminal gap penalty -namespace: data +id: EDAM_data:2902 +name: Data resource definition accession +subset: bioinformatics subset: data -def: "A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1410 ! Terminal gap opening penalty -consider: EDAM_data:1411 ! Terminal gap extension penalty +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a data definition (catalogued in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1084 ! Data resource definition identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1404 -name: Gap opening penalty (integer) -namespace: data +id: EDAM_data:2903 +name: Genome accession +subset: bioinformatics subset: data -def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1397 ! Gap opening penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An accession of a particular genome (in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2749 ! Genome identifier [Term] -id: EDAM_data:1405 -name: Gap opening penalty (float) -namespace: data +id: EDAM_data:2904 +name: Map accession +subset: bioinformatics subset: data -def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1397 ! Gap opening penalty +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An accession of a map of a molecular sequence (deposited in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2117 ! Map identifier [Term] -id: EDAM_data:1406 -name: Gap extension penalty (integer) -namespace: data +id: EDAM_data:2905 +name: Lipid accession +subset: bioinformatics subset: data -def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1398 ! Gap extension penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of an entry from a database of lipids." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2812 ! Lipid identifier +is_a: EDAM_data:2901 ! Molecule accession [Term] -id: EDAM_data:1407 -name: Gap extension penalty (float) -namespace: data +id: EDAM_data:2906 +name: Peptide ID +subset: bioinformatics subset: data -def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1398 ! Gap extension penalty +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a peptide deposited in a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0988 ! Peptide identifier +is_a: EDAM_data:2901 ! Molecule accession [Term] -id: EDAM_data:1408 -name: Gap separation penalty (integer) -namespace: data +id: EDAM_data:2907 +name: Protein accession +subset: bioinformatics subset: data -def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1399 ! Gap separation penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a protein deposited in a database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0989 ! Protein identifier +is_a: EDAM_data:2901 ! Molecule accession [Term] -id: EDAM_data:1409 -name: Gap separation penalty (float) -namespace: data +id: EDAM_data:2908 +name: Organism accession +subset: bioinformatics subset: data -def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1399 ! Gap separation penalty - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An accession of annotation on a (group of) organisms (catalogued in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1869 ! Organism identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1410 -name: Terminal gap opening penalty -namespace: data +id: EDAM_data:2909 +name: Organism name +subset: bioinformatics subset: data -def: "A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org] -is_a: EDAM_data:1397 ! Gap opening penalty +subset: edam +subset: identifiers +xref: Moby:BriefOccurrenceRecord +xref: Moby:FirstEpithet +xref: Moby:InfraspecificEpithet +xref: Moby:OccurrenceRecord +xref: Moby:Organism_Name +xref: Moby:OrganismsLongName +xref: Moby:OrganismsShortName +created_in: "beta12orEarlier" +def: "The name of an organism (or group of organisms)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1869 ! Organism identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM_data:1411 -name: Terminal gap extension penalty -namespace: data +id: EDAM_data:2910 +name: Protein family accession +subset: bioinformatics subset: data -def: "A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org] -is_a: EDAM_data:1398 ! Gap extension penalty +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of a protein family (that is deposited in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1075 ! Protein family identifier +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:2007 -name: UniProt keyword -namespace: data +id: EDAM_data:2911 +name: Transcription factor accession +subset: bioinformatics subset: data -def: "A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org] -xref: Moby_namespace:SP_KW -xref: http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW -is_a: EDAM_data:0968 ! Keyword - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Accession of an entry from a database of transcription factors or binding sites." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1077 ! Transcription factor identifier +is_a: EDAM_data:2091 ! Accession +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1877 -name: Synonym -namespace: data +id: EDAM_data:2912 +name: Strain accession +subset: bioinformatics subset: data -def: "An alternative for a word." [http://edamontology.org] -synonym: "Alternative name" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0968 ! Keyword - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2379 ! Strain identifier +is_a: EDAM_data:2908 ! Organism accession +relationship: is_identifier_of EDAM_data:0963 ! Cell line annotation [Term] -id: EDAM_data:1878 -name: Misspelling -namespace: data +id: EDAM_data:2913 +name: Virus identifier +subset: bioinformatics subset: data -def: "A common misspelling of a word." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0968 ! Keyword - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1869 ! Organism identifier +relationship: is_identifier_of EDAM_data:2307 ! Virus annotation [Term] -id: EDAM_data:1879 -name: Acronym -namespace: data +id: EDAM_data:2914 +name: Sequence features metadata +subset: bioinformatics subset: data -def: "An abbreviation of a phrase or word." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0968 ! Keyword - +subset: edam +created_in: "beta12orEarlier" +def: "Metadata on sequence features." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0855 ! Sequence metadata [Term] -id: EDAM_data:1880 -name: Misnomer -namespace: data +id: EDAM_data:2915 +name: Gramene identifier +subset: bioinformatics subset: data -def: "A term which is likely to be misleading of its meaning." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0968 ! Keyword +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a Gramene database entry." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] -id: EDAM_data:1591 -name: Vienna RNA parameters -namespace: data +id: EDAM_data:2916 +name: DDBJ accession +subset: bioinformatics subset: data -def: "RNA parameters used by the Vienna package." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2527 ! Parameter +subset: edam +subset: identifiers +synonym: "DDBJ accession number" EXACT [] +synonym: "DDBJ ID" EXACT [] +synonym: "DDBJ identifier" EXACT [] +created_in: "beta12orEarlier" +def: "An identifier of an entry from the DDBJ sequence database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID [Term] -id: EDAM_data:1592 -name: Vienna RNA structure constraints -namespace: data +id: EDAM_data:2917 +name: ConsensusPathDB identifier +subset: bioinformatics subset: data -def: "Structure constraints used by the Vienna package." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2527 ! Parameter - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "An identifier of an entity from the ConsensusPathDB database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM_data:1593 -name: Vienna RNA concentration data -namespace: data +id: EDAM_data:2925 +name: Sequence data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "RNA concentration data used by the Vienna package." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2527 ! Parameter +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning molecular sequence(s)." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2044 ! Sequence +consider: EDAM_data:2955 ! Sequence report [Term] -id: EDAM_data:1696 -name: Drug annotation -namespace: data +id: EDAM_data:2927 +name: Codon usage data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "An informative report on a specific drug." [http://edamontology.org] -is_a: EDAM_data:0962 ! Small molecule annotation -relationship: has_topic EDAM_topic:0620 ! Drugs and targets +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning codon usage." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0914 ! Codon usage report +consider: EDAM_data:1597 ! Codon usage table [Term] -id: EDAM_data:2400 -name: Toxin annotation -namespace: data +id: EDAM_data:2954 +name: Article report +subset: bioinformatics subset: data -def: "An informative report on a specific toxin." [http://edamontology.org] -is_a: EDAM_data:0962 ! Small molecule annotation +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning or derived from the analysis of a scientific article." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_data:2240 -name: Heterogen annotation -namespace: data +id: EDAM_data:2955 +name: Sequence report +subset: bioinformatics subset: data -def: "An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files." [http://edamontology.org] -is_a: EDAM_data:0962 ! Small molecule annotation - +subset: edam +synonym: "Sequence-derived report" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM_data:2726 -name: Inhibitor annotation -namespace: data +id: EDAM_data:2956 +name: Protein secondary structure report +subset: bioinformatics subset: data -def: "An informative report on one or more small molecules that are enzyme inhibitors." [http://edamontology.org] -is_a: EDAM_data:0962 ! Small molecule annotation +subset: edam +created_in: "beta12orEarlier" +def: "An informative report about the properties or features of one or more protein secondary structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2881 ! Secondary structure report [Term] -id: EDAM_data:2396 -name: Fungi annotation (anamorph) -namespace: data +id: EDAM_data:2957 +name: Hopp and Woods plot +subset: bioinformatics subset: data -def: "An informative report on a specific fungus anamorph." [http://edamontology.org] -is_a: EDAM_data:2395 ! Fungi annotation +subset: edam +created_in: "beta12orEarlier" +def: "A Hopp and Woods plot of predicted antigenicity of a peptide or protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1534 ! Peptide immunogenicity data [Term] -id: EDAM_data:2142 -name: EMBOSS graph -namespace: data +id: EDAM_data:2958 +name: Nucleic acid melting curve +comment: Shows the proportion of nucleic acid which are double-stranded versus temperature. +subset: bioinformatics subset: data -def: "An image of a graph generated by the EMBOSS suite." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2968 ! Image - +subset: edam +created_in: "beta12orEarlier" +def: "A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] -id: EDAM_data:1707 -name: Phylogenetic tree image -namespace: data +id: EDAM_data:2959 +name: Nucleic acid probability profile +comment: Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature +subset: bioinformatics subset: data -def: "An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information." [http://edamontology.org] -comment: See also 'Phylogenetic tree' -is_a: EDAM_data:2968 ! Image -is_a: EDAM_data:1438 ! Phylogenetic tree report - +subset: edam +created_in: "beta12orEarlier" +def: "A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] -id: EDAM_data:1708 -name: RNA secondary structure image -namespace: data +id: EDAM_data:2960 +name: Nucleic acid temperature profile +comment: Plots melting temperature versus base position. +subset: bioinformatics subset: data -def: "Image of RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] -is_a: EDAM_data:2880 ! Secondary structure image +subset: edam +synonym: "Melting map" EXACT [] +created_in: "beta12orEarlier" +def: "A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] -id: EDAM_data:1709 -name: Protein secondary structure image -namespace: data +id: EDAM_data:2961 +name: Pathway or network (gene regulation) +subset: bioinformatics subset: data -def: "Image of protein secondary structure." [http://edamontology.org] -is_a: EDAM_data:2880 ! Secondary structure image -is_a: EDAM_data:2956 ! Protein secondary structure report +subset: edam +created_in: "beta12orEarlier" +def: "A report typically including a map (diagram) of a gene regulatory network." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network +relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks [Term] -id: EDAM_data:1710 -name: Structure image -namespace: data +id: EDAM_data:2965 +name: 2D PAGE image (annotated) +subset: bioinformatics subset: data -! alt_id: EDAM_data:2604 -def: "Image of one or more molecular tertiary (3D) structures." [http://edamontology.org] -is_a: EDAM_data:2085 ! Structure report -is_a: EDAM_data:2968 ! Image +subset: edam +synonym: "2D PAGE image annotation" EXACT [] +created_in: "beta12orEarlier" +def: "An informative report on a two-dimensional (2D PAGE) gel." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0942 ! 2D PAGE image [Term] -id: EDAM_data:2880 -name: Secondary structure image -namespace: data +id: EDAM_data:2966 +name: Oligonucleotide probe sets annotation +subset: bioinformatics subset: data -def: "Image of one or more molecular secondary structures." [http://edamontology.org] -is_a: EDAM_data:2881 ! Secondary structure report +subset: edam +created_in: "beta12orEarlier" +def: "General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2717 ! Oligonucleotide probe annotation [Term] -id: EDAM_data:1711 -name: Sequence alignment image -namespace: data +id: EDAM_data:2967 +name: Microarray image +subset: bioinformatics subset: data -def: "Image of two or more aligned molecular sequences possibly annotated with alignment features." [http://edamontology.org] +subset: edam +synonym: "Gene expression image" EXACT [] +created_in: "beta12orEarlier" +def: "An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2603 ! Microarray data is_a: EDAM_data:2968 ! Image -is_a: EDAM_data:0867 ! Sequence alignment report - +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] -id: EDAM_data:2168 -name: Sequence trace image -namespace: data +id: EDAM_data:2968 +name: Image +subset: bioinformatics subset: data -def: "Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases)." [http://edamontology.org] -is_a: EDAM_data:2969 ! Sequence image +subset: edam +synonym: "SIO:000079" BROAD [] +synonym: "SIO:000081" NARROW [] +created_in: "beta12orEarlier" +def: "Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2969 name: Sequence image -namespace: data +subset: bioinformatics subset: data +subset: edam +created_in: "beta12orEarlier" def: "Image of a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org] -is_a: EDAM_data:2968 ! Image +namespace: data is_a: EDAM_data:2955 ! Sequence report +is_a: EDAM_data:2968 ! Image +[Term] +id: EDAM_data:2970 +name: Protein hydropathy data +subset: bioinformatics +subset: data +subset: edam +synonym: "Protein hydropathy report" EXACT [] +created_in: "beta12orEarlier" +def: "A report on protein properties concerning hydropathy." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:1712 -name: Structure image (small molecule) +id: EDAM_data:2971 +name: Workflow data +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning a computational workflow." [http://edamontology.org] namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0949 ! Workflow metadata +consider: EDAM_data:2972 ! Workflow + +[Term] +id: EDAM_data:2972 +name: Workflow +subset: bioinformatics subset: data -def: "An image of the structure of a small chemical compound." [http://edamontology.org] -comment: The molecular identifier and formula are typically included. -synonym: "Chemical structure image" EXACT [http://edamontology.org] -synonym: "Small molecule structure image" EXACT [http://edamontology.org] -is_a: EDAM_data:1710 ! Structure image -is_a: EDAM_data:0962 ! Small molecule annotation +subset: edam +created_in: "beta12orEarlier" +def: "A computational workflow." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data +[Term] +id: EDAM_data:2973 +name: Secondary structure data +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning molecular secondary structure data." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2081 ! Secondary structure +consider: EDAM_data:2881 ! Secondary structure report [Term] -id: EDAM_data:2992 -name: Protein structure image +id: EDAM_data:2974 +name: Raw sequence (protein) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A raw protein sequence (string of characters)." [http://edamontology.org] namespace: data +is_a: EDAM_data:0848 ! Raw sequence +is_a: EDAM_data:2976 ! Protein sequence + +[Term] +id: EDAM_data:2975 +name: Raw sequence (nucleic acid) +subset: bioinformatics subset: data -def: "An image of protein structure." [http://edamontology.org] -synonym: "Structure image (protein)" EXACT [http://edamontology.org] -is_a: EDAM_data:1710 ! Structure image -is_a: EDAM_data:3153 ! Protein image +subset: edam +created_in: "beta12orEarlier" +def: "A raw nucleic acid sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0848 ! Raw sequence +is_a: EDAM_data:2977 ! Nucleic acid sequence +[Term] +id: EDAM_data:2976 +name: Protein sequence +subset: bioinformatics +subset: data +subset: edam +synonym: "AminoAcidSequenceInformation" RELATED [] +created_in: "beta12orEarlier" +def: "One or more protein sequences, possibly with associated annotation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2044 ! Sequence [Term] -id: EDAM_data:3154 !{since=beta13} -name: Protein alignment +id: EDAM_data:2977 +name: Nucleic acid sequence +subset: bioinformatics +subset: data +subset: edam +synonym: "NucleotideSequenceInformation" RELATED [] +created_in: "beta12orEarlier" +def: "One or more nucleic acid sequences, possibly with associated annotation." [http://edamontology.org] namespace: data +is_a: EDAM_data:2044 ! Sequence + +[Term] +id: EDAM_data:2978 +name: Reaction data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "An alignment of protein sequences and/or structures." [http://edamontology.org] -is_a: EDAM_data:0896 ! Protein report -is_a: EDAM_data:1916 ! Alignment +subset: edam +synonym: "Enzyme kinetics annotation" EXACT [] +synonym: "Reaction annotation" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:3153 !{since=beta13} -name: Protein image +id: EDAM_data:2979 +name: Peptide property +subset: bioinformatics +subset: data +subset: edam +synonym: "Peptide data" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning small peptides." [http://edamontology.org] namespace: data +is_a: EDAM_data:2087 ! Molecular property + +[Term] +id: EDAM_data:2980 +name: Protein classification +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "An image of a protein." [http://edamontology.org] +subset: edam +synonym: "Protein classification data" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning the classification of protein sequences or structures." [http://edamontology.org] +namespace: data is_a: EDAM_data:0896 ! Protein report - +is_a: EDAM_data:2987 ! Classification +relationship: has_topic EDAM_topic:0595 ! Protein classification [Term] -id: EDAM_data:1713 -name: Fate map -namespace: data +id: EDAM_data:2981 +name: Sequence motif data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: " A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development." [http://edamontology.org] -is_a: EDAM_data:2724 ! Embryo annotation - +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning specific or conserved pattern in molecular sequences." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1353 ! Sequence motif [Term] -id: EDAM_data:2967 -name: Microarray image -namespace: data +id: EDAM_data:2982 +name: Sequence profile data +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -! alt_id: EDAM_data:1635 -def: "An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data." [http://edamontology.org] -synonym: "Gene expression image" EXACT [http://edamontology.org] -is_a: EDAM_data:2603 ! Microarray data -is_a: EDAM_data:2968 ! Image -relationship: has_topic EDAM_topic:0200 ! Microarrays +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning models representing a (typically multiple) sequence alignment." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1354 ! Sequence profile [Term] -id: EDAM_data:1714 -name: Microarray spots image -namespace: data +id: EDAM_data:2983 +name: Pathway or network data +subset: bioinformatics subset: data -def: "An image of spots from a microarray experiment." [http://edamontology.org] -is_a: EDAM_data:2967 ! Microarray image -is_a: EDAM_data:3108 ! Experimental measurement +subset: edam +created_in: "beta12orEarlier" +def: "Data concerning a specific biological pathway or network." [http://edamontology.org] +namespace: data +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2600 ! Pathway or network +consider: EDAM_data:2984 ! Pathway or network report [Term] -id: EDAM_data:2162 -name: Helical wheel -namespace: data +id: EDAM_data:2984 +name: Pathway or network report +subset: bioinformatics subset: data -def: "An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties." [http://edamontology.org] -is_a: EDAM_data:1709 ! Protein secondary structure image - +subset: edam +created_in: "beta12orEarlier" +def: "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2048 ! Report +relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM_data:2163 -name: Helical net -namespace: data +id: EDAM_data:2985 +name: Nucleic acid thermodynamic data +subset: bioinformatics subset: data -def: "An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix." [http://edamontology.org] -comment: Useful for highlighting amphipathicity and other properties. -is_a: EDAM_data:1709 ! Protein secondary structure image +subset: edam +synonym: "Nucleic acid property (thermodynamic or kinetic)" EXACT [] +synonym: "Nucleic acid thermodynamic property" EXACT [] +created_in: "beta12orEarlier" +def: "A thermodynamic or kinetic property of a nucleic acid molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0912 ! Nucleic acid property [Term] -id: EDAM_data:2308 -name: Virus annotation (taxonomy) -namespace: data +id: EDAM_data:2986 +name: Nucleic acid classification +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "An informative report on the taxonomy of a specific virus." [http://edamontology.org] -is_a: EDAM_data:2307 ! Virus annotation +subset: edam +synonym: "Nucleic acid classification data" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning the classification of nucleic acid sequences or structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2084 ! Nucleic acid report +is_a: EDAM_data:2987 ! Classification +relationship: has_topic EDAM_topic:0722 ! Nucleic acid classification [Term] -id: EDAM_data:0582 -name: Ontology -namespace: data +id: EDAM_data:2987 +name: Classification +comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. +subset: bioinformatics subset: data -! alt_id: EDAM_data:0829 -! alt_id: EDAM_data:0830 -! alt_id: EDAM_data:0834 -! alt_id: EDAM_data:0836 -! alt_id: EDAM_data:0837 -! alt_id: EDAM_data:0838 -! alt_id: EDAM_data:0839 -! alt_id: EDAM_data:0840 -! alt_id: EDAM_data:2221 -def: "An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc." [http://edamontology.org] +subset: edam +synonym: "Classification data" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning a classification of molecular sequences, structures or other entities." [http://edamontology.org] +namespace: data is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0089 ! Ontology +relationship: has_topic EDAM_topic:2829 ! Ontologies, nomenclature and classification + +[Term] +id: EDAM_data:2989 +name: Protein features (key folding sites) +subset: bioinformatics +subset: data +subset: edam +created_in: "beta12orEarlier" +def: "A report on key residues involved in protein folding." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +[Term] +id: EDAM_data:2991 +name: Protein torsion angle data +subset: bioinformatics +subset: data +subset: edam +synonym: "Torsion angle data" EXACT [] +created_in: "beta12orEarlier" +def: "Torsion angle data for a protein structure." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM_data:2858 -name: Ontology concept +id: EDAM_data:2992 +name: Protein structure image +subset: bioinformatics +subset: data +subset: edam +synonym: "Structure image (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "An image of protein structure." [http://edamontology.org] namespace: data +is_a: EDAM_data:1710 ! Structure image +is_a: EDAM_data:3153 ! Protein image + +[Term] +id: EDAM_data:2994 +name: Phylogenetic character weights +subset: bioinformatics subset: data -def: "A concept from a biological ontology." [http://edamontology.org] -comment: This includes any fields from the concept definition such as concept name, definition, comments and so on. -is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0089 ! Ontology +subset: edam +created_in: "beta12orEarlier" +def: "Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2523 ! Phylogenetic raw data +[Term] +id: EDAM_data:3002 +name: Sequence annotation track +subset: bioinformatics +subset: data +subset: edam +synonym: "Annotation track" EXACT [] +synonym: "Genome annotation track" EXACT [] +synonym: "Genome track" EXACT [] +synonym: "Genome-browser track" EXACT [] +synonym: "Genomic track" EXACT [] +created_in: "beta12orEarlier" +def: "Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1255 ! Feature record [Term] -id: EDAM_data:0966 -name: Ontology term -namespace: data +id: EDAM_data:3021 +name: UniProt accession +subset: bioinformatics subset: data -def: "A term (name) from an ontology." [http://edamontology.org] -is_a: EDAM_data:0967 ! Ontology concept metadata - +subset: edam +subset: identifiers +synonym: "Swiss-Prot entry accession" NARROW [] +synonym: "TrEMBL entry accession" NARROW [] +synonym: "UniProt accession number" EXACT [] +synonym: "UniProt entry accession" EXACT [] +synonym: "UniProtKB accession" EXACT [] +synonym: "UniProtKB accession number" EXACT [] +created_in: "beta12orEarlier" +def: "Accession number of a UniProt (protein sequence) database entry." [http://edamontology.org] +example: "P43353|Q7M1G0|Q9C199|A5A6J6" +regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]" +namespace: identifier +is_a: EDAM_data:1096 ! Sequence accession (protein) +relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] -id: EDAM_data:0967 -name: Ontology concept metadata -namespace: data +id: EDAM_data:3022 +name: NCBI genetic code ID +subset: bioinformatics subset: data -def: "Data concerning or derived from a concept from a biological ontology." [http://edamontology.org] -is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:0089 ! Ontology - +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a genetic code in the NCBI list of genetic codes." [http://edamontology.org] +example: "16" +regex: "[1-9][0-9]?" +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM_data:1715 -name: BioPax -namespace: data +id: EDAM_data:3025 +name: Ontology concept identifier +subset: bioinformatics subset: data -def: "A term from the BioPax ontology." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "Identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:2858 ! Ontology concept [Term] -id: EDAM_data:1716 -name: GO -namespace: data +id: EDAM_data:3026 +name: GO concept name (biological process) +subset: bioinformatics subset: data -def: "A term definition from The Gene Ontology (GO)." [http://edamontology.org] -synonym: "Gene Ontology term" EXACT [http://edamontology.org] -xref: Moby:GO_Term -xref: Moby:GOTerm -xref: Moby:Annotated_GO_Term -xref: Moby:Annotated_GO_Term_With_Probability -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a concept for a biological process from the GO ontology." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2339 ! Ontology concept name [Term] -id: EDAM_data:1717 -name: MeSH -namespace: data +id: EDAM_data:3027 +name: GO concept name (molecular function) +subset: bioinformatics subset: data -def: "A term from the MeSH vocabulary." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +subset: identifiers +created_in: "beta12orEarlier" +def: "The name of a concept for a molecular function from the GO ontology." [http://edamontology.org] +namespace: identifier +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:2339 ! Ontology concept name [Term] -id: EDAM_data:1718 -name: HGNC -namespace: data +id: EDAM_data:3028 +name: Taxonomy +comment: This is a broad data type and is used a placeholder for other, more specific types. +subset: bioinformatics subset: data -def: "A term from the HGNC controlled vocabulary." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +synonym: "Taxonomic data" EXACT [] +created_in: "beta12orEarlier" +def: "Data concerning the classification, identification and naming of organisms." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2987 ! Classification +relationship: has_topic EDAM_topic:0637 ! Taxonomy [Term] -id: EDAM_data:1719 -name: NCBI taxonomy vocabulary -namespace: data +id: EDAM_data:3029 +name: Protein ID (EMBL/GenBank/DDBJ) +comment: This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. +subset: bioinformatics subset: data -def: "A term from the NCBI taxonomy vocabulary." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +subset: identifiers +created_in: "beta13" +def: "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM_data:1720 -name: Plant ontology term -namespace: data +id: EDAM_data:3031 +name: Core data +comment: Core data entities typically have a format and may be identified by an accession number. +subset: bioinformatics subset: data -def: "A term from the Plant Ontology (PO)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +created_in: "beta13" +def: "A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0006 ! Data [Term] -id: EDAM_data:1721 -name: UMLS -namespace: data +id: EDAM_data:3034 +name: Sequence feature identifier +subset: bioinformatics subset: data -def: "A term from the UMLS vocabulary." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +subset: identifiers +created_in: "beta13" +def: "Name or other identifier of molecular sequence feature(s)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:1255 ! Feature record [Term] -id: EDAM_data:1722 -name: FMA -namespace: data +id: EDAM_data:3035 +name: Structure identifier +subset: bioinformatics subset: data -def: "A term from Foundational Model of Anatomy." [http://edamontology.org] -comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +subset: identifiers +created_in: "beta13" +def: "An identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:0883 ! Structure [Term] -id: EDAM_data:1723 -name: EMAP -namespace: data +id: EDAM_data:3036 +name: Matrix identifier +subset: bioinformatics subset: data -def: "A term from the EMAP mouse ontology." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +subset: identifiers +created_in: "beta13" +def: "An identifier of an array of numerical values, such as a comparison matrix." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:2082 ! Matrix [Term] -id: EDAM_data:1724 -name: ChEBI -namespace: data +id: EDAM_data:3085 +name: Protein sequence composition +subset: bioinformatics subset: data -def: "A term from the ChEBI ontology." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +synonym: "Sequence property (protein composition)" EXACT [] +created_in: "beta13" +def: "A report (typically a table) on character or word composition / frequency of protein sequence(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1261 ! Sequence composition [Term] -id: EDAM_data:1725 -name: MGED -namespace: data +id: EDAM_data:3086 +name: Nucleic acid sequence composition +subset: bioinformatics subset: data -def: "A term from the MGED ontology." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term +subset: edam +synonym: "Sequence property (nucleic acid composition)" EXACT [] +created_in: "beta13" +def: "A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0912 ! Nucleic acid property +is_a: EDAM_data:1261 ! Sequence composition [Term] -id: EDAM_data:1726 -name: myGrid -namespace: data +id: EDAM_data:3101 +name: Protein domain classification node +subset: bioinformatics subset: data -def: "A term from the myGrid ontology." [http://edamontology.org] -comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0966 ! Ontology term - +subset: edam +created_in: "beta13" +def: "A node from a classification of protein structural domain(s)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0900 ! Protein domain classification [Term] -id: EDAM_data:1727 -name: GO (biological process) -namespace: data +id: EDAM_data:3102 +name: CAS number +subset: bioinformatics subset: data -def: "A term definition for a biological process from the Gene Ontology (GO)." [http://edamontology.org] -comment: Data Type is an enumerated string. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2858 ! Ontology concept +subset: edam +subset: identifiers +synonym: "CAS registry number" EXACT [] +created_in: "beta13" +def: "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2895 ! Drug accession [Term] -id: EDAM_data:1728 -name: GO (molecular function) -namespace: data +id: EDAM_data:3103 +name: ATC code +subset: bioinformatics subset: data -def: "A term definition for a molecular function from the Gene Ontology (GO)." [http://edamontology.org] -comment: Data Type is an enumerated string. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2858 ! Ontology concept +subset: edam +subset: identifiers +created_in: "beta13" +def: "Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2895 ! Drug accession [Term] -id: EDAM_data:1729 -name: GO (cellular component) -namespace: data +id: EDAM_data:3104 +name: UNII +subset: bioinformatics subset: data -def: "A term definition for a cellular component from the Gene Ontology (GO)." [http://edamontology.org] -comment: Data Type is an enumerated string. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2858 ! Ontology concept - +subset: edam +subset: identifiers +synonym: "Unique Ingredient Identifier" EXACT [] +created_in: "beta13" +def: "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:1086 ! Compound identifier [Term] -id: EDAM_data:1730 -name: Ontology relation type -namespace: data +id: EDAM_data:3105 +name: Geotemporal metadata +subset: bioinformatics subset: data -def: "A relation type defined in an ontology." [http://edamontology.org] -is_a: EDAM_data:0967 ! Ontology concept metadata +subset: edam +created_in: "beta13" +def: "Basic information concerning geographical location or time." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata [Term] -id: EDAM_data:1731 -name: Ontology concept definition -namespace: data +id: EDAM_data:3106 +name: System metadata +subset: bioinformatics subset: data -def: "The definition of a concept from an ontology." [http://edamontology.org] -is_a: EDAM_data:0967 ! Ontology concept metadata +subset: edam +created_in: "beta13" +def: "Metadata concerning the software, hardware or other aspects of a computer system." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2337 ! Metadata [Term] -id: EDAM_data:1732 -name: Ontology concept comment -namespace: data +id: EDAM_data:3107 +name: Sequence feature name +subset: bioinformatics subset: data -def: "A comment on a concept from an ontology." [http://edamontology.org] -is_a: EDAM_data:0967 ! Ontology concept metadata +subset: edam +subset: identifiers +created_in: "beta13" +def: "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." [http://edamontology.org] +namespace: identifier +is_a: EDAM_data:2099 ! Name +is_a: EDAM_data:3034 ! Sequence feature identifier [Term] -id: EDAM_data:1733 -name: Ontology concept reference +id: EDAM_data:3108 +name: Experimental measurement +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: bioinformatics +subset: data +subset: edam +synonym: "Experimental measurement data" EXACT [] +synonym: "Experimentally measured data" EXACT [] +synonym: "Measured data" EXACT [] +synonym: "Measurement" EXACT [] +synonym: "Measurement data" EXACT [] +synonym: "Measurement metadata" NARROW [] +synonym: "Raw experimental data" NARROW [] +created_in: "beta13" +def: "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware." [http://edamontology.org] namespace: data -subset: data -def: "Reference for a concept from an ontology." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2093 ! Data reference - +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM_data:1738 -name: doc2loc document information -namespace: data +id: EDAM_data:3110 +name: Raw microarray data +comment: Such data as found in Affymetrix CEL or GPR files. +subset: bioinformatics subset: data -def: "Information on a published article provided by the doc2loc program." [http://edamontology.org] -comment: The doc2loc output includes the url, format, type and availability code of a document for every service provider. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0970 ! Bibliographic reference +subset: edam +created_in: "beta13" +def: "Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3108 ! Experimental measurement +is_a: EDAM_data:3117 ! Microarray hybridisation data +[Term] +id: EDAM_data:3111 +name: Processed microarray data +comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. +subset: bioinformatics +subset: data +subset: edam +synonym: "Gene annotation (expression)" EXACT [] +synonym: "Gene expression report" EXACT [] +synonym: "Microarray probe set data" EXACT [] +created_in: "beta13" +def: "Data generated from processing and analysis of probe set data from a microarray experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0928 ! Gene expression profile +is_a: EDAM_data:3117 ! Microarray hybridisation data +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] -id: EDAM_data:2177 -name: Exactly 1 -namespace: data +id: EDAM_data:3112 +name: Normalised microarray data +comment: This combines data from all hybridisations. +subset: bioinformatics subset: data -def: "A single thing." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} - +subset: edam +synonym: "Gene expression data matrix" EXACT [] +synonym: "Gene expression matrix" EXACT [] +created_in: "beta13" +def: "The final processed (normalised) data for a set of hybridisations in a microarray experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3117 ! Microarray hybridisation data [Term] -id: EDAM_data:2178 -name: 1 or more -namespace: data +id: EDAM_data:3113 +name: Sample annotation +comment: This might include compound and dose in a dose response experiment. +subset: bioinformatics subset: data -def: "One or more things." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} - +subset: edam +created_in: "beta13" +def: "Annotation on a biological sample, for example experimental factors and their values." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0931 ! Experiment annotation (microarray) [Term] -id: EDAM_data:2179 -name: Exactly 2 -namespace: data +id: EDAM_data:3115 +name: Microarray annotation +comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. +subset: bioinformatics subset: data -def: "Exactly two things." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} - +subset: edam +created_in: "beta13" +def: "Annotation on the array itself used in a microarray experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0931 ! Experiment annotation (microarray) [Term] -id: EDAM_data:2180 -name: 2 or more -namespace: data +id: EDAM_data:3116 +name: Microarray protocol annotation +comment: This might describe e.g. the normalisation methods used to process the raw data. +subset: bioinformatics subset: data -def: "Two or more things." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} - - - -! -! Identifier -! - +subset: edam +created_in: "beta13" +def: "Annotation on laboratory and/or data processing protocols used in an microarray experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0931 ! Experiment annotation (microarray) [Term] -id: EDAM_data:1121 -name: BLAST sequence alignment type -namespace: identifier -subset: identifiers +id: EDAM_data:3117 +name: Microarray hybridisation data +subset: bioinformatics subset: data -def: "The type of a BLAST sequence alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1120 ! Sequence alignment type +subset: edam +created_in: "beta13" +def: "Data concerning the hybridisations measured during a microarray experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2603 ! Microarray data +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] -id: EDAM_data:0974 -name: Entity identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3118 +name: Protein features (topological domains) +subset: bioinformatics subset: data -def: "An identifier of a biological entity or phenomenon." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0842 ! Identifier +subset: edam +synonym: "Protein topological domains" EXACT [] +created_in: "beta13" +def: "Summary of topological domains such as cytoplasmic regions in a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] -id: EDAM_data:0975 -name: Data resource identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3119 +name: Sequence features (compositionally-biased regions) +subset: bioinformatics subset: data -def: "An identifier of a data resource." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0842 ! Identifier +subset: edam +created_in: "beta13" +def: "A report of regions in a molecular sequence that are biased to certain characters." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1261 ! Sequence composition [Term] -id: EDAM_data:0978 -name: Discrete entity identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3120 +name: Protein features (sequence variants) +subset: bioinformatics subset: data -def: "Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0842 ! Identifier - +subset: edam +created_in: "beta13" +def: "A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features [Term] -id: EDAM_data:0979 -name: Entity feature identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3122 +name: Nucleic acid features (difference and change) +subset: bioinformatics subset: data -def: "Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0842 ! Identifier +subset: edam +created_in: "beta13" +def: "A report on features in a nucleic acid sequence that indicate changes to or differences between sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_data:0980 -name: Entity collection identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3123 +name: Nucleic acid features (expression signal) +subset: bioinformatics subset: data -def: "Name or other identifier of a collection of discrete biological entities." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0842 ! Identifier +subset: edam +created_in: "beta13" +def: "A report on regions within a nucleic acid sequence containing a signal that alters a biological function." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_data:0981 -name: Phenomenon identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3125 +name: Nucleic acid features (binding) +comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). +subset: bioinformatics subset: data -def: "Name or other identifier of a physical, observable biological occurrence or event." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0842 ! Identifier - +subset: edam +created_in: "beta13" +def: "A report on regions of a nucleic acid sequence that bind some other molecule." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_data:2091 -name: Accession -namespace: identifier -subset: identifiers +id: EDAM_data:3126 +name: Nucleic acid features (repeats) +comment: This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. +subset: bioinformatics subset: data -! alt_id: EDAM_data:2862 -def: "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." [http://edamontology.org] -synonym: "information entity identifier" BROAD [http://semanticscience.org/resource/SIO_000731] -synonym: "unique identifier" BROAD [http://semanticscience.org/resource/SIO_000675] -is_a: EDAM_data:0842 ! Identifier +subset: edam +created_in: "beta13" +def: "A report on repetitive elements within a nucleic acid sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features +is_a: EDAM_data:1299 ! Sequence features (repeats) [Term] -id: EDAM_data:2099 -name: Name -namespace: identifier -subset: identifiers +id: EDAM_data:3127 +name: Nucleic acid features (replication and recombination) +comment: This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. +subset: bioinformatics subset: data -! alt_id: EDAM_data:2863 -def: "A name of a thing, which need not necessarily uniquely identify it." [http://edamontology.org] -synonym: "Symbolic name" EXACT [http://edamontology.org] -synonym: "name" EXACT [http://usefulinc.com/ns/doap#name] -synonym: "name" EXACT [http://semanticscience.org/resource/SIO_000116] -synonym: "label" BROAD [http://www.w3.org/2000/01/rdf-schema#label] !{note="Almost exact, but focusing on human readability and not on identification."} -is_a: EDAM_data:0842 ! Identifier +subset: edam +created_in: "beta13" +def: "A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_data:0976 -name: Identifier (typed) -namespace: identifier -subset: identifiers +id: EDAM_data:3128 +name: Nucleic acid features (structure) +subset: bioinformatics subset: data -def: "An identifier that identifies a particular type of data." [http://edamontology.org] -comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. -is_a: EDAM_data:0842 ! Identifier +subset: edam +created_in: "beta13" +def: "A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_data:2109 -name: Identifier (hybrid) -namespace: identifier -subset: identifiers +id: EDAM_data:3129 +name: Protein features (repeats) +subset: bioinformatics subset: data -def: "An identifier that is re-used for data objects of fundamentally different types (typically served from a single database)." [http://edamontology.org] -comment: This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. -is_a: EDAM_data:0842 ! Identifier - - +subset: edam +created_in: "beta13" +def: "Location of short repetitive subsequences (repeat sequences) in a protein sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +is_a: EDAM_data:1299 ! Sequence features (repeats) [Term] -id: EDAM_data:0977 -name: Tool identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3130 +name: Protein features (motifs) +comment: Use this concept if another, more specific concept is not available. +subset: bioinformatics subset: data -def: "An identifier of a bioinformatics tool, e.g. an application or web service." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) +subset: edam +created_in: "beta13" +def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1277 ! Protein features +is_a: EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_data:1190 -name: Tool name -namespace: identifier -subset: identifiers +id: EDAM_data:3131 +name: Nucleic acid features (motifs) +comment: Use this concept if another, more specific concept is not available. +subset: bioinformatics subset: data -def: "The name of a computer package, application, method or function." [http://edamontology.org] -is_a: EDAM_data:0977 ! Tool identifier - +subset: edam +created_in: "beta13" +def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features +is_a: EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_data:1191 -name: Tool name (signature) -namespace: identifier -subset: identifiers +id: EDAM_data:3132 +name: Nucleic acid features (d-loop) +comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. +subset: bioinformatics subset: data -def: "The unique name of a signature (sequence classifier) method." [http://edamontology.org] -comment: Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. -is_a: EDAM_data:1190 ! Tool name +subset: edam +created_in: "beta13" +def: "A report on displacement loops in a mitochondrial DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] -id: EDAM_data:1192 -name: Tool name (BLAST) -namespace: identifier -subset: identifiers +id: EDAM_data:3133 +name: Nucleic acid features (stem loop) +comment: A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. +subset: bioinformatics subset: data -def: "The name of a BLAST tool." [http://edamontology.org] -comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. -synonym: "BLAST name" EXACT [http://edamontology.org] -is_a: EDAM_data:1190 ! Tool name +subset: edam +created_in: "beta13" +def: "A report on stem loops in a DNA sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] -id: EDAM_data:1193 -name: Tool name (FASTA) -namespace: identifier -subset: identifiers +id: EDAM_data:3134 +name: Nucleic acid features (mRNA features) +comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). +subset: bioinformatics subset: data -def: "The name of a FASTA tool." [http://edamontology.org] -comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. -is_a: EDAM_data:1190 ! Tool name +subset: edam +synonym: "mRNA features" EXACT [] +created_in: "beta13" +def: "Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) [Term] -id: EDAM_data:1194 -name: Tool name (EMBOSS) -namespace: identifier -subset: identifiers +id: EDAM_data:3135 +name: Nucleic acid features (signal or transit peptide) +comment: A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. +subset: bioinformatics subset: data -def: "The name of an EMBOSS application." [http://edamontology.org] -is_a: EDAM_data:1190 ! Tool name +subset: edam +created_in: "beta13" +def: "A report on a coding sequence for a signal or transit peptide." [http://edamontology.org] +namespace: data +is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] -id: EDAM_data:1195 -name: Tool name (EMBASSY package) -namespace: identifier -subset: identifiers +id: EDAM_data:3137 +name: Nucleic acid features (non-coding RNA) +subset: bioinformatics subset: data -def: "The name of an EMBASSY package." [http://edamontology.org] -is_a: EDAM_data:1190 ! Tool name +subset: edam +synonym: "ncRNA features" EXACT [] +synonym: "Non-coding RNA features" EXACT [] +created_in: "beta13" +def: "Features concerning non-coding or functional RNA molecules, including tRNA and rRNA." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) +[Term] +id: EDAM_data:3138 +name: Nucleic acid features (transcriptional) +comment: This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. +subset: bioinformatics +subset: data +subset: edam +created_in: "beta13" +def: "Features concerning transcription of DNA into RNA including the regulation of transcription." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) [Term] -id: EDAM_data:2098 -name: Job identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3139 +name: Nucleic acid features (STS) +comment: Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. +subset: bioinformatics subset: data -def: "An identifier of a submitted job." [http://edamontology.org] -synonym: "Computation ID" EXACT [http://wsio.org/data_009] -is_a: EDAM_data:0976 ! Identifier (typed) +subset: edam +created_in: "beta13" +def: "A report on sequence tagged sites (STS) in nucleic acid sequences." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM_data:1676 -name: Job ID -namespace: identifier -subset: identifiers +id: EDAM_data:3140 +name: Nucleic acid features (immunoglobulin gene structure) +subset: bioinformatics subset: data -def: "The (typically numeric) unique identifier of a submitted job." [http://edamontology.org] -! is_a: EDAM_data:2098 ! Job identifier -is_obsolete: true !{since=1.0} -replaced_by: EDAM_data:2098 ! Job identifier - +subset: edam +created_in: "beta13" +def: "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] -id: EDAM_data:2118 -name: Person identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3141 +name: SCOP class +subset: bioinformatics subset: data -def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) - +subset: edam +created_in: "beta13" +def: "Information on a 'class' node from the SCOP database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM_data:2101 -name: User ID -namespace: identifier -subset: identifiers +id: EDAM_data:3142 +name: SCOP fold +subset: bioinformatics subset: data -def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] -is_a: EDAM_data:2118 ! Person identifier - +subset: edam +created_in: "beta13" +def: "Information on a 'fold' node from the SCOP database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM_data:1689 -name: Username -namespace: identifier -subset: identifiers +id: EDAM_data:3143 +name: SCOP superfamily +subset: bioinformatics subset: data -def: "A username on a computer system." [http://edamontology.org] -is_a: EDAM_data:2101 ! User ID - +subset: edam +created_in: "beta13" +def: "Information on a 'superfamily' node from the SCOP database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM_data:1690 -name: Password -namespace: identifier -subset: identifiers +id: EDAM_data:3144 +name: SCOP family +subset: bioinformatics subset: data -def: "A password on a computer system." [http://edamontology.org] -is_a: EDAM_data:2101 ! User ID - +subset: edam +created_in: "beta13" +def: "Information on a 'family' node from the SCOP database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM_data:1691 -name: Email address -namespace: identifier -subset: identifiers +id: EDAM_data:3145 +name: SCOP protein +subset: bioinformatics subset: data -def: "A valid email address of an end-user." [http://edamontology.org] -xref: Moby:Email -xref: Moby:EmailAddress -is_a: EDAM_data:2101 ! User ID - +subset: edam +created_in: "beta13" +def: "Information on a 'protein' node from the SCOP database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM_data:1692 -name: Person name -namespace: identifier -subset: identifiers +id: EDAM_data:3146 +name: SCOP species +subset: bioinformatics subset: data -def: "The name of a person." [http://edamontology.org] -is_a: EDAM_data:2118 ! Person identifier - +subset: edam +created_in: "beta13" +def: "Information on a 'species' node from the SCOP database." [http://edamontology.org] +namespace: data +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM_data:1881 -name: Author ID -namespace: identifier -subset: identifiers +id: EDAM_data:3147 +name: Experiment annotation (mass spectrometry) +subset: bioinformatics subset: data -def: "Information on the authors of a published work." [http://edamontology.org] -xref: Moby:Author -is_a: EDAM_data:2118 ! Person identifier +subset: edam +created_in: "beta13" +def: "General annotation on a mass spectrometry experiment." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2531 ! Experiment annotation [Term] -id: EDAM_data:1882 -name: DragonDB author identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3148 +name: Gene family annotation +subset: bioinformatics subset: data -def: "An identifier representing an author in the DragonDB database." [http://edamontology.org] -is_a: EDAM_data:1881 ! Author ID - - - +subset: edam +created_in: "beta13" +def: "An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0916 ! Gene annotation +is_a: EDAM_data:2986 ! Nucleic acid classification [Term] -id: EDAM_data:2596 -name: Catalogue identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3153 +name: Protein image +subset: bioinformatics subset: data -def: "An identifier of a catalogue of biological resources." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) +subset: edam +created_in: "beta13" +def: "An image of a protein." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0896 ! Protein report [Term] -id: EDAM_data:2779 -name: Stock number -namespace: identifier -subset: identifiers +id: EDAM_data:3154 +name: Protein alignment +subset: bioinformatics subset: data -def: "An identifier of stock from a catalogue of biological resources." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession +subset: edam +created_in: "beta13" +def: "An alignment of protein sequences and/or structures." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0896 ! Protein report +is_a: EDAM_data:1916 ! Alignment [Term] -id: EDAM_data:3022 -name: NCBI genetic code ID -namespace: identifier -subset: identifiers +id: EDAM_data:3165 +name: Experiment annotation (sequencing) +subset: bioinformatics subset: data -def: "Identifier of a genetic code in the NCBI list of genetic codes." [http://edamontology.org] -regex: "[1-9][0-9]?" -example: "16" -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession +subset: edam +created_in: "1.0" +def: "Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2531 ! Experiment annotation +relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] -id: EDAM_data:0982 -name: Molecule identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3181 +name: Sequence assembly report +subset: bioinformatics subset: data -def: "Name or other identifier of a molecule." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:2529 ! Molecule report +subset: edam +created_in: "1.1" +def: "An informative report about a DNA sequence assembly." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2955 ! Sequence report [Term] -id: EDAM_data:1015 -name: Sequence feature ID -namespace: identifier -subset: identifiers +id: EDAM_data:3210 +name: Genome index +comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. +subset: bioinformatics subset: data -def: "A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file." [http://edamontology.org] -is_a: EDAM_data:2091 ! Accession -is_a: EDAM_data:3034 ! Sequence feature identifier +subset: edam +created_in: "1.1" +def: "An index of a genome sequence." [http://edamontology.org] +namespace: data +is_a: EDAM_data:0955 ! Data index [Term] -id: EDAM_data:3107 !{since=beta13} -name: Sequence feature name -namespace: identifier -subset: identifiers +id: EDAM_data:3231 +name: Experiment annotation (GWAS) +subset: bioinformatics subset: data -def: "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." [http://edamontology.org] -is_a: EDAM_data:2099 ! Name -is_a: EDAM_data:3034 ! Sequence feature identifier - - - +subset: edam +synonym: "Experiment annotation (genome-wide association study)" EXACT [] +created_in: "1.1" +def: "Metadata on a genome-wide association study (GWAS)." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2531 ! Experiment annotation [Term] -id: EDAM_data:3034 !{since=beta13} -name: Sequence feature identifier -namespace: identifier -subset: identifiers +id: EDAM_data:3236 +name: Cytoband position +comment: Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on. +subset: bioinformatics subset: data -def: "Name or other identifier of molecular sequence feature(s)." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2914 ! Sequence features metadata -relationship: is_identifier_of EDAM_data:1255 ! Feature record +subset: edam +created_in: "1.2" +def: "The position of a cytogenetic band in a genome." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2012 ! Map position [Term] -id: EDAM_data:1023 -name: EMBOSS Uniform Feature Object -namespace: data +id: EDAM_data:3238 +name: Cell type ontology ID +subset: bioinformatics subset: data -def: "The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications." [http://edamontology.org] -synonym: "UFO" EXACT [http://edamontology.org] -is_a: EDAM_data:3034 ! Sequence feature identifier -is_a: EDAM_data:2099 ! Name - - - +subset: edam +subset: identifiers +synonym: "CL ID" EXACT [] +created_in: "beta12orEarlier" +def: "Cell type ontology concept ID." [http://edamontology.org] +regex: "CL_[0-9]{7}" +namespace: identifier +is_a: EDAM_data:1087 ! Ontology concept ID +is_a: EDAM_data:2893 ! Cell type accession [Term] -id: EDAM_data:1893 -name: Locus ID -namespace: identifier -subset: identifiers +id: EDAM_data:3241 +name: Kinetic model +subset: bioinformatics subset: data -def: "A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [http://edamontology.org] -synonym: "Locus name" EXACT [http://edamontology.org] -synonym: "Locus identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:2012 ! Map position - +subset: edam +created_in: "1.2" +def: "Mathematical model of a network, that contains biochemical kinetics." [http://edamontology.org] +namespace: data +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM_data:2340 -name: Genome build identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a build of a particular genome." [http://edamontology.org] -is_a: EDAM_data:2749 ! Genome identifier +id: EDAM_format:1196 +name: SMILES +subset: bioinformatics +subset: edam +subset: formats +xref: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification +xref: http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html +created_in: "beta12orEarlier" +def: "Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation." [http://edamontology.org] +documentation: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification +documentation: http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html +namespace: format +is_a: EDAM_format:2035 ! Chemical formula format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2749 -name: Genome identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a particular genome." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1197 +name: InChI +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2035 ! Chemical formula format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2903 -name: Genome accession -namespace: identifier -subset: identifiers -subset: data -def: "An accession of a particular genome (in a database)." [http://edamontology.org] -is_a: EDAM_data:2749 ! Genome identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1198 +name: mf +comment: The general MF query format consists of a series of valid atomic symbols, with an optional number or range. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2035 ! Chemical formula format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1199 +name: inchikey +comment: An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2035 ! Chemical formula format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1025 -name: Gene identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." [http://edamontology.org] -xref: Moby:GeneAccessionList -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:0916 ! Gene annotation +id: EDAM_format:1200 +name: smarts +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1196 ! SMILES +[Term] +id: EDAM_format:1206 +name: unambiguous pure +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2094 ! pure +is_a: EDAM_format:2096 ! unambiguous sequence [Term] -id: EDAM_data:2795 -name: ORF identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of an open reading frame." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1207 +name: nucleotide +comment: Non-sequence characters may be used for example for gaps. +subset: bioinformatics +subset: edam +subset: formats +synonym: "Nucleotide_sequence" RELATED [] +created_in: "beta12orEarlier" +def: "Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2571 ! Raw sequence format +[Term] +id: EDAM_format:1208 +name: protein +comment: Non-sequence characters may be used for gaps and translation stop. +subset: bioinformatics +subset: edam +subset: formats +synonym: "Amino_acid_sequence" RELATED [] +created_in: "beta12orEarlier" +def: "Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2571 ! Raw sequence format [Term] -id: EDAM_data:2727 -name: Promoter ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a promoter of a gene that is catalogued in a database." [http://edamontology.org] -xref: Moby:GeneAccessionList -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1209 +name: consensus +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for the consensus of two or more molecular sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2095 ! unpure +is_a: EDAM_format:2097 ! ambiguous +[Term] +id: EDAM_format:1210 +name: pure nucleotide +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1207 ! nucleotide +is_a: EDAM_format:2094 ! pure [Term] -id: EDAM_data:2630 -name: Mobile genetic element ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a mobile genetic element." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1211 +name: unambiguous pure nucleotide +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters ." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1206 ! unambiguous pure +is_a: EDAM_format:1207 ! nucleotide [Term] -id: EDAM_data:2127 -name: Genetic code identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a genetic code." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:1598 ! Genetic code +id: EDAM_format:1212 +name: dna +subset: bioinformatics +subset: edam +subset: formats +synonym: "DNA_sequence" RELATED [] +created_in: "beta12orEarlier" +def: "Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1207 ! nucleotide [Term] -id: EDAM_data:1038 -name: Protein domain ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein structural domain." [http://edamontology.org] -comment: This is typically a character or string concatenated with a PDB identifier and a chain identifier. -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:1468 ! Protein domain +id: EDAM_format:1213 +name: rna +subset: bioinformatics +subset: edam +subset: formats +synonym: "RNA_sequence" RELATED [] +created_in: "beta12orEarlier" +def: "Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1207 ! nucleotide [Term] -id: EDAM_data:2618 -name: Protein modification ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein modification catalogued in a database." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1214 +name: unambiguous pure dna +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1206 ! unambiguous pure +is_a: EDAM_format:1212 ! dna [Term] -id: EDAM_data:1867 -name: Protein fold name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a protein fold." [http://edamontology.org] -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1215 +name: pure dna +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1210 ! pure nucleotide +is_a: EDAM_format:1212 ! dna +[Term] +id: EDAM_format:1216 +name: unambiguous pure rna sequence +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1206 ! unambiguous pure +is_a: EDAM_format:1213 ! rna [Term] -id: EDAM_data:2655 -name: Cell type identifier -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of a type or group of cells." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1217 +name: pure rna +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1210 ! pure nucleotide +is_a: EDAM_format:1213 ! rna +[Term] +id: EDAM_format:1218 +name: unambiguous pure protein +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1206 ! unambiguous pure +is_a: EDAM_format:1208 ! protein [Term] -id: EDAM_data:2893 -name: Cell type accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a type or group of cells (catalogued in a database)." [http://edamontology.org] -is_a: EDAM_data:2655 ! Cell type identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1219 +name: pure protein +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1208 ! protein +is_a: EDAM_format:2094 ! pure +[Term] +id: EDAM_format:1228 +name: UniGene entry format +comment: A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from UniGene." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1869 -name: Organism identifier -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of a (group of) organisms." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:2530 ! Organism annotation +id: EDAM_format:1247 +name: COG sequence cluster format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the COG database of clusters of (related) protein sequences." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2908 -name: Organism accession -namespace: identifier -subset: identifiers -subset: data -def: "An accession of annotation on a (group of) organisms (catalogued in a database)." [http://edamontology.org] -is_a: EDAM_data:1869 ! Organism identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1248 +name: EMBL feature location +subset: bioinformatics +subset: edam +subset: formats +synonym: "Feature location" EXACT [] +created_in: "beta12orEarlier" +def: "Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2078 ! Sequence range format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2909 -name: Organism name -namespace: identifier -subset: identifiers -subset: data -def: "The name of an organism (or group of organisms)." [http://edamontology.org] -xref: Moby:Organism_Name -xref: Moby:OrganismsLongName -xref: Moby:OrganismsShortName -xref: Moby:FirstEpithet -xref: Moby:InfraspecificEpithet -xref: Moby:OccurrenceRecord -xref: Moby:BriefOccurrenceRecord -is_a: EDAM_data:1869 ! Organism identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1295 +name: quicktandem +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2155 ! Sequence features (repeats) format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1296 +name: Sanger inverted repeats +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2155 ! Sequence features (repeats) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1048 -name: Database identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a biological or bioinformatics database." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:0957 ! Database metadata +id: EDAM_format:1297 +name: EMBOSS repeat +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Report format for tandem repeats in a sequence (an EMBOSS report format)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2155 ! Sequence features (repeats) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1049 -name: Directory name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a directory." [http://edamontology.org] -is_a: EDAM_data:2099 ! Name -is_a: EDAM_data:0583 ! Directory metadata +id: EDAM_format:1316 +name: est2genome format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on exon-intron structure generated by EMBOSS est2genome." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2159 ! Gene features (coding region) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1050 -name: File name -namespace: identifier -subset: identifiers -subset: data -def: "The name (or part of a name) of a file (of any type)." [http://edamontology.org] -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1318 +name: restrict format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Report format for restriction enzyme recognition sites used by EMBOSS restrict program." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1051 -name: Ontology name -namespace: identifier -subset: identifiers -subset: data -def: "Name of an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] -is_a: EDAM_data:2099 ! Name -is_a: EDAM_data:2338 ! Ontology identifier -relationship: is_identifier_of EDAM_data:0582 ! Ontology +id: EDAM_format:1319 +name: restover format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Report format for restriction enzyme recognition sites used by EMBOSS restover program." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2110 -name: Molecular property identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a molecular property." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:2087 ! Molecular property +id: EDAM_format:1320 +name: REBASE restriction sites +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Report format for restriction enzyme recognition sites used by REBASE database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1332 +name: FASTA search results format +comment: This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of results of a sequence database search using FASTA." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1062 -name: Database entry identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type." [http://edamontology.org] -comment: This concept is required for completeness. It should never have child concepts. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0842 ! Identifier +id: EDAM_format:1333 +name: BLAST results +comment: This includes score data, alignment data and summary table. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of results of a sequence database search using some variant of BLAST." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1334 +name: mspcrunch +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of results of a sequence database search using some variant of MSPCrunch." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2117 -name: Map identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a map of a molecular sequence." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:1274 ! Map +id: EDAM_format:1335 +name: Smith-Waterman format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of results of a sequence database search using some variant of Smith Waterman." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2904 -name: Map accession -namespace: identifier -subset: identifiers -subset: data -def: "An accession of a map of a molecular sequence (deposited in a database)." [http://edamontology.org] -is_a: EDAM_data:2117 ! Map identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1336 +name: dhf +comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1063 -name: Sequence identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of molecular sequence(s) or entries from a molecular sequence database." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:0855 ! Sequence metadata -relationship: is_identifier_of EDAM_data:2044 ! Sequence +id: EDAM_format:1337 +name: lhf +comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1341 +name: InterPro hits format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Results format for searches of the InterPro database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2294 -name: Sequence variation ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of an entry from a database of molecular sequence variation." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1342 +name: InterPro protein view report format +comment: The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1341 ! InterPro hits format +[Term] +id: EDAM_format:1343 +name: InterPro match table format +comment: The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1341 ! InterPro hits format [Term] -id: EDAM_data:1064 -name: Sequence set ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a set of molecular sequence(s)." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:0850 ! Sequence set +id: EDAM_format:1349 +name: HMMER Dirichlet prior +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Dirichlet distribution HMMER format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2074 ! Dirichlet distribution format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1065 -name: Sequence signature identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1114 ! Sequence motif identifier -consider: EDAM_data:1115 ! Sequence profile ID +id: EDAM_format:1350 +name: MEME Dirichlet prior +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Dirichlet distribution MEME format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2074 ! Dirichlet distribution format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1066 -name: Sequence alignment ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a molecular sequence alignment, for example a record from an alignment database." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:0863 ! Sequence alignment +id: EDAM_format:1351 +name: HMMER emission and transition +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2075 ! HMM emission and transition counts format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1067 -name: Phylogenetic distance matrix identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a phylogenetic distance matrix." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1356 +name: prosite-pattern +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a regular expression pattern from the Prosite database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2068 ! Sequence motif format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1068 -name: Phylogenetic tree ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a phylogenetic tree for example from a phylogenetic tree database." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:0872 ! Phylogenetic tree +id: EDAM_format:1357 +name: EMBOSS sequence pattern +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an EMBOSS sequence pattern." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2068 ! Sequence motif format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1360 +name: meme-motif +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A motif in the format generated by the MEME program." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2068 ! Sequence motif format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:3036 !{since=beta13} -name: Matrix identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of an array of numerical values, such as a comparison matrix." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:2082 ! Matrix +id: EDAM_format:1366 +name: prosite-profile +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Sequence profile (sequence classifier) format used in the PROSITE database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2069 ! Sequence profile format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1367 +name: JASPAR format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A profile (sequence classifier) in the format used in the JASPAR database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2069 ! Sequence profile format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1069 -name: Comparison matrix identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a comparison matrix." [http://edamontology.org] -synonym: "Substitution matrix identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:3036 ! Matrix identifier -relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix +id: EDAM_format:1369 +name: MEME background Markov model +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of the model of random sequences used by MEME." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2072 ! Hidden Markov model format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1370 +name: HMMER format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a hidden Markov model representation used by the HMMER package." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2072 ! Hidden Markov model format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:3035 !{since=beta13} -name: Structure identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:0883 ! Structure +id: EDAM_format:1391 +name: HMMER-aln +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "FASTA-style format for multiple sequences aligned by HMMER package to an HMM." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2200 ! FASTA-like (text) +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:1070 -name: Structure ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org] -is_a: EDAM_data:3035 ! Structure identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1392 +name: DIALIGN format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of multiple sequences aligned by DIALIGN package." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) +[Term] +id: EDAM_format:1393 +name: daf +comment: The format is clustal-like and includes annotation of domain family classification information. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:1759 -name: PDB model number -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a model structure from a PDB file." [http://edamontology.org] -synonym: "Model number" EXACT [http://edamontology.org] -xref: WHATIF: model_number -is_a: EDAM_data:3035 ! Structure identifier -! pdbx_PDB_model_num in PDBML +id: EDAM_format:1419 +name: Sequence-MEME profile alignment +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2014 ! Sequence-profile alignment format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1421 +name: HMMER profile alignment (sequences versus HMMs) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2014 ! Sequence-profile alignment format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1071 -name: Structural (3D) profile ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org] -synonym: "Structural profile identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:0889 ! Structural (3D) profile +id: EDAM_format:1422 +name: HMMER profile alignment (HMM versus sequences) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2014 ! Sequence-profile alignment format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1072 -name: Structure alignment ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from a database of tertiary structure alignments." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:0886 ! Structure alignment +id: EDAM_format:1423 +name: Phylip distance matrix +comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of PHYLIP phylogenetic distance matrix data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2067 ! Sequence distance matrix format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1073 -name: Amino acid index ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an index of amino acid physicochemical and biochemical property data." [http://edamontology.org] -is_a: EDAM_data:3036 ! Matrix identifier -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:1501 ! Amino acid index +id: EDAM_format:1424 +name: ClustalW dendrogram +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Dendrogram (tree file) format generated by ClustalW." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) +[Term] +id: EDAM_format:1425 +name: Phylip tree raw +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] -id: EDAM_data:2627 -name: Molecular interaction ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a report of molecular interactions from a database (typically)." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:2599 ! Molecular interaction +id: EDAM_format:1430 +name: Phylip continuous quantitative characters +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "PHYLIP file format for continuous quantitative character data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1075 -name: Protein family identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein family." [http://edamontology.org] -synonym: "Protein secondary database record identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:0907 ! Protein family +id: EDAM_format:1431 +name: Phylogenetic property values format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of phylogenetic property data." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2036 ! Phylogenetic character data format [Term] -id: EDAM_data:2910 -name: Protein family accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a protein family (that is deposited in a database)." [http://edamontology.org] -is_a: EDAM_data:2091 ! Accession -is_a: EDAM_data:1075 ! Protein family identifier +id: EDAM_format:1432 +name: Phylip character frequencies format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "PHYLIP file format for phylogenetics character frequency data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1131 -name: Protein family name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a protein family." [http://edamontology.org] -is_a: EDAM_data:1075 ! Protein family identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1433 +name: Phylip discrete states format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of PHYLIP discrete states data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2038 ! Phylogenetic discrete states format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2355 -name: RNA family identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an RNA family, typically an entry from a RNA sequence classification database." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:2354 ! RNA family annotation +id: EDAM_format:1434 +name: Phylip cliques format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of PHYLIP cliques data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2039 ! Phylogenetic tree report (cliques) format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1435 +name: Phylip tree format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Phylogenetic tree data format used by the PHYLIP program." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] -id: EDAM_data:2111 -name: Codon usage table identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a codon usage table, for example a genetic code." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:1597 ! Codon usage table -relationship: is_identifier_of EDAM_data:1598 ! Genetic code +id: EDAM_format:1436 +name: TreeBASE format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "The format of an entry from the TreeBASE database of phylogenetic data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) +[Term] +id: EDAM_format:1437 +name: TreeFam format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "The format of an entry from the TreeFam database of phylogenetic data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] -id: EDAM_data:1077 -name: Transcription factor identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a transcription factor (or a TF binding site)." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:0989 ! Protein identifier -relationship: is_identifier_of EDAM_data:1315 ! Gene features (TFBS) +id: EDAM_format:1445 +name: Phylip tree distance format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2049 ! Phylogenetic tree report (tree distances) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2911 -name: Transcription factor accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of an entry from a database of transcription factors or binding sites." [http://edamontology.org] -is_a: EDAM_data:1077 ! Transcription factor identifier -is_a: EDAM_data:2907 ! Protein accession -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1454 +name: dssp +comment: The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2077 ! Protein secondary structure format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1078 -name: Microarray experiment annotation ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from a database of microarray data." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:0931 ! Experiment annotation (microarray) +id: EDAM_format:1455 +name: hssp +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2077 ! Protein secondary structure format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1079 -name: Electron microscopy model ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from a database of electron microscopy data." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:0941 ! Electron microscopy model +id: EDAM_format:1457 +name: Dot-bracket format +subset: bioinformatics +subset: edam +subset: formats +synonym: "Vienna RNA format" EXACT [] +synonym: "Vienna RNA secondary structure format" EXACT [] +created_in: "beta12orEarlier" +def: "Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2076 ! RNA secondary structure format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1458 +name: Vienna local RNA secondary structure format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1457 ! Dot-bracket format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1080 -name: Gene expression report ID -namespace: identifier -subset: identifiers -subset: data -! alt_id: EDAM_data:2708 -def: "Accession of a report of gene expression (e.g. a gene expression profile) from a database." [http://edamontology.org] -synonym: "Gene expression profile identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:3111 ! Processed microarray data +id: EDAM_format:1475 +name: PDB database entry format +subset: bioinformatics +subset: edam +subset: formats +synonym: "PDB entry format" EXACT [] +created_in: "beta12orEarlier" +def: "Format of an entry (or part of an entry) from the PDB database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2033 ! Tertiary structure format +relationship: is_format_of EDAM_data:0883 ! Structure [Term] -id: EDAM_data:1081 -name: Genotype and phenotype annotation ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from a database of genotypes and phenotypes." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:0920 ! Genotype/phenotype annotation +id: EDAM_format:1476 +name: PDB format +subset: bioinformatics +subset: edam +subset: formats +synonym: "PDB" EXACT [] +created_in: "beta12orEarlier" +def: "Entry format of PDB database in PDB format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1475 ! PDB database entry format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1477 +name: mmCIF +subset: bioinformatics +subset: edam +subset: formats +synonym: "mmcif" EXACT [] +created_in: "beta12orEarlier" +def: "Entry format of PDB database in mmCIF format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1475 ! PDB database entry format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2382 -name: Genotype experiment ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from a database of genotype experiment metadata." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:2381 ! Experiment annotation (genotype) +id: EDAM_format:1478 +name: PDBML +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of PDB database in PDBML (XML) format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1475 ! PDB database entry format +is_a: EDAM_format:2332 ! XML [Term] -id: EDAM_data:2638 -name: PubChem bioassay ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an assay from the PubChem database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2639 ! PubChem identifier +id: EDAM_format:1500 +name: Domainatrix 3D-1D scoring matrix format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:1082 -name: Pathway or network identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from a database of biological pathways or networks." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:2600 ! Pathway or network +id: EDAM_format:1504 +name: aaindex +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Amino acid index format used by the AAindex database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2017 ! Amino acid index format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2590 -name: Hierarchy identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from a database of biological hierarchies." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2891 ! Biological model accession +id: EDAM_format:1511 +name: IntEnz enzyme report format +comment: IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from IntEnz (The Integrated Relational Enzyme Database)." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2108 -name: Reaction ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a biological reaction from a database." [http://edamontology.org] -is_a: EDAM_data:2091 ! Accession -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:2978 ! Reaction data +id: EDAM_format:1512 +name: BRENDA enzyme report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the BRENDA enzyme database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1513 +name: KEGG REACTION enzyme report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the KEGG REACTION database of biochemical reactions." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1083 -name: Workflow ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a biological or biomedical workflow, typically from a database of workflows." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:2972 ! Workflow +id: EDAM_format:1514 +name: KEGG ENZYME enzyme report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the KEGG ENZYME database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1084 -name: Data resource definition identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a data type definition from some provider." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1515 +name: REBASE proto enzyme report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the proto section of the REBASE enzyme database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2219 -name: Database field name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a field in a database." [http://edamontology.org] -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1516 +name: REBASE withrefm enzyme report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the withrefm section of the REBASE enzyme database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1551 +name: Pcons report format +comment: Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of output of the Pcons Model Quality Assessment Program (MQAP)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1085 -name: Biological model identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a mathematical model, typically an entry from a database." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:0950 ! Biological model +id: EDAM_format:1552 +name: ProQ report format +comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of output of the ProQ protein model quality predictor." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2891 -name: Biological model accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a mathematical model, typically an entry from a database." [http://edamontology.org] -is_a: EDAM_data:1085 ! Biological model identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1563 +name: SMART domain assignment report format +comment: The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of SMART domain assignment data." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1568 +name: BIND entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the BIND database of protein interaction." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1086 -name: Compound identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from a database of chemicals." [http://edamontology.org] -synonym: "Small molecule identifier" EXACT [http://edamontology.org] -synonym: "Chemical compound identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:0982 ! Molecule identifier -relationship: is_identifier_of EDAM_data:0962 ! Small molecule annotation -relationship: is_identifier_of EDAM_data:1712 ! Structure image (small molecule) -relationship: is_identifier_of EDAM_data:0846 ! Chemical formula +id: EDAM_format:1569 +name: IntAct entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the IntAct database of protein interaction." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2894 -name: Compound accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of an entry from a database of chemicals." [http://edamontology.org] -synonym: "Small molecule accession" EXACT [http://edamontology.org] -synonym: "Chemical compound accession" EXACT [http://edamontology.org] -is_a: EDAM_data:1086 ! Compound identifier -is_a: EDAM_data:2901 ! Molecule accession +id: EDAM_format:1570 +name: InterPro entry format +comment: This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2338 -name: Ontology identifier -namespace: identifier -subset: identifiers -subset: data -def: "Any arbitrary identifier of an ontology." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:0582 ! Ontology +id: EDAM_format:1571 +name: InterPro entry abstract format +comment: References are included and a functional inference is made where possible. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the textual abstract of signatures in an InterPro entry and its protein matches." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1572 +name: Gene3D entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the Gene3D protein secondary database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:3025 -name: Ontology concept identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:2858 ! Ontology concept +id: EDAM_format:1573 +name: PIRSF entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the PIRSF protein secondary database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1087 -name: Ontology concept ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] -synonym: "Ontology concept ID" EXACT [http://edamontology.org] -is_a: EDAM_data:3025 ! Ontology concept identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1574 +name: PRINTS entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the PRINTS protein secondary database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1575 +name: Panther Families and HMMs entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the Panther library of protein families and subfamilies." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1088 -name: Article ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a scientific article." [http://edamontology.org] -is_a: EDAM_data:2091 ! Accession -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:0971 ! Article +id: EDAM_format:1576 +name: Pfam entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the Pfam protein secondary database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2633 -name: Book ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a book." [http://edamontology.org] -is_a: EDAM_data:2091 ! Accession -is_a: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1577 +name: SMART entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the SMART protein secondary database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2790 -name: Gel identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a two-dimensional (protein) gel." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1578 +name: Superfamily entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the Superfamily protein secondary database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1579 +name: TIGRFam entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the TIGRFam protein secondary database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2791 -name: Reference map name (SWISS-2DPAGE) -namespace: identifier -subset: identifiers -subset: data -def: "Name of a reference map gel from the SWISS-2DPAGE database." [http://edamontology.org] -is_a: EDAM_data:2790 ! Gel identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1580 +name: ProDom entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the ProDom protein domain classification database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2373 -name: Spot ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a spot from a two-dimensional (protein) gel." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1581 +name: FSSP entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the FSSP database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2587 -name: Blot ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a blot from a Northern Blot." [http://edamontology.org] -is_a: EDAM_data:2091 ! Accession -is_a: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1582 +name: findkm +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2027 ! Enzyme kinetics report format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2379 -name: Strain identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] -is_a: EDAM_data:1869 ! Organism identifier +id: EDAM_format:1603 +name: Ensembl gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of Ensembl genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2912 -name: Strain accession -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] -is_a: EDAM_data:2379 ! Strain identifier -is_a: EDAM_data:2908 ! Organism accession -relationship: is_identifier_of EDAM_data:0963 ! Cell line annotation +id: EDAM_format:1604 +name: DictyBase gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of DictyBase genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1605 +name: CGD gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of Candida Genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2917 -name: ConsensusPathDB identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of an entity from the ConsensusPathDB database." [http://edamontology.org] -is_a: EDAM_data:2109 ! Identifier (hybrid) - +id: EDAM_format:1606 +name: DragonDB gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of DragonDB genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2776 -name: ConsensusPathDB entity ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a physical entity from the ConsensusPathDB database." [http://edamontology.org] -is_a: EDAM_data:2917 ! ConsensusPathDB identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1607 +name: EcoCyc gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of EcoCyc genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2777 -name: ConsensusPathDB entity name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a physical entity from the ConsensusPathDB database." [http://edamontology.org] -is_a: EDAM_data:2917 ! ConsensusPathDB identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1608 +name: FlyBase gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of FlyBase genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2639 -name: PubChem identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the PubChem database." [http://edamontology.org] -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1609 +name: Gramene gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of Gramene genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2367 -name: ASTD ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an object from the ASTD database." [http://edamontology.org] -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1610 +name: KEGG GENES gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of KEGG GENES genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1089 -name: FlyBase ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an object from the FlyBase database." [http://edamontology.org] -regex: "FB[a-zA-Z_0-9]{2}[0-9]{7}" -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1611 +name: MaizeGDB gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of the Maize genetics and genomics database (MaizeGDB)." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2113 -name: WormBase identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an object from the WormBase database." [http://edamontology.org] -is_a: EDAM_data:2109 ! Identifier (hybrid) +id: EDAM_format:1612 +name: MGD gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of the Mouse Genome Database (MGD)." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2104 -name: BioCyc ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an object from one of the BioCyc databases." [http://edamontology.org] -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1613 +name: RGD gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of the Rat Genome Database (RGD)." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1154 -name: KEGG object identifier -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an object from one of the KEGG databases (excluding the GENES division)." [http://edamontology.org] -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1614 +name: SGD gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of the Saccharomyces Genome Database (SGD)." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1615 +name: GeneDB gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of the Sanger GeneDB genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2380 -name: CABRI accession -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of an item from the CABRI database." [http://edamontology.org] -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1616 +name: TAIR gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of The Arabidopsis Information Resource (TAIR) genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2387 -name: TAIR accession -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the TAIR database." [http://edamontology.org] -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1617 +name: WormBase gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of the WormBase genomes database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2610 -name: Ensembl ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database." [http://edamontology.org] -regex: "ENS[A-Z]*[FPTG][0-9]{11}" -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1618 +name: ZFIN gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of the Zebrafish Information Network (ZFIN) genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2620 -name: RGD ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the RGD database." [http://edamontology.org] -regex: "[0-9]{4,7}" -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1619 +name: TIGR gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format of the TIGR genome database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1620 +name: dbSNP polymorphism report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the dbSNP database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2632 -name: SGD ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the Saccharomyces genome database (SGD)." [http://edamontology.org] -regex: "PWY[a-zA-Z_0-9]{2}\-[0-9]{3}" -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1623 +name: OMIM entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the OMIM database of genotypes and phenotypes." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2649 -name: PharmGKB ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] -regex: "PA[0-9]+" -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1624 +name: HGVbase entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a record from the HGVbase database of genotypes and phenotypes." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1625 +name: HIVDB entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a record from the HIVDB database of genotypes and phenotypes." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2368 -name: ASTD ID (exon) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an exon from the ASTD database." [http://edamontology.org] -is_a: EDAM_data:2367 ! ASTD ID +id: EDAM_format:1626 +name: KEGG DISEASE entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the KEGG DISEASE database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1627 +name: Primer3 primer +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2061 ! Nucleic acid features (primers) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2369 -name: ASTD ID (intron) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an intron from the ASTD database." [http://edamontology.org] -is_a: EDAM_data:2367 ! ASTD ID - +id: EDAM_format:1628 +name: ABI +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A format of raw sequence read data from an Applied Biosystems sequencing machine." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2057 ! Sequence trace format +is_a: EDAM_format:2333 ! Binary format [Term] -id: EDAM_data:2370 -name: ASTD ID (polya) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a polyA signal from the ASTD database." [http://edamontology.org] -is_a: EDAM_data:2367 ! ASTD ID +id: EDAM_format:1629 +name: mira +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of MIRA sequence trace information file." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2057 ! Sequence trace format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1630 +name: CAF +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.sanger.ac.uk/resources/software/caf/ +created_in: "beta12orEarlier" +def: "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." [http://edamontology.org] +documentation: http://www.sanger.ac.uk/resources/software/caf/ +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2561 ! Sequence assembly format (text) [Term] -id: EDAM_data:2371 -name: ASTD ID (tss) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a transcription start site from the ASTD database." [http://edamontology.org] -is_a: EDAM_data:2367 ! ASTD ID +id: EDAM_format:1631 +name: exp +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Sequence assembly project file EXP format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2561 ! Sequence assembly format (text) [Term] -id: EDAM_data:2671 -name: Ensembl ID (Homo sapiens) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division)." [http://edamontology.org] -regex: "ENS([EGTP])[0-9]{11}" -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:1632 +name: SCF +subset: bioinformatics +subset: edam +subset: formats +xref: http://staden.sourceforge.net/manual/formats_unix_2.html +created_in: "beta12orEarlier" +def: "Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata." [http://edamontology.org] +documentation: http://staden.sourceforge.net/manual/formats_unix_2.html +namespace: format +is_a: EDAM_format:2057 ! Sequence trace format +is_a: EDAM_format:2333 ! Binary format [Term] -id: EDAM_data:2672 -name: Ensembl ID ('Bos taurus') -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division)." [http://edamontology.org] -regex: "ENSBTA([EGTP])[0-9]{11}" -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:1633 +name: PHD +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.bioperl.org/wiki/PHD_sequence_format +created_in: "beta12orEarlier" +def: "PHD sequence trace format to store serialised chromatogram data (reads)." [http://edamontology.org] +documentation: http://www.bioperl.org/wiki/PHD_sequence_format +namespace: format +is_a: EDAM_format:2057 ! Sequence trace format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2673 -name: Ensembl ID ('Canis familiaris') -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division)." [http://edamontology.org] -regex: "ENSCAF([EGTP])[0-9]{11}" -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:1637 +name: dat +subset: bioinformatics +subset: edam +subset: formats +synonym: "Affymetrix image data file format" EXACT [] +created_in: "beta12orEarlier" +def: "Format of Affymetrix data file of raw image data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2058 ! Gene expression report format +is_a: EDAM_format:2330 ! Textual format +relationship: is_format_of EDAM_data:1714 ! Microarray spots image [Term] -id: EDAM_data:2674 -name: Ensembl ID ('Cavia porcellus') -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division)." [http://edamontology.org] -regex: "ENSCPO([EGTP])[0-9]{11}" -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:1638 +name: cel +subset: bioinformatics +subset: edam +subset: formats +synonym: "Affymetrix probe raw data format" EXACT [] +created_in: "beta12orEarlier" +def: "Format of Affymetrix data file of information about (raw) expression levels of the individual probes." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2058 ! Gene expression report format +is_a: EDAM_format:2330 ! Textual format +relationship: is_format_of EDAM_data:3110 ! Raw microarray data [Term] -id: EDAM_data:2675 -name: Ensembl ID ('Ciona intestinalis') -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division)." [http://edamontology.org] -regex: "ENSCIN([EGTP])[0-9]{11}" -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:1639 +name: affymetrix +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2172 ! Sequence cluster format (nucleic acid) +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2676 -name: Ensembl ID ('Ciona savignyi') -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division)." [http://edamontology.org] -regex: "ENSCSAV([EGTP])[0-9]{11}" -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:1640 +name: ArrayExpress entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the ArrayExpress microarrays database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! 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[http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2695 -name: Ensembl ID ('Rattus norvegicus') -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division)." [http://edamontology.org] -regex: "ENSRNO([EGTP])[0-9]{11}" -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:1701 +name: PubChem entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "The format of an entry from PubChem." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2696 -name: Ensembl ID ('Spermophilus tridecemlineatus') -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division)." [http://edamontology.org] -regex: "ENSSTO([EGTP])[0-9]{11}" -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:1702 +name: ChemSpider entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "The format of an entry from a database of chemical structures and property predictions." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! 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[http://edamontology.org] -synonym: "Ensembl Transcript ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2610 ! Ensembl ID -is_a: EDAM_data:2769 ! Transcript ID - +id: EDAM_format:1706 +name: KEGG DRUG entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "The format of an entry from the KEGG DRUG database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2597 -name: CABRI catalogue name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a catalogue of biological resources from the CABRI database." [http://edamontology.org] -is_a: EDAM_data:2596 ! Catalogue identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1734 +name: PubMed citation +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of bibliographic reference as used by the PubMed database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2848 ! Bibliographic reference format [Term] -id: EDAM_data:2780 -name: Stock number (TAIR) -namespace: identifier -subset: identifiers -subset: data -def: "A stock number from The Arabidopsis information resource (TAIR)." [http://edamontology.org] -is_a: EDAM_data:2779 ! Stock number +id: EDAM_format:1735 +name: Medline Display Format +comment: Bibliographic reference information including citation information is included +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for abstracts of scientific articles from the Medline database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! 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Name +id: EDAM_format:1737 +name: CiteXplore-all +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2848 ! Bibliographic reference format +[Term] +id: EDAM_format:1739 +name: pmc +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Article format of the PubMed Central database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2020 ! Article format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2538 -name: Mutation identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a mutation." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1740 +name: iHOP text mining abstract format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "iHOP abstract format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2021 ! Text mining report format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1741 +name: Oscar3 +comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Text mining abstract format from the Oscar 3 application." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2021 ! Text mining report format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2209 -name: Mutation ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of a specific mutation catalogued in a database." [http://edamontology.org] -is_a: EDAM_data:2538 ! Mutation identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1747 +name: PDB atom record format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an ATOM record (describing data for an individual atom) from a PDB file." [http://edamontology.org] +namespace: format +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1476 ! PDB format [Term] -id: EDAM_data:2133 -name: Logical operator -namespace: identifier -subset: identifiers -subset: data -def: "A logical operator such as OR, AND, XOR, and NOT." [http://edamontology.org] -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1760 +name: CATH chain report format +comment: The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of CATH domain classification information for a polypeptide chain." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1114 -name: Sequence motif identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a sequence motif, for example an entry from a motif database." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:1353 ! Sequence motif +id: EDAM_format:1761 +name: CATH PDB report format +comment: The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of CATH domain classification information for a protein PDB file." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1115 -name: Sequence profile ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a sequence profile." [http://edamontology.org] -comment: A sequence profile typically represents a sequence alignment. -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:1354 ! Sequence profile +id: EDAM_format:1782 +name: NCBI gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry (gene) format of the NCBI database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1808 +name: GeneIlluminator gene report format +comment: This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. +subset: bioinformatics +subset: edam +subset: formats +xref: Moby:GI_Gene +created_in: "beta12orEarlier" +def: "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2660 -name: BioNumbers ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1809 +name: BacMap gene card format +subset: bioinformatics +subset: edam +subset: formats +xref: Moby:BacMapGeneCard +created_in: "beta12orEarlier" +def: "Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:0983 -name: Atom identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier (e.g. character symbol) of a specific atom." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) +id: EDAM_format:1810 +name: ColiCard report format +subset: bioinformatics +subset: edam +subset: formats +xref: Moby:ColiCard +created_in: "beta12orEarlier" +def: "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML +[Term] +id: EDAM_format:1861 +name: PlasMapper TextMap +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Map of a plasmid (circular DNA) in PlasMapper TextMap format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2060 ! Map format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:0984 -name: Molecule name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a specific molecule." [http://edamontology.org] -is_a: EDAM_data:0982 ! Molecule identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1910 +name: newick +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Phylogenetic tree Newick (text) format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) +[Term] +id: EDAM_format:1911 +name: TreeCon format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Phylogenetic tree TreeCon (text) format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] -id: EDAM_data:2901 -name: Molecule accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a specific molecule (catalogued in a database)." [http://edamontology.org] -is_a: EDAM_data:0982 ! Molecule identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1912 +name: Nexus format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Phylogenetic tree Nexus (text) format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] -id: EDAM_data:0986 -name: Chemical identifier -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a chemical compound." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1086 ! Compound identifier +id: EDAM_format:1915 +name: Format +comment: The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. +subset: bioinformatics +subset: edam +subset: formats +synonym: "WSIO_compression:004" RELATED [] +synonym: "Continuant" BROAD [] +synonym: "Data format" EXACT [] +synonym: "Data model" BROAD [] +synonym: "Exchange format" EXACT [] +synonym: "File format" NARROW [] +synonym: "File:format" RELATED [] +synonym: "http://en.wikipedia.org/wiki/List_of_file_formats" RELATED [] +synonym: "http://purl.org/dc/elements/1.1/format" BROAD [] +synonym: "IAO:0000098" RELATED [] +synonym: "MachineLanguage" RELATED [] +synonym: "Perpetuant" RELATED [] +synonym: "Quality" BROAD [] +synonym: "Quality" RELATED [] +synonym: "quality" RELATED [] +synonym: "SIO:000612" RELATED [] +synonym: "SIO:000618" RELATED [] +synonym: "Symbol_structure" RELATED [] +created_in: "beta12orEarlier" +def: "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere." [http://edamontology.org] +namespace: format +disjoint_from: EDAM_operation:0004 ! Operation +disjoint_from: EDAM_topic:0003 ! Topic +[Term] +id: EDAM_format:1918 +name: Atomic data format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for an individual atom." [http://edamontology.org] +namespace: format +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1475 ! PDB database entry format [Term] -id: EDAM_data:2119 -name: Nucleic acid identifier -namespace: identifier -subset: identifiers -subset: data -def: "Name or other identifier of a nucleic acid molecule." [http://edamontology.org] -is_a: EDAM_data:0982 ! Molecule identifier -relationship: is_identifier_of EDAM_data:2084 ! Nucleic acid report +id: EDAM_format:1919 +name: Sequence record format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a molecular sequence record." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0849 ! Sequence record +[Term] +id: EDAM_format:1920 +name: Sequence feature annotation format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for molecular sequence feature information." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1255 ! Feature record [Term] -id: EDAM_data:0988 -name: Peptide identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a peptide chain." [http://edamontology.org] -is_a: EDAM_data:0982 ! Molecule identifier +id: EDAM_format:1921 +name: Alignment format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for molecular sequence alignment information." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM_data:2906 -name: Peptide ID -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a peptide deposited in a database." [http://edamontology.org] -is_a: EDAM_data:0988 ! Peptide identifier -is_a: EDAM_data:2901 ! Molecule accession +id: EDAM_format:1923 +name: acedb +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "ACEDB sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:1008 -name: Polypeptide chain ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a polypeptide chain from a protein." [http://edamontology.org] -comment: This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA -synonym: "Polypeptide chain identifier" EXACT [http://edamontology.org] -synonym: "Protein chain identifier" EXACT [http://edamontology.org] -synonym: "PDB chain identifier" EXACT [http://edamontology.org] -synonym: "Chain identifier" EXACT [http://edamontology.org] -synonym: "PDB strand id" EXACT [http://edamontology.org] -xref: WHATIF: chain -is_a: EDAM_data:0988 ! Peptide identifier -relationship: is_identifier_of EDAM_data:1467 ! Protein chain -! pdbx_PDB_strand_id in PDBML +id: EDAM_format:1924 +name: clustal sequence format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Clustalw output format." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1982 ! ClustalW format [Term] -id: EDAM_data:0989 -name: Protein identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein." [http://edamontology.org] -is_a: EDAM_data:0982 ! Molecule identifier -relationship: is_identifier_of EDAM_data:0896 ! Protein report +id: EDAM_format:1925 +name: codata +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Codata entry format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2907 -name: Protein accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a protein deposited in a database." [http://edamontology.org] -is_a: EDAM_data:0989 ! Protein identifier -is_a: EDAM_data:2901 ! Molecule accession +id: EDAM_format:1926 +name: dbid +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Fasta format variant with database name before ID." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2200 ! FASTA-like (text) [Term] -id: EDAM_data:1757 -name: Atom name -namespace: identifier -subset: identifiers -subset: data -def: "Name of an atom." [http://edamontology.org] -is_a: EDAM_data:0983 ! Atom identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1927 +name: EMBL format +subset: bioinformatics +subset: edam +subset: formats +synonym: "EMBL" EXACT [] +synonym: "EMBL sequence format" EXACT [] +created_in: "beta12orEarlier" +def: "EMBL entry format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2181 ! EMBL-like (text) +is_a: EDAM_format:2206 ! Sequence feature table format (text) [Term] -id: EDAM_data:1748 -name: PDB atom name -namespace: identifier -subset: identifiers -subset: data -def: "Identifier (a string) of a specific atom from a PDB file for a molecular structure." [http://edamontology.org] -xref: WHATIF: atom_type -xref: WHATIF: alternate_atom -xref: WHATIF: PDBx_auth_atom_id -xref: WHATIF: PDBx_type_symbol -is_a: EDAM_data:1757 ! Atom name -! pdbx_PDB_atom_name in PDBML +id: EDAM_format:1928 +name: Staden experiment format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Staden experiment file format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:0990 -name: Compound name -namespace: identifier -subset: identifiers -subset: data -def: "Unique name of a chemical compound." [http://edamontology.org] -synonym: "Chemical name" EXACT [http://edamontology.org] -is_a: EDAM_data:1086 ! Compound identifier -is_a: EDAM_data:0984 ! Molecule name +id: EDAM_format:1929 +name: FASTA format +subset: bioinformatics +subset: edam +subset: formats +synonym: "FASTA" EXACT [] +synonym: "FASTA sequence format" EXACT [] +created_in: "beta12orEarlier" +def: "FASTA format including NCBI-style IDs." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2200 ! FASTA-like (text) +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:0991 -name: Chemical registry number -namespace: identifier -subset: identifiers -subset: data -def: "Unique registry number of a chemical compound." [http://edamontology.org] -is_a: EDAM_data:2894 ! Compound accession +id: EDAM_format:1930 +name: FASTQ +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "FASTQ short read format ignoring quality scores." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2182 ! FASTQ-like format (text) +[Term] +id: EDAM_format:1931 +name: FASTQ-illumina +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "FASTQ Illumina 1.3 short read format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] -id: EDAM_data:0992 -name: Ligand identifier -namespace: identifier -subset: identifiers -subset: data -def: "Code word for a ligand, for example from a PDB file." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1086 ! Compound identifier +id: EDAM_format:1932 +name: FASTQ-sanger +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "FASTQ short read format with phred quality." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] -id: EDAM_data:0993 -name: Drug identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a drug." [http://edamontology.org] -is_a: EDAM_data:1086 ! Compound identifier -relationship: is_identifier_of EDAM_data:2851 ! Drug structure +id: EDAM_format:1933 +name: FASTQ-solexa +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "FASTQ Solexa/Illumina 1.0 short read format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2182 ! FASTQ-like format (text) +[Term] +id: EDAM_format:1934 +name: fitch program +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Fitch program format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2895 -name: Drug accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a drug." [http://edamontology.org] -is_a: EDAM_data:0993 ! Drug identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1935 +name: gcg +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "GCG sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +[Term] +id: EDAM_format:1936 +name: GenBank format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Genbank entry format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2205 ! GenBank-like format (text) +is_a: EDAM_format:2206 ! Sequence feature table format (text) [Term] -id: EDAM_data:2899 -name: Drug name -namespace: identifier -subset: identifiers -subset: data -def: "Common name of a drug." [http://edamontology.org] -is_a: EDAM_data:0993 ! Drug identifier -is_a: EDAM_data:0990 ! Compound name +id: EDAM_format:1937 +name: genpept +comment: Currently identical to refseqp format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Genpept protein entry format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2205 ! GenBank-like format (text) +[Term] +id: EDAM_format:1938 +name: GFF2-seq +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "GFF feature file format with sequence in the header." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1974 ! GFF2 +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2576 -name: Toxin identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a toxin." [http://edamontology.org] -is_a: EDAM_data:1086 ! Compound identifier -relationship: is_identifier_of EDAM_data:2852 ! Toxin structure +id: EDAM_format:1939 +name: GFF3-seq +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "GFF3 feature file format with sequence." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1975 ! GFF3 +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2896 -name: Toxin name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a toxin." [http://edamontology.org] -is_a: EDAM_data:2576 ! Toxin identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:1940 +name: giFASTA format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "FASTA sequence format including NCBI-style GIs." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2200 ! FASTA-like (text) [Term] -id: EDAM_data:2897 -name: Toxin accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a toxin (catalogued in a database)." [http://edamontology.org] -is_a: EDAM_data:2576 ! Toxin identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1941 +name: hennig86 +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Hennig86 output sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +[Term] +id: EDAM_format:1942 +name: ig +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Intelligenetics sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:0994 -name: Amino acid identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an amino acid." [http://edamontology.org] -synonym: "Residue identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:1086 ! Compound identifier -relationship: is_identifier_of EDAM_data:2016 ! Amino acid property - +id: EDAM_format:1943 +name: igstrict +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Intelligenetics sequence format (strict version)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:0995 -name: Nucleotide identifier -namespace: identifier -subset: identifiers -subset: data -def: "Name or other identifier of a nucleotide." [http://edamontology.org] -is_a: EDAM_data:1086 ! Compound identifier +id: EDAM_format:1944 +name: jackknifer +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Jackknifer interleaved and non-interleaved sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:0996 -name: Monosaccharide identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a monosaccharide." [http://edamontology.org] -is_a: EDAM_data:1086 ! Compound identifier +id: EDAM_format:1945 +name: mase format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Mase program sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +[Term] +id: EDAM_format:1946 +name: mega-seq +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Mega interleaved and non-interleaved sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2898 -name: Monosaccharide accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a monosaccharide (catalogued in a database)." [http://edamontology.org] -is_a: EDAM_data:0996 ! Monosaccharide identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_format:1947 +name: msf +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "GCG MSF (multiple sequence file) file format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:2812 -name: Lipid identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a lipid." [http://edamontology.org] -is_a: EDAM_data:0982 ! Molecule identifier -relationship: is_identifier_of EDAM_data:2850 ! Lipid structure -relationship: is_identifier_of EDAM_data:2879 ! Lipid structure report +id: EDAM_format:1948 +name: nbrf +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "NBRF/PIR entry sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2202 ! Sequence record full format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1949 +name: nexus-seq +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Nexus/paup interleaved sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:2905 -name: Lipid accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of an entry from a database of lipids." [http://edamontology.org] -is_a: EDAM_data:2812 ! Lipid identifier -is_a: EDAM_data:2901 ! Molecule accession +id: EDAM_format:1950 +name: pdbatom +comment: pdb format in EMBOSS. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "PDB sequence format (ATOM lines)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1475 ! PDB database entry format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2663 -name: Carbohydrate identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a carbohydrate." [http://edamontology.org] -is_a: EDAM_data:1086 ! Compound identifier -relationship: is_identifier_of EDAM_data:2313 ! Carbohydrate structure report -relationship: is_identifier_of EDAM_data:1462 ! Carbohydrate structure +id: EDAM_format:1951 +name: pdbatomnuc +comment: pdbnuc format in EMBOSS. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "PDB nucleotide sequence format (ATOM lines)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1475 ! PDB database entry format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +[Term] +id: EDAM_format:1952 +name: pdbseqresnuc +comment: pdbnucseq format in EMBOSS. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "PDB nucleotide sequence format (SEQRES lines)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1475 ! PDB database entry format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2900 -name: Carbohydrate accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of an entry from a database of carbohydrates." [http://edamontology.org] -is_a: EDAM_data:2663 ! Carbohydrate identifier -is_a: EDAM_data:2901 ! Molecule accession +id: EDAM_format:1953 +name: pdbseqres +comment: pdbseq format in EMBOSS. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "PDB sequence format (SEQRES lines)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1475 ! PDB database entry format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +[Term] +id: EDAM_format:1954 +name: Pearson format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Plain old FASTA sequence format (unspecified format for IDs)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2200 ! FASTA-like (text) [Term] -id: EDAM_data:2605 -name: Compound ID (KEGG) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a chemical compound from the KEGG database." [http://edamontology.org] -synonym: "KEGG compound ID" EXACT [http://edamontology.org] -synonym: "KEGG compound identifier" EXACT [http://edamontology.org] -regex: "C[0-9]+" -is_a: EDAM_data:2894 ! Compound accession -is_a: EDAM_data:1154 ! KEGG object identifier +id: EDAM_format:1955 +name: phylip sequence format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Phylip interleaved sequence format." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1997 ! Phylip format [Term] -id: EDAM_data:2580 -name: BindingDB Monomer ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a monomer from the BindingDB database." [http://edamontology.org] -is_a: EDAM_data:2894 ! Compound accession +id: EDAM_format:1956 +name: phylipnon sequence format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Phylip non-interleaved sequence format." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1998 ! Phylipnon +[Term] +id: EDAM_format:1957 +name: raw +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Raw sequence format with no non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2571 ! Raw sequence format [Term] -id: EDAM_data:1172 -name: PubChem CID -namespace: identifier -subset: identifiers -subset: data -def: "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure." [http://edamontology.org] -synonym: "PubChem compound accession identifier" EXACT [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2894 ! Compound accession -is_a: EDAM_data:2639 ! PubChem identifier +id: EDAM_format:1958 +name: refseqp +comment: Currently identical to genpept format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Refseq protein entry sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:1173 -name: ChemSpider ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the ChemSpider database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2894 ! Compound accession +id: EDAM_format:1959 +name: selex sequence format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Selex sequence format." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2000 ! selex [Term] -id: EDAM_data:1174 -name: ChEBI ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the ChEBI database." [http://edamontology.org] -synonym: "ChEBI identifier" EXACT [http://edamontology.org] -regex: "CHEBI:[0-9]+" -is_a: EDAM_data:2894 ! Compound accession +id: EDAM_format:1960 +name: Staden format +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html +xref: staden +created_in: "beta12orEarlier" +def: "Staden suite sequence format." [http://edamontology.org] +documentation: http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html +documentation: "staden" +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2105 -name: Compound ID (BioCyc) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a compound from the BioCyc chemical compounds database." [http://edamontology.org] -synonym: "BioCyc compound ID" EXACT [http://edamontology.org] -synonym: "BioCyc compound identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:2104 ! BioCyc ID -is_a: EDAM_data:2894 ! Compound accession +id: EDAM_format:1961 +name: Stockholm format +subset: bioinformatics +subset: edam +subset: formats +xref: Stockholm:format +created_in: "beta12orEarlier" +def: "Stockholm multiple sequence alignment format (used by Pfam and Rfam)." [http://edamontology.org] +documentation: Stockholm:format +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:2622 -name: Compound ID (HMDB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB)." [http://edamontology.org] -synonym: "HMDB ID" EXACT [http://edamontology.org] -regex: "HMDB[0-9]{5}" -is_a: EDAM_data:2894 ! Compound accession - +id: EDAM_format:1962 +name: strider format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "DNA strider output sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2635 -name: Compound ID (3DMET) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a metabolite from the 3DMET database." [http://edamontology.org] -synonym: "3DMET ID" EXACT [http://edamontology.org] -regex: "B[0-9]{5}" -is_a: EDAM_data:2894 ! Compound accession +id: EDAM_format:1963 +name: UniProtKB format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "UniProtKB entry sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2187 ! UniProt-like (text) [Term] -id: EDAM_data:2646 -name: Compound ID (ChEMBL) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a small molecular from the ChEMBL database." [http://edamontology.org] -synonym: "ChEMBL ID" EXACT [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2894 ! Compound accession +id: EDAM_format:1964 +name: plain text format (unformatted) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Plain text sequence format (essentially unformatted)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:2658 -name: Compound ID (ChemIDplus) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a chemical from the ChemIDplus database." [http://edamontology.org] -synonym: "ChemIDplus ID" EXACT [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2894 ! Compound accession +id: EDAM_format:1965 +name: treecon sequence format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Treecon output sequence format." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2005 ! TreeCon-seq [Term] -id: EDAM_data:0997 -name: Chemical name (ChEBI) -namespace: identifier -subset: identifiers -subset: data -def: "Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound." [http://edamontology.org] -comment: This is the recommended chemical name for use for example in database annotation. -synonym: "ChEBI chemical name" EXACT [http://edamontology.org] -is_a: EDAM_data:0990 ! Compound name +id: EDAM_format:1966 +name: ASN.1 sequence format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "NCBI ASN.1-based sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:0998 -name: Chemical name (IUPAC) -namespace: identifier -subset: identifiers -subset: data -def: "IUPAC recommended name of a chemical compound." [http://edamontology.org] -synonym: "IUPAC chemical name" EXACT [http://edamontology.org] -is_a: EDAM_data:0990 ! Compound name +id: EDAM_format:1967 +name: DAS format +subset: bioinformatics +subset: edam +subset: formats +synonym: "das sequence format" EXACT [] +created_in: "beta12orEarlier" +def: "DAS sequence (XML) format (any type)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:2552 ! Sequence record format (XML) [Term] -id: EDAM_data:0999 -name: Chemical name (INN) -namespace: identifier -subset: identifiers -subset: data -def: "International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO)." [http://edamontology.org] -synonym: "INN chemical name" EXACT [http://edamontology.org] -is_a: EDAM_data:0990 ! Compound name +id: EDAM_format:1968 +name: dasdna +comment: The use of this format is deprecated. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "DAS sequence (XML) format (nucleotide-only)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:2552 ! Sequence record format (XML) [Term] -id: EDAM_data:1000 -name: Chemical name (brand) -namespace: identifier -subset: identifiers -subset: data -def: "Brand name of a chemical compound." [http://edamontology.org] -synonym: "Brand chemical name" EXACT [http://edamontology.org] -is_a: EDAM_data:0990 ! Compound name +id: EDAM_format:1969 +name: debug-seq +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "EMBOSS debugging trace sequence format of full internal data content." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:1001 -name: Chemical name (synonymous) -namespace: identifier -subset: identifiers -subset: data -def: "Synonymous name of a chemical compound." [http://edamontology.org] -synonym: "Synonymous chemical name" EXACT [http://edamontology.org] -is_a: EDAM_data:0990 ! Compound name +id: EDAM_format:1970 +name: jackknifernon +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Jackknifer output sequence non-interleaved format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM_data:1002 -name: Chemical registry number (CAS) -namespace: identifier -subset: identifiers -subset: data -def: "CAS registry number of a chemical compound." [http://edamontology.org] -synonym: "CAS chemical registry number" EXACT [http://edamontology.org] -is_a: EDAM_data:0991 ! Chemical registry number +id: EDAM_format:1971 +name: meganon sequence format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Mega non-interleaved output sequence format." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1992 ! meganon [Term] -id: EDAM_data:1003 -name: Chemical registry number (Beilstein) -namespace: identifier -subset: identifiers -subset: data -def: "Beilstein registry number of a chemical compound." [http://edamontology.org] -synonym: "Beilstein chemical registry number" EXACT [http://edamontology.org] -is_a: EDAM_data:0991 ! Chemical registry number +id: EDAM_format:1972 +name: NCBI format +comment: There are several variants of this. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "NCBI FASTA sequence format with NCBI-style IDs." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2200 ! FASTA-like (text) [Term] -id: EDAM_data:1004 -name: Chemical registry number (Gmelin) -namespace: identifier -subset: identifiers -subset: data -def: "Gmelin registry number of a chemical compound." [http://edamontology.org] -synonym: "Gmelin chemical registry number" EXACT [http://edamontology.org] -is_a: EDAM_data:0991 ! Chemical registry number +id: EDAM_format:1973 +name: nexusnon +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Nexus/paup non-interleaved sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:1005 -name: HET group name -namespace: identifier -subset: identifiers -subset: data -def: "3-letter code word for a ligand (HET group) from a PDB file, for example ATP." [http://edamontology.org] -synonym: "Short ligand name" EXACT [http://edamontology.org] -synonym: "Component identifier code" EXACT [http://edamontology.org] -is_a: EDAM_data:0990 ! Compound name +id: EDAM_format:1974 +name: GFF2 +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.sanger.ac.uk/resources/software/gff/spec.html +created_in: "beta12orEarlier" +def: "General Feature Format (GFF) of sequence features." [http://edamontology.org] +documentation: http://www.sanger.ac.uk/resources/software/gff/spec.html +namespace: format +is_a: EDAM_format:2305 ! GFF +[Term] +id: EDAM_format:1975 +name: GFF3 +subset: bioinformatics +subset: edam +subset: formats +xref: http://sequenceontology.org/resources/gff3.html +created_in: "beta12orEarlier" +def: "Generic Feature Format version 3 (GFF3) of sequence features." [http://edamontology.org] +documentation: http://sequenceontology.org/resources/gff3.html +namespace: format +is_a: EDAM_format:2305 ! GFF [Term] -id: EDAM_data:2613 -name: KEGG Glycan ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND)." [http://edamontology.org] -regex: "G[0-9]+" -is_a: EDAM_data:2900 ! Carbohydrate accession -is_a: EDAM_data:1154 ! KEGG object identifier +id: EDAM_format:1976 +name: pir +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "PIR feature format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2206 ! Sequence feature table format (text) +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:1977 +name: swiss feature +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Swiss-Prot feature format." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1963 ! UniProtKB format [Term] -id: EDAM_data:2326 -name: DrugBank ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a drug from the DrugBank database." [http://edamontology.org] -regex: "DB[0-9]{5}" -is_a: EDAM_data:2895 ! Drug accession +id: EDAM_format:1978 +name: DASGFF +subset: bioinformatics +subset: edam +subset: formats +synonym: "das feature" EXACT [] +synonym: "DASGFF feature" EXACT [] +created_in: "beta12orEarlier" +def: "DAS GFF (XML) feature format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:2553 ! Sequence feature table format (XML) [Term] -id: EDAM_data:2609 -name: Drug ID (KEGG) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a drug from the KEGG Drug database." [http://edamontology.org] -regex: "D[0-9]+" -is_a: EDAM_data:2895 ! Drug accession -is_a: EDAM_data:1154 ! KEGG object identifier +id: EDAM_format:1979 +name: debug-feat +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "EMBOSS debugging trace feature format of full internal data content." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1920 ! Sequence feature annotation format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2652 -name: Drug ID (PharmGKB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] -regex: "PA[0-9]+" -is_a: EDAM_data:2895 ! Drug accession -is_a: EDAM_data:2649 ! PharmGKB ID +id: EDAM_format:1980 +name: EMBL feature +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "EMBL feature format." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1927 ! EMBL format +[Term] +id: EDAM_format:1981 +name: GenBank feature +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Genbank feature format." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1936 ! GenBank format [Term] -id: EDAM_data:2653 -name: Drug ID (TTD) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a drug from the Therapeutic Target Database (TTD)." [http://edamontology.org] -regex: "DAP[0-9]+" -is_a: EDAM_data:2895 ! Drug accession +id: EDAM_format:1982 +name: ClustalW format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "ClustalW format for (aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:3102 !{since=beta13} -name: CAS number -namespace: identifier -subset: identifiers -subset: data -def: "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." [http://edamontology.org] -synonym: "CAS registry number" EXACT [http://edamontology.org] -is_a: EDAM_data:2895 ! Drug accession +id: EDAM_format:1983 +name: debug +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "EMBOSS alignment format for debugging trace of full internal data content." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:3103 !{since=beta13} -name: ATC code -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC)." [http://edamontology.org] -is_a: EDAM_data:2895 ! Drug accession +id: EDAM_format:1984 +name: FASTA-aln +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Fasta format for (aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2200 ! FASTA-like (text) +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:3104 !{since=beta13} -name: UNII -namespace: identifier -subset: identifiers -subset: data -def: "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." [http://edamontology.org] -synonym: "Unique Ingredient Identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:1086 ! Compound identifier +id: EDAM_format:1985 +name: markx0 +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Pearson MARKX0 alignment format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2922 ! markx0 variant +[Term] +id: EDAM_format:1986 +name: markx1 +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Pearson MARKX1 alignment format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2922 ! markx0 variant +[Term] +id: EDAM_format:1987 +name: markx10 +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Pearson MARKX10 alignment format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2922 ! markx0 variant +[Term] +id: EDAM_format:1988 +name: markx2 +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Pearson MARKX2 alignment format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2922 ! markx0 variant +[Term] +id: EDAM_format:1989 +name: markx3 +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Pearson MARKX3 alignment format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2922 ! markx0 variant [Term] -id: EDAM_data:2578 -name: ArachnoServer ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a toxin from the ArachnoServer database." [http://edamontology.org] -is_a: EDAM_data:2897 ! Toxin accession +id: EDAM_format:1990 +name: match +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alignment format for start and end of matches between sequence pairs." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) +[Term] +id: EDAM_format:1991 +name: mega +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Mega format for (typically aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2923 ! mega variant [Term] -id: EDAM_data:2662 -name: T3DB ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database." [http://edamontology.org] -regex: "T3D[0-9]+" -is_a: EDAM_data:2897 ! Toxin accession +id: EDAM_format:1992 +name: meganon +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Mega non-interleaved format for (typically aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2923 ! mega variant [Term] -id: EDAM_data:1006 -name: Amino acid name -namespace: identifier -subset: identifiers -subset: data -def: "String of one or more ASCII characters representing an amino acid." [http://edamontology.org] -is_a: EDAM_data:0994 ! Amino acid identifier +id: EDAM_format:1993 +name: msf alignment format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "MSF format for (aligned) sequences." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1947 ! msf [Term] -id: EDAM_data:2563 -name: Amino acid name (single letter) -namespace: identifier -subset: identifiers -subset: data -def: "Single letter amino acid identifier, e.g. G." [http://edamontology.org] -is_a: EDAM_data:1006 ! Amino acid name +id: EDAM_format:1994 +name: nexus alignment format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Nexus/paup format for (aligned) sequences." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1949 ! nexus-seq [Term] -id: EDAM_data:2564 -name: Amino acid name (three letter) -namespace: identifier -subset: identifiers -subset: data -def: "Three letter amino acid identifier, e.g. GLY." [http://edamontology.org] -is_a: EDAM_data:1006 ! Amino acid name +id: EDAM_format:1995 +name: nexusnon alignment format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Nexus/paup non-interleaved format for (aligned) sequences." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:1973 ! nexusnon +[Term] +id: EDAM_format:1996 +name: pair +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "EMBOSS simple sequence pair alignment format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:1758 -name: PDB residue name -namespace: identifier -subset: identifiers -subset: data -def: "Three-letter amino acid residue names as used in PDB files." [http://edamontology.org] -xref: WHATIF: type -is_a: EDAM_data:2564 ! Amino acid name (three letter) +id: EDAM_format:1997 +name: Phylip format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Phylip format for (aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2924 ! Phylip format variant +[Term] +id: EDAM_format:1998 +name: Phylipnon +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Phylip non-interleaved format for (aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2924 ! Phylip format variant +[Term] +id: EDAM_format:1999 +name: scores format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alignment format for score values for pairs of sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:2565 -name: Amino acid name (full name) -namespace: identifier -subset: identifiers -subset: data -def: "Full name of an amino acid, e.g. Glycine." [http://edamontology.org] -is_a: EDAM_data:1006 ! Amino acid name +id: EDAM_format:2000 +name: selex +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "SELEX format for (aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +is_a: EDAM_format:2554 ! Alignment format (text) +[Term] +id: EDAM_format:2001 +name: EMBOSS simple format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "EMBOSS simple multiple alignment format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:1007 -name: Nucleotide code -namespace: identifier -subset: identifiers -subset: data -def: "String of one or more ASCII characters representing a nucleotide." [http://edamontology.org] -is_a: EDAM_data:0995 ! Nucleotide identifier -is_a: EDAM_data:0990 ! Compound name +id: EDAM_format:2002 +name: srs format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Simple multiple sequence (alignment) format for SRS." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:2746 -name: MonosaccharideDB ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a monosaccharide from the MonosaccharideDB database." [http://edamontology.org] -is_a: EDAM_data:2898 ! Monosaccharide accession +id: EDAM_format:2003 +name: srspair +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Simple sequence pair (alignment) format for SRS." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] -id: EDAM_data:2625 -name: LIPID MAPS ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the LIPID MAPS database." [http://edamontology.org] -synonym: "LM ID" EXACT [http://edamontology.org] -regex: "LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?" -is_a: EDAM_data:2905 ! Lipid accession +id: EDAM_format:2004 +name: T-Coffee format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "T-Coffee program alignment format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) +[Term] +id: EDAM_format:2005 +name: TreeCon-seq +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Treecon format for (aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:2665 -name: LipidBank ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the LipidBank database." [http://edamontology.org] -regex: "[a-zA-Z_0-9]+[0-9]+" -is_a: EDAM_data:2905 ! Lipid accession - +id: EDAM_format:2006 +name: Phylogenetic tree format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a phylogenetic tree." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0872 ! Phylogenetic tree [Term] -id: EDAM_data:2664 -name: GlycomeDB ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the GlycomeDB database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2900 ! Carbohydrate accession +id: EDAM_format:2013 +name: Biological pathway or network format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a biological pathway or network." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:2600 ! Pathway or network +[Term] +id: EDAM_format:2014 +name: Sequence-profile alignment format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a sequence-profile alignment." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0869 ! Sequence-profile alignment [Term] -id: EDAM_data:2752 -name: GlycoMap ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2900 ! Carbohydrate accession +id: EDAM_format:2015 +name: Sequence-profile alignment (HMM) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a sequence-HMM profile alignment." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2014 ! Sequence-profile alignment format [Term] -id: EDAM_data:2796 -name: Linucs ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] -is_a: EDAM_data:2900 ! Carbohydrate accession +id: EDAM_format:2017 +name: Amino acid index format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for an amino acid index." [http://edamontology.org] +namespace: format +is_a: EDAM_format:3033 ! Matrix format +relationship: is_format_of EDAM_data:1501 ! Amino acid index +[Term] +id: EDAM_format:2020 +name: Article format +subset: bioinformatics +subset: edam +subset: formats +synonym: "Literature format" EXACT [] +created_in: "beta12orEarlier" +def: "Data format for a full-text scientific article." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0971 ! Article [Term] -id: EDAM_data:0987 -name: Chromosome name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a chromosome." [http://edamontology.org] -is_a: EDAM_data:2119 ! Nucleic acid identifier -is_a: EDAM_data:0984 ! Molecule name -relationship: is_identifier_of EDAM_data:0919 ! Gene annotation (chromosome) +id: EDAM_format:2021 +name: Text mining report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for an abstract (report) from text mining." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0972 ! Text mining report [Term] -id: EDAM_data:2208 -name: Plasmid identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a plasmid in a database." [http://edamontology.org] -is_a: EDAM_data:2119 ! Nucleic acid identifier +id: EDAM_format:2027 +name: Enzyme kinetics report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for reports on enzyme kinetics." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:2024 ! Enzyme kinetics data [Term] -id: EDAM_data:2718 -name: Oligonucleotide ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an oligonucleotide from a database." [http://edamontology.org] -is_a: EDAM_data:2119 ! Nucleic acid identifier -is_a: EDAM_data:2901 ! Molecule accession +id: EDAM_format:2030 +name: Small molecule report format +subset: bioinformatics +subset: edam +subset: formats +synonym: "Chemical compound annotation format" EXACT [] +created_in: "beta12orEarlier" +def: "Format of a report on a chemical compound." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0962 ! Small molecule annotation +[Term] +id: EDAM_format:2031 +name: Gene annotation format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0916 ! Gene annotation [Term] -id: EDAM_data:2769 -name: Transcript ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a RNA transcript." [http://edamontology.org] -is_a: EDAM_data:2119 ! Nucleic acid identifier -is_a: EDAM_data:2901 ! Molecule accession -relationship: is_identifier_of EDAM_data:2399 ! Gene annotation (transcript) +id: EDAM_format:2032 +name: Workflow format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a workflow." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:2972 ! Workflow [Term] -id: EDAM_data:2706 -name: Chromosome name (BioCyc) -namespace: identifier -subset: identifiers -subset: data -def: "Name of a chromosome as used in the BioCyc database." [http://edamontology.org] -is_a: EDAM_data:0987 ! Chromosome name +id: EDAM_format:2033 +name: Tertiary structure format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a molecular tertiary structure." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +[Term] +id: EDAM_format:2034 +name: Biological model format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a biological model." [http://edamontology.org] +namespace: format +obsolete_since: "1.2" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2013 ! Biological pathway or network format [Term] -id: EDAM_data:2719 -name: dbProbe ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an oligonucleotide probe from the dbProbe database." [http://edamontology.org] -is_a: EDAM_data:2718 ! Oligonucleotide ID +id: EDAM_format:2035 +name: Chemical formula format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Text format of a chemical formula." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0846 ! Chemical formula [Term] -id: EDAM_data:2721 -name: DiProDB ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an dinucleotide property from the DiProDB database." [http://edamontology.org] -is_a: EDAM_data:2718 ! Oligonucleotide ID +id: EDAM_format:2036 +name: Phylogenetic character data format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of raw (unplotted) phylogenetic data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0871 ! Phylogenetic character data [Term] -id: EDAM_data:2770 -name: HIT ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an RNA transcript from the H-InvDB database." [http://edamontology.org] -is_a: EDAM_data:2769 ! Transcript ID +id: EDAM_format:2037 +name: Phylogenetic continuous quantitative character format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of phylogenetic continuous quantitative character data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2036 ! Phylogenetic character data format +relationship: is_format_of EDAM_data:1426 ! Phylogenetic continuous quantitative data +[Term] +id: EDAM_format:2038 +name: Phylogenetic discrete states format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of phylogenetic discrete states data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2036 ! Phylogenetic character data format +relationship: is_format_of EDAM_data:1427 ! Phylogenetic discrete data [Term] -id: EDAM_data:2626 -name: PeptideAtlas ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a peptide from the PeptideAtlas peptide databases." [http://edamontology.org] -regex: "PAp[0-9]{8}" -is_a: EDAM_data:2906 ! Peptide ID -! pdbx_PDB_strand_id in PDBML +id: EDAM_format:2039 +name: Phylogenetic tree report (cliques) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of phylogenetic cliques data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2036 ! Phylogenetic character data format +relationship: is_format_of EDAM_data:1428 ! Phylogenetic character cliques [Term] -id: EDAM_data:1009 -name: Protein name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a protein." [http://edamontology.org] -is_a: EDAM_data:0989 ! Protein identifier -is_a: EDAM_data:0984 ! Molecule name +id: EDAM_format:2040 +name: Phylogenetic tree report (invariants) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of phylogenetic invariants data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2036 ! Phylogenetic character data format +relationship: is_format_of EDAM_data:1429 ! Phylogenetic invariants [Term] -id: EDAM_data:1010 -name: Enzyme identifier -namespace: identifier -subset: identifiers -subset: data -def: "Name or other identifier of an enzyme or record from a database of enzymes." [http://edamontology.org] -is_a: EDAM_data:0989 ! Protein identifier -relationship: is_identifier_of EDAM_data:1509 ! Enzyme property +id: EDAM_format:2045 +name: Electron microscopy model format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Annotation format for electron microscopy models." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2350 ! Format (typed) +[Term] +id: EDAM_format:2049 +name: Phylogenetic tree report (tree distances) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for phylogenetic tree distance data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1442 ! Phylogenetic tree report (tree distances) [Term] -id: EDAM_data:2114 -name: WormBase wormpep ID -namespace: identifier -subset: identifiers -subset: data -def: "Protein identifier used by WormBase database." [http://edamontology.org] -regex: "CE[0-9]{5}" -is_a: EDAM_data:2907 ! Protein accession -is_a: EDAM_data:2113 ! WormBase identifier +id: EDAM_format:2051 +name: Polymorphism report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for sequence polymorphism data." [http://edamontology.org] +namespace: format +obsolete_since: "1.0" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_data:2804 -name: Protein ID (ConoServer) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a cone snail toxin protein from the ConoServer database." [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2052 +name: Protein family report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for reports on a protein family." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0907 ! Protein family +[Term] +id: EDAM_format:2054 +name: Molecular interaction format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for molecular interaction data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:2599 ! Molecular interaction [Term] -id: EDAM_data:2802 -name: Protein ID (EcID) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a protein from the EcID database." [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2055 +name: Sequence assembly format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for sequence assembly data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0925 ! Sequence assembly +[Term] +id: EDAM_format:2056 +name: Microarray experiment data format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for microarray experimental data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0931 ! Experiment annotation (microarray) [Term] -id: EDAM_data:3029 !{since=beta13} -name: Protein ID (EMBL/GenBank/DDBJ) -namespace: identifier -subset: identifiers -subset: data -def: "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators." [http://edamontology.org] -comment: This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2057 +name: Sequence trace format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for sequence trace data (i.e. including base call information)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1919 ! Sequence record format +relationship: is_format_of EDAM_data:0924 ! Sequence trace +[Term] +id: EDAM_format:2058 +name: Gene expression report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for a report on gene expression." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2031 ! Gene annotation format +relationship: is_format_of EDAM_data:3111 ! Processed microarray data +[Term] +id: EDAM_format:2059 +name: Genotype and phenotype annotation format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on genotype / phenotype information." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2350 ! Format (typed) [Term] -id: EDAM_data:2398 -name: Protein ID (Ensembl) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a protein from the Ensembl database." [http://edamontology.org] -synonym: "Ensembl protein ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession -is_a: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:2060 +name: Map format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a map of (typically one) molecular sequence annotated with features." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1274 ! Map +[Term] +id: EDAM_format:2061 +name: Nucleic acid features (primers) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0922 ! Nucleic acid features (primers) [Term] -id: EDAM_data:2713 -name: Protein ID (CORUM) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a protein complex from the CORUM database." [http://edamontology.org] -synonym: "CORUM complex ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2062 +name: Protein report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report of general information about a specific protein." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0896 ! Protein report +[Term] +id: EDAM_format:2063 +name: Protein report (enzyme) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report of general information about a specific enzyme." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2350 ! Format (typed) [Term] -id: EDAM_data:2715 -name: Protein ID (CuticleDB) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a protein from the CuticleDB database." [http://edamontology.org] -synonym: "CuticleDB ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2064 +name: 3D-1D scoring matrix format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:3033 ! Matrix format +relationship: is_format_of EDAM_data:1499 ! 3D-1D scoring matrix +[Term] +id: EDAM_format:2065 +name: Protein structure report (quality evaluation) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on the quality of a protein three-dimensional model." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1539 ! Protein structural quality report [Term] -id: EDAM_data:2723 -name: Protein ID (DisProt) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a protein from the DisProt database." [http://edamontology.org] -synonym: "DisProt ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2066 +name: Database hits (sequence) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on sequence hits and associated data from searching a sequence database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0857 ! Database hits (sequence) +[Term] +id: EDAM_format:2067 +name: Sequence distance matrix format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a matrix of genetic distances between molecular sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0870 ! Sequence distance matrix [Term] -id: EDAM_data:2789 -name: Protein ID (TopDB) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a membrane protein from the TopDB database." [http://edamontology.org] -synonym: "TopDB ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2068 +name: Sequence motif format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a sequence motif." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1353 ! Sequence motif +[Term] +id: EDAM_format:2069 +name: Sequence profile format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a sequence profile." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1354 ! Sequence profile [Term] -id: EDAM_data:2792 -name: Protein ID (PeroxiBase) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a peroxidase protein from the PeroxiBase database." [http://edamontology.org] -synonym: "PeroxiBase ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2072 +name: Hidden Markov model format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a hidden Markov model." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2069 ! Sequence profile format +relationship: is_format_of EDAM_data:1364 ! Hidden Markov model +[Term] +id: EDAM_format:2074 +name: Dirichlet distribution format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format of a dirichlet distribution." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1347 ! Dirichlet distribution [Term] -id: EDAM_data:2797 -name: Protein ID (LGICdb) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a ligand-gated ion channel protein from the LGICdb database." [http://edamontology.org] -synonym: "LGICdb ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2075 +name: HMM emission and transition counts format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for the emission and transition counts of a hidden Markov model." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1348 ! HMM emission and transition counts [Term] -id: EDAM_data:2617 -name: Signaling Gateway protein ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database." [http://edamontology.org] -regex: "A[0-9]{6}" -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2076 +name: RNA secondary structure format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0880 ! RNA secondary structure record [Term] -id: EDAM_data:2647 -name: LGICdb identifier -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database." [http://edamontology.org] -regex: "[a-zA-Z_0-9]+" -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2077 +name: Protein secondary structure format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for secondary structure (predicted or real) of a protein molecule." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0876 ! Protein features (secondary structure) [Term] -id: EDAM_data:2654 -name: Target ID (TTD) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a target protein from the Therapeutic Target Database (TTD)." [http://edamontology.org] -regex: "TTDS[0-9]+" -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2078 +name: Sequence range format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used to specify range(s) of sequence positions." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1017 ! Sequence range [Term] -id: EDAM_data:2756 -name: TCID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a membrane transport proteins from the transport classification database (TCDB)." [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2094 +name: pure +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for molecular sequence with possible unknown positions but without non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2571 ! Raw sequence format +[Term] +id: EDAM_format:2095 +name: unpure +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2571 ! Raw sequence format [Term] -id: EDAM_data:2772 -name: HPA antibody id -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a antibody from the HPA database." [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2096 +name: unambiguous sequence +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2571 ! Raw sequence format [Term] -id: EDAM_data:2773 -name: IMGT/HLA ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database." [http://edamontology.org] -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2097 +name: ambiguous +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2571 ! Raw sequence format [Term] -id: EDAM_data:2764 -name: Protein name (UniProt) -namespace: identifier -subset: identifiers -subset: data -def: "Official name of a protein as used in the UniProt database." [http://edamontology.org] -is_a: EDAM_data:1009 ! Protein name +id: EDAM_format:2155 +name: Sequence features (repeats) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used for map of repeats in molecular (typically nucleotide) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1299 ! Sequence features (repeats) [Term] -id: EDAM_data:2775 -name: Kinase name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a kinase protein." [http://edamontology.org] -is_a: EDAM_data:1009 ! Protein name +id: EDAM_format:2158 +name: Nucleic acid features (restriction sites) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used for report on restriction enzyme recognition sites in nucleotide sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1305 ! Nucleic acid features (restriction sites) [Term] -id: EDAM_data:2321 -name: Enzyme ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique, persistent identifier of an enzyme." [http://edamontology.org] -synonym: "Enzyme accession" EXACT [http://edamontology.org] -is_a: EDAM_data:1010 ! Enzyme identifier -is_a: EDAM_data:2907 ! Protein accession +id: EDAM_format:2159 +name: Gene features (coding region) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used for report on coding regions in nucleotide sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2031 ! Gene annotation format +relationship: is_format_of EDAM_data:1313 ! Nucleic acid features (coding sequence) +[Term] +id: EDAM_format:2170 +name: Sequence cluster format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used for clusters of molecular sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:1235 ! Sequence cluster [Term] -id: EDAM_data:1012 -name: Enzyme name -namespace: identifier -subset: identifiers -subset: data -def: "Name of an enzyme." [http://edamontology.org] -is_a: EDAM_data:1010 ! Enzyme identifier -is_a: EDAM_data:1009 ! Protein name +id: EDAM_format:2171 +name: Sequence cluster format (protein) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used for clusters of protein sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2170 ! Sequence cluster format +[Term] +id: EDAM_format:2172 +name: Sequence cluster format (nucleic acid) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used for clusters of nucleotide sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2170 ! Sequence cluster format [Term] -id: EDAM_data:1011 -name: EC number -namespace: identifier -subset: identifiers -subset: data -def: "An Enzyme Commission (EC) number of an enzyme." [http://edamontology.org] -synonym: "EC code" EXACT [http://edamontology.org] -synonym: "EC" EXACT [http://edamontology.org] -synonym: "Enzyme Commission number" EXACT [http://edamontology.org] -xref: Moby:EC_Number -xref: Moby:Annotated_EC_Number -regex: "[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+" -is_a: EDAM_data:2321 ! Enzyme ID +id: EDAM_format:2175 +name: Gene cluster format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used for clusters of genes." [http://edamontology.org] +namespace: format +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2172 ! Sequence cluster format (nucleic acid) [Term] -id: EDAM_data:2107 -name: Enzyme ID (BioCyc) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an enzyme from the BioCyc enzymes database." [http://edamontology.org] -synonym: "BioCyc enzyme ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2104 ! BioCyc ID -is_a: EDAM_data:2321 ! Enzyme ID +id: EDAM_format:2181 +name: EMBL-like (text) +comment: This concept may be used for the many non-standard EMBL-like text formats. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A text format resembling EMBL entry format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2543 ! EMBL-like format [Term] -id: EDAM_data:2629 -name: Enzyme ID (MEROPS) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a peptidase enzyme from the MEROPS database." [http://edamontology.org] -synonym: "MEROPS ID" EXACT [http://edamontology.org] -regex: "S[0-9]{2}\.[0-9]{3}" -is_a: EDAM_data:2321 ! Enzyme ID +id: EDAM_format:2182 +name: FASTQ-like format (text) +comment: This concept may be used for non-standard FASTQ short read-like formats. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A text format resembling FASTQ short read format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2545 ! FASTQ-like format [Term] -id: EDAM_data:2702 -name: Enzyme ID (CAZy) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an enzyme from the CAZy enzymes database." [http://edamontology.org] -synonym: "CAZy ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2321 ! Enzyme ID +id: EDAM_format:2183 +name: EMBLXML +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "XML format for EMBL entries." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2204 ! EMBL format (XML) [Term] -id: EDAM_data:2325 -name: REBASE enzyme number -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an enzyme from the REBASE enzymes database." [http://edamontology.org] -is_a: EDAM_data:2321 ! Enzyme ID +id: EDAM_format:2184 +name: cdsxml +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "XML format for EMBL entries." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2204 ! EMBL format (XML) +[Term] +id: EDAM_format:2185 +name: insdxml +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "XML format for EMBL entries." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2204 ! EMBL format (XML) [Term] -id: EDAM_data:1013 -name: Restriction enzyme name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a restriction enzyme." [http://edamontology.org] -is_a: EDAM_data:1012 ! Enzyme name -relationship: is_identifier_of EDAM_data:1517 ! Restriction enzyme property +id: EDAM_format:2186 +name: geneseq +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Geneseq sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2181 ! EMBL-like (text) [Term] -id: EDAM_data:1018 -name: Nucleic acid feature identifier -namespace: identifier -subset: identifiers -subset: data -def: "Name or other identifier of an nucleic acid feature." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1015 ! Sequence feature ID +id: EDAM_format:2187 +name: UniProt-like (text) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A text sequence format resembling uniprotkb entry format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2547 ! uniprotkb-like format [Term] -id: EDAM_data:1019 -name: Protein feature identifier -namespace: identifier -subset: identifiers -subset: data -def: "Name or other identifier of a protein feature." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1015 ! Sequence feature ID - +id: EDAM_format:2188 +name: UniProt format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "UniProt entry sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2187 ! UniProt-like (text) [Term] -id: EDAM_data:2736 -name: Sequence feature ID (SwissRegulon) -namespace: identifier -subset: identifiers -subset: data -def: "A feature identifier as used in the SwissRegulon database." [http://edamontology.org] -comment: This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". -is_a: EDAM_data:1015 ! Sequence feature ID +id: EDAM_format:2189 +name: ipi +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "ipi sequence format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2187 ! UniProt-like (text) [Term] -id: EDAM_data:1024 -name: Codon name -namespace: identifier -subset: identifiers -subset: data -def: "String of one or more ASCII characters representing a codon." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1276 ! Nucleic acid features +id: EDAM_format:2194 +name: medline +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Abstract format used by MedLine database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2020 ! Article format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:2195 +name: Ontology format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format used for ontologies." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0582 ! Ontology -! Don't know whether the loci identifiers listed here are 'ordered' or not. +[Term] +id: EDAM_format:2196 +name: OBO format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A serialisation format conforming to the Open Biomedical Ontologies (OBO) model." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2195 ! Ontology format [Term] -id: EDAM_data:2009 -name: Ordered locus name -namespace: identifier -subset: identifiers -subset: data -def: "A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1893 ! Locus ID +id: EDAM_format:2197 +name: OWL format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A serialisation format conforming to the Web Ontology Language (OWL) model." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2195 ! Ontology format +is_a: EDAM_format:2332 ! XML [Term] -id: EDAM_data:1895 -name: Locus ID (AGI) -namespace: identifier -subset: identifiers -subset: data -def: "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" [http://edamontology.org] -synonym: "AGI locus code" EXACT [http://edamontology.org] -synonym: "AGI ID" EXACT [http://edamontology.org] -synonym: "AGI identifier" EXACT [http://edamontology.org] -synonym: "Arabidopsis gene loci number" EXACT [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode -regex: "AT[1-5]G[0-9]{5}" -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2200 +name: FASTA-like (text) +comment: This concept may also be used for the many non-standard FASTA-like formats. +subset: bioinformatics +subset: edam +subset: formats +synonym: "http://filext.com/file-extension/FASTA" NARROW [] +created_in: "beta12orEarlier" +def: "A text format resembling FASTA format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2546 ! FASTA-like [Term] -id: EDAM_data:1896 -name: Locus ID (ASPGD) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for loci from ASPGD (Aspergillus Genome Database)." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD -xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2202 +name: Sequence record full format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1919 ! Sequence record format +relationship: is_format_of EDAM_data:2201 ! Sequence record full [Term] -id: EDAM_data:1897 -name: Locus ID (MGG) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for loci from Magnaporthe grisea Database at the Broad Institute." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2203 +name: Sequence record lite format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1919 ! Sequence record format +relationship: is_format_of EDAM_data:2043 ! Sequence record lite +[Term] +id: EDAM_format:2204 +name: EMBL format (XML) +comment: This is a placeholder for other more specific concepts. It should not normally be used for annotation. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "An XML format for EMBL entries." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2558 ! EMBL-like (XML) [Term] -id: EDAM_data:1898 -name: Locus ID (CGD) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for loci from CGD (Candida Genome Database)." [http://edamontology.org] -synonym: "CGD locus identifier" EXACT [http://edamontology.org] -synonym: "CGDID" EXACT [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGD -xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGDID -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2205 +name: GenBank-like format (text) +comment: This concept may be used for the non-standard GenBank-like text formats. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A text format resembling GenBank entry (plain text) format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2559 ! GenBank-like format +[Term] +id: EDAM_format:2206 +name: Sequence feature table format (text) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Text format for a sequence feature table." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2548 ! Sequence feature table format [Term] -id: EDAM_data:1899 -name: Locus ID (CMR) -namespace: identifier -subset: identifiers -subset: data -def: "Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR -xref: http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2210 +name: Strain data format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on organism strain data / cell line." [http://edamontology.org] +namespace: format +obsolete_since: "1.0" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +[Term] +id: EDAM_format:2211 +name: CIP strain data format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for a report of strain data as used for CIP database entries." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1900 -name: NCBI locus tag -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for loci from NCBI database." [http://edamontology.org] -synonym: "Locus ID (NCBI)" EXACT [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag -xref: Moby_namespace:LocusID -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2243 +name: phylip property values +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "PHYLIP file format for phylogenetic property data." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2036 ! Phylogenetic character data format +[Term] +id: EDAM_format:2303 +name: STRING entry format (HTML) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format (HTML) for the STRING database of protein interaction." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1901 -name: Locus ID (SGD) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for loci from SGD (Saccharomyces Genome Database)." [http://edamontology.org] -synonym: "SGDID" EXACT [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGD -xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGDID -is_a: EDAM_data:1893 ! Locus ID -is_a: EDAM_data:2632 ! SGD ID +id: EDAM_format:2304 +name: STRING entry format (XML) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format (XML) for the STRING database of protein interaction." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2054 ! Molecular interaction format +is_a: EDAM_format:2332 ! XML +[Term] +id: EDAM_format:2305 +name: GFF +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "GFF feature format (of indeterminate version)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2206 ! Sequence feature table format (text) +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1902 -name: Locus ID (MMP) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of loci from Maize Mapping Project." [http://edamontology.org] -xref: Moby_namespace:MMP_Locus -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2306 +name: GTF +subset: bioinformatics +subset: edam +subset: formats +xref: format4 +xref: http://mblab.wustl.edu/GTF22.html +created_in: "beta12orEarlier" +def: "Gene Transfer Format (GTF), a restricted version of GFF." [http://edamontology.org] +documentation: http://mblab.wustl.edu/GTF22.html +namespace: format +is_a: EDAM_format:2305 ! GFF +[Term] +id: EDAM_format:2310 +name: FASTA-HTML +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "FASTA format wrapped in HTML elements." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2331 ! HTML +is_a: EDAM_format:2546 ! FASTA-like [Term] -id: EDAM_data:1903 -name: Locus ID (DictyBase) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of locus from DictyBase (Dictyostelium discoideum)." [http://edamontology.org] -xref: Moby_namespace:DDB_gene -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2311 +name: EMBL-HTML +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "EMBL entry format wrapped in HTML elements." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2331 ! HTML +is_a: EDAM_format:2543 ! EMBL-like format +[Term] +id: EDAM_format:2322 +name: BioCyc enzyme report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the BioCyc enzyme database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1904 -name: Locus ID (EntrezGene) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a locus from EntrezGene database." [http://edamontology.org] -xref: Moby_namespace:EntrezGene_EntrezGeneID -xref: Moby_namespace:EntrezGene_ID -is_a: EDAM_data:1893 ! Locus ID - +id: EDAM_format:2323 +name: ENZYME enzyme report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of an entry from the Enzyme nomenclature database (ENZYME)." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1905 -name: Locus ID (MaizeGDB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of locus from MaizeGDB (Maize genome database)." [http://edamontology.org] -xref: Moby_namespace:MaizeGDB_Locus -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2328 +name: PseudoCAP gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on a gene from the PseudoCAP database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1908 -name: Locus ID (Tropgene) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a locus from the Tropgene database." [http://edamontology.org] -xref: Moby:Tropgene_locus -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2329 +name: GeneCards gene report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on a gene from the GeneCards database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2744 -name: Locus ID (PseudoCAP) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a locus from the PseudoCAP database." [http://edamontology.org] -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2330 +name: Textual format +comment: Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). +subset: bioinformatics +subset: edam +subset: formats +synonym: "http://filext.com/file-extension/TSV" NARROW [] +synonym: "http://filext.com/file-extension/TXT" NARROW [] +synonym: "Plain text" NARROW [] +synonym: "Tabular format" NARROW [] +created_in: "beta12orEarlier" +def: "Textual format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1915 ! Format +[Term] +id: EDAM_format:2331 +name: HTML +subset: bioinformatics +subset: edam +subset: formats +synonym: "http://filext.com/file-extension/HTML" EXACT [] +synonym: "Hypertext Markup Language" EXACT [] +created_in: "beta12orEarlier" +def: "HTML format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1915 ! Format +relationship: is_format_of EDAM_data:2048 ! Report [Term] -id: EDAM_data:2745 -name: Locus ID (UTR) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a locus from the UTR database." [http://edamontology.org] -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2332 +name: XML +comment: Data in XML format can be serialised into text, or binary format. +subset: bioinformatics +subset: edam +subset: formats +synonym: "Extensible Markup Language" EXACT [] +synonym: "http://filext.com/file-extension/XML" EXACT [] +created_in: "beta12orEarlier" +def: "eXtensible Markup Language (XML) format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1915 ! Format [Term] -id: EDAM_data:2794 -name: ORF ID -namespace: identifier -subset: identifiers -subset: data -def: "Accession of an open reading frame (catalogued in a database)." [http://edamontology.org] -is_a: EDAM_data:2795 ! ORF identifier -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2333 +name: Binary format +comment: Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Binary format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1915 ! Format +[Term] +id: EDAM_format:2334 +name: URI format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Typical textual representation of a URI." [http://edamontology.org] +namespace: format +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:1047 ! URI [Term] -id: EDAM_data:1026 -name: Gene symbol -namespace: identifier -subset: identifiers -subset: data -def: "The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name." [http://edamontology.org] -xref: Moby_namespace:Global_GeneSymbol -xref: Moby_namespace:Global_GeneCommonName -is_a: EDAM_data:2299 ! Gene name +id: EDAM_format:2341 +name: NCI-Nature pathway entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "The format of an entry from the NCI-Nature pathways database." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:2299 -name: Gene name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol." [http://edamontology.org] -is_a: EDAM_data:1025 ! Gene identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:2350 +name: Format (typed) +comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A broad class of format distinguished by the scientific nature of the data that is identified." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1915 ! Format +[Term] +id: EDAM_format:2352 +name: BioXSD +subset: bioinformatics +subset: edam +subset: formats +synonym: "BioXSD XML format" EXACT [] +xref: http://bioxsd.org +created_in: "beta12orEarlier" +def: "BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more)." [http://edamontology.org] +documentation: http://bioxsd.org +namespace: format +is_a: EDAM_format:1919 ! Sequence record format +is_a: EDAM_format:1920 ! Sequence feature annotation format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:2555 ! Alignment format (XML) +is_a: EDAM_format:2571 ! Raw sequence format +relationship: is_format_of EDAM_data:0863 ! Sequence alignment +relationship: is_format_of EDAM_data:1255 ! Feature record +relationship: is_format_of EDAM_data:2044 ! Sequence [Term] -id: EDAM_data:2295 -name: Gene ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." [http://edamontology.org] -synonym: "Gene code" EXACT [http://edamontology.org] -synonym: "Gene accession" EXACT [http://edamontology.org] -is_a: EDAM_data:1025 ! Gene identifier -is_a: EDAM_data:1893 ! Locus ID +id: EDAM_format:2376 +name: RDF format +subset: bioinformatics +subset: edam +subset: formats +synonym: "SWO:3000006" EXACT [] +created_in: "beta12orEarlier" +def: "A serialisation format conforming to the Resource Description Framework (RDF) model." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2195 ! Ontology format +is_a: EDAM_format:2332 ! XML +[Term] +id: EDAM_format:2532 +name: GenBank-HTML +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Genbank entry format wrapped in HTML elements." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2331 ! HTML +is_a: EDAM_format:2559 ! GenBank-like format [Term] -id: EDAM_data:1891 -name: iHOP symbol -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of a protein or gene used in the iHOP database." [http://edamontology.org] -xref: Moby_namespace:iHOPsymbol -is_a: EDAM_data:2295 ! Gene ID -is_a: EDAM_data:2907 ! Protein accession -is_a: EDAM_data:2109 ! Identifier (hybrid) +id: EDAM_format:2542 +name: Protein features (domains) format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a report on protein features (domain composition)." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2350 ! Format (typed) +[Term] +id: EDAM_format:2543 +name: EMBL-like format +comment: This concept may be used for the many non-standard EMBL-like formats. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A format resembling EMBL entry (plain text) format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2202 ! Sequence record full format -! Suspect this identifiers more than just genes +[Term] +id: EDAM_format:2545 +name: FASTQ-like format +comment: This concept may be used for non-standard FASTQ short read-like formats. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A format resembling FASTQ short read format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2057 ! Sequence trace format [Term] -id: EDAM_data:1036 -name: TIGR identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the TIGR database." [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID -is_a: EDAM_data:2109 ! Identifier (hybrid) +id: EDAM_format:2546 +name: FASTA-like +comment: This concept may be used for the many non-standard FASTA-like formats. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A format resembling FASTA format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2203 ! Sequence record lite format [Term] -id: EDAM_data:1037 -name: TAIR accession (gene) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an gene from the TAIR database." [http://edamontology.org] -regex: "Gene:[0-9]{7}" -is_a: EDAM_data:2295 ! Gene ID -is_a: EDAM_data:2387 ! TAIR accession +id: EDAM_format:2547 +name: uniprotkb-like format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A sequence format resembling uniprotkb entry format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2202 ! Sequence record full format +is_a: EDAM_format:2206 ! Sequence feature table format (text) [Term] -id: EDAM_data:2388 -name: TAIR accession (At gene) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an Arabidopsis thaliana gene from the TAIR database." [http://edamontology.org] -is_a: EDAM_data:1037 ! TAIR accession (gene) +id: EDAM_format:2548 +name: Sequence feature table format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format for a sequence feature table." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1920 ! Sequence feature annotation format +relationship: is_format_of EDAM_data:1255 ! Feature record [Term] -id: EDAM_data:1806 -name: Gene synonym -namespace: identifier -subset: identifiers -subset: data -def: "Any name (other than the recommended one) for a gene." [http://edamontology.org] -synonym: "Gene name synonym" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2549 +name: OBO +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "OBO ontology text format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2196 ! OBO format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:2550 +name: OBO-XML +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "OBO ontology XML format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2196 ! OBO format +is_a: EDAM_format:2332 ! XML [Term] -id: EDAM_data:1807 -name: ORF name -namespace: identifier -subset: identifiers -subset: data -def: "The name of an open reading frame attributed by a sequencing project." [http://edamontology.org] -is_a: EDAM_data:2795 ! ORF identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_format:2551 +name: Sequence record format (text) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a molecular sequence record." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1919 ! Sequence record format +[Term] +id: EDAM_format:2552 +name: Sequence record format (XML) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a molecular sequence record." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1919 ! Sequence record format -! GeneFarm gene ID is also given +[Term] +id: EDAM_format:2553 +name: Sequence feature table format (XML) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "XML format for a sequence feature table." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2548 ! Sequence feature table format [Term] -id: EDAM_data:1892 -name: Gene name (GeneFarm) -namespace: identifier -subset: identifiers -subset: data -def: "Name of a gene from the GeneFarm database." [http://edamontology.org] -xref: Moby_namespace:GENEFARM_GeneName -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2554 +name: Alignment format (text) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Text format for molecular sequence alignment information." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1921 ! Alignment format +[Term] +id: EDAM_format:2555 +name: Alignment format (XML) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "XML format for molecular sequence alignment information." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1921 ! Alignment format [Term] -id: EDAM_data:1889 -name: Gene name (DragonDB) -namespace: identifier -subset: identifiers -subset: data -def: "The name of an Antirrhinum Gene from the DragonDB database." [http://edamontology.org] -xref: Moby_namespace:DragonDB_Gene -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2556 +name: Phylogenetic tree format (text) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Text format for a phylogenetic tree." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2006 ! Phylogenetic tree format +[Term] +id: EDAM_format:2557 +name: Phylogenetic tree format (XML) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "XML format for a phylogenetic tree." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2006 ! Phylogenetic tree format [Term] -id: EDAM_data:1890 -name: Gene name (Arabidopsis) -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." [http://edamontology.org] -xref: Moby_namespace:ArabidopsisGeneSymbol -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2558 +name: EMBL-like (XML) +comment: This concept may be used for the any non-standard EMBL-like XML formats. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "An XML format resembling EMBL entry format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:2543 ! EMBL-like format [Term] -id: EDAM_data:1783 -name: Gene name (ASPGD) -namespace: identifier -subset: identifiers -subset: data -def: "Name of a gene from Aspergillus Genome Database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2559 +name: GenBank-like format +comment: This concept may be used for the non-standard GenBank-like formats. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "A format resembling GenBank entry (plain text) format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2202 ! Sequence record full format [Term] -id: EDAM_data:1784 -name: Gene name (CGD) -namespace: identifier -subset: identifiers -subset: data -def: "Name of a gene from Candida Genome Database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2560 +name: STRING entry format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Entry format for the STRING database of protein interaction." [http://edamontology.org] +namespace: format +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM_data:1785 -name: Gene name (dictyBase) -namespace: identifier -subset: identifiers -subset: data -def: "Name of a gene from dictyBase database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2561 +name: Sequence assembly format (text) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Text format for sequence assembly data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2055 ! Sequence assembly format [Term] -id: EDAM_data:1786 -name: Gene name (EcoGene primary) -namespace: identifier -subset: identifiers -subset: data -def: "Primary name of a gene from EcoGene Database." [http://edamontology.org] -synonym: "EcoGene primary gene name" EXACT [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2562 +name: Amino acid identifier format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Text format (representation) of amino acid residues." [http://edamontology.org] +namespace: format +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_data:0994 ! Amino acid identifier [Term] -id: EDAM_data:1787 -name: Gene name (MaizeGDB) -namespace: identifier -subset: identifiers -subset: data -def: "Name of a gene from MaizeGDB (maize genes) database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2566 +name: completely unambiguous +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a molecular sequence without any unknown positions or ambiguity characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2571 ! Raw sequence format [Term] -id: EDAM_data:1788 -name: Gene name (SGD) -namespace: identifier -subset: identifiers -subset: data -def: "Name of a gene from Saccharomyces Genome Database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS -is_a: EDAM_data:1026 ! Gene symbol -is_a: EDAM_data:2632 ! SGD ID +id: EDAM_format:2567 +name: completely unambiguous pure +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2094 ! pure +is_a: EDAM_format:2566 ! completely unambiguous [Term] -id: EDAM_data:1789 -name: Gene name (TGD) -namespace: identifier -subset: identifiers -subset: data -def: "Name of a gene from Tetrahymena Genome Database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2568 +name: completely unambiguous pure nucleotide +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters ." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1207 ! nucleotide +is_a: EDAM_format:2567 ! completely unambiguous pure [Term] -id: EDAM_data:1790 -name: Gene name (CGSC) -namespace: identifier -subset: identifiers -subset: data -def: "Symbol of a gene from E.coli Genetic Stock Center." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2569 +name: completely unambiguous pure dna +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1212 ! dna +is_a: EDAM_format:2567 ! completely unambiguous pure [Term] -id: EDAM_data:1791 -name: Gene name (HGNC) -namespace: identifier -subset: identifiers -subset: data -def: "Symbol of a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org] -synonym: "Official gene name" EXACT [http://edamontology.org] -synonym: "Gene name (HUGO)" EXACT [http://edamontology.org] -synonym: "HGNC symbol" EXACT [http://edamontology.org] -synonym: "HUGO symbol" EXACT [http://edamontology.org] -synonym: "HGNC gene symbol" EXACT [http://edamontology.org] -synonym: "HUGO gene symbol" EXACT [http://edamontology.org] -synonym: "HUGO gene name" EXACT [http://edamontology.org] -synonym: "HGNC gene name" EXACT [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene -regex: "HGNC:[0-9]{1,5}" -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2570 +name: completely unambiguous pure rna sequence +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1213 ! rna +is_a: EDAM_format:2567 ! completely unambiguous pure [Term] -id: EDAM_data:1792 -name: Gene name (MGD) -namespace: identifier -subset: identifiers -subset: data -def: "Symbol of a gene from the Mouse Genome Database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD -regex: "MGI:[0-9]+" -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2571 +name: Raw sequence format +subset: bioinformatics +subset: edam +subset: formats +synonym: "Symbol_sequence" RELATED [] +created_in: "beta12orEarlier" +def: "Format of a raw molecular sequence (i.e. the alphabet used)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0848 ! Raw sequence [Term] -id: EDAM_data:1793 -name: Gene name (Bacillus subtilis) -namespace: identifier -subset: identifiers -subset: data -def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2572 +name: BAM +subset: bioinformatics +subset: edam +subset: formats +xref: http://samtools.sourceforge.net/SAM-1.3.pdf +created_in: "beta12orEarlier" +def: "BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [http://edamontology.org] +documentation: http://samtools.sourceforge.net/SAM-1.3.pdf +namespace: format +is_a: EDAM_format:1921 ! Alignment format +is_a: EDAM_format:2057 ! Sequence trace format +is_a: EDAM_format:2333 ! Binary format [Term] -id: EDAM_data:2103 -name: Gene name (KEGG GENES) -namespace: identifier -subset: identifiers -subset: data -def: "Name of an entry (gene) from the KEGG GENES database." [http://edamontology.org] -synonym: "KEGG GENES entry name" EXACT [http://edamontology.org] -xref: Moby_namespace:GeneId -regex: "[a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*" -is_a: EDAM_data:1026 ! Gene symbol -is_a: EDAM_data:1154 ! KEGG object identifier +id: EDAM_format:2573 +name: SAM +comment: The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. +subset: bioinformatics +subset: edam +subset: formats +xref: http://samtools.sourceforge.net/SAM-1.3.pdf +created_in: "beta12orEarlier" +def: "Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [http://edamontology.org] +documentation: http://samtools.sourceforge.net/SAM-1.3.pdf +namespace: format +is_a: EDAM_format:2057 ! Sequence trace format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] -id: EDAM_data:2296 -name: Gene name (AceView) -namespace: identifier -subset: identifiers -subset: data -def: "Name of an entry (gene) from the AceView genes database." [http://edamontology.org] -synonym: "AceView gene name" EXACT [http://edamontology.org] -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2585 +name: SBML +subset: bioinformatics +subset: edam +subset: formats +xref: http://sbml.org +created_in: "beta12orEarlier" +def: "Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation." [http://edamontology.org] +documentation: http://sbml.org +namespace: format +is_a: EDAM_format:2013 ! Biological pathway or network format +is_a: EDAM_format:2332 ! XML [Term] -id: EDAM_data:2300 -name: Gene name (NCBI) -namespace: identifier -subset: identifiers -subset: data -def: "Name of an entry (gene) from the NCBI genes database." [http://edamontology.org] -synonym: "NCBI gene name" EXACT [http://edamontology.org] -is_a: EDAM_data:1026 ! Gene symbol - +id: EDAM_format:2607 +name: completely unambiguous pure protein +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1208 ! protein +is_a: EDAM_format:2567 ! completely unambiguous pure [Term] -id: EDAM_data:2740 -name: Gene name (Genolist) -namespace: identifier -subset: identifiers -subset: data -def: "Name of an entry (gene) from the Genolist genes database." [http://edamontology.org] -synonym: "Genolist gene name" EXACT [http://edamontology.org] -is_a: EDAM_data:1026 ! Gene symbol +id: EDAM_format:2848 +name: Bibliographic reference format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a bibliographic reference." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0970 ! Bibliographic reference +relationship: is_format_of EDAM_data:2849 ! Abstract [Term] -id: EDAM_data:2743 -name: Gene name (HUGO) -namespace: identifier -subset: identifiers -subset: data -def: "Name of an entry (gene) from the HUGO database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1791 ! Gene name (HGNC) +id: EDAM_format:2919 +name: Sequence annotation track format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of a sequence annotation track." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1920 ! Sequence feature annotation format +relationship: is_format_of EDAM_data:3002 ! Sequence annotation track +[Term] +id: EDAM_format:2920 +name: Alignment format (pair only) +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:1921 ! Alignment format +relationship: is_format_of EDAM_data:1381 ! Sequence alignment (pair) [Term] -id: EDAM_data:2771 -name: HIX ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of gene cluster in the H-InvDB database." [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:2921 +name: Sequence variation annotation format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Format of sequence variation annotation." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0918 ! Nucleic acid features (variation) [Term] -id: EDAM_data:2737 -name: FIG ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of gene in the NMPDR database." [http://edamontology.org] -comment: A FIG ID consists of four parts: a prefix, genome id, locus type and id number. -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:2922 +name: markx0 variant +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Some variant of Pearson MARKX alignment format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:2774 -name: Gene ID (JCVI) -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI)." [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:2923 +name: mega variant +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Some variant of Mega format for (typically aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:2738 -name: Gene ID (Xenbase) -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of gene in the Xenbase database." [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:2924 +name: Phylip format variant +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Some variant of Phylip format for (aligned) sequences." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2551 ! Sequence record format (text) +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM_data:2799 -name: Gene ID (MfunGD) -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of gene in the MfunGD database." [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3000 +name: AB1 +comment: AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2057 ! Sequence trace format +is_a: EDAM_format:2333 ! Binary format +[Term] +id: EDAM_format:3001 +name: ACE +subset: bioinformatics +subset: edam +subset: formats +xref: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt +created_in: "beta12orEarlier" +def: "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." [http://edamontology.org] +documentation: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt +namespace: format +is_a: EDAM_format:2055 ! Sequence assembly format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2739 -name: Gene ID (Genolist) -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of gene in the Genolist database." [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3003 +name: BED +comment: BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). +subset: bioinformatics +subset: edam +subset: formats +xref: format1 +created_in: "beta12orEarlier" +def: "Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser." [http://edamontology.org] +documentation: "format1" +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2919 ! Sequence annotation track format +[Term] +id: EDAM_format:3004 +name: bigBed +subset: bioinformatics +subset: edam +subset: formats +xref: format1.5 +created_in: "beta12orEarlier" +def: "bigBed format for large sequence annotation tracks, similar to textual BED format." [http://edamontology.org] +documentation: "format1.5" +namespace: format +is_a: EDAM_format:2333 ! Binary format +is_a: EDAM_format:2919 ! Sequence annotation track format [Term] -id: EDAM_data:1028 -name: Gene identifier (NCBI RefSeq) -namespace: identifier -subset: identifiers -subset: data -def: "An NCBI RefSeq unique identifier of a gene." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1027 ! Gene ID (NCBI) +id: EDAM_format:3005 +name: WIG +subset: bioinformatics +subset: edam +subset: formats +xref: http://genome.ucsc.edu/goldenPath/help/wiggle.html +created_in: "beta12orEarlier" +def: "Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser." [http://edamontology.org] +documentation: http://genome.ucsc.edu/goldenPath/help/wiggle.html +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2919 ! Sequence annotation track format [Term] -id: EDAM_data:1029 -name: Gene identifier (NCBI UniGene) -namespace: identifier -subset: identifiers -subset: data -def: "An NCBI UniGene unique identifier of a gene." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1104 ! Sequence cluster ID (UniGene) +id: EDAM_format:3006 +name: bigWig +subset: bioinformatics +subset: edam +subset: formats +xref: format6.1 +created_in: "beta12orEarlier" +def: "bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format." [http://edamontology.org] +documentation: "format6.1" +namespace: format +is_a: EDAM_format:2333 ! Binary format +is_a: EDAM_format:2919 ! Sequence annotation track format [Term] -id: EDAM_data:1030 -name: Gene identifier (Entrez) -namespace: identifier -subset: identifiers -subset: data -def: "An Entrez unique identifier of a gene." [http://edamontology.org] -regex: "[0-9]+" -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1027 ! Gene ID (NCBI) +id: EDAM_format:3007 +name: PSL +subset: bioinformatics +subset: edam +subset: formats +xref: format2 +created_in: "beta12orEarlier" +def: "PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track." [http://edamontology.org] +documentation: "format2" +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2919 ! Sequence annotation track format +is_a: EDAM_format:2920 ! Alignment format (pair only) +[Term] +id: EDAM_format:3008 +name: MAF +comment: Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. +subset: bioinformatics +subset: edam +subset: formats +xref: format5 +created_in: "beta12orEarlier" +def: "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth." [http://edamontology.org] +documentation: "format5" +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2554 ! Alignment format (text) +is_a: EDAM_format:2919 ! Sequence annotation track format [Term] -id: EDAM_data:1886 -name: Blattner number -namespace: identifier -subset: identifiers -subset: data -def: "The blattner identifier for a gene." [http://edamontology.org] -xref: Moby_namespace:Blattner_number -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3009 +name: 2bit +subset: bioinformatics +subset: edam +subset: formats +xref: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD +xref: http://jcomeau.freeshell.org/www/genome/2bitformat.html +created_in: "beta12orEarlier" +def: "2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'." [http://edamontology.org] +documentation: http://jcomeau.freeshell.org/www/genome/2bitformat.html +namespace: format +is_a: EDAM_format:2333 ! Binary format +is_a: EDAM_format:2571 ! Raw sequence format [Term] -id: EDAM_data:1027 -name: Gene ID (NCBI) -namespace: identifier -subset: identifiers -subset: data -def: "An NCBI unique identifier of a gene." [http://edamontology.org] -synonym: "Gene identifier (NCBI)" EXACT [http://edamontology.org] -synonym: "NCBI gene ID" EXACT [http://edamontology.org] -synonym: "NCBI geneid" EXACT [http://edamontology.org] -synonym: "Gene identifier (Entrez)" EXACT [http://edamontology.org] -synonym: "Entrez gene ID" EXACT [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene -xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID -is_a: EDAM_data:2295 ! Gene ID -is_a: EDAM_data:1098 ! RefSeq accession +id: EDAM_format:3010 +name: .nib +subset: bioinformatics +subset: edam +subset: formats +xref: format8 +created_in: "beta12orEarlier" +def: ".nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'." [http://edamontology.org] +documentation: "format8" +namespace: format +is_a: EDAM_format:2333 ! Binary format +is_a: EDAM_format:2571 ! Raw sequence format [Term] -id: EDAM_data:1031 -name: Gene ID (CGD) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a gene or feature from the CGD database." [http://edamontology.org] -synonym: "CGD ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3011 +name: genePred +comment: genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. +subset: bioinformatics +subset: edam +subset: formats +xref: format9 +created_in: "beta12orEarlier" +def: "genePred table format for gene prediction tracks." [http://edamontology.org] +documentation: "format9" +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2919 ! Sequence annotation track format +[Term] +id: EDAM_format:3012 +name: pgSnp +subset: bioinformatics +subset: edam +subset: formats +xref: format10 +created_in: "beta12orEarlier" +def: "Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser." [http://edamontology.org] +documentation: "format10" +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2919 ! Sequence annotation track format [Term] -id: EDAM_data:1032 -name: Gene ID (DictyBase) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a gene from DictyBase." [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3013 +name: axt +subset: bioinformatics +subset: edam +subset: formats +xref: http://genome.ucsc.edu/goldenPath/help/axt.html +created_in: "beta12orEarlier" +def: "axt format of alignments, typically produced from BLASTZ." [http://edamontology.org] +documentation: http://genome.ucsc.edu/goldenPath/help/axt.html +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2920 ! Alignment format (pair only) +[Term] +id: EDAM_format:3014 +name: LAV +subset: bioinformatics +subset: edam +subset: formats +xref: lav:format.html +created_in: "beta12orEarlier" +def: "LAV format of alignments generated by BLASTZ and LASTZ." [http://edamontology.org] +documentation: lav:format.html +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] -id: EDAM_data:1033 -name: Gene ID (Ensembl) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier for a gene (or other feature) from the Ensembl database." [http://edamontology.org] -synonym: "Ensembl Gene ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID -is_a: EDAM_data:2610 ! Ensembl ID +id: EDAM_format:3015 +name: Pileup +subset: bioinformatics +subset: edam +subset: formats +xref: http://samtools.sourceforge.net/pileup.shtml +created_in: "beta12orEarlier" +def: "Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s)." [http://edamontology.org] +documentation: http://samtools.sourceforge.net/pileup.shtml +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2920 ! Alignment format (pair only) +[Term] +id: EDAM_format:3016 +name: VCF +subset: bioinformatics +subset: edam +subset: formats +xref: http://vcftools.sourceforge.net/specs.html +created_in: "beta12orEarlier" +def: "Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org] +documentation: http://vcftools.sourceforge.net/specs.html +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2921 ! Sequence variation annotation format [Term] -id: EDAM_data:1034 -name: Gene ID (SGD) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the SGD database." [http://edamontology.org] -synonym: "SGD identifier" EXACT [http://edamontology.org] -regex: "S[0-9]+" -is_a: EDAM_data:2295 ! Gene ID -is_a: EDAM_data:2632 ! SGD ID +id: EDAM_format:3017 +name: SRF +subset: bioinformatics +subset: edam +subset: formats +xref: http://srf.sourceforge.net/ +created_in: "beta12orEarlier" +def: "Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive." [http://edamontology.org] +documentation: http://srf.sourceforge.net/ +namespace: format +is_a: EDAM_format:2057 ! Sequence trace format +is_a: EDAM_format:2333 ! Binary format +[Term] +id: EDAM_format:3018 +name: ZTR +subset: bioinformatics +subset: edam +subset: formats +xref: http://staden.sourceforge.net/manual/formats_unix_12.html +created_in: "beta12orEarlier" +def: "ZTR format for storing chromatogram data from DNA sequencing instruments." [http://edamontology.org] +documentation: http://staden.sourceforge.net/manual/formats_unix_12.html +namespace: format +is_a: EDAM_format:2057 ! Sequence trace format +is_a: EDAM_format:2333 ! Binary format [Term] -id: EDAM_data:1885 -name: Gene ID (GeneFarm) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a gene from the GeneFarm database." [http://edamontology.org] -xref: Moby_namespace:GENEFARM_GeneID -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3019 +name: GVF +subset: bioinformatics +subset: edam +subset: formats +xref: http://sequenceontology.org/gvf.html +created_in: "beta12orEarlier" +def: "Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation." [http://edamontology.org] +documentation: http://sequenceontology.org/gvf.html +namespace: format +is_a: EDAM_format:1975 ! GFF3 +is_a: EDAM_format:2921 ! Sequence variation annotation format +[Term] +id: EDAM_format:3020 +name: BCF +subset: bioinformatics +subset: edam +subset: formats +xref: http://samtools.sourceforge.net/mpileup.shtml +created_in: "beta12orEarlier" +def: "BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2333 ! Binary format +is_a: EDAM_format:2921 ! Sequence variation annotation format [Term] -id: EDAM_data:1907 -name: Gene ID (KOME) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a gene from the KOME database." [http://edamontology.org] -xref: Moby_namespace:GeneId -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3033 +name: Matrix format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta13" +def: "Format of a matrix (array) of numerical values." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:2082 ! Matrix +[Term] +id: EDAM_format:3097 +name: Protein domain classification format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta13" +def: "Format of data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:0900 ! Protein domain classification [Term] -id: EDAM_data:1794 -name: Gene ID (PlasmoDB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3098 +name: Raw SCOP domain classification format +comment: These are the parsable data files provided by SCOP. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta13" +def: "Format of raw SCOP domain classification data files." [http://edamontology.org] +namespace: format +is_a: EDAM_format:3097 ! Protein domain classification format +[Term] +id: EDAM_format:3099 +name: Raw CATH domain classification format +comment: These are the parsable data files provided by CATH. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta13" +def: "Format of raw CATH domain classification data files." [http://edamontology.org] +namespace: format +is_a: EDAM_format:3097 ! Protein domain classification format [Term] -id: EDAM_data:1795 -name: Gene ID (EcoGene) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a gene from EcoGene Database." [http://edamontology.org] -synonym: "EcoGene Accession" EXACT [http://edamontology.org] -synonym: "EcoGene ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3100 +name: CATH domain report format +comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta13" +def: "Format of summary of domain classification information for a CATH domain." [http://edamontology.org] +namespace: format +is_a: EDAM_format:3097 ! Protein domain classification format +[Term] +id: EDAM_format:3155 +name: SBRML +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.comp-sys-bio.org/tiki-index.php?page=SBRML +created_in: "1.0" +def: "Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models." [http://edamontology.org] +documentation: http://www.comp-sys-bio.org/tiki-index.php?page=SBRML +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:3166 ! Biological pathway or network report format [Term] -id: EDAM_data:2297 -name: Gene ID (ECK) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an E. coli K-12 gene from EcoGene Database." [http://edamontology.org] -synonym: "E. coli K-12 gene identifier" EXACT [http://edamontology.org] -synonym: "ECK accession" EXACT [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK -is_a: EDAM_data:1795 ! Gene ID (EcoGene) +id: EDAM_format:3156 +name: BioPAX +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.biopax.org +created_in: "1.0" +def: "BioPAX is an exchange format for pathway data, with its data model defined in OWL." [http://edamontology.org] +documentation: http://www.biopax.org +namespace: format +is_a: EDAM_format:2013 ! Biological pathway or network format [Term] -id: EDAM_data:1796 -name: Gene ID (FlyBase) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier from FlyBase database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB -xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3157 +name: EBI Application Result XML +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.ebi.ac.uk/schema/ApplicationResult.xsd +created_in: "1.0" +def: "EBI Application Result XML is a format returned by sequence similarity search Web services at EBI." [http://edamontology.org] +documentation: http://www.ebi.ac.uk/schema/ApplicationResult.xsd +namespace: format +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] -id: EDAM_data:1802 -name: Gene ID (Gramene) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier from Gramene database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene -xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3158 +name: PSI MI XML (MIF) +subset: bioinformatics +subset: edam +subset: formats +synonym: "MIF" EXACT [] +xref: http://www.psidev.info/mif +created_in: "1.0" +def: "XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI." [http://edamontology.org] +documentation: http://www.psidev.info/mif +namespace: format +is_a: EDAM_format:2054 ! Molecular interaction format +is_a: EDAM_format:2332 ! XML +[Term] +id: EDAM_format:3159 +name: phyloXML +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.phyloxml.org +created_in: "1.0" +def: "phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data." [http://edamontology.org] +documentation: http://www.phyloxml.org +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:2557 ! Phylogenetic tree format (XML) [Term] -id: EDAM_data:1803 -name: Gene ID (Virginia microbial) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier from Virginia Bioinformatics Institute microbial database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD -xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3160 +name: NeXML +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.nexml.org +created_in: "1.0" +def: "NeXML is a standardised XML format for rich phyloinformatic data." [http://edamontology.org] +documentation: http://www.nexml.org +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:2557 ! Phylogenetic tree format (XML) +[Term] +id: EDAM_format:3161 +name: MAGE-ML +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.mged.org/Workgroups/MAGE/mage-ml.html +created_in: "1.0" +def: "MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org] +documentation: http://www.mged.org/Workgroups/MAGE/mage-ml.html +namespace: format +is_a: EDAM_format:2056 ! Microarray experiment data format +is_a: EDAM_format:2058 ! Gene expression report format +is_a: EDAM_format:2332 ! XML [Term] -id: EDAM_data:1804 -name: Gene ID (SGN) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier from Sol Genomics Network." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3162 +name: MAGE-TAB +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.mged.org/mage-tab +created_in: "1.0" +def: "MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org] +documentation: http://www.mged.org/mage-tab +namespace: format +is_a: EDAM_format:2056 ! Microarray experiment data format +is_a: EDAM_format:2058 ! Gene expression report format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:3163 +name: GCDML +subset: bioinformatics +subset: edam +subset: formats +xref: http://gcdml.gensc.org +created_in: "1.0" +def: "GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC)." [http://edamontology.org] +documentation: http://gcdml.gensc.org +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:3167 ! Experiment annotation format +relationship: is_format_of EDAM_data:3165 ! Experiment annotation (sequencing) [Term] -id: EDAM_data:1805 -name: Gene ID (WormBase) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier used by WormBase database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB -xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase -regex: "WBGene[0-9]{8}" -is_a: EDAM_data:2295 ! Gene ID -is_a: EDAM_data:2113 ! WormBase identifier +id: EDAM_format:3164 +name: GTrack +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.gtrack.no +created_in: "1.0" +def: "GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG)." [http://edamontology.org] +documentation: http://www.gtrack.no +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2919 ! Sequence annotation track format +[Term] +id: EDAM_format:3166 +name: Biological pathway or network report format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for a report of information derived from a biological pathway or network." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:2984 ! Pathway or network report [Term] -id: EDAM_data:1035 -name: Gene ID (GeneDB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a gene from the GeneDB database." [http://edamontology.org] -synonym: "GeneDB identifier" EXACT [http://edamontology.org] -xref: Moby_namespace:GeneDB -regex: "[a-zA-Z_0-9\.-]*" -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3167 +name: Experiment annotation format +subset: bioinformatics +subset: edam +subset: formats +created_in: "beta12orEarlier" +def: "Data format for annotation on a laboratory experiment." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +[Term] +id: EDAM_format:3235 +name: Cytoband format +comment: Reflects a UCSC Browser DB table. +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.broadinstitute.org/software/igv/Cytoband +created_in: "1.2" +def: "Cytoband format for chromosome cytobands." [http://edamontology.org] +documentation: http://www.broadinstitute.org/software/igv/Cytoband +namespace: format +is_a: EDAM_format:2078 ! Sequence range format +is_a: EDAM_format:2330 ! Textual format +relationship: is_format_of EDAM_data:3236 ! Cytoband position [Term] -id: EDAM_data:2285 -name: Gene ID (MIPS) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for genetic elements in MIPS database." [http://edamontology.org] -synonym: "MIPS genetic element identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3239 +name: CopasiML +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.copasi.org/tiki-index.php?page_ref_id=128 +created_in: "1.2" +def: "CopasiML, the native format of COPASI." [http://edamontology.org] +documentation: http://www.copasi.org/tiki-index.php?page_ref_id=128 +namespace: format +is_a: EDAM_format:2013 ! Biological pathway or network format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:3166 ! Biological pathway or network report format [Term] -id: EDAM_data:2298 -name: Gene ID (HGNC) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org] -synonym: "HGNC ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3240 +name: CellML +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.cellml.org +created_in: "1.2" +def: "CellML, the format for mathematical models of biological and other networks." [http://edamontology.org] +documentation: http://www.cellml.org +namespace: format +is_a: EDAM_format:2013 ! Biological pathway or network format +is_a: EDAM_format:2332 ! XML +[Term] +id: EDAM_format:3242 +name: PSI MI TAB (MITAB) +subset: bioinformatics +subset: edam +subset: formats +xref: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README +created_in: "1.2" +def: "Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI." [http://edamontology.org] +documentation: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README +namespace: format +is_a: EDAM_format:2054 ! Molecular interaction format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:2642 -name: Gene ID (miRBase) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for a gene from the miRBase database." [http://edamontology.org] -synonym: "miRNA name" EXACT [http://edamontology.org] -synonym: "miRNA identifier" EXACT [http://edamontology.org] -synonym: "miRNA ID" EXACT [http://edamontology.org] -regex: "MI[0-9]{7}" -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3243 +name: PSI-PAR +subset: bioinformatics +subset: edam +subset: formats +xref: http://www.psidev.info/psi-par +created_in: "1.2" +def: "Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema." [http://edamontology.org] +documentation: http://www.psidev.info/psi-par +namespace: format +is_a: EDAM_format:3158 ! PSI MI XML (MIF) [Term] -id: EDAM_data:2643 -name: Gene ID (ZFIN) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for a gene from the Zebrafish information network genome (ZFIN) database." [http://edamontology.org] -regex: "ZDB\-GENE\-[0-9]+\-[0-9]+" -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3244 +name: mzML +comment: mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. +subset: bioinformatics +subset: edam +subset: formats +xref: http://psidev.info/mzml +created_in: "1.2" +def: "mzML format for raw spectrometer output data, standardised by HUPO PSI MSS." [http://edamontology.org] +documentation: http://psidev.info/mzml +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:3245 ! Mass spectrometry data format [Term] -id: EDAM_data:2759 -name: Gene ID (VectorBase) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for a gene from the VectorBase database." [http://edamontology.org] -synonym: "VectorBase ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3245 +name: Mass spectrometry data format +subset: bioinformatics +subset: edam +subset: formats +created_in: "1.2" +def: "Format for mass spectrometry data." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2350 ! Format (typed) +relationship: is_format_of EDAM_data:2536 ! Mass spectrometry data +[Term] +id: EDAM_format:3246 +name: TraML +subset: bioinformatics +subset: edam +subset: formats +xref: http://psidev.info/traml +created_in: "1.2" +def: "TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS." [http://edamontology.org] +documentation: http://psidev.info/traml +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:3245 ! Mass spectrometry data format [Term] -id: EDAM_data:2835 -name: Gene ID (VBASE2) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for a gene from the VBASE2 database." [http://edamontology.org] -synonym: "VBASE2 ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_format:3247 +name: mzIdentML +subset: bioinformatics +subset: edam +subset: formats +xref: http://psidev.info/mzidentml +created_in: "1.2" +def: "mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines." [http://edamontology.org] +documentation: http://psidev.info/mzidentml +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:3245 ! Mass spectrometry data format +[Term] +id: EDAM_format:3248 +name: mzQuantML +subset: bioinformatics +subset: edam +subset: formats +xref: http://psidev.info/mzquantml +created_in: "1.2" +def: "mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics." [http://edamontology.org] +documentation: http://psidev.info/mzquantml +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:3245 ! Mass spectrometry data format [Term] -id: EDAM_data:1797 -name: Gene ID (GeneDB Glossina morsitans) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier from Glossina morsitans GeneDB database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans -is_obsolete: true !{since=beta13} -consider: EDAM_data:1035 ! Gene ID (GeneDB) +id: EDAM_format:3249 +name: GelML +subset: bioinformatics +subset: edam +subset: formats +xref: http://psidev.info/gelml +created_in: "1.2" +def: "GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS." [http://edamontology.org] +documentation: http://psidev.info/gelml +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:3167 ! Experiment annotation format +relationship: is_format_of EDAM_data:3147 ! Experiment annotation (mass spectrometry) +[Term] +id: EDAM_format:3250 +name: spML +subset: bioinformatics +subset: edam +subset: formats +xref: http://psidev.info +created_in: "1.2" +def: "spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics." [http://edamontology.org] +documentation: http://psidev.info +namespace: format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:3167 ! Experiment annotation format +relationship: is_format_of EDAM_data:3147 ! Experiment annotation (mass spectrometry) [Term] -id: EDAM_data:1798 -name: Gene ID (GeneDB Leishmania major) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier from Leishmania major GeneDB database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor -is_obsolete: true !{since=beta13} -consider: EDAM_data:1035 ! Gene ID (GeneDB) +id: EDAM_format:3252 +name: OWL Functional Syntax +subset: bioinformatics +subset: edam +subset: formats +created_in: "1.2" +def: "A human-readable encoding for the Web Ontology Language (OWL)." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2197 ! OWL format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:3253 +name: Manchester OWL Syntax +comment: This format was influenced by the OWL Abstract Syntax and the DL style syntax. +subset: bioinformatics +subset: edam +subset: formats +created_in: "1.2" +def: "A syntax for writing OWL class expressions." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2197 ! OWL format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM_data:1799 -name: Gene ID (GeneDB Plasmodium falciparum) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier from Plasmodium falciparum GeneDB database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum -is_obsolete: true !{since=beta13} -consider: EDAM_data:1035 ! Gene ID (GeneDB) +id: EDAM_format:3254 +name: KRSS2 Syntax +comment: This format is used in Protege 4. +subset: bioinformatics +subset: edam +subset: formats +created_in: "1.2" +def: "A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort"." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2195 ! Ontology format +is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_format:3255 +name: Turtle +comment: The SPARQL Query Language incorporates a very similar syntax. +subset: bioinformatics +subset: edam +subset: formats +created_in: "1.2" +def: "The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2376 ! RDF format [Term] -id: EDAM_data:1800 -name: Gene ID (GeneDB Schizosaccharomyces pombe) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe -is_obsolete: true !{since=beta13} -consider: EDAM_data:1035 ! Gene ID (GeneDB) +id: EDAM_format:3256 +name: N-Triples +comment: N-Triples should not be confused with Notation 3 which is a superset of Turtle. +subset: bioinformatics +subset: edam +subset: formats +created_in: "1.2" +def: "A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2376 ! RDF format +[Term] +id: EDAM_format:3257 +name: Notation3 +subset: bioinformatics +subset: edam +subset: formats +synonym: "N3" EXACT [] +created_in: "1.2" +def: "A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2330 ! Textual format +is_a: EDAM_format:2376 ! RDF format [Term] -id: EDAM_data:1801 -name: Gene ID (GeneDB Trypanosoma brucei) -namespace: identifier -subset: identifiers -subset: data -def: "Gene identifier from Trypanosoma brucei GeneDB database." [http://edamontology.org] -xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei -is_obsolete: true !{since=beta13} -consider: EDAM_data:1035 ! Gene ID (GeneDB) +id: EDAM_format:3261 +name: RDF/XML +comment: RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. +subset: bioinformatics +subset: edam +subset: formats +synonym: "RDF" EXACT [] +synonym: "SWO:3000006" EXACT [] +created_in: "beta12orEarlier" +def: "Resource Description Framework (RDF) XML format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2197 ! OWL format +is_a: EDAM_format:2332 ! XML +is_a: EDAM_format:2376 ! RDF format [Term] -id: EDAM_data:1887 -name: Gene ID (MIPS Maize) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for genetic elements in MIPS Maize database." [http://edamontology.org] -synonym: "MIPS genetic element identifier (Maize)" EXACT [http://edamontology.org] -xref: Moby_namespace:MIPS_GE_Maize -is_obsolete: true !{since=beta13} -consider: EDAM_data:2285 ! Gene ID (MIPS) +id: EDAM_format:3262 +name: OWL/XML +subset: bioinformatics +subset: edam +subset: formats +synonym: "OWL" EXACT [] +created_in: "beta12orEarlier" +def: "OWL ontology XML serialisation format." [http://edamontology.org] +namespace: format +is_a: EDAM_format:2197 ! OWL format +is_a: EDAM_format:2332 ! XML +[Term] +id: EDAM_operation:0004 +name: Operation +subset: bioinformatics +subset: edam +subset: operations +synonym: "Computational method" NARROW [] +synonym: "Computational operation" NARROW [] +synonym: "Computational procedure" NARROW [] +synonym: "Computational subroutine" NARROW [] +synonym: "Computational tool" RELATED [] +synonym: "Continuant" BROAD [] +synonym: "Function" BROAD [] +synonym: "Function" BROAD [] +synonym: "Function" BROAD [] +synonym: "Function" RELATED [] +synonym: "Function (programming)" NARROW [] +synonym: "Function:(mathematics)" NARROW [] +synonym: "http://en.wikipedia.org/wiki/Function_(computer_science)" NARROW [] +synonym: "http://en.wikipedia.org/wiki/Subroutine" NARROW [] +synonym: "Lambda abstraction" NARROW [] +synonym: "Mathematical function" NARROW [] +synonym: "Mathematical operation" NARROW [] +synonym: "Method" RELATED [] +synonym: "WSIO_operation:001" EXACT [] +synonym: "Perpetuant" RELATED [] +synonym: "Process" RELATED [] +synonym: "Process" RELATED [] +synonym: "process" RELATED [] +synonym: "Quality" RELATED [] +synonym: "quality" RELATED [] +synonym: "SIO:000017" BROAD [] +synonym: "SIO:000649" RELATED [] +synonym: "sumo:Function" RELATED [] +synonym: "SWO:0000003" RELATED [] +created_in: "beta12orEarlier" +def: "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state." [http://edamontology.org] +namespace: operation +disjoint_from: EDAM_topic:0003 ! Topic [Term] -id: EDAM_data:1888 -name: Gene ID (MIPS Medicago) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier for genetic elements in MIPS Medicago database." [http://edamontology.org] -synonym: "MIPS genetic element identifier (Medicago)" EXACT [http://edamontology.org] -xref: Moby_namespace:MIPS_GE_Medicago -is_obsolete: true !{since=beta13} -consider: EDAM_data:2285 ! Gene ID (MIPS) +id: EDAM_operation:0224 +name: Search and retrieval +subset: bioinformatics +subset: edam +subset: operations +synonym: "Database retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Search or query a data resource and retrieve entries and / or annotation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation +relationship: has_output EDAM_data:0006 ! Data +relationship: has_topic EDAM_topic:0090 ! Data search and retrieval [Term] -id: EDAM_data:2751 -name: GenomeReviews ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a particular genome." [http://edamontology.org] -is_a: EDAM_data:2903 ! Genome accession +id: EDAM_operation:0225 +name: Data retrieval (database cross-reference) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search database to retrieve all relevant references to a particular entity or entry." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval +[Term] +id: EDAM_operation:0226 +name: Annotation +comment: This is a broad concept and is used a placeholder for other, more specific concepts. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation +relationship: has_input EDAM_data:0582 ! Ontology +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] -id: EDAM_data:2786 -name: NCBI Genome Project ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a genome project assigned by NCBI." [http://edamontology.org] -is_a: EDAM_data:2903 ! Genome accession +id: EDAM_operation:0227 +name: Data indexing +subset: bioinformatics +subset: edam +subset: operations +synonym: "Database indexing" EXACT [] +created_in: "beta12orEarlier" +def: "Generate an index of (typically a file of) biological data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2412 ! Data index processing +relationship: has_output EDAM_data:0955 ! Data index +[Term] +id: EDAM_operation:0228 +name: Data index analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Database index analysis" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse an index of biological data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2412 ! Data index processing +relationship: has_input EDAM_data:0955 ! Data index +relationship: has_output EDAM_data:0956 ! Data index report [Term] -id: EDAM_data:2787 -name: NCBI genome accession -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of a whole genome assigned by the NCBI." [http://edamontology.org] -is_a: EDAM_data:2903 ! Genome accession +id: EDAM_operation:0229 +name: Annotation retrieval (sequence) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Retrieve basic information about a molecular sequence." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:1813 ! Sequence retrieval +[Term] +id: EDAM_operation:0230 +name: Sequence generation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a molecular sequence by some means." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2121 ! Sequence file processing [Term] -id: EDAM_data:2631 -name: ACLAME ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a mobile genetic element from the Aclame database." [http://edamontology.org] -regex: "mge:[0-9]+" -is_a: EDAM_data:2630 ! Mobile genetic element ID +id: EDAM_operation:0231 +name: Sequence editing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Edit or change a molecular sequence, either randomly or specifically." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2121 ! Sequence file processing +is_a: EDAM_operation:3096 ! Editing [Term] -id: EDAM_data:2128 -name: Genetic code name -namespace: identifier -subset: identifiers -subset: data -def: "Informal name for a genetic code, typically an organism name." [http://edamontology.org] -is_a: EDAM_data:2127 ! Genetic code identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_operation:0232 +name: Sequence merging +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence splicing" EXACT [] +created_in: "beta12orEarlier" +def: "Merge two or more (typically overlapping) molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0231 ! Sequence editing +[Term] +id: EDAM_operation:0233 +name: Sequence conversion +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Convert a molecular sequence from one type to another." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0231 ! Sequence editing [Term] -id: EDAM_data:1039 -name: SCOP domain identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein domain (or other node) from the SCOP database." [http://edamontology.org] -is_a: EDAM_data:1038 ! Protein domain ID -relationship: is_identifier_of EDAM_data:1554 ! SCOP node +id: EDAM_operation:0234 +name: Sequence complexity calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0236 ! Sequence composition calculation +relationship: has_output EDAM_data:1259 ! Sequence complexity +relationship: has_topic EDAM_topic:0642 ! Low complexity sequences [Term] -id: EDAM_data:2700 -name: CATH identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein domain (or other node) from the CATH database." [http://edamontology.org] -is_a: EDAM_data:1038 ! Protein domain ID -relationship: is_identifier_of EDAM_data:1553 ! CATH node +id: EDAM_operation:0235 +name: Sequence ambiguity calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0236 ! Sequence composition calculation +relationship: has_output EDAM_data:1260 ! Sequence ambiguity +relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis +[Term] +id: EDAM_operation:0236 +name: Sequence composition calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate character or word composition or frequency of a molecular sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2403 ! Sequence analysis +relationship: has_output EDAM_data:1261 ! Sequence composition +relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] -id: EDAM_data:2666 -name: CDD ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a conserved domain from the Conserved Domain Database." [http://edamontology.org] -regex: "cd[0-9]{5}" -is_a: EDAM_data:1038 ! Protein domain ID +id: EDAM_operation:0237 +name: Repeat sequence analysis +comment: Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Find and/or analyse repeat sequences in (typically nucleotide) sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2403 ! Sequence analysis +relationship: has_topic EDAM_topic:0641 ! Repeat sequences [Term] -id: EDAM_data:1041 -name: SCOP concise classification string (sccs) -namespace: identifier -subset: identifiers -subset: data -def: "A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification." [http://edamontology.org] -comment: An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. -is_a: EDAM_data:1039 ! SCOP domain identifier +id: EDAM_operation:0238 +name: Sequence motif discovery +comment: Motifs and patterns might be conserved or over-represented (occur with improbable frequency). +subset: bioinformatics +subset: edam +subset: operations +synonym: "Motif discovery" EXACT [] +created_in: "beta12orEarlier" +def: "Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0253 ! Feature prediction +is_a: EDAM_operation:2404 ! Sequence motif processing +relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_data:1042 -name: SCOP sunid -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229." [http://edamontology.org] -comment: A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. -example: "33229" -synonym: "sunid" EXACT [http://edamontology.org] -synonym: "SCOP unique identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:1039 ! SCOP domain identifier +id: EDAM_operation:0239 +name: Sequence motif recognition +subset: bioinformatics +subset: edam +subset: operations +synonym: "Motif detection" EXACT [] +synonym: "Motif recognition" EXACT [] +synonym: "Sequence motif detection" EXACT [] +created_in: "beta12orEarlier" +def: "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0253 ! Feature prediction +is_a: EDAM_operation:2404 ! Sequence motif processing +relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_data:1040 -name: CATH domain ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein domain from CATH." [http://edamontology.org] -example: "1nr3A00" -synonym: "CATH domain identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:2700 ! CATH identifier +id: EDAM_operation:0240 +name: Sequence motif comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Find motifs shared by molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2404 ! Sequence motif processing +is_a: EDAM_operation:2451 ! Sequence comparison +relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_data:1043 -name: CATH node ID -namespace: identifier -subset: identifiers -subset: data -def: "A code number identifying a node from the CATH database." [http://edamontology.org] -example: "3.30.1190.10.1.1.1.1.1" -synonym: "CATH code" EXACT [http://edamontology.org] -synonym: "CATH node identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:2700 ! CATH identifier +id: EDAM_operation:0241 +name: Transcription regulatory sequence analysis +comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] -id: EDAM_data:2701 -name: CATH node ID (family) -namespace: identifier -subset: identifiers -subset: data -def: "A code number identifying a family from the CATH database." [http://edamontology.org] -example: "2.10.10.10" -is_a: EDAM_data:1043 ! CATH node ID -relationship: is_identifier_of EDAM_data:1553 ! CATH node +id: EDAM_operation:0242 +name: Conserved transcription regulatory sequence identification +comment: For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction +relationship: has_output EDAM_data:1315 ! Gene features (TFBS) [Term] -id: EDAM_data:2619 -name: RESID ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein modification catalogued in the RESID database." [http://edamontology.org] -regex: "AA[0-9]{4}" -is_a: EDAM_data:2618 ! Protein modification ID +id: EDAM_operation:0243 +name: Protein property calculation (from structure) +comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein structural property calculation" EXACT [] +created_in: "beta12orEarlier" +def: "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0250 ! Protein property calculation +is_a: EDAM_operation:2406 ! Protein structure analysis +relationship: has_output EDAM_data:0897 ! Protein property +relationship: has_topic EDAM_topic:2814 ! Protein structure analysis [Term] -id: EDAM_data:2892 -name: Cell type name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a type or group of cells." [http://edamontology.org] -is_a: EDAM_data:2655 ! Cell type identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_operation:0244 +name: Protein flexibility and motion analysis +comment: Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse flexibility and motion in protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0243 ! Protein property calculation (from structure) +is_a: EDAM_operation:2476 ! Molecular dynamics simulation +relationship: has_output EDAM_data:1541 ! Protein flexibility or motion report [Term] -id: EDAM_data:2656 -name: NeuronDB ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of a neuron from the NeuronDB database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2893 ! Cell type accession +id: EDAM_operation:0245 +name: Protein structural motif recognition +comment: This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein structural feature identification" EXACT [] +created_in: "beta12orEarlier" +def: "Identify or screen for 3D structural motifs in protein structure(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) +relationship: has_output EDAM_data:0899 ! Protein features (3D motif) +relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces [Term] -id: EDAM_data:2657 -name: NeuroMorpho ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of a neuron from the NeuroMorpho database." [http://edamontology.org] -regex: "[a-zA-Z_0-9]+" -is_a: EDAM_data:2893 ! Cell type accession - +id: EDAM_operation:0246 +name: Protein domain recognition +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) +relationship: has_output EDAM_data:0901 ! Protein features (domains) +relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] -id: EDAM_data:1868 -name: Taxon -namespace: identifier -subset: identifiers -subset: data -def: "The name of a group of organisms belonging to the same taxonomic rank." [http://edamontology.org] -comment: For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. -synonym: "Taxonomy rank" EXACT [http://edamontology.org] -synonym: "Taxonomic rank" EXACT [http://edamontology.org] -xref: Moby:BriefTaxonConcept -xref: Moby:PotentialTaxon -is_a: EDAM_data:2909 ! Organism name +id: EDAM_operation:0247 +name: Protein architecture analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2406 ! Protein structure analysis +relationship: has_output EDAM_data:0902 ! Protein architecture report [Term] -id: EDAM_data:1872 -name: Taxonomic classification -namespace: identifier -subset: identifiers -subset: data -def: "The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature." [http://edamontology.org] -comment: Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. -synonym: "Taxonomic name" EXACT [http://edamontology.org] -synonym: "Taxonomic information" EXACT [http://edamontology.org] -xref: Moby:GCP_Taxon -xref: Moby:TaxonName -xref: Moby:TaxonTCS -xref: Moby:TaxonScientificName -xref: Moby:iANT_organism-xml -is_a: EDAM_data:2909 ! Organism name +id: EDAM_operation:0248 +name: Residue interaction calculation +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: SymShellFiveXML +xref: WHATIF: SymShellOneXML +xref: WHATIF: SymShellTenXML +xref: WHATIF: SymShellTwoXML +xref: WHATIF:ListContactsNormal +xref: WHATIF:ListContactsRelaxed +xref: WHATIF:ListSideChainContactsNormal +xref: WHATIF:ListSideChainContactsRelaxed +created_in: "beta12orEarlier" +def: "Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0243 ! Protein property calculation (from structure) +relationship: has_output EDAM_data:1540 ! Protein residue interactions +relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] -id: EDAM_data:1874 -name: Genbank common name -namespace: identifier -subset: identifiers -subset: data -def: "Common name for an organism as used in the GenBank database." [http://edamontology.org] -is_a: EDAM_data:2909 ! Organism name +id: EDAM_operation:0249 +name: Torsion angle calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0243 ! Protein property calculation (from structure) +relationship: has_output EDAM_data:2991 ! Protein torsion angle data [Term] -id: EDAM_data:1873 -name: iHOP organism ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier for an organism used in the iHOP database." [http://edamontology.org] -xref: Moby_namespace:iHOPorganism -is_a: EDAM_data:2908 ! Organism accession - +id: EDAM_operation:0250 +name: Protein property calculation +comment: This includes methods to render and visualise the properties of a protein sequence. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein property rendering" EXACT [] +created_in: "beta12orEarlier" +def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2502 ! Protein data processing +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_input EDAM_data:0897 ! Protein property +relationship: has_output EDAM_data:0897 ! Protein property +relationship: has_topic EDAM_topic:0123 ! Protein properties [Term] -id: EDAM_data:2102 -name: KEGG organism code -namespace: identifier -subset: identifiers -subset: data -def: "A three-letter code used in the KEGG databases to uniquely identify organisms." [http://edamontology.org] -is_a: EDAM_data:2909 ! Organism name -is_a: EDAM_data:1154 ! KEGG object identifier - +id: EDAM_operation:0252 +name: Peptide immunogenicity prediction +comment: This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2492 ! Protein interaction prediction +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) +relationship: has_output EDAM_data:1534 ! Peptide immunogenicity data +relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] -id: EDAM_data:2593 -name: BRENDA organism ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier for an organism used in the BRENDA database." [http://edamontology.org] -is_a: EDAM_data:2908 ! Organism accession - +id: EDAM_operation:0253 +name: Feature prediction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence feature detection" EXACT [] +synonym: "SO:0000110" RELATED [] +created_in: "beta12orEarlier" +def: "Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2403 ! Sequence analysis +is_a: EDAM_operation:2423 ! Prediction, detection and recognition +relationship: has_output EDAM_data:1255 ! Feature record +relationship: has_topic EDAM_topic:3072 ! Sequence feature detection [Term] -id: EDAM_data:2913 -name: Virus identifier -namespace: identifier -subset: identifiers -subset: data -def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org] -is_a: EDAM_data:1869 ! Organism identifier -relationship: is_identifier_of EDAM_data:2307 ! Virus annotation +id: EDAM_operation:0254 +name: Data retrieval (feature table) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Extract a sequence feature table from a sequence database entry." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_data:2785 -name: Virus ID -namespace: identifier -subset: identifiers -subset: data -def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org] -is_a: EDAM_data:2913 ! Virus identifier -is_a: EDAM_data:2908 ! Organism accession - +id: EDAM_operation:0255 +name: Feature table query +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Query the features (in a feature table) of molecular sequence(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2453 ! Feature table processing +relationship: has_input EDAM_data:1270 ! Sequence feature table +relationship: has_input EDAM_data:2201 ! Sequence record full +relationship: has_output EDAM_data:1255 ! Feature record [Term] -id: EDAM_data:2836 -name: DPVweb ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier for a virus from the DPVweb database." [http://edamontology.org] -synonym: "DPVweb virus ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2785 ! Virus ID +id: EDAM_operation:0256 +name: Feature comparison +subset: bioinformatics +subset: edam +subset: operations +synonym: "Feature table comparison" EXACT [] +synonym: "Sequence feature comparison" EXACT [] +created_in: "beta12orEarlier" +def: "Compare the feature tables of two or more molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2424 ! Comparison +is_a: EDAM_operation:2453 ! Feature table processing +relationship: has_input EDAM_data:1270 ! Sequence feature table +relationship: has_input EDAM_data:2201 ! Sequence record full [Term] -id: EDAM_data:2784 -name: RNAVirusDB ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier for a virus from the RNAVirusDB database." [http://edamontology.org] -is_a: EDAM_data:2785 ! Virus ID +id: EDAM_operation:0257 +name: Data retrieval (sequence alignment) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Display basic information about a sequence alignment." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval -! Could list (or cross-reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. +[Term] +id: EDAM_operation:0258 +name: Sequence alignment analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse a molecular sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2463 ! Sequence alignment processing +is_a: EDAM_operation:2946 ! Alignment analysis +relationship: has_input EDAM_data:0863 ! Sequence alignment +relationship: has_output EDAM_data:0867 ! Sequence alignment report [Term] -id: EDAM_data:1875 -name: NCBI taxon -namespace: identifier -subset: identifiers -subset: data -def: "The name of a taxon from the NCBI taxonomy database." [http://edamontology.org] -is_a: EDAM_data:1868 ! Taxon +id: EDAM_operation:0259 +name: Sequence alignment comparison +comment: See also 'Sequence profile alignment'. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare (typically by aligning) two molecular sequence alignments." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0258 ! Sequence alignment analysis +is_a: EDAM_operation:2424 ! Comparison +[Term] +id: EDAM_operation:0260 +name: Sequence alignment conversion +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3081 ! Sequence alignment editing [Term] -id: EDAM_data:2594 -name: UniGene taxon -namespace: identifier -subset: identifiers -subset: data -def: "The name of a taxon using the controlled vocabulary of the UniGene database." [http://edamontology.org] -synonym: "UniGene organism abbreviation" EXACT [http://edamontology.org] -is_a: EDAM_data:1868 ! Taxon +id: EDAM_operation:0261 +name: Nucleic acid property processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) physicochemical property data of nucleic acids." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0262 ! Nucleic acid property calculation [Term] -id: EDAM_data:2595 -name: UTRdb taxon -namespace: identifier -subset: identifiers -subset: data -def: "The name of a taxon using the controlled vocabulary of the UTRdb database." [http://edamontology.org] -is_a: EDAM_data:1868 ! Taxon +id: EDAM_operation:0262 +name: Nucleic acid property calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_output EDAM_data:0912 ! Nucleic acid property [Term] -id: EDAM_data:1044 -name: Kingdom name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." [http://edamontology.org] -is_a: EDAM_data:1868 ! Taxon +id: EDAM_operation:0264 +name: Splice transcript prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2499 ! Splicing analysis +relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] -id: EDAM_data:1870 -name: Genus name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a genus of organism." [http://edamontology.org] -is_a: EDAM_data:1868 ! Taxon +id: EDAM_operation:0265 +name: Frameshift error detection +comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3195 ! Sequencing error detection +is_a: EDAM_operation:3202 ! Mutation detection +relationship: has_topic EDAM_topic:3168 ! Sequencing +[Term] +id: EDAM_operation:0266 +name: Vector sequence detection +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison [Term] -id: EDAM_data:2732 -name: Family name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a family of organism." [http://edamontology.org] -is_a: EDAM_data:1868 ! Taxon +id: EDAM_operation:0267 +name: Protein secondary structure prediction +comment: Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Secondary structure prediction (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "Predict secondary structure of protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) +is_a: EDAM_operation:2444 ! Protein secondary structure processing +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_output EDAM_data:0876 ! Protein features (secondary structure) +relationship: has_topic EDAM_topic:0178 ! Protein secondary structure prediction [Term] -id: EDAM_data:1045 -name: Species name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a species (typically a taxonomic group) of organism." [http://edamontology.org] -synonym: "Organism species" EXACT [http://edamontology.org] -is_a: EDAM_data:1868 ! Taxon +id: EDAM_operation:0268 +name: Protein super-secondary structure prediction +comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict super-secondary structure of protein sequence(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0267 ! Protein secondary structure prediction +relationship: has_output EDAM_data:0877 ! Protein features (super-secondary) +[Term] +id: EDAM_operation:0269 +name: Transmembrane protein prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0267 ! Protein secondary structure prediction +is_a: EDAM_operation:0270 ! Transmembrane protein analysis +relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) [Term] -id: EDAM_data:2733 -name: Genus name (virus) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a genus of viruses." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1870 ! Genus name +id: EDAM_operation:0270 +name: Transmembrane protein analysis +comment: Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2502 ! Protein data processing +relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) +relationship: has_topic EDAM_topic:0820 ! Membrane proteins [Term] -id: EDAM_data:2734 -name: Family name (virus) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a family of viruses." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:2732 ! Family name +id: EDAM_operation:0271 +name: Structure prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict tertiary structure of a molecular (biopolymer) sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2423 ! Prediction, detection and recognition +is_a: EDAM_operation:2465 ! Structure processing +relationship: has_output EDAM_data:0883 ! Structure +relationship: has_topic EDAM_topic:0082 ! Structure prediction +[Term] +id: EDAM_operation:0272 +name: Residue interaction prediction +comment: Methods usually involve multiple sequence alignment analysis. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0243 ! Protein property calculation (from structure) +is_a: EDAM_operation:2506 ! Sequence alignment analysis (protein) +relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] -id: EDAM_data:2317 -name: Cell line name (exact) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a cell line." [http://edamontology.org] -is_a: EDAM_data:2316 ! Cell line name +id: EDAM_operation:0273 +name: Protein interaction raw data analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2949 ! Protein interaction analysis +relationship: has_input EDAM_data:0905 ! Protein interaction raw data +relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] -id: EDAM_data:2318 -name: Cell line name (truncated) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a cell line." [http://edamontology.org] -is_a: EDAM_data:2316 ! Cell line name +id: EDAM_operation:0274 +name: Protein-protein interaction prediction (from protein sequence) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2464 ! Protein-protein interaction prediction +is_a: EDAM_operation:3084 ! Protein function prediction (from sequence) [Term] -id: EDAM_data:2319 -name: Cell line name (no punctuation) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a cell line." [http://edamontology.org] -is_a: EDAM_data:2316 ! Cell line name +id: EDAM_operation:0275 +name: Protein-protein interaction prediction (from protein structure) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2464 ! Protein-protein interaction prediction +is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) [Term] -id: EDAM_data:2320 -name: Cell line name (assonant) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a cell line." [http://edamontology.org] -is_a: EDAM_data:2316 ! Cell line name +id: EDAM_operation:0276 +name: Protein interaction network analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse a network of protein interactions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2445 ! Protein interaction network processing +is_a: EDAM_operation:2497 ! Pathway or network analysis +is_a: EDAM_operation:2949 ! Protein interaction analysis +relationship: has_input EDAM_data:1663 ! Pathway or network (protein-protein interaction) +relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] -id: EDAM_data:1056 -name: Database name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a biological or bioinformatics database." [http://edamontology.org] -is_a: EDAM_data:1048 ! Database identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_operation:0277 +name: Protein interaction network comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more networks of protein interactions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0276 ! Protein interaction network analysis +is_a: EDAM_operation:1778 ! Protein function comparison +relationship: has_input EDAM_data:1663 ! Pathway or network (protein-protein interaction) [Term] -id: EDAM_data:2149 -name: Database category name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a category of biological or bioinformatics database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1056 ! Database name +id: EDAM_operation:0278 +name: RNA secondary structure prediction +comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +is_a: EDAM_operation:2439 ! RNA secondary structure processing +relationship: has_output EDAM_data:0880 ! RNA secondary structure record +relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] -id: EDAM_data:1057 -name: Sequence database name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a molecular sequence database." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1056 ! Database name +id: EDAM_operation:0279 +name: Nucleic acid folding analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Nucleic acid folding" EXACT [] +synonym: "Nucleic acid folding modelling" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2426 ! Modelling and simulation +is_a: EDAM_operation:2501 ! Nucleic acid data processing +relationship: has_output EDAM_data:1596 ! Nucleic acid folding report +relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] -id: EDAM_data:2735 -name: Database name (SwissRegulon) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a SwissRegulon database." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1056 ! Database name +id: EDAM_operation:0280 +name: Data retrieval (restriction enzyme annotation) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Restriction enzyme information retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Retrieve information on restriction enzymes or restriction enzyme sites." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval +[Term] +id: EDAM_operation:0281 +name: Genetic marker identification +comment: A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify genetic markers in DNA sequences." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] -id: EDAM_data:2747 -name: Database name (CMD) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a subdivision of the Collagen Mutation Database (CMD) database." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1056 ! Database name +id: EDAM_operation:0282 +name: Genetic mapping +comment: Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Genetic map generation" EXACT [] +synonym: "Linkage mapping" EXACT [] +created_in: "beta12orEarlier" +def: "Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2520 ! DNA mapping +relationship: has_output EDAM_data:1278 ! Genetic map +relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage +[Term] +id: EDAM_operation:0283 +name: Linkage analysis +comment: For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse genetic linkage." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_output EDAM_data:0927 ! Gene annotation (linkage) +relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] -id: EDAM_data:2748 -name: Database name (Osteogenesis) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a subdivision of the Osteogenesis database." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1056 ! Database name +id: EDAM_operation:0284 +name: Codon usage table generation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate codon usage statistics and create a codon usage table." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2433 ! Codon usage table processing +relationship: has_output EDAM_data:1597 ! Codon usage table [Term] -id: EDAM_data:1058 -name: Enumerated file name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a file (of any type) with restricted possible values." [http://edamontology.org] -is_a: EDAM_data:1050 ! File name +id: EDAM_operation:0285 +name: Codon usage table comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more codon usage tables." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2433 ! Codon usage table processing +is_a: EDAM_operation:2998 ! Nucleic acid comparison [Term] -id: EDAM_data:1059 -name: File name extension -namespace: identifier -subset: identifiers -subset: data -def: "The extension of a file name." [http://edamontology.org] -comment: A file extension is the characters appearing after the final '.' in the file name. -is_a: EDAM_data:1050 ! File name +id: EDAM_operation:0286 +name: Codon usage analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "synon: Codon usage data analysis" EXACT [] +synonym: "synon: Codon usage table analysis" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2501 ! Nucleic acid data processing +relationship: has_input EDAM_data:1597 ! Codon usage table +relationship: has_input EDAM_data:2977 ! Nucleic acid sequence +relationship: has_output EDAM_data:0914 ! Codon usage report +relationship: has_output EDAM_data:1597 ! Codon usage table +relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] -id: EDAM_data:1060 -name: File base name -namespace: identifier -subset: identifiers -subset: data -def: "The base name of a file." [http://edamontology.org] -comment: A file base name is the file name stripped of its directory specification and extension. -is_a: EDAM_data:1050 ! File name +id: EDAM_operation:0287 +name: Base position variability plotting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify and plot third base position variability in a nucleotide sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0286 ! Codon usage analysis +relationship: has_output EDAM_data:1263 ! Sequence composition (base position variability) +relationship: has_topic EDAM_topic:0109 ! Gene finding +[Term] +id: EDAM_operation:0288 +name: Sequence word comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Find exact character or word matches between molecular sequences without full sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2451 ! Sequence comparison +relationship: has_output EDAM_data:0861 ! Sequence alignment (words) [Term] -id: EDAM_data:1061 -name: QSAR descriptor name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a QSAR descriptor." [http://edamontology.org] -is_a: EDAM_data:2110 ! Molecular property identifier -is_a: EDAM_data:2099 ! Name -relationship: is_identifier_of EDAM_data:0847 ! QSAR descriptor +id: EDAM_operation:0289 +name: Sequence distance matrix generation +subset: bioinformatics +subset: edam +subset: operations +synonym: "Phylogenetic distance matrix generation" EXACT [] +created_in: "beta12orEarlier" +def: "Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2451 ! Sequence comparison +relationship: has_output EDAM_data:0870 ! Sequence distance matrix +relationship: has_topic EDAM_topic:0084 ! Phylogenetics +[Term] +id: EDAM_operation:0290 +name: Sequence redundancy removal +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0291 ! Sequence clustering +relationship: has_output EDAM_data:2044 ! Sequence +relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] -id: EDAM_data:2288 -name: Sequence identifier (protein) -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of protein sequence(s) or protein sequence database entries." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1096 ! Sequence accession (protein) +id: EDAM_operation:0291 +name: Sequence clustering +comment: The clusters may be output or used internally for some other purpose. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence cluster generation" EXACT [] +created_in: "beta12orEarlier" +def: "Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2451 ! Sequence comparison +is_a: EDAM_operation:2452 ! Sequence cluster processing +is_a: EDAM_operation:2995 ! Sequence classification +relationship: has_output EDAM_data:1235 ! Sequence cluster +[Term] +id: EDAM_operation:0292 +name: Sequence alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence alignment" EXACT [] +synonym: "Sequence alignment computation" EXACT [] +synonym: "Sequence alignment generation" EXACT [] +created_in: "beta12orEarlier" +def: "Align (identify equivalent sites within) molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2451 ! Sequence comparison +is_a: EDAM_operation:2463 ! Sequence alignment processing +is_a: EDAM_operation:2928 ! Alignment construction +relationship: has_input EDAM_data:2044 ! Sequence +relationship: has_output EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM_data:2289 -name: Sequence identifier (nucleic acid) -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of nucleotide sequence(s) or nucleotide sequence database entries." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1097 ! Sequence accession (nucleic acid) +id: EDAM_operation:0293 +name: Hybrid sequence alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Hybrid sequence alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0292 ! Sequence alignment construction +[Term] +id: EDAM_operation:0294 +name: Structure-based sequence alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Structure-based sequence alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align molecular sequences using sequence and structural information." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0292 ! Sequence alignment construction +relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] -id: EDAM_data:1093 -name: Sequence accession -namespace: identifier -subset: identifiers -subset: data -def: "A persistent, unique identifier of a molecular sequence database entry." [http://edamontology.org] -synonym: "Sequence accession number" EXACT [http://edamontology.org] -is_a: EDAM_data:1063 ! Sequence identifier -is_a: EDAM_data:2091 ! Accession -is_a: EDAM_data:2914 ! Sequence features metadata +id: EDAM_operation:0295 +name: Structure alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Structure alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align (superimpose) molecular tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2483 ! Structure comparison +is_a: EDAM_operation:2928 ! Alignment construction +is_a: EDAM_operation:2952 ! Structure alignment processing +relationship: has_output EDAM_data:0886 ! Structure alignment +[Term] +id: EDAM_operation:0296 +name: Sequence profile generation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2413 ! Sequence profile processing +is_a: EDAM_operation:2463 ! Sequence alignment processing +relationship: has_input EDAM_data:0863 ! Sequence alignment +relationship: has_output EDAM_data:1354 ! Sequence profile [Term] -id: EDAM_data:2154 -name: Sequence name -namespace: identifier -subset: identifiers -subset: data -def: "Any arbitrary name of a molecular sequence." [http://edamontology.org] -is_a: EDAM_data:1063 ! Sequence identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_operation:0297 +name: Structural (3D) profile generation +subset: bioinformatics +subset: edam +subset: operations +synonym: "Structural profile generation" EXACT [] +created_in: "beta12orEarlier" +def: "Generate some type of structural (3D) profile or template from a structure or structure alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2411 ! Structural (3D) profile processing +is_a: EDAM_operation:2465 ! Structure processing +is_a: EDAM_operation:2952 ! Structure alignment processing +relationship: has_input EDAM_data:0883 ! Structure +relationship: has_input EDAM_data:0886 ! Structure alignment +relationship: has_output EDAM_data:0889 ! Structural (3D) profile +[Term] +id: EDAM_operation:0298 +name: Sequence profile alignment construction +comment: See also 'Sequence alignment comparison'. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence profile alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align sequence profiles (representing sequence alignments)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2413 ! Sequence profile processing +is_a: EDAM_operation:2928 ! Alignment construction +relationship: has_input EDAM_data:1354 ! Sequence profile +relationship: has_output EDAM_data:0868 ! Sequence profile alignment [Term] -id: EDAM_data:1095 -name: EMBOSS Uniform Sequence Address -namespace: identifier -subset: identifiers -subset: data -def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [http://edamontology.org] -synonym: "EMBOSS USA" EXACT [http://edamontology.org] -is_a: EDAM_data:1063 ! Sequence identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_operation:0299 +name: Structural (3D) profile alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Structural (3D) profile alignment" EXACT [] +synonym: "Structural profile alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align structural (3D) profiles or templates (representing structures or structure alignments)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2411 ! Structural (3D) profile processing +is_a: EDAM_operation:2928 ! Alignment construction +relationship: has_input EDAM_data:0889 ! Structural (3D) profile +relationship: has_output EDAM_data:0890 ! Structural (3D) profile alignment +relationship: has_topic EDAM_topic:0183 ! Structure alignment +[Term] +id: EDAM_operation:0300 +name: Sequence-profile alignment construction +comment: A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence-profile alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align molecular sequence(s) to sequence profile(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2403 ! Sequence analysis +is_a: EDAM_operation:2413 ! Sequence profile processing +is_a: EDAM_operation:2928 ! Alignment construction +relationship: has_input EDAM_data:1354 ! Sequence profile +relationship: has_output EDAM_data:0869 ! Sequence-profile alignment +[Term] +id: EDAM_operation:0301 +name: Sequence-3D profile alignment construction +comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence-3D profile alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0303 ! Protein fold recognition +is_a: EDAM_operation:2403 ! Sequence analysis +is_a: EDAM_operation:2928 ! Alignment construction +relationship: has_input EDAM_data:0889 ! Structural (3D) profile +relationship: has_output EDAM_data:0891 ! Sequence-3D profile alignment +relationship: has_topic EDAM_topic:0184 ! Threading [Term] -id: EDAM_data:2291 -name: UniProt ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a polypeptide in the UniProt database." [http://edamontology.org] -synonym: "UniProt identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:1096 ! Sequence accession (protein) -relationship: is_identifier_of EDAM_data:0849 ! Sequence record +id: EDAM_operation:0302 +name: Protein threading +comment: Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence-structure alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align molecular sequence to structure in 3D space (threading)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0303 ! Protein fold recognition +is_a: EDAM_operation:2928 ! Alignment construction +relationship: has_input EDAM_data:1460 ! Protein structure +relationship: has_output EDAM_data:0893 ! Sequence-structure alignment +relationship: has_topic EDAM_topic:0175 ! Homology modelling +relationship: has_topic EDAM_topic:0184 ! Threading [Term] -id: EDAM_data:1100 -name: PIR identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of PIR sequence database entry." [http://edamontology.org] -synonym: "PIR accession number" EXACT [http://edamontology.org] -synonym: "PIR ID" EXACT [http://edamontology.org] -is_a: EDAM_data:1096 ! Sequence accession (protein) -relationship: is_identifier_of EDAM_data:0849 ! Sequence record +id: EDAM_operation:0303 +name: Protein fold recognition +comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein domain prediction" EXACT [] +synonym: "Protein fold prediction" EXACT [] +created_in: "beta12orEarlier" +def: "Recognize (predict and identify) known protein structural domains or folds in protein sequence(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) +is_a: EDAM_operation:0474 ! Protein structure prediction +is_a: EDAM_operation:2997 ! Protein comparison +relationship: has_output EDAM_data:0901 ! Protein features (domains) +relationship: has_topic EDAM_topic:0184 ! Threading [Term] -id: EDAM_data:1101 -name: TREMBL accession -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a TREMBL sequence database entry." [http://edamontology.org] -is_a: EDAM_data:3021 ! UniProt accession -synonym: "TREMBL accession number" EXACT [http://edamontology.org] -synonym: "TREMBL ID" EXACT [http://edamontology.org] -relationship: is_identifier_of EDAM_data:0849 ! Sequence record +id: EDAM_operation:0304 +name: Data retrieval (metadata and documentation) +comment: This includes documentation, general information and other metadata on entities such as databases, database entries and tools. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Data retrieval (documentation)" EXACT [] +synonym: "Data retrieval (metadata)" EXACT [] +created_in: "beta12orEarlier" +def: "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2422 ! Data retrieval +relationship: has_output EDAM_data:2337 ! Metadata [Term] -id: EDAM_data:2621 -name: TAIR accession (protein) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein sequence from the TAIR database." [http://edamontology.org] -regex: "AASequence:[0-9]{10}" -is_a: EDAM_data:1096 ! Sequence accession (protein) -is_a: EDAM_data:2387 ! TAIR accession -relationship: is_identifier_of EDAM_data:0849 ! Sequence record +id: EDAM_operation:0305 +name: Literature search +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Query the biomedical and informatics literature." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2421 ! Database search +relationship: has_output EDAM_data:0970 ! Bibliographic reference +relationship: has_topic EDAM_topic:0217 ! Literature analysis [Term] -id: EDAM_data:2290 -name: EMBL accession -namespace: identifier -subset: identifiers -subset: data -! alt_id: EDAM_data:1107 -def: "An accession number of an entry from the EMBL sequence database." [http://edamontology.org] -synonym: "EMBL accession number" EXACT [http://edamontology.org] -synonym: "EMBL identifier" EXACT [http://edamontology.org] -synonym: "EMBL ID" EXACT [http://edamontology.org] -is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID - +id: EDAM_operation:0306 +name: Text mining +subset: bioinformatics +subset: edam +subset: operations +synonym: "Text data mining" EXACT [] +created_in: "beta12orEarlier" +def: "Process and analyse text (typically the biomedical and informatics literature) to extract information from it." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2947 ! Article analysis +relationship: has_input EDAM_data:2048 ! Report +relationship: has_output EDAM_data:0972 ! Text mining report +relationship: has_topic EDAM_topic:0218 ! Text mining [Term] -id: EDAM_data:2292 -name: GenBank accession -namespace: identifier -subset: identifiers -subset: data -! alt_id: EDAM_data:1108 -def: "Accession number of an entry from the GenBank sequence database." [http://edamontology.org] -is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID -synonym: "GenBank accession number" EXACT [http://edamontology.org] -synonym: "GenBank identifier" EXACT [http://edamontology.org] -synonym: "GenBank ID" EXACT [http://edamontology.org] +id: EDAM_operation:0307 +name: Virtual PCR +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Perform in-silico (virtual) PCR." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis +[Term] +id: EDAM_operation:0308 +name: PCR primer design +comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. +subset: bioinformatics +subset: edam +subset: operations +synonym: "PCR primer prediction" EXACT [] +created_in: "beta12orEarlier" +def: "Design or predict oligonucleotide primers for PCR and DNA amplification etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2419 ! Primer and probe design +relationship: has_input EDAM_data:2977 ! Nucleic acid sequence +relationship: has_output EDAM_data:1240 ! PCR primers +relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] -id: EDAM_data:2916 -name: DDBJ accession -namespace: identifier -subset: identifiers -subset: data -! alt_id: EDAM_data:1109 -def: "An identifier of an entry from the DDBJ sequence database." [http://edamontology.org] -is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID -synonym: "DDBJ accession number" EXACT [http://edamontology.org] -synonym: "DDBJ identifier" EXACT [http://edamontology.org] -synonym: "DDBJ ID" EXACT [http://edamontology.org] +id: EDAM_operation:0309 +name: Microarray probe design +subset: bioinformatics +subset: edam +subset: operations +synonym: "Microarray probe prediction" EXACT [] +created_in: "beta12orEarlier" +def: "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2419 ! Primer and probe design +is_a: EDAM_operation:2425 ! Optimisation and refinement +relationship: has_input EDAM_data:2977 ! Nucleic acid sequence +relationship: has_output EDAM_data:2717 ! Oligonucleotide probe annotation +relationship: has_topic EDAM_topic:0200 ! Microarrays +relationship: has_topic EDAM_topic:3032 ! Primer or probe design +[Term] +id: EDAM_operation:0310 +name: Sequence assembly +comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2429 ! Mapping and assembly +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_output EDAM_data:0925 ! Sequence assembly +relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] -id: EDAM_data:1855 -name: Clone ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a clone (cloned molecular sequence) from a database." [http://edamontology.org] -is_a: EDAM_data:2769 ! Transcript ID +id: EDAM_operation:0311 +name: Microarray data standardization and normalization +comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Standardize or normalize microarray data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2428 ! Evaluation and validation +is_a: EDAM_operation:2495 ! Gene expression data processing +relationship: has_input EDAM_data:3117 ! Microarray hybridisation data +relationship: has_output EDAM_data:3117 ! Microarray hybridisation data +[Term] +id: EDAM_operation:0312 +name: Sequencing-based expression profile data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) SAGE, MPSS or SBS experimental data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2495 ! Gene expression data processing [Term] -id: EDAM_data:2386 -name: EPD ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (promoter) from the EPD database." [http://edamontology.org] -synonym: "EPD identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:2727 ! Promoter ID +id: EDAM_operation:0313 +name: Gene expression profile clustering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0315 ! Gene expression profile comparison +relationship: has_output EDAM_data:3111 ! Processed microarray data +[Term] +id: EDAM_operation:0314 +name: Gene expression profile generation +subset: bioinformatics +subset: edam +subset: operations +synonym: "Expression profiling" EXACT [] +synonym: "Gene expression profiling" EXACT [] +created_in: "beta12orEarlier" +def: "Generate a gene expression profile or pattern, for example from microarray data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2435 ! Gene expression profile processing +relationship: has_output EDAM_data:0928 ! Gene expression profile [Term] -id: EDAM_data:2741 -name: ABS ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry (promoter) from the ABS database." [http://edamontology.org] -synonym: "ABS identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:2727 ! Promoter ID +id: EDAM_operation:0315 +name: Gene expression profile comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare gene expression profiles or patterns." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0532 ! Gene expression profile analysis +is_a: EDAM_operation:2998 ! Nucleic acid comparison +relationship: has_output EDAM_data:3111 ! Processed microarray data [Term] -id: EDAM_data:1096 -name: Sequence accession (protein) -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a protein sequence database entry." [http://edamontology.org] -synonym: "Protein sequence accession number" EXACT [http://edamontology.org] -is_a: EDAM_data:1093 ! Sequence accession -relationship: is_identifier_of EDAM_data:2976 ! Protein sequence +id: EDAM_operation:0316 +name: Functional profiling +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Interpret (in functional terms) and annotate gene expression data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0532 ! Gene expression profile analysis [Term] -id: EDAM_data:1097 -name: Sequence accession (nucleic acid) -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a nucleotide sequence database entry." [http://edamontology.org] -synonym: "Nucleotide sequence accession number" EXACT [http://edamontology.org] -is_a: EDAM_data:1093 ! Sequence accession -relationship: is_identifier_of EDAM_data:2977 ! Nucleic acid sequence +id: EDAM_operation:0317 +name: EST and cDNA sequence analysis +comment: For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse EST or cDNA sequences." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2403 ! Sequence analysis +[Term] +id: EDAM_operation:0318 +name: Structural genomics target selection +comment: Methods will typically navigate a graph of protein families of known structure. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify and select targets for protein structural determination." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2406 ! Protein structure analysis [Term] -id: EDAM_data:2362 -name: Sequence accession (hybrid) -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a nucleotide or protein sequence database entry." [http://edamontology.org] -is_a: EDAM_data:1093 ! Sequence accession -relationship: is_identifier_of EDAM_data:0849 ! Sequence record +id: EDAM_operation:0319 +name: Protein secondary structure assignment +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign secondary structure from protein coordinate or experimental data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2444 ! Protein secondary structure processing +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_output EDAM_data:0876 ! Protein features (secondary structure) +relationship: has_topic EDAM_topic:2226 ! Structure determination +[Term] +id: EDAM_operation:0320 +name: Protein structure assignment +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign a protein tertiary structure (3D coordinates) from raw experimental data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2459 ! Structure processing (protein) +relationship: has_output EDAM_data:1460 ! Protein structure +relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] -id: EDAM_data:1098 -name: RefSeq accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a RefSeq database entry." [http://edamontology.org] -regex: "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+" -is_a: EDAM_data:2362 ! Sequence accession (hybrid) -synonym: "RefSeq ID" EXACT [http://edamontology.org] +id: EDAM_operation:0321 +name: Protein model evaluation +comment: Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: UseFileDB +created_in: "beta12orEarlier" +def: "Evaluate the quality or correctness a protein three-dimensional model." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0477 ! Protein modelling +is_a: EDAM_operation:2428 ! Evaluation and validation +relationship: has_output EDAM_data:1539 ! Protein structural quality report +relationship: has_topic EDAM_topic:0175 ! Homology modelling +relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction +relationship: has_topic EDAM_topic:2275 ! Molecular modelling [Term] -id: EDAM_data:2314 -name: GI number -namespace: identifier -subset: identifiers -subset: data -def: "A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record." [http://edamontology.org] -comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. -synonym: "NCBI GI number" EXACT [http://edamontology.org] -synonym: "gi number" EXACT [http://edamontology.org] -is_a: EDAM_data:2362 ! Sequence accession (hybrid) +id: EDAM_operation:0322 +name: Protein model refinement +comment: The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: CorrectedPDBasXML +created_in: "beta12orEarlier" +def: "Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0321 ! Protein model evaluation +is_a: EDAM_operation:2425 ! Optimisation and refinement [Term] -id: EDAM_data:2315 -name: NCBI version -namespace: identifier -subset: identifiers -subset: data -def: "An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number." [http://edamontology.org] -comment: Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. -synonym: "accession.version" EXACT [http://edamontology.org] -synonym: "NCBI accession.version" EXACT [http://edamontology.org] -is_a: EDAM_data:2362 ! Sequence accession (hybrid) +id: EDAM_operation:0323 +name: Phylogenetic tree construction +comment: Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Phylogenetic tree construction" EXACT [] +synonym: "Phylogenetic tree generation" EXACT [] +created_in: "beta12orEarlier" +def: "Construct a phylogenetic tree." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2443 ! Phylogenetic tree processing +is_a: EDAM_operation:2995 ! Sequence classification +relationship: has_output EDAM_data:0872 ! Phylogenetic tree +relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM_data:2385 -name: RefSeq accession (protein) -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a protein from the RefSeq database." [http://edamontology.org] -is_a: EDAM_data:1098 ! RefSeq accession -synonym: "RefSeq protein ID" EXACT [http://edamontology.org] +id: EDAM_operation:0324 +name: Phylogenetic tree analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2443 ! Phylogenetic tree processing +relationship: has_input EDAM_data:0872 ! Phylogenetic tree +relationship: has_output EDAM_data:1438 ! Phylogenetic tree report [Term] -id: EDAM_data:2327 -name: GI number (protein) -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier assigned to NCBI protein sequence records." [http://edamontology.org] -comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. -synonym: "protein gi number" EXACT [http://edamontology.org] -synonym: "protein gi" EXACT [http://edamontology.org] -is_a: EDAM_data:2314 ! GI number +id: EDAM_operation:0325 +name: Phylogenetic tree comparison +comment: For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more phylogenetic trees." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0324 ! Phylogenetic tree analysis +is_a: EDAM_operation:2424 ! Comparison [Term] -id: EDAM_data:1099 -name: UniProt accession (extended) -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number." [http://edamontology.org] -regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+" -example: "Q7M1G0" "P43353-2" "P01012.107" -! is_a: EDAM_data:3021 ! UniProt accession -! relationship: is_identifier_of EDAM_format:1208 ! Protein sequence ! now 'protein' format -! relationship: is_identifier_of EDAM_data:0849 ! Sequence record -is_obsolete: true !{since=1.0} -consider: EDAM_data:3021 ! UniProt accession +id: EDAM_operation:0326 +name: Phylogenetic tree editing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Edit a phylogenetic tree." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2443 ! Phylogenetic tree processing +is_a: EDAM_operation:3096 ! Editing +relationship: has_input EDAM_data:0872 ! Phylogenetic tree +relationship: has_output EDAM_data:0872 ! Phylogenetic tree [Term] -id: EDAM_data:3021 -name: UniProt accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a UniProt (protein sequence) database entry." [http://edamontology.org] -regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]" -example: "P43353" "Q7M1G0" "Q9C199" "A5A6J6" -synonym: "UniProtKB accession number" EXACT [http://edamontology.org] -synonym: "UniProtKB entry accession" EXACT [http://edamontology.org] -synonym: "UniProt accession number" EXACT [http://edamontology.org] -synonym: "Swiss-Prot accession" EXACT [http://edamontology.org] -is_a: EDAM_data:2291 ! UniProt ID -relationship: is_identifier_of EDAM_data:0849 ! Sequence record ! Of protein/peptide (feature) record? Also of a class of protein molecules? +id: EDAM_operation:0327 +name: Phylogenetic footprinting / shadowing +comment: A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences) +relationship: has_topic EDAM_topic:0194 ! Phylogenomics [Term] -id: EDAM_data:2392 -name: UniParc accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a UniParc (protein sequence) database entry." [http://edamontology.org] -synonym: "UniParc ID" EXACT [http://edamontology.org] -synonym: "UPI" EXACT [http://edamontology.org] -regex: "UPI[A-F0-9]{10}" -is_a: EDAM_data:2291 ! UniProt ID +id: EDAM_operation:0328 +name: Protein folding simulation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Simulate the folding of a protein." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2415 ! Protein folding analysis [Term] -id: EDAM_data:2915 -name: Gramene identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a Gramene database entry." [http://edamontology.org] -is_a: EDAM_data:1096 ! Sequence accession (protein) +id: EDAM_operation:0329 +name: Protein folding pathway prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict the folding pathway(s) or non-native structural intermediates of a protein." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2415 ! Protein folding analysis +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) [Term] -id: EDAM_data:1102 -name: Gramene primary identifier -namespace: identifier -subset: identifiers -subset: data -def: "Primary identifier of a Gramene database entry." [http://edamontology.org] -synonym: "Gramene primary ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2915 ! Gramene identifier +id: EDAM_operation:0330 +name: Protein SNP mapping +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0331 ! Protein modelling (mutation) +relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) +relationship: has_topic EDAM_topic:2277 ! SNPs [Term] -id: EDAM_data:2293 -name: Gramene secondary identifier -namespace: identifier -subset: identifiers -subset: data -def: "Secondary (internal) identifier of a Gramene database entry." [http://edamontology.org] -synonym: "Gramene secondary ID" EXACT [http://edamontology.org] -synonym: "Gramene internal ID" EXACT [http://edamontology.org] -synonym: "Gramene internal identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:2915 ! Gramene identifier +id: EDAM_operation:0331 +name: Protein modelling (mutation) +comment: Methods might predict silent or pathological mutations. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein mutation modelling" EXACT [] +created_in: "beta12orEarlier" +def: "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0477 ! Protein modelling +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_topic EDAM_topic:0130 ! Protein folding and stability +relationship: has_topic EDAM_topic:0199 ! Genetic variation [Term] -id: EDAM_data:2384 -name: IPI protein ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a protein entry catalogued in the International Protein Index (IPI) database." [http://edamontology.org] -regex: "IPI[0-9]{8}" -is_a: EDAM_data:1096 ! Sequence accession (protein) - +id: EDAM_operation:0332 +name: Immunogen design +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Design molecules that elicit an immune response (immunogens)." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0559 ! Peptide immunogen prediction and optimisation [Term] -id: EDAM_data:2728 -name: EST accession -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an EST sequence." [http://edamontology.org] -is_a: EDAM_data:1855 ! Clone ID +id: EDAM_operation:0333 +name: Zinc finger protein domain prediction and optimisation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0420 ! Protein-nucleic acid binding prediction +is_a: EDAM_operation:2425 ! Optimisation and refinement +relationship: has_output EDAM_data:1567 ! Protein-nucleic acid interaction +relationship: has_topic EDAM_topic:0150 ! Protein design [Term] -id: EDAM_data:1103 -name: EMBL/GenBank/DDBJ ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases." [http://edamontology.org] -is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) +id: EDAM_operation:0334 +name: Enzyme kinetics calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate Km, Vmax and derived data for an enzyme reaction." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) +relationship: has_output EDAM_data:2024 ! Enzyme kinetics data +relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions [Term] -id: EDAM_data:2389 -name: UniSTS accession -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the UniSTS database." [http://edamontology.org] -is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) +id: EDAM_operation:0335 +name: File reformatting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Reformat a file of data (or equivalent entity in memory)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2409 ! File processing [Term] -id: EDAM_data:2390 -name: UNITE accession -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the UNITE database." [http://edamontology.org] -is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) +id: EDAM_operation:0336 +name: File validation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Test and validate the format and content of a data file." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2409 ! File processing +is_a: EDAM_operation:2428 ! Evaluation and validation [Term] -id: EDAM_data:2391 -name: UTR accession -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the UTR database." [http://edamontology.org] -is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) +id: EDAM_operation:0337 +name: Plotting and rendering +subset: bioinformatics +subset: edam +subset: operations +synonym: "Visualisation" EXACT [] +created_in: "beta12orEarlier" +def: "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation +relationship: has_input EDAM_data:0006 ! Data +relationship: has_output EDAM_data:2968 ! Image +relationship: has_topic EDAM_topic:0092 ! Data visualisation [Term] -id: EDAM_data:2393 -name: mFLJ/mKIAA number -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the Rouge or HUGE databases." [http://edamontology.org] -is_a: EDAM_data:2295 ! Gene ID +id: EDAM_operation:0338 +name: Sequence database search +comment: This excludes direct retrieval methods (e.g. the dbfetch program). +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search a sequence database by sequence comparison and retrieve similar sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2403 ! Sequence analysis +is_a: EDAM_operation:2421 ! Database search +relationship: has_output EDAM_data:0857 ! Database hits (sequence) +relationship: has_topic EDAM_topic:0159 ! Sequence comparison +[Term] +id: EDAM_operation:0339 +name: Structure database search +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2421 ! Database search +is_a: EDAM_operation:2996 ! Structure classification +relationship: has_output EDAM_data:0885 ! Database hits (structure) +relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM_data:2781 -name: REDIdb ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the RNA editing database (REDIdb)." [http://edamontology.org] -is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) +id: EDAM_operation:0340 +name: Protein secondary database search +comment: Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein sequence classification" EXACT [] +created_in: "beta12orEarlier" +def: "Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2421 ! Database search +is_a: EDAM_operation:3093 ! Sequence screening +relationship: has_output EDAM_data:0858 ! Database hits (secondary) +relationship: has_topic EDAM_topic:0595 ! Protein classification +[Term] +id: EDAM_operation:0341 +name: Motif database search +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Screen a sequence against a motif or pattern database." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0239 ! Sequence motif recognition +is_a: EDAM_operation:2421 ! Database search +is_a: EDAM_operation:3093 ! Sequence screening +relationship: has_output EDAM_data:1298 ! Sequence features (motifs) +relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] -id: EDAM_data:2729 -name: COGEME EST ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an EST sequence from the COGEME database." [http://edamontology.org] -is_a: EDAM_data:2728 ! EST accession +id: EDAM_operation:0342 +name: Sequence profile database search +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search a database of sequence profiles with a query sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0300 ! Sequence-profile alignment construction +is_a: EDAM_operation:2421 ! Database search +is_a: EDAM_operation:3093 ! Sequence screening +relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM_data:2730 -name: COGEME unisequence ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a unisequence from the COGEME database." [http://edamontology.org] -comment: A unisequence is a single sequence assembled from ESTs. -is_a: EDAM_data:2728 ! EST accession +id: EDAM_operation:0343 +name: Transmembrane protein database search +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search a database of transmembrane proteins, for example for sequence or structural similarities." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2421 ! Database search [Term] -id: EDAM_data:2798 -name: MaizeDB ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an EST sequence from the MaizeDB database." [http://edamontology.org] -is_a: EDAM_data:2728 ! EST accession +id: EDAM_operation:0344 +name: Sequence retrieval (by code) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Query a database and retrieve sequences with a given entry code or accession number." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1813 ! Sequence retrieval +[Term] +id: EDAM_operation:0345 +name: Sequence retrieval (by keyword) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Query a database and retrieve sequences containing a given keyword." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1813 ! Sequence retrieval [Term] -id: EDAM_data:1105 -name: dbEST accession -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a dbEST database entry." [http://edamontology.org] -synonym: "dbEST ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2292 ! GenBank accession -is_a: EDAM_data:2728 ! EST accession +id: EDAM_operation:0346 +name: Sequence database search (by sequence) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence similarity search" EXACT [] +created_in: "beta12orEarlier" +def: "Search a sequence database and retrieve sequences that are similar to a query sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0338 ! Sequence database search +is_a: EDAM_operation:2451 ! Sequence comparison +is_a: EDAM_operation:3093 ! Sequence screening [Term] -id: EDAM_data:2704 -name: Clone ID (IMAGE) -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence)." [http://edamontology.org] -synonym: "I.M.A.G.E. cloneID" EXACT [http://edamontology.org] -synonym: "IMAGE cloneID" EXACT [http://edamontology.org] -is_a: EDAM_data:1855 ! Clone ID +id: EDAM_operation:0347 +name: Sequence database search (by motif or pattern) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0239 ! Sequence motif recognition +is_a: EDAM_operation:0338 ! Sequence database search +relationship: has_input EDAM_data:1353 ! Sequence motif +relationship: has_topic EDAM_topic:0158 ! Sequence motifs +[Term] +id: EDAM_operation:0348 +name: Sequence database search (by amino acid composition) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search a sequence database and retrieve sequences of a given amino acid composition." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0338 ! Sequence database search +relationship: has_input EDAM_data:1267 ! Amino acid frequencies +relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] -id: EDAM_data:2803 -name: Clone ID (RefSeq) -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of a cDNA molecule catalogued in the RefSeq database." [http://edamontology.org] -is_a: EDAM_data:1855 ! Clone ID -is_a: EDAM_data:1098 ! RefSeq accession +id: EDAM_operation:0349 +name: Sequence database search (by physicochemical property) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search a sequence database and retrieve sequences with a specified physicochemical property." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0338 ! Sequence database search [Term] -id: EDAM_data:1110 -name: EMBOSS sequence type -namespace: identifier -subset: identifiers -subset: data -def: "The EMBOSS type of a molecular sequence." [http://edamontology.org] -comment: See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1094 ! Sequence type +id: EDAM_operation:0350 +name: Sequence database search (by sequence using word-based methods) +comment: Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence similarity search (word-based methods)" EXACT [] +created_in: "beta12orEarlier" +def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0288 ! Sequence word comparison +is_a: EDAM_operation:0346 ! Sequence database search (by sequence) [Term] -id: EDAM_data:1106 -name: dbSNP ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a dbSNP database entry." [http://edamontology.org] -synonym: "dbSNP identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:2294 ! Sequence variation ID +id: EDAM_operation:0351 +name: Sequence database search (by sequence using profile-based methods) +comment: This includes tools based on PSI-BLAST. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence similarity search (profile-based methods)" EXACT [] +created_in: "beta12orEarlier" +def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0300 ! Sequence-profile alignment construction +is_a: EDAM_operation:0346 ! Sequence database search (by sequence) +[Term] +id: EDAM_operation:0352 +name: Sequence database search (by sequence using local alignment-based methods) +comment: This includes tools based on the Smith-Waterman algorithm or FASTA. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence similarity search (local alignment-based methods) " EXACT [] +created_in: "beta12orEarlier" +def: "Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0346 ! Sequence database search (by sequence) +is_a: EDAM_operation:0493 ! Pairwise sequence alignment construction (local) +relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] -id: EDAM_data:2805 -name: GeneSNP ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a GeneSNP database entry." [http://edamontology.org] -is_a: EDAM_data:2294 ! Sequence variation ID +id: EDAM_operation:0353 +name: Sequence database search (by sequence using global alignment-based methods) +comment: This includes tools based on the Needleman and Wunsch algorithm. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence similarity search (global alignment-based methods)" EXACT [] +created_in: "beta12orEarlier" +def: "Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0346 ! Sequence database search (by sequence) +is_a: EDAM_operation:0494 ! Pairwise sequence alignment construction (global) +relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] -id: EDAM_data:1112 -name: Sequence cluster ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a cluster of molecular sequence(s)." [http://edamontology.org] -is_a: EDAM_data:1064 ! Sequence set ID -relationship: is_identifier_of EDAM_data:1235 ! Sequence cluster +id: EDAM_operation:0354 +name: Sequence database search (by sequence for primer sequences) +comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence similarity search (primer sequences)" EXACT [] +created_in: "beta12orEarlier" +def: "Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0346 ! Sequence database search (by sequence) +relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] -id: EDAM_data:2346 -name: Sequence cluster ID (UniRef) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the UniRef database." [http://edamontology.org] -synonym: "UniRef entry accession" EXACT [http://edamontology.org] -synonym: "UniRef cluster id" EXACT [http://edamontology.org] -is_a: EDAM_data:1112 ! Sequence cluster ID +id: EDAM_operation:0355 +name: Sequence database search (by molecular weight) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Peptide mass fingerprinting" EXACT [] +synonym: "Protein fingerprinting" EXACT [] +created_in: "beta12orEarlier" +def: "Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property) +relationship: has_input EDAM_data:0944 ! Peptide mass fingerprint +relationship: has_topic EDAM_topic:0123 ! Protein properties +relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] -id: EDAM_data:1113 -name: Sequence cluster ID (COG) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the COG database." [http://edamontology.org] -synonym: "COG ID" EXACT [http://edamontology.org] -is_a: EDAM_data:1112 ! Sequence cluster ID +id: EDAM_operation:0356 +name: Sequence database search (by isoelectric point) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property) +relationship: has_topic EDAM_topic:0123 ! Protein properties [Term] -id: EDAM_data:1104 -name: Sequence cluster ID (UniGene) -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of an entry (gene cluster) from the NCBI UniGene database." [http://edamontology.org] -synonym: "UniGene ID" EXACT [http://edamontology.org] -synonym: "UniGene identifier" EXACT [http://edamontology.org] -synonym: "UniGene cluster ID" EXACT [http://edamontology.org] -synonym: "UniGene cluster id" EXACT [http://edamontology.org] -is_a: EDAM_data:1112 ! Sequence cluster ID +id: EDAM_operation:0357 +name: Structure retrieval (by code) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Query a tertiary structure database and retrieve entries with a given entry code or accession number." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1814 ! Structure retrieval [Term] -id: EDAM_data:2220 -name: Sequence cluster ID (SYSTERS) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a sequence cluster from the SYSTERS database." [http://edamontology.org] -synonym: "SYSTERS cluster ID" EXACT [http://edamontology.org] -is_a: EDAM_data:1112 ! Sequence cluster ID +id: EDAM_operation:0358 +name: Structure retrieval (by keyword) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Query a tertiary structure database and retrieve entries containing a given keyword." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1814 ! Structure retrieval [Term] -id: EDAM_data:2612 -name: Sequence cluster ID (CluSTr) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a sequence cluster from the CluSTr database." [http://edamontology.org] -synonym: "CluSTr cluster ID" EXACT [http://edamontology.org] -synonym: "CluSTr ID" EXACT [http://edamontology.org] -regex: "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?" -is_a: EDAM_data:1112 ! Sequence cluster ID +id: EDAM_operation:0359 +name: Structure database search (by sequence) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Structure retrieval by sequence" EXACT [] +created_in: "beta12orEarlier" +def: "Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0339 ! Structure database search +is_a: EDAM_operation:2451 ! Sequence comparison +is_a: EDAM_operation:3093 ! Sequence screening [Term] -id: EDAM_data:2347 -name: Sequence cluster ID (UniRef100) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the UniRef100 database." [http://edamontology.org] -synonym: "UniRef100 entry accession" EXACT [http://edamontology.org] -synonym: "UniRef100 cluster id" EXACT [http://edamontology.org] -is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) +id: EDAM_operation:0360 +name: Structure database search (by structure) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Structural similarity search" EXACT [] +synonym: "Structure retrieval by structure" EXACT [] +created_in: "beta12orEarlier" +def: "Search a tertiary structure database and retrieve structures that are similar to a query structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0339 ! Structure database search +relationship: has_topic EDAM_topic:1770 ! Structure comparison [Term] -id: EDAM_data:2348 -name: Sequence cluster ID (UniRef90) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the UniRef90 database." [http://edamontology.org] -synonym: "UniRef90 entry accession" EXACT [http://edamontology.org] -synonym: "UniRef90 cluster id" EXACT [http://edamontology.org] -is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) +id: EDAM_operation:0361 +name: Sequence annotation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Annotate a molecular sequence record with terms from a controlled vocabulary." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0226 ! Annotation +relationship: has_input EDAM_data:0849 ! Sequence record +relationship: has_output EDAM_data:0849 ! Sequence record [Term] -id: EDAM_data:2349 -name: Sequence cluster ID (UniRef50) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the UniRef50 database." [http://edamontology.org] -synonym: "UniRef50 entry accession" EXACT [http://edamontology.org] -synonym: "UniRef50 cluster id" EXACT [http://edamontology.org] -is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) +id: EDAM_operation:0362 +name: Genome annotation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Annotate a genome sequence with terms from a controlled vocabulary." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0361 ! Sequence annotation +[Term] +id: EDAM_operation:0363 +name: Nucleic acid sequence reverse and complement +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate the reverse and / or complement of a nucleotide sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid) [Term] -id: EDAM_data:2761 -name: UTRSite ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs." [http://edamontology.org] -is_a: EDAM_data:1114 ! Sequence motif identifier +id: EDAM_operation:0364 +name: Random sequence generation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a random sequence, for example, with a specific character composition." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0230 ! Sequence generation +[Term] +id: EDAM_operation:0365 +name: Nucleic acid restriction digest +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate digest fragments for a nucleotide sequence containing restriction sites." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0262 ! Nucleic acid property calculation +is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid) +relationship: has_output EDAM_data:1239 ! Restriction digest +relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] -id: EDAM_data:1116 -name: ELM ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the ELMdb database of protein functional sites." [http://edamontology.org] -is_a: EDAM_data:1114 ! Sequence motif identifier +id: EDAM_operation:0366 +name: Protein sequence cleavage +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2514 ! Sequence generation (protein) +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) +relationship: has_output EDAM_data:1238 ! Proteolytic digest +relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification +[Term] +id: EDAM_operation:0367 +name: Sequence mutation and randomization +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0231 ! Sequence editing [Term] -id: EDAM_data:1117 -name: Prosite accession number -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry from the Prosite database." [http://edamontology.org] -synonym: "Prosite ID" EXACT [http://edamontology.org] -regex: "PS[0-9]{5}" -is_a: EDAM_data:1114 ! Sequence motif identifier +id: EDAM_operation:0368 +name: Sequence masking +comment: For example, SNPs or repeats in a DNA sequence might be masked. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Mask characters in a molecular sequence (replacing those characters with a mask character)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0231 ! Sequence editing +relationship: has_input EDAM_data:0851 ! Sequence mask character [Term] -id: EDAM_data:2714 -name: CDD PSSM-ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a position-specific scoring matrix from the CDD database." [http://edamontology.org] -is_a: EDAM_data:1115 ! Sequence profile ID +id: EDAM_operation:0369 +name: Sequence cutting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Cut (remove) characters or a region from a molecular sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0231 ! Sequence editing +[Term] +id: EDAM_operation:0370 +name: Restriction site creation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Create (or remove) restriction sites in sequences, for example using silent mutations." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid) +relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] -id: EDAM_data:1118 -name: HMMER hidden Markov model ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier or name of a HMMER hidden Markov model." [http://edamontology.org] -is_a: EDAM_data:1115 ! Sequence profile ID -relationship: is_identifier_of EDAM_data:1364 ! Hidden Markov model +id: EDAM_operation:0371 +name: DNA translation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Translate a DNA sequence into protein." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0233 ! Sequence conversion +relationship: has_topic EDAM_topic:0108 ! Translation [Term] -id: EDAM_data:1119 -name: JASPAR profile ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier or name of a profile from the JASPAR database." [http://edamontology.org] -is_a: EDAM_data:1115 ! Sequence profile ID +id: EDAM_operation:0372 +name: DNA transcription +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Transcribe a nucleotide sequence into mRNA sequence(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0233 ! Sequence conversion +relationship: has_topic EDAM_topic:0110 ! Transcription +[Term] +id: EDAM_operation:0377 +name: Sequence composition calculation (nucleic acid) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate base frequency or word composition of a nucleotide sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0236 ! Sequence composition calculation +is_a: EDAM_operation:0262 ! Nucleic acid property calculation [Term] -id: EDAM_data:2150 -name: Sequence profile name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a sequence profile." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1115 ! Sequence profile ID +id: EDAM_operation:0378 +name: Sequence composition calculation (protein) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate amino acid frequency or word composition of a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0236 ! Sequence composition calculation +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) [Term] -id: EDAM_data:1123 -name: TreeBASE study accession number -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry from the TreeBASE database." [http://edamontology.org] -is_a: EDAM_data:1068 ! Phylogenetic tree ID +id: EDAM_operation:0379 +name: Repeat sequence detection +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0237 ! Repeat sequence analysis +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1299 ! Sequence features (repeats) [Term] -id: EDAM_data:1124 -name: TreeFam accession number -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry from the TreeFam database." [http://edamontology.org] -is_a: EDAM_data:1068 ! Phylogenetic tree ID +id: EDAM_operation:0380 +name: Repeat sequence organisation analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse repeat sequence organization such as periodicity." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0236 ! Sequence composition calculation +is_a: EDAM_operation:0237 ! Repeat sequence analysis [Term] -id: EDAM_data:1126 -name: Comparison matrix name -namespace: identifier -subset: identifiers -subset: data -def: "Unique name or identifier of a comparison matrix." [http://edamontology.org] -comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. -synonym: "Substitution matrix name" EXACT [http://edamontology.org] -is_a: EDAM_data:1069 ! Comparison matrix identifier -is_a: EDAM_data:2099 ! Name -relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix +id: EDAM_operation:0383 +name: Protein hydropathy calculation (from structure) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0243 ! Protein property calculation (from structure) +is_a: EDAM_operation:2574 ! Protein hydropathy calculation +[Term] +id: EDAM_operation:0384 +name: Protein solvent accessibility calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate solvent accessible or buried surface areas in protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0243 ! Protein property calculation (from structure) +relationship: has_output EDAM_data:1542 ! Protein solvent accessibility +relationship: has_topic EDAM_topic:0137 ! Protein hydropathy [Term] -id: EDAM_data:1127 -name: PDB ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of an entry from the PDB database." [http://edamontology.org] -synonym: "PDB identifier" EXACT [http://edamontology.org] -synonym: "PDBID" EXACT [http://edamontology.org] -regex: "[a-zA-Z_0-9]{4}" -is_a: EDAM_data:1070 ! Structure ID +id: EDAM_operation:0385 +name: Protein hydropathy cluster calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify clusters of hydrophobic or charged residues in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0383 ! Protein hydropathy calculation (from structure) +is_a: EDAM_operation:0393 ! Protein residue cluster calculation +[Term] +id: EDAM_operation:0386 +name: Protein dipole moment calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate whether a protein structure has an unusually large net charge (dipole moment)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) +relationship: has_output EDAM_data:1545 ! Protein dipole moment [Term] -id: EDAM_data:2667 -name: MMDB ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of an entry from the MMDB database." [http://edamontology.org] -synonym: "MMDB accession" EXACT [http://edamontology.org] -regex: "[0-9]{1,5}" -is_a: EDAM_data:1070 ! Structure ID +id: EDAM_operation:0387 +name: Protein surface and interior calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0384 ! Protein solvent accessibility calculation +relationship: has_output EDAM_data:1543 ! Protein surface report +relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces +[Term] +id: EDAM_operation:0388 +name: Binding site prediction (from structure) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Ligand-binding and active site prediction (from structure)" EXACT [] +created_in: "beta12orEarlier" +def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0245 ! Protein structural motif recognition +is_a: EDAM_operation:2575 ! Binding site prediction [Term] -id: EDAM_data:2793 -name: SISYPHUS ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the SISYPHUS database of tertiary structure alignments." [http://edamontology.org] -is_a: EDAM_data:1072 ! Structure alignment ID +id: EDAM_operation:0389 +name: Protein-nucleic acid binding site analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse RNA or DNA-binding sites in protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2949 ! Protein interaction analysis +relationship: has_input EDAM_data:1567 ! Protein-nucleic acid interaction +relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions +[Term] +id: EDAM_operation:0390 +name: Protein peeling +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Decompose a structure into compact or globular fragments (protein peeling)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0246 ! Protein domain recognition +relationship: has_output EDAM_data:0901 ! Protein features (domains) [Term] -id: EDAM_data:1128 -name: AAindex ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the AAindex database." [http://edamontology.org] -is_a: EDAM_data:1073 ! Amino acid index ID +id: EDAM_operation:0391 +name: Protein distance matrix calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0248 ! Residue interaction calculation +relationship: has_output EDAM_data:1546 ! Protein distance matrix [Term] -id: EDAM_data:1074 -name: Protein interaction ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a report of protein interactions from a protein interaction database (typically)." [http://edamontology.org] -is_a: EDAM_data:2627 ! Molecular interaction ID +id: EDAM_operation:0392 +name: Protein contact map calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) +relationship: has_output EDAM_data:1547 ! Protein contact map +[Term] +id: EDAM_operation:0393 +name: Protein residue cluster calculation +comment: Cluster of contacting residues might be key structural residues. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate clusters of contacting residues in protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) +relationship: has_output EDAM_data:1548 ! Protein residue 3D cluster [Term] -id: EDAM_data:2628 -name: BioGRID interaction ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of an interaction from the BioGRID database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2627 ! Molecular interaction ID +id: EDAM_operation:0394 +name: Hydrogen bond calculation +comment: The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:HasHydrogenBonds +xref: WHATIF:ShowHydrogenBonds +xref: WHATIF:ShowHydrogenBondsM +created_in: "beta12orEarlier" +def: "Identify potential hydrogen bonds between amino acids and other groups." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0248 ! Residue interaction calculation +relationship: has_output EDAM_data:1549 ! Protein hydrogen bonds [Term] -id: EDAM_data:2636 -name: MatrixDB interaction ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of an interaction from the MatrixDB database." [http://edamontology.org] -regex: "([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)" -is_a: EDAM_data:2627 ! Molecular interaction ID +id: EDAM_operation:0395 +name: Residue non-canonical interaction detection +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate non-canonical atomic interactions in protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0248 ! Residue interaction calculation +is_a: EDAM_operation:0321 ! Protein model evaluation +relationship: has_output EDAM_data:1550 ! Protein non-canonical interactions [Term] -id: EDAM_data:1129 -name: BIND accession number -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry from the BIND database." [http://edamontology.org] -is_a: EDAM_data:1074 ! Protein interaction ID +id: EDAM_operation:0396 +name: Ramachandran plot calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate a Ramachandran plot of a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0249 ! Torsion angle calculation +relationship: has_output EDAM_data:1544 ! Ramachandran plot [Term] -id: EDAM_data:1130 -name: IntAct accession number -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry from the IntAct database." [http://edamontology.org] -regex: "EBI\-[0-9]+" -is_a: EDAM_data:1074 ! Protein interaction ID +id: EDAM_operation:0397 +name: Ramachandran plot evaluation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse (typically to validate) a Ramachandran plot of a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1844 ! Dihedral angle validation +relationship: has_input EDAM_data:1544 ! Ramachandran plot +relationship: has_output EDAM_data:1539 ! Protein structural quality report +[Term] +id: EDAM_operation:0398 +name: Protein molecular weight calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate the molecular weight of a protein sequence or fragments." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) +relationship: has_output EDAM_data:1519 ! Peptide molecular weights +relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] -id: EDAM_data:2302 -name: STRING ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the STRING database of protein-protein interactions." [http://edamontology.org] -is_a: EDAM_data:1074 ! Protein interaction ID +id: EDAM_operation:0399 +name: Protein extinction coefficient calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict extinction coefficients or optical density of a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) +relationship: has_output EDAM_data:1531 ! Protein extinction coefficient [Term] -id: EDAM_data:2615 -name: MINT ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the MINT database of protein-protein interactions." [http://edamontology.org] -regex: "MINT\-[0-9]{1,5}" -is_a: EDAM_data:1074 ! Protein interaction ID +id: EDAM_operation:0400 +name: Protein pH-dependent property calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate pH-dependent properties from pKa calculations of a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) +relationship: has_output EDAM_data:0897 ! Protein property +relationship: has_topic EDAM_topic:0137 ! Protein hydropathy [Term] -id: EDAM_data:2616 -name: DIP ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the DIP database of protein-protein interactions." [http://edamontology.org] -regex: "DIP[\:\-][0-9]{3}[EN]" -is_a: EDAM_data:1074 ! Protein interaction ID +id: EDAM_operation:0401 +name: Protein hydropathy calculation (from sequence) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Hydropathy calculation on a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2574 ! Protein hydropathy calculation [Term] -id: EDAM_data:2668 -name: iRefIndex ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the iRefIndex database of protein-protein interactions." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:1074 ! Protein interaction ID +id: EDAM_operation:0402 +name: Protein titration curve plotting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Plot a protein titration curve." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation +relationship: has_output EDAM_data:1527 ! Protein titration curve +[Term] +id: EDAM_operation:0403 +name: Protein isoelectric point calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate isoelectric point of a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation +relationship: has_output EDAM_data:1528 ! Protein isoelectric point [Term] -id: EDAM_data:1076 -name: Codon usage table name -namespace: identifier -subset: identifiers -subset: data -def: "Unique name of a codon usage table." [http://edamontology.org] -is_a: EDAM_data:2111 ! Codon usage table identifier -is_a: EDAM_data:2099 ! Name -relationship: is_identifier_of EDAM_data:1597 ! Codon usage table -relationship: is_identifier_of EDAM_data:1598 ! Genetic code +id: EDAM_operation:0404 +name: Protein hydrogen exchange rate calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Estimate hydrogen exchange rate of a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation +relationship: has_output EDAM_data:1530 ! Protein hydrogen exchange rate [Term] -id: EDAM_data:2356 -name: RFAM accession -namespace: identifier -subset: identifiers -subset: data -def: "Stable accession number of an entry (RNA family) from the RFAM database." [http://edamontology.org] -is_a: EDAM_data:2355 ! RNA family identifier -is_a: EDAM_data:2091 ! Accession +id: EDAM_operation:0405 +name: Protein hydrophobic region calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate hydrophobic or hydrophilic / charged regions of a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) +[Term] +id: EDAM_operation:0406 +name: Protein aliphatic index calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) +relationship: has_output EDAM_data:1521 ! Protein aliphatic index [Term] -id: EDAM_data:2606 -name: RFAM name -namespace: identifier -subset: identifiers -subset: data -def: "Name (not necessarily stable) an entry (RNA family) from the RFAM database." [http://edamontology.org] -is_a: EDAM_data:2355 ! RNA family identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_operation:0407 +name: Protein hydrophobic moment plotting +comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) +relationship: has_output EDAM_data:1520 ! Peptide hydrophobic moment [Term] -id: EDAM_data:2766 -name: HAMAP ID -namespace: identifier -subset: identifiers -subset: data -def: "Name of a protein family from the HAMAP database." [http://edamontology.org] -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0408 +name: Protein globularity prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) +relationship: has_output EDAM_data:1526 ! Protein globularity +[Term] +id: EDAM_operation:0409 +name: Protein solubility prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict the solubility or atomic solvation energy of a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) +relationship: has_output EDAM_data:1524 ! Protein solubility [Term] -id: EDAM_data:1132 -name: InterPro entry name -namespace: identifier -subset: identifiers -subset: data -def: "Name of an InterPro entry, usually indicating the type of protein matches for that entry." [http://edamontology.org] -is_a: EDAM_data:1131 ! Protein family name -relationship: is_identifier_of EDAM_data:1355 ! Protein signature +id: EDAM_operation:0410 +name: Protein crystallizability prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict crystallizability of a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) +relationship: has_output EDAM_data:1525 ! Protein crystallizability [Term] -id: EDAM_data:1133 -name: InterPro accession -namespace: identifier -subset: identifiers -subset: data -def: "Primary accession number of an InterPro entry." [http://edamontology.org] -comment: Every InterPro entry has a unique accession number to provide a persistent citation of database records. -synonym: "InterPro primary accession number" EXACT [http://edamontology.org] -synonym: "InterPro primary accession" EXACT [http://edamontology.org] -regex: "IPR[0-9]{6}" -example: "IPR015590" -is_a: EDAM_data:2910 ! Protein family accession -relationship: is_identifier_of EDAM_data:1355 ! Protein signature +id: EDAM_operation:0411 +name: Protein signal peptide detection (eukaryotes) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0418 ! Protein signal peptide detection +[Term] +id: EDAM_operation:0412 +name: Protein signal peptide detection (bacteria) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0418 ! Protein signal peptide detection [Term] -id: EDAM_data:1134 -name: InterPro secondary accession -namespace: identifier -subset: identifiers -subset: data -def: "Secondary accession number of an InterPro entry." [http://edamontology.org] -synonym: "InterPro secondary accession number" EXACT [http://edamontology.org] -is_a: EDAM_data:1133 ! InterPro accession -relationship: is_identifier_of EDAM_data:1355 ! Protein signature +id: EDAM_operation:0413 +name: MHC peptide immunogenicity prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction +[Term] +id: EDAM_operation:0414 +name: Protein feature prediction (from sequence) +comment: Methods typically involve scanning for known motifs, patterns and regular expressions. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence feature detection (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2479 ! Protein sequence analysis +is_a: EDAM_operation:3092 ! Protein feature prediction [Term] -id: EDAM_data:1135 -name: Gene3D ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the Gene3D database." [http://edamontology.org] -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0415 +name: Nucleic acid feature prediction +comment: Methods typically involve scanning for known motifs, patterns and regular expressions. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence feature detection (nucleic acid)" EXACT [] +created_in: "beta12orEarlier" +def: "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0239 ! Sequence motif recognition +is_a: EDAM_operation:0253 ! Feature prediction +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) +relationship: has_output EDAM_data:1276 ! Nucleic acid features +relationship: has_topic EDAM_topic:3073 ! Nucleic acid feature detection [Term] -id: EDAM_data:1136 -name: PIRSF ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the PIRSF database." [http://edamontology.org] -regex: "PIRSF[0-9]{6}" -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0416 +name: Epitope mapping +comment: Epitope mapping is commonly done during vaccine design. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict antigenic determinant sites (epitopes) in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2429 ! Mapping and assembly +is_a: EDAM_operation:3087 ! Protein site detection +relationship: has_output EDAM_data:1326 ! Protein features (binding sites) +relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] -id: EDAM_data:1137 -name: PRINTS code -namespace: identifier -subset: identifiers -subset: data -def: "The unique identifier of an entry in the PRINTS database." [http://edamontology.org] -regex: "PR[0-9]{5}" -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0417 +name: Protein post-translation modification site prediction +comment: Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict post-translation modification sites in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3087 ! Protein site detection +relationship: has_output EDAM_data:1324 ! Protein features (post-translation modifications) +relationship: has_topic EDAM_topic:0601 ! Protein modifications [Term] -id: EDAM_data:1138 -name: Pfam accession number -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a Pfam entry." [http://edamontology.org] -regex: "PF[0-9]{5}" -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0418 +name: Protein signal peptide detection +comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect or predict signal peptides and signal peptide cleavage sites in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2489 ! Protein subcellular localization prediction +is_a: EDAM_operation:3087 ! Protein site detection +relationship: has_output EDAM_data:1322 ! Protein features (signal peptides) +relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization +[Term] +id: EDAM_operation:0419 +name: Binding site prediction (from sequence) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Ligand-binding and active site prediction (from sequence)" EXACT [] +created_in: "beta12orEarlier" +def: "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2575 ! Binding site prediction +is_a: EDAM_operation:3087 ! Protein site detection [Term] -id: EDAM_data:2758 -name: Pfam clan ID -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of a Pfam clan." [http://edamontology.org] -regex: "CL[0-9]{4}" -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0420 +name: Protein-nucleic acid binding prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict RNA and DNA-binding binding sites in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0419 ! Binding site prediction (from sequence) +relationship: has_output EDAM_data:1326 ! Protein features (binding sites) +[Term] +id: EDAM_operation:0421 +name: Protein folding site prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2415 ! Protein folding analysis +is_a: EDAM_operation:3087 ! Protein site detection +relationship: has_output EDAM_data:2989 ! Protein features (key folding sites) [Term] -id: EDAM_data:2757 -name: Pfam domain name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a domain from the Pfam database." [http://edamontology.org] -regex: "PF[0-9]{5}" -is_a: EDAM_data:1131 ! Protein family name +id: EDAM_operation:0422 +name: Protein cleavage site prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect or predict cleavage sites (enzymatic or chemical) in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3087 ! Protein site detection +relationship: has_output EDAM_data:1323 ! Protein features (cleavage sites) +relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification +[Term] +id: EDAM_operation:0423 +name: Epitope mapping (MHC Class I) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict epitopes that bind to MHC class I molecules." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0416 ! Epitope mapping [Term] -id: EDAM_data:2782 -name: SMART domain name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a domain from the SMART database." [http://edamontology.org] -is_a: EDAM_data:1131 ! Protein family name - +id: EDAM_operation:0424 +name: Epitope mapping (MHC Class II) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict epitopes that bind to MHC class II molecules." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0416 ! Epitope mapping [Term] -id: EDAM_data:1139 -name: SMART accession number -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry from the SMART database." [http://edamontology.org] -regex: "SM[0-9]{5}" -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0425 +name: Whole gene prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2454 ! Gene and gene component prediction [Term] -id: EDAM_data:1140 -name: Superfamily hidden Markov model number -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier (number) of a hidden Markov model from the Superfamily database." [http://edamontology.org] -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0426 +name: Gene component prediction +comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2454 ! Gene and gene component prediction +[Term] +id: EDAM_operation:0427 +name: Transposon prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1301 ! Nucleic acid features (mobile genetic elements) [Term] -id: EDAM_data:1141 -name: TIGRFam ID -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org] -synonym: "TIGRFam accession number" EXACT [http://edamontology.org] -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0428 +name: PolyA signal detection +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect polyA signals in nucleotide sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1302 ! Nucleic acid features (PolyA signal or site) +[Term] +id: EDAM_operation:0429 +name: Quadruplex formation site detection +comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Quadruplex structure prediction" EXACT [] +created_in: "beta12orEarlier" +def: "Detect quadruplex-forming motifs in nucleotide sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1303 ! Nucleic acid features (quadruplexes) +relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] -id: EDAM_data:1142 -name: ProDom accession number -namespace: identifier -subset: identifiers -subset: data -def: "A ProDom domain family accession number." [http://edamontology.org] -comment: ProDom is a protein domain family database. -regex: "PD[0-9]+" -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0430 +name: CpG island and isochore detection +comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. +subset: bioinformatics +subset: edam +subset: operations +synonym: "CpG island and isochores detection" EXACT [] +synonym: "CpG island and isochores rendering" EXACT [] +created_in: "beta12orEarlier" +def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1304 ! Nucleic acid features (CpG island and isochore) +relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis +[Term] +id: EDAM_operation:0431 +name: Restriction site recognition +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1305 ! Nucleic acid features (restriction sites) +relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] -id: EDAM_data:2614 -name: TCDB ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins." [http://edamontology.org] -comment: OBO file for regular expression. -synonym: "TC number" EXACT [http://edamontology.org] -regex: "[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+" -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0432 +name: Nucleosome formation or exclusion sequence prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1306 ! Nucleic acid features (nucleosome exclusion sequences) [Term] -id: EDAM_data:2731 -name: Protein family ID (GeneFarm) -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org] -synonym: "GeneFarm family ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0433 +name: Splice site prediction +comment: Methods might require a pre-mRNA or genomic DNA sequence. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify, predict or analyse splice sites in nucleotide sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1307 ! Nucleic acid features (splice sites) +relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing +[Term] +id: EDAM_operation:0434 +name: Integrated gene prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict whole gene structure using a combination of multiple methods to achieve better predictions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0425 ! Whole gene prediction [Term] -id: EDAM_data:2783 -name: Protein family ID (PANTHER) -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry (family) from the PANTHER database." [http://edamontology.org] -synonym: "Panther family ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2910 ! Protein family accession +id: EDAM_operation:0435 +name: Operon prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Find operons (operators, promoters and genes) in bacteria genes." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0425 ! Whole gene prediction [Term] -id: EDAM_data:1143 -name: TRANSFAC accession number -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the TRANSFAC database." [http://edamontology.org] -is_a: EDAM_data:2911 ! Transcription factor accession +id: EDAM_operation:0436 +name: Coding region prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0426 ! Gene component prediction +relationship: has_output EDAM_data:1313 ! Nucleic acid features (coding sequence) +[Term] +id: EDAM_operation:0437 +name: Selenocysteine insertion sequence (SECIS) prediction +comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0426 ! Gene component prediction +relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] -id: EDAM_data:2716 -name: DBD ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a predicted transcription factor from the DBD database." [http://edamontology.org] -is_a: EDAM_data:2911 ! Transcription factor accession +id: EDAM_operation:0438 +name: Transcription regulatory element prediction +comment: This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0426 ! Gene component prediction +relationship: has_topic EDAM_topic:0110 ! Transcription +relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites [Term] -id: EDAM_data:2742 -name: AraC-XylS ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a transcription factor from the AraC-XylS database." [http://edamontology.org] -is_a: EDAM_data:2911 ! Transcription factor accession +id: EDAM_operation:0439 +name: Translation initiation site prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict translation initiation sites, possibly by searching a database of sites." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0436 ! Coding region prediction +relationship: has_topic EDAM_topic:0108 ! Translation [Term] -id: EDAM_data:2755 -name: Transcription factor name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a transcription factor." [http://edamontology.org] -is_a: EDAM_data:1077 ! Transcription factor identifier -is_a: EDAM_data:1009 ! Protein name +id: EDAM_operation:0440 +name: Promoter prediction +comment: Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction +relationship: has_output EDAM_data:1312 ! Gene features (promoter) [Term] -id: EDAM_data:1144 -name: ArrayExpress accession number -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry from the ArrayExpress database." [http://edamontology.org] -synonym: "ArrayExpress experiment ID" EXACT [http://edamontology.org] -regex: "[AEP]-[a-zA-Z_0-9]{4}-[0-9]+" -is_a: EDAM_data:1078 ! Microarray experiment annotation ID +id: EDAM_operation:0441 +name: Transcription regulatory element prediction (DNA-cis) +comment: Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction +[Term] +id: EDAM_operation:0442 +name: Transcription regulatory element prediction (RNA-cis) +comment: Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] -id: EDAM_data:1145 -name: PRIDE experiment accession number -namespace: identifier -subset: identifiers -subset: data -def: "PRIDE experiment accession number." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:1078 ! Microarray experiment annotation ID +id: EDAM_operation:0443 +name: Transcription regulatory element prediction (trans) +comment: Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Functional RNA identification" EXACT [] +created_in: "beta12orEarlier" +def: "Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction +relationship: has_topic EDAM_topic:3060 ! Regulatory RNA +[Term] +id: EDAM_operation:0444 +name: Matrix/scaffold attachment site prediction +comment: MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction +relationship: has_output EDAM_data:1308 ! Nucleic acid features (matrix/scaffold attachment sites) [Term] -id: EDAM_data:2710 -name: CleanEx dataset code -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database." [http://edamontology.org] -is_a: EDAM_data:1078 ! Microarray experiment annotation ID +id: EDAM_operation:0445 +name: Transcription factor binding site prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict transcription factor binding sites in DNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0440 ! Promoter prediction +relationship: has_output EDAM_data:1315 ! Gene features (TFBS) [Term] -id: EDAM_data:1146 -name: EMDB ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the EMDB electron microscopy database." [http://edamontology.org] -is_a: EDAM_data:1079 ! Electron microscopy model ID +id: EDAM_operation:0446 +name: Exonic splicing enhancer prediction +comment: An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict exonic splicing enhancers (ESE) in exons." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0440 ! Promoter prediction +relationship: has_output EDAM_data:2397 ! Nucleic acid features (exon) +relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] -id: EDAM_data:1147 -name: GEO accession number -namespace: identifier -subset: identifiers -subset: data -def: "Accession number of an entry from the GEO database." [http://edamontology.org] -regex: "o^GDS[0-9]+" -is_a: EDAM_data:1080 ! Gene expression report ID +id: EDAM_operation:0447 +name: Sequence alignment quality evaluation +comment: Evaluation might be purely sequence-based or use structural information. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Evaluate molecular sequence alignment accuracy." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0258 ! Sequence alignment analysis +is_a: EDAM_operation:2428 ! Evaluation and validation [Term] -id: EDAM_data:1148 -name: GermOnline ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the GermOnline database." [http://edamontology.org] -is_a: EDAM_data:1080 ! Gene expression report ID +id: EDAM_operation:0448 +name: Sequence alignment analysis (conservation) +comment: Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0258 ! Sequence alignment analysis +relationship: has_output EDAM_data:1415 ! Sequence alignment report (site conservation) +[Term] +id: EDAM_operation:0449 +name: Sequence alignment analysis (site correlation) +comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse correlations between sites in a molecular sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0258 ! Sequence alignment analysis +relationship: has_output EDAM_data:1416 ! Sequence alignment report (site correlation) [Term] -id: EDAM_data:1149 -name: EMAGE ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the EMAGE database." [http://edamontology.org] -is_a: EDAM_data:1080 ! Gene expression report ID +id: EDAM_operation:0450 +name: Sequence alignment analysis (chimeric sequence detection) +comment: A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detects chimeric sequences (chimeras) from a sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] -id: EDAM_data:2709 -name: CleanEx entry name -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a gene expression profile from the CleanEx database." [http://edamontology.org] -is_a: EDAM_data:1080 ! Gene expression report ID +id: EDAM_operation:0451 +name: Sequence alignment analysis (recombination detection) +comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] -id: EDAM_data:1150 -name: Disease ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from a database of disease." [http://edamontology.org] -is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:1622 ! Disease annotation +id: EDAM_operation:0452 +name: Sequence alignment analysis (indel detection) +comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify insertion, deletion and duplication events from a sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] -id: EDAM_data:1151 -name: HGVbase ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the HGVbase database." [http://edamontology.org] -is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID +id: EDAM_operation:0453 +name: Nucleosome formation potential prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict nucleosome formation potential of DNA sequences." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0432 ! Nucleosome formation or exclusion sequence prediction [Term] -id: EDAM_data:1152 -name: HIVDB identifier -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the HIVDB database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0842 ! Identifier +id: EDAM_operation:0455 +name: Nucleic acid thermodynamic property calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0262 ! Nucleic acid property calculation +relationship: has_output EDAM_data:2985 ! Nucleic acid thermodynamic data +[Term] +id: EDAM_operation:0456 +name: Nucleic acid melting profile plotting +comment: A melting profile is used to visualise and analyse partly melted DNA conformations. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate and plot a DNA or DNA/RNA melting profile." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0262 ! Nucleic acid property calculation +relationship: has_output EDAM_data:1583 ! Nucleic acid melting profile [Term] -id: EDAM_data:1153 -name: OMIM ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the OMIM database." [http://edamontology.org] -regex: "[*#+%^]?[0-9]{6}" -is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID +id: EDAM_operation:0457 +name: Nucleic acid stitch profile plotting +comment: A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate and plot a DNA or DNA/RNA stitch profile." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting +relationship: has_output EDAM_data:1587 ! Nucleic acid stitch profile [Term] -id: EDAM_data:2611 -name: ICD identifier -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a disease from the International Classification of Diseases (ICD) database." [http://edamontology.org] -regex: "[A-Z][0-9]+(\.[-[0-9]+])?" -is_a: EDAM_data:1150 ! Disease ID -relationship: is_identifier_of EDAM_data:1622 ! Disease annotation +id: EDAM_operation:0458 +name: Nucleic acid melting curve plotting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate and plot a DNA or DNA/RNA melting curve." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting +relationship: has_output EDAM_data:2958 ! Nucleic acid melting curve [Term] -id: EDAM_data:2800 -name: Orpha number -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a disease from the Orpha database." [http://edamontology.org] -is_a: EDAM_data:1150 ! Disease ID -relationship: is_identifier_of EDAM_data:1622 ! Disease annotation +id: EDAM_operation:0459 +name: Nucleic acid probability profile plotting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate and plot a DNA or DNA/RNA probability profile." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting +relationship: has_output EDAM_data:2959 ! Nucleic acid probability profile [Term] -id: EDAM_data:2651 -name: Disease ID (PharmGKB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] -regex: "PA[0-9]+" -is_a: EDAM_data:1150 ! Disease ID -is_a: EDAM_data:2649 ! PharmGKB ID +id: EDAM_operation:0460 +name: Nucleic acid temperature profile plotting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate and plot a DNA or DNA/RNA temperature profile." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting +relationship: has_output EDAM_data:2960 ! Nucleic acid temperature profile +[Term] +id: EDAM_operation:0461 +name: Nucleic acid curvature calculation +comment: This includes properties such as. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate curvature and flexibility / stiffness of a nucleotide sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0262 ! Nucleic acid property calculation +relationship: has_output EDAM_data:0912 ! Nucleic acid property +relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_data:2383 -name: EGA accession -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the EGA database." [http://edamontology.org] -is_a: EDAM_data:2382 ! Genotype experiment ID +id: EDAM_operation:0463 +name: microRNA detection +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) +relationship: has_output EDAM_data:1310 ! Nucleic acid features (microRNA) [Term] -id: EDAM_data:2342 -name: Pathway or network name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a biological pathway or network." [http://edamontology.org] -is_a: EDAM_data:1082 ! Pathway or network identifier +id: EDAM_operation:0464 +name: tRNA gene prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0425 ! Whole gene prediction +relationship: has_topic EDAM_topic:0663 ! tRNA [Term] -id: EDAM_data:2365 -name: Pathway or network accession -namespace: identifier -subset: identifiers -subset: data -def: "A persistent, unique identifier of a biological pathway or network (typically a database entry)." [http://edamontology.org] -is_a: EDAM_data:1082 ! Pathway or network identifier -is_a: EDAM_data:2091 ! Accession - +id: EDAM_operation:0465 +name: siRNA binding specificity prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) +relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] -id: EDAM_data:2637 -name: cPath ID -namespace: identifier -subset: identifiers -subset: data -def: "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database." [http://edamontology.org] -comment: These identifiers are unique within the cPath database, however, they are not stable between releases. -regex: "[0-9]+" -is_a: EDAM_data:2109 ! Identifier (hybrid) -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0467 +name: Protein secondary structure prediction (integrated) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0267 ! Protein secondary structure prediction +[Term] +id: EDAM_operation:0468 +name: Protein secondary structure prediction (helices) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict helical secondary structure of protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] -id: EDAM_data:2659 -name: Pathway ID (SMPDB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a pathway from the Small Molecule Pathway Database (SMPDB)." [http://edamontology.org] -regex: "SMP[0-9]{5}" -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0469 +name: Protein secondary structure prediction (turns) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict turn structure (for example beta hairpin turns) of protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0267 ! Protein secondary structure prediction +[Term] +id: EDAM_operation:0470 +name: Protein secondary structure prediction (coils) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] -id: EDAM_data:2837 -name: Pathway ID (BioSystems) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a pathway from the BioSystems pathway database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0471 +name: Protein secondary structure prediction (disulfide bonds) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict cysteine bonding state and disulfide bond partners in protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0267 ! Protein secondary structure prediction +[Term] +id: EDAM_operation:0472 +name: GPCR prediction +subset: bioinformatics +subset: edam +subset: operations +synonym: "G protein-coupled receptor (GPCR) prediction" EXACT [] +created_in: "beta12orEarlier" +def: "Predict G protein-coupled receptors (GPCR)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0269 ! Transmembrane protein prediction +is_a: EDAM_operation:0473 ! GPCR analysis [Term] -id: EDAM_data:2650 -name: Pathway ID (PharmGKB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] -regex: "PA[0-9]+" -is_a: EDAM_data:2365 ! Pathway or network accession -is_a: EDAM_data:2649 ! PharmGKB ID +id: EDAM_operation:0473 +name: GPCR analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "G protein-coupled receptor (GPCR) analysis" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse G-protein coupled receptor proteins (GPCRs)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0270 ! Transmembrane protein analysis +relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) +relationship: has_topic EDAM_topic:0820 ! Membrane proteins [Term] -id: EDAM_data:2345 -name: Pathway ID (ConsensusPathDB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a pathway from the ConsensusPathDB pathway database." [http://edamontology.org] -is_a: EDAM_data:2917 ! ConsensusPathDB identifier -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0474 +name: Protein structure prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict tertiary structure (backbone and side-chain conformation) of protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0271 ! Structure prediction +is_a: EDAM_operation:2459 ! Structure processing (protein) +is_a: EDAM_operation:2479 ! Protein sequence analysis +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_output EDAM_data:1460 ! Protein structure +relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction +[Term] +id: EDAM_operation:0475 +name: Nucleic acid structure prediction +comment: Methods might identify thermodynamically stable or evolutionarily conserved structures. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict tertiary structure of DNA or RNA." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0271 ! Structure prediction +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +is_a: EDAM_operation:2519 ! Structure processing (nucleic acid) +is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) +relationship: has_output EDAM_data:1459 ! Nucleic acid structure +relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] -id: EDAM_data:2343 -name: Pathway ID (KEGG) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a pathway from the KEGG pathway database." [http://edamontology.org] -synonym: "KEGG pathway ID" EXACT [http://edamontology.org] -regex: "[a-zA-Z_0-9]{2,3}[0-9]{5}" -is_a: EDAM_data:2365 ! Pathway or network accession -is_a: EDAM_data:1154 ! KEGG object identifier +id: EDAM_operation:0476 +name: Ab initio structure prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict tertiary structure of protein sequence(s) without homologs of known structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0474 ! Protein structure prediction +relationship: has_topic EDAM_topic:0174 ! Ab initio structure prediction [Term] -id: EDAM_data:2344 -name: Pathway ID (NCI-Nature) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a pathway from the NCI-Nature pathway database." [http://edamontology.org] -regex: "[a-zA-Z_0-9]+" -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0477 +name: Protein modelling +comment: The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Comparative modelling" EXACT [] +synonym: "Homology modelling" EXACT [] +synonym: "Homology structure modelling" EXACT [] +synonym: "Protein structure comparative modelling" EXACT [] +created_in: "beta12orEarlier" +def: "Build a three-dimensional protein model based on known (for example homologs) structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0474 ! Protein structure prediction +is_a: EDAM_operation:2406 ! Protein structure analysis +is_a: EDAM_operation:2426 ! Modelling and simulation +relationship: has_topic EDAM_topic:0175 ! Homology modelling +[Term] +id: EDAM_operation:0478 +name: Protein docking +comment: This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0477 ! Protein modelling +is_a: EDAM_operation:2492 ! Protein interaction prediction +relationship: has_output EDAM_data:1461 ! Protein-ligand complex +relationship: has_output EDAM_data:2877 ! Protein complex +relationship: has_topic EDAM_topic:0177 ! Molecular docking [Term] -id: EDAM_data:1155 -name: Pathway ID (reactome) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the Reactome database." [http://edamontology.org] -synonym: "Reactome ID" EXACT [http://edamontology.org] -regex: "REACT_[0-9]+(\.[0-9]+)?" -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0479 +name: Protein modelling (backbone) +comment: Methods might require a preliminary C(alpha) trace. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Model protein backbone conformation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0477 ! Protein modelling [Term] -id: EDAM_data:1156 -name: Pathway ID (aMAZE) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the aMAZE database." [http://edamontology.org] -synonym: "aMAZE ID" EXACT [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1082 ! Pathway or network identifier +id: EDAM_operation:0480 +name: Protein modelling (side chains) +comment: Methods might use a residue rotamer library. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0477 ! Protein modelling [Term] -id: EDAM_data:1157 -name: Pathway ID (BioCyc) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an pathway from the BioCyc biological pathways database." [http://edamontology.org] -synonym: "BioCyc pathway ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2365 ! Pathway or network accession -is_a: EDAM_data:2104 ! BioCyc ID +id: EDAM_operation:0481 +name: Protein modelling (loops) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Model loop conformation in protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0477 ! Protein modelling +[Term] +id: EDAM_operation:0482 +name: Protein-ligand docking +comment: Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Virtual ligand screening" EXACT [] +created_in: "beta12orEarlier" +def: "Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0478 ! Protein docking +relationship: has_output EDAM_data:1461 ! Protein-ligand complex +relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] -id: EDAM_data:1158 -name: Pathway ID (INOH) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the INOH database." [http://edamontology.org] -synonym: "INOH identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0483 +name: Structured RNA prediction and optimisation +subset: bioinformatics +subset: edam +subset: operations +synonym: "Nucleic acid folding family identification" EXACT [] +synonym: "RNA inverse folding" EXACT [] +created_in: "beta12orEarlier" +def: "Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2425 ! Optimisation and refinement +is_a: EDAM_operation:3095 ! Nucleic acid design +relationship: has_output EDAM_data:1234 ! Sequence set (nucleic acid) +relationship: has_topic EDAM_topic:2953 ! Nucleic acid design +[Term] +id: EDAM_operation:0484 +name: SNP detection +comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Single nucleotide polymorphism detection" EXACT [] +created_in: "beta12orEarlier" +def: "Find single nucleotide polymorphisms (SNPs) between sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0258 ! Sequence alignment analysis +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +is_a: EDAM_operation:3202 ! Mutation detection +relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] -id: EDAM_data:1159 -name: Pathway ID (PATIKA) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the PATIKA database." [http://edamontology.org] -synonym: "PATIKA ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0485 +name: Radiation Hybrid Mapping +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2944 ! Physical mapping +relationship: has_output EDAM_data:2870 ! Radiation hybrid map [Term] -id: EDAM_data:1160 -name: Pathway ID (CPDB) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB." [http://edamontology.org] -comment: This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. -synonym: "CPDB ID" EXACT [http://edamontology.org] -is_a: EDAM_data:2365 ! Pathway or network accession - +id: EDAM_operation:0486 +name: Functional mapping +comment: This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Map the genetic architecture of dynamic complex traits." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0282 ! Genetic mapping [Term] -id: EDAM_data:1161 -name: Pathway ID (Panther) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a biological pathway from the Panther Pathways database." [http://edamontology.org] -synonym: "Panther Pathways ID" EXACT [http://edamontology.org] -regex: "PTHR[0-9]{5}" -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0487 +name: Haplotype inference +comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). +subset: bioinformatics +subset: edam +subset: operations +synonym: "Haplotype mapping" EXACT [] +synonym: "Haplotype reconstruction" EXACT [] +created_in: "beta12orEarlier" +def: "Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0283 ! Linkage analysis +relationship: has_output EDAM_data:1863 ! Haplotype map [Term] -id: EDAM_data:2645 -name: Pathway ID (Unipathway) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a biological pathway from the Unipathway database." [http://edamontology.org] -synonym: "upaid" EXACT [http://edamontology.org] -regex: "UPA[0-9]{5}" -is_a: EDAM_data:2365 ! Pathway or network accession - +id: EDAM_operation:0488 +name: Linkage disequilibrium calculation +comment: Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0283 ! Linkage analysis +relationship: has_output EDAM_data:1634 ! Gene annotation (linkage disequilibrium) [Term] -id: EDAM_data:2670 -name: Pathway ID (DQCS) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS)." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2365 ! Pathway or network accession +id: EDAM_operation:0489 +name: Genetic code prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict genetic code from analysis of codon usage data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0286 ! Codon usage analysis +is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) +relationship: has_output EDAM_data:1598 ! Genetic code [Term] -id: EDAM_data:2591 -name: Brite hierarchy ID -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an entry from the Brite database of biological hierarchies." [http://edamontology.org] -is_a: EDAM_data:2891 ! Biological model accession +id: EDAM_operation:0490 +name: Dotplot plotting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Draw a dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0288 ! Sequence word comparison +is_a: EDAM_operation:0565 ! Sequence alignment rendering +relationship: has_output EDAM_data:0862 ! Dotplot [Term] -id: EDAM_data:1162 -name: MIRIAM identifier -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a MIRIAM data resource." [http://edamontology.org] -comment: This is the identifier used internally by MIRIAM for a data type. -regex: "MIR:[0-9]{8}" -example: "MIR:00100005" -is_a: EDAM_data:2902 ! Data resource definition accession -relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype +id: EDAM_operation:0491 +name: Pairwise sequence alignment construction +comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Pairwise sequence alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align exactly two molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0292 ! Sequence alignment construction +relationship: has_output EDAM_data:1381 ! Sequence alignment (pair) [Term] -id: EDAM_data:1163 -name: MIRIAM data type name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a data type from the MIRIAM database." [http://edamontology.org] -is_a: EDAM_data:2253 ! Data resource definition name -relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype +id: EDAM_operation:0492 +name: Multiple sequence alignment construction +comment: This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Multiple sequence alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align two or more molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0292 ! Sequence alignment construction [Term] -id: EDAM_data:2253 -name: Data resource definition name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a data type." [http://edamontology.org] -is_a: EDAM_data:1084 ! Data resource definition identifier -is_a: EDAM_data:2099 ! Name - +id: EDAM_operation:0493 +name: Pairwise sequence alignment construction (local) +comment: Local alignment methods identify regions of local similarity. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Local pairwise sequence alignment construction" EXACT [] +synonym: "Pairwise sequence alignment (local)" EXACT [] +created_in: "beta12orEarlier" +def: "Locally align exactly two molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction [Term] -id: EDAM_data:2902 -name: Data resource definition accession -namespace: identifier -subset: identifiers -subset: data -def: "Accession of a data definition (catalogued in a database)." [http://edamontology.org] -is_a: EDAM_data:1084 ! Data resource definition identifier -is_a: EDAM_data:2091 ! Accession - +id: EDAM_operation:0494 +name: Pairwise sequence alignment construction (global) +comment: Global alignment methods identify similarity across the entire length of the sequences. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Global pairwise sequence alignment construction" EXACT [] +synonym: "Pairwise sequence alignment (global)" EXACT [] +created_in: "beta12orEarlier" +def: "Globally align exactly two molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction [Term] -id: EDAM_data:1164 -name: MIRIAM URI -namespace: identifier -subset: identifiers -subset: data -def: "The URI (URL or URN) of a data entity from the MIRIAM database." [http://edamontology.org] -comment: A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. -example: "urn:miriam:pubmed:16333295" "urn:miriam:obo.go:GO%3A0045202" !{note="'urn:miriam:pubmed:16333295' is the MIRIAM URI of the publication about MIRIAM, whereas 'urn:miriam:obo.go:GO%3A0045202' refers to GO"} -is_a: EDAM_data:2902 ! Data resource definition accession -is_a: EDAM_data:1047 ! URI -relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype +id: EDAM_operation:0495 +name: Multiple sequence alignment construction (local) +comment: Local alignment methods identify regions of local similarity. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Local multiple sequence alignment construction" EXACT [] +synonym: "Multiple sequence alignment (local)" EXACT [] +created_in: "beta12orEarlier" +def: "Locally align two or more molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] -id: EDAM_data:1165 -name: MIRIAM data type primary name -namespace: identifier -subset: identifiers -subset: data -def: "The primary name of a data type from the MIRIAM database." [http://edamontology.org] -comment: The primary name of a MIRIAM data type is taken from a controlled vocabulary. -example: "UniProt" "Enzyme Nomenclature" !{note="A protein entity has the data type 'UniProt', an enzyme has the type 'Enzyme Nomenclature' etc."} -is_a: EDAM_data:1163 ! MIRIAM data type name +id: EDAM_operation:0496 +name: Multiple sequence alignment construction (global) +comment: Global alignment methods identify similarity across the entire length of the sequences. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Global multiple sequence alignment construction" EXACT [] +synonym: "Multiple sequence alignment (global)" EXACT [] +created_in: "beta12orEarlier" +def: "Globally align two or more molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] -id: EDAM_data:1166 -name: MIRIAM data type synonymous name -namespace: identifier -subset: identifiers -subset: data -def: "A synonymous name of a data type from the MIRIAM database." [http://edamontology.org] -comment: A synonymous name for a MIRIAM data type taken from a controlled vocabulary. -is_a: EDAM_data:1163 ! MIRIAM data type name - +id: EDAM_operation:0497 +name: Multiple sequence alignment construction (constrained) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Constrained multiple sequence alignment construction" EXACT [] +synonym: "Multiple sequence alignment (constrained)" EXACT [] +created_in: "beta12orEarlier" +def: "Align two or more molecular sequences with user-defined constraints." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] -id: EDAM_data:2106 -name: Reaction ID (BioCyc) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a biological reaction from the BioCyc reactions database." [http://edamontology.org] -is_a: EDAM_data:2108 ! Reaction ID -is_a: EDAM_data:2104 ! BioCyc ID -relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids - +id: EDAM_operation:0498 +name: Multiple sequence alignment construction (consensus) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Consensus multiple sequence alignment construction" EXACT [] +synonym: "Multiple sequence alignment (consensus)" EXACT [] +created_in: "beta12orEarlier" +def: "Align two or more molecular sequences using multiple methods to achieve higher quality." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] -id: EDAM_data:2309 -name: Reaction ID (SABIO-RK) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a biological reaction from the SABIO-RK reactions database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2108 ! Reaction ID +id: EDAM_operation:0499 +name: Multiple sequence alignment construction (phylogenetic tree-based) +comment: This is supposed to give a more biologically meaningful alignment than standard alignments. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Multiple sequence alignment (phylogenetic tree-based)" EXACT [] +synonym: "Phylogenetic tree-based multiple sequence alignment construction" EXACT [] +created_in: "beta12orEarlier" +def: "Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0492 ! Multiple sequence alignment construction +relationship: has_topic EDAM_topic:0084 ! Phylogenetics +[Term] +id: EDAM_operation:0500 +name: Secondary structure alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Secondary structure alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align molecular secondary structure (represented as a 1D string)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0294 ! Structure-based sequence alignment construction +is_a: EDAM_operation:2482 ! Secondary structure processing +is_a: EDAM_operation:2931 ! Secondary structure comparison +relationship: has_output EDAM_data:2366 ! Secondary structure alignment +relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] -id: EDAM_data:2648 -name: Reaction kinetics ID (SABIO-RK) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2309 ! Reaction ID (SABIO-RK) +id: EDAM_operation:0501 +name: Protein secondary structure alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein secondary structure alignment" EXACT [] +synonym: "Secondary structure alignment (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "Align protein secondary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0500 ! Secondary structure alignment construction +is_a: EDAM_operation:2488 ! Protein secondary structure comparison +relationship: has_output EDAM_data:0878 ! Secondary structure alignment (protein) [Term] -id: EDAM_data:2608 -name: Reaction ID (KEGG) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of a biological reaction from the KEGG reactions database." [http://edamontology.org] -regex: "R[0-9]+" -is_a: EDAM_data:2108 ! Reaction ID -is_a: EDAM_data:1154 ! KEGG object identifier +id: EDAM_operation:0502 +name: RNA secondary structure alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "RNA secondary structure alignment" EXACT [] +synonym: "Secondary structure alignment (RNA)" EXACT [] +created_in: "beta12orEarlier" +def: "Align RNA secondary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0500 ! Secondary structure alignment construction +is_a: EDAM_operation:2439 ! RNA secondary structure processing +relationship: has_input EDAM_data:0880 ! RNA secondary structure record +relationship: has_output EDAM_data:0881 ! Secondary structure alignment (RNA) [Term] -id: EDAM_data:2641 -name: Reaction ID (MACie) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an enzyme reaction mechanism from the MACie database." [http://edamontology.org] -synonym: "MACie entry number" EXACT [http://edamontology.org] -regex: "M[0-9]{4}" -is_a: EDAM_data:2108 ! Reaction ID +id: EDAM_operation:0503 +name: Pairwise structure alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Pairwise structure alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0295 ! Structure alignment construction [Term] -id: EDAM_data:2644 -name: Reaction ID (Rhea) -namespace: identifier -subset: identifiers -subset: data -def: "Identifier of an enzyme-catalysed reaction from the Rhea database." [http://edamontology.org] -regex: "[0-9]{5}" -is_a: EDAM_data:2108 ! Reaction ID +id: EDAM_operation:0504 +name: Multiple structure alignment construction +comment: This includes methods that use an existing alignment. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Multiple structure alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0295 ! Structure alignment construction [Term] -id: EDAM_data:1167 -name: Taverna workflow ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a Taverna workflow." [http://edamontology.org] -is_a: EDAM_data:1083 ! Workflow ID - +id: EDAM_operation:0505 +name: Structure alignment (protein) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Align protein tertiary structures." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0295 ! Structure alignment construction [Term] -id: EDAM_data:1170 -name: Biological model name -namespace: identifier -subset: identifiers -subset: data -def: "Name of a biological (mathematical) model." [http://edamontology.org] -is_a: EDAM_data:1085 ! Biological model identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_operation:0506 +name: Structure alignment (RNA) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Align RNA tertiary structures." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0295 ! Structure alignment construction [Term] -id: EDAM_data:1171 -name: BioModel ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the BioModel database." [http://edamontology.org] -regex: "(BIOMD|MODEL)[0-9]{10}" -is_a: EDAM_data:2891 ! Biological model accession +id: EDAM_operation:0507 +name: Pairwise structure alignment construction (local) +comment: Local alignment methods identify regions of local similarity, common substructures etc. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Local pairwise structure alignment construction" EXACT [] +synonym: "Pairwise structure alignment (local)" EXACT [] +created_in: "beta12orEarlier" +def: "Locally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0503 ! Pairwise structure alignment construction [Term] -id: EDAM_data:2669 -name: ModelDB ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of an entry from the ModelDB database." [http://edamontology.org] -regex: "[0-9]+" -is_a: EDAM_data:2891 ! Biological model accession +id: EDAM_operation:0508 +name: Pairwise structure alignment construction (global) +comment: Global alignment methods identify similarity across the entire structures. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Global pairwise structure alignment construction" EXACT [] +synonym: "Pairwise structure alignment (global)" EXACT [] +created_in: "beta12orEarlier" +def: "Globally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0503 ! Pairwise structure alignment construction +[Term] +id: EDAM_operation:0509 +name: Multiple structure alignment construction (local) +comment: Local alignment methods identify regions of local similarity, common substructures etc. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Local multiple structure alignment construction" EXACT [] +synonym: "Multiple structure alignment (local)" EXACT [] +created_in: "beta12orEarlier" +def: "Locally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0504 ! Multiple structure alignment construction [Term] -id: EDAM_data:2339 -name: Ontology concept name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a concept in an ontology." [http://edamontology.org] -is_a: EDAM_data:3025 ! Ontology concept identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_operation:0510 +name: Multiple structure alignment construction (global) +comment: Global alignment methods identify similarity across the entire structures. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Global multiple structure alignment construction" EXACT [] +synonym: "Multiple structure alignment (global)" EXACT [] +created_in: "beta12orEarlier" +def: "Globally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0504 ! Multiple structure alignment construction +[Term] +id: EDAM_operation:0511 +name: Sequence profile alignment construction (pairwise) +comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Pairwise sequence profile alignment construction" EXACT [] +synonym: "Sequence profile alignment (pairwise)" EXACT [] +created_in: "beta12orEarlier" +def: "Align exactly two molecular profiles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0298 ! Sequence profile alignment construction [Term] -id: EDAM_data:1175 -name: BioPax concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from the BioPax ontology." [http://edamontology.org] -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0512 +name: Sequence profile alignment construction (multiple) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Multiple sequence profile alignment construction" EXACT [] +synonym: "Sequence profile alignment (multiple)" EXACT [] +created_in: "beta12orEarlier" +def: "Align two or more molecular profiles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0298 ! Sequence profile alignment construction [Term] -id: EDAM_data:1176 -name: GO concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from The Gene Ontology." [http://edamontology.org] -synonym: "GO concept identifier" EXACT [http://edamontology.org] -regex: "[0-9]{7}" "GO:[0-9]{7}" -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0513 +name: Structural (3D) profile alignment construction (pairwise) +comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Pairwise structural (3D) profile alignment construction" EXACT [] +synonym: "Structural (3D) profile alignment (pairwise)" EXACT [] +created_in: "beta12orEarlier" +def: "Align exactly two molecular Structural (3D) profiles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction [Term] -id: EDAM_data:1177 -name: MeSH concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from the MeSH vocabulary." [http://edamontology.org] -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0514 +name: Structural (3D) profile alignment construction (multiple) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Multiple structural (3D) profile alignment construction" EXACT [] +synonym: "Structural (3D) profile alignment (multiple)" EXACT [] +created_in: "beta12orEarlier" +def: "Align two or more molecular 3D profiles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction [Term] -id: EDAM_data:1178 -name: HGNC concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from the HGNC controlled vocabulary." [http://edamontology.org] -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0515 +name: Data retrieval (tool metadata) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Data retrieval (tool annotation)" EXACT [] +synonym: "Tool information retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) +relationship: has_output EDAM_data:0958 ! Tool metadata [Term] -id: EDAM_data:1179 -name: NCBI taxonomy ID -namespace: identifier -subset: identifiers -subset: data -def: "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." [http://edamontology.org] -regex: "[1-9][0-9]{0,8}" -example: "9662" "3483" "182682" -synonym: "NCBI taxonomy identifier" EXACT [http://edamontology.org] -synonym: "NCBI tax ID" EXACT [http://edamontology.org] -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0516 +name: Data retrieval (database metadata) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Data retrieval (database annotation)" EXACT [] +synonym: "Database information retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) +relationship: has_output EDAM_data:0957 ! Database metadata [Term] -id: EDAM_data:1180 -name: Plant Ontology concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from the Plant Ontology (PO)." [http://edamontology.org] -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0517 +name: PCR primer design (for large scale sequencing) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict primers for large scale sequencing." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0308 ! PCR primer design +relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] -id: EDAM_data:1181 -name: UMLS concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from the UMLS vocabulary." [http://edamontology.org] -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0518 +name: PCR primer design (for genotyping polymorphisms) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0308 ! PCR primer design [Term] -id: EDAM_data:1182 -name: FMA concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from Foundational Model of Anatomy." [http://edamontology.org] -comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. -regex: "FMA:[0-9]+" -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0519 +name: PCR primer design (for gene transcription profiling) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict primers for gene transcription profiling." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0308 ! PCR primer design +relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] -id: EDAM_data:1183 -name: EMAP concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from the EMAP mouse ontology." [http://edamontology.org] -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0520 +name: PCR primer design (for conserved primers) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict primers that are conserved across multiple genomes or species." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0308 ! PCR primer design [Term] -id: EDAM_data:1184 -name: ChEBI concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from the ChEBI ontology." [http://edamontology.org] -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0521 +name: PCR primer design (based on gene structure) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict primers based on gene structure, promoters, exon-exon junctions etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0308 ! PCR primer design +relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] -id: EDAM_data:1185 -name: MGED concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from the MGED ontology." [http://edamontology.org] -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0522 +name: PCR primer design (for methylation PCRs) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict primers for methylation PCRs." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0308 ! PCR primer design [Term] -id: EDAM_data:1186 -name: myGrid concept ID -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a concept from the myGrid ontology." [http://edamontology.org] -comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. -is_a: EDAM_data:1087 ! Ontology concept ID +id: EDAM_operation:0523 +name: Sequence assembly (mapping assembly) +comment: The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Sequence assembly by combining fragments using an existing backbone sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0310 ! Sequence assembly [Term] -id: EDAM_data:2705 -name: GO concept ID (cellular compartment) -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a 'cellular compartment' concept from the Gene Ontology." [http://edamontology.org] -synonym: "GO concept identifier (cellular compartment)" EXACT [http://edamontology.org] -regex: "[0-9]{7}" "GO:[0-9]{7}" -is_a: EDAM_data:1176 ! GO concept ID +id: EDAM_operation:0524 +name: Sequence assembly (de-novo assembly) +comment: De-novo assemblers are much slower and more memory intensive than mapping assemblers. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Sequence assembly by combining fragments into a new, previously unknown sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0310 ! Sequence assembly +[Term] +id: EDAM_operation:0525 +name: Sequence assembly (genome assembly) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Sequence assembly capable on a very large scale such as assembly of whole genomes." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0310 ! Sequence assembly [Term] -id: EDAM_data:2582 -name: GO concept ID (biological process) -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a 'biological process' concept from the the Gene Ontology." [http://edamontology.org] -regex: "[0-9]{7}" "GO:[0-9]{7}" -is_a: EDAM_data:1176 ! GO concept ID +id: EDAM_operation:0526 +name: Sequence assembly (EST assembly) +comment: Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Sequence assembly for EST sequences (transcribed mRNA)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0310 ! Sequence assembly [Term] -id: EDAM_data:2583 -name: GO concept ID (molecular function) -namespace: identifier -subset: identifiers -subset: data -def: "An identifier of a 'molecular function' concept from the the Gene Ontology." [http://edamontology.org] -regex: "[0-9]{7}" "GO:[0-9]{7}" -is_a: EDAM_data:1176 ! GO concept ID +id: EDAM_operation:0527 +name: Tag mapping +comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Tag to gene assignment" EXACT [] +created_in: "beta12orEarlier" +def: "Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2436 ! Gene expression profile annotation +relationship: has_output EDAM_data:0936 ! Sequence tag profile (with gene assignment) [Term] -id: EDAM_data:2581 -name: GO concept name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a concept from the GO ontology." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2339 ! Ontology concept name +id: EDAM_operation:0528 +name: SAGE data processing +subset: bioinformatics +subset: edam +subset: operations +synonym: "Serial analysis of gene expression data processing" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) serial analysis of gene expression (SAGE) data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2495 ! Gene expression data processing [Term] -id: EDAM_data:3026 -name: GO concept name (biological process) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a concept for a biological process from the GO ontology." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2339 ! Ontology concept name +id: EDAM_operation:0529 +name: MPSS data processing +subset: bioinformatics +subset: edam +subset: operations +synonym: "Massively parallel signature sequencing data processing" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) massively parallel signature sequencing (MPSS) data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2495 ! Gene expression data processing [Term] -id: EDAM_data:3027 -name: GO concept name (molecular function) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a concept for a molecular function from the GO ontology." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2339 ! Ontology concept name +id: EDAM_operation:0530 +name: SBS data processing +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequencing by synthesis data processing" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) sequencing by synthesis (SBS) data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2495 ! Gene expression data processing [Term] -id: EDAM_data:2584 -name: GO concept name (cellular component) -namespace: identifier -subset: identifiers -subset: data -def: "The name of a concept for a cellular component from the GO ontology." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:2339 ! Ontology concept name +id: EDAM_operation:0531 +name: Heat map generation +comment: The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a heat map of gene expression from microarray data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering +relationship: has_output EDAM_data:1636 ! Heat map +[Term] +id: EDAM_operation:0532 +name: Gene expression profile analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Functional profiling" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse one or more gene expression profiles, typically to interpret them in functional terms." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2435 ! Gene expression profile processing +relationship: has_input EDAM_data:0928 ! Gene expression profile +[Term] +id: EDAM_operation:0533 +name: Gene expression profile pathway mapping +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0532 ! Gene expression profile analysis +is_a: EDAM_operation:2497 ! Pathway or network analysis +relationship: has_output EDAM_data:2984 ! Pathway or network report +[Term] +id: EDAM_operation:0534 +name: Protein secondary structure assignment (from coordinate data) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign secondary structure from protein coordinate data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0319 ! Protein secondary structure assignment +is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) -! Different biological types of signature are listed below. Bioinformatics types (motif, profile, HMM etc) are given elsewhere +[Term] +id: EDAM_operation:0535 +name: Protein secondary structure assignment (from CD data) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign secondary structure from circular dichroism (CD) spectroscopic data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0319 ! Protein secondary structure assignment +relationship: has_input EDAM_data:0939 ! Protein circular dichroism (CD) spectroscopic data [Term] -id: EDAM_data:1187 -name: PubMed ID -namespace: identifier -subset: identifiers -subset: data -def: "PubMed unique identifier of an article." [http://edamontology.org] -synonym: "PMID" EXACT [http://edamontology.org] -regex: "[1-9][0-9]{0,8}" -example: "4963447" -is_a: EDAM_data:1088 ! Article ID +id: EDAM_operation:0536 +name: Protein structure assignment (from X-ray crystallographic data) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0320 ! Protein structure assignment +relationship: has_input EDAM_data:0937 ! Protein X-ray crystallographic data [Term] -id: EDAM_data:1188 -name: Digital Object Identifier -namespace: identifier -subset: identifiers -subset: data -def: "Digital Object Identifier (DOI) of a published article." [http://edamontology.org] -regex: "(doi\:)?[0-9]{2}\.[0-9]{4}/.*" -is_a: EDAM_data:1088 ! Article ID +id: EDAM_operation:0537 +name: Protein structure assignment (from NMR data) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0320 ! Protein structure assignment +relationship: has_input EDAM_data:0938 ! Protein NMR data [Term] -id: EDAM_data:1189 -name: Medline UI -namespace: identifier -subset: identifiers -subset: data -def: "Medline UI (unique identifier) of an article." [http://edamontology.org] -comment: The use of Medline UI has been replaced by the PubMed unique identifier. -synonym: "Medline unique identifier" EXACT [http://edamontology.org] -is_a: EDAM_data:1088 ! Article ID +id: EDAM_operation:0538 +name: Phylogenetic tree construction (data centric) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Construct a phylogenetic tree from a specific type of data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0323 ! Phylogenetic tree construction +[Term] +id: EDAM_operation:0539 +name: Phylogenetic tree construction (method centric) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Construct a phylogenetic tree using a specific method." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0323 ! Phylogenetic tree construction [Term] -id: EDAM_data:2634 -name: ISBN -namespace: identifier -subset: identifiers -subset: data -def: "The International Standard Book Number (ISBN) is for identifying printed books." [http://edamontology.org] -regex: "(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)" -is_a: EDAM_data:2633 ! Book ID +id: EDAM_operation:0540 +name: Phylogenetic tree construction (from molecular sequences) +comment: Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Phylogenetic tree construction from molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) +is_a: EDAM_operation:2403 ! Sequence analysis [Term] -id: EDAM_data:2374 -name: Spot serial number -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database." [http://edamontology.org] -is_a: EDAM_data:2373 ! Spot ID +id: EDAM_operation:0541 +name: Phylogenetic tree construction (from continuous quantitative characters) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Phylogenetic tree construction from continuous quantitative character data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) +relationship: has_input EDAM_data:1426 ! Phylogenetic continuous quantitative data +[Term] +id: EDAM_operation:0542 +name: Phylogenetic tree construction (from gene frequencies) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Phylogenetic tree construction from gene frequency data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) +relationship: has_input EDAM_data:2873 ! Phylogenetic gene frequencies data +relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] -id: EDAM_data:2375 -name: Spot ID (HSC-2DPAGE) -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database." [http://edamontology.org] -is_a: EDAM_data:2373 ! Spot ID +id: EDAM_operation:0543 +name: Phylogenetic tree construction (from polymorphism data) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) +relationship: has_topic EDAM_topic:0199 ! Genetic variation [Term] -id: EDAM_data:2588 -name: BlotBase blot ID -namespace: identifier -subset: identifiers -subset: data -def: "Unique identifier of a blot from a Northern Blot from the BlotBase database." [http://edamontology.org] -is_a: EDAM_data:2587 ! Blot ID +id: EDAM_operation:0544 +name: Phylogenetic species tree construction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences) [Term] -id: EDAM_data:1046 -name: Strain name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] -is_a: EDAM_data:2909 ! Organism name -is_a: EDAM_data:2379 ! Strain identifier +id: EDAM_operation:0545 +name: Phylogenetic tree construction (parsimony methods) +comment: This includes evolutionary parsimony (invariants) methods. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) +[Term] +id: EDAM_operation:0546 +name: Phylogenetic tree construction (minimum distance methods) +comment: This includes neighbor joining (NJ) clustering method. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] -id: EDAM_data:2778 -name: CCAP strain number -namespace: identifier -subset: identifiers -subset: data -def: "The number of a strain of algae and protozoa from the CCAP database." [http://edamontology.org] -is_a: EDAM_data:2912 ! Strain accession +id: EDAM_operation:0547 +name: Phylogenetic tree construction (maximum likelihood and Bayesian methods) +comment: Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] -id: EDAM_data:2316 -name: Cell line name -namespace: identifier -subset: identifiers -subset: data -def: "The name of a cell line." [http://edamontology.org] -is_a: EDAM_data:1046 ! Strain name +id: EDAM_operation:0548 +name: Phylogenetic tree construction (quartet methods) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] -id: EDAM_data:2112 -name: FlyBase primary identifier -namespace: identifier -subset: identifiers -subset: data -def: "Primary identifier of an object from the FlyBase database." [http://edamontology.org] -is_a: EDAM_data:1089 ! FlyBase ID +id: EDAM_operation:0549 +name: Phylogenetic tree construction (AI methods) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) +[Term] +id: EDAM_operation:0550 +name: Sequence alignment analysis (phylogenetic modelling) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify a plausible model of DNA substitution that explains a DNA sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2426 ! Modelling and simulation +is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) +relationship: has_output EDAM_data:1439 ! DNA substitution model +relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] -id: EDAM_data:2174 -name: FlyBase secondary identifier -namespace: identifier -subset: identifiers -subset: data -def: "Secondary identifier of an object from the FlyBase database." [http://edamontology.org] -comment: Secondary identifier are used to handle entries that were merged with or split from other entries in the database. -is_a: EDAM_data:1089 ! FlyBase ID +id: EDAM_operation:0551 +name: Phylogenetic tree analysis (shape) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Phylogenetic tree topology analysis" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse the shape (topology) of a phylogenetic tree." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0324 ! Phylogenetic tree analysis +relationship: has_output EDAM_data:1440 ! Phylogenetic tree report (tree shape) +[Term] +id: EDAM_operation:0552 +name: Phylogenetic tree bootstrapping +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0324 ! Phylogenetic tree analysis +is_a: EDAM_operation:2428 ! Evaluation and validation +relationship: has_output EDAM_data:1441 ! Phylogenetic tree report (tree evaluation) [Term] -id: EDAM_data:1091 -name: WormBase name -namespace: identifier -subset: identifiers -subset: data -def: "Name of an object from the WormBase database, usually a human-readable name." [http://edamontology.org] -is_a: EDAM_data:2113 ! WormBase identifier -is_a: EDAM_data:2099 ! Name +id: EDAM_operation:0553 +name: Phylogenetic tree analysis (gene family prediction) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict families of genes and gene function based on their position in a phylogenetic tree." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0324 ! Phylogenetic tree analysis +relationship: has_output EDAM_data:0916 ! Gene annotation +relationship: has_topic EDAM_topic:0194 ! Phylogenomics [Term] -id: EDAM_data:1092 -name: WormBase class -namespace: identifier -subset: identifiers -subset: data -def: "Class of an object from the WormBase database." [http://edamontology.org] -comment: A WormBase class describes the type of object such as 'sequence' or 'protein'. -is_a: EDAM_data:2113 ! WormBase identifier +id: EDAM_operation:0554 +name: Phylogenetic tree analysis (natural selection) +comment: Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0324 ! Phylogenetic tree analysis +[Term] +id: EDAM_operation:0555 +name: Phylogenetic tree construction (consensus) +comment: Methods typically test for topological similarity between trees using for example a congruence index. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more phylogenetic trees to produce a consensus tree." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0323 ! Phylogenetic tree construction +is_a: EDAM_operation:0325 ! Phylogenetic tree comparison [Term] -id: EDAM_data:2254 -name: OBO file format name -namespace: identifier -subset: identifiers -subset: data -def: "Name of an OBO file format such as OBO-XML, plain and so on." [http://edamontology.org] -is_a: EDAM_data:2129 ! File format name +id: EDAM_operation:0556 +name: Phylogenetic sub/super tree detection +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more phylogenetic trees to detect subtrees or supertrees." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0325 ! Phylogenetic tree comparison +[Term] +id: EDAM_operation:0557 +name: Phylogenetic tree distances calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more phylogenetic trees to calculate distances between trees." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0325 ! Phylogenetic tree comparison +relationship: has_output EDAM_data:1442 ! Phylogenetic tree report (tree distances) +[Term] +id: EDAM_operation:0558 +name: Phylogenetic tree annotation +subset: bioinformatics +subset: edam +subset: operations +synonym: "CDAOAnnotation" RELATED [] +created_in: "beta12orEarlier" +def: "Annotate a phylogenetic tree with terms from a controlled vocabulary." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0226 ! Annotation +is_a: EDAM_operation:0326 ! Phylogenetic tree editing -! -! Format -! +[Term] +id: EDAM_operation:0559 +name: Peptide immunogen prediction and optimisation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict and optimise peptide ligands that elicit an immunological response." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction +is_a: EDAM_operation:2425 ! Optimisation and refinement +relationship: has_output EDAM_data:1460 ! Protein structure +relationship: has_topic EDAM_topic:0150 ! Protein design +relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] -id: EDAM_format:2350 -name: Format (typed) -namespace: format -subset: formats -def: "A broad class of format distinguished by the scientific nature of the data that is identified." [http://edamontology.org] -comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. -is_a: EDAM_format:1915 ! Format +id: EDAM_operation:0560 +name: DNA vaccine prediction and optimisation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict or optimise DNA to elicit (via DNA vaccination) an immunological response." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2425 ! Optimisation and refinement +is_a: EDAM_operation:3095 ! Nucleic acid design +relationship: has_topic EDAM_topic:0804 ! Immunoinformatics +relationship: has_topic EDAM_topic:2953 ! Nucleic acid design +[Term] +id: EDAM_operation:0561 +name: Sequence reformatting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Reformat (a file or other report of) molecular sequence(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0335 ! File reformatting +is_a: EDAM_operation:2121 ! Sequence file processing [Term] -id: EDAM_format:2330 -name: Textual format -namespace: format -subset: formats -def: "Textual format." [http://edamontology.org] -comment: Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or very precisely not plain-textual). -synonym: "Tabular format" NARROW [http://edamontology.org, http://filext.com/file-extension/TSV] !{note="Many textual formats used in bioinformatics are tabular (tab-separated values, TSV)."} -synonym: "Plain text" NARROW [http://edamontology.org] -synonym: "TXT" NARROW [http://filext.com/file-extension/TXT] -synonym: "Text File" NARROW [http://filext.com/file-extension/TXT] -synonym: "TSV" NARROW [http://filext.com/file-extension/TSV] -synonym: "Tab-Separated Values" NARROW [http://filext.com/file-extension/TSV] -is_a: EDAM_format:1915 ! Format +id: EDAM_operation:0562 +name: Sequence alignment reformatting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Reformat (a file or other report of) molecular sequence alignment(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0335 ! File reformatting +is_a: EDAM_operation:2122 ! Sequence alignment file processing [Term] -id: EDAM_format:2331 -name: HTML -namespace: format -subset: formats -def: "HTML format." [http://edamontology.org] -synonym: "Hypertext Markup Language" EXACT [http://edamontology.org, http://filext.com/file-extension/HTML] -synonym: "HTML" EXACT [http://filext.com/file-extension/HTML] !{note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."} -synonym: "HTM" EXACT [http://filext.com/file-extension/HTM] !{note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."} -is_a: EDAM_format:1915 ! Format -relationship: is_format_of EDAM_data:2048 ! Report +id: EDAM_operation:0563 +name: Codon usage table reformatting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Reformat a codon usage table." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0335 ! File reformatting +is_a: EDAM_operation:2433 ! Codon usage table processing +relationship: has_input EDAM_data:1597 ! Codon usage table +relationship: has_output EDAM_data:1597 ! Codon usage table [Term] -id: EDAM_format:2332 -name: XML -namespace: format -subset: formats -def: "eXtensible Markup Language (XML) format." [http://edamontology.org] -comment: Data in XML format can be serialised into text, or binary format. -synonym: "Extensible Markup Language" EXACT [http://edamontology.org, http://filext.com/file-extension/XML] -synonym: "XML" EXACT [http://filext.com/file-extension/XML] !{note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."} -is_a: EDAM_format:1915 ! Format +id: EDAM_operation:0564 +name: Sequence rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise, format or render a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering +is_a: EDAM_operation:2446 ! Sequence processing +relationship: has_input EDAM_data:2044 ! Sequence +relationship: has_output EDAM_data:2969 ! Sequence image [Term] -id: EDAM_format:2333 -name: Binary format -namespace: format -subset: formats -def: "Binary format." [http://edamontology.org] -comment: Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. -is_a: EDAM_format:1915 ! Format +id: EDAM_operation:0565 +name: Sequence alignment rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise, format or print a molecular sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering +is_a: EDAM_operation:2463 ! Sequence alignment processing +relationship: has_input EDAM_data:0863 ! Sequence alignment +relationship: has_output EDAM_data:1711 ! Sequence alignment image +[Term] +id: EDAM_operation:0566 +name: Sequence cluster rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise, format or render sequence clusters." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering +is_a: EDAM_operation:2452 ! Sequence cluster processing +relationship: has_input EDAM_data:1235 ! Sequence cluster [Term] -id: EDAM_format:2376 -name: RDF -namespace: format -subset: formats -def: "Resource Description Framework (RDF) format." [http://edamontology.org] -comment: Data in RDF format can be serialised into XML, textual, or binary format. -is_a: EDAM_format:1915 ! Format +id: EDAM_operation:0567 +name: Phylogenetic tree rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise or plot a phylogenetic tree." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering +is_a: EDAM_operation:2443 ! Phylogenetic tree processing +relationship: has_output EDAM_data:0872 ! Phylogenetic tree [Term] -id: EDAM_format:2921 -name: Sequence variation annotation format -namespace: format -subset: formats -def: "Format of sequence variation annotation." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0918 ! Nucleic acid features (variation) +id: EDAM_operation:0568 +name: RNA secondary structure rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering +is_a: EDAM_operation:2439 ! RNA secondary structure processing +relationship: has_input EDAM_data:0880 ! RNA secondary structure record +[Term] +id: EDAM_operation:0569 +name: Protein secondary structure rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Render and visualise protein secondary structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering +is_a: EDAM_operation:2444 ! Protein secondary structure processing +relationship: has_input EDAM_data:0876 ! Protein features (secondary structure) [Term] -id: EDAM_format:2919 -name: Sequence annotation track format -namespace: format -subset: formats -def: "Format of a sequence annotation track." [http://edamontology.org] -is_a: EDAM_format:1920 ! Sequence feature annotation format -relationship: is_format_of EDAM_data:3002 ! Sequence annotation track +id: EDAM_operation:0570 +name: Structure rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering +is_a: EDAM_operation:2465 ! Structure processing +relationship: has_input EDAM_data:0883 ! Structure +relationship: has_output EDAM_data:1710 ! Structure image [Term] -id: EDAM_format:2352 -name: BioXSD -namespace: format -subset: formats -def: "BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more)." [http://edamontology.org] -synonym: "BioXSD XML format" EXACT [http://edamontology.org] -xref: http://bioxsd.org !{documentation=true} -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:1919 ! Sequence record format -is_a: EDAM_format:1920 ! Sequence feature annotation format -is_a: EDAM_format:2555 ! Alignment format (XML) -is_a: EDAM_format:2332 ! XML -relationship: is_format_of EDAM_data:2044 ! Sequence -relationship: is_format_of EDAM_data:1255 ! Feature record -relationship: is_format_of EDAM_data:0863 ! Sequence alignment +id: EDAM_operation:0571 +name: Microarray data rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise microarray data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering +is_a: EDAM_operation:2435 ! Gene expression profile processing +relationship: has_input EDAM_data:3117 ! Microarray hybridisation data +relationship: has_output EDAM_data:2967 ! Microarray image [Term] -id: EDAM_format:2848 -name: Bibliographic reference format -namespace: format -subset: formats -def: "Format of a bibliographic reference." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0970 ! Bibliographic reference -relationship: is_format_of EDAM_data:2849 ! Abstract +id: EDAM_operation:0572 +name: Protein interaction network rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify and analyse networks of protein interactions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2445 ! Protein interaction network processing +is_a: EDAM_operation:3083 ! Pathway or network rendering +relationship: has_input EDAM_data:1663 ! Pathway or network (protein-protein interaction) +[Term] +id: EDAM_operation:0573 +name: Map rendering +subset: bioinformatics +subset: edam +subset: operations +synonym: "DNA map rendering" EXACT [] +created_in: "beta12orEarlier" +def: "Render and visualise a DNA map." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) +is_a: EDAM_operation:2521 ! Map data processing +relationship: has_input EDAM_data:1274 ! Map [Term] -id: EDAM_format:2334 -name: URI format -namespace: format -subset: formats -def: "Typical textual representation of a URI." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:1047 ! URI +id: EDAM_operation:0574 +name: Sequence motif rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Render a sequence with motifs." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0564 ! Sequence rendering [Term] -id: EDAM_format:1918 -name: Atomic data format -namespace: format -subset: formats -def: "Data format for an individual atom." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_format:1475 ! PDB database entry format +id: EDAM_operation:0575 +name: Restriction map rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise restriction maps in DNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0431 ! Restriction site recognition +is_a: EDAM_operation:0573 ! Map rendering +relationship: has_output EDAM_data:1289 ! Restriction map [Term] -id: EDAM_format:1919 -name: Sequence record format -namespace: format -subset: formats -def: "Data format for a molecular sequence record." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0849 ! Sequence record +id: EDAM_operation:0577 +name: DNA linear map rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Draw a linear maps of DNA." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0573 ! Map rendering [Term] -id: EDAM_format:1920 -name: Sequence feature annotation format -namespace: format -subset: formats -def: "Data format for molecular sequence feature information." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1255 ! Feature record +id: EDAM_operation:0578 +name: DNA circular map rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Draw a circular maps of DNA, for example a plasmid map." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0573 ! Map rendering [Term] -id: EDAM_format:1921 -name: Alignment format -namespace: format -subset: formats -def: "Data format for molecular sequence alignment information." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0863 ! Sequence alignment +id: EDAM_operation:0579 +name: Operon rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise operon structure etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0573 ! Map rendering +relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] -id: EDAM_format:2920 -name: Alignment format (pair only) -namespace: format -subset: formats -def: "Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences." [http://edamontology.org] -is_a: EDAM_format:1921 ! Alignment format -relationship: is_format_of EDAM_data:1381 ! Sequence alignment (pair) +id: EDAM_operation:1768 +name: Nucleic acid folding family identification +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify folding families of related RNAs." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0483 ! Structured RNA prediction and optimisation [Term] -id: EDAM_format:2006 -name: Phylogenetic tree format -namespace: format -subset: formats -def: "Data format for a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0872 ! Phylogenetic tree +id: EDAM_operation:1769 +name: Nucleic acid folding energy calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0279 ! Nucleic acid folding analysis [Term] -id: EDAM_format:2033 -name: Tertiary structure format -namespace: format -subset: formats -def: "Data format for a molecular tertiary structure." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) +id: EDAM_operation:1774 +name: Annotation retrieval +comment: Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Retrieve existing annotation (or documentation), typically annotation on a database entity." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:3167 -name: Experiment annotation format -namespace: format -subset: formats -def: "Data format for annotation on a laboratory experiment." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) +id: EDAM_operation:1777 +name: Protein function prediction +comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict general functional properties of a protein." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2414 ! Protein function analysis +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_topic EDAM_topic:2276 ! Protein function prediction +[Term] +id: EDAM_operation:1778 +name: Protein function comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare the functional properties of two or more proteins." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2414 ! Protein function analysis +is_a: EDAM_operation:2997 ! Protein comparison +relationship: has_topic EDAM_topic:1775 ! Protein function analysis [Term] -id: EDAM_format:2034 -name: Biological model format -namespace: format -subset: formats -def: "Data format for a biological model." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0950 ! Biological model +id: EDAM_operation:1780 +name: Sequence submission +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Submit a molecular sequence to a database." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2446 ! Sequence processing +relationship: has_input EDAM_data:2044 ! Sequence +relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition [Term] -id: EDAM_format:2014 -name: Sequence-profile alignment format -namespace: format -subset: formats -def: "Data format for a sequence-profile alignment." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0869 ! Sequence-profile alignment +id: EDAM_operation:1781 +name: Gene regulatory network analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse a known network of gene regulation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2496 ! Gene regulatory network processing +is_a: EDAM_operation:2497 ! Pathway or network analysis +relationship: has_input EDAM_data:2961 ! Pathway or network (gene regulation) [Term] -id: EDAM_format:2562 -name: Amino acid identifier format -namespace: format -subset: formats -def: "Text format (representation) of amino acid residues." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_data:0994 ! Amino acid identifier +id: EDAM_operation:1812 +name: Data loading +subset: bioinformatics +subset: edam +subset: operations +synonym: "Data submission" EXACT [] +synonym: "Database submission" EXACT [] +xref: WHATIF:UploadPDB +created_in: "beta12orEarlier" +def: "Prepare or load a user-specified data file so that it is available for use." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2409 ! File processing +relationship: has_input EDAM_data:0842 ! Identifier [Term] -id: EDAM_format:2017 -name: Amino acid index format -namespace: format -subset: formats -def: "Data format for an amino acid index." [http://edamontology.org] -is_a: EDAM_format:3033 ! Matrix format -relationship: is_format_of EDAM_data:1501 ! Amino acid index +id: EDAM_operation:1813 +name: Sequence retrieval +comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Data retrieval (sequences)" EXACT [] +created_in: "beta12orEarlier" +def: "Query a sequence data resource (typically a database) and retrieve sequences and / or annotation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2422 ! Data retrieval +is_a: EDAM_operation:2446 ! Sequence processing +relationship: has_output EDAM_data:2044 ! Sequence [Term] -id: EDAM_format:2020 -name: Article format -namespace: format -subset: formats -def: "Data format for a full-text scientific article." [http://edamontology.org] -synonym: "Literature format" EXACT [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0971 ! Article +id: EDAM_operation:1814 +name: Structure retrieval +comment: This includes direct retrieval methods but not those that perform calculations on the sequence or structure. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:DownloadPDB +xref: WHATIF:EchoPDB +created_in: "beta12orEarlier" +def: "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2422 ! Data retrieval +is_a: EDAM_operation:2465 ! Structure processing +relationship: has_output EDAM_data:0883 ! Structure [Term] -id: EDAM_format:2021 -name: Text mining report format -namespace: format -subset: formats -def: "Data format for an abstract (report) from text mining." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0972 ! Text mining report +id: EDAM_operation:1816 +name: Surface rendering +comment: A dot has three coordinates (x,y,z) and (typically) a color. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:GetSurfaceDots +created_in: "beta12orEarlier" +def: "Calculate the positions of dots that are homogeneously distributed over the surface of a molecule." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0570 ! Structure rendering +is_a: EDAM_operation:2462 ! Protein surface calculation [Term] -id: EDAM_format:2027 -name: Enzyme kinetics report format -namespace: format -subset: formats -def: "Data format for reports on enzyme kinetics." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:2024 ! Enzyme kinetics data +id: EDAM_operation:1817 +name: Protein atom surface calculation (accessible) +comment: Waters are not considered. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:AtomAccessibilitySolvent +xref: WHATIF:AtomAccessibilitySolventPlus +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility ('accessible surface') for each atom in a structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2460 ! Protein atom surface calculation [Term] -id: EDAM_format:2030 -name: Small molecule report format -namespace: format -subset: formats -def: "Format of a report on a chemical compound." [http://edamontology.org] -synonym: "Chemical compound annotation format" EXACT [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0962 ! Small molecule annotation +id: EDAM_operation:1818 +name: Protein atom surface calculation (accessible molecular) +comment: Waters are not considered. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:AtomAccessibilityMolecular +xref: WHATIF:AtomAccessibilityMolecularPlus +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2460 ! Protein atom surface calculation [Term] -id: EDAM_format:2031 -name: Gene annotation format -namespace: format -subset: formats -def: "Format of a report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0916 ! Gene annotation +id: EDAM_operation:1819 +name: Protein residue surface calculation (accessible) +comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ResidueAccessibilitySolvent +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility ('accessible surface') for each residue in a structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] -id: EDAM_format:2032 -name: Workflow format -namespace: format -subset: formats -def: "Format of a workflow." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:2972 ! Workflow +id: EDAM_operation:1820 +name: Protein residue surface calculation (vacuum accessible) +comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ResidueAccessibilityVacuum +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] -id: EDAM_format:2035 -name: Chemical formula format -namespace: format -subset: formats -def: "Text format of a chemical formula." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0846 ! Chemical formula +id: EDAM_operation:1821 +name: Protein residue surface calculation (accessible molecular) +comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ResidueAccessibilityMolecular +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] -id: EDAM_format:2036 -name: Phylogenetic character data format -namespace: format -subset: formats -def: "Format of raw (unplotted) phylogenetic data." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0871 ! Phylogenetic character data +id: EDAM_operation:1822 +name: Protein residue surface calculation (vacuum molecular) +comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ResidueAccessibilityVacuumMolecular +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] -id: EDAM_format:3097 !{since=beta13} -name: Protein domain classification format -namespace: format -subset: formats -def: "Format of data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0900 ! Protein domain classification +id: EDAM_operation:1823 +name: Protein surface calculation (accessible molecular) +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:TotAccessibilityMolecular +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2462 ! Protein surface calculation +[Term] +id: EDAM_operation:1824 +name: Protein surface calculation (accessible) +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:TotAccessibilitySolvent +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility ('accessible surface') for a structure as a whole." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2462 ! Protein surface calculation [Term] -id: EDAM_format:3098 !{since=beta13} -name: Raw SCOP domain classification format -namespace: format -subset: formats -def: "Format of raw SCOP domain classification data files." [http://edamontology.org] -comment: These are the parsable data files provided by SCOP. -is_a: EDAM_format:3097 ! Protein domain classification format +id: EDAM_operation:1825 +name: Backbone torsion angle calculation +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ResidueTorsionsBB +created_in: "beta12orEarlier" +def: "Calculate for each residue in a protein structure all its backbone torsion angles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] -id: EDAM_format:3099 !{since=beta13} -name: Raw CATH domain classification format -namespace: format -subset: formats -def: "Format of raw CATH domain classification data files." [http://edamontology.org] -comment: These are the parsable data files provided by CATH. -is_a: EDAM_format:3097 ! Protein domain classification format +id: EDAM_operation:1826 +name: Full torsion angle calculation +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ResidueTorsions +created_in: "beta12orEarlier" +def: "Calculate for each residue in a protein structure all its torsion angles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] -id: EDAM_format:3100 !{since=beta13} -name: CATH domain report format -namespace: format -subset: formats -def: "Format of summary of domain classification information for a CATH domain." [http://edamontology.org] -comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. -is_a: EDAM_format:3097 ! Protein domain classification format +id: EDAM_operation:1827 +name: Cysteine torsion angle calculation +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:CysteineTorsions +created_in: "beta12orEarlier" +def: "Calculate for each cysteine (bridge) all its torsion angles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0249 ! Torsion angle calculation +[Term] +id: EDAM_operation:1828 +name: Tau angle calculation +comment: Tau is the backbone angle N-Calpha-C (angle over the C-alpha). +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ShowTauAngle +created_in: "beta12orEarlier" +def: "For each amino acid in a protein structure calculate the backbone angle tau." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] -id: EDAM_format:2045 -name: Electron microscopy model format -namespace: format -subset: formats -def: "Annotation format for electron microscopy models." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2350 ! Format (typed) +id: EDAM_operation:1829 +name: Cysteine bridge detection +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ShowCysteineBridge +created_in: "beta12orEarlier" +def: "Detect cysteine bridges (from coordinate data) in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment +[Term] +id: EDAM_operation:1830 +name: Free cysteine detection +comment: A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ShowCysteineFree +created_in: "beta12orEarlier" +def: "Detect free cysteines in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] -id: EDAM_format:2049 -name: Phylogenetic tree report (tree distances) format -namespace: format -subset: formats -def: "Format for phylogenetic tree distance data." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1442 ! Phylogenetic tree report (tree distances) +id: EDAM_operation:1831 +name: Metal-bound cysteine detection +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ShowCysteineMetal +created_in: "beta12orEarlier" +def: "Detect cysteines that are bound to metal in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] -id: EDAM_format:2051 -name: Polymorphism report format -namespace: format -subset: formats -def: "Format for sequence polymorphism data." [http://edamontology.org] -is_obsolete: true !{since=1.0} -! is_a: EDAM_format:2350 ! Format (typed) -! relationship: is_format_of EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) +id: EDAM_operation:1832 +name: Residue contact calculation (residue-nucleic acid) +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:HasNucleicContacts +xref: WHATIF:ShowProteiNucleicContacts +created_in: "beta12orEarlier" +def: "Calculate protein residue contacts with nucleic acids in a structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0245 ! Protein structural motif recognition +is_a: EDAM_operation:0389 ! Protein-nucleic acid binding site analysis +is_a: EDAM_operation:2950 ! Residue contact calculation [Term] -id: EDAM_format:2052 -name: Protein family report format -namespace: format -subset: formats -def: "Format for reports on a protein family." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0907 ! Protein family +id: EDAM_operation:1834 +name: Residue contact calculation (residue-metal) +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:HasMetalContacts +xref: WHATIF:HasMetalContactsPlus +created_in: "beta12orEarlier" +def: "Calculate protein residue contacts with metal in a structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0388 ! Binding site prediction (from structure) +is_a: EDAM_operation:2950 ! Residue contact calculation [Term] -id: EDAM_format:2054 -name: Protein interaction format -namespace: format -subset: formats -def: "Format for protein interaction data." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0906 ! Protein interaction - +id: EDAM_operation:1835 +name: Residue contact calculation (residue-negative ion) +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:HasNegativeIonContacts +xref: WHATIF:HasNegativeIonContactsPlus +created_in: "beta12orEarlier" +def: "Calculate ion contacts in a structure (all ions for all side chain atoms)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2950 ! Residue contact calculation [Term] -id: EDAM_format:2055 -name: Sequence assembly format -namespace: format -subset: formats -def: "Format for sequence assembly data." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0925 ! Sequence assembly +id: EDAM_operation:1836 +name: Residue bump detection +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ShowBumps +created_in: "beta12orEarlier" +def: "Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection [Term] -id: EDAM_format:2056 -name: Microarray experiment data format -namespace: format -subset: formats -def: "Format for microarray experimental data." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0931 ! Experiment annotation (microarray) +id: EDAM_operation:1837 +name: Residue symmetry contact calculation +comment: A symmetry contact is a contact between two atoms in different asymmetric unit. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:SymmetryContact +created_in: "beta12orEarlier" +def: "Calculate the number of symmetry contacts made by residues in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] -id: EDAM_format:2058 -name: Gene expression report format -namespace: format -subset: formats -def: "Format for a report on gene expression." [http://edamontology.org] -is_a: EDAM_format:2031 ! Gene annotation format -relationship: is_format_of EDAM_data:3111 ! Processed microarray data +id: EDAM_operation:1838 +name: Residue contact calculation (residue-ligand) +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ShowDrugContacts +xref: WHATIF:ShowDrugContactsShort +xref: WHATIF:ShowLigandContacts +created_in: "beta12orEarlier" +def: "Calculate contacts between residues and ligands in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0388 ! Binding site prediction (from structure) +is_a: EDAM_operation:2950 ! Residue contact calculation [Term] -id: EDAM_format:2059 -name: Genotype and phenotype annotation format -namespace: format -subset: formats -def: "Format of a report on genotype / phenotype information." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0920 ! Genotype/phenotype annotation +id: EDAM_operation:1839 +name: Salt bridge calculation +comment: Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:HasSaltBridge +xref: WHATIF:HasSaltBridgePlus +xref: WHATIF:ShowSaltBridges +xref: WHATIF:ShowSaltBridgesH +created_in: "beta12orEarlier" +def: "Calculate (and possibly score) salt bridges in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] -id: EDAM_format:2060 -name: Map format -namespace: format -subset: formats -def: "Format of a map of (typically one) molecular sequence annotated with features." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1274 ! Map +id: EDAM_operation:1841 +name: Rotamer likelihood prediction +comment: Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ShowLikelyRotamers +xref: WHATIF:ShowLikelyRotamers100 +xref: WHATIF:ShowLikelyRotamers200 +xref: WHATIF:ShowLikelyRotamers300 +xref: WHATIF:ShowLikelyRotamers400 +xref: WHATIF:ShowLikelyRotamers500 +xref: WHATIF:ShowLikelyRotamers600 +xref: WHATIF:ShowLikelyRotamers700 +xref: WHATIF:ShowLikelyRotamers800 +xref: WHATIF:ShowLikelyRotamers900 +created_in: "beta12orEarlier" +def: "Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0480 ! Protein modelling (side chains) [Term] -id: EDAM_format:2061 -name: Nucleic acid features (primers) format -namespace: format -subset: formats -def: "Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0922 ! Nucleic acid features (primers) +id: EDAM_operation:1842 +name: Proline mutation value calculation +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:ProlineMutationValue +created_in: "beta12orEarlier" +def: "Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0331 ! Protein modelling (mutation) [Term] -id: EDAM_format:2062 -name: Protein report format -namespace: format -subset: formats -def: "Format of a report of general information about a specific protein." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0896 ! Protein report +id: EDAM_operation:1843 +name: Residue packing validation +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: PackingQuality +created_in: "beta12orEarlier" +def: "Identify poorly packed residues in protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection [Term] -id: EDAM_format:3033 !{since=beta13} -name: Matrix format -namespace: format -subset: formats -def: "Format of a matrix (array) of numerical values." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:2082 ! Matrix +id: EDAM_operation:1844 +name: Dihedral angle validation +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: ImproperQualityMax +xref: WHATIF: ImproperQualitySum +created_in: "beta12orEarlier" +def: "Identify for each residue in a protein structure any improper dihedral (phi/psi) angles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0321 ! Protein model evaluation [Term] -id: EDAM_format:2064 -name: 3D-1D scoring matrix format -namespace: format -subset: formats -def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [http://edamontology.org] -is_a: EDAM_format:3033 ! Matrix format -relationship: is_format_of EDAM_data:1499 ! 3D-1D scoring matrix +id: EDAM_operation:1845 +name: PDB file sequence retrieval +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: PDB_sequence +created_in: "beta12orEarlier" +def: "Extract a molecular sequence from a PDB file." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0344 ! Sequence retrieval (by code) [Term] -id: EDAM_format:2065 -name: Protein structure report (quality evaluation) format -namespace: format -subset: formats -def: "Format of a report on the quality of a protein three-dimensional model." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1539 ! Protein structural quality report +id: EDAM_operation:1846 +name: HET group detection +comment: A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: HETGroupNames +created_in: "beta12orEarlier" +def: "Identify HET groups in PDB files." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1838 ! Residue contact calculation (residue-ligand) +[Term] +id: EDAM_operation:1847 +name: DSSP secondary structure assignment +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: ResidueDSSP +created_in: "beta12orEarlier" +def: "Determine for residue the DSSP determined secondary structure in three-state (HSC)." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data) [Term] -id: EDAM_format:2066 -name: Database hits (sequence) format -namespace: format -subset: formats -def: "Format of a report on sequence hits and associated data from searching a sequence database." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0857 ! Database hits (sequence) +id: EDAM_operation:1848 +name: Structure reformatting +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: PDBasXML +created_in: "beta12orEarlier" +def: "Reformat (a file or other report of) tertiary structure data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0335 ! File reformatting +is_a: EDAM_operation:2234 ! Structure file processing [Term] -id: EDAM_format:2067 -name: Sequence distance matrix format -namespace: format -subset: formats -def: "Format of a matrix of genetic distances between molecular sequences." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0870 ! Sequence distance matrix +id: EDAM_operation:1850 +name: Protein cysteine and disulfide bond assignment +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign cysteine bonding state and disulfide bond partners in protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data) +relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] -id: EDAM_format:2068 -name: Sequence motif format -namespace: format -subset: formats -def: "Format of a sequence motif." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1353 ! Sequence motif +id: EDAM_operation:1913 +name: Residue validation +comment: The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF: UseResidueDB +created_in: "beta12orEarlier" +def: "Identify poor quality amino acid positions in protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0321 ! Protein model evaluation [Term] -id: EDAM_format:2069 -name: Sequence profile format -namespace: format -subset: formats -def: "Format of a sequence profile." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1354 ! Sequence profile +id: EDAM_operation:1914 +name: Structure retrieval (water) +subset: bioinformatics +subset: edam +subset: operations +xref: WHATIF:MovedWaterPDB +created_in: "beta12orEarlier" +def: "Query a tertiary structure database and retrieve water molecules." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1814 ! Structure retrieval [Term] -id: EDAM_format:2074 -name: Dirichlet distribution format -namespace: format -subset: formats -def: "Data format of a dirichlet distribution." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1347 ! Dirichlet distribution +id: EDAM_operation:2008 +name: siRNA duplex prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict siRNA duplexes in RNA." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) +relationship: has_output EDAM_data:2169 ! Nucleic acid features (siRNA) +relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] -id: EDAM_format:2075 -name: HMM emission and transition counts format -namespace: format -subset: formats -def: "Data format for the emission and transition counts of a hidden Markov model." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1348 ! HMM emission and transition counts +id: EDAM_operation:2089 +name: Sequence alignment refinement +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Refine an existing sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0258 ! Sequence alignment analysis +is_a: EDAM_operation:2425 ! Optimisation and refinement [Term] -id: EDAM_format:2077 -name: Protein secondary structure format -namespace: format -subset: formats -def: "Format for secondary structure (predicted or real) of a protein molecule." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0876 ! Protein features (secondary structure) +id: EDAM_operation:2120 +name: Listfile processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2409 ! File processing [Term] -id: EDAM_format:2076 -name: RNA secondary structure format -namespace: format -subset: formats -def: "Format for secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0880 ! RNA secondary structure record +id: EDAM_operation:2121 +name: Sequence file processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2409 ! File processing +is_a: EDAM_operation:2446 ! Sequence processing [Term] -id: EDAM_format:2078 -name: Sequence range format -namespace: format -subset: formats -def: "Format used to specify range(s) of sequence positions." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1017 ! Sequence range +id: EDAM_operation:2122 +name: Sequence alignment file processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2409 ! File processing +is_a: EDAM_operation:2463 ! Sequence alignment processing [Term] -id: EDAM_format:2155 -name: Sequence features (repeats) format -namespace: format -subset: formats -def: "Format used for map of repeats in molecular (typically nucleotide) sequences." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1299 ! Sequence features (repeats) +id: EDAM_operation:2123 +name: Small molecule data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) physicochemical property data for small molecules." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2420 ! Analysis and processing [Term] -id: EDAM_format:2158 -name: Nucleic acid features (restriction sites) format -namespace: format -subset: formats -def: "Format used for report on restriction enzyme recognition sites in nucleotide sequences." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1305 ! Nucleic acid features (restriction sites) +id: EDAM_operation:2222 +name: Data retrieval (ontology annotation) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Ontology information retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Search and retrieve documentation on a bioinformatics ontology." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:2159 -name: Gene features (coding region) format -namespace: format -subset: formats -def: "Format used for report on coding regions in nucleotide sequences." [http://edamontology.org] -is_a: EDAM_format:2031 ! Gene annotation format -relationship: is_format_of EDAM_data:1313 ! Nucleic acid features (coding sequence) +id: EDAM_operation:2224 +name: Data retrieval (ontology concept) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Ontology retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Query an ontology and retrieve concepts or relations." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:2170 -name: Sequence cluster format -namespace: format -subset: formats -def: "Format used for clusters of molecular sequences." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1235 ! Sequence cluster +id: EDAM_operation:2233 +name: Representative sequence identification +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0291 ! Sequence clustering +relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] -id: EDAM_format:2195 -name: Ontology format -namespace: format -subset: formats -def: "Format used for ontologies." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0582 ! Ontology +id: EDAM_operation:2234 +name: Structure file processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Perform basic (non-analytical) operations on a file of molecular tertiary structural data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2409 ! File processing +is_a: EDAM_operation:2465 ! Structure processing [Term] -id: EDAM_format:2210 -name: Strain data format -namespace: format -subset: formats -def: "Format of a report on organism strain data / cell line." [http://edamontology.org] -is_obsolete: true !{since=1.0} -! is_a: EDAM_format:2350 ! Format (typed) -! relationship: is_format_of EDAM_data:0963 ! Cell line annotation +id: EDAM_operation:2237 +name: Data retrieval (sequence profile) +comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Query a profile data resource and retrieve one or more profile(s) and / or associated annotation." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:2542 -name: Protein features (domains) format -namespace: format -subset: formats -def: "Format of a report on protein features (domain composition)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2350 ! Format (typed) +id: EDAM_operation:2238 +name: Statistical calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Perform a statistical data operation of some type, e.g. calibration or validation." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0004 ! Operation [Term] -id: EDAM_format:2571 -name: Raw sequence format -namespace: format -subset: formats -def: "Format of a raw molecular sequence (i.e. the alphabet used)." [http://edamontology.org] -synonym: "Symbol sequence" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0848 ! Raw sequence +id: EDAM_operation:2239 +name: 3D-1D scoring matrix generation +comment: A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0243 ! Protein property calculation (from structure) +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) +relationship: has_output EDAM_data:1499 ! 3D-1D scoring matrix +relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] -id: EDAM_format:1734 -name: PubMed citation -namespace: format -subset: formats -def: "Format of bibliographic reference as used by the PubMed database." [http://edamontology.org] -is_a: EDAM_format:2848 ! Bibliographic reference format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2241 +name: Transmembrane protein rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0270 ! Transmembrane protein analysis +is_a: EDAM_operation:0569 ! Protein secondary structure rendering +relationship: has_input EDAM_data:1456 ! Protein features (membrane regions) +relationship: has_output EDAM_data:2992 ! Protein structure image [Term] -id: EDAM_format:1735 -name: Medline Display Format -namespace: format -subset: formats -def: "Format for abstracts of scientific articles from the Medline database." [http://edamontology.org] -comment: Bibliographic reference information including citation information is included -xref: Moby:PubMed-MEDLINE -is_a: EDAM_format:2848 ! Bibliographic reference format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2246 +name: Demonstration +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "An operation performing purely illustrative (pedagogical) purposes." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_format:1736 -name: CiteXplore-core -namespace: format -subset: formats -def: "CiteXplore 'core' citation format including title, journal, authors and abstract." [http://edamontology.org] -is_a: EDAM_format:2848 ! Bibliographic reference format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2264 +name: Data retrieval (pathway or network) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Query a biological pathways database and retrieve annotation on one or more pathways." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:1737 -name: CiteXplore-all -namespace: format -subset: formats -def: "CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references." [http://edamontology.org] -is_a: EDAM_format:2848 ! Bibliographic reference format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2265 +name: Data retrieval (identifier) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Query a database and retrieve one or more data identifiers." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:1747 -name: PDB atom record format -namespace: format -subset: formats -def: "Format of an ATOM record (describing data for an individual atom) from a PDB file." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_format:1476 ! PDB format +id: EDAM_operation:2284 +name: Nucleic acid density plotting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate a density plot (of base composition) for a nucleotide sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0377 ! Sequence composition calculation (nucleic acid) [Term] -id: EDAM_format:2551 -name: Sequence record format (text) -namespace: format -subset: formats -def: "Data format for a molecular sequence record." [http://edamontology.org] -is_a: EDAM_format:1919 ! Sequence record format +id: EDAM_operation:2403 +name: Sequence analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence analysis (general)" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse one or more known molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2446 ! Sequence processing +relationship: has_input EDAM_data:2044 ! Sequence +relationship: has_output EDAM_data:2955 ! Sequence report +relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM_format:2552 -name: Sequence record format (XML) -namespace: format -subset: formats -def: "Data format for a molecular sequence record." [http://edamontology.org] -is_a: EDAM_format:1919 ! Sequence record format +id: EDAM_operation:2404 +name: Sequence motif processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) molecular sequence motifs." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] -id: EDAM_format:2203 -name: Sequence record lite format -namespace: format -subset: formats -def: "Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment." [http://edamontology.org] -is_a: EDAM_format:1919 ! Sequence record format -relationship: is_format_of EDAM_data:2043 ! Sequence record lite +id: EDAM_operation:2405 +name: Protein interaction data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) protein interaction data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2502 ! Protein data processing +relationship: has_topic EDAM_topic:0128 ! Protein interactions [Term] -id: EDAM_format:2202 -name: Sequence record full format -namespace: format -subset: formats -def: "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] -is_a: EDAM_format:1919 ! Sequence record format -relationship: is_format_of EDAM_data:2201 ! Sequence record full - +id: EDAM_operation:2406 +name: Protein structure analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Structure analysis (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse protein tertiary structural data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2459 ! Structure processing (protein) +is_a: EDAM_operation:2480 ! Structure analysis +relationship: has_input EDAM_data:1460 ! Protein structure +relationship: has_output EDAM_data:0897 ! Protein property [Term] -id: EDAM_format:2057 -name: Sequence trace format -namespace: format -subset: formats -def: "Format for sequence trace data (i.e. including base call information)." [http://edamontology.org] -is_a: EDAM_format:1919 ! Sequence record format -relationship: is_format_of EDAM_data:0924 ! Sequence trace +id: EDAM_operation:2407 +name: Annotation processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:1923 -name: acedb -namespace: format -subset: formats -def: "ACEDB sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) +id: EDAM_operation:2408 +name: Sequence feature analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse features in molecular sequences." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0253 ! Feature prediction +[Term] +id: EDAM_operation:2409 +name: File processing +subset: bioinformatics +subset: edam +subset: operations +synonym: "Data file processing" EXACT [] +synonym: "File handling" EXACT [] +synonym: "Report handling" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] -id: EDAM_format:1924 -name: clustal sequence format -namespace: format -subset: formats -def: "Clustalw output format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1982 ! clustal +id: EDAM_operation:2410 +name: Gene expression analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse gene expression and regulation data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2495 ! Gene expression data processing [Term] -id: EDAM_format:1925 -name: codata -namespace: format -subset: formats -def: "Codata entry format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2411 +name: Structural (3D) profile processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] -id: EDAM_format:1928 -name: experiment -namespace: format -subset: formats -def: "Staden experiment file format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2412 +name: Data index processing +subset: bioinformatics +subset: edam +subset: operations +synonym: "Database index processing" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) an index of (typically a file of) biological data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2409 ! File processing [Term] -id: EDAM_format:1934 -name: fitch -namespace: format -subset: formats -def: "Fitch program format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2413 +name: Sequence profile processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) some type of sequence profile." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] -id: EDAM_format:1935 -name: gcg -namespace: format -subset: formats -def: "GCG sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2414 +name: Protein function analysis +comment: This is a broad concept and is used a placeholder for other, more specific concepts. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2502 ! Protein data processing +relationship: has_output EDAM_data:0896 ! Protein report [Term] -id: EDAM_format:1938 -name: GFF2-seq -namespace: format -subset: formats -def: "GFF feature file format with sequence in the header." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:1974 ! GFF2 +id: EDAM_operation:2415 +name: Protein folding analysis +comment: This is a broad concept and is used a placeholder for other, more specific concepts. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein folding modelling" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2426 ! Modelling and simulation +is_a: EDAM_operation:2502 ! Protein data processing +relationship: has_output EDAM_data:0903 ! Protein folding report +relationship: has_topic EDAM_topic:0130 ! Protein folding and stability +[Term] +id: EDAM_operation:2416 +name: Protein secondary structure analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Secondary structure analysis (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse known protein secondary structure data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2444 ! Protein secondary structure processing +relationship: has_input EDAM_data:0876 ! Protein features (secondary structure) +relationship: has_output EDAM_data:2956 ! Protein secondary structure report [Term] -id: EDAM_format:1939 -name: GFF3-seq -namespace: format -subset: formats -def: "GFF3 feature file format with sequence." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:1975 ! GFF3 +id: EDAM_operation:2417 +name: Physicochemical property data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) data on the physicochemical property of a molecule." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2420 ! Analysis and processing +[Term] +id: EDAM_operation:2419 +name: Primer and probe design +subset: bioinformatics +subset: edam +subset: operations +synonym: "Primer and probe prediction" EXACT [] +created_in: "beta12orEarlier" +def: "Predict oligonucleotide primers or probes." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) +is_a: EDAM_operation:3095 ! Nucleic acid design +relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] -id: EDAM_format:1941 -name: hennig86 -namespace: format -subset: formats -def: "Hennig86 output sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2420 +name: Analysis and processing +subset: bioinformatics +subset: edam +subset: operations +synonym: "Calculation" EXACT [] +synonym: "Computation" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) data of a specific type, for example applying analytical methods." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation [Term] -id: EDAM_format:1942 -name: ig -namespace: format -subset: formats -def: "Intelligenetics sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2421 +name: Database search +comment: Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0224 ! Search and retrieval +is_a: EDAM_operation:2424 ! Comparison +relationship: has_output EDAM_data:2080 ! Database hits [Term] -id: EDAM_format:1943 -name: igstrict -namespace: format -subset: formats -def: "Intelligenetics sequence format (strict version)." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2422 +name: Data retrieval +subset: bioinformatics +subset: edam +subset: operations +synonym: "Information retrieval" BROAD [] +created_in: "beta12orEarlier" +def: "Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0224 ! Search and retrieval +relationship: has_input EDAM_data:0842 ! Identifier [Term] -id: EDAM_format:1944 -name: jackknifer -namespace: format -subset: formats -def: "Jackknifer interleaved and non-interleaved sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2423 +name: Prediction, detection and recognition +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict, recognise, detect or identify some properties of a biomolecule." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation [Term] -id: EDAM_format:1945 -name: mase -namespace: format -subset: formats -def: "Mase program sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2424 +name: Comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more things to identify similarities." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation [Term] -id: EDAM_format:1946 -name: mega-seq -namespace: format -subset: formats -def: "Mega interleaved and non-interleaved sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2425 +name: Optimisation and refinement +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Refine or optimise some data model." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation [Term] -id: EDAM_format:1947 -name: msf -namespace: format -subset: formats -def: "GCG MSF (multiple sequence file) file format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2426 +name: Modelling and simulation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Model or simulate some biological entity or system." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation +relationship: has_topic EDAM_topic:2275 ! Molecular modelling [Term] -id: EDAM_format:1949 -name: nexus-seq -namespace: format -subset: formats -def: "Nexus/paup interleaved sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2427 +name: Data handling +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Perform basic operations on some data or a database." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2420 ! Analysis and processing [Term] -id: EDAM_format:1950 -name: pdbatom -namespace: format -subset: formats -def: "PDB sequence format (ATOM lines)." [http://edamontology.org] -comment: pdb format in EMBOSS. -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:1475 ! PDB database entry format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2428 +name: Evaluation and validation +subset: bioinformatics +subset: edam +subset: operations +synonym: "Validation and standardisation" EXACT [] +created_in: "beta12orEarlier" +def: "Validate or standardise some data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation [Term] -id: EDAM_format:1951 -name: pdbatomnuc -namespace: format -subset: formats -def: "PDB nucleotide sequence format (ATOM lines)." [http://edamontology.org] -comment: pdbnuc format in EMBOSS. -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:1475 ! PDB database entry format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2429 +name: Mapping and assembly +comment: This is a broad concept and is used a placeholder for other, more specific concepts. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation +relationship: has_topic EDAM_topic:0102 ! Mapping +relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] -id: EDAM_format:1952 -name: pdbseqresnuc -namespace: format -subset: formats -def: "PDB nucleotide sequence format (SEQRES lines)." [http://edamontology.org] -comment: pdbnucseq format in EMBOSS. -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:1475 ! PDB database entry format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2430 +name: Design +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Design a biological entity (typically a molecular sequence or structure) with specific properties." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) [Term] -id: EDAM_format:1953 -name: pdbseqres -namespace: format -subset: formats -def: "PDB sequence format (SEQRES lines)." [http://edamontology.org] -comment: pdbseq format in EMBOSS. -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:1475 ! PDB database entry format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2432 +name: Microarray data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) microarray data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2495 ! Gene expression data processing [Term] -id: EDAM_format:1955 -name: phylip sequence format -namespace: format -subset: formats -def: "Phylip interleaved sequence format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1997 ! phylip +id: EDAM_operation:2433 +name: Codon usage table processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a codon usage table." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0286 ! Codon usage analysis [Term] -id: EDAM_format:1956 -name: phylipnon sequence format -namespace: format -subset: formats -def: "Phylip non-interleaved sequence format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1998 ! phylipnon +id: EDAM_operation:2434 +name: Data retrieval (codon usage table) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Retrieve a codon usage table and / or associated annotation." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval +[Term] +id: EDAM_operation:2435 +name: Gene expression profile processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a gene expression profile." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2495 ! Gene expression data processing [Term] -id: EDAM_format:1957 -name: raw -namespace: format -subset: formats -def: "Raw sequence format with no non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2436 +name: Gene expression profile annotation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Annotate a gene expression profile with concepts from an ontology of gene functions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0226 ! Annotation +is_a: EDAM_operation:0532 ! Gene expression profile analysis +relationship: has_output EDAM_data:0928 ! Gene expression profile -! For now, identical to genpept [Term] -id: EDAM_format:1958 -name: refseqp -namespace: format -subset: formats -def: "Refseq protein entry sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2437 +name: Gene regulatory network prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict a network of gene regulation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2496 ! Gene regulatory network processing +is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) +relationship: has_output EDAM_data:2961 ! Pathway or network (gene regulation) [Term] -id: EDAM_format:1959 -name: selex sequence format -namespace: format -subset: formats -def: "Selex sequence format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2000 ! selex +id: EDAM_operation:2438 +name: Pathway or network processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate, analyse or handle a biological pathway or network." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models +[Term] +id: EDAM_operation:2439 +name: RNA secondary structure processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) RNA secondary structure data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2482 ! Secondary structure processing +is_a: EDAM_operation:2501 ! Nucleic acid data processing +relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis +relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] -id: EDAM_format:1960 -name: Staden format -namespace: format -subset: formats -def: "Staden suite sequence format." [http://edamontology.org] -xref: http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html !{documentation=true} -xref: http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden !{documentation=true} -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2440 +name: Structure processing (RNA) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) RNA tertiary structure data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2519 ! Structure processing (nucleic acid) [Term] -id: EDAM_format:1961 -name: stockholm -namespace: format -subset: formats -def: "Stockholm multiple sequence alignment format (used by Pfam and Rfam)." [http://edamontology.org] -xref: http://en.wikipedia.org/wiki/Stockholm_format !{documentation=true} -is_a: EDAM_format:2330 ! Textual format -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2441 +name: RNA structure prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict RNA tertiary structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0475 ! Nucleic acid structure prediction +relationship: has_output EDAM_data:1465 ! RNA structure record [Term] -id: EDAM_format:1962 -name: strider -namespace: format -subset: formats -def: "DNA strider output sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2442 +name: DNA structure prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict DNA tertiary structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0475 ! Nucleic acid structure prediction +relationship: has_output EDAM_data:1464 ! DNA structure +[Term] +id: EDAM_operation:2443 +name: Phylogenetic tree processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a phylogenetic tree." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] -id: EDAM_format:1964 -name: text -namespace: format -subset: formats -def: "Plain text sequence format (essentially unformatted)." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2444 +name: Protein secondary structure processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) protein secondary structure data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2482 ! Secondary structure processing +is_a: EDAM_operation:2502 ! Protein data processing +relationship: has_topic EDAM_topic:0694 ! Protein secondary structure [Term] -id: EDAM_format:1965 -name: treecon sequence format -namespace: format -subset: formats -def: "Treecon output sequence format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2005 ! treecon-seq - +id: EDAM_operation:2445 +name: Protein interaction network processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a network of protein interactions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2405 ! Protein interaction data processing +is_a: EDAM_operation:2438 ! Pathway or network processing +relationship: has_topic EDAM_topic:3044 ! Protein interaction networks [Term] -id: EDAM_format:1966 -name: asn1 sequence format -namespace: format -subset: formats -def: "NCBI ASN.1 sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2446 +name: Sequence processing +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence processing (general)" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) one or more molecular sequences and associated annotation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing [Term] -id: EDAM_format:1969 -name: debug-seq -namespace: format -subset: formats -def: "EMBOSS debugging trace sequence format of full internal data content." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2447 +name: Sequence processing (protein) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a protein sequence and associated annotation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2446 ! Sequence processing +is_a: EDAM_operation:2502 ! Protein data processing [Term] -id: EDAM_format:1970 -name: jackknifernon -namespace: format -subset: formats -def: "Jackknifer output sequence non-interleaved format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2448 +name: Sequence processing (nucleic acid) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a nucleotide sequence and associated annotation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2446 ! Sequence processing +is_a: EDAM_operation:2501 ! Nucleic acid data processing [Term] -id: EDAM_format:1971 -name: meganon sequence format -namespace: format -subset: formats -def: "Mega non-interleaved output sequence format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1992 ! meganon +id: EDAM_operation:2451 +name: Sequence comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more molecular sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2403 ! Sequence analysis +is_a: EDAM_operation:2424 ! Comparison +relationship: has_input EDAM_data:2044 ! Sequence +relationship: has_output EDAM_data:2955 ! Sequence report +relationship: has_topic EDAM_topic:0159 ! Sequence comparison [Term] -id: EDAM_format:1973 -name: nexusnon -namespace: format -subset: formats -def: "Nexus/paup non-interleaved sequence format." [http://edamontology.org] -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2452 +name: Sequence cluster processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a sequence cluster." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] -id: EDAM_format:1967 -name: das -namespace: format -subset: formats -def: "DAS sequence (XML) format (any type)." [http://edamontology.org] -synonym: "das sequence format" EXACT [http://edamontology.org] -is_a: EDAM_format:2552 ! Sequence record format (XML) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2453 +name: Feature table processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a sequence feature table." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2446 ! Sequence processing +relationship: has_input EDAM_data:1270 ! Sequence feature table +relationship: has_input EDAM_data:2201 ! Sequence record full +relationship: has_output EDAM_data:1255 ! Feature record +relationship: has_topic EDAM_topic:0160 ! Sequence sites and features [Term] -id: EDAM_format:1968 -name: dasdna -namespace: format -subset: formats -def: "DAS sequence (XML) format (nucleotide-only)." [http://edamontology.org] -comment: The use of this format is deprecated. -is_a: EDAM_format:2552 ! Sequence record format (XML) -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:2454 +name: Gene and gene component prediction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Gene finding" EXACT [] +created_in: "beta12orEarlier" +def: "Detect, predict and identify genes or components of genes in DNA sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) +relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] -id: EDAM_format:2546 -name: FASTA-like -namespace: format -subset: formats -def: "A format resembling FASTA format." [http://edamontology.org] -comment: This concept may be used for the many non-standard FASTA-like formats. -is_a: EDAM_format:2203 ! Sequence record lite format - +id: EDAM_operation:2456 +name: GPCR classification +subset: bioinformatics +subset: edam +subset: operations +synonym: "G protein-coupled receptor (GPCR) classification" EXACT [] +created_in: "beta12orEarlier" +def: "Classify G-protein coupled receptors (GPCRs) into families and subfamilies." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0473 ! GPCR analysis +is_a: EDAM_operation:2995 ! Sequence classification +relationship: has_output EDAM_data:0907 ! Protein family [Term] -id: EDAM_format:2200 ! This is the one used for annotation in eSysbio -name: FASTA-like (text) -namespace: format -subset: formats -def: "A text format resembling FASTA format." [http://edamontology.org] -comment: This concept may also be used for the many non-standard FASTA-like formats. -synonym: "DNA and Protein Sequence Alignment" NARROW [http://filext.com/file-extension/FASTA] -is_a: EDAM_format:2546 ! FASTA-like -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2457 +name: GPCR coupling selectivity prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict G-protein coupled receptor (GPCR) coupling selectivity." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0473 ! GPCR analysis +is_a: EDAM_operation:2492 ! Protein interaction prediction +is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) +relationship: has_output EDAM_data:0896 ! Protein report [Term] -id: EDAM_format:2310 -name: FASTA-HTML -namespace: format -subset: formats -def: "FASTA format wrapped in HTML elements." [http://edamontology.org] -is_a: EDAM_format:2546 ! FASTA-like -is_a: EDAM_format:2331 ! HTML +id: EDAM_operation:2459 +name: Structure processing (protein) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a protein tertiary structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2465 ! Structure processing +is_a: EDAM_operation:2502 ! Protein data processing +relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure [Term] -id: EDAM_format:1929 -name: FASTA format -namespace: format -subset: formats -def: "FASTA format including NCBI-style IDs." [http://edamontology.org] ! Is it different from 1972? -synonym: "FASTA" EXACT [http://edamontology.org] -synonym: "FASTA sequence format" EXACT [http://edamontology.org] -is_a: EDAM_format:2200 ! FASTA-like (text) -is_a: EDAM_format:2554 ! Alignment format (text) +id: EDAM_operation:2460 +name: Protein atom surface calculation +comment: Waters are not considered. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility for each atom in a structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] -id: EDAM_format:1926 -name: dbid -namespace: format -subset: formats -def: "Fasta format variant with database name before ID." [http://edamontology.org] -is_a: EDAM_format:2200 ! FASTA-like (text) +id: EDAM_operation:2461 +name: Protein residue surface calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility for each residue in a structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] -id: EDAM_format:1940 -name: giFASTA format -namespace: format -subset: formats -def: "FASTA sequence format including NCBI-style GIs." [http://edamontology.org] -is_a: EDAM_format:2200 ! FASTA-like (text) +id: EDAM_operation:2462 +name: Protein surface calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate the solvent accessibility of a structure as a whole." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] -id: EDAM_format:1954 -name: Pearson format -namespace: format -subset: formats -def: "Plain old FASTA sequence format (unspecified format for IDs)." [http://edamontology.org] -is_a: EDAM_format:2200 ! FASTA-like (text) +id: EDAM_operation:2463 +name: Sequence alignment processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a molecular sequence alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2951 ! Alignment processing +relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] -id: EDAM_format:1972 -name: NCBI format -namespace: format -subset: formats -def: "NCBI FASTA sequence format with NCBI-style IDs." [http://edamontology.org] -comment: There are several variants of this. -is_a: EDAM_format:2200 ! FASTA-like (text) +id: EDAM_operation:2464 +name: Protein-protein interaction prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify or predict protein-protein interactions, interfaces, binding sites etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2492 ! Protein interaction prediction +relationship: has_output EDAM_data:1565 ! Protein-protein interaction +relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] -id: EDAM_format:2543 -name: EMBL-like format -namespace: format -subset: formats -def: "A format resembling EMBL entry (plain text) format." [http://edamontology.org] -comment: This concept may be used for the many non-standard EMBL-like formats. -is_a: EDAM_format:2202 ! Sequence record full format +id: EDAM_operation:2465 +name: Structure processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a molecular tertiary structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +[Term] +id: EDAM_operation:2466 +name: Map annotation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Annotate a DNA map of some type with terms from a controlled vocabulary." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0226 ! Annotation +is_a: EDAM_operation:2521 ! Map data processing +relationship: has_input EDAM_data:1274 ! Map +relationship: has_output EDAM_data:1274 ! Map [Term] -id: EDAM_format:2559 -name: GenBank-like format -namespace: format -subset: formats -def: "A format resembling GenBank entry (plain text) format." [http://edamontology.org] -comment: This concept may be used for the non-standard GenBank-like formats. -is_a: EDAM_format:2202 ! Sequence record full format +id: EDAM_operation:2467 +name: Data retrieval (protein annotation) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein information retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Retrieve information on a protein." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:2547 -name: uniprotkb-like format -namespace: format -subset: formats -def: "A sequence format resembling uniprotkb entry format." [http://edamontology.org] -is_a: EDAM_format:2202 ! Sequence record full format -is_a: EDAM_format:2206 ! Sequence feature table format (text) +id: EDAM_operation:2468 +name: Data retrieval (phylogenetic tree) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Retrieve a phylogenetic tree from a data resource." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:1948 -name: nbrf -namespace: format -subset: formats -def: "NBRF/PIR entry sequence format." [http://edamontology.org] -is_a: EDAM_format:2202 ! Sequence record full format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2469 +name: Data retrieval (protein interaction annotation) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Retrieve information on a protein interaction." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:2181 -name: EMBL-like (text) -namespace: format -subset: formats -def: "A text format resembling EMBL entry format." [http://edamontology.org] -comment: This concept may be used for the many non-standard EMBL-like text formats. -is_a: EDAM_format:2543 ! EMBL-like format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2470 +name: Data retrieval (protein family annotation) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein family information retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Retrieve information on a protein family." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:2558 -name: EMBL-like (XML) -namespace: format -subset: formats -def: "An XML format resembling EMBL entry format." [http://edamontology.org] -comment: This concept may be used for the any non-standard EMBL-like XML formats. -is_a: EDAM_format:2543 ! EMBL-like format -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:2471 +name: Data retrieval (RNA family annotation) +subset: bioinformatics +subset: edam +subset: operations +synonym: "RNA family information retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Retrieve information on an RNA family." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:2311 -name: EMBL-HTML -namespace: format -subset: formats -def: "EMBL entry format wrapped in HTML elements." [http://edamontology.org] -is_a: EDAM_format:2543 ! EMBL-like format -is_a: EDAM_format:2331 ! HTML +id: EDAM_operation:2472 +name: Data retrieval (gene annotation) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Gene information retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Retrieve information on a specific gene." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval +[Term] +id: EDAM_operation:2473 +name: Data retrieval (genotype and phenotype annotation) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Genotype and phenotype information retrieval" EXACT [] +created_in: "beta12orEarlier" +def: "Retrieve information on a specific genotype or phenotype." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM_format:1927 -name: EMBL format -namespace: format -subset: formats -def: "EMBL entry format." [http://edamontology.org] -synonym: "EMBL sequence format" EXACT [http://edamontology.org] -synonym: "EMBL" EXACT [http://edamontology.org] -is_a: EDAM_format:2181 ! EMBL-like (text) -is_a: EDAM_format:2206 ! Sequence feature table format (text) +id: EDAM_operation:2474 +name: Protein architecture comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare the architecture of two or more protein structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0247 ! Protein architecture analysis +is_a: EDAM_operation:2488 ! Protein secondary structure comparison +relationship: has_output EDAM_data:0902 ! Protein architecture report [Term] -id: EDAM_format:2186 -name: geneseq -namespace: format -subset: formats -def: "Geneseq sequence format." [http://edamontology.org] -is_a: EDAM_format:2181 ! EMBL-like (text) +id: EDAM_operation:2475 +name: Protein architecture recognition +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify the architecture of a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0247 ! Protein architecture analysis +is_a: EDAM_operation:2996 ! Structure classification +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_output EDAM_data:0902 ! Protein architecture report [Term] -id: EDAM_format:2204 -name: EMBL format (XML) -namespace: format -subset: formats -def: "An XML format for EMBL entries." [http://edamontology.org] -comment: This is a placeholder for other more specific concepts. It should not normally be used for annotation. -is_a: EDAM_format:2558 ! EMBL-like (XML) +id: EDAM_operation:2476 +name: Molecular dynamics simulation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2423 ! Prediction, detection and recognition +is_a: EDAM_operation:2426 ! Modelling and simulation +is_a: EDAM_operation:2480 ! Structure analysis +relationship: has_output EDAM_data:0883 ! Structure +relationship: has_topic EDAM_topic:0082 ! Structure prediction +relationship: has_topic EDAM_topic:0176 ! Molecular dynamics [Term] -id: EDAM_format:2183 -name: EMBLXML -namespace: format -subset: formats -def: "XML format for EMBL entries." [http://edamontology.org] -is_a: EDAM_format:2204 ! EMBL format (XML) +id: EDAM_operation:2478 +name: Nucleic acid sequence analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence analysis (nucleic acid)" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2403 ! Sequence analysis +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +relationship: has_input EDAM_data:2977 ! Nucleic acid sequence +relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis +[Term] +id: EDAM_operation:2479 +name: Protein sequence analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence analysis (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2403 ! Sequence analysis +is_a: EDAM_operation:2447 ! Sequence processing (protein) +relationship: has_input EDAM_data:2976 ! Protein sequence +relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis [Term] -id: EDAM_format:2184 -name: cdsxml -namespace: format -subset: formats -def: "XML format for EMBL entries." [http://edamontology.org] -is_a: EDAM_format:2204 ! EMBL format (XML) +id: EDAM_operation:2480 +name: Structure analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse known molecular tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2465 ! Structure processing +relationship: has_input EDAM_data:0883 ! Structure +relationship: has_output EDAM_data:2085 ! Structure report +relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM_format:2185 -name: insdxml -namespace: format -subset: formats -def: "XML format for EMBL entries." [http://edamontology.org] -is_a: EDAM_format:2204 ! EMBL format (XML) +id: EDAM_operation:2481 +name: Nucleic acid structure analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse nucleic acid tertiary structural data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2480 ! Structure analysis +is_a: EDAM_operation:2519 ! Structure processing (nucleic acid) +relationship: has_input EDAM_data:1459 ! Nucleic acid structure +relationship: has_output EDAM_data:0912 ! Nucleic acid property +[Term] +id: EDAM_operation:2482 +name: Secondary structure processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a molecular secondary structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM_format:2205 -name: GenBank-like format (text) -namespace: format -subset: formats -def: "A text format resembling GenBank entry (plain text) format." [http://edamontology.org] -comment: This concept may be used for the non-standard GenBank-like text formats. -is_a: EDAM_format:2559 ! GenBank-like format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2483 +name: Structure comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more molecular tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2424 ! Comparison +is_a: EDAM_operation:2480 ! Structure analysis +relationship: has_topic EDAM_topic:1770 ! Structure comparison [Term] -id: EDAM_format:2532 -name: GenBank-HTML -namespace: format -subset: formats -def: "Genbank entry format wrapped in HTML elements." [http://edamontology.org] -is_a: EDAM_format:2559 ! GenBank-like format -is_a: EDAM_format:2331 ! HTML +id: EDAM_operation:2485 +name: Helical wheel rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Render a helical wheel representation of protein secondary structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0569 ! Protein secondary structure rendering +relationship: has_output EDAM_data:2162 ! Helical wheel [Term] -id: EDAM_format:1936 -name: GenBank format -namespace: format -subset: formats -def: "Genbank entry format." [http://edamontology.org] -is_a: EDAM_format:2205 ! GenBank-like format (text) -is_a: EDAM_format:2206 ! Sequence feature table format (text) +id: EDAM_operation:2486 +name: Topology diagram rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Render a topology diagram of protein secondary structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0569 ! Protein secondary structure rendering +relationship: has_output EDAM_data:2992 ! Protein structure image +[Term] +id: EDAM_operation:2487 +name: Protein structure comparison +comment: Methods might identify structural neighbors, find structural similarities or define a structural core. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Structure comparison (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "Compare protein tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2459 ! Structure processing (protein) +is_a: EDAM_operation:2483 ! Structure comparison +is_a: EDAM_operation:2997 ! Protein comparison +relationship: has_input EDAM_data:1460 ! Protein structure +relationship: has_output EDAM_data:0897 ! Protein property -! For now, identical to refseqp [Term] -id: EDAM_format:1937 -name: genpept -namespace: format -subset: formats -def: "Genpept protein entry format." [http://edamontology.org] -is_a: EDAM_format:2205 ! GenBank-like format (text) +id: EDAM_operation:2488 +name: Protein secondary structure comparison +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein secondary structure" EXACT [] +synonym: "Secondary structure comparison (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "Compare protein secondary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2416 ! Protein secondary structure analysis +is_a: EDAM_operation:2931 ! Secondary structure comparison +is_a: EDAM_operation:2997 ! Protein comparison +relationship: has_input EDAM_data:0876 ! Protein features (secondary structure) +[Term] +id: EDAM_operation:2489 +name: Protein subcellular localization prediction +comment: The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein targeting prediction" EXACT [] +created_in: "beta12orEarlier" +def: "Predict the subcellular localization of a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +is_a: EDAM_operation:3084 ! Protein function prediction (from sequence) +relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization [Term] -id: EDAM_format:2187 -name: uniprotkb-like (text) -namespace: format -subset: formats -def: "A text sequence format resembling uniprotkb entry format." [http://edamontology.org] -is_a: EDAM_format:2547 ! uniprotkb-like format -is_a: EDAM_format:2330 ! Textual format - +id: EDAM_operation:2490 +name: Residue contact calculation (residue-residue) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate contacts between residues in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2950 ! Residue contact calculation [Term] -id: EDAM_format:1963 -name: Swiss-Prot format -namespace: format -subset: formats -def: "Swiss-Prot entry sequence format." [http://edamontology.org] -is_a: EDAM_format:2187 ! uniprotkb-like (text) - +id: EDAM_operation:2491 +name: Hydrogen bond calculation (inter-residue) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify potential hydrogen bonds between amino acid residues." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0394 ! Hydrogen bond calculation +is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] -id: EDAM_format:2188 -name: uniprot -namespace: format -subset: formats -def: "UniProt entry sequence format." [http://edamontology.org] -is_a: EDAM_format:2187 ! uniprotkb-like (text) +id: EDAM_operation:2492 +name: Protein interaction prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict the interactions of proteins with other molecules." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2405 ! Protein interaction data processing +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_output EDAM_data:0906 ! Protein interaction [Term] -id: EDAM_format:2189 -name: ipi -namespace: format -subset: formats -def: "ipi sequence format." [http://edamontology.org] -is_a: EDAM_format:2187 ! uniprotkb-like (text) - +id: EDAM_operation:2493 +name: Codon usage data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) codon usage data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:0286 ! Codon usage analysis [Term] -id: EDAM_format:1628 -name: ABI -namespace: format -subset: formats -def: "A format of raw sequence read data from an Applied Biosystems sequencing machine." [http://edamontology.org] -is_a: EDAM_format:2057 ! Sequence trace format -is_a: EDAM_format:2333 ! Binary format +id: EDAM_operation:2495 +name: Gene expression data processing +subset: bioinformatics +subset: edam +subset: operations +synonym: "Gene expression (microarray) data processing" EXACT [] +synonym: "Microarray data processing" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) gene expression (typically microarray) data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0200 ! Microarrays +relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] -id: EDAM_format:1629 -name: mira -namespace: format -subset: formats -def: "Format of MIRA sequence trace information file." [http://edamontology.org] -is_a: EDAM_format:2057 ! Sequence trace format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2496 +name: Gene regulatory network processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a network of gene regulation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2438 ! Pathway or network processing +relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks [Term] -id: EDAM_format:2545 -name: FASTQ-like format -namespace: format -subset: formats -def: "A format resembling FASTQ short read format." [http://edamontology.org] -comment: This concept may be used for non-standard FASTQ short read-like formats. -is_a: EDAM_format:2057 ! Sequence trace format - +id: EDAM_operation:2497 +name: Pathway or network analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Network analysis" EXACT [] +synonym: "Pathway analysis" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse a known biological pathway or network." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2438 ! Pathway or network processing +relationship: has_input EDAM_data:2600 ! Pathway or network +relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] -id: EDAM_format:2572 -name: BAM -namespace: format -subset: formats -def: "BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [http://edamontology.org] -xref: http://samtools.sourceforge.net/SAM-1.3.pdf !{documentation=true} -is_a: EDAM_format:2057 ! Sequence trace format -is_a: EDAM_format:1921 ! Alignment format -is_a: EDAM_format:2333 ! Binary format +id: EDAM_operation:2498 +name: Sequencing-based expression profile data analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2495 ! Gene expression data processing [Term] -id: EDAM_format:2573 -name: SAM -namespace: format -subset: formats -def: "Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [http://edamontology.org] -comment: The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. -xref: http://samtools.sourceforge.net/SAM-1.3.pdf !{documentation=true} -is_a: EDAM_format:2057 ! Sequence trace format -is_a: EDAM_format:2920 ! Alignment format (pair only) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2499 +name: Splicing analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Splicing modelling" EXACT [] +created_in: "beta12orEarlier" +def: "Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2426 ! Modelling and simulation +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison +is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) +relationship: has_output EDAM_data:1307 ! Nucleic acid features (splice sites) +relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] -id: EDAM_format:2182 -name: FASTQ-like format (text) -namespace: format -subset: formats -def: "A text format resembling FASTQ short read format." [http://edamontology.org] -comment: This concept may be used for non-standard FASTQ short read-like formats. -is_a: EDAM_format:2545 ! FASTQ-like format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2500 +name: Microarray raw data analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse raw microarray data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2495 ! Gene expression data processing [Term] -id: EDAM_format:1930 -name: FASTQ -namespace: format -subset: formats -def: "FASTQ short read format ignoring quality scores." [http://edamontology.org] -is_a: EDAM_format:2182 ! FASTQ-like format (text) +id: EDAM_operation:2501 +name: Nucleic acid data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) nucleic acid sequence or structural data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] -id: EDAM_format:1931 -name: FASTQ-illumina -namespace: format -subset: formats -def: "FASTQ Illumina 1.3 short read format." [http://edamontology.org] -is_a: EDAM_format:2182 ! FASTQ-like format (text) +id: EDAM_operation:2502 +name: Protein data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) protein sequence or structural data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing +relationship: has_topic EDAM_topic:0078 ! Protein analysis [Term] -id: EDAM_format:1932 -name: FASTQ-sanger -namespace: format -subset: formats -def: "FASTQ short read format with phred quality." [http://edamontology.org] -is_a: EDAM_format:2182 ! FASTQ-like format (text) +id: EDAM_operation:2503 +name: Sequence data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) molecular sequence data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2446 ! Sequence processing [Term] -id: EDAM_format:1933 -name: FASTQ-solexa -namespace: format -subset: formats -def: "FASTQ Solexa/Illumina 1.0 short read format." [http://edamontology.org] -is_a: EDAM_format:2182 ! FASTQ-like format (text) +id: EDAM_operation:2504 +name: Structural data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) molecular structural data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2465 ! Structure processing [Term] -id: EDAM_format:2548 -name: Sequence feature table format -namespace: format -subset: formats -def: "Format for a sequence feature table." [http://edamontology.org] -is_a: EDAM_format:1920 ! Sequence feature annotation format -relationship: is_format_of EDAM_data:1255 ! Feature record +id: EDAM_operation:2505 +name: Text processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) text." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing [Term] -id: EDAM_format:1979 -name: debug-feat -namespace: format -subset: formats -def: "EMBOSS debugging trace feature format of full internal data content." [http://edamontology.org] -is_a: EDAM_format:1920 ! Sequence feature annotation format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2506 +name: Sequence alignment analysis (protein) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0258 ! Sequence alignment analysis +is_a: EDAM_operation:2502 ! Protein data processing +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_input EDAM_data:1384 ! Sequence alignment (protein) +relationship: has_topic EDAM_topic:0741 ! Protein sequence alignment [Term] -id: EDAM_format:2206 -name: Sequence feature table format (text) -namespace: format -subset: formats -def: "Text format for a sequence feature table." [http://edamontology.org] -is_a: EDAM_format:2548 ! Sequence feature table format +id: EDAM_operation:2507 +name: Sequence alignment analysis (nucleic acid) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0258 ! Sequence alignment analysis +is_a: EDAM_operation:2501 ! Nucleic acid data processing +is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) +relationship: has_input EDAM_data:1383 ! Sequence alignment (nucleic acid) +relationship: has_topic EDAM_topic:0740 ! Nucleic acid sequence alignment [Term] -id: EDAM_format:2553 -name: Sequence feature table format (XML) -namespace: format -subset: formats -def: "XML format for a sequence feature table." [http://edamontology.org] -is_a: EDAM_format:2548 ! Sequence feature table format - +id: EDAM_operation:2508 +name: Nucleic acid sequence comparison +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence comparison (nucleic acid)" EXACT [] +created_in: "beta12orEarlier" +def: "Compare two or more nucleic acid sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2451 ! Sequence comparison +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +is_a: EDAM_operation:2998 ! Nucleic acid comparison [Term] -id: EDAM_format:2305 -name: GFF -namespace: format -subset: formats -def: "GFF feature format (of indeterminate version)." [http://edamontology.org] -is_a: EDAM_format:2206 ! Sequence feature table format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2509 +name: Protein sequence comparison +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence comparison (protein)" EXACT [] +created_in: "beta12orEarlier" +def: "Compare two or more protein sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2451 ! Sequence comparison +is_a: EDAM_operation:2479 ! Protein sequence analysis +is_a: EDAM_operation:2997 ! Protein comparison +[Term] +id: EDAM_operation:2510 +name: DNA back-translation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Back-translate a protein sequence into DNA." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0233 ! Sequence conversion +relationship: has_topic EDAM_topic:0108 ! Translation [Term] -id: EDAM_format:1976 -name: pir -namespace: format -subset: formats -def: "PIR feature format." [http://edamontology.org] -is_a: EDAM_format:2206 ! Sequence feature table format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2511 +name: Sequence editing (nucleic acid) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Edit or change a nucleic acid sequence, either randomly or specifically." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0231 ! Sequence editing +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) [Term] -id: EDAM_format:1977 -name: swiss feature -namespace: format -subset: formats -def: "Swiss-Prot feature format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1963 ! Swiss-Prot format +id: EDAM_operation:2512 +name: Sequence editing (protein) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Edit or change a protein sequence, either randomly or specifically." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0231 ! Sequence editing +is_a: EDAM_operation:2447 ! Sequence processing (protein) +[Term] +id: EDAM_operation:2513 +name: Sequence generation (nucleic acid) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a nucleic acid sequence by some means." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0230 ! Sequence generation +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:1980 -name: EMBL feature -namespace: format -subset: formats -def: "EMBL feature format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1927 ! EMBL format +id: EDAM_operation:2514 +name: Sequence generation (protein) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a protein sequence by some means." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0230 ! Sequence generation +is_a: EDAM_operation:2447 ! Sequence processing (protein) +relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis +[Term] +id: EDAM_operation:2515 +name: Sequence rendering (nucleic acid) +comment: Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise, format or render a nucleic acid sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0564 ! Sequence rendering +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:1981 -name: GenBank feature -namespace: format -subset: formats -def: "Genbank feature format." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1936 ! GenBank format +id: EDAM_operation:2516 +name: Sequence rendering (protein) +comment: Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise, format or render a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0564 ! Sequence rendering +is_a: EDAM_operation:2447 ! Sequence processing (protein) +[Term] +id: EDAM_operation:2518 +name: Nucleic acid structure comparison +subset: bioinformatics +subset: edam +subset: operations +synonym: "Structure comparison (nucleic acid)" EXACT [] +created_in: "beta12orEarlier" +def: "Compare nucleic acid tertiary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2481 ! Nucleic acid structure analysis +is_a: EDAM_operation:2483 ! Structure comparison +is_a: EDAM_operation:2998 ! Nucleic acid comparison [Term] -id: EDAM_format:1974 -name: GFF2 -namespace: format -subset: formats -def: "General Feature Format (GFF) of sequence features." [http://edamontology.org] -xref: http://www.sanger.ac.uk/resources/software/gff/spec.html !{documentation=true} -is_a: EDAM_format:2305 ! GFF +id: EDAM_operation:2519 +name: Structure processing (nucleic acid) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) nucleic acid tertiary structure data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2465 ! Structure processing +is_a: EDAM_operation:2501 ! Nucleic acid data processing +relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis +[Term] +id: EDAM_operation:2520 +name: DNA mapping +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a map of a DNA sequence annotated with positional or non-positional features of some type." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2429 ! Mapping and assembly +is_a: EDAM_operation:2521 ! Map data processing +relationship: has_output EDAM_data:1274 ! Map [Term] -id: EDAM_format:1975 -name: GFF3 -namespace: format -subset: formats -def: "Generic Feature Format version 3 (GFF3) of sequence features." [http://edamontology.org] -xref: http://sequenceontology.org/resources/gff3.html !{documentation=true} -is_a: EDAM_format:2305 ! GFF +id: EDAM_operation:2521 +name: Map data processing +subset: bioinformatics +subset: edam +subset: operations +synonym: "DNA map data processing" EXACT [] +created_in: "beta12orEarlier" +def: "Process (read and / or write) a DNA map of some type." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2501 ! Nucleic acid data processing +relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage +[Term] +id: EDAM_operation:2574 +name: Protein hydropathy calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0250 ! Protein property calculation +relationship: has_output EDAM_data:2970 ! Protein hydropathy data +relationship: has_topic EDAM_topic:0137 ! Protein hydropathy [Term] -id: EDAM_format:2306 -name: GTF -namespace: format -subset: formats -def: "Gene Transfer Format (GTF), a restricted version of GFF." [http://edamontology.org] -xref: http://mblab.wustl.edu/GTF22.html !{documentation=true} -xref: http://genome.ucsc.edu/FAQ/FAQformat#format4 !{documentation=true} -is_a: EDAM_format:2305 ! GFF +id: EDAM_operation:2575 +name: Binding site prediction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Ligand-binding and active site prediction" EXACT [] +created_in: "beta12orEarlier" +def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2492 ! Protein interaction prediction +relationship: has_output EDAM_data:1325 ! Protein features (active sites) +relationship: has_output EDAM_data:1326 ! Protein features (binding sites) +relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions +[Term] +id: EDAM_operation:2871 +name: Sequence tagged site (STS) mapping +comment: An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence mapping" EXACT [] +created_in: "beta12orEarlier" +def: "Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2944 ! Physical mapping +relationship: has_output EDAM_data:1279 ! Sequence map [Term] -id: EDAM_format:1978 -name: DASGFF -namespace: format -subset: formats -def: "DAS GFF (XML) feature format." [http://edamontology.org] -synonym: "DASGFF feature" EXACT [http://edamontology.org] -synonym: "das feature" EXACT [http://edamontology.org] -is_a: EDAM_format:2553 ! Sequence feature table format (XML) -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:2928 +name: Alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2951 ! Alignment processing +relationship: has_output EDAM_data:1916 ! Alignment [Term] -id: EDAM_format:2554 -name: Alignment format (text) -namespace: format -subset: formats -def: "Text format for molecular sequence alignment information." [http://edamontology.org] -is_a: EDAM_format:1921 ! Alignment format +id: EDAM_operation:2929 +name: Protein fragment weight comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0398 ! Protein molecular weight calculation +is_a: EDAM_operation:2930 ! Protein property comparison +[Term] +id: EDAM_operation:2930 +name: Protein property comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare the physicochemical properties of two or more proteins (or reference data)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2997 ! Protein comparison +relationship: has_output EDAM_data:0897 ! Protein property [Term] -id: EDAM_format:2555 -name: Alignment format (XML) -namespace: format -subset: formats -def: "XML format for molecular sequence alignment information." [http://edamontology.org] -is_a: EDAM_format:1921 ! Alignment format +id: EDAM_operation:2931 +name: Secondary structure comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more molecular secondary structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2424 ! Comparison +relationship: has_input EDAM_data:2081 ! Secondary structure +relationship: has_output EDAM_data:2881 ! Secondary structure report +relationship: has_topic EDAM_topic:1770 ! Structure comparison [Term] -id: EDAM_format:1982 -name: clustal -namespace: format -subset: formats -def: "Clustalw format for (aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2932 +name: Hopp and Woods plotting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a Hopp and Woods plot of antigenicity of a protein." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction [Term] -id: EDAM_format:1983 -name: debug -namespace: format -subset: formats -def: "EMBOSS alignment format for debugging trace of full internal data content." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2934 +name: Microarray cluster textual view rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise gene clusters with gene names." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering [Term] -id: EDAM_format:1984 -name: FASTA-aln -namespace: format -subset: formats -def: "Fasta format for (aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2200 ! FASTA-like (text) +id: EDAM_operation:2935 +name: Microarray wave graph rendering +comment: This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Microarray cluster temporal graph rendering" EXACT [] +created_in: "beta12orEarlier" +def: "Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering [Term] -id: EDAM_format:2922 -name: markx0 variant -namespace: format -subset: formats -def: "Some variant of Pearson MARKX alignment format." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2936 +name: Microarray dendrograph rendering +subset: bioinformatics +subset: edam +subset: operations +synonym: "Microarray checks view rendering" EXACT [] +synonym: "Microarray view rendering" EXACT [] +created_in: "beta12orEarlier" +def: "Generate a dendrograph of raw, preprocessed or clustered microarray data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering [Term] -id: EDAM_format:1985 -name: markx0 -namespace: format -subset: formats -def: "Pearson MARKX0 alignment format." [http://edamontology.org] -is_a: EDAM_format:2922 ! markx0 variant - +id: EDAM_operation:2937 +name: Microarray proximity map rendering +subset: bioinformatics +subset: edam +subset: operations +synonym: "Microarray distance map rendering" EXACT [] +created_in: "beta12orEarlier" +def: "Generate a plot of distances (distance matrix) between genes." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering [Term] -id: EDAM_format:1986 -name: markx1 -namespace: format -subset: formats -def: "Pearson MARKX1 alignment format." [http://edamontology.org] -is_a: EDAM_format:2922 ! markx0 variant +id: EDAM_operation:2938 +name: Microarray tree or dendrogram view rendering +subset: bioinformatics +subset: edam +subset: operations +synonym: "Microarray 2-way dendrogram rendering" EXACT [] +synonym: "Microarray matrix tree plot rendering" EXACT [] +created_in: "beta12orEarlier" +def: "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering +[Term] +id: EDAM_operation:2939 +name: Microarray principal component rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering [Term] -id: EDAM_format:1987 -name: markx10 -namespace: format -subset: formats -def: "Pearson MARKX10 alignment format." [http://edamontology.org] -is_a: EDAM_format:2922 ! markx0 variant +id: EDAM_operation:2940 +name: Microarray scatter plot rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a scatter plot of microarray data, typically after principal component analysis." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering +[Term] +id: EDAM_operation:2941 +name: Whole microarray graph view rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise gene expression data where each band (or line graph) corresponds to a sample." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering [Term] -id: EDAM_format:1988 -name: markx2 -namespace: format -subset: formats -def: "Pearson MARKX2 alignment format." [http://edamontology.org] -is_a: EDAM_format:2922 ! markx0 variant +id: EDAM_operation:2942 +name: Microarray tree-map rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise gene expression data after hierarchical clustering for representing hierarchical relationships." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering +[Term] +id: EDAM_operation:2943 +name: Microarray Box-Whisker plot rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0571 ! Microarray data rendering [Term] -id: EDAM_format:1989 -name: markx3 -namespace: format -subset: formats -def: "Pearson MARKX3 alignment format." [http://edamontology.org] -is_a: EDAM_format:2922 ! markx0 variant +id: EDAM_operation:2944 +name: Physical mapping +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2520 ! DNA mapping +relationship: has_output EDAM_data:1280 ! Physical map +relationship: has_topic EDAM_topic:0102 ! Mapping +[Term] +id: EDAM_operation:2945 +name: Analysis +comment: For non-analytical operations, see the 'Processing' branch. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Apply analytical methods to existing data of a specific type." [http://edamontology.org] +namespace: operation +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_operation:2420 ! Analysis and processing [Term] -id: EDAM_format:1990 -name: match -namespace: format -subset: formats -def: "Alignment format for start and end of matches between sequence pairs." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2946 +name: Alignment analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse an existing alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2951 ! Alignment processing +relationship: has_input EDAM_data:1916 ! Alignment +relationship: has_output EDAM_data:2083 ! Alignment report +[Term] +id: EDAM_operation:2947 +name: Article analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse a body of scientific text (typically a full text article from a scientific journal.)" [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2505 ! Text processing +relationship: has_input EDAM_data:0971 ! Article +relationship: has_output EDAM_data:2954 ! Article report +relationship: has_topic EDAM_topic:0217 ! Literature analysis [Term] -id: EDAM_format:2923 -name: mega variant -namespace: format -subset: formats -def: "Some variant of Mega format for (typically aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2948 +name: Molecular interaction analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_format:1991 -name: mega -namespace: format -subset: formats -def: "Mega format for (typically aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2923 ! mega variant +id: EDAM_operation:2949 +name: Protein interaction analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2405 ! Protein interaction data processing +relationship: has_output EDAM_data:0906 ! Protein interaction [Term] -id: EDAM_format:1992 -name: meganon -namespace: format -subset: formats -def: "Mega non-interleaved format for (typically aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2923 ! mega variant +id: EDAM_operation:2950 +name: Residue contact calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate contacts between residues and some other group in a protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0248 ! Residue interaction calculation +[Term] +id: EDAM_operation:2951 +name: Alignment processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing [Term] -id: EDAM_format:1993 -name: msf alignment format -namespace: format -subset: formats -def: "MSF format for (aligned) sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1947 ! msf +id: EDAM_operation:2952 +name: Structure alignment processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) a molecular tertiary (3D) structure alignment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2951 ! Alignment processing +relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] -id: EDAM_format:1994 -name: nexus alignment format -namespace: format -subset: formats -def: "Nexus/paup format for (aligned) sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1949 ! nexus-seq +id: EDAM_operation:2962 +name: Codon usage bias calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate codon usage bias." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0286 ! Codon usage analysis +relationship: has_output EDAM_data:2865 ! Codon usage bias [Term] -id: EDAM_format:1995 -name: nexusnon alignment format -namespace: format -subset: formats -def: "Nexus/paup non-interleaved format for (aligned) sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1973 ! nexusnon +id: EDAM_operation:2963 +name: Codon usage bias plotting +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Generate a codon usage bias plot." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2962 ! Codon usage bias calculation +relationship: has_output EDAM_data:1600 ! Codon usage bias plot [Term] -id: EDAM_format:1996 -name: pair -namespace: format -subset: formats -def: "EMBOSS simple sequence pair alignment format." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) +id: EDAM_operation:2964 +name: Codon usage fraction calculation +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0286 ! Codon usage analysis +relationship: has_output EDAM_data:1602 ! Codon usage fraction difference [Term] -id: EDAM_format:2924 -name: phylip variant -namespace: format -subset: formats -def: "Some variant of Phylip format for (aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2990 +name: Classification +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation +relationship: has_output EDAM_data:2987 ! Classification [Term] -id: EDAM_format:1997 -name: phylip -namespace: format -subset: formats -def: "Phylip format for (aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2924 ! phylip variant +id: EDAM_operation:2993 +name: Molecular interaction data processing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Process (read and / or write) molecular interaction data." [http://edamontology.org] +namespace: operation +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_format:1998 -name: phylipnon -namespace: format -subset: formats -def: "Phylip non-interleaved format for (aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2924 ! phylip variant +id: EDAM_operation:2995 +name: Sequence classification +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign molecular sequence(s) to a group or category." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2403 ! Sequence analysis +is_a: EDAM_operation:2990 ! Classification +[Term] +id: EDAM_operation:2996 +name: Structure classification +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Assign molecular structure(s) to a group or category." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2480 ! Structure analysis +is_a: EDAM_operation:2990 ! Classification [Term] -id: EDAM_format:1999 -name: score -namespace: format -subset: formats -def: "Alignment format for score values for pairs of sequences." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2997 +name: Protein comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more proteins (or some aspect) to identify similarities." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2424 ! Comparison [Term] -id: EDAM_format:2000 -name: selex -namespace: format -subset: formats -def: "SELEX format for (aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:2998 +name: Nucleic acid comparison +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Compare two or more nucleic acids to identify similarities." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2424 ! Comparison [Term] -id: EDAM_format:2001 -name: simple -namespace: format -subset: formats -def: "EMBOSS simple multiple alignment format." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3023 +name: Prediction, detection and recognition (protein) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict, recognise, detect or identify some properties of proteins." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2423 ! Prediction, detection and recognition [Term] -id: EDAM_format:2002 -name: srs -namespace: format -subset: formats -def: "Simple multiple sequence (alignment) format for SRS." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3024 +name: Prediction, detection and recognition (nucleic acid) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Predict, recognise, detect or identify some properties of nucleic acids." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2423 ! Prediction, detection and recognition [Term] -id: EDAM_format:2003 -name: srspair -namespace: format -subset: formats -def: "Simple sequence pair (alignment) format for SRS." [http://edamontology.org] -is_a: EDAM_format:2920 ! Alignment format (pair only) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3080 +name: Structure editing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2234 ! Structure file processing +is_a: EDAM_operation:3096 ! Editing +relationship: has_input EDAM_data:0883 ! Structure [Term] -id: EDAM_format:2004 -name: tcoffee -namespace: format -subset: formats -def: "TCOFFEE program alignment format." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3081 +name: Sequence alignment editing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2122 ! Sequence alignment file processing +is_a: EDAM_operation:3096 ! Editing [Term] -id: EDAM_format:2005 -name: treecon-seq -namespace: format -subset: formats -def: "Treecon format for (aligned) sequences." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3083 +name: Pathway or network rendering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Render (visualise) a biological pathway or network." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering +is_a: EDAM_operation:2438 ! Pathway or network processing +relationship: has_input EDAM_data:2600 ! Pathway or network [Term] -id: EDAM_format:1391 -name: hmmer-aln -namespace: format -subset: formats -def: "FASTA-style format for multiple sequences aligned by HMMER package to an HMM." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format - +id: EDAM_operation:3084 +name: Protein function prediction (from sequence) +comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Predict general (non-positional) functional properties of a protein from analysing its sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:1777 ! Protein function prediction +is_a: EDAM_operation:2479 ! Protein sequence analysis +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_topic EDAM_topic:2276 ! Protein function prediction [Term] -id: EDAM_format:1392 -name: dialign -namespace: format +id: EDAM_operation:3087 +name: Protein site detection +subset: bioinformatics +subset: edam +subset: operations +synonym: "name: Sequence motif recognition (protein)" EXACT [] +created_in: "beta13" +def: "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0239 ! Sequence motif recognition +is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) -subset: formats -def: "Multiple sequences aligned by DIALIGN package." [http://edamontology.org] -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_operation:3088 +name: Protein property calculation (from sequence) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0250 ! Protein property calculation +is_a: EDAM_operation:2479 ! Protein sequence analysis +[Term] +id: EDAM_operation:3090 +name: Protein feature prediction (from structure) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Predict, recognise and identify positional features in proteins from analysing protein structure." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2406 ! Protein structure analysis +is_a: EDAM_operation:3092 ! Protein feature prediction [Term] -id: EDAM_format:1393 -name: daf -namespace: format -subset: formats -def: "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family." [http://edamontology.org] -comment: The format is clustal-like and includes annotation of domain family classification information. -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3092 +name: Protein feature prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0253 ! Feature prediction +is_a: EDAM_operation:2502 ! Protein data processing +is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) +relationship: has_output EDAM_data:1277 ! Protein features +relationship: has_topic EDAM_topic:3074 ! Protein feature detection +[Term] +id: EDAM_operation:3093 +name: Sequence screening +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2995 ! Sequence classification [Term] -id: EDAM_format:2556 -name: Phylogenetic tree format (text) -namespace: format -subset: formats -def: "Text format for a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_format:2006 ! Phylogenetic tree format +id: EDAM_operation:3094 +name: Protein interaction network prediction +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Predict a network of protein interactions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2445 ! Protein interaction network processing +relationship: has_output EDAM_data:1663 ! Pathway or network (protein-protein interaction) [Term] -id: EDAM_format:2557 -name: Phylogenetic tree format (XML) -namespace: format -subset: formats -def: "XML format for a phylogenetic tree." [http://edamontology.org] -is_a: EDAM_format:2006 ! Phylogenetic tree format +id: EDAM_operation:3095 +name: Nucleic acid design +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Design (or predict) nucleic acid sequences with specific chemical or physical properties." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +[Term] +id: EDAM_operation:3096 +name: Editing +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta13" +def: "Edit, convert or otherwise change a data entity, either randomly or specifically." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0004 ! Operation [Term] -id: EDAM_format:1435 -name: phylip tree -namespace: format -subset: formats -def: "Phylogenetic tree data format used by the PHYLIP program." [http://edamontology.org] -is_a: EDAM_format:2556 ! Phylogenetic tree format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3180 +name: Sequence assembly evaluation +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Evaluate a DNA sequence assembly, typically for purposes of quality control." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2425 ! Optimisation and refinement +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_input EDAM_data:0925 ! Sequence assembly +relationship: has_output EDAM_data:3181 ! Sequence assembly report +relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] -id: EDAM_format:1425 -name: Phylip tree raw -namespace: format -subset: formats -def: "Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted." [http://edamontology.org] -is_a: EDAM_format:2556 ! Phylogenetic tree format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3182 +name: Genome alignment construction +subset: bioinformatics +subset: edam +subset: operations +synonym: "Genome alignment" EXACT [] +created_in: "1.1" +def: "Align two or more (tpyically huge) molecular sequences that represent genomes." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0292 ! Sequence alignment construction [Term] -id: EDAM_format:1424 -name: Clustalw dendrogram -namespace: format -subset: formats -def: "Dendrogram (tree file) format generated by Clustalw." [http://edamontology.org] -is_a: EDAM_format:2556 ! Phylogenetic tree format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3183 +name: Localized reassembly +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Reconstruction of a sequence assembly in a localised area." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0310 ! Sequence assembly [Term] -id: EDAM_format:1436 -name: treebase -namespace: format -subset: formats -def: "The format of an entry from the TreeBASE database of phylogenetic data." [http://edamontology.org] -is_a: EDAM_format:2556 ! Phylogenetic tree format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3184 +name: Sequence assembly rendering +subset: bioinformatics +subset: edam +subset: operations +synonym: "Assembly rendering" EXACT [] +synonym: "Assembly visualisation" EXACT [] +synonym: "Sequence assembly visualisation" EXACT [] +created_in: "1.1" +def: "Render and visualise a DNA sequence assembly." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) [Term] -id: EDAM_format:1437 -name: treefam -namespace: format -subset: formats -def: "The format of an entry from the TreeFam database of phylogenetic data." [http://edamontology.org] -is_a: EDAM_format:2556 ! Phylogenetic tree format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3185 +name: Base-calling +subset: bioinformatics +subset: edam +subset: operations +synonym: "Base calling" EXACT [] +synonym: "Phred base calling" EXACT [] +synonym: "Phred base-calling" EXACT [] +created_in: "1.1" +def: "Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] -id: EDAM_format:1910 -name: newick -namespace: format -subset: formats -def: "Phylogenetic tree Newick (text) format." [http://edamontology.org] -xref: Moby:Newick_Text -is_a: EDAM_format:2556 ! Phylogenetic tree format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3186 +name: Bisulfite mapping +comment: Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Bisulfite sequence alignment" EXACT [] +synonym: "Bisulfite sequence mapping" EXACT [] +created_in: "1.1" +def: "The mapping of methylation sites in a DNA (genome) sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2944 ! Physical mapping [Term] -id: EDAM_format:1911 -name: treecon -namespace: format -subset: formats -def: "Phylogenetic tree TreeCon (text) format." [http://edamontology.org] -xref: Moby:TreeCon -is_a: EDAM_format:2556 ! Phylogenetic tree format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3187 +name: Sequence contamination filtering +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] -id: EDAM_format:1912 -name: nexus -namespace: format -subset: formats -def: "Phylogenetic tree Nexus (text) format." [http://edamontology.org] -xref: Moby:Nexus_Text -is_a: EDAM_format:2556 ! Phylogenetic tree format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3189 +name: Trim ends +comment: For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Trim sequences (typically from an automated DNA sequencer) to remove misleading ends." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3192 ! Sequence trimming [Term] -id: EDAM_format:1475 -name: PDB database entry format -namespace: format -subset: formats -def: "Format of an entry (or part of an entry) from the PDB database." [http://edamontology.org] -synonym: "PDB entry" EXACT [http://edamontology.org] -is_a: EDAM_format:2033 ! Tertiary structure format +id: EDAM_operation:3190 +name: Trim vector +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3192 ! Sequence trimming [Term] -id: EDAM_format:1476 -name: PDB format -namespace: format -subset: formats -def: "Entry format of PDB database in PDB format." [http://edamontology.org] -synonym: "PDB" EXACT [http://edamontology.org] -xref: Moby:PDB-formatted-text -xref: Moby:PDB-Text -is_a: EDAM_format:1475 ! PDB database entry format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3191 +name: Trim to reference +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3192 ! Sequence trimming [Term] -id: EDAM_format:1477 -name: mmCIF -namespace: format -subset: formats -def: "Entry format of PDB database in mmCIF format." [http://edamontology.org] -synonym: "mmcif" EXACT [http://edamontology.org] -xref: Moby:mmCIF-Text -xref: Moby:mmCIF_Text -is_a: EDAM_format:1475 ! PDB database entry format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3192 +name: Sequence trimming +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Cut (remove) the end from a molecular sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0369 ! Sequence cutting [Term] -id: EDAM_format:1478 -name: PDBML -namespace: format -subset: formats -def: "Entry format of PDB database in PDBML (XML) format." [http://edamontology.org] -is_a: EDAM_format:1475 ! PDB database entry format -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:3194 +name: Genome feature comparison +comment: Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Compare the features of two genome sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0256 ! Feature comparison +[Term] +id: EDAM_operation:3195 +name: Sequencing error detection +subset: bioinformatics +subset: edam +subset: operations +synonym: "Short read error correction" EXACT [] +synonym: "Short-read error correction" EXACT [] +created_in: "beta12orEarlier" +def: "Detect errors in DNA sequences generated from sequencing projects)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison +relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] -id: EDAM_format:2013 -name: Biological pathway or network format -namespace: format -subset: formats -def: "Data format for a biological pathway or network." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:2600 ! Pathway or network +id: EDAM_operation:3196 +name: Genotyping +comment: Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3197 ! Genetic variation analysis +[Term] +id: EDAM_operation:3197 +name: Genetic variation analysis +comment: Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Genetic variation annotation" EXACT [] +synonym: "Sequence variation analysis" EXACT [] +created_in: "1.1" +def: "Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison +relationship: has_output EDAM_data:0918 ! Nucleic acid features (variation) [Term] -id: EDAM_format:3166 -name: Biological pathway or network report format -namespace: format -subset: formats -def: "Data format for a report of information derived from a biological pathway or network." [http://edamontology.org] -is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:2984 ! Pathway or network report +id: EDAM_operation:3198 +name: Oligonucleotide alignment construction +comment: The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Oligonucleotide alignment" EXACT [] +synonym: "Oligonucleotide mapping" EXACT [] +synonym: "Read alignment" EXACT [] +synonym: "Read mapping" EXACT [] +synonym: "Short oligonucleotide alignment" EXACT [] +synonym: "Short read alignment" EXACT [] +synonym: "Short read mapping" EXACT [] +synonym: "Short sequence read mapping" EXACT [] +created_in: "1.1" +def: "Align short oligonucleotide sequences (reads) to a larger (genomic) sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0292 ! Sequence alignment construction +[Term] +id: EDAM_operation:3199 +name: Split read mapping +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3198 ! Oligonucleotide alignment construction +[Term] +id: EDAM_operation:3200 +name: DNA barcoding +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sample barcoding" EXACT [] +created_in: "1.1" +def: "Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] -id: EDAM_format:2585 -name: SBML -namespace: format -subset: formats -def: "Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation." [http://edamontology.org] -xref: http://sbml.org !{documentation=true} -is_a: EDAM_format:2034 ! Biological model format -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:3201 +name: SNP calling +comment: Operations usually score confidence in the prediction or some other statistical measure of evidence. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0484 ! SNP detection [Term] -id: EDAM_format:3155 !{since=1.0} -name: SBRML -namespace: format -subset: formats -def: "Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models." [http://edamontology.org] -xref: http://www.comp-sys-bio.org/tiki-index.php?page=SBRML !{documentation=true} -is_a: EDAM_format:3166 ! Biological pathway or network report format -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:3202 +name: Mutation detection +subset: bioinformatics +subset: edam +subset: operations +synonym: "Polymorphism detection" EXACT [] +created_in: "1.1" +def: "Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3197 ! Genetic variation analysis +[Term] +id: EDAM_operation:3203 +name: Chromatogram visualisation +subset: bioinformatics +subset: edam +subset: operations +synonym: "Chromatogram viewing" EXACT [] +created_in: "1.1" +def: "Visualise, format or render an image of a Chromatogram." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0337 ! Plotting and rendering [Term] -id: EDAM_format:3156 !{since=1.0} -name: BioPAX -namespace: format -subset: formats -def: "BioPAX is an exchange format for pathway data, with its data model defined in OWL." [http://edamontology.org] -xref: http://www.biopax.org !{documentation=true} -is_a: EDAM_format:2013 ! Biological pathway or network format -is_a: EDAM_format:2197 ! OWL +id: EDAM_operation:3204 +name: Methylation analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Determine cytosine methylation states in nucleic acid sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] -id: EDAM_format:3157 !{since=1.0} -name: EBI Application Result XML -namespace: format -subset: formats -def: "EBI Application Result XML is a format returned by sequence similarity search Web services at EBI." [http://edamontology.org] -xref: http://www.ebi.ac.uk/schema/ApplicationResult.xsd !{documentation=true} -is_a: EDAM_format:2066 ! Database hits (sequence) format -is_a: EDAM_format:2920 ! Alignment format (pair only) -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:3205 +name: Methylation calling +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Determine cytosine methylation status of specific positions in a nucleic acid sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3204 ! Methylation analysis [Term] -id: EDAM_format:3158 !{since=1.0} -name: PSI MI XML (MIF) -namespace: format -subset: formats -def: "XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI." [http://edamontology.org] -xref: http://psidev.sourceforge.net/mi/xml/doc/user !{documentation=true} -is_a: EDAM_format:2054 ! Protein interaction format -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:3206 +name: Methylation level analysis (global) +subset: bioinformatics +subset: edam +subset: operations +synonym: "Global methylation analysis" EXACT [] +created_in: "1.1" +def: "Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3205 ! Methylation calling [Term] -id: EDAM_format:3159 !{since=1.0} -name: phyloXML -namespace: format -subset: formats -def: "phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data." [http://edamontology.org] -xref: http://www.phyloxml.org !{documentation=true} -is_a: EDAM_format:2557 ! Phylogenetic tree format (XML) -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:3207 +name: Methylation level analysis (gene-specific) +comment: Many different techniques are available for this. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Gene-specific methylation analysis" EXACT [] +created_in: "1.1" +def: "Measure the level of methyl cytosines in specific genes." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3205 ! Methylation calling [Term] -id: EDAM_format:3160 !{since=1.0} -name: NeXML -namespace: format -subset: formats -def: "NeXML is a standardised XML format for rich phyloinformatic data." [http://edamontology.org] -xref: http://www.nexml.org !{documentation=true} -is_a: EDAM_format:2557 ! Phylogenetic tree format (XML) ! And more -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:3208 +name: Genome rendering +subset: bioinformatics +subset: edam +subset: operations +synonym: "Genome browsing" EXACT [] +synonym: "Genome viewing" EXACT [] +synonym: "Genome visualisation" EXACT [] +synonym: "Genome visualization" EXACT [] +created_in: "1.1" +def: "Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) [Term] -id: EDAM_format:3161 !{since=1.0} -name: MAGE-ML -namespace: format -subset: formats -def: "MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org] -xref: http://www.mged.org/Workgroups/MAGE/mage-ml.html !{documentation=true} -is_a: EDAM_format:2058 ! Gene expression report format -is_a: EDAM_format:2056 ! Microarray experiment data format -is_a: EDAM_format:2332 ! XML +id: EDAM_operation:3209 +name: Genome comparison +subset: bioinformatics +subset: edam +subset: operations +synonym: "Genomic region matching" EXACT [] +created_in: "1.1" +def: "Compare the sequence or features of two or more genomes, for example, to find matching regions." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison [Term] -id: EDAM_format:3162 !{since=1.0} -name: MAGE-TAB -namespace: format -subset: formats -def: "MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org] -xref: http://www.mged.org/mage-tab !{documentation=true} -is_a: EDAM_format:2058 ! Gene expression report format -is_a: EDAM_format:2056 ! Microarray experiment data format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3211 +name: Genome indexing +comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Generate an index of a genome sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0227 ! Data indexing +relationship: has_output EDAM_data:3210 ! Genome index [Term] -id: EDAM_format:3163 !{since=1.0} -name: GCDML -namespace: format -subset: formats -def: "GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC)." [http://edamontology.org] -xref: http://gcdml.gensc.org !{documentation=true} -is_a: EDAM_format:3167 ! Experiment annotation format -is_a: EDAM_format:2332 ! XML -relationship: is_format_of EDAM_data:3165 ! Experiment annotation (sequencing) +id: EDAM_operation:3212 +name: Genome indexing (Burrows-Wheeler) +comment: The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Generate an index of a genome sequence using the Burrows-Wheeler algorithm." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3211 ! Genome indexing [Term] -id: EDAM_format:3164 !{since=1.0} -name: GTrack -namespace: format -subset: formats -def: "GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG)." [http://edamontology.org] -xref: http://www.gtrack.no !{documentation=true} -is_a: EDAM_format:2919 ! Sequence annotation track format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3213 +name: Genome indexing (suffix arrays) +comment: A suffix array consists of the lexicographically sorted list of suffixes of a genome. +subset: bioinformatics +subset: edam +subset: operations +synonym: "suffix arrays" EXACT [] +created_in: "1.1" +def: "Generate an index of a genome sequence using a suffix arrays algorithm." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3211 ! Genome indexing [Term] -id: EDAM_format:1666 -name: BioModel mathematical model format -namespace: format -subset: formats -def: "Format of mathematical models from the BioModel database." [http://edamontology.org] -comment: Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3214 +name: Spectrum analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "Mass spectrum analysis" EXACT [] +synonym: "Spectral analysis" EXACT [] +created_in: "1.1" +def: "Analyse a spectrum from a mass spectrometry (or other) experiment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2420 ! Analysis and processing [Term] -id: EDAM_format:1647 -name: KEGG PATHWAY entry format -namespace: format -subset: formats -def: "The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML - +id: EDAM_operation:3215 +name: Peak detection +subset: bioinformatics +subset: edam +subset: operations +synonym: "Peak finding" EXACT [] +created_in: "1.1" +def: "Identify peaks in a spectrum from a mass spectrometry experiment." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3214 ! Spectrum analysis +relationship: has_input EDAM_data:0943 ! Mass spectrometry spectra [Term] -id: EDAM_format:1648 -name: MetaCyc entry format -namespace: format -subset: formats -def: "The format of an entry from the MetaCyc metabolic pathways database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3216 +name: Scaffolding +comment: Scaffold may be positioned along a chromosome physical map to create a "golden path". +subset: bioinformatics +subset: edam +subset: operations +synonym: "Scaffold construction" EXACT [] +created_in: "1.1" +def: "Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2429 ! Mapping and assembly +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +[Term] +id: EDAM_operation:3217 +name: Scaffold gap completion +comment: Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2429 ! Mapping and assembly +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:1649 -name: HumanCyc entry format -namespace: format -subset: formats -def: "The format of a report from the HumanCyc metabolic pathways database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3218 +name: Sequencing quality control +subset: bioinformatics +subset: edam +subset: operations +synonym: "Analyse raw sequence data from a sequencing pipeline and identify problems." EXACT [] +synonym: "Sequencing QC" EXACT [] +created_in: "1.1" +def: "Raw sequence data quality control." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2428 ! Evaluation and validation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +[Term] +id: EDAM_operation:3219 +name: Read pre-processing +comment: This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Sequence read pre-processing" EXACT [] +created_in: "1.1" +def: "Pre-process sequence reads to ensure (or improve) quality and reliability." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:1650 -name: INOH entry format -namespace: format -subset: formats -def: "The format of an entry from the INOH signal transduction pathways database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3221 +name: Species frequency estimation +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_topic EDAM_topic:3174 ! Metagenomics +[Term] +id: EDAM_operation:3222 +name: Peak calling +comment: Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). +subset: bioinformatics +subset: edam +subset: operations +synonym: "Protein binding peak detection" EXACT [] +created_in: "1.1" +def: "Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +[Term] +id: EDAM_operation:3223 +name: Differential expression analysis +comment: Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Differentially expressed gene identification" EXACT [] +created_in: "1.1" +def: "Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0315 ! Gene expression profile comparison [Term] -id: EDAM_format:1651 -name: PATIKA entry format -namespace: format -subset: formats -def: "The format of an entry from the PATIKA biological pathways database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3224 +name: Gene set testing +comment: Gene sets can be defined beforehand by biological function, chromosome locations and so on. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2435 ! Gene expression profile processing +[Term] +id: EDAM_operation:3225 +name: Variant classification +comment: Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +is_a: EDAM_operation:2995 ! Sequence classification [Term] -id: EDAM_format:1652 -name: Reactome entry format -namespace: format -subset: formats -def: "The format of an entry from the reactome biological pathways database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3226 +name: Variant prioritization +comment: Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +[Term] +id: EDAM_operation:3227 +name: Variant mapping +comment: Methods often utilise a database of aligned reads. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Variant calling" EXACT [] +created_in: "1.1" +def: "Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3197 ! Genetic variation analysis [Term] -id: EDAM_format:1653 -name: aMAZE entry format -namespace: format -subset: formats -def: "The format of an entry from the aMAZE biological pathways and molecular interactions database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3228 +name: Structural variation discovery +comment: Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3197 ! Genetic variation analysis +[Term] +id: EDAM_operation:3229 +name: Exome analysis +comment: Exome sequencing is considered a cheap alternative to whole genome sequencing. +subset: bioinformatics +subset: edam +subset: operations +synonym: "Exome sequence analysis" EXACT [] +synonym: "Targeted exome capture" EXACT [] +created_in: "1.1" +def: "Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:1654 -name: CPDB entry format -namespace: format -subset: formats -def: "The format of an entry from the CPDB database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3230 +name: Read depth analysis +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +[Term] +id: EDAM_operation:3232 +name: Gene expression QTL analysis +subset: bioinformatics +subset: edam +subset: operations +synonym: "eQTL profiling" EXACT [] +synonym: "expression QTL profiling" EXACT [] +synonym: "expression quantitative trait loci profiling" EXACT [] +created_in: "1.1" +def: "Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0532 ! Gene expression profile analysis +relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] -id: EDAM_format:1655 -name: Panther Pathways entry format -namespace: format -subset: formats -def: "The format of an entry from the Panther Pathways database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3233 +name: Copy number estimation +comment: Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). +subset: bioinformatics +subset: edam +subset: operations +synonym: "Transcript copy number estimation" EXACT [] +created_in: "1.1" +def: "Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:2341 -name: NCI-Nature pathway entry format -namespace: format -subset: formats -def: "The format of an entry from the NCI-Nature pathways database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_operation:3237 +name: Primer removal +subset: bioinformatics +subset: edam +subset: operations +created_in: "1.1" +def: "Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products)." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:0369 ! Sequence cutting +is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid) [Term] -id: EDAM_format:2015 -name: Sequence-profile alignment (HMM) format -namespace: format -subset: formats -def: "Data format for a sequence-HMM profile alignment." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2014 ! Sequence-profile alignment format +id: EDAM_operation:3258 +name: Transcriptome assembly +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Infer a transcriptome sequence by analysis of short sequence reads." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:2429 ! Mapping and assembly +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_output EDAM_data:0925 ! Sequence assembly +relationship: has_topic EDAM_topic:0196 ! Sequence assembly +[Term] +id: EDAM_operation:3259 +name: Transcriptome assembly (de novo) +subset: bioinformatics +subset: edam +subset: operations +synonym: "de novo transcriptome assembly" EXACT [] +created_in: "beta12orEarlier" +def: "Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3258 ! Transcriptome assembly [Term] -id: EDAM_format:1419 -name: Sequence-MEME profile alignment -namespace: format -subset: formats -def: "Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package." [http://edamontology.org] -is_a: EDAM_format:2014 ! Sequence-profile alignment format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_operation:3260 +name: Transcriptome assembly (mapping) +subset: bioinformatics +subset: edam +subset: operations +created_in: "beta12orEarlier" +def: "Infer a transcriptome sequence by mapping short reads to a reference genome." [http://edamontology.org] +namespace: operation +is_a: EDAM_operation:3258 ! Transcriptome assembly [Term] -id: EDAM_format:1421 -name: HMMER profile alignment (sequences versus HMMs) -namespace: format -subset: formats -def: "Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database." [http://edamontology.org] -is_a: EDAM_format:2014 ! Sequence-profile alignment format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0003 +name: Topic +subset: bioinformatics +subset: edam +subset: topics +synonym: "Area_of_Research" RELATED [] +synonym: "Category" RELATED [] +synonym: "Continuant" BROAD [] +synonym: "Method" RELATED [] +synonym: "Perpetuant" RELATED [] +synonym: "Quality" BROAD [] +synonym: "Quality" RELATED [] +synonym: "quality" RELATED [] +synonym: "sumo:FieldOfStudy" RELATED [] +created_in: "beta12orEarlier" +def: "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other." [http://edamontology.org] +namespace: topic [Term] -id: EDAM_format:1422 -name: HMMER profile alignment (HMM versus sequences) -namespace: format -subset: formats -def: "Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database." [http://edamontology.org] -is_a: EDAM_format:2014 ! Sequence-profile alignment format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0077 +name: Nucleic acid analysis +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D017422" NARROW [] +synonym: "http://purl.bioontology.org/ontology/MSH/D017423" NARROW [] +synonym: "Nucleic acid bioinformatics" EXACT [] +synonym: "Nucleic acid informatics" EXACT [] +synonym: "Nucleic acids" EXACT [] +created_in: "beta12orEarlier" +def: "Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic +[Term] +id: EDAM_topic:0078 +name: Protein analysis +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D020539" NARROW [] +synonym: "Protein bioinformatics" EXACT [] +synonym: "Protein informatics" EXACT [] +synonym: "Proteins" EXACT [] +created_in: "beta12orEarlier" +def: "Processing and analysis of protein data, typically molecular sequence and structural data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic +[Term] +id: EDAM_topic:0079 +name: Metabolites +comment: This concept excludes macromolecules such as proteins and nucleic acids. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0154 ! Small molecules +is_a: EDAM_topic:3172 ! Metabolomics [Term] -id: EDAM_format:1504 -name: aaindex -namespace: format -subset: formats -def: "Amino acid index format used by the AAindex database." [http://edamontology.org] -is_a: EDAM_format:2017 ! Amino acid index format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0080 +name: Sequence analysis +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D017421" EXACT [] +synonym: "Sequences" EXACT [] +xref: BioCatalogue:Sequence Analysis +created_in: "beta12orEarlier" +def: "Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1739 -name: pmc -namespace: format -subset: formats -def: "Article format of the PubMed Central database." [http://edamontology.org] -is_a: EDAM_format:2020 ! Article format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0081 +name: Structure analysis +comment: This includes related concepts such as structural properties, alignments and structural motifs. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Computation structural biology" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D015394" RELATED [] +synonym: "Structural bioinformatics" EXACT [] +created_in: "beta12orEarlier" +def: "Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:2194 -name: medline -namespace: format -subset: formats -def: "Abstract format used by MedLine database." [http://edamontology.org] -is_a: EDAM_format:2020 ! Article format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0082 +name: Structure prediction +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the prediction of molecular (secondary or tertiary) structure." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM_format:1740 -name: iHOP text mining abstract format -namespace: format -subset: formats -def: "iHOP abstract format." [http://edamontology.org] -is_a: EDAM_format:2021 ! Text mining report format -is_a: EDAM_format:2330 ! Textual format - +id: EDAM_topic:0083 +name: Alignment +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0182 ! Sequence alignment +consider: EDAM_topic:0183 ! Structure alignment +consider: EDAM_topic:0184 ! Threading [Term] -id: EDAM_format:1741 -name: Oscar3 -namespace: format -subset: formats -def: "Text mining abstract format from the Oscar 3 application." [http://edamontology.org] -comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. -is_a: EDAM_format:2021 ! Text mining report format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0084 +name: Phylogenetics +comment: This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data. +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D010802" NARROW [] +synonym: "Phylogenetic clocks, dating and stratigraphy" EXACT [] +synonym: "Phylogenetic simulation" EXACT [] +xref: BioCatalogue:Phylogeny +xref: BioCatalogue:Statistical Robustness +created_in: "beta12orEarlier" +def: "Topic concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1582 -name: findkm -namespace: format -subset: formats -def: "A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax)." [http://edamontology.org] -is_a: EDAM_format:2027 ! Enzyme kinetics report format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0085 +name: Functional genomics +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the study of gene or protein functions and their interactions." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0622 ! Genomics +[Term] +id: EDAM_topic:0089 +name: Ontology +comment: This includes the annotation of entities (typically biological database entries) with concepts from a controlled vocabulary. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Applied ontology" NARROW [] +synonym: "Ontologies" EXACT [] +xref: BioCatalogue:Ontology Lookup +xref: BioCatalogue:Ontology +created_in: "beta12orEarlier" +def: "Topic concerning ontologies, controlled vocabularies, structured glossary or other related resource." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] -id: EDAM_format:1697 -name: KEGG LIGAND entry format -namespace: format -subset: formats -def: "The format of an entry from the KEGG LIGAND chemical database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0090 +name: Data search and retrieval +comment: This includes, for example, search, query and retrieval of molecular sequences and associated data. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Data retrieval" EXACT [] +xref: BioCatalogue:Data Retrieval +xref: BioCatalogue:Identifier Retrieval +xref: BioCatalogue:Image Retrieval +xref: BioCatalogue:Sequence Retrieval +xref: BioCatalogue:Structure Retrieval +created_in: "beta12orEarlier" +def: "Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0091 ! Data handling +[Term] +id: EDAM_topic:0091 +name: Data handling +subset: bioinformatics +subset: edam +subset: topics +synonym: "Data types, processing and visualisation" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D016247" NARROW [] +created_in: "beta12orEarlier" +def: "Topic for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1698 -name: KEGG COMPOUND entry format -namespace: format -subset: formats -def: "The format of an entry from the KEGG COMPOUND database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0092 +name: Data visualisation +subset: bioinformatics +subset: edam +subset: topics +synonym: "Data plotting" EXACT [] +synonym: "Data rendering" EXACT [] +synonym: "Data rendering and visualisation" EXACT [] +created_in: "beta12orEarlier" +def: "Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0091 ! Data handling +[Term] +id: EDAM_topic:0094 +name: Nucleic acid thermodynamics +comment: This includes the study of thermal and conformational properties including DNA or DNA/RNA denaturation (melting). +subset: bioinformatics +subset: edam +subset: topics +synonym: "DNA melting" EXACT [] +synonym: "Nucleic acid denaturation" EXACT [] +synonym: "Nucleic acid physicochemistry" EXACT [] +synonym: "Nucleic acid properties" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the study of the thermodynamic properties of a nucleic acid." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:1699 -name: KEGG PLANT entry format -namespace: format -subset: formats -def: "The format of an entry from the KEGG PLANT database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0097 +name: Nucleic acid structure analysis +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "The processing and analysis of nucleic acid (secondary or tertiary) structural data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0077 ! Nucleic acid analysis +is_a: EDAM_topic:0081 ! Structure analysis +[Term] +id: EDAM_topic:0099 +name: RNA +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning RNA sequences and structures." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3042 ! Nucleic acid sequences [Term] -id: EDAM_format:1700 -name: KEGG GLYCAN entry format -namespace: format -subset: formats -def: "The format of an entry from the KEGG GLYCAN database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0100 +name: Nucleic acid restriction +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis +is_a: EDAM_topic:0821 ! Enzymes and reactions [Term] -id: EDAM_format:1706 -name: KEGG DRUG entry format -namespace: format -subset: formats -def: "The format of an entry from the KEGG DRUG database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0102 +name: Mapping +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the mapping of complete (typically nucleotide) sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:1701 -name: PubChem entry format -namespace: format -subset: formats -def: "The format of an entry from PubChem." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0107 +name: Codon usage analysis +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0110 ! Transcription +[Term] +id: EDAM_topic:0108 +name: Translation +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the translation of mRNA into protein." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:1702 -name: ChemSpider entry format -namespace: format -subset: formats -def: "The format of an entry from a database of chemical structures and property predictions." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0109 +name: Gene finding +comment: This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Gene discovery" EXACT [] +synonym: "Gene prediction" EXACT [] +xref: BioCatalogue:Gene Prediction +created_in: "beta12orEarlier" +def: "Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3073 ! Nucleic acid feature detection +[Term] +id: EDAM_topic:0110 +name: Transcription +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Transcription Factors +created_in: "beta12orEarlier" +def: "Topic concerning the transcription of DNA into mRNA." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:1703 -name: ChEBI entry format -namespace: format -subset: formats -def: "The format of an entry from Chemical Entities of Biological Interest (ChEBI)." [http://edamontology.org] -comment: ChEBI includes an ontological classification defining relations between entities or classes of entities. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0111 +name: Promoters +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Promoter Prediction +created_in: "beta12orEarlier" +def: "Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins)." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0749 ! Transcription factors and regulatory sites +[Term] +id: EDAM_topic:0112 +name: Nucleic acid folding +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the folding (in 3D space) of nucleic acid molecules." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0173 ! Nucleic acid structure prediction [Term] -id: EDAM_format:1704 -name: MSDchem ligand dictionary entry format -namespace: format -subset: formats -def: "The format of an entry from the MSDchem ligand dictionary." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0114 +name: Gene structure and RNA splicing +comment: This includes splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Gene structure" EXACT [] +synonym: "RNA splicing" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0747 ! Nucleic acid sites and features +is_a: EDAM_topic:3062 ! Genetic organisation +[Term] +id: EDAM_topic:0121 +name: Proteomics +comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues). +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D040901" EXACT [] +synonym: "Protein expression" EXACT [] +xref: BioCatalogue:Proteomics +created_in: "beta12orEarlier" +def: "Topic concerning the study of whole proteomes of organisms." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1705 -name: HET group dictionary entry format -namespace: format -subset: formats -def: "The format of an entry from the HET group dictionary (HET groups from PDB files)." [http://edamontology.org] -is_a: EDAM_format:2030 ! Small molecule report format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0122 +name: Structural genomics +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Structural Genomics +created_in: "beta12orEarlier" +def: "Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0622 ! Genomics +is_a: EDAM_topic:2226 ! Structure determination [Term] -id: EDAM_format:1808 -name: GeneIlluminator gene report format -namespace: format -subset: formats -def: "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service." [http://edamontology.org] -comment: This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. -xref: Moby:GI_Gene -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0123 +name: Protein properties +subset: bioinformatics +subset: edam +subset: topics +synonym: "Protein physicochemistry" EXACT [] +created_in: "beta12orEarlier" +def: "Topic for the study of the physical and biochemical properties of peptides and proteins." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0639 ! Protein sequence analysis [Term] -id: EDAM_format:1809 -name: BacMap gene card format -namespace: format -subset: formats -def: "Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database." [http://edamontology.org] -xref: Moby:BacMapGeneCard -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0128 +name: Protein interactions +comment: This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Protein Interaction +created_in: "beta12orEarlier" +def: "Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:1775 ! Protein function analysis +is_a: EDAM_topic:2225 ! Protein databases [Term] -id: EDAM_format:1810 -name: ColiCard report format -namespace: format -subset: formats -def: "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [http://edamontology.org] -xref: Moby:ColiCard -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0130 +name: Protein folding and stability +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2814 ! Protein structure analysis [Term] -id: EDAM_format:2328 -name: PseudoCAP gene report format -namespace: format -subset: formats -def: "Format of a report on a gene from the PseudoCAP database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0133 +name: Two-dimensional gel electrophoresis +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning two-dimensional gel electrophoresis image and related data." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0121 ! Proteomics [Term] -id: EDAM_format:2329 -name: GeneCards gene report format -namespace: format -subset: formats -def: "Format of a report on a gene from the GeneCards database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0134 +name: Mass spectrometry +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning mass spectrometry and related data." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0121 ! Proteomics [Term] -id: EDAM_format:1603 -name: Ensembl gene report format -namespace: format -subset: formats -def: "Entry format of Ensembl genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0135 +name: Protein microarrays +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning protein microarray data." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0121 ! Proteomics +consider: EDAM_topic:0200 ! Microarrays [Term] -id: EDAM_format:1604 -name: DictyBase gene report format -namespace: format -subset: formats -def: "Entry format of DictyBase genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0137 +name: Protein hydropathy +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0123 ! Protein properties [Term] -id: EDAM_format:1605 -name: CGD gene report format -namespace: format -subset: formats -def: "Entry format of Candida Genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML - +id: EDAM_topic:0140 +name: Protein targeting and localization +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2225 ! Protein databases +is_a: EDAM_topic:2276 ! Protein function prediction [Term] -id: EDAM_format:1606 -name: DragonDB gene report format -namespace: format -subset: formats -def: "Entry format of DragonDB genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0141 +name: Protein cleavage sites and proteolysis +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0639 ! Protein sequence analysis [Term] -id: EDAM_format:1607 -name: EcoCyc gene report format -namespace: format -subset: formats -def: "Entry format of EcoCyc genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0143 +name: Protein structure comparison +comment: Use this concept for methods that are exclusively for protein structure. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the comparison of two or more protein structures." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0698 ! Protein tertiary structure +consider: EDAM_topic:1770 ! Structure comparison [Term] -id: EDAM_format:1608 -name: FlyBase gene report format -namespace: format -subset: formats -def: "Entry format of FlyBase genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0144 +name: Protein residue interaction analysis +subset: bioinformatics +subset: edam +subset: topics +synonym: "Protein residue interactions" EXACT [] +created_in: "beta12orEarlier" +def: "The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2814 ! Protein structure analysis +[Term] +id: EDAM_topic:0147 +name: Protein-protein interactions +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning protein-protein interactions, protein complexes, protein functional coupling etc." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0128 ! Protein interactions [Term] -id: EDAM_format:1609 -name: Gramene gene report format -namespace: format -subset: formats -def: "Entry format of Gramene genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0148 +name: Protein-ligand interactions +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Ligand Interaction +created_in: "beta12orEarlier" +def: "Topic concerning protein-ligand (small molecule) interactions." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0128 ! Protein interactions +[Term] +id: EDAM_topic:0149 +name: Protein-nucleic acid interactions +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning protein-DNA/RNA interactions." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0128 ! Protein interactions [Term] -id: EDAM_format:1610 -name: KEGG GENES gene report format -namespace: format -subset: formats -def: "Entry format of KEGG GENES genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0150 +name: Protein design +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0172 ! Protein structure prediction [Term] -id: EDAM_format:1611 -name: MaizeGDB gene report format -namespace: format -subset: formats -def: "Entry format of the Maize genetics and genomics database (MaizeGDB)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0151 +name: G protein-coupled receptors (GPCR) +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning G-protein coupled receptors (GPCRs)." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0820 ! Membrane proteins +[Term] +id: EDAM_topic:0152 +name: Carbohydrates +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning carbohydrates, typically including structural information." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3038 ! Structure databases [Term] -id: EDAM_format:1612 -name: MGD gene report format -namespace: format -subset: formats -def: "Entry format of the Mouse Genome Database (MGD)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0153 +name: Lipids +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning lipids and their structures." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3038 ! Structure databases [Term] -id: EDAM_format:1613 -name: RGD gene report format -namespace: format -subset: formats -def: "Entry format of the Rat Genome Database (RGD)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0154 +name: Small molecules +comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. +subset: bioinformatics +subset: edam +subset: topics +synonym: "CHEBI:23367" RELATED [] +created_in: "beta12orEarlier" +def: "Topic concerning small molecules of biological significance, typically including structural information." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3038 ! Structure databases [Term] -id: EDAM_format:1614 -name: SGD gene report format -namespace: format -subset: formats -def: "Entry format of the Saccharomyces Genome Database (SGD)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0156 +name: Sequence editing +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0080 ! Sequence analysis +consider: EDAM_topic:0091 ! Data handling +[Term] +id: EDAM_topic:0157 +name: Sequence composition analysis +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM_format:1615 -name: GeneDB gene report format -namespace: format -subset: formats -def: "Entry format of the Sanger GeneDB genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0158 +name: Sequence motifs +subset: bioinformatics +subset: edam +subset: topics +synonym: "Motifs" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0594 ! Sequence classification [Term] -id: EDAM_format:1616 -name: TAIR gene report format -namespace: format -subset: formats -def: "Entry format of The Arabidopsis Information Resource (TAIR) genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0159 +name: Sequence comparison +comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Nucleotide Sequence Similarity +xref: BioCatalogue:Protein Sequence Similarity +created_in: "beta12orEarlier" +def: "Topic concerning the comparison of two or more molecular sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0080 ! Sequence analysis +[Term] +id: EDAM_topic:0160 +name: Sequence sites and features +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM_format:1617 -name: WormBase gene report format -namespace: format -subset: formats -def: "Entry format of the WormBase genomes database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0163 +name: Sequence database search +comment: The query is a sequence-based entity such as another sequence, a motif or profile. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence)." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0159 ! Sequence comparison [Term] -id: EDAM_format:1618 -name: ZFIN gene report format -namespace: format -subset: formats -def: "Entry format of the Zebrafish Information Network (ZFIN) genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0164 +name: Sequence clustering +comment: This includes systems that generate, process and analyse sequence clusters. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0159 ! Sequence comparison +[Term] +id: EDAM_topic:0166 +name: Protein structural motifs and surfaces +comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Protein structural features" EXACT [] +synonym: "Protein structural motifs" EXACT [] +synonym: "Protein surfaces" EXACT [] +synonym: "Structural motifs" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0698 ! Protein tertiary structure [Term] -id: EDAM_format:1619 -name: TIGR gene report format -namespace: format -subset: formats -def: "Entry format of the TIGR genome database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0167 +name: Structural (3D) profiles +subset: bioinformatics +subset: edam +subset: topics +synonym: "Structural profiles" EXACT [] +created_in: "beta12orEarlier" +def: "The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:1770 ! Structure comparison [Term] -id: EDAM_format:1782 -name: NCBI gene report format -namespace: format -subset: formats -def: "Entry (gene) format of the NCBI database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0172 +name: Protein structure prediction +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Protein Structure Prediction +created_in: "beta12orEarlier" +def: "Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0082 ! Structure prediction +is_a: EDAM_topic:2814 ! Protein structure analysis [Term] -id: EDAM_format:1665 -name: Taverna workflow format -namespace: format -subset: formats -def: "Format of Taverna workflows." [http://edamontology.org] -is_a: EDAM_format:2032 ! Workflow format -is_a: EDAM_format:2332 ! XML +id: EDAM_topic:0173 +name: Nucleic acid structure prediction +subset: bioinformatics +subset: edam +subset: topics +synonym: "Nucleic acid folding" EXACT [] +synonym: "RNA/DNA structure prediction" EXACT [] +xref: BioCatalogue:Nucleotide Secondary Structure +xref: BioCatalogue:Nucleotide Structure Prediction +xref: BioCatalogue:Nucleotide Tertiary Structure +created_in: "beta12orEarlier" +def: "Topic concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0082 ! Structure prediction +is_a: EDAM_topic:0097 ! Nucleic acid structure analysis [Term] -id: EDAM_format:1196 -name: smiles -namespace: format -subset: formats -def: "Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation." [http://edamontology.org] -is_a: EDAM_format:2035 ! Chemical formula format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0174 +name: Ab initio structure prediction +subset: bioinformatics +subset: edam +subset: topics +synonym: "de novo protein structure prediction" EXACT [] +created_in: "beta12orEarlier" +def: "Topic for the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0082 ! Structure prediction [Term] -id: EDAM_format:1197 -name: inchi -namespace: format -subset: formats -def: "Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation." [http://edamontology.org] -is_a: EDAM_format:2035 ! Chemical formula format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0175 +name: Homology modelling +subset: bioinformatics +subset: edam +subset: topics +synonym: "Comparative modelling" EXACT [] +created_in: "beta12orEarlier" +def: "Topic for the modelling of the three-dimensional structure of a protein using known sequence and structural data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2275 ! Molecular modelling [Term] -id: EDAM_format:1198 -name: mf -namespace: format -subset: formats -def: "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound." [http://edamontology.org] -comment: The general MF query format consists of a series of valid atomic symbols, with an optional number or range. -is_a: EDAM_format:2035 ! Chemical formula format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0176 +name: Molecular dynamics +comment: This includes resources concerning flexibility and motion in protein and other molecular structures. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Molecular flexibility" EXACT [] +synonym: "Molecular motions" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2275 ! Molecular modelling [Term] -id: EDAM_format:1199 -name: inchikey -namespace: format -subset: formats -def: "The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound." [http://edamontology.org] -comment: An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. -is_a: EDAM_format:2035 ! Chemical formula format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0177 +name: Molecular docking +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic for modelling the structure of proteins in complex with small molecules or other macromolecules." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2275 ! Molecular modelling [Term] -id: EDAM_format:1200 -name: smarts -namespace: format -subset: formats -def: "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." [http://edamontology.org] -is_a: EDAM_format:1196 ! smiles +id: EDAM_topic:0178 +name: Protein secondary structure prediction +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Protein Secondary Structure +created_in: "beta12orEarlier" +def: "Topic concerning the prediction of secondary or supersecondary structure of protein sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0172 ! Protein structure prediction +is_a: EDAM_topic:0694 ! Protein secondary structure [Term] -id: EDAM_format:2037 -name: Phylogenetic continuous quantitative character format -namespace: format -subset: formats -def: "Format of phylogenetic continuous quantitative character data." [http://edamontology.org] -is_a: EDAM_format:2036 ! Phylogenetic character data format -relationship: is_format_of EDAM_data:1426 ! Phylogenetic continuous quantitative data +id: EDAM_topic:0179 +name: Protein tertiary structure prediction +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Protein Tertiary Structure +created_in: "beta12orEarlier" +def: "Topic concerning the prediction of tertiary structure of protein sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0172 ! Protein structure prediction +is_a: EDAM_topic:0698 ! Protein tertiary structure [Term] -id: EDAM_format:1431 -name: Phylogenetic property values format -namespace: format -subset: formats -def: "Format of phylogenetic property data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2036 ! Phylogenetic character data format +id: EDAM_topic:0180 +name: Protein fold recognition +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0172 ! Protein structure prediction +[Term] +id: EDAM_topic:0182 +name: Sequence alignment +comment: This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D016415" EXACT [] +xref: BioCatalogue:Nucleotide Multiple Alignment +xref: BioCatalogue:Nucleotide Pairwise Alignment +xref: BioCatalogue:Nucleotide Sequence Alignment +xref: BioCatalogue:Protein Multiple Alignment +xref: BioCatalogue:Protein Pairwise Alignment +xref: BioCatalogue:Protein Sequence Alignment +created_in: "beta12orEarlier" +def: "Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0159 ! Sequence comparison +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM_format:2038 -name: Phylogenetic discrete states format -namespace: format -subset: formats -def: "Format of phylogenetic discrete states data." [http://edamontology.org] -is_a: EDAM_format:2036 ! Phylogenetic character data format -relationship: is_format_of EDAM_data:1427 ! Phylogenetic discrete data +id: EDAM_topic:0183 +name: Structure alignment +comment: This includes the generation, storage, analysis, rendering etc. of structure alignments. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Structure alignment generation" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:1770 ! Structure comparison +is_a: EDAM_topic:3038 ! Structure databases [Term] -id: EDAM_format:2039 -name: Phylogenetic tree report (cliques) format -namespace: format -subset: formats -def: "Format of phylogenetic cliques data." [http://edamontology.org] -is_a: EDAM_format:2036 ! Phylogenetic character data format -relationship: is_format_of EDAM_data:1428 ! Phylogenetic character cliques +id: EDAM_topic:0184 +name: Threading +subset: bioinformatics +subset: edam +subset: topics +synonym: "Sequence-structure alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0180 ! Protein fold recognition +[Term] +id: EDAM_topic:0188 +name: Sequence profiles and HMMs +comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0594 ! Sequence classification [Term] -id: EDAM_format:2040 -name: Phylogenetic tree report (invariants) format -namespace: format -subset: formats -def: "Format of phylogenetic invariants data." [http://edamontology.org] -is_a: EDAM_format:2036 ! Phylogenetic character data format -relationship: is_format_of EDAM_data:1429 ! Phylogenetic invariants +id: EDAM_topic:0191 +name: Phylogeny reconstruction +comment: Currently too specific for the topic sub-ontology (but might be unobsoleted). +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Evolutionary Distance Measurements +xref: BioCatalogue:Tree Inference +created_in: "beta12orEarlier" +def: "Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0084 ! Phylogenetics [Term] -id: EDAM_format:1430 -name: phylip continuous quantitative characters -namespace: format -subset: formats -def: "PHYLIP file format for continuous quantitative character data." [http://edamontology.org] -is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0194 +name: Phylogenomics +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0084 ! Phylogenetics +is_a: EDAM_topic:0622 ! Genomics [Term] -id: EDAM_format:1432 -name: phylip character frequencies -namespace: format -subset: formats -def: "PHYLIP file format for phylogenetics character frequency data." [http://edamontology.org] -is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0195 +name: Virtual PCR +subset: bioinformatics +subset: edam +subset: topics +synonym: "PCR" EXACT [] +synonym: "Polymerase chain reaction" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning simulated polymerase chain reaction (PCR)." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0077 ! Nucleic acid analysis [Term] -id: EDAM_format:2243 -name: phylip property values -namespace: format -subset: formats -def: "PHYLIP file format for phylogenetic property data." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2036 ! Phylogenetic character data format +id: EDAM_topic:0196 +name: Sequence assembly +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3168 ! Sequencing [Term] -id: EDAM_format:1433 -name: phylip discrete states -namespace: format -subset: formats -def: "Format of PHYLIP discrete states data." [http://edamontology.org] -is_a: EDAM_format:2038 ! Phylogenetic discrete states format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0199 +name: Genetic variation +subset: bioinformatics +subset: edam +subset: topics +synonym: "DNA variation" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D014644" EXACT [] +synonym: "Mutation and polymorphism" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning DNA sequence variation (mutation and polymorphism) data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0625 ! Genotype and phenotype +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM_format:1434 -name: phylip cliques -namespace: format -subset: formats -def: "Format of PHYLIP cliques data." [http://edamontology.org] -is_a: EDAM_format:2039 ! Phylogenetic tree report (cliques) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0200 +name: Microarrays +subset: bioinformatics +subset: edam +subset: topics +synonym: "DNA microarrays" NARROW [] +synonym: "http://purl.bioontology.org/ontology/MSH/D046228" NARROW [] +xref: BioCatalogue:Microarrays +created_in: "beta12orEarlier" +def: "Topic concerning microarrays, for example, to process microarray data or design probes and experiments." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0607 ! Laboratory resources +[Term] +id: EDAM_topic:0202 +name: Pharmacoinformatics +subset: bioinformatics +subset: edam +subset: topics +synonym: "Computational pharmacology" EXACT [] +created_in: "beta12orEarlier" +def: "Topic for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2258 ! Chemoinformatics [Term] -id: EDAM_format:1645 -name: EMDB entry format -namespace: format -subset: formats -def: "Format of an entry from the Electron Microscopy DataBase (EMDB)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0203 +name: Transcriptomics +alt_id: topic_0197 +comment: This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Expression profiling" EXACT [] +synonym: "Gene expression analysis" EXACT [] +synonym: "Gene expression profiling" EXACT [] +synonym: "Gene expression resources" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D015870" RELATED [] +created_in: "beta12orEarlier" +def: "Topic concerning primarily raw or processed gene (mRNA) expression (typically microarray) data, including the analysis of gene expression levels, by identifying, quantifying or comparing mRNA transcripts and the interpretation (in functional terms) of gene expression data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic +is_a: EDAM_topic:2816 ! Gene resources [Term] -id: EDAM_format:1445 -name: phylip tree distance -namespace: format -subset: formats -def: "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." [http://edamontology.org] -is_a: EDAM_format:2049 ! Phylogenetic tree report (tree distances) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0204 +name: Gene regulation +subset: bioinformatics +subset: edam +subset: topics +synonym: "Gene regulation resources" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning primarily the regulation of gene expression." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2816 ! Gene resources [Term] -id: EDAM_format:1620 -name: dbSNP polymorphism report format -namespace: format -subset: formats -def: "Entry format for the dbSNP database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0208 +name: Pharmacogenomics +subset: bioinformatics +subset: edam +subset: topics +synonym: "Pharmacogenetics" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0202 ! Pharmacoinformatics +is_a: EDAM_topic:0622 ! Genomics [Term] -id: EDAM_format:1570 -name: InterPro entry format -namespace: format -subset: formats -def: "Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences." [http://edamontology.org] -comment: This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0209 +name: Drug design +comment: This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the design of drugs or potential drug compounds." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0202 ! Pharmacoinformatics [Term] -id: EDAM_format:1571 -name: InterPro entry abstract format -namespace: format -subset: formats -def: "Entry format for the textual abstract of signatures in an InterPro entry and its protein matches." [http://edamontology.org] -comment: References are included and a functional inference is made where possible. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0210 +name: Fish +comment: The resource may be specific to a fish, a group of fish or all fish. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2820 ! Vertebrates +[Term] +id: EDAM_topic:0211 +name: Flies +comment: The resource may be specific to a fly, a group of flies or all flies. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Fly" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2819 ! Invertebrates [Term] -id: EDAM_format:1572 -name: Gene3D entry format -namespace: format -subset: formats -def: "Entry format for the Gene3D protein secondary database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0213 +name: Mice or rats +comment: The resource may be specific to a group of mice / rats or all mice / rats. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Mouse or rat" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3048 ! Mammals +[Term] +id: EDAM_topic:0215 +name: Worms +comment: The resource may be specific to a worm, a group of worms or all worms. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Worm" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2819 ! Invertebrates [Term] -id: EDAM_format:1573 -name: PIRSF entry format -namespace: format -subset: formats -def: "Entry format for the PIRSF protein secondary database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0217 +name: Literature analysis +subset: bioinformatics +subset: edam +subset: topics +synonym: "Literature search and analysis" EXACT [] +synonym: "Literature sources" EXACT [] +xref: BioCatalogue: Document Discovery +xref: BioCatalogue: Literature retrieval +created_in: "beta12orEarlier" +def: "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3068 ! Literature and reference [Term] -id: EDAM_format:1574 -name: PRINTS entry format -namespace: format -subset: formats -def: "Entry format for the PRINTS protein secondary database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0218 +name: Text mining +subset: bioinformatics +subset: edam +subset: topics +synonym: "Text data mining" EXACT [] +xref: BioCatalogue:Document Clustering +xref: BioCatalogue:Document Similarity +xref: BioCatalogue:Named Entity Recognition +xref: BioCatalogue:Text Mining +created_in: "beta12orEarlier" +def: "Topic concerning the analysis of the biomedical and informatics literature." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0217 ! Literature analysis +[Term] +id: EDAM_topic:0219 +name: Annotation +subset: bioinformatics +subset: edam +subset: topics +synonym: "Ontology annotation" EXACT [] +xref: BioCatalogue:Genome Annotation +xref: BioCatalogue:Ontology Annotation +created_in: "beta12orEarlier" +def: "Topic for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] -id: EDAM_format:1575 -name: Panther Families and HMMs entry format -namespace: format -subset: formats -def: "Entry format for the Panther library of protein families and subfamilies." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0220 +name: Data processing and validation +comment: This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Data file handling" EXACT [] +synonym: "File handling" EXACT [] +synonym: "Report handling" EXACT [] +synonym: "Report processing" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning basic manipulations of files or reports of generic biological data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0091 ! Data handling [Term] -id: EDAM_format:1576 -name: Pfam entry format -namespace: format -subset: formats -def: "Entry format for the Pfam protein secondary database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0221 +name: Sequence annotation +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Annotate a molecular sequence." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0219 ! Annotation +[Term] +id: EDAM_topic:0222 +name: Genome annotation +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Genome Annotation +created_in: "beta12orEarlier" +def: "Annotate a genome." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0219 ! Annotation +consider: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] -id: EDAM_format:1577 -name: SMART entry format -namespace: format -subset: formats -def: "Entry format for the SMART protein secondary database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0593 +name: NMR +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning raw NMR data." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:2226 ! Structure determination [Term] -id: EDAM_format:1578 -name: Superfamily entry format -namespace: format -subset: formats -def: "Entry format for the Superfamily protein secondary database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0594 +name: Sequence classification +comment: Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the classification of molecular sequences based on some measure of their similarity." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0080 ! Sequence analysis +[Term] +id: EDAM_topic:0595 +name: Protein classification +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0078 ! Protein analysis +is_a: EDAM_topic:0594 ! Sequence classification +is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] -id: EDAM_format:1579 -name: TIGRFam entry format -namespace: format -subset: formats -def: "Entry format for the TIGRFam protein secondary database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0598 +name: Sequence motif or profile +comment: This includes comparison, discovery, recognition etc. of sequence motifs. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0158 ! Sequence motifs +consider: EDAM_topic:0188 ! Sequence profiles and HMMs [Term] -id: EDAM_format:1580 -name: ProDom entry format -namespace: format -subset: formats -def: "Entry format for the ProDom protein domain classification database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0601 +name: Protein modifications +comment: EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) +subset: bioinformatics +subset: edam +subset: topics +synonym: "GO:0006464" RELATED [] +synonym: "MOD:00000" RELATED [] +synonym: "Protein post-translational modification" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning protein chemical modifications, e.g. post-translational modifications." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0123 ! Protein properties +is_a: EDAM_topic:2225 ! Protein databases +[Term] +id: EDAM_topic:0602 +name: Pathways, networks and models +alt_id: topic_3076 +subset: bioinformatics +subset: edam +subset: topics +synonym: "Network or pathway analysis" EXACT [] +xref: BioCatalogue:Pathway Retrieval +xref: BioCatalogue:Pathways +created_in: "beta13" +def: "Topic concerning biological pathways, networks and other models, including their construction and analysis." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2259 ! Systems biology +is_a: EDAM_topic:3071 ! Biological data resources [Term] -id: EDAM_format:1581 -name: FSSP entry format -namespace: format -subset: formats -def: "Entry format for the FSSP database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0605 +name: Informatics +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0091 ! Data handling +[Term] +id: EDAM_topic:0606 +name: Literature data resources +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3068 ! Literature and reference +is_a: EDAM_topic:3071 ! Biological data resources [Term] -id: EDAM_format:1568 -name: BIND entry format -namespace: format -subset: formats -def: "Entry format for the BIND database of protein interaction." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0607 +name: Laboratory resources +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3071 ! Biological data resources +[Term] +id: EDAM_topic:0608 +name: Cell culture resources +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning general cell culture or data on a specific cell lines." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0607 ! Laboratory resources [Term] -id: EDAM_format:1569 -name: IntAct entry format -namespace: format -subset: formats -def: "Entry format for the IntAct database of protein interaction." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0610 +name: Ecoinformatics +subset: bioinformatics +subset: edam +subset: topics +synonym: "Computational ecology" EXACT [] +synonym: "Ecological informatics" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D004777" RELATED [] +created_in: "beta12orEarlier" +def: "Topic concerning the application of information technology to the ecological and environmental sciences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic +[Term] +id: EDAM_topic:0611 +name: Electron microscopy +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning electron microscopy data." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:2226 ! Structure determination [Term] -id: EDAM_format:2560 -name: STRING entry format -namespace: format -subset: formats -def: "Entry format for the STRING database of protein interaction." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0612 +name: Cell cycle +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the cell cycle including key genes and proteins." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:2229 ! Cell biology resources +[Term] +id: EDAM_topic:0613 +name: Peptides and amino acids +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0154 ! Small molecules [Term] -id: EDAM_format:2303 -name: STRING entry format (HTML) -namespace: format -subset: formats -def: "Entry format (HTML) for the STRING database of protein interaction." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0616 +name: Organelle genes and proteins +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3078 ! Gene and protein resources [Term] -id: EDAM_format:2304 -name: STRING entry format (XML) -namespace: format -subset: formats -def: "Entry format (XML) for the STRING database of protein interaction." [http://edamontology.org] -is_a: EDAM_format:2054 ! Protein interaction format -is_a: EDAM_format:2332 ! XML +id: EDAM_topic:0617 +name: Ribosomal genes and proteins +subset: bioinformatics +subset: edam +subset: topics +synonym: "Ribosome genes and proteins" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning ribosomes, typically of ribosome-related genes and proteins." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0616 ! Organelle genes and proteins +[Term] +id: EDAM_topic:0618 +name: Scents +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "A database about scents." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0154 ! Small molecules [Term] -id: EDAM_format:2561 -name: Sequence assembly format (text) -namespace: format -subset: formats -def: "Text format for sequence assembly data." [http://edamontology.org] -is_a: EDAM_format:2055 ! Sequence assembly format +id: EDAM_topic:0620 +name: Drugs and targets +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the structures of drugs, drug target, their interactions and binding affinities." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0154 ! Small molecules +is_a: EDAM_topic:0202 ! Pharmacoinformatics [Term] -id: EDAM_format:1630 -name: CAF -namespace: format -subset: formats -def: "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." [http://edamontology.org] -xref: http://www.sanger.ac.uk/resources/software/caf/ !{documentation=true} -is_a: EDAM_format:2561 ! Sequence assembly format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0621 +name: Genome, proteome and model organisms +comment: General information on or more organisms, genomes (including molecular sequences and map, genes and annotation) and proteomes may be included. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Genome map" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0121 ! Proteomics +is_a: EDAM_topic:0622 ! Genomics +is_a: EDAM_topic:0625 ! Genotype and phenotype +[Term] +id: EDAM_topic:0622 +name: Genomics +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D023281" EXACT [] +xref: BioCatalogue:Functional Genomics +xref: BioCatalogue:Genomics +created_in: "beta12orEarlier" +def: "Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1631 -name: exp -namespace: format -subset: formats -def: "Sequence assembly project file EXP format." [http://edamontology.org] -is_a: EDAM_format:2561 ! Sequence assembly format (text) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0623 +name: Genes, gene family or system +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning particular gene(s), gene system or groups of genes." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2816 ! Gene resources +is_a: EDAM_topic:3052 ! Sequence clusters and classification [Term] -id: EDAM_format:1632 -name: SCF -namespace: format -subset: formats -def: "Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata." [http://edamontology.org] -xref: http://staden.sourceforge.net/manual/formats_unix_2.html !{documentation=true} -is_a: EDAM_format:2057 ! Sequence trace format -is_a: EDAM_format:2333 ! Binary format +id: EDAM_topic:0624 +name: Chromosomes +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning chromosomes." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3062 ! Genetic organisation +[Term] +id: EDAM_topic:0625 +name: Genotype and phenotype +subset: bioinformatics +subset: edam +subset: topics +synonym: "Genotype and phenotype resources" EXACT [] +synonym: "Genotyping" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2816 ! Gene resources [Term] -id: EDAM_format:1633 -name: PHD -namespace: format -subset: formats -def: "PHD sequence trace format to store serialised chromatogram data (reads)." [http://edamontology.org] -xref: http://www.bioperl.org/wiki/PHD_sequence_format !{documentation=true} -is_a: EDAM_format:2057 ! Sequence trace format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0629 +name: Gene expression and microarray +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0200 ! Microarrays +consider: EDAM_topic:0203 ! Transcriptomics +[Term] +id: EDAM_topic:0632 +name: Probes and primers +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D015335" RELATED [] +created_in: "beta12orEarlier" +def: "Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0607 ! Laboratory resources +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM_format:1640 -name: ArrayExpress entry format -namespace: format -subset: formats -def: "Entry format for the ArrayExpress microarrays database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0634 +name: Disease resources +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning diseases." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0625 ! Genotype and phenotype +[Term] +id: EDAM_topic:0635 +name: Specific protein resources +subset: bioinformatics +subset: edam +subset: topics +synonym: "Specific protein" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning a particular protein, protein family or other group of proteins." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2225 ! Protein databases [Term] -id: EDAM_format:1641 -name: affymetrix-exp -namespace: format -subset: formats -def: "Affymetrix data file format for information about experimental conditions and protocols." [http://edamontology.org] -synonym: "Affymetrix experimental conditions data file format" EXACT [http://edamontology.org] -is_a: EDAM_format:2056 ! Microarray experiment data format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0637 +name: Taxonomy +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning organism classification, identification and naming." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification +[Term] +id: EDAM_topic:0639 +name: Protein sequence analysis +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Protein Sequence Analysis +created_in: "beta12orEarlier" +def: "Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0078 ! Protein analysis +is_a: EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM_format:1638 -name: cel -namespace: format -subset: formats -def: "Format of Affymetrix data file of information about (raw) expression levels of the individual probes." [http://edamontology.org] -synonym: "Affymetrix probe raw data format" EXACT [http://edamontology.org] -is_a: EDAM_format:2058 ! Gene expression report format -is_a: EDAM_format:2330 ! Textual format -relationship: is_format_of EDAM_data:3110 ! Raw microarray data +id: EDAM_topic:0640 +name: Nucleic acid sequence analysis +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Nucleotide Sequence Analysis +created_in: "beta12orEarlier" +def: "Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0077 ! Nucleic acid analysis +is_a: EDAM_topic:0080 ! Sequence analysis +[Term] +id: EDAM_topic:0641 +name: Repeat sequences +subset: bioinformatics +subset: edam +subset: topics +synonym: "Repeat sequence" EXACT [] +xref: BioCatalogue:Repeats +created_in: "beta12orEarlier" +def: "Topic concerning the repetitive nature of molecular sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0157 ! Sequence composition analysis +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM_format:1644 -name: CHP -namespace: format -subset: formats -def: "Format of Affymetrix data file of information about (normalised) expression levels of the individual probes." [http://edamontology.org] -synonym: "Affymetrix probe normalised data format" EXACT [http://edamontology.org] -is_a: EDAM_format:2058 ! Gene expression report format -is_a: EDAM_format:2330 ! Textual format -relationship: is_format_of EDAM_data:3111 ! Processed microarray data +id: EDAM_topic:0642 +name: Low complexity sequences +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0157 ! Sequence composition analysis +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM_format:1637 -name: dat -namespace: format -subset: formats -def: "Format of Affymetrix data file of raw image data." [http://edamontology.org] -synonym: "Affymetrix image data file format" EXACT [http://edamontology.org] -is_a: EDAM_format:2058 ! Gene expression report format -is_a: EDAM_format:2330 ! Textual format -relationship: is_format_of EDAM_data:1714 ! Microarray spots image +id: EDAM_topic:0644 +name: Proteome +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning a specific proteome including protein sequences and annotation." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM_format:1623 -name: OMIM entry format -namespace: format -subset: formats -def: "Format of an entry from the OMIM database of genotypes and phenotypes." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0654 +name: DNA +comment: The DNA sequences might be coding or non-coding sequences. +subset: bioinformatics +subset: edam +subset: topics +synonym: "DNA analysis" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning DNA sequences and structure, including processes such as methylation and replication." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0077 ! Nucleic acid analysis +is_a: EDAM_topic:3042 ! Nucleic acid sequences [Term] -id: EDAM_format:1624 -name: HGVbase entry format -namespace: format -subset: formats -def: "Format of a record from the HGVbase database of genotypes and phenotypes." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0655 +name: mRNA, EST or cDNA database +subset: bioinformatics +subset: edam +subset: topics +synonym: "mRNA, EST or cDNA" EXACT [] +synonym: "Transcriptome" EXACT [] +synonym: "Transcriptome database" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning data resources for messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0099 ! RNA [Term] -id: EDAM_format:1625 -name: HIVDB entry format -namespace: format -subset: formats -def: "Format of a record from the HIVDB database of genotypes and phenotypes." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0659 +name: Functional and non-coding RNA +comment: For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). +subset: bioinformatics +subset: edam +subset: topics +synonym: "Functional RNA" EXACT [] +synonym: "Non-coding RNA" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning functional or non-coding RNA sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0099 ! RNA +[Term] +id: EDAM_topic:0660 +name: rRNA +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning one or more ribosomal RNA (rRNA) sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] -id: EDAM_format:1626 -name: KEGG DISEASE entry format -namespace: format -subset: formats -def: "Format of an entry from the KEGG DISEASE database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0663 +name: tRNA +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning one or more transfer RNA (tRNA) sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0659 ! Functional and non-coding RNA +[Term] +id: EDAM_topic:0694 +name: Protein secondary structure +comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Protein secondary structure analysis" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning protein secondary structure or secondary structure alignments." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2814 ! Protein structure analysis [Term] -id: EDAM_format:1861 -name: PlasMapper TextMap -namespace: format -subset: formats -def: "Map of a plasmid (circular DNA) in PlasMapper TextMap format." [http://edamontology.org] -xref: Moby:PlasMapperTextMap -is_a: EDAM_format:2060 ! Map format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0697 +name: RNA structure and alignment +subset: bioinformatics +subset: edam +subset: topics +synonym: "RNA alignment" EXACT [] +synonym: "RNA structure" EXACT [] +synonym: "RNA structure alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning RNA secondary or tertiary structure and alignments." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0183 ! Structure alignment [Term] -id: EDAM_format:1627 -name: Primer3 primer -namespace: format -subset: formats -def: "Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program." [http://edamontology.org] -is_a: EDAM_format:2061 ! Nucleic acid features (primers) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0698 +name: Protein tertiary structure +subset: bioinformatics +subset: edam +subset: topics +synonym: "Protein tertiary structure analysis" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning protein tertiary structures." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2814 ! Protein structure analysis [Term] -id: EDAM_format:2063 -name: Protein report (enzyme) format -namespace: format -subset: formats -def: "Format of a report of general information about a specific enzyme." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2350 ! Format (typed) +id: EDAM_topic:0722 +name: Nucleic acid classification +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning nucleic acid classification (typically sequence classification)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0077 ! Nucleic acid analysis +is_a: EDAM_topic:0594 ! Sequence classification +is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] -id: EDAM_format:1511 -name: IntEnz enzyme report format -namespace: format -subset: formats -def: "Format of an entry from IntEnz (The Integrated Relational Enzyme Database)." [http://edamontology.org] -comment: IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0724 +name: Protein families +comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Protein secondary" EXACT [] +synonym: "Protein sequence classification" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning primarily proteins that have been classified as members of a protein family (or other grouping)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2225 ! Protein databases +is_a: EDAM_topic:3052 ! Sequence clusters and classification [Term] -id: EDAM_format:1512 -name: BRENDA enzyme report format -namespace: format -subset: formats -def: "Format of an entry from the BRENDA enzyme database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0736 +name: Protein domains and folds +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Domains +created_in: "beta12orEarlier" +def: "Topic concerning protein tertiary structural domains and folds." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0698 ! Protein tertiary structure +is_a: EDAM_topic:0724 ! Protein families [Term] -id: EDAM_format:2322 -name: BioCyc enzyme report format -namespace: format -subset: formats -def: "Format of an entry from the BioCyc enzyme database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0740 +name: Nucleic acid sequence alignment +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning nucleotide sequence alignments." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0182 ! Sequence alignment +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:2323 -name: ENZYME enzyme report format -namespace: format -subset: formats -def: "Format of an entry from the Enzyme nomenclature database (ENZYME)." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0741 +name: Protein sequence alignment +comment: A sequence profile typically represents a sequence alignment. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning protein sequence alignments." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0182 ! Sequence alignment +is_a: EDAM_topic:0639 ! Protein sequence analysis [Term] -id: EDAM_format:1513 -name: KEGG REACTION enzyme report format -namespace: format -subset: formats -def: "Format of an entry from the KEGG REACTION database of biochemical reactions." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0747 +name: Nucleic acid sites and features +subset: bioinformatics +subset: edam +subset: topics +synonym: "Nucleic acid features" EXACT [] +synonym: "Nucleic acid functional sites" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning positional features such as functional sites in nucleotide sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0160 ! Sequence sites and features +is_a: EDAM_topic:3042 ! Nucleic acid sequences [Term] -id: EDAM_format:1514 -name: KEGG ENZYME enzyme report format -namespace: format -subset: formats -def: "Format of an entry from the KEGG ENZYME database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML - +id: EDAM_topic:0748 +name: Protein sites and features +subset: bioinformatics +subset: edam +subset: topics +synonym: "Protein functional sites" EXACT [] +synonym: "Protein sequence features" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning positional features such as functional sites in protein sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0160 ! Sequence sites and features +is_a: EDAM_topic:3043 ! Protein sequences [Term] -id: EDAM_format:1515 -name: REBASE proto enzyme report format -namespace: format -subset: formats -def: "Format of an entry from the proto section of the REBASE enzyme database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML - +id: EDAM_topic:0749 +name: Transcription factors and regulatory sites +comment: This includes promoters, enhancers, silencers and boundary elements / insulators. This includes sequence and structural information, binding profiles etc, and may also include the transcription factor binding site in DNA. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Transcription factor and binding site" EXACT [] +synonym: "Transcription factors" EXACT [] +synonym: "Transcriptional regulatory sites" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning transcription factors; proteins that bind to DNA and control transcription of DNA to mRNA, either promoting (as an activator) or blocking (as a repressor) the binding to DNA of RNA polymerase, and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0110 ! Transcription +is_a: EDAM_topic:0204 ! Gene regulation +is_a: EDAM_topic:0635 ! Specific protein resources +is_a: EDAM_topic:0747 ! Nucleic acid sites and features +is_a: EDAM_topic:3062 ! Genetic organisation +is_a: EDAM_topic:3073 ! Nucleic acid feature detection [Term] -id: EDAM_format:1516 -name: REBASE withrefm enzyme report format -namespace: format -subset: formats -def: "Format of an entry from the withrefm section of the REBASE enzyme database." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:0751 +name: Phosphorylation sites +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning protein phosphorylation and phosphorylation sites in protein sequences." [http://edamontology.org] +namespace: topic +obsolete_since: "1.0" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0601 ! Protein modifications +consider: EDAM_topic:0748 ! Protein sites and features [Term] -id: EDAM_format:1500 -name: Domainatrix 3D-1D scoring matrix format -namespace: format -subset: formats -def: "Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} +id: EDAM_topic:0753 +name: Metabolic pathways +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning metabolic pathways." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0602 ! Pathways, networks and models +is_a: EDAM_topic:3172 ! Metabolomics [Term] -id: EDAM_format:1551 -name: Pcons report format -namespace: format -subset: formats -def: "Format of output of the Pcons Model Quality Assessment Program (MQAP)." [http://edamontology.org] -comment: Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. -is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format -is_a: EDAM_format:2330 ! Textual format - +id: EDAM_topic:0754 +name: Signaling pathways +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning signaling pathways." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM_format:1552 -name: ProQ report format -namespace: format -subset: formats -def: "Format of output of the ProQ protein model quality predictor." [http://edamontology.org] -comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. -is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format -is_a: EDAM_format:2330 ! Textual format - +id: EDAM_topic:0767 +name: Protein and peptide identification +comment: This includes the results of any methods that separate, characterize and identify expressed proteins. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Peptide identification and proteolysis" EXACT [] +synonym: "Proteomics data" EXACT [] +synonym: "Proteomics data resources" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0121 ! Proteomics +is_a: EDAM_topic:0639 ! Protein sequence analysis +is_a: EDAM_topic:2225 ! Protein databases [Term] -id: EDAM_format:1341 -name: InterPro hits format -namespace: format -subset: formats -def: "Results format for searches of the InterPro database." [http://edamontology.org] -is_a: EDAM_format:2066 ! Database hits (sequence) format -is_a: EDAM_format:2330 ! Textual format - +id: EDAM_topic:0769 +name: Workflows +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning biological or biomedical analytical workflows or pipelines." [http://edamontology.org] +namespace: topic +obsolete_since: "1.0" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_format:1342 -name: InterPro protein view report format -namespace: format -subset: formats -def: "Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries." [http://edamontology.org] -comment: The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. -is_a: EDAM_format:1341 ! InterPro hits format - +id: EDAM_topic:0770 +name: Data types and objects +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning structuring data into basic types and (computational) objects." [http://edamontology.org] +namespace: topic +obsolete_since: "1.0" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0091 ! Data handling [Term] -id: EDAM_format:1343 -name: InterPro match table format -namespace: format -subset: formats -def: "Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry." [http://edamontology.org] -comment: The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. -is_a: EDAM_format:1341 ! InterPro hits format +id: EDAM_topic:0771 +name: Biological models +comment: This includes databases of models and methods to construct or analyse a model. +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Model Creation +created_in: "beta12orEarlier" +def: "Topic concerning mathematical or other models of biological processes." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM_format:1332 -name: FASTA search results format -namespace: format -subset: formats -def: "Format of results of a sequence database search using FASTA." [http://edamontology.org] -comment: This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) -is_a: EDAM_format:2066 ! Database hits (sequence) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0779 +name: Mitochondrial genes and proteins +subset: bioinformatics +subset: edam +subset: topics +synonym: "Mitochondria genes and proteins" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning mitochondria, typically of mitochondrial genes and proteins." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0616 ! Organelle genes and proteins [Term] -id: EDAM_format:1333 -name: BLAST results -namespace: format -subset: formats -def: "Format of results of a sequence database search using some variant of BLAST." [http://edamontology.org] -comment: This includes score data, alignment data and summary table. -is_a: EDAM_format:2066 ! Database hits (sequence) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0780 +name: Plants +comment: The resource may be specific to a plant, a group of plants or all plants. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Plant" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2818 ! Eukaryotes [Term] -id: EDAM_format:1334 -name: mspcrunch -namespace: format -subset: formats -def: "Format of results of a sequence database search using some variant of MSPCrunch." [http://edamontology.org] -is_a: EDAM_format:2066 ! Database hits (sequence) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0781 +name: Viruses +comment: The resource may be specific to a virus, a group of viruses or all viruses. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Virus" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0621 ! Genome, proteome and model organisms +[Term] +id: EDAM_topic:0782 +name: Fungi +comment: The resource may be specific to a fungus, a group of fungi or all fungi. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Fungal" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2818 ! Eukaryotes [Term] -id: EDAM_format:1335 -name: smith-waterman -namespace: format -subset: formats -def: "Format of results of a sequence database search using some variant of Smith Waterman." [http://edamontology.org] -is_a: EDAM_format:2066 ! Database hits (sequence) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0783 +name: Pathogens +comment: The resource may be specific to a pathogen, a group of pathogens or all pathogens. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Pathogen" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] -id: EDAM_format:1336 -name: dhf -namespace: format -subset: formats -def: "Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information." [http://edamontology.org] -comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. -is_a: EDAM_format:2066 ! Database hits (sequence) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0786 +name: Arabidopsis +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning Arabidopsis-specific data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0780 ! Plants +[Term] +id: EDAM_topic:0787 +name: Rice +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning rice-specific data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0780 ! Plants [Term] -id: EDAM_format:1337 -name: lhf -namespace: format -subset: formats -def: "Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information." [http://edamontology.org] -comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database. -is_a: EDAM_format:2066 ! Database hits (sequence) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0796 +name: Genetic mapping and linkage +subset: bioinformatics +subset: edam +subset: topics +synonym: "Genetic linkage" EXACT [] +synonym: "Linkage mapping" EXACT [] +created_in: "beta12orEarlier" +def: "Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0102 ! Mapping +[Term] +id: EDAM_topic:0797 +name: Comparative genomics +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Comparative Genomics +created_in: "beta12orEarlier" +def: "Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0622 ! Genomics [Term] -id: EDAM_format:1423 -name: phylip distance matrix -namespace: format -subset: formats -def: "Format of PHYLIP phylogenetic distance matrix data." [http://edamontology.org] -comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). -is_a: EDAM_format:2067 ! Sequence distance matrix format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0798 +name: Mobile genetic elements +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3062 ! Genetic organisation +[Term] +id: EDAM_topic:0803 +name: Human disease +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0634 ! Disease resources [Term] -id: EDAM_format:1360 -name: meme-motif -namespace: format -subset: formats -def: "A motif in the format generated by the MEME program." [http://edamontology.org] -is_a: EDAM_format:2068 ! Sequence motif format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0804 +name: Immunoinformatics +subset: bioinformatics +subset: edam +subset: topics +synonym: "Computational immunology" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D007120" RELATED [] +synonym: "http://purl.bioontology.org/ontology/MSH/D007125" RELATED [] +created_in: "beta12orEarlier" +def: "Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1356 -name: prosite-pattern -namespace: format -subset: formats -def: "Format of a regular expression pattern from the Prosite database." [http://edamontology.org] -is_a: EDAM_format:2068 ! Sequence motif format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:0820 +name: Membrane proteins +subset: bioinformatics +subset: edam +subset: topics +synonym: "Transmembrane proteins" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning a protein or region of a protein that spans a membrane." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0635 ! Specific protein resources +[Term] +id: EDAM_topic:0821 +name: Enzymes and reactions +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0635 ! Specific protein resources [Term] -id: EDAM_format:1357 -name: EMBOSS sequence pattern -namespace: format -subset: formats -def: "Format of an EMBOSS sequence pattern." [http://edamontology.org] -is_a: EDAM_format:2068 ! Sequence motif format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:1770 +name: Structure comparison +comment: This might involve comparison of secondary or tertiary (3D) structural information. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the comparison of two or more molecular structures." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM_format:2072 -name: Hidden Markov model format -namespace: format -subset: formats -def: "Format of a hidden Markov model." [http://edamontology.org] -is_a: EDAM_format:2069 ! Sequence profile format -relationship: is_format_of EDAM_data:1364 ! Hidden Markov model +id: EDAM_topic:1775 +name: Protein function analysis +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic for the study of protein function." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0078 ! Protein analysis [Term] -id: EDAM_format:1367 -name: jaspar -namespace: format -subset: formats -def: "A profile (sequence classifier) in the format used in the JASPAR database." [http://edamontology.org] -is_a: EDAM_format:2069 ! Sequence profile format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:1811 +name: Prokaryotes and archae +comment: The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Prokaryote and archae" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0621 ! Genome, proteome and model organisms +[Term] +id: EDAM_topic:2225 +name: Protein databases +subset: bioinformatics +subset: edam +subset: topics +synonym: "Protein data resources" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning protein data resources." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0078 ! Protein analysis +is_a: EDAM_topic:3071 ! Biological data resources [Term] -id: EDAM_format:1366 -name: prosite-profile -namespace: format -subset: formats -def: "Sequence profile (sequence classifier) format used in the PROSITE database." [http://edamontology.org] -is_a: EDAM_format:2069 ! Sequence profile format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2226 +name: Structure determination +subset: bioinformatics +subset: edam +subset: topics +synonym: "Raw structural data analysis" EXACT [] +synonym: "Structural assignment" EXACT [] +synonym: "Structural determination" EXACT [] +synonym: "Structure assignment" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, including the assignment or modelling of molecular structure from such data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM_format:1369 -name: MEME background Markov model -namespace: format -subset: formats -def: "Format of the model of random sequences used by MEME." [http://edamontology.org] -is_a: EDAM_format:2072 ! Hidden Markov model format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2229 +name: Cell biology resources +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning cells, such as key genes and proteins involved in the cell cycle." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3070 ! Biological science resources +[Term] +id: EDAM_topic:2230 +name: Classification +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] -id: EDAM_format:1370 -name: hmmer -namespace: format -subset: formats -def: "Format of a hidden Markov model representation used by the HMMER package." [http://edamontology.org] -is_a: EDAM_format:2072 ! Hidden Markov model format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2232 +name: Lipoproteins +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning lipoproteins (protein-lipid assemblies)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0635 ! Specific protein resources [Term] -id: EDAM_format:1349 -name: HMMER Dirichlet prior -namespace: format -subset: formats -def: "Dirichlet distribution HMMER format." [http://edamontology.org] -is_a: EDAM_format:2074 ! Dirichlet distribution format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2257 +name: Phylogeny visualisation +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Tree Display +created_in: "beta12orEarlier" +def: "Visualise a phylogeny, for example, render a phylogenetic tree." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0084 ! Phylogenetics [Term] -id: EDAM_format:1350 -name: MEME Dirichlet prior -namespace: format -subset: formats -def: "Dirichlet distribution MEME format." [http://edamontology.org] -is_a: EDAM_format:2074 ! Dirichlet distribution format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2258 +name: Chemoinformatics +subset: bioinformatics +subset: edam +subset: topics +synonym: "Chemical informatics" EXACT [] +synonym: "Cheminformatics" EXACT [] +synonym: "Computational chemistry" EXACT [] +xref: BioCatalogue:Chemoinformatics +created_in: "beta12orEarlier" +def: "Topic for the application of information technology to chemistry." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1351 -name: HMMER emission and transition -namespace: format -subset: formats -def: "Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model." [http://edamontology.org] -is_a: EDAM_format:2075 ! HMM emission and transition counts format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2259 +name: Systems biology +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D049490" EXACT [] +synonym: "Systems:biology" EXACT [] +xref: BioCatalogue:Systems Biology +created_in: "beta12orEarlier" +def: "Topic concerning the holistic modelling and analysis of biological systems and the interactions therein." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1454 -name: dssp -namespace: format -subset: formats -def: "Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins)." [http://edamontology.org] -comment: The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. -is_a: EDAM_format:2077 ! Protein secondary structure format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2269 +name: Biostatistics +subset: bioinformatics +subset: edam +subset: topics +synonym: "Biometrics" EXACT [] +synonym: "Biometry" EXACT [] +synonym: "http://en.wikipedia.org/wiki/Biostatistics" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D056808" EXACT [] +xref: BioCatalogue:Biostatistics +created_in: "beta12orEarlier" +def: "Topic for the application of statistical methods to biological problems." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0091 ! Data handling +[Term] +id: EDAM_topic:2271 +name: Structure database search +comment: The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure)." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:1770 ! Structure comparison [Term] -id: EDAM_format:1455 -name: hssp -namespace: format -subset: formats -def: "Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins)." [http://edamontology.org] -is_a: EDAM_format:2077 ! Protein secondary structure format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2275 +name: Molecular modelling +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. " [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0082 ! Structure prediction +is_a: EDAM_topic:0172 ! Protein structure prediction +[Term] +id: EDAM_topic:2276 +name: Protein function prediction +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Function Prediction +created_in: "beta12orEarlier" +def: "Topic concerning the prediction of functional properties of a protein." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:1775 ! Protein function analysis [Term] -id: EDAM_format:1457 -name: Vienna RNA secondary structure -namespace: format -subset: formats -def: "Format of RNA secondary structure (in bracket notation) with free energy values, generated by the Vienna program." [http://edamontology.org] -synonym: "Dot-bracket format" EXACT [http://edamontology.org] -is_a: EDAM_format:2076 ! RNA secondary structure format -is_a: EDAM_format:2330 ! Textual format - +id: EDAM_topic:2277 +name: SNPs +comment: A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0199 ! Genetic variation [Term] -id: EDAM_format:1458 -name: Vienna local RNA secondary structure -namespace: format -subset: formats -def: "Format of local RNA secondary structure components with free energy values, generated by the Vienna program." [http://edamontology.org] -is_a: EDAM_format:1457 ! Vienna RNA secondary structure -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2278 +name: Transmembrane protein prediction +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Predict transmembrane domains and topology in protein sequences." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0178 ! Protein secondary structure prediction +consider: EDAM_topic:0820 ! Membrane proteins [Term] -id: EDAM_format:1248 -name: EMBL feature location -namespace: format -subset: formats -def: "Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database." [http://edamontology.org] -synonym: "Feature location" EXACT [http://edamontology.org] -is_a: EDAM_format:2078 ! Sequence range format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2280 +name: Nucleic acid structure comparison +comment: Use this concept for methods that are exclusively for nucleic acid structures. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0097 ! Nucleic acid structure analysis +consider: EDAM_topic:1770 ! Structure comparison [Term] -id: EDAM_format:1295 -name: quicktandem -namespace: format -subset: formats -def: "Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program)." [http://edamontology.org] -is_a: EDAM_format:2155 ! Sequence features (repeats) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2640 +name: Cancer +subset: bioinformatics +subset: edam +subset: topics +synonym: "Cancer resources" EXACT [] +created_in: "beta12orEarlier" +def: "Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0634 ! Disease resources [Term] -id: EDAM_format:1296 -name: Sanger inverted repeats -namespace: format -subset: formats -def: "Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program)." [http://edamontology.org] -is_a: EDAM_format:2155 ! Sequence features (repeats) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2661 +name: Toxins and targets +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning structural and associated data for toxic chemical substances." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0154 ! Small molecules +is_a: EDAM_topic:2840 ! Toxicoinformatics [Term] -id: EDAM_format:1297 -name: EMBOSS repeat -namespace: format -subset: formats -def: "Report format for tandem repeats in a sequence (an EMBOSS report format)." [http://edamontology.org] -is_a: EDAM_format:2155 ! Sequence features (repeats) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2807 +name: Tool topic +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1318 -name: restrict -namespace: format -subset: formats -def: "Report format for restriction enzyme recognition sites used by EMBOSS restrict program." [http://edamontology.org] -is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2809 +name: Study topic +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0003 ! Topic +[Term] +id: EDAM_topic:2811 +name: Nomenclature +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning biological nomenclature (naming), symbols and terminology." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] -id: EDAM_format:1319 -name: restover -namespace: format -subset: formats -def: "Report format for restriction enzyme recognition sites used by EMBOSS restover program." [http://edamontology.org] -is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2813 +name: Disease genes and proteins +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning the genes, gene variations and proteins involved in one or more specific diseases." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0634 ! Disease resources +is_a: EDAM_topic:3078 ! Gene and protein resources +[Term] +id: EDAM_topic:2814 +name: Protein structure analysis +alt_id: topic_3040 +subset: bioinformatics +subset: edam +subset: topics +synonym: "Protein structure" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning protein secondary or tertiary structural data and/or associated annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0078 ! Protein analysis +is_a: EDAM_topic:0081 ! Structure analysis +is_a: EDAM_topic:2225 ! Protein databases +is_a: EDAM_topic:3038 ! Structure databases [Term] -id: EDAM_format:1320 -name: REBASE restriction sites -namespace: format -subset: formats -def: "Report format for restriction enzyme recognition sites used by REBASE database." [http://edamontology.org] -is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2815 +name: Humans +comment: The resource may be specific to a human, a group of humans or all humans. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Human" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3048 ! Mammals [Term] -id: EDAM_format:1316 -name: est2genome -namespace: format -subset: formats -def: "Format of a report on exon-intron structure generated by EMBOSS est2genome." [http://edamontology.org] -is_a: EDAM_format:2159 ! Gene features (coding region) format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2816 +name: Gene resources +subset: bioinformatics +subset: edam +subset: topics +synonym: "Gene database" EXACT [] +synonym: "Gene resource" EXACT [] +created_in: "beta12orEarlier" +def: "Informatics resource (typically a database) primarily focussed on genes." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3053 ! Genetics +is_a: EDAM_topic:3071 ! Biological data resources [Term] -id: EDAM_format:2171 -name: Sequence cluster format (protein) -namespace: format -subset: formats -def: "Format used for clusters of protein sequences." [http://edamontology.org] -is_a: EDAM_format:2170 ! Sequence cluster format +id: EDAM_topic:2817 +name: Yeast +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0782 ! Fungi [Term] -id: EDAM_format:2172 -name: Sequence cluster format (nucleic acid) -namespace: format -subset: formats -def: "Format used for clusters of nucleotide sequences." [http://edamontology.org] -is_a: EDAM_format:2170 ! Sequence cluster format +id: EDAM_topic:2818 +name: Eukaryotes +comment: The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Eukaryote" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] -id: EDAM_format:1247 -name: COG sequence cluster format -namespace: format -subset: formats -def: "Format of an entry from the COG database of clusters of (related) protein sequences." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:2819 +name: Invertebrates +comment: The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2818 ! Eukaryotes +[Term] +id: EDAM_topic:2820 +name: Vertebrates +comment: The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Vertebrate" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2818 ! Eukaryotes [Term] -id: EDAM_format:2175 -name: Gene cluster format -namespace: format -subset: formats -! alt_id: EDAM_format:2918 -def: "Format used for clusters of genes." [http://edamontology.org] -is_obsolete: true !{since=beta13} -consider: EDAM_format:2172 ! Sequence cluster format (nucleic acid) +id: EDAM_topic:2821 +name: Unicellular eukaryotes +comment: The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Unicellular eukaryote" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2818 ! Eukaryotes +[Term] +id: EDAM_topic:2826 +name: Protein structure alignment +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning protein secondary or tertiary structure alignments." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0183 ! Structure alignment +is_a: EDAM_topic:2814 ! Protein structure analysis [Term] -id: EDAM_format:1228 -name: UniGene entry format -namespace: format -subset: formats -def: "Format of an entry from UniGene." [http://edamontology.org] -comment: A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:2828 +name: X-ray crystallography +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning X-ray crystallography data." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:2226 ! Structure determination [Term] -id: EDAM_format:1639 -name: affymetrix -namespace: format -subset: formats -def: "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [http://edamontology.org] -is_a: EDAM_format:2330 ! Textual format -is_a: EDAM_format:2172 ! Sequence cluster format (nucleic acid) +id: EDAM_topic:2829 +name: Ontologies, nomenclature and classification +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D002965" NARROW [] +created_in: "beta12orEarlier" +def: "Topic concerning conceptualisation, categorisation and naming, or that help to identify, group, or name things in a structured way according to some schema based on observable relationships." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:2196 -name: OBO format -namespace: format -subset: formats -def: "OBO ontology format." [http://edamontology.org] -is_a: EDAM_format:2195 ! Ontology format +id: EDAM_topic:2830 +name: Immunity genes, immunoproteins and antigens +comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." +subset: bioinformatics +subset: edam +subset: topics +synonym: "Immunoproteins and immunopeptides" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning immunity-related genes, proteins and their ligands." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0804 ! Immunoinformatics +is_a: EDAM_topic:3078 ! Gene and protein resources [Term] -id: EDAM_format:2549 -name: OBO -namespace: format -subset: formats -def: "OBO ontology text format." [http://edamontology.org] -is_a: EDAM_format:2196 ! OBO format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2839 +name: Molecules +subset: bioinformatics +subset: edam +subset: topics +synonym: "CHEBI:23367" RELATED [] +created_in: "beta12orEarlier" +def: "Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true [Term] -id: EDAM_format:2197 -name: OWL -namespace: format -subset: formats -def: "OWL ontology format." [http://edamontology.org] -is_a: EDAM_format:2195 ! Ontology format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:2840 +name: Toxicoinformatics +subset: bioinformatics +subset: edam +subset: topics +synonym: "Computational toxicology" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the adverse effects of chemical substances on living organisms." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2258 ! Chemoinformatics [Term] -id: EDAM_format:2550 -name: OBO-XML -namespace: format -subset: formats -def: "OBO ontology XML format." [http://edamontology.org] -is_a: EDAM_format:2196 ! OBO format -is_a: EDAM_format:2332 ! XML +id: EDAM_topic:2842 +name: High-throughput sequencing +subset: bioinformatics +subset: edam +subset: topics +synonym: "Next-generation sequencing" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [http://edamontology.org] +namespace: topic +obsolete_since: "beta13" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:3168 ! Sequencing [Term] -id: EDAM_format:2211 -name: CIP strain data format -namespace: format -subset: formats -def: "Format for a report of strain data as used for CIP database entries." [http://edamontology.org] -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:2844 +name: Structural clustering +subset: bioinformatics +subset: edam +subset: topics +synonym: "Structure classification" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:1770 ! Structure comparison [Term] -id: EDAM_format:1760 -name: CATH chain report format -namespace: format -subset: formats -def: "Format of CATH domain classification information for a polypeptide chain." [http://edamontology.org] -comment: The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:2846 +name: Gene regulatory networks +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic concerning gene regulatory networks." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0204 ! Gene regulation +is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM_format:1761 -name: CATH PDB report format -namespace: format -subset: formats -def: "Format of CATH domain classification information for a protein PDB file." [http://edamontology.org] -comment: The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:2847 +name: Disease (specific) +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Informatics resources dedicated to one or more specific diseases (not diseases in general)." [http://edamontology.org] +namespace: topic +obsolete_since: "beta12orEarlier" +!is_a: ObsoleteClass ! Obsolete concept (EDAM) +is_obsolete: true +consider: EDAM_topic:0634 ! Disease resources [Term] -id: EDAM_format:1563 -name: SMART domain assignment report format -namespace: format -subset: formats -def: "Format of SMART domain assignment data." [http://edamontology.org] -comment: The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. -is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2331 ! HTML +id: EDAM_topic:2953 +name: Nucleic acid design +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta12orEarlier" +def: "Topic for the design of nucleic acid sequences with specific conformations." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0077 ! Nucleic acid analysis [Term] -id: EDAM_format:3000 -name: AB1 -namespace: format -subset: formats -def: "AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence." [http://www.fileinfo.com/extension/ab1, http://edamontology.org] -comment: AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). -is_a: EDAM_format:2333 ! Binary format -is_a: EDAM_format:2057 ! Sequence trace format +id: EDAM_topic:3032 +name: Primer or probe design +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM_format:3001 -name: ACE -namespace: format -subset: formats -def: "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." [http://edamontology.org] -xref: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt !{documentation=true} -is_a: EDAM_format:2330 ! Textual format -is_a: EDAM_format:2055 ! Sequence assembly format - +id: EDAM_topic:3038 +name: Structure databases +subset: bioinformatics +subset: edam +subset: topics +synonym: "Structure data resources" EXACT [] +created_in: "beta13" +def: "Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0081 ! Structure analysis +is_a: EDAM_topic:3071 ! Biological data resources [Term] -id: EDAM_format:3003 -name: BED -namespace: format -subset: formats -def: "Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser." [http://edamontology.org] -comment: BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). -xref: http://genome.ucsc.edu/FAQ/FAQformat#format1 !{documentation=true} -is_a: EDAM_format:2919 ! Sequence annotation track format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3039 +name: Nucleic acid structure +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3038 ! Structure databases [Term] -id: EDAM_format:3004 -name: bigBed -namespace: format -subset: formats -def: "bigBed format for large sequence annotation tracks, similar to textual BED format." [http://edamontology.org] -xref: http://genome.ucsc.edu/FAQ/FAQformat#format1.5 !{documentation=true} -is_a: EDAM_format:2919 ! Sequence annotation track format -is_a: EDAM_format:2333 ! Binary format - +id: EDAM_topic:3041 +name: Sequence databases +subset: bioinformatics +subset: edam +subset: topics +synonym: "Sequence data" EXACT [] +synonym: "Sequence data resource" EXACT [] +synonym: "Sequence data resources" EXACT [] +created_in: "beta13" +def: "Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0080 ! Sequence analysis +is_a: EDAM_topic:3071 ! Biological data resources [Term] -id: EDAM_format:3005 -name: WIG -namespace: format -subset: formats -def: "Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser." [http://edamontology.org] -xref: http://genome.ucsc.edu/goldenPath/help/wiggle.html !{documentation=true} -is_a: EDAM_format:2919 ! Sequence annotation track format -is_a: EDAM_format:2330 ! Textual format - +id: EDAM_topic:3042 +name: Nucleic acid sequences +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM_format:3006 -name: bigWig -namespace: format -subset: formats -def: "bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format." [http://edamontology.org] -xref: http://genome.ucsc.edu/FAQ/FAQformat#format6.1 !{documentation=true} -is_a: EDAM_format:2919 ! Sequence annotation track format -is_a: EDAM_format:2333 ! Binary format +id: EDAM_topic:3043 +name: Protein sequences +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Protein Sequence Analysis +created_in: "beta13" +def: "Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2225 ! Protein databases +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM_format:3007 -name: PSL -namespace: format -subset: formats -def: "PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track." [http://edamontology.org] -xref: http://genome.ucsc.edu/FAQ/FAQformat#format2 !{documentation=true} -is_a: EDAM_format:2919 ! Sequence annotation track format -is_a: EDAM_format:2920 ! Alignment format (pair only) -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3044 +name: Protein interaction networks +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning protein-protein interaction networks." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0147 ! Protein-protein interactions +is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM_format:3008 -name: MAF -namespace: format -subset: formats -def: "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth." [http://edamontology.org] -comment: Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. -xref: http://genome.ucsc.edu/FAQ/FAQformat#format5 !{documentation=true} -is_a: EDAM_format:2554 ! Alignment format (text) -is_a: EDAM_format:2919 ! Sequence annotation track format - - +id: EDAM_topic:3047 +name: Molecular biology reference +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue: Document Discovery +xref: BioCatalogue: Literature retrieval +created_in: "beta13" +def: "Topic concerning general molecular biology information extracted from the literature." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0606 ! Literature data resources [Term] -id: EDAM_format:3009 -name: 2bit -namespace: format -subset: formats -def: "2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'." [http://edamontology.org] -xref: http://jcomeau.freeshell.org/www/genome/2bitformat.html !{documentation=true} -xref: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD !{documentation=true} -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2333 ! Binary format +id: EDAM_topic:3048 +name: Mammals +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2820 ! Vertebrates [Term] -id: EDAM_format:3010 -name: .nib -namespace: format -subset: formats -def: ".nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'." [http://edamontology.org] -xref: http://genome.ucsc.edu/FAQ/FAQformat#format8 !{documentation=true} -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2333 ! Binary format +id: EDAM_topic:3050 +name: Biodiversity +subset: bioinformatics +subset: edam +subset: topics +synonym: "Biodiversity data resource" EXACT [] +synonym: "Biodiversity data resources" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D044822" EXACT [] +created_in: "beta13" +def: "Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0610 ! Ecoinformatics [Term] -id: EDAM_format:2094 -name: pure -namespace: format -subset: formats -def: "Alphabet for molecular sequence with possible unknown positions but without non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3052 +name: Sequence clusters and classification +comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Sequence clusters" EXACT [] +synonym: "Sequence families" EXACT [] +created_in: "beta13" +def: "Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM_format:2095 -name: unpure -namespace: format -subset: formats -def: "Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3053 +name: Genetics +subset: bioinformatics +subset: edam +subset: topics +synonym: "Genetics data resources" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D005823" EXACT [] +created_in: "beta13" +def: "Topic concerning the study of genes, genetic variation and heredity in living organisms." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:2096 -name: unambiguous sequence -namespace: format -subset: formats -def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters." [http://edamontology.org] +id: EDAM_topic:3055 +name: Quantitative genetics +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3053 ! Genetics -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2330 ! Textual format +[Term] +id: EDAM_topic:3056 +name: Population genetics +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3053 ! Genetics [Term] -id: EDAM_format:2566 -name: completely unambiguous -namespace: format -subset: formats -def: "Alphabet for a molecular sequence without any unknown positions or ambiguity characters." [http://edamontology.org] -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3060 +name: Regulatory RNA +comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA)." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] -id: EDAM_format:2097 -name: ambiguous -namespace: format -subset: formats -def: "Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters." [http://edamontology.org] -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3061 +name: Documentation and help +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning documentation and getting help." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3068 ! Literature and reference [Term] -id: EDAM_format:1207 -name: nucleotide -namespace: format -subset: formats -def: "Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] -comment: Non-sequence characters may be used for example for gaps. -synonym: "Nucleotide sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence] -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3062 +name: Genetic organisation +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning the structural and functional organisation of genes and other genetic elements." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2816 ! Gene resources [Term] -id: EDAM_format:1208 -name: protein -namespace: format -subset: formats -def: "Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] -comment: Non-sequence characters may be used for gaps and translation stop. -synonym: "Amino acid sequence" EXACT [http://edamontology.org] -synonym: "Amino acid sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence] -is_a: EDAM_format:2571 ! Raw sequence format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3063 +name: Medical informatics resources +subset: bioinformatics +subset: edam +subset: topics +synonym: "Biomedical informatics" EXACT [] +synonym: "Clinical informatics" EXACT [] +synonym: "Health and disease" EXACT [] +synonym: "Health informatics" EXACT [] +synonym: "Healthcare informatics" EXACT [] +created_in: "beta13" +def: "Topic for the application of information technology to health, disease and biomedicine." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0607 ! Laboratory resources +[Term] +id: EDAM_topic:3064 +name: Developmental biology resources +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning how organisms grow and develop." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3070 ! Biological science resources [Term] -id: EDAM_format:1206 -name: unambiguous pure -namespace: format -subset: formats -def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2094 ! pure -is_a: EDAM_format:2096 ! unambiguous sequence +id: EDAM_topic:3065 +name: Embryology resources +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3064 ! Developmental biology resources [Term] -id: EDAM_format:2567 -name: completely unambiguous pure -namespace: format -subset: formats -def: "Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2094 ! pure -is_a: EDAM_format:2566 ! completely unambiguous +id: EDAM_topic:3067 +name: Anatomy resources +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning the structures of living organisms." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3070 ! Biological science resources +[Term] +id: EDAM_topic:3068 +name: Literature and reference +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D011642" RELATED [] +created_in: "beta13" +def: "Topic concerning the scientific literature, reference information and documentation." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1209 -name: consensus -namespace: format -subset: formats -def: "Alphabet for the consensus of two or more molecular sequences." [http://edamontology.org] -is_a: EDAM_format:2097 ! ambiguous -is_a: EDAM_format:2095 ! unpure +id: EDAM_topic:3070 +name: Biological science resources +subset: bioinformatics +subset: edam +subset: topics +synonym: "Phenotype resource" EXACT [] +created_in: "beta13" +def: "Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3071 ! Biological data resources [Term] -id: EDAM_format:1210 -name: pure nucleotide -namespace: format -subset: formats -def: "Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2094 ! pure -is_a: EDAM_format:1207 ! nucleotide +id: EDAM_topic:3071 +name: Biological data resources +subset: bioinformatics +subset: edam +subset: topics +synonym: "Biological data resource" EXACT [] +synonym: "Biological databases" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D030541" NARROW [] +created_in: "beta13" +def: "A topic concerning primarily a specific type of bioinformatics data, typically the broad category of content of a digital archives of biological data, including databanks, databases proper, web portals and other data resources." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1211 -name: unambiguous pure nucleotide -namespace: format -subset: formats -def: "Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters ." [http://edamontology.org] -is_a: EDAM_format:1207 ! nucleotide -is_a: EDAM_format:1206 ! unambiguous pure +id: EDAM_topic:3072 +name: Sequence feature detection +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D058977" RELATED [] +created_in: "beta13" +def: "Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0080 ! Sequence analysis +[Term] +id: EDAM_topic:3073 +name: Nucleic acid feature detection +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning the detection of positional features such as functional sites in nucleotide sequences." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis +is_a: EDAM_topic:3072 ! Sequence feature detection [Term] -id: EDAM_format:2568 -name: completely unambiguous pure nucleotide -namespace: format -subset: formats -def: "Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters ." [http://edamontology.org] -is_a: EDAM_format:1207 ! nucleotide -is_a: EDAM_format:2567 ! completely unambiguous pure +id: EDAM_topic:3074 +name: Protein feature detection +subset: bioinformatics +subset: edam +subset: topics +created_in: "beta13" +def: "Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0639 ! Protein sequence analysis +is_a: EDAM_topic:3072 ! Sequence feature detection +[Term] +id: EDAM_topic:3075 +name: Biological system modelling +subset: bioinformatics +subset: edam +subset: topics +xref: BioCatalogue:Model Analysis +xref: BioCatalogue:Model Execution +created_in: "beta13" +def: "Topic for modelling biological systems in mathematical terms." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:2259 ! Systems biology [Term] -id: EDAM_format:1212 -name: dna -namespace: format -subset: formats -def: "Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] -synonym: "DNA sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence] -is_a: EDAM_format:1207 ! nucleotide +id: EDAM_topic:3077 +name: Data acquisition and deposition +subset: bioinformatics +subset: edam +subset: topics +synonym: "Database submission" EXACT [] +created_in: "beta13" +def: "Topic concerning the acquisition and deposition of biological data." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0091 ! Data handling [Term] -id: EDAM_format:1213 -name: rna -namespace: format -subset: formats -def: "Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] -synonym: "RNA sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence] -is_a: EDAM_format:1207 ! nucleotide +id: EDAM_topic:3078 +name: Gene and protein resources +subset: bioinformatics +subset: edam +subset: topics +synonym: "Genes and proteins resources" EXACT [] +created_in: "beta13" +def: "Topic concerning specific genes and their encoded proteins or a related group of such genes and proteins." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0623 ! Genes, gene family or system +is_a: EDAM_topic:0635 ! Specific protein resources [Term] -id: EDAM_format:1214 -name: unambiguous pure dna -namespace: format -subset: formats -def: "Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:1206 ! unambiguous pure -is_a: EDAM_format:1212 ! dna +id: EDAM_topic:3168 +name: Sequencing +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D059014" NARROW [] +created_in: "1.1" +def: "Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_format:2569 -name: completely unambiguous pure dna -namespace: format -subset: formats -def: "Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2567 ! completely unambiguous pure -is_a: EDAM_format:1212 ! dna +id: EDAM_topic:3169 +name: ChIP-seq +subset: bioinformatics +subset: edam +subset: topics +synonym: "Chip seq" EXACT [] +synonym: "Chip sequencing" EXACT [] +synonym: "Chip-sequencing" EXACT [] +created_in: "1.1" +def: "Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0128 ! Protein interactions +is_a: EDAM_topic:3168 ! Sequencing [Term] -id: EDAM_format:1215 -name: pure dna -namespace: format -subset: formats -def: "Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:1210 ! pure nucleotide -is_a: EDAM_format:1212 ! dna +id: EDAM_topic:3170 +name: RNA-Seq +comment: This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. +subset: bioinformatics +subset: edam +subset: topics +synonym: "RNA-seq" EXACT [] +synonym: "Small RNA-Seq" EXACT [] +synonym: "Small RNA-seq" EXACT [] +synonym: "Whole transcriptome shotgun sequencing" EXACT [] +synonym: "WTSS" EXACT [] +created_in: "1.1" +def: "A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. " [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0203 ! Transcriptomics +is_a: EDAM_topic:3168 ! Sequencing [Term] -id: EDAM_format:1216 -name: unambiguous pure rna sequence -namespace: format -subset: formats -def: "Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:1206 ! unambiguous pure -is_a: EDAM_format:1213 ! rna +id: EDAM_topic:3171 +name: DNA methylation +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D019175" EXACT [] +created_in: "1.1" +def: "Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0654 ! DNA [Term] -id: EDAM_format:2570 -name: completely unambiguous pure rna sequence -namespace: format -subset: formats -def: "Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2567 ! completely unambiguous pure -is_a: EDAM_format:1213 ! rna +id: EDAM_topic:3172 +name: Metabolomics +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D055432" EXACT [] +created_in: "1.1" +def: "Topic concerning the study of metabolites and the chemical processes they are involved in, especially the systematic study of the chemical fingerprints of specific cellular processes." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM_format:1217 -name: pure rna -namespace: format -subset: formats -def: "Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:1210 ! pure nucleotide -is_a: EDAM_format:1213 ! rna +id: EDAM_topic:3173 +name: Epigenomics +comment: Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. +subset: bioinformatics +subset: edam +subset: topics +synonym: "Epigenetics" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D057890" EXACT [] +created_in: "1.1" +def: "A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0622 ! Genomics [Term] -id: EDAM_format:1218 -name: unambiguous pure protein -namespace: format -subset: formats -def: "Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:1206 ! unambiguous pure -is_a: EDAM_format:1208 ! protein +id: EDAM_topic:3174 +name: Metagenomics +subset: bioinformatics +subset: edam +subset: topics +synonym: "Community genomics" EXACT [] +synonym: "Ecogenomics" EXACT [] +synonym: "Environmental genomics" EXACT [] +synonym: "http://purl.bioontology.org/ontology/MSH/D056186" EXACT [] +created_in: "1.1" +def: "Topic concerning the study of genetic material recovered from environmental samples." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0610 ! Ecoinformatics +is_a: EDAM_topic:0622 ! Genomics [Term] -id: EDAM_format:2607 -name: completely unambiguous pure protein -namespace: format -subset: formats -def: "Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2567 ! completely unambiguous pure -is_a: EDAM_format:1208 ! protein +id: EDAM_topic:3175 +name: Structural variation +subset: bioinformatics +subset: edam +subset: topics +synonym: "Genomic structural variation" EXACT [] +created_in: "1.1" +def: "Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0199 ! Genetic variation +is_a: EDAM_topic:0624 ! Chromosomes [Term] -id: EDAM_format:1219 -name: pure protein -namespace: format -subset: formats -def: "Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] -is_a: EDAM_format:2094 ! pure -is_a: EDAM_format:1208 ! protein +id: EDAM_topic:3176 +name: DNA packaging +subset: bioinformatics +subset: edam +subset: topics +synonym: "http://purl.bioontology.org/ontology/MSH/D042003" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0624 ! Chromosomes +is_a: EDAM_topic:0654 ! DNA [Term] -id: EDAM_format:3011 -name: genePred -namespace: format -subset: formats -def: "genePred table format for gene prediction tracks." [http://edamontology.org] -comment: genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. -xref: http://genome.ucsc.edu/FAQ/FAQformat#format9 !{documentation=true} -is_a: EDAM_format:2919 ! Sequence annotation track format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3177 +name: DNA-Seq +subset: bioinformatics +subset: edam +subset: topics +synonym: "DNA-seq" EXACT [] +created_in: "1.1" +def: "A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:3168 ! Sequencing [Term] -id: EDAM_format:3012 -name: pgSnp -namespace: format -subset: formats -def: "Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser." [http://edamontology.org] ! UCSC-specific,but also for custom tracks & useful -xref: http://genome.ucsc.edu/FAQ/FAQformat#format10 !{documentation=true} -is_a: EDAM_format:2919 ! Sequence annotation track format -is_a: EDAM_format:2330 ! Textual format +id: EDAM_topic:3178 +name: RNA-Seq alignment +subset: bioinformatics +subset: edam +subset: topics +synonym: "RNA-seq alignment" EXACT [] +created_in: "beta12orEarlier" +def: "Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0182 ! Sequence alignment -! [Term] -! id: EDAM_format:todo if desired (but then we could include 100 ucsc db tables) At least, this one is used also in IGV (for importing genome cytobands) -! name: Cytoband format -! namespace: format -! subset: formats -! def: "Cytoband format for chromosome cytobands." [http://edamontology.org] -! comment: Reflects a UCSC Browser DB table. -! xref: http://www.broadinstitute.org/software/igv/Cytoband !{documentation=true} +[Term] +id: EDAM_topic:3179 +name: ChIP-on-chip +subset: bioinformatics +subset: edam +subset: topics +synonym: "ChIP-chip" EXACT [] +created_in: "1.1" +def: "Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions." [http://edamontology.org] +namespace: topic +is_a: EDAM_topic:0128 ! Protein interactions +is_a: EDAM_topic:3168 ! Sequencing +[Typedef] +id: has_format +name: has format +comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. +subset: bioinformatics +subset: edam +subset: relations +synonym: "has-quality" RELATED [] +synonym: "OBI:0000298" RELATED [] +def: "'A has_format B' defines for the subject A, that it has the object B as its data format." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: false +transitive_over: OBO_REL:is_a +domain: EDAM_data:0006 ! Data +range: EDAM_format:1915 ! Format -[Term] -id: EDAM_format:3013 -name: axt -namespace: format -subset: formats -def: "axt format of alignments, typically produced from BLASTZ." [http://edamontology.org] -xref: http://genome.ucsc.edu/goldenPath/help/axt.html !{documentation=true} -is_a: EDAM_format:2920 ! Alignment format (pair only) -is_a: EDAM_format:2330 ! Textual format +[Typedef] +id: has_function +name: has function +comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. +subset: bioinformatics +subset: edam +subset: relations +synonym: "has-quality" RELATED [] +synonym: "has_function" EXACT [] +synonym: "OBI:0000306" NARROW [] +synonym: "OBO_REL:bearer_of" RELATED [] +def: "'A has_function B' defines for the subject A, that it has the object B as its function." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: true +transitive_over: OBO_REL:is_a +range: EDAM_operation:0004 ! Operation +[Typedef] +id: has_identifier +name: has identifier +comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. +subset: bioinformatics +subset: edam +subset: relations +def: "'A has_identifier B' defines for the subject A, that it has the object B as its identifier." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: false +transitive_over: OBO_REL:is_a +domain: EDAM_data:0006 ! Data +range: EDAM_data:0842 ! Identifier -[Term] -id: EDAM_format:3014 -name: LAV -namespace: format -subset: formats -def: "LAV format of alignments generated by BLASTZ and LASTZ." [http://genome.ucsc.edu/goldenPath/help/axt.html] ! Can be used by UCSC and Galaxy -xref: http://www.bx.psu.edu/miller_lab/dist/lav_format.html !{documentation=true} -is_a: EDAM_format:2920 ! Alignment format (pair only) -is_a: EDAM_format:2330 ! Textual format +[Typedef] +id: has_input +name: has input +comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. +subset: bioinformatics +subset: edam +subset: relations +synonym: "has_input" EXACT [] +synonym: "OBI:0000293" NARROW [] +synonym: "OBO_REL:has_participant" RELATED [] +def: "'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: true +transitive_over: OBO_REL:is_a +domain: EDAM_operation:0004 ! Operation +range: EDAM_data:0006 ! Data +[Typedef] +id: has_output +name: has output +comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. +subset: bioinformatics +subset: edam +subset: relations +synonym: "has_output" EXACT [] +synonym: "OBI:0000299" NARROW [] +synonym: "OBO_REL:has_participant" RELATED [] +def: "'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: true +transitive_over: OBO_REL:is_a +domain: EDAM_operation:0004 ! Operation +range: EDAM_data:0006 ! Data -[Term] -id: EDAM_format:3015 -name: Pileup -namespace: format -subset: formats -def: "Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s)." [http://edamontology.org] -xref: http://samtools.sourceforge.net/pileup.shtml !{documentation=true} -is_a: EDAM_format:2920 ! Alignment format (pair only) -is_a: EDAM_format:2330 ! Textual format -! and of track? (encoded as points, but could be 'function', like wig) +[Typedef] +id: has_topic +name: has topic +comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. +subset: bioinformatics +subset: edam +subset: relations +synonym: "has-quality" RELATED [] +synonym: "hasTopic" RELATED [] +synonym: "IAO:0000136" RELATED [] +synonym: "OBI:0000298" RELATED [] +def: "'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B)." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: true +transitive_over: OBO_REL:is_a +range: EDAM_topic:0003 ! Topic +[Typedef] +id: is_format_of +name: is format of +comment: Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. +subset: bioinformatics +subset: edam +subset: relations +synonym: "inherent-in" RELATED [] +synonym: "OBO_REL:quality_of" RELATED [] +def: "'A is_format_of B' defines for the subject A, that it is a data format of the object B." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: false +transitive_over: OBO_REL:is_a +domain: EDAM_format:1915 ! Format +range: EDAM_data:0006 ! Data +inverse_of: has_format ! has format -[Term] -id: EDAM_format:3016 -name: VCF -namespace: format -subset: formats -def: "Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org] -xref: http://vcftools.sourceforge.net/specs.html !{documentation=true} -is_a: EDAM_format:2921 ! Sequence variation annotation format -is_a: EDAM_format:2330 ! Textual format +[Typedef] +id: is_function_of +name: is function of +comment: Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. +subset: bioinformatics +subset: edam +subset: relations +synonym: "http://wsio.org/is_function_of" EXACT [] +synonym: "inherent-in" RELATED [] +synonym: "OBO_REL:function_of" NARROW [] +synonym: "OBO_REL:inheres_in" RELATED [] +def: "'A is_function_of B' defines for the subject A, that it is a function of the object B." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: true +transitive_over: OBO_REL:is_a +domain: EDAM_operation:0004 ! Operation +inverse_of: has_function ! has function -[Term] -id: EDAM_format:3017 -name: SRF -namespace: format -subset: formats -def: "Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive." [http://edamontology.org, http://srf.sourceforge.net/ShortSequenceFormatDec18th_v_1_3.htm] -xref: http://srf.sourceforge.net/ !{documentation=true} -is_a: EDAM_format:2057 ! Sequence trace format -is_a: EDAM_format:2333 ! Binary format +[Typedef] +id: is_identifier_of +name: is identifier of +comment: Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. +subset: bioinformatics +subset: edam +subset: relations +def: "'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: false +transitive_over: OBO_REL:is_a +domain: EDAM_data:0842 ! Identifier +range: EDAM_data:0006 ! Data +inverse_of: has_identifier ! has identifier -[Term] -id: EDAM_format:3018 -name: ZTR -namespace: format -subset: formats -def: "ZTR format for storing chromatogram data from DNA sequencing instruments." [http://staden.sourceforge.net/manual/formats_unix_12.html, http://edamontology.org] -xref: http://staden.sourceforge.net/manual/formats_unix_12.html !{documentation=true} -is_a: EDAM_format:2057 ! Sequence trace format -is_a: EDAM_format:2333 ! Binary format +[Typedef] +id: is_input_of +name: is input of +comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. +subset: bioinformatics +subset: edam +subset: relations +synonym: "http://wsio.org/is_input_of" EXACT [] +synonym: "OBI:0000295" NARROW [] +synonym: "OBO_REL:participates_in" RELATED [] +def: "'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: true +transitive_over: OBO_REL:is_a +domain: EDAM_data:0006 ! Data +range: EDAM_operation:0004 ! Operation +inverse_of: has_input ! has input -[Term] -id: EDAM_format:3019 -name: GVF -namespace: format -subset: formats -def: "Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation." [http://edamontology.org] -xref: http://sequenceontology.org/gvf.html !{documentation=true} -is_a: EDAM_format:1975 ! GFF3 -! is_format_of (1255, Sequence feature annotation) is defined in parent (+ here has special tags for a particular class of seqfeatures: variation (indels,polymphs,structvar)) +[Typedef] +id: is_output_of +name: is output of +comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. +subset: bioinformatics +subset: edam +subset: relations +synonym: "http://wsio.org/is_output_of" EXACT [] +synonym: "OBI:0000312" NARROW [] +synonym: "OBO_REL:participates_in" RELATED [] +def: "'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: true +transitive_over: OBO_REL:is_a +domain: EDAM_data:0006 ! Data +range: EDAM_operation:0004 ! Operation +inverse_of: has_output ! has output -[Term] -id: EDAM_format:3020 -name: BCF -namespace: format -subset: formats -def: "BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org] -xref: http://samtools.sourceforge.net/mpileup.shtml !{documentation=true, note="BCF described on this site"} -is_a: EDAM_format:2921 ! Sequence variation annotation format -is_a: EDAM_format:2333 ! Binary format +[Typedef] +id: is_topic_of +name: is topic of +comment: Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. +subset: bioinformatics +subset: edam +subset: relations +synonym: "inherent-in" RELATED [] +synonym: "OBO_REL:quality_of" RELATED [] +def: "'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B)." [http://edamontology.org] +is_anti_symmetric: false +is_reflexive: false +is_symmetric: false +is_cyclic: true +transitive_over: OBO_REL:is_a +domain: EDAM_topic:0003 ! Topic +inverse_of: has_topic ! has topic diff --git a/releases/EDAM.owl b/releases/EDAM.owl new file mode 100644 index 0000000..b39f42e --- /dev/null +++ b/releases/EDAM.owl @@ -0,0 +1,52059 @@ + + + + EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics, and formats + + + 1.2 + application/rdf+xml + + + 14:12:2012 12:45 + 3263 + EDAM + EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web. + EDAM editors: Jon Ison and Matus Kalas. Co-authors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE (FP6, EU), EMBOSS (BBSRC, UK), eSysbio and FUGE Bioinformatics Platform (both Research Council of Norway). See http://edamontology.org for documentation and licence. + Jon Ison + Matúš Kalaš + EDAM http://edamontology.org/ "EDAM relations and concept properties" + EDAM_data http://edamontology.org/data_ "EDAM types of data" + EDAM_format http://edamontology.org/format_ "EDAM data formats" + EDAM_operation http://edamontology.org/operation_ "EDAM operations" + EDAM_topic http://edamontology.org/topic_ "EDAM topics" + Jon Ison, Matus Kalas + operations "EDAM operations" + data "EDAM types of data" + topics "EDAM topics" + formats "EDAM data formats" + identifiers "EDAM types of identifiers" + relations "EDAM relations" + concept_properties "EDAM concept properties" + edam "EDAM" + bioinformatics "Bioinformatics" + + + Singular, bioinformatics-specific operations that are functions of tools, workflows, or scripts, or can be performed manually. + operations "EDAM operations" + + + + + Types of data that are relevant in bioinformatics, commonly used as inputs, outputs, or intermediate data of analyses, or provided by databases and portals. + data "EDAM types of data" + + + + + Application domains of bioinformatics tools and resources; topics of research, studies, or analyses; approaches, techniques, and paradigms within - or directly related to - bioinformatics. + topics "EDAM topics" + + + + + Data formats commonly used in - and specific to - bioinformatics. Many format concepts in EDAM include references to their definition and documentation. + formats "EDAM data formats" + + + + + Types of identifiers that identify biological or computational entities; including resource-specific data accessions. Several identifier concepts in EDAM include regular expressions and examples. + identifiers "EDAM types of identifiers" + + + + + Types of relations - defined in EDAM - that apply between concepts, entities subject to semantic annotation, and entities and concepts (or possibly even vice versa). + relations "EDAM relations" + + + + + Types of concept properties and property modifiers, that are defined and used in EDAM in addition to the standard markup from the OBO and OWL formats and the standard Semantic Web vocabularies. + concept_properties "EDAM concept properties" + + + + + + + + + + + Created in + concept_properties + Version in which a concept was created. + true + + + + + Obsolete since + Version in which a concept was made obsolete. + concept_properties + true + + + + + Regular expression + true + 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. + concept_properties + + + + + Example + true + 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + concept_properties + + + + + Documentation + 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. + true + concept_properties + Specification + + + + + + + + + + + + relations + edam + bioinformatics + has format + 'A has_format B' defines for the subject A, that it has the object B as its data format. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. + false + false + false + OBO_REL:is_a + false + + + + + + + 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. + + + + + + + + + + + relations + edam + bioinformatics + has function + 'A has_function B' defines for the subject A, that it has the object B as its function. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. + false + false + false + true + OBO_REL:is_a + + + + + OBO_REL:bearer_of + + + In very unusual cases. + true + + + + + 'OBI:has_function' only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes, with objects that are a 'function' (snap:Function). It does not define explicitly that the object is a function of the subject. + + + + + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. + OBO_REL:bearer_of + + + + + + + + + + relations + edam + bioinformatics + has identifier + 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. + false + false + false + false + OBO_REL:is_a + + + + + + + + + + relations + edam + bioinformatics + has input + 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. + Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. + false + false + false + OBO_REL:is_a + true + + + + + OBO_REL:has_participant + + + In very unusual cases. + true + + + + + 'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). + + + + + + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. + OBO_REL:has_participant + + + + + + + + + + relations + edam + bioinformatics + has output + 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. + Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. + false + false + false + OBO_REL:is_a + true + + + + + OBO_REL:has_participant + + + In very unusual cases. + true + + + + + 'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). + + + + + + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. + OBO_REL:has_participant + + + + + + + + + + relations + edam + bioinformatics + has topic + 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. + false + false + false + OBO_REL:is_a + true + + + + + + + + + + + + + + + + In very unusual cases. + true + + + + + 'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource. + + + + + + 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. + + + + + + 'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object. + + + + + + + + + + + relations + edam + bioinformatics + is format of + 'A is_format_of B' defines for the subject A, that it is a data format of the object B. + Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. + false + false + false + false + OBO_REL:is_a + + + + + OBO_REL:quality_of + + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + OBO_REL:quality_of + + + + + + + + + + relations + edam + bioinformatics + is function of + 'A is_function_of B' defines for the subject A, that it is a function of the object B. + Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. + false + false + false + true + OBO_REL:is_a + + + + OBO_REL:function_of + + OBO_REL:inheres_in + + + In very unusual cases. + true + + + + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. + OBO_REL:function_of + + + + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. + OBO_REL:inheres_in + + + + + + + + + + relations + edam + bioinformatics + is identifier of + 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. + Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. + false + false + false + OBO_REL:is_a + false + + + + + + + + + + + relations + edam + bioinformatics + is input of + 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. + false + false + false + OBO_REL:is_a + true + + + + + + OBO_REL:participates_in + + + In very unusual cases. + true + + + + + 'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). + + + + + + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. + OBO_REL:participates_in + + + + + + + + + + relations + edam + bioinformatics + is output of + 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. + false + false + false + OBO_REL:is_a + true + + + + + + OBO_REL:participates_in + + + In very unusual cases. + true + + + + + 'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). + + + + + + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. + OBO_REL:participates_in + + + + + + + + + + relations + edam + bioinformatics + is topic of + 'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B). + Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. + false + false + false + OBO_REL:is_a + true + + + + + + + + + + + + OBO_REL:quality_of + + + In very unusual cases. + true + + + + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + OBO_REL:quality_of + + + + + + + + + + + + + + + + Resource type + + true + data + edam + A type of computational resource used in bioinformatics. + data + beta12orEarlier + beta12orEarlier + bioinformatics + + + + + + + + beta12orEarlier + data + edam + bioinformatics + data + + + Data + Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. + Data record + Datum + Data set + + + + + + + + + + + EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). + Data record + + + + + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Datum + + + + + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Data set + + + + + GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. + + + + + + Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019). + + + + + + IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something. + + + + + + IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity. + + + + + + Data does however not necessarily contain statements and not necessarily about an entity. + + + + + + + + + + + Tool + + true + edam + beta12orEarlier + beta12orEarlier + A bioinformatics package or tool, e.g. a standalone application or web service. + data + bioinformatics + data + + + + + + + + Database + + true + beta12orEarlier + data + beta12orEarlier + bioinformatics + A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model. + edam + data + + + + + + + + Ontology + + + + + + + + An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. + bioinformatics + edam + data + beta12orEarlier + data + + + + + + + + Directory metadata + + bioinformatics + data + edam + beta12orEarlier + A directory on disk from which files are read. + data + + + + + + + + MeSH vocabulary + + true + data + beta12orEarlier + Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. + data + bioinformatics + beta12orEarlier + edam + + + + + + + + + HGNC vocabulary + + true + bioinformatics + data + Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. + beta12orEarlier + beta12orEarlier + edam + data + + + + + + + + + UMLS vocabulary + + true + edam + bioinformatics + data + beta12orEarlier + beta12orEarlier + data + Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). + + + + + + + + + beta12orEarlier + data + identifiers + bioinformatics + edam + identifier + Identifier + A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). + + + + + + + + + + ID + + + + + + Almost exact but limited to identifying resources. + + + + + + + + + + + Database entry + + true + data + An entry (retrievable via URL) from a biological database. + bioinformatics + beta12orEarlier + beta12orEarlier + data + edam + + + + + + + + + Molecular mass + + data + bioinformatics + edam + data + beta12orEarlier + Mass of a molecule. + + + + + + + + Molecular charge + + PDBML:pdbx_formal_charge + bioinformatics + data + beta12orEarlier + Net charge of a molecule. + edam + data + + + + + + + + Chemical formula + + beta12orEarlier + A specification of a chemical structure. + bioinformatics + data + Chemical structure specification + edam + data + + + + + + + + QSAR descriptor + + QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. + edam + beta12orEarlier + data + A QSAR quantitative descriptor (name-value pair) of chemical structure. + data + bioinformatics + + + + + + + + Raw sequence + + Non-sequence characters may be used for example for gaps and translation stop. + data + edam + A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters. + data + bioinformatics + beta12orEarlier + + + + + + + + Sequence record + + data + data + A molecular sequence and associated metadata. + edam + beta12orEarlier + bioinformatics + + + + + + + + Sequence set + + data + bioinformatics + data + SO:0001260 + beta12orEarlier + This concept may be used for arbitrary sequence sets and associated data arising from processing. + edam + A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method. + + + + + + + + Sequence mask character + + A character used to replace (mask) other characters in a molecular sequence. + data + bioinformatics + edam + beta12orEarlier + data + + + + + + + + Sequence mask type + + + bioinformatics + data + beta12orEarlier + Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. + A label (text token) describing the type of sequence masking to perform. + edam + data + + + + + + + + DNA sense specification + + + bioinformatics + data + beta12orEarlier + edam + DNA strand specification + data + The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. + The strand of a DNA sequence (forward or reverse). + Strand + + + + + + + + Sequence length specification + + bioinformatics + data + beta12orEarlier + A specification of sequence length(s). + data + edam + + + + + + + + Sequence metadata + + + + This is used for such things as a report including the sequence identifier, type and length. + Basic or general information concerning molecular sequences. + beta12orEarlier + data + edam + data + bioinformatics + + + + + + + + Sequence feature source + + + data + beta12orEarlier + How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. + edam + This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). + data + bioinformatics + + + + + + + + Database hits (sequence) + + data + A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. + The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. + edam + data + bioinformatics + beta12orEarlier + + + + + + + + Database hits (secondary) + + bioinformatics + A report of hits from a search of a protein secondary or domain database. + data + data + edam + beta12orEarlier + Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'. + + + + + + + + Sequence signature model + + true + data + bioinformatics + data + edam + beta12orEarlier + beta12orEarlier + Data files used by motif or profile methods. + + + + + + + + + Sequence signature + + true + data + edam + beta12orEarlier + A classifier of sequences such as a sequence motif, profile or other diagnostic element. + beta12orEarlier + data + bioinformatics + + + + + + + + + + Sequence alignment (words) + + Alignment of exact matches between subsequences (words) within two or more molecular sequences. + data + Sequence word alignment + data + beta12orEarlier + edam + bioinformatics + + + + + + + + Dotplot + + data + beta12orEarlier + edam + bioinformatics + A dotplot of sequence similarities identified from word-matching or character comparison. + data + + + + + + + + Sequence alignment + + + + + + + + Alignment of multiple molecular sequences. + beta12orEarlier + data + edam + bioinformatics + data + + + + + + + + + + + Sequence alignment parameter + + beta12orEarlier + bioinformatics + edam + data + data + Some simple value controlling a sequence alignment (or similar 'match') operation. + + + + + + + + Sequence similarity score + + edam + data + beta12orEarlier + bioinformatics + data + A value representing molecular sequence similarity. + + + + + + + + Sequence alignment metadata + + + bioinformatics + edam + data + data + beta12orEarlier + Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score. + + + + + + + + Sequence alignment report + + beta12orEarlier + edam + data + An informative report of molecular sequence alignment-derived data or metadata. + bioinformatics + This is a broad data type and is used a placeholder for other, more specific types. + data + + + + + + + + Sequence profile alignment + + bioinformatics + data + data + A profile-profile alignment (each profile typically representing a sequence alignment). + beta12orEarlier + edam + + + + + + + + Sequence-profile alignment + + Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. + bioinformatics + data + edam + data + Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment). + beta12orEarlier + + + + + + + + Sequence distance matrix + + Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. + data + A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. + bioinformatics + edam + Phylogenetic distance matrix + data + Moby:phylogenetic_distance_matrix + beta12orEarlier + + + + + + + + Phylogenetic character data + + data + beta12orEarlier + edam + bioinformatics + data + Basic character data from which a phylogenetic tree may be generated. + As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments + + + + + + + + + Phylogenetic tree + + + + + + + + bioinformatics + Moby:myTree + beta12orEarlier + data + The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length. + Moby:phylogenetic_tree + data + A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. + Moby:Tree + Phylogeny + edam + + + + + + + + + + Comparison matrix + + data + bioinformatics + Substitution matrix + edam + Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. + beta12orEarlier + data + The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). + + + + + + + + Protein topology + + true + edam + beta12orEarlier + bioinformatics + beta12orEarlier + data + The location and size of the secondary structure elements and intervening loop regions is usually indicated. + data + Predicted or actual protein topology represented as a string of protein secondary structure elements. + + + + + + + + + Protein features (secondary structure) + + + + + + + + + edam + beta12orEarlier + data + bioinformatics + data + The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). + Protein secondary structure + Secondary structure assignment (predicted or real) of a protein. + + + + + + + + Protein features (super-secondary) + + + data + bioinformatics + edam + A report of predicted or actual super-secondary structure of protein sequence(s). + data + Protein structure report (super-secondary) + beta12orEarlier + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. + + + + + + + + Secondary structure alignment (protein) + + + beta12orEarlier + Alignment of the (1D representations of) secondary structure of two or more proteins. + data + bioinformatics + edam + data + + + + + + + + Secondary structure alignment metadata (protein) + + true + beta12orEarlier + edam + beta12orEarlier + data + An informative report on protein secondary structure alignment-derived data or metadata. + bioinformatics + data + + + + + + + + + RNA secondary structure record + + + + + + + + beta12orEarlier + bioinformatics + data + edam + Moby:RNAStructML + This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. + data + An informative report of secondary structure (predicted or real) of an RNA molecule. + + + + + + + + Secondary structure alignment (RNA) + + edam + beta12orEarlier + data + Alignment of the (1D representations of) secondary structure of two or more RNA molecules. + bioinformatics + data + Moby:RNAStructAlignmentML + + + + + + + + Secondary structure alignment metadata (RNA) + + true + beta12orEarlier + data + data + edam + An informative report of RNA secondary structure alignment-derived data or metadata. + beta12orEarlier + bioinformatics + + + + + + + + + Structure + + + + + + + + 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. + Structure data + data + The coordinate data may be predicted or real. + bioinformatics + data + beta12orEarlier + edam + + + + + + + + + Tertiary structure record + + true + An entry from a molecular tertiary (3D) structure database. + beta12orEarlier + beta12orEarlier + bioinformatics + data + data + edam + + + + + + + + + Database hits (structure) + + This includes alignment and score data. + edam + beta12orEarlier + Results (hits) from searching a database of tertiary structure. + data + data + bioinformatics + + + + + + + + Structure alignment + + + + + + + + + edam + data + bioinformatics + Alignment (superimposition) of molecular tertiary (3D) structures. + data + beta12orEarlier + A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. + + + + + + + + Structure alignment report + + bioinformatics + data + An informative report on molecular tertiary structure alignment-derived data. + edam + data + This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + + + + + + + + Structure similarity score + + data + bioinformatics + edam + A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. + data + beta12orEarlier + + + + + + + + Structural (3D) profile + + + + + + + + bioinformatics + edam + data + data + Some type of structural (3D) profile or template (representing a structure or structure alignment). + beta12orEarlier + 3D profile + + + + + + + + Structural (3D) profile alignment + + A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). + data + data + edam + bioinformatics + Structural profile alignment + beta12orEarlier + + + + + + + + Sequence-3D profile alignment + + beta12orEarlier + data + bioinformatics + data + An alignment of a sequence to a 3D profile (representing structures or a structure alignment). + edam + Sequence-structural profile alignment + + + + + + + + Protein sequence-structure scoring matrix + + edam + Matrix of values used for scoring sequence-structure compatibility. + data + beta12orEarlier + bioinformatics + data + + + + + + + + Sequence-structure alignment + + data + An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). + data + beta12orEarlier + bioinformatics + edam + + + + + + + + Amino acid annotation + + + beta12orEarlier + data + edam + bioinformatics + An informative report about a specific amino acid. + data + + + + + + + + Peptide annotation + + + + + + + + + beta12orEarlier + data + An informative report about a specific peptide. + bioinformatics + edam + data + + + + + + + + Protein report + + + + + + + + bioinformatics + edam + data + Gene product annotation + beta12orEarlier + An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. + data + + + + + + + + Protein property + + + data + edam + A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. + bioinformatics + The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. + data + beta12orEarlier + Protein physicochemical property + + + + + + + + Protein features (3D motif) + + + + + + + + + beta12orEarlier + data + Protein structure report (3D motif) + edam + data + An informative report on the 3D structural motifs in a protein. + This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. + bioinformatics + + + + + + + + Protein domain classification + + + + + + + + bioinformatics + beta12orEarlier + data + Data concerning the classification of the sequences and/or structures of protein structural domain(s). + edam + data + + + + + + + + Protein features (domains) + + + + + + + + edam + beta12orEarlier + The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. + Protein structural domains + Protein domain assignment + Summary of structural domains or 3D folds in a protein or polypeptide chain. + bioinformatics + data + data + + + + + + + + Protein architecture report + + + beta12orEarlier + bioinformatics + edam + data + data + Protein structure report (architecture) + Protein property (architecture) + An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. + + + + + + + + Protein folding report + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Protein report (folding) + data + data + edam + bioinformatics + Protein property (folding) + A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. + beta12orEarlier + + + + + + + + Protein features (mutation) + + true + Protein report (mutation) + beta13 + Protein structure report (mutation) + data + data + Protein property (mutation) + beta12orEarlier + bioinformatics + Data on the effect of (typically point) mutation on protein folding, stability, structure and function. + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + edam + + + + + + + + + Protein interaction raw data + + data + beta12orEarlier + edam + Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. + bioinformatics + data + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + + + + + + + + Protein interaction + + + + + + + + + bioinformatics + data + data + Protein report (interaction) + beta12orEarlier + An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand. + edam + + + + + + + + Protein family + + + + + + + + edam + Protein family annotation + bioinformatics + data + beta12orEarlier + data + An informative report on a specific protein family or other group of classified proteins. + + + + + + + + Vmax + + The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. + data + data + edam + beta12orEarlier + bioinformatics + + + + + + + + Km + + data + beta12orEarlier + data + Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. + edam + bioinformatics + + + + + + + + Nucleotide base annotation + + bioinformatics + An informative report about a specific nucleotide base. + data + edam + beta12orEarlier + data + + + + + + + + Nucleic acid property + + + Nucleic acid physicochemical property + data + bioinformatics + data + beta12orEarlier + The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. + A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule. + edam + + + + + + + + Codon usage report + + + + + + + + This is a broad data type and is used a placeholder for other, more specific types. + data + bioinformatics + data + Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences. + edam + beta12orEarlier + + + + + + + + Gene annotation + + + + + + + + data + bioinformatics + Gene annotation (functional) + data + Moby:GeneInfo + Moby_namespace:Human_Readable_Description + beta12orEarlier + edam + This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). + Moby:gene + Gene report + An informative report on a particular locus, gene, gene system or groups of genes. + + + + + + + + Gene classification + + true + beta12orEarlier + edam + A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. + bioinformatics + data + beta12orEarlier + data + + + + + + + + + Nucleic acid features (variation) + + + + + + + + beta12orEarlier + data + A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. + bioinformatics + Sequence variation annotation + data + edam + SO:0001059 + + + + + + + + Gene annotation (chromosome) + + + + + + + + This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. + data + data + An informative report on a specific chromosome. + edam + beta12orEarlier + bioinformatics + + + + + + + + Genotype/phenotype annotation + + beta12orEarlier + data + data + edam + bioinformatics + An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes. + + + + + + + + Nucleic acid features (primers) + + + + + + + + edam + data + beta12orEarlier + bioinformatics + data + Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence. + + + + + + + + Experiment annotation (PCR assay data) + + + + + + + + data + PCR assay data + beta12orEarlier + bioinformatics + Data on a PCR assay or electronic / virtual PCR. + edam + data + + + + + + + + Sequence trace + + + edam + beta12orEarlier + data + bioinformatics + This is the raw data produced by a DNA sequencing machine. + Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores. + data + + + + + + + + Sequence assembly + + data + SO:0000353 + SO:0001248 + beta12orEarlier + An assembly of fragments of a (typically genomic) DNA sequence. + + edam + data + Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. + bioinformatics + + + Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. + SO:0001248 + + + + + + + + + + Radiation Hybrid (RH) scores + + bioinformatics + data + edam + Radiation hybrid scores (RH) scores for one or more markers. + data + Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. + beta12orEarlier + + + + + + + + Gene annotation (linkage) + + An informative report on the linkage of alleles. + data + data + beta12orEarlier + edam + bioinformatics + + + + + + + + Gene expression profile + + Gene expression pattern + bioinformatics + Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. + beta12orEarlier + edam + data + data + + + + + + + + Experiment annotation (microarray) + + + + + + + + beta12orEarlier + This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. + data + bioinformatics + edam + Information on a microarray experiment such as conditions, protocol, sample:data relationships etc. + data + Experimental design annotation + + + + + + + + Oligonucleotide probe data + + true + Data on oligonucleotide probes (typically for use with DNA microarrays). + bioinformatics + data + beta13 + edam + data + beta12orEarlier + + + + + + + + + SAGE experimental data + + true + edam + data + beta12orEarlier + data + beta12orEarlier + Serial analysis of gene expression (SAGE) experimental data + bioinformatics + Output from a serial analysis of gene expression (SAGE) experiment. + + + + + + + + + MPSS experimental data + + true + data + edam + beta12orEarlier + beta12orEarlier + Massively parallel signature sequencing (MPSS) experimental data + Massively parallel signature sequencing (MPSS) data. + bioinformatics + data + + + + + + + + + SBS experimental data + + true + data + bioinformatics + edam + beta12orEarlier + Sequencing by synthesis (SBS) experimental data + Sequencing by synthesis (SBS) data. + data + beta12orEarlier + + + + + + + + + Sequence tag profile (with gene assignment) + + Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. + bioinformatics + data + beta12orEarlier + edam + data + + + + + + + + Protein X-ray crystallographic data + + beta12orEarlier + data + X-ray crystallography data. + bioinformatics + edam + data + + + + + + + + Protein NMR data + + bioinformatics + beta12orEarlier + data + edam + data + Protein nuclear magnetic resonance (NMR) raw data. + + + + + + + + Protein circular dichroism (CD) spectroscopic data + + data + data + Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. + bioinformatics + beta12orEarlier + edam + + + + + + + + Electron microscopy volume map + + + + + + + + edam + EM volume map + Volume map data from electron microscopy. + bioinformatics + data + beta12orEarlier + data + + + + + + + + Electron microscopy model + + + + + + + + This might include the location in the model of the known features of a particular macromolecule. + Annotation on a structural 3D model (volume map) from electron microscopy. + data + edam + beta12orEarlier + bioinformatics + data + + + + + + + + 2D PAGE image + + + + + + + + + beta12orEarlier + Two-dimensional gel electrophoresis image. + edam + data + data + Two-dimensional gel electrophoresis image + bioinformatics + + + + + + + + Mass spectrometry spectra + + + + + + + + data + Spectra from mass spectrometry. + beta12orEarlier + data + edam + bioinformatics + + + + + + + + Peptide mass fingerprint + + + + + + + + + edam + beta12orEarlier + A set of peptide masses (peptide mass fingerprint) from mass spectrometry. + bioinformatics + data + data + Protein fingerprint + Peak list + + + + + + + + Peptide identification + + + + + + + + beta12orEarlier + bioinformatics + data + Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database. + edam + data + + + + + + + + Pathway or network annotation + + true + beta12orEarlier + bioinformatics + data + An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. + data + edam + beta12orEarlier + + + + + + + + + Biological pathway map + + true + beta12orEarlier + data + A map (typically a diagram) of a biological pathway. + data + bioinformatics + edam + beta12orEarlier + + + + + + + + + Data resource definition + + edam + data + A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. + bioinformatics + data + beta12orEarlier + + + + + + + + Workflow metadata + + beta12orEarlier + edam + data + bioinformatics + Basic information, annotation or documentation concerning a workflow (but not the workflow itself). + data + + + + + + + + Biological model + + + + + + + + edam + data + bioinformatics + beta12orEarlier + A biological model which can be represented in mathematical terms. + data + + + + + + + + Statistical estimate score + + + data + bioinformatics + A value representing estimated statistical significance of some observed data; typically sequence database hits. + beta12orEarlier + data + edam + + + + + + + + EMBOSS database resource definition + + data + edam + beta12orEarlier + Resource definition for an EMBOSS database. + bioinformatics + data + + + + + + + + Version information + + beta12orEarlier + Information on a version of software or data, for example name, version number and release date. + Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. + bioinformatics + + + data + + data + edam + + + + Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. + + + + + + + + + + + Database cross-mapping + + The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. + A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases. + data + edam + data + bioinformatics + beta12orEarlier + + + + + + + + Data index + + + + + + + + beta12orEarlier + bioinformatics + An index of data of biological relevance. + data + edam + data + + + + + + + + Data index report + + + + + + + + beta12orEarlier + data + data + edam + bioinformatics + Database index annotation + A report of an analysis of an index of biological data. + + + + + + + + Database metadata + + bioinformatics + edam + data + data + beta12orEarlier + Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. + + + + + + + + Tool metadata + + data + edam + data + Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. + beta12orEarlier + bioinformatics + + + + + + + + Job metadata + + data + Textual metadata on a submitted or completed job. + edam + Moby:PDGJOB + data + bioinformatics + beta12orEarlier + + + + + + + + User metadata + + data + edam + data + Textual metadata on a software author or end-user, for example a person or other software. + bioinformatics + beta12orEarlier + + + + + + + + Small molecule annotation + + + + + + + + + data + data + An informative report on a specific chemical compound. + Small molecule report + bioinformatics + Chemical compound annotation + beta12orEarlier + edam + + + + + + + + Cell line annotation + + beta12orEarlier + Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on. + bioinformatics + data + data + edam + Organism strain data + + + + + + + + Scent annotation + + bioinformatics + data + An informative report about a specific scent. + edam + beta12orEarlier + data + + + + + + + + Ontology term + + bioinformatics + A term (name) from an ontology. + edam + data + beta12orEarlier + data + + + + + + + + Ontology concept metadata + + + + + + + + bioinformatics + data + Data concerning or derived from a concept from a biological ontology. + data + beta12orEarlier + edam + + + + + + + + Keyword + + Moby:Global_Keyword + Moby:Wildcard_Query + Moby:BooleanQueryString + data + beta12orEarlier + data + Moby:QueryString + bioinformatics + edam + Keyword(s) or phrase(s) used (typically) for text-searching purposes. + Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. + + + + + + + + Bibliographic reference + + + beta12orEarlier + Moby:Publication + edam + Citation + Reference + data + A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. + Bibliographic data that uniquely identifies a scientific article, book or other published material. + bioinformatics + data + Moby:GCP_SimpleCitation + + + + + + + + Article + + + + + + + + data + A body of scientific text, typically a full text article from a scientific journal. + beta12orEarlier + edam + data + bioinformatics + + + + + + + + Text mining report + + A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. + beta12orEarlier + data + data + bioinformatics + An abstract of the results of text mining. + edam + + + + + + + + Entity identifier + + true + An identifier of a biological entity or phenomenon. + identifier + beta12orEarlier + beta12orEarlier + data + bioinformatics + edam + identifiers + + + + + + + + + Data resource identifier + + true + beta12orEarlier + An identifier of a data resource. + edam + identifier + identifiers + beta12orEarlier + bioinformatics + data + + + + + + + + + Identifier (typed) + + identifiers + edam + data + bioinformatics + An identifier that identifies a particular type of data. + This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. + identifier + beta12orEarlier + + + + + + + + Tool identifier + + data + beta12orEarlier + An identifier of a bioinformatics tool, e.g. an application or web service. + bioinformatics + identifier + identifiers + edam + + + + + + + + Discrete entity identifier + + true + identifier + identifiers + bioinformatics + data + beta12orEarlier + Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). + beta12orEarlier + edam + + + + + + + + + Entity feature identifier + + true + identifiers + identifier + data + edam + beta12orEarlier + Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing). + beta12orEarlier + bioinformatics + + + + + + + + + Entity collection identifier + + true + edam + Name or other identifier of a collection of discrete biological entities. + data + identifiers + identifier + bioinformatics + beta12orEarlier + beta12orEarlier + + + + + + + + + Phenomenon identifier + + true + data + identifiers + edam + beta12orEarlier + Name or other identifier of a physical, observable biological occurrence or event. + beta12orEarlier + bioinformatics + identifier + + + + + + + + + Molecule identifier + + + + + + + + identifier + edam + identifiers + beta12orEarlier + data + bioinformatics + Name or other identifier of a molecule. + + + + + + + + Atom identifier + + beta12orEarlier + data + Identifier (e.g. character symbol) of a specific atom. + identifier + bioinformatics + identifiers + edam + + + + + + + + Molecule name + + + identifiers + edam + beta12orEarlier + identifier + bioinformatics + data + Name of a specific molecule. + + + + + + + + Molecule type + + Protein|DNA|RNA + bioinformatics + beta12orEarlier + A label (text token) describing the type a molecule. + data + edam + data + For example, 'Protein', 'DNA', 'RNA' etc. + + + + + + + + Chemical identifier + + true + bioinformatics + edam + beta12orEarlier + beta12orEarlier + Unique identifier of a chemical compound. + identifiers + identifier + data + + + + + + + + + Chromosome name + + + + + + + + + identifier + beta12orEarlier + edam + Name of a chromosome. + identifiers + bioinformatics + data + + + + + + + + Peptide identifier + + beta12orEarlier + identifier + Identifier of a peptide chain. + data + bioinformatics + identifiers + edam + + + + + + + + Protein identifier + + + + + + + + identifiers + bioinformatics + edam + identifier + data + Identifier of a protein. + beta12orEarlier + + + + + + + + Compound name + + + identifier + beta12orEarlier + bioinformatics + edam + identifiers + Chemical name + Unique name of a chemical compound. + data + + + + + + + + Chemical registry number + + identifiers + edam + identifier + Unique registry number of a chemical compound. + bioinformatics + beta12orEarlier + data + + + + + + + + Ligand identifier + + true + beta12orEarlier + Code word for a ligand, for example from a PDB file. + identifier + edam + data + identifiers + beta12orEarlier + bioinformatics + + + + + + + + + Drug identifier + + + + + + + + edam + data + Identifier of a drug. + identifier + beta12orEarlier + bioinformatics + identifiers + + + + + + + + Amino acid identifier + + + + + + + + bioinformatics + identifier + Residue identifier + beta12orEarlier + Identifier of an amino acid. + data + identifiers + edam + + + + + + + + Nucleotide identifier + + identifier + Name or other identifier of a nucleotide. + bioinformatics + data + beta12orEarlier + identifiers + edam + + + + + + + + Monosaccharide identifier + + Identifier of a monosaccharide. + bioinformatics + beta12orEarlier + identifiers + edam + data + identifier + + + + + + + + Chemical name (ChEBI) + + This is the recommended chemical name for use for example in database annotation. + edam + Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. + identifier + identifiers + bioinformatics + data + beta12orEarlier + ChEBI chemical name + + + + + + + + Chemical name (IUPAC) + + bioinformatics + beta12orEarlier + edam + identifiers + IUPAC chemical name + data + identifier + IUPAC recommended name of a chemical compound. + + + + + + + + Chemical name (INN) + + edam + identifier + data + International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). + bioinformatics + identifiers + beta12orEarlier + INN chemical name + + + + + + + + Chemical name (brand) + + data + identifiers + edam + bioinformatics + Brand chemical name + beta12orEarlier + identifier + Brand name of a chemical compound. + + + + + + + + Chemical name (synonymous) + + identifiers + Synonymous name of a chemical compound. + edam + data + bioinformatics + identifier + Synonymous chemical name + beta12orEarlier + + + + + + + + Chemical registry number (CAS) + + identifiers + bioinformatics + identifier + edam + data + beta12orEarlier + CAS registry number of a chemical compound. + CAS chemical registry number + + + + + + + + Chemical registry number (Beilstein) + + data + identifiers + Beilstein registry number of a chemical compound. + bioinformatics + identifier + Beilstein chemical registry number + beta12orEarlier + edam + + + + + + + + Chemical registry number (Gmelin) + + bioinformatics + Gmelin registry number of a chemical compound. + identifier + beta12orEarlier + identifiers + edam + data + Gmelin chemical registry number + + + + + + + + HET group name + + beta12orEarlier + Component identifier code + bioinformatics + Short ligand name + identifier + data + 3-letter code word for a ligand (HET group) from a PDB file, for example ATP. + identifiers + edam + + + + + + + + Amino acid name + + identifier + edam + data + bioinformatics + identifiers + String of one or more ASCII characters representing an amino acid. + beta12orEarlier + + + + + + + + Nucleotide code + + + data + bioinformatics + edam + String of one or more ASCII characters representing a nucleotide. + identifier + identifiers + beta12orEarlier + + + + + + + + Polypeptide chain ID + + + + + + + + Polypeptide chain identifier + This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA + PDB chain identifier + Protein chain identifier + PDB strand id + PDBML:pdbx_PDB_strand_id + edam + Identifier of a polypeptide chain from a protein. + data + identifiers + Chain identifier + bioinformatics + identifier + WHATIF: chain + beta12orEarlier + + + + + + + + Protein name + + + identifiers + bioinformatics + beta12orEarlier + edam + data + identifier + Name of a protein. + + + + + + + + Enzyme identifier + + + + + + + + data + Name or other identifier of an enzyme or record from a database of enzymes. + bioinformatics + identifiers + beta12orEarlier + edam + identifier + + + + + + + + EC number + + bioinformatics + Enzyme Commission number + beta12orEarlier + data + Moby:Annotated_EC_Number + edam + EC + An Enzyme Commission (EC) number of an enzyme. + EC code + Moby:EC_Number + [0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ + identifier + identifiers + + + + + + + + Enzyme name + + + beta12orEarlier + Name of an enzyme. + data + identifier + identifiers + bioinformatics + edam + + + + + + + + Restriction enzyme name + + + + + + + + identifier + data + beta12orEarlier + edam + Name of a restriction enzyme. + bioinformatics + identifiers + + + + + + + + Sequence position specification + + beta12orEarlier + A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. + data + data + bioinformatics + edam + + + + + + + + Sequence feature ID + + + beta12orEarlier + edam + bioinformatics + A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file. + identifier + data + identifiers + + + + + + + + Sequence position + + PDBML:_atom_site.id + beta12orEarlier + data + WHATIF: number + data + SO:0000735 + A position of a single point (base or residue) in a sequence, or part of such a specification. + bioinformatics + edam + WHATIF: PDBx_atom_site + + + + + + + + Sequence range + + edam + data + data + Specification of range(s) of sequence positions. + bioinformatics + beta12orEarlier + + + + + + + + Nucleic acid feature identifier + + true + bioinformatics + Name or other identifier of an nucleic acid feature. + beta12orEarlier + beta12orEarlier + data + identifiers + identifier + edam + + + + + + + + + Protein feature identifier + + true + edam + bioinformatics + identifier + Name or other identifier of a protein feature. + beta12orEarlier + data + identifiers + beta12orEarlier + + + + + + + + + Sequence feature key + + A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. + data + bioinformatics + beta12orEarlier + The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key. + Sequence feature type + edam + data + Sequence feature method + + + + + + + + Sequence feature qualifier + + Feature qualifiers hold information about a feature beyond that provided by the feature key and location. + data + edam + bioinformatics + data + Typically one of the EMBL or Swiss-Prot feature qualifiers. + beta12orEarlier + + + + + + + + Sequence feature label + + A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. + beta12orEarlier + bioinformatics + Typically an EMBL or Swiss-Prot feature label. + data + Sequence feature name + edam + data + + + + + + + + EMBOSS Uniform Feature Object + + + The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. + bioinformatics + data + beta12orEarlier + UFO + edam + data + + + + + + + + Codon name + + true + bioinformatics + beta12orEarlier + identifier + beta12orEarlier + data + String of one or more ASCII characters representing a codon. + identifiers + edam + + + + + + + + + Gene identifier + + + + + + + + edam + beta12orEarlier + An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database. + data + bioinformatics + identifier + identifiers + Moby:GeneAccessionList + + + + + + + + Gene symbol + + edam + data + The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name. + Moby_namespace:Global_GeneCommonName + identifier + identifiers + beta12orEarlier + Moby_namespace:Global_GeneSymbol + bioinformatics + + + + + + + + Gene ID (NCBI) + + + bioinformatics + beta12orEarlier + NCBI gene ID + identifiers + An NCBI unique identifier of a gene. + edam + http://www.geneontology.org/doc/GO.xrf_abbs:LocusID + data + Gene identifier (Entrez) + http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene + Entrez gene ID + identifier + Gene identifier (NCBI) + NCBI geneid + + + + + + + + Gene identifier (NCBI RefSeq) + + true + beta12orEarlier + An NCBI RefSeq unique identifier of a gene. + edam + bioinformatics + data + identifier + identifiers + beta12orEarlier + + + + + + + + + Gene identifier (NCBI UniGene) + + true + edam + identifiers + An NCBI UniGene unique identifier of a gene. + bioinformatics + identifier + data + beta12orEarlier + beta12orEarlier + + + + + + + + + Gene identifier (Entrez) + + true + data + [0-9]+ + edam + beta12orEarlier + beta12orEarlier + identifier + An Entrez unique identifier of a gene. + bioinformatics + identifiers + + + + + + + + + Gene ID (CGD) + + beta12orEarlier + Identifier of a gene or feature from the CGD database. + data + edam + CGD ID + identifiers + bioinformatics + identifier + + + + + + + + Gene ID (DictyBase) + + identifiers + bioinformatics + Identifier of a gene from DictyBase. + data + identifier + beta12orEarlier + edam + + + + + + + + Gene ID (Ensembl) + + + bioinformatics + data + edam + Unique identifier for a gene (or other feature) from the Ensembl database. + beta12orEarlier + identifier + identifiers + Ensembl Gene ID + + + + + + + + Gene ID (SGD) + + + identifiers + data + identifier + edam + bioinformatics + beta12orEarlier + SGD identifier + S[0-9]+ + Identifier of an entry from the SGD database. + + + + + + + + Gene ID (GeneDB) + + data + [a-zA-Z_0-9\.-]* + bioinformatics + edam + Moby_namespace:GeneDB + Identifier of a gene from the GeneDB database. + identifier + beta12orEarlier + identifiers + GeneDB identifier + + + + + + + + TIGR identifier + + + bioinformatics + identifiers + identifier + data + edam + Identifier of an entry from the TIGR database. + beta12orEarlier + + + + + + + + TAIR accession (gene) + + + Identifier of an gene from the TAIR database. + beta12orEarlier + edam + data + identifiers + bioinformatics + identifier + Gene:[0-9]{7} + + + + + + + + Protein domain ID + + + + + + + + + bioinformatics + identifier + identifiers + This is typically a character or string concatenated with a PDB identifier and a chain identifier. + edam + data + Identifier of a protein structural domain. + beta12orEarlier + + + + + + + + SCOP domain identifier + + + + + + + + identifier + bioinformatics + beta12orEarlier + identifiers + edam + data + Identifier of a protein domain (or other node) from the SCOP database. + + + + + + + + CATH domain ID + + identifiers + bioinformatics + CATH domain identifier + 1nr3A00 + data + identifier + edam + Identifier of a protein domain from CATH. + beta12orEarlier + + + + + + + + SCOP concise classification string (sccs) + + edam + identifiers + An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. + data + beta12orEarlier + identifier + bioinformatics + A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification. + + + + + + + + SCOP sunid + + 33229 + A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. + identifier + edam + bioinformatics + data + SCOP unique identifier + sunid + identifiers + Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229. + beta12orEarlier + + + + + + + + CATH node ID + + beta12orEarlier + CATH node identifier + A code number identifying a node from the CATH database. + identifiers + bioinformatics + CATH code + data + identifier + 3.30.1190.10.1.1.1.1.1 + edam + + + + + + + + Kingdom name + + identifier + beta12orEarlier + identifiers + The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes). + bioinformatics + data + edam + + + + + + + + Species name + + beta12orEarlier + identifier + Organism species + The name of a species (typically a taxonomic group) of organism. + identifiers + bioinformatics + edam + data + + + + + + + + Strain name + + + The name of a strain of an organism variant, typically a plant, virus or bacterium. + beta12orEarlier + identifier + bioinformatics + identifiers + edam + data + + + + + + + + URI + + + edam + bioinformatics + beta12orEarlier + A string of characters that name or otherwise identify a resource on the Internet. + data + data + + + + + + + + Database identifier + + + + + + + + edam + identifier + data + beta12orEarlier + An identifier of a biological or bioinformatics database. + bioinformatics + identifiers + + + + + + + + Directory name + + + identifiers + bioinformatics + data + edam + The name of a directory. + beta12orEarlier + identifier + + + + + + + + File name + + beta12orEarlier + data + edam + The name (or part of a name) of a file (of any type). + bioinformatics + identifier + identifiers + + + + + + + + Ontology name + + + + + + + + + identifiers + bioinformatics + data + Name of an ontology of biological or bioinformatics concepts and relations. + identifier + edam + beta12orEarlier + + + + + + + + URL + + Moby:Link + beta12orEarlier + data + Moby:URL + A Uniform Resource Locator (URL). + edam + bioinformatics + data + + + + + + + + URN + + edam + data + data + beta12orEarlier + A Uniform Resource Name (URN). + bioinformatics + + + + + + + + LSID + + A Life Science Identifier (LSID) - a unique identifier of some data. + data + Life Science Identifier + LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>] + data + beta12orEarlier + bioinformatics + edam + + + + + + + + Database name + + + edam + identifiers + bioinformatics + beta12orEarlier + The name of a biological or bioinformatics database. + data + identifier + + + + + + + + Sequence database name + + true + beta13 + edam + bioinformatics + The name of a molecular sequence database. + identifier + beta12orEarlier + identifiers + data + + + + + + + + + Enumerated file name + + edam + The name of a file (of any type) with restricted possible values. + data + beta12orEarlier + bioinformatics + identifier + identifiers + + + + + + + + File name extension + + beta12orEarlier + data + bioinformatics + identifier + A file extension is the characters appearing after the final '.' in the file name. + identifiers + edam + The extension of a file name. + + + + + + + + File base name + + A file base name is the file name stripped of its directory specification and extension. + edam + data + identifier + The base name of a file. + beta12orEarlier + bioinformatics + identifiers + + + + + + + + QSAR descriptor name + + + + + + + + + bioinformatics + Name of a QSAR descriptor. + beta12orEarlier + data + identifiers + identifier + edam + + + + + + + + Database entry identifier + + true + beta12orEarlier + edam + identifier + This concept is required for completeness. It should never have child concepts. + identifiers + beta12orEarlier + An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. + bioinformatics + data + + + + + + + + + Sequence identifier + + + + + + + + + beta12orEarlier + identifier + An identifier of molecular sequence(s) or entries from a molecular sequence database. + edam + identifiers + bioinformatics + data + + + + + + + + Sequence set ID + + + + + + + + + beta12orEarlier + identifiers + edam + data + bioinformatics + An identifier of a set of molecular sequence(s). + identifier + + + + + + + + Sequence signature identifier + + true + Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. + identifiers + bioinformatics + data + edam + beta12orEarlier + beta12orEarlier + identifier + + + + + + + + + + Sequence alignment ID + + + + + + + + + bioinformatics + identifier + beta12orEarlier + identifiers + edam + Identifier of a molecular sequence alignment, for example a record from an alignment database. + data + + + + + + + + Phylogenetic distance matrix identifier + + true + identifiers + data + Identifier of a phylogenetic distance matrix. + beta12orEarlier + beta12orEarlier + identifier + edam + bioinformatics + + + + + + + + + Phylogenetic tree ID + + + + + + + + + identifier + beta12orEarlier + identifiers + Identifier of a phylogenetic tree for example from a phylogenetic tree database. + bioinformatics + edam + data + + + + + + + + Comparison matrix identifier + + + + + + + + identifiers + beta12orEarlier + data + Substitution matrix identifier + bioinformatics + edam + identifier + An identifier of a comparison matrix. + + + + + + + + Structure ID + + + bioinformatics + A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. + identifiers + identifier + data + edam + beta12orEarlier + + + + + + + + Structural (3D) profile ID + + + + + + + + + bioinformatics + beta12orEarlier + identifiers + edam + identifier + Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). + Structural profile identifier + data + + + + + + + + Structure alignment ID + + + + + + + + + data + identifier + edam + Identifier of an entry from a database of tertiary structure alignments. + beta12orEarlier + bioinformatics + identifiers + + + + + + + + Amino acid index ID + + + + + + + + + data + beta12orEarlier + identifiers + bioinformatics + edam + identifier + Identifier of an index of amino acid physicochemical and biochemical property data. + + + + + + + + Protein interaction ID + + identifiers + data + Identifier of a report of protein interactions from a protein interaction database (typically). + edam + bioinformatics + identifier + beta12orEarlier + + + + + + + + Protein family identifier + + + + + + + + identifier + beta12orEarlier + bioinformatics + identifiers + Identifier of a protein family. + edam + Protein secondary database record identifier + data + + + + + + + + Codon usage table name + + + + + + + + + + + + + + + identifiers + Unique name of a codon usage table. + bioinformatics + data + identifier + edam + beta12orEarlier + + + + + + + + Transcription factor identifier + + + + + + + + + edam + Identifier of a transcription factor (or a TF binding site). + data + identifier + beta12orEarlier + bioinformatics + identifiers + + + + + + + + Microarray experiment annotation ID + + + + + + + + identifiers + Identifier of an entry from a database of microarray data. + edam + data + beta12orEarlier + bioinformatics + identifier + + + + + + + + Electron microscopy model ID + + + + + + + + + edam + beta12orEarlier + Identifier of an entry from a database of electron microscopy data. + identifier + bioinformatics + identifiers + data + + + + + + + + Gene expression report ID + + + + + + + + + Gene expression profile identifier + edam + identifier + identifiers + data + beta12orEarlier + Accession of a report of gene expression (e.g. a gene expression profile) from a database. + bioinformatics + + + + + + + + Genotype and phenotype annotation ID + + + + + + + + + data + beta12orEarlier + edam + identifier + bioinformatics + identifiers + Identifier of an entry from a database of genotypes and phenotypes. + + + + + + + + Pathway or network identifier + + + + + + + + data + edam + identifiers + bioinformatics + beta12orEarlier + identifier + Identifier of an entry from a database of biological pathways or networks. + + + + + + + + Workflow ID + + + + + + + + + bioinformatics + identifiers + data + beta12orEarlier + edam + Identifier of a biological or biomedical workflow, typically from a database of workflows. + identifier + + + + + + + + Data resource definition identifier + + identifier + Identifier of a data type definition from some provider. + identifiers + bioinformatics + data + beta12orEarlier + edam + + + + + + + + Biological model identifier + + + + + + + + beta12orEarlier + Identifier of a mathematical model, typically an entry from a database. + bioinformatics + identifiers + data + edam + identifier + + + + + + + + Compound identifier + + + + + + + + + + + + + + + + + + + + beta12orEarlier + identifier + Small molecule identifier + Identifier of an entry from a database of chemicals. + edam + bioinformatics + Chemical compound identifier + data + identifiers + + + + + + + + Ontology concept ID + + + A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. + identifier + bioinformatics + Ontology concept ID + edam + beta12orEarlier + data + identifiers + + + + + + + + Article ID + + + + + + + + + identifier + Unique identifier of a scientific article. + data + bioinformatics + identifiers + beta12orEarlier + edam + + + + + + + + FlyBase ID + + + edam + identifier + data + identifiers + bioinformatics + FB[a-zA-Z_0-9]{2}[0-9]{7} + beta12orEarlier + Identifier of an object from the FlyBase database. + + + + + + + + WormBase name + + + edam + data + identifier + identifiers + beta12orEarlier + Name of an object from the WormBase database, usually a human-readable name. + bioinformatics + + + + + + + + WormBase class + + data + A WormBase class describes the type of object such as 'sequence' or 'protein'. + edam + bioinformatics + Class of an object from the WormBase database. + identifier + identifiers + beta12orEarlier + + + + + + + + Sequence accession + + + + Sequence accession number + data + identifiers + bioinformatics + identifier + A persistent, unique identifier of a molecular sequence database entry. + beta12orEarlier + edam + + + + + + + + Sequence type + + + + data + edam + Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). + A label (text token) describing a type of molecular sequence. + beta12orEarlier + bioinformatics + data + + + + + + + + EMBOSS Uniform Sequence Address + + + bioinformatics + beta12orEarlier + data + identifiers + edam + The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. + EMBOSS USA + identifier + + + + + + + + Sequence accession (protein) + + + + + + + + beta12orEarlier + identifiers + Protein sequence accession number + data + bioinformatics + edam + Accession number of a protein sequence database entry. + identifier + + + + + + + + Sequence accession (nucleic acid) + + + + + + + + beta12orEarlier + Accession number of a nucleotide sequence database entry. + bioinformatics + data + Nucleotide sequence accession number + identifier + identifiers + edam + + + + + + + + RefSeq accession + + RefSeq ID + identifiers + beta12orEarlier + identifier + Accession number of a RefSeq database entry. + (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ + data + edam + bioinformatics + + + + + + + + UniProt accession (extended) + + true + bioinformatics + 1.0 + Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. + [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+ + data + edam + identifiers + Q7M1G0|P43353-2|P01012.107 + beta12orEarlier + identifier + + + + + + + + + PIR identifier + + + + + + + + edam + PIR ID + beta12orEarlier + identifiers + An identifier of PIR sequence database entry. + PIR accession number + data + bioinformatics + identifier + + + + + + + + TREMBL accession + + true + data + identifier + bioinformatics + identifiers + 1.2 + edam + Identifier of a TREMBL sequence database entry. + beta12orEarlier + + + + + + + + + + Gramene primary identifier + + Primary identifier of a Gramene database entry. + data + identifiers + Gramene primary ID + edam + identifier + bioinformatics + beta12orEarlier + + + + + + + + EMBL/GenBank/DDBJ ID + + beta12orEarlier + identifiers + Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. + data + identifier + bioinformatics + edam + + + + + + + + Sequence cluster ID (UniGene) + + A unique identifier of an entry (gene cluster) from the NCBI UniGene database. + UniGene cluster ID + bioinformatics + UniGene identifier + edam + identifiers + beta12orEarlier + identifier + UniGene ID + UniGene cluster id + data + + + + + + + + dbEST accession + + + beta12orEarlier + identifier + data + dbEST ID + edam + Identifier of a dbEST database entry. + identifiers + bioinformatics + + + + + + + + dbSNP ID + + Identifier of a dbSNP database entry. + data + edam + dbSNP identifier + bioinformatics + beta12orEarlier + identifier + identifiers + + + + + + + + EMBOSS sequence type + + true + edam + identifiers + bioinformatics + data + The EMBOSS type of a molecular sequence. + beta12orEarlier + identifier + See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. + beta12orEarlier + + + + + + + + + EMBOSS listfile + + bioinformatics + data + beta12orEarlier + List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). + edam + data + + + + + + + + Sequence cluster ID + + + + + + + + identifier + beta12orEarlier + edam + identifiers + data + An identifier of a cluster of molecular sequence(s). + bioinformatics + + + + + + + + Sequence cluster ID (COG) + + identifier + identifiers + bioinformatics + edam + Unique identifier of an entry from the COG database. + beta12orEarlier + data + COG ID + + + + + + + + Sequence motif identifier + + + + + + + + identifier + beta12orEarlier + edam + identifiers + bioinformatics + data + Identifier of a sequence motif, for example an entry from a motif database. + + + + + + + + Sequence profile ID + + + + + + + + + A sequence profile typically represents a sequence alignment. + edam + Identifier of a sequence profile. + identifier + data + bioinformatics + identifiers + beta12orEarlier + + + + + + + + ELM ID + + bioinformatics + beta12orEarlier + data + Identifier of an entry from the ELMdb database of protein functional sites. + edam + identifier + identifiers + + + + + + + + Prosite accession number + + Prosite ID + edam + PS[0-9]{5} + data + Accession number of an entry from the Prosite database. + bioinformatics + identifiers + identifier + beta12orEarlier + + + + + + + + HMMER hidden Markov model ID + + + + + + + + identifiers + edam + beta12orEarlier + data + Unique identifier or name of a HMMER hidden Markov model. + identifier + bioinformatics + + + + + + + + JASPAR profile ID + + Unique identifier or name of a profile from the JASPAR database. + bioinformatics + data + identifier + beta12orEarlier + identifiers + edam + + + + + + + + Sequence alignment type + + + bioinformatics + data + A label (text token) describing the type of a sequence alignment. + Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. + data + edam + beta12orEarlier + + + + + + + + BLAST sequence alignment type + + true + The type of a BLAST sequence alignment. + identifiers + bioinformatics + edam + beta12orEarlier + data + beta12orEarlier + identifier + + + + + + + + + Phylogenetic tree type + + + nj|upgmp + data + edam + A label (text token) describing the type of a phylogenetic tree. + bioinformatics + data + beta12orEarlier + For example 'nj', 'upgmp' etc. + + + + + + + + TreeBASE study accession number + + bioinformatics + identifier + identifiers + beta12orEarlier + data + edam + Accession number of an entry from the TreeBASE database. + + + + + + + + TreeFam accession number + + identifiers + edam + data + Accession number of an entry from the TreeFam database. + bioinformatics + identifier + beta12orEarlier + + + + + + + + Comparison matrix type + + + For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. + A label (text token) describing the type of a comparison matrix. + Substitution matrix type + beta12orEarlier + bioinformatics + blosum|pam|gonnet|id + data + edam + data + + + + + + + + Comparison matrix name + + + + + + + + + Unique name or identifier of a comparison matrix. + identifiers + identifier + Substitution matrix name + bioinformatics + edam + See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. + data + beta12orEarlier + + + + + + + + PDB ID + + edam + identifier + [a-zA-Z_0-9]{4} + identifiers + beta12orEarlier + PDB identifier + bioinformatics + data + PDBID + An identifier of an entry from the PDB database. + + + + + + + + AAindex ID + + data + edam + Identifier of an entry from the AAindex database. + bioinformatics + identifier + beta12orEarlier + identifiers + + + + + + + + BIND accession number + + data + beta12orEarlier + Accession number of an entry from the BIND database. + identifier + edam + bioinformatics + identifiers + + + + + + + + IntAct accession number + + data + identifier + Accession number of an entry from the IntAct database. + edam + beta12orEarlier + bioinformatics + identifiers + EBI\-[0-9]+ + + + + + + + + Protein family name + + + Name of a protein family. + identifiers + identifier + beta12orEarlier + data + edam + bioinformatics + + + + + + + + InterPro entry name + + + + + + + + identifier + edam + identifiers + data + Name of an InterPro entry, usually indicating the type of protein matches for that entry. + beta12orEarlier + bioinformatics + + + + + + + + InterPro accession + + + + + + + + IPR[0-9]{6} + bioinformatics + IPR015590 + edam + identifier + InterPro primary accession number + beta12orEarlier + Every InterPro entry has a unique accession number to provide a persistent citation of database records. + data + InterPro primary accession + identifiers + Primary accession number of an InterPro entry. + + + + + + + + InterPro secondary accession + + + + + + + + identifiers + Secondary accession number of an InterPro entry. + identifier + InterPro secondary accession number + bioinformatics + data + beta12orEarlier + edam + + + + + + + + Gene3D ID + + identifiers + bioinformatics + Unique identifier of an entry from the Gene3D database. + identifier + edam + beta12orEarlier + data + + + + + + + + PIRSF ID + + Unique identifier of an entry from the PIRSF database. + identifiers + edam + beta12orEarlier + bioinformatics + identifier + PIRSF[0-9]{6} + data + + + + + + + + PRINTS code + + The unique identifier of an entry in the PRINTS database. + edam + PR[0-9]{5} + data + identifier + identifiers + beta12orEarlier + bioinformatics + + + + + + + + Pfam accession number + + beta12orEarlier + data + edam + identifier + bioinformatics + Accession number of a Pfam entry. + PF[0-9]{5} + identifiers + + + + + + + + SMART accession number + + data + SM[0-9]{5} + beta12orEarlier + identifier + bioinformatics + identifiers + Accession number of an entry from the SMART database. + edam + + + + + + + + Superfamily hidden Markov model number + + identifiers + beta12orEarlier + data + Unique identifier (number) of a hidden Markov model from the Superfamily database. + identifier + bioinformatics + edam + + + + + + + + TIGRFam ID + + identifier + beta12orEarlier + Accession number of an entry (family) from the TIGRFam database. + identifiers + edam + TIGRFam accession number + data + bioinformatics + + + + + + + + ProDom accession number + + beta12orEarlier + identifiers + bioinformatics + data + ProDom is a protein domain family database. + PD[0-9]+ + edam + identifier + A ProDom domain family accession number. + + + + + + + + TRANSFAC accession number + + edam + identifiers + Identifier of an entry from the TRANSFAC database. + identifier + beta12orEarlier + bioinformatics + data + + + + + + + + ArrayExpress accession number + + [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ + bioinformatics + identifiers + edam + ArrayExpress experiment ID + beta12orEarlier + identifier + data + Accession number of an entry from the ArrayExpress database. + + + + + + + + PRIDE experiment accession number + + identifier + PRIDE experiment accession number. + beta12orEarlier + identifiers + [0-9]+ + bioinformatics + edam + data + + + + + + + + EMDB ID + + bioinformatics + edam + data + Identifier of an entry from the EMDB electron microscopy database. + identifiers + beta12orEarlier + identifier + + + + + + + + GEO accession number + + beta12orEarlier + data + edam + o^GDS[0-9]+ + bioinformatics + identifiers + identifier + Accession number of an entry from the GEO database. + + + + + + + + GermOnline ID + + bioinformatics + identifier + data + beta12orEarlier + Identifier of an entry from the GermOnline database. + edam + identifiers + + + + + + + + EMAGE ID + + data + identifiers + identifier + beta12orEarlier + bioinformatics + edam + Identifier of an entry from the EMAGE database. + + + + + + + + Disease ID + + + + + + + + + bioinformatics + beta12orEarlier + Identifier of an entry from a database of disease. + edam + data + identifier + identifiers + + + + + + + + HGVbase ID + + data + beta12orEarlier + identifiers + Identifier of an entry from the HGVbase database. + identifier + bioinformatics + edam + + + + + + + + HIVDB identifier + + true + Identifier of an entry from the HIVDB database. + beta12orEarlier + identifier + bioinformatics + beta12orEarlier + identifiers + edam + data + + + + + + + + + OMIM ID + + Identifier of an entry from the OMIM database. + [*#+%^]?[0-9]{6} + identifiers + bioinformatics + edam + beta12orEarlier + identifier + data + + + + + + + + KEGG object identifier + + + bioinformatics + data + Unique identifier of an object from one of the KEGG databases (excluding the GENES division). + identifier + edam + beta12orEarlier + identifiers + + + + + + + + Pathway ID (reactome) + + identifier + identifiers + bioinformatics + data + Reactome ID + edam + beta12orEarlier + REACT_[0-9]+(\.[0-9]+)? + Identifier of an entry from the Reactome database. + + + + + + + + Pathway ID (aMAZE) + + true + identifier + Identifier of an entry from the aMAZE database. + bioinformatics + beta12orEarlier + identifiers + aMAZE ID + beta12orEarlier + data + edam + + + + + + + + + Pathway ID (BioCyc) + + + edam + identifiers + data + Identifier of an pathway from the BioCyc biological pathways database. + identifier + beta12orEarlier + bioinformatics + BioCyc pathway ID + + + + + + + + Pathway ID (INOH) + + bioinformatics + identifiers + Identifier of an entry from the INOH database. + INOH identifier + identifier + edam + beta12orEarlier + data + + + + + + + + Pathway ID (PATIKA) + + edam + beta12orEarlier + identifiers + identifier + bioinformatics + PATIKA ID + Identifier of an entry from the PATIKA database. + data + + + + + + + + Pathway ID (CPDB) + + beta12orEarlier + identifiers + data + bioinformatics + CPDB ID + This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. + edam + identifier + Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB. + + + + + + + + Pathway ID (Panther) + + beta12orEarlier + data + Identifier of a biological pathway from the Panther Pathways database. + identifier + bioinformatics + edam + Panther Pathways ID + PTHR[0-9]{5} + identifiers + + + + + + + + MIRIAM identifier + + + + + + + + MIR:[0-9]{8} + identifier + MIR:00100005 + edam + Unique identifier of a MIRIAM data resource. + This is the identifier used internally by MIRIAM for a data type. + beta12orEarlier + data + bioinformatics + identifiers + + + + + + + + MIRIAM data type name + + + + + + + + identifier + The name of a data type from the MIRIAM database. + data + identifiers + beta12orEarlier + edam + bioinformatics + + + + + + + + MIRIAM URI + + + + + + + + + identifier + urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 + A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. + data + identifiers + The URI (URL or URN) of a data entity from the MIRIAM database. + beta12orEarlier + bioinformatics + edam + + + + + + + + MIRIAM data type primary name + + bioinformatics + identifiers + The primary name of a MIRIAM data type is taken from a controlled vocabulary. + UniProt|Enzyme Nomenclature + data + edam + The primary name of a data type from the MIRIAM database. + beta12orEarlier + identifier + + + A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. + UniProt|Enzyme Nomenclature + + + + + + + + + + MIRIAM data type synonymous name + + identifiers + bioinformatics + data + beta12orEarlier + identifier + edam + A synonymous name for a MIRIAM data type taken from a controlled vocabulary. + A synonymous name of a data type from the MIRIAM database. + + + + + + + + Taverna workflow ID + + identifier + identifiers + bioinformatics + Unique identifier of a Taverna workflow. + edam + data + beta12orEarlier + + + + + + + + Biological model name + + + data + identifiers + identifier + Name of a biological (mathematical) model. + bioinformatics + beta12orEarlier + edam + + + + + + + + BioModel ID + + (BIOMD|MODEL)[0-9]{10} + data + identifier + bioinformatics + edam + beta12orEarlier + Unique identifier of an entry from the BioModel database. + identifiers + + + + + + + + PubChem CID + + + identifier + beta12orEarlier + edam + Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure. + bioinformatics + PubChem compound accession identifier + [0-9]+ + identifiers + data + + + + + + + + ChemSpider ID + + identifier + bioinformatics + edam + [0-9]+ + beta12orEarlier + data + Identifier of an entry from the ChemSpider database. + identifiers + + + + + + + + ChEBI ID + + beta12orEarlier + identifiers + edam + bioinformatics + CHEBI:[0-9]+ + identifier + data + ChEBI identifier + Identifier of an entry from the ChEBI database. + + + + + + + + BioPax concept ID + + identifier + An identifier of a concept from the BioPax ontology. + beta12orEarlier + bioinformatics + identifiers + data + edam + + + + + + + + GO concept ID + + data + [0-9]{7}|GO:[0-9]{7} + identifiers + edam + An identifier of a concept from The Gene Ontology. + beta12orEarlier + bioinformatics + identifier + GO concept identifier + + + + + + + + MeSH concept ID + + identifiers + identifier + edam + data + bioinformatics + An identifier of a concept from the MeSH vocabulary. + beta12orEarlier + + + + + + + + HGNC concept ID + + identifier + An identifier of a concept from the HGNC controlled vocabulary. + beta12orEarlier + data + edam + bioinformatics + identifiers + + + + + + + + NCBI taxonomy ID + + beta12orEarlier + identifier + 9662|3483|182682 + A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database. + NCBI tax ID + edam + [1-9][0-9]{0,8} + data + identifiers + NCBI taxonomy identifier + bioinformatics + + + + + + + + Plant Ontology concept ID + + data + beta12orEarlier + identifier + bioinformatics + edam + An identifier of a concept from the Plant Ontology (PO). + identifiers + + + + + + + + UMLS concept ID + + identifier + beta12orEarlier + identifiers + An identifier of a concept from the UMLS vocabulary. + bioinformatics + edam + data + + + + + + + + FMA concept ID + + identifier + Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. + An identifier of a concept from Foundational Model of Anatomy. + FMA:[0-9]+ + beta12orEarlier + bioinformatics + edam + data + identifiers + + + + + + + + EMAP concept ID + + identifier + identifiers + edam + An identifier of a concept from the EMAP mouse ontology. + data + beta12orEarlier + bioinformatics + + + + + + + + ChEBI concept ID + + bioinformatics + edam + data + An identifier of a concept from the ChEBI ontology. + identifiers + identifier + beta12orEarlier + + + + + + + + MGED concept ID + + data + bioinformatics + identifiers + edam + identifier + An identifier of a concept from the MGED ontology. + beta12orEarlier + + + + + + + + myGrid concept ID + + An identifier of a concept from the myGrid ontology. + The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. + edam + beta12orEarlier + data + identifier + identifiers + bioinformatics + + + + + + + + PubMed ID + + 4963447 + beta12orEarlier + edam + PubMed unique identifier of an article. + data + [1-9][0-9]{0,8} + bioinformatics + identifier + PMID + identifiers + + + + + + + + Digital Object Identifier + + data + bioinformatics + Digital Object Identifier (DOI) of a published article. + identifier + (doi\:)?[0-9]{2}\.[0-9]{4}/.* + identifiers + beta12orEarlier + edam + + + + + + + + Medline UI + + identifier + The use of Medline UI has been replaced by the PubMed unique identifier. + Medline UI (unique identifier) of an article. + beta12orEarlier + edam + Medline unique identifier + identifiers + data + bioinformatics + + + + + + + + Tool name + + identifier + bioinformatics + data + beta12orEarlier + The name of a computer package, application, method or function. + identifiers + edam + + + + + + + + Tool name (signature) + + Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. + edam + bioinformatics + identifiers + The unique name of a signature (sequence classifier) method. + identifier + data + beta12orEarlier + + + + + + + + Tool name (BLAST) + + BLAST name + beta12orEarlier + The name of a BLAST tool. + identifiers + edam + data + bioinformatics + identifier + This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. + + + + + + + + Tool name (FASTA) + + identifiers + This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. + identifier + edam + data + bioinformatics + The name of a FASTA tool. + beta12orEarlier + + + + + + + + Tool name (EMBOSS) + + bioinformatics + edam + identifier + beta12orEarlier + data + identifiers + The name of an EMBOSS application. + + + + + + + + Tool name (EMBASSY package) + + beta12orEarlier + The name of an EMBASSY package. + bioinformatics + identifier + identifiers + edam + data + + + + + + + + QSAR descriptor (constitutional) + + QSAR constitutional descriptor + bioinformatics + edam + data + beta12orEarlier + data + A QSAR constitutional descriptor. + + + + + + + + QSAR descriptor (electronic) + + data + QSAR electronic descriptor + bioinformatics + data + A QSAR electronic descriptor. + edam + beta12orEarlier + + + + + + + + QSAR descriptor (geometrical) + + bioinformatics + beta12orEarlier + edam + A QSAR geometrical descriptor. + data + data + QSAR geometrical descriptor + + + + + + + + QSAR descriptor (topological) + + edam + A QSAR topological descriptor. + QSAR topological descriptor + data + bioinformatics + data + beta12orEarlier + + + + + + + + QSAR descriptor (molecular) + + data + edam + QSAR molecular descriptor + beta12orEarlier + data + A QSAR molecular descriptor. + bioinformatics + + + + + + + + Sequence set (protein) + + beta12orEarlier + data + bioinformatics + edam + data + Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. + + + + + + + + Sequence set (nucleic acid) + + + data + data + edam + Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. + beta12orEarlier + bioinformatics + + + + + + + + Sequence cluster + + + + + + + + + + + + + + beta12orEarlier + The cluster might include sequences identifiers, short descriptions, alignment and summary information. + bioinformatics + edam + data + data + A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. + + + + + + + + Psiblast checkpoint file + + true + A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. + bioinformatics + beta12orEarlier + A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. + beta12orEarlier + edam + data + data + + + + + + + + + HMMER synthetic sequences set + + true + beta12orEarlier + data + beta12orEarlier + Sequences generated by HMMER package in FASTA-style format. + bioinformatics + edam + data + + + + + + + + + Proteolytic digest + + + + + + + + edam + data + A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. + beta12orEarlier + bioinformatics + data + + + + + + + + Restriction digest + + beta12orEarlier + data + data + edam + SO:0000412 + Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. + bioinformatics + + + + + + + + PCR primers + + bioinformatics + edam + data + Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. + data + beta12orEarlier + + + + + + + + vectorstrip cloning vector definition file + + true + beta12orEarlier + File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. + data + edam + data + bioinformatics + beta12orEarlier + + + + + + + + + Primer3 internal oligo mishybridizing library + + true + beta12orEarlier + bioinformatics + edam + data + A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. + beta12orEarlier + data + + + + + + + + + Primer3 mispriming library file + + true + edam + beta12orEarlier + data + beta12orEarlier + data + A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format. + bioinformatics + + + + + + + + + primersearch primer pairs sequence record + + true + data + edam + File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. + beta12orEarlier + bioinformatics + beta12orEarlier + data + + + + + + + + + Sequence cluster (protein) + + + beta12orEarlier + Protein sequence cluster + bioinformatics + A cluster of protein sequences. + data + The sequences are typically related, for example a family of sequences. + edam + data + + + + + + + + Sequence cluster (nucleic acid) + + + bioinformatics + beta12orEarlier + Nucleotide sequence cluster + data + data + The sequences are typically related, for example a family of sequences. + A cluster of nucleotide sequences. + edam + + + + + + + + Sequence length + + edam + data + data + beta12orEarlier + The size (length) of a sequence, subsequence or region in a sequence. + bioinformatics + + + + + + + + Word size + + data + data + edam + beta12orEarlier + Size of a sequence word. + bioinformatics + Word length + Word size is used for example in word-based sequence database search methods. + + + + + + + + Window size + + edam + Size of a sequence window. + data + beta12orEarlier + A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. + data + bioinformatics + + + + + + + + Sequence length range + + data + Specification of range(s) of length of sequences. + beta12orEarlier + data + bioinformatics + edam + + + + + + + + Sequence information report + + true + edam + bioinformatics + Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. + beta12orEarlier + data + beta12orEarlier + data + + + + + + + + + + Sequence property + + Sequence properties report + edam + An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis. + data + bioinformatics + data + beta12orEarlier + + + + + + + + Feature record + + Sequence features + Features + Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. + data + edam + data + General sequence features + This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. + SO:0000110 + bioinformatics + beta12orEarlier + Sequence features report + + + + + + + + + Sequence features (comparative) + + true + bioinformatics + beta12orEarlier + data + edam + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + beta13 + Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc. + data + + + + + + + + + Sequence property (protein) + + true + data + beta12orEarlier + data + bioinformatics + beta12orEarlier + edam + A report of general sequence properties derived from protein sequence data. + + + + + + + + + Sequence property (nucleic acid) + + true + beta12orEarlier + edam + data + A report of general sequence properties derived from nucleotide sequence data. + beta12orEarlier + data + bioinformatics + + + + + + + + + Sequence complexity + + bioinformatics + Sequence property (complexity) + data + edam + beta12orEarlier + data + A report on sequence complexity, for example low-complexity or repeat regions in sequences. + + + + + + + + Sequence ambiguity + + beta12orEarlier + bioinformatics + Sequence property (ambiguity) + A report on ambiguity in molecular sequence(s). + edam + data + data + + + + + + + + Sequence composition + + Sequence property (composition) + edam + data + bioinformatics + data + A report (typically a table) on character or word composition / frequency of a molecular sequence(s). + beta12orEarlier + + + + + + + + Peptide molecular weight hits + + edam + data + beta12orEarlier + data + bioinformatics + A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. + + + + + + + + Sequence composition (base position variability) + + data + edam + data + bioinformatics + Report on or plot of third base position variability in a nucleotide sequence. + beta12orEarlier + + + + + + + + Sequence composition table + + true + data + beta12orEarlier + data + edam + beta12orEarlier + A table of character or word composition / frequency of a molecular sequence. + bioinformatics + + + + + + + + + Sequence composition (base frequencies) + + bioinformatics + data + edam + A table of base frequencies of a nucleotide sequence. + data + beta12orEarlier + + + + + + + + Sequence composition (base words) + + data + edam + data + A table of word composition of a nucleotide sequence. + beta12orEarlier + bioinformatics + + + + + + + + Amino acid frequencies + + data + data + A table of amino acid frequencies of a protein sequence. + beta12orEarlier + bioinformatics + Sequence composition (amino acid frequencies) + edam + + + + + + + + Amino acid word frequencies + + data + edam + beta12orEarlier + Sequence composition (amino acid words) + bioinformatics + data + A table of amino acid word composition of a protein sequence. + + + + + + + + DAS sequence feature annotation + + true + edam + data + beta12orEarlier + bioinformatics + Annotation of a molecular sequence in DAS format. + beta12orEarlier + data + + + + + + + + + Sequence feature table + + Feature table + Annotation of positional sequence features, organized into a standard feature table. + data + beta12orEarlier + edam + bioinformatics + data + + + + + + + + Map + + + + + + + + bioinformatics + A map of (typically one) DNA sequence annotated with positional or non-positional features. + data + beta12orEarlier + DNA map + edam + data + + + + + + + + Nucleic acid features + + + edam + bioinformatics + Feature table (nucleic acid) + Nucleic acid feature table + Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence). + data + This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. + data + beta12orEarlier + + + + + + + + Protein features + + + Protein feature table + This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. + edam + data + Feature table (protein) + bioinformatics + data + Protein sequence-specific feature annotation (positional features of a protein sequence). + beta12orEarlier + + + + + + + + Genetic map + + + + + + + + Moby:GeneticMap + Linkage map + beta12orEarlier + data + edam + A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. + data + bioinformatics + A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies. + + + + + + + + Sequence map + + A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs. + data + data + beta12orEarlier + bioinformatics + A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. + edam + + + + + + + + Physical map + + data + beta12orEarlier + bioinformatics + Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. + edam + data + A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them. + + + + + + + + Sequence signature map + + true + bioinformatics + beta12orEarlier + edam + beta12orEarlier + data + data + Image of a sequence with matches to signatures, motifs or profiles. + + + + + + + + + Cytogenetic map + + bioinformatics + This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. + Cytogenic map + data + Chromosome map + edam + Cytologic map + A map showing banding patterns derived from direct observation of a stained chromosome. + data + beta12orEarlier + + + + + + + + DNA transduction map + + A gene map showing distances between loci based on relative cotransduction frequencies. + data + data + bioinformatics + beta12orEarlier + edam + + + + + + + + Gene map + + beta12orEarlier + data + edam + data + Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene. + bioinformatics + + + + + + + + Plasmid map + + beta12orEarlier + Sequence map of a plasmid (circular DNA). + bioinformatics + data + data + edam + + + + + + + + Genome map + + edam + bioinformatics + data + data + Sequence map of a whole genome. + beta12orEarlier + + + + + + + + Restriction map + + + + data + data + beta12orEarlier + Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. + bioinformatics + edam + + + + + + + + InterPro compact match image + + true + edam + data + data + bioinformatics + beta12orEarlier + The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. + Image showing matches between protein sequence(s) and InterPro Entries. + beta12orEarlier + + + + + + + + + InterPro detailed match image + + true + The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. + Image showing detailed information on matches between protein sequence(s) and InterPro Entries. + beta12orEarlier + data + edam + bioinformatics + data + beta12orEarlier + + + + + + + + + InterPro architecture image + + true + bioinformatics + beta12orEarlier + data + Image showing the architecture of InterPro domains in a protein sequence. + The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. + data + edam + beta12orEarlier + + + + + + + + + SMART protein schematic + + true + SMART protein schematic in PNG format. + beta12orEarlier + beta12orEarlier + edam + data + data + bioinformatics + + + + + + + + + GlobPlot domain image + + true + data + bioinformatics + edam + Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. + beta12orEarlier + beta12orEarlier + data + + + + + + + + + Sequence features (motifs) + + data + Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. + beta12orEarlier + Use this concept if another, more specific concept is not available. + bioinformatics + data + edam + + + + + + + + Sequence features (repeats) + + data + data + Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. + The report might include derived data map such as classification, annotation, organization, periodicity etc. + Repeat sequence map + edam + beta12orEarlier + bioinformatics + + + + + + + + Nucleic acid features (gene and transcript structure) + + + edam + bioinformatics + data + A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. + beta12orEarlier + data + Gene annotation (structure) + + + + + + + + Nucleic acid features (mobile genetic elements) + + data + data + edam + beta12orEarlier + A report on a region of a nucleic acid sequence containin mobile genetic elements. + Nucleic acid features (transposons) + This includes transposons, Plasmids, Bacteriophage elements and Group II introns. + bioinformatics + + + + + + + + Nucleic acid features (PolyA signal or site) + + beta12orEarlier + A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. + bioinformatics + data + A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. + data + PolyA site + PolyA signal + edam + + + + + + + + Nucleic acid features (quadruplexes) + + beta12orEarlier + data + bioinformatics + data + A report on quadruplex-forming motifs in a nucleotide sequence. + edam + + + + + + + + Nucleic acid features (CpG island and isochore) + + data + A report or plot of CpG rich regions (isochores) in a nucleotide sequence. + bioinformatics + beta12orEarlier + edam + data + + + + + + + + Nucleic acid features (restriction sites) + + bioinformatics + data + Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. + edam + data + beta12orEarlier + + + + + + + + Nucleic acid features (nucleosome exclusion sequences) + + A report on nucleosome formation potential or exclusion sequence(s). + data + beta12orEarlier + edam + bioinformatics + data + + + + + + + + Nucleic acid features (splice sites) + + Nucleic acid report (RNA splicing) + Nucleic acid report (RNA splice model) + bioinformatics + data + data + beta12orEarlier + A report on splice sites in a nucleotide sequence or alternative RNA splicing events. + edam + + + + + + + + Nucleic acid features (matrix/scaffold attachment sites) + + edam + data + beta12orEarlier + bioinformatics + A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. + data + + + + + + + + Gene features (exonic splicing enhancer) + + true + data + A report on exonic splicing enhancers (ESE) in an exon. + edam + bioinformatics + beta13 + beta12orEarlier + data + + + + + + + + + Nucleic acid features (microRNA) + + + + + + + + data + A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. + edam + beta12orEarlier + data + bioinformatics + + + + + + + + Nucleic acid features (operon) + + data + beta12orEarlier + A report on operons (operators, promoters and genes) from a bacterial genome. + edam + bioinformatics + The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. + Gene features (operon) + data + + + + + + + + Gene features (promoter) + + beta12orEarlier + data + data + A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. + edam + bioinformatics + + + + + + + + Nucleic acid features (coding sequence) + + Gene features (coding sequence) + beta12orEarlier + Gene features (coding region) + A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. + Gene annotation (translation) + bioinformatics + data + edam + data + + + + + + + + Gene features (SECIS element) + + true + data + data + beta13 + A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. + beta12orEarlier + edam + bioinformatics + + + + + + + + + Gene features (TFBS) + + + + + + + + + data + A report on the transcription factor binding sites (TFBS) in a DNA sequence. + bioinformatics + data + edam + beta12orEarlier + + + + + + + + Protein features (sites) + + true + A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites. + bioinformatics + beta12orEarlier + beta12orEarlier + data + Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. + edam + data + + + + + + + + + Protein features (signal peptides) + + beta12orEarlier + edam + A report on the location of signal peptides or signal peptide cleavage sites in protein sequences. + data + bioinformatics + data + + + + + + + + Protein features (cleavage sites) + + + + + + + + data + bioinformatics + edam + beta12orEarlier + A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. + data + + + + + + + + Protein features (post-translation modifications) + + data + data + Post-translation modification + beta12orEarlier + bioinformatics + A report on post-translation modifications in a protein sequence, typically describing the specific sites involved. + edam + Protein features (post-translation modification sites) + + + + + + + + Protein features (active sites) + + data + beta12orEarlier + Enzyme active site + A report on catalytic residues (active site) of an enzyme. + data + edam + bioinformatics + + + + + + + + Protein features (binding sites) + + bioinformatics + A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. + beta12orEarlier + data + data + edam + + + + + + + + Protein features (epitopes) + + true + A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. + beta13 + data + Epitope mapping is commonly done during vaccine design. + beta12orEarlier + bioinformatics + edam + data + + + + + + + + + Protein features (nucleic acid binding sites) + + bioinformatics + beta12orEarlier + edam + data + data + A report on RNA and DNA-binding proteins and binding sites in protein sequences. + + + + + + + + MHC Class I epitopes report + + true + data + edam + A report on epitopes that bind to MHC class I molecules. + beta12orEarlier + bioinformatics + data + beta12orEarlier + + + + + + + + + MHC Class II epitopes report + + true + A report on predicted epitopes that bind to MHC class II molecules. + data + data + beta12orEarlier + beta12orEarlier + edam + bioinformatics + + + + + + + + + Protein features (PEST sites) + + true + data + bioinformatics + beta13 + 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. + data + edam + A report or plot of PEST sites in a protein sequence. + beta12orEarlier + + + + + + + + + Sequence database hits scores list + + true + data + beta12orEarlier + bioinformatics + edam + beta12orEarlier + Scores from a sequence database search (for example a BLAST search). + data + + + + + + + + + Sequence database hits alignments list + + true + edam + beta12orEarlier + data + Alignments from a sequence database search (for example a BLAST search). + beta12orEarlier + bioinformatics + data + + + + + + + + + Sequence database hits evaluation data + + true + data + data + bioinformatics + edam + beta12orEarlier + A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). + beta12orEarlier + + + + + + + + + MEME motif alphabet + + true + bioinformatics + data + data + beta12orEarlier + beta12orEarlier + Alphabet for the motifs (patterns) that MEME will search for. + edam + + + + + + + + + MEME background frequencies file + + true + beta12orEarlier + data + beta12orEarlier + bioinformatics + edam + data + MEME background frequencies file. + + + + + + + + + MEME motifs directive file + + true + beta12orEarlier + edam + File of directives for ordering and spacing of MEME motifs. + data + beta12orEarlier + data + bioinformatics + + + + + + + + + Dirichlet distribution + + data + data + edam + bioinformatics + beta12orEarlier + Dirichlet distribution used by hidden Markov model analysis programs. + + + + + + + + HMM emission and transition counts + + bioinformatics + beta12orEarlier + data + Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states. + data + edam + + + + + + + + Regular expression + + bioinformatics + beta12orEarlier + data + Regular expression pattern. + data + edam + + + + + + + + Sequence motif + + + + + + + + edam + bioinformatics + Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. + data + beta12orEarlier + data + + + + + + + + Sequence profile + + + + + + + + edam + bioinformatics + data + data + beta12orEarlier + Some type of statistical model representing a (typically multiple) sequence alignment. + + + + + + + + + Protein signature + + data + edam + beta12orEarlier + InterPro entry + data + An entry (sequence classifier and associated data) from the InterPro database. + bioinformatics + + + + + + + + Prosite nucleotide pattern + + true + beta12orEarlier + data + A nucleotide regular expression pattern from the Prosite database. + beta12orEarlier + bioinformatics + data + edam + + + + + + + + + Prosite protein pattern + + true + beta12orEarlier + data + edam + beta12orEarlier + bioinformatics + data + A protein regular expression pattern from the Prosite database. + + + + + + + + + Position frequency matrix + + PFM + A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. + bioinformatics + beta12orEarlier + edam + data + data + + + + + + + + Position weight matrix + + Contributions of individual sequences to the matrix might be uneven (weighted). + data + A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. + data + edam + beta12orEarlier + PWM + bioinformatics + + + + + + + + Information content matrix + + edam + A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position. + data + ICM + bioinformatics + data + beta12orEarlier + + + + + + + + Hidden Markov model + + edam + data + data + A hidden Markov model representation of a set or alignment of sequences. + beta12orEarlier + bioinformatics + HMM + + + + + + + + Fingerprint + + bioinformatics + One or more fingerprints (sequence classifiers) as used in the PRINTS database. + data + edam + data + beta12orEarlier + + + + + + + + Domainatrix signature + + true + beta12orEarlier + beta12orEarlier + bioinformatics + data + edam + A protein signature of the type used in the EMBASSY Signature package. + data + + + + + + + + + HMMER NULL hidden Markov model + + true + bioinformatics + NULL hidden Markov model representation used by the HMMER package. + data + data + beta12orEarlier + edam + beta12orEarlier + + + + + + + + + Protein family signature + + A protein family signature (sequence classifier) from the InterPro database. + data + data + bioinformatics + edam + beta12orEarlier + Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. + + + + + + + + Protein domain signature + + Protein domain signatures identify structural or functional domains or other units with defined boundaries. + bioinformatics + A protein domain signature (sequence classifier) from the InterPro database. + edam + data + beta12orEarlier + data + + + + + + + + Protein region signature + + A protein region signature defines a region which cannot be described as a protein family or domain signature. + bioinformatics + data + beta12orEarlier + A protein region signature (sequence classifier) from the InterPro database. + edam + data + + + + + + + + Protein repeat signature + + A protein repeat signature (sequence classifier) from the InterPro database. + beta12orEarlier + data + edam + A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. + data + bioinformatics + + + + + + + + Protein site signature + + edam + data + bioinformatics + A protein site signature (sequence classifier) from the InterPro database. + data + beta12orEarlier + A protein site signature is a classifier for a specific site in a protein. + + + + + + + + Protein conserved site signature + + beta12orEarlier + edam + A protein conserved site signature (sequence classifier) from the InterPro database. + bioinformatics + A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. + data + data + + + + + + + + Protein active site signature + + beta12orEarlier + edam + data + bioinformatics + data + A protein active site signature (sequence classifier) from the InterPro database. + A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. + + + + + + + + Protein binding site signature + + data + beta12orEarlier + A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. + data + bioinformatics + A protein binding site signature (sequence classifier) from the InterPro database. + edam + + + + + + + + Protein post-translational modification signature + + beta12orEarlier + A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. + A protein post-translational modification signature (sequence classifier) from the InterPro database. + data + bioinformatics + edam + data + + + + + + + + Sequence alignment (pair) + + data + Alignment of exactly two molecular sequences. + bioinformatics + beta12orEarlier + data + edam + + + + + + + + + Sequence alignment (multiple) + + true + data + edam + Alignment of more than two molecular sequences. + beta12orEarlier + beta12orEarlier + bioinformatics + data + + + + + + + + + Sequence alignment (nucleic acid) + + + data + Alignment of multiple nucleotide sequences. + edam + bioinformatics + data + beta12orEarlier + + + + + + + + Sequence alignment (protein) + + + bioinformatics + beta12orEarlier + data + edam + data + Alignment of multiple protein sequences. + + + + + + + + Sequence alignment (hybrid) + + data + bioinformatics + beta12orEarlier + Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. + data + Alignment of multiple molecular sequences of different types. + edam + + + + + + + + Sequence alignment (nucleic acid pair) + + + bioinformatics + Alignment of exactly two nucleotide sequences. + beta12orEarlier + data + edam + data + + + + + + + + Sequence alignment (protein pair) + + + beta12orEarlier + Alignment of exactly two protein sequences. + data + edam + bioinformatics + data + + + + + + + + Hybrid sequence alignment (pair) + + true + Alignment of exactly two molecular sequences of different types. + edam + bioinformatics + beta12orEarlier + data + data + beta12orEarlier + + + + + + + + + Multiple nucleotide sequence alignment + + true + edam + beta12orEarlier + data + Alignment of more than two nucleotide sequences. + bioinformatics + data + beta12orEarlier + + + + + + + + + Multiple protein sequence alignment + + true + data + edam + Alignment of more than two protein sequences. + beta12orEarlier + data + beta12orEarlier + bioinformatics + + + + + + + + + Alignment score or penalty + + + A simple floating point number defining the penalty for opening or extending a gap in an alignment. + data + edam + bioinformatics + data + beta12orEarlier + + + + + + + + Score end gaps control + + true + bioinformatics + edam + Whether end gaps are scored or not. + beta12orEarlier + beta12orEarlier + data + data + + + + + + + + + Aligned sequence order + + true + Controls the order of sequences in an output sequence alignment. + data + data + bioinformatics + edam + beta12orEarlier + beta12orEarlier + + + + + + + + + Gap opening penalty + + bioinformatics + beta12orEarlier + data + edam + A penalty for opening a gap in an alignment. + data + + + + + + + + Gap extension penalty + + edam + beta12orEarlier + data + A penalty for extending a gap in an alignment. + bioinformatics + data + + + + + + + + Gap separation penalty + + data + edam + bioinformatics + A penalty for gaps that are close together in an alignment. + data + beta12orEarlier + + + + + + + + Terminal gap penalty + + true + beta12orEarlier + data + bioinformatics + A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + data + edam + beta12orEarlier + + + + + + + + + + Match reward score + + The score for a 'match' used in various sequence database search applications with simple scoring schemes. + data + edam + beta12orEarlier + data + bioinformatics + + + + + + + + Mismatch penalty score + + The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. + beta12orEarlier + bioinformatics + data + edam + data + + + + + + + + Drop off score + + beta12orEarlier + data + bioinformatics + data + This is the threshold drop in score at which extension of word alignment is halted. + edam + + + + + + + + Gap opening penalty (integer) + + true + data + beta12orEarlier + A simple floating point number defining the penalty for opening a gap in an alignment. + beta12orEarlier + bioinformatics + edam + data + + + + + + + + + Gap opening penalty (float) + + true + A simple floating point number defining the penalty for opening a gap in an alignment. + beta12orEarlier + bioinformatics + beta12orEarlier + data + data + edam + + + + + + + + + Gap extension penalty (integer) + + true + edam + beta12orEarlier + beta12orEarlier + A simple floating point number defining the penalty for extending a gap in an alignment. + bioinformatics + data + data + + + + + + + + + Gap extension penalty (float) + + true + data + beta12orEarlier + edam + data + A simple floating point number defining the penalty for extending a gap in an alignment. + beta12orEarlier + bioinformatics + + + + + + + + + Gap separation penalty (integer) + + true + edam + beta12orEarlier + data + data + bioinformatics + beta12orEarlier + A simple floating point number defining the penalty for gaps that are close together in an alignment. + + + + + + + + + Gap separation penalty (float) + + true + A simple floating point number defining the penalty for gaps that are close together in an alignment. + data + bioinformatics + beta12orEarlier + data + beta12orEarlier + edam + + + + + + + + + Terminal gap opening penalty + + data + A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + edam + data + beta12orEarlier + bioinformatics + + + + + + + + Terminal gap extension penalty + + bioinformatics + data + data + edam + beta12orEarlier + A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + + + + + + + + Sequence identity + + beta12orEarlier + data + edam + bioinformatics + data + Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. + + + + + + + + Sequence similarity + + Data Type is float probably. + edam + Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension. + data + data + bioinformatics + beta12orEarlier + + + + + + + + Sequence alignment metadata (quality report) + + true + Data on molecular sequence alignment quality (estimated accuracy). + beta12orEarlier + edam + data + bioinformatics + data + beta12orEarlier + + + + + + + + + Sequence alignment report (site conservation) + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. + data + data + Data on character conservation in a molecular sequence alignment. + beta12orEarlier + edam + bioinformatics + + + + + + + + Sequence alignment report (site correlation) + + Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures. + beta12orEarlier + data + bioinformatics + edam + data + + + + + + + + Sequence-profile alignment (Domainatrix signature) + + true + beta12orEarlier + data + Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). + edam + beta12orEarlier + bioinformatics + data + + + + + + + + + Sequence-profile alignment (HMM) + + bioinformatics + data + Alignment of molecular sequence(s) to a hidden Markov model(s). + edam + data + beta12orEarlier + + + + + + + + Sequence-profile alignment (fingerprint) + + edam + beta12orEarlier + bioinformatics + data + data + Alignment of molecular sequences to a protein fingerprint from the PRINTS database. + + + + + + + + Phylogenetic continuous quantitative data + + Continuous quantitative data that may be read during phylogenetic tree calculation. + edam + Quantitative traits + Phylogenetic continuous quantitative characters + beta12orEarlier + data + bioinformatics + data + + + + + + + + Phylogenetic discrete data + + Discretely coded characters + data + bioinformatics + beta12orEarlier + Phylogenetic discrete states + edam + data + Character data with discrete states that may be read during phylogenetic tree calculation. + Discrete characters + + + + + + + + Phylogenetic character cliques + + data + beta12orEarlier + edam + Phylogenetic report (cliques) + data + One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny. + bioinformatics + + + + + + + + Phylogenetic invariants + + bioinformatics + Phylogenetic report (invariants) + data + data + beta12orEarlier + Phylogenetic invariants data for testing alternative tree topologies. + edam + + + + + + + + Phylogenetic tree report + + data + data + A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. + This is a broad data type and is used a placeholder for other, more specific types. + bioinformatics + beta12orEarlier + Phylogenetic tree-derived report + edam + + + + + + + + DNA substitution model + + + + beta12orEarlier + Sequence alignment report (DNA substitution model) + edam + data + A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. + data + bioinformatics + Phylogenetic tree report (DNA substitution model) + + + + + + + + Phylogenetic tree report (tree shape) + + data + Data about the shape of a phylogenetic tree. + data + edam + beta12orEarlier + bioinformatics + + + + + + + + Phylogenetic tree report (tree evaluation) + + bioinformatics + Data on the confidence of a phylogenetic tree. + edam + data + data + beta12orEarlier + + + + + + + + Phylogenetic tree report (tree distances) + + Distances, such as Branch Score distance, between two or more phylogenetic trees. + data + edam + data + beta12orEarlier + bioinformatics + + + + + + + + Phylogenetic tree report (tree stratigraphic) + + bioinformatics + data + edam + Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. + data + beta12orEarlier + + + + + + + + Phylogenetic character contrasts + + beta12orEarlier + edam + data + Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts. + bioinformatics + Phylogenetic report (character contrasts) + data + + + + + + + + Comparison matrix (integers) + + true + bioinformatics + beta12orEarlier + Matrix of integer numbers for sequence comparison. + data + edam + data + Substitution matrix (integers) + beta12orEarlier + + + + + + + + + Comparison matrix (floats) + + true + data + beta12orEarlier + bioinformatics + edam + Substitution matrix (floats) + data + Matrix of floating point numbers for sequence comparison. + beta12orEarlier + + + + + + + + + Comparison matrix (nucleotide) + + data + data + bioinformatics + Nucleotide substitution matrix + beta12orEarlier + edam + Matrix of integer or floating point numbers for nucleotide comparison. + + + + + + + + Comparison matrix (amino acid) + + + Amino acid substitution matrix + edam + data + data + Matrix of integer or floating point numbers for amino acid comparison. + beta12orEarlier + bioinformatics + + + + + + + + Nucleotide comparison matrix (integers) + + true + Matrix of integer numbers for nucleotide comparison. + beta12orEarlier + beta12orEarlier + data + Nucleotide substitution matrix (integers) + edam + data + bioinformatics + + + + + + + + + Nucleotide comparison matrix (floats) + + true + edam + Nucleotide substitution matrix (floats) + beta12orEarlier + data + bioinformatics + Matrix of floating point numbers for nucleotide comparison. + data + beta12orEarlier + + + + + + + + + Amino acid comparison matrix (integers) + + true + data + beta12orEarlier + data + beta12orEarlier + bioinformatics + Amino acid substitution matrix (integers) + edam + Matrix of integer numbers for amino acid comparison. + + + + + + + + + Amino acid comparison matrix (floats) + + true + data + beta12orEarlier + data + Amino acid substitution matrix (floats) + bioinformatics + edam + Matrix of floating point numbers for amino acid comparison. + beta12orEarlier + + + + + + + + + Protein features (membrane regions) + + bioinformatics + An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. + This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. + beta12orEarlier + Intramembrane region report + data + edam + data + Transmembrane region report + Protein report (membrane protein) + + + + + + + + Nucleic acid structure + + + + + + + + data + edam + bioinformatics + beta12orEarlier + 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. + data + + + + + + + + Protein structure + + + + + + + + + + + + + + beta12orEarlier + data + edam + 3D coordinate and associated data for a protein tertiary (3D) structure. + bioinformatics + data + + + + + + + + Protein-ligand complex + + This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. + data + bioinformatics + edam + beta12orEarlier + The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule. + data + + + + + + + + Carbohydrate structure + + + + + + + + + + + + + + bioinformatics + 3D coordinate and associated data for a carbohydrate (3D) structure. + beta12orEarlier + edam + data + data + + + + + + + + Small molecule structure + + + + + + + + data + beta12orEarlier + bioinformatics + CHEBI:23367 + edam + data + 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound. + + + + + + + + DNA structure + + data + data + bioinformatics + 3D coordinate and associated data for a DNA tertiary (3D) structure. + beta12orEarlier + edam + + + + + + + + RNA structure record + + + + + + + + edam + 3D coordinate and associated data for an RNA tertiary (3D) structure. + bioinformatics + beta12orEarlier + data + data + + + + + + + + tRNA structure record + + data + beta12orEarlier + 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. + data + edam + bioinformatics + + + + + + + + Protein chain + + bioinformatics + 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. + data + beta12orEarlier + edam + data + + + + + + + + Protein domain + + + + + + + + data + data + beta12orEarlier + bioinformatics + edam + 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. + + + + + + + + Protein structure (all atoms) + + 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). + data + bioinformatics + data + edam + beta12orEarlier + + + + + + + + Protein structure (C-alpha atoms) + + data + beta12orEarlier + data + bioinformatics + edam + C-beta atoms from amino acid side-chains may be included. + 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). + + + + + + + + Protein chain (all atoms) + + true + data + edam + beta12orEarlier + 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). + data + beta12orEarlier + bioinformatics + + + + + + + + + + Protein chain (C-alpha atoms) + + true + data + edam + beta12orEarlier + 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). + data + bioinformatics + C-beta atoms from amino acid side-chains may be included. + beta12orEarlier + + + + + + + + + + Protein domain (all atoms) + + true + data + data + beta12orEarlier + 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). + beta12orEarlier + bioinformatics + edam + + + + + + + + + + Protein domain (C-alpha atoms) + + true + beta12orEarlier + beta12orEarlier + bioinformatics + C-beta atoms from amino acid side-chains may be included. + data + edam + data + 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). + + + + + + + + + + Structure alignment (pair) + + data + data + beta12orEarlier + edam + bioinformatics + Alignment (superimposition) of exactly two molecular tertiary (3D) structures. + + + + + + + + Structure alignment (multiple) + + true + data + edam + Alignment (superimposition) of more than two molecular tertiary (3D) structures. + data + beta12orEarlier + bioinformatics + beta12orEarlier + + + + + + + + + Structure alignment (protein) + + + data + edam + bioinformatics + data + Alignment (superimposition) of protein tertiary (3D) structures. + beta12orEarlier + + + + + + + + Structure alignment (nucleic acid) + + + bioinformatics + data + Alignment (superimposition) of nucleic acid tertiary (3D) structures. + beta12orEarlier + edam + data + + + + + + + + Structure alignment (protein pair) + + + Alignment (superimposition) of exactly two protein tertiary (3D) structures. + beta12orEarlier + data + bioinformatics + data + edam + + + + + + + + Multiple protein tertiary structure alignment + + true + bioinformatics + beta12orEarlier + beta12orEarlier + Alignment (superimposition) of more than two protein tertiary (3D) structures. + edam + data + data + + + + + + + + + Structure alignment (protein all atoms) + + data + beta12orEarlier + Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). + edam + bioinformatics + data + + + + + + + + Structure alignment (protein C-alpha atoms) + + beta12orEarlier + bioinformatics + edam + data + C-beta atoms from amino acid side-chains may be considered. + data + Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). + + + + + + + + Pairwise protein tertiary structure alignment (all atoms) + + true + edam + beta12orEarlier + beta12orEarlier + data + data + Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). + bioinformatics + + + + + + + + + Pairwise protein tertiary structure alignment (C-alpha atoms) + + true + beta12orEarlier + edam + data + data + beta12orEarlier + bioinformatics + Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). + C-beta atoms from amino acid side-chains may be included. + + + + + + + + + Multiple protein tertiary structure alignment (all atoms) + + true + edam + beta12orEarlier + Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). + data + data + bioinformatics + beta12orEarlier + + + + + + + + + Multiple protein tertiary structure alignment (C-alpha atoms) + + true + data + data + beta12orEarlier + bioinformatics + beta12orEarlier + C-beta atoms from amino acid side-chains may be included. + edam + Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). + + + + + + + + + Structure alignment (nucleic acid pair) + + + Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. + data + data + bioinformatics + beta12orEarlier + edam + + + + + + + + Multiple nucleic acid tertiary structure alignment + + true + beta12orEarlier + data + Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. + data + edam + beta12orEarlier + bioinformatics + + + + + + + + + Structure alignment (RNA) + + beta12orEarlier + Alignment (superimposition) of RNA tertiary (3D) structures. + edam + data + bioinformatics + data + + + + + + + + Structural transformation matrix + + beta12orEarlier + edam + Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures. + data + data + bioinformatics + + + + + + + + DaliLite hit table + + true + data + data + beta12orEarlier + DaliLite hit table of protein chain tertiary structure alignment data. + beta12orEarlier + bioinformatics + The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. + edam + + + + + + + + + Molecular similarity score + + true + beta12orEarlier + bioinformatics + edam + A score reflecting structural similarities of two molecules. + data + data + beta12orEarlier + + + + + + + + + Root-mean-square deviation + + Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. + bioinformatics + edam + beta12orEarlier + data + data + RMSD + + + + + + + + Tanimoto similarity score + + bioinformatics + A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. + edam + data + A measure of the similarity between two ligand fingerprints. + data + beta12orEarlier + + + + + + + + 3D-1D scoring matrix + + data + beta12orEarlier + data + A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. + bioinformatics + edam + + + + + + + + Amino acid index + + + edam + A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. + bioinformatics + data + data + beta12orEarlier + + + + + + + + Amino acid index (chemical classes) + + data + beta12orEarlier + Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. + bioinformatics + data + edam + + + + + + + + Amino acid pair-wise contact potentials + + beta12orEarlier + edam + bioinformatics + data + data + Statistical protein contact potentials. + + + + + + + + Amino acid index (molecular weight) + + edam + bioinformatics + beta12orEarlier + data + Molecular weights of amino acids. + data + + + + + + + + Amino acid index (hydropathy) + + beta12orEarlier + data + Hydrophobic, hydrophilic or charge properties of amino acids. + edam + data + bioinformatics + + + + + + + + Amino acid index (White-Wimley data) + + edam + data + Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. + data + bioinformatics + beta12orEarlier + + + + + + + + Amino acid index (van der Waals radii) + + beta12orEarlier + data + data + edam + Van der Waals radii of atoms for different amino acid residues. + bioinformatics + + + + + + + + Enzyme property + + + + + + + + An informative report on a specific enzyme. + bioinformatics + data + data + Enzyme report + edam + beta12orEarlier + Protein report (enzyme) + + + + + + + + Restriction enzyme property + + edam + data + data + Restriction enzyme report + Protein report (restriction enzyme) + This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. + beta12orEarlier + bioinformatics + Restriction enzyme pattern data + An informative report on a specific restriction enzyme such as enzyme reference data. + + + + + + + + Peptide molecular weights + + The report might include associated data such as frequency of peptide fragment molecular weights. + data + List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents. + beta12orEarlier + bioinformatics + edam + data + + + + + + + + Peptide hydrophobic moment + + data + Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. + Report on the hydrophobic moment of a polypeptide sequence. + bioinformatics + data + beta12orEarlier + edam + + + + + + + + Protein aliphatic index + + The aliphatic index is the relative protein volume occupied by aliphatic side chains. + beta12orEarlier + The aliphatic index of a protein. + bioinformatics + data + edam + data + + + + + + + + Protein sequence hydropathy plot + + edam + beta12orEarlier + A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc. + Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. + data + data + bioinformatics + + + + + + + + Protein charge plot + + data + A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence. + data + edam + bioinformatics + beta12orEarlier + + + + + + + + Protein solubility + + Protein solubility data + edam + data + data + The solubility or atomic solvation energy of a protein sequence or structure. + bioinformatics + beta12orEarlier + + + + + + + + Protein crystallizability + + data + data + edam + Data on the crystallizability of a protein sequence. + Protein crystallizability data + bioinformatics + beta12orEarlier + + + + + + + + Protein globularity + + data + edam + Data on the stability, intrinsic disorder or globularity of a protein sequence. + beta12orEarlier + data + Protein globularity data + bioinformatics + + + + + + + + Protein titration curve + + data + bioinformatics + beta12orEarlier + data + The titration curve of a protein. + edam + + + + + + + + Protein isoelectric point + + The isoelectric point of one proteins. + data + bioinformatics + data + edam + beta12orEarlier + + + + + + + + Protein pKa value + + data + bioinformatics + beta12orEarlier + The pKa value of a protein. + data + edam + + + + + + + + Protein hydrogen exchange rate + + data + data + The hydrogen exchange rate of a protein. + bioinformatics + edam + beta12orEarlier + + + + + + + + Protein extinction coefficient + + beta12orEarlier + data + edam + The extinction coefficient of a protein. + data + bioinformatics + + + + + + + + Protein optical density + + bioinformatics + beta12orEarlier + data + edam + data + The optical density of a protein. + + + + + + + + Protein subcellular localization + + true + beta13 + An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). + data + data + Protein report (subcellular localization) + beta12orEarlier + edam + bioinformatics + + + + + + + + + Peptide immunogenicity data + + This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. + beta12orEarlier + Peptide immunogenicity report + data + bioinformatics + data + edam + Peptide immunogenicity + An report on allergenicity / immunogenicity of peptides and proteins. + + + + + + + + MHC peptide immunogenicity report + + true + edam + data + bioinformatics + beta12orEarlier + data + A report on the immunogenicity of MHC class I or class II binding peptides. + beta13 + + + + + + + + + Protein structure report + + + Protein structure report (domain) + Protein report (structure) + Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains. + beta12orEarlier + Protein property (structural) + edam + data + bioinformatics + data + Protein structure-derived report + Protein structural property + + + + + + + + Protein structural quality report + + + beta12orEarlier + Protein report (structural quality) + data + edam + Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. + data + Protein property (structural quality) + Protein structure report (quality evaluation) + bioinformatics + Report on the quality of a protein three-dimensional model. + + + + + + + + Protein residue interactions + + + + + + + + + bioinformatics + Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups. + data + edam + Atom interaction data + beta12orEarlier + Residue interaction data + data + + + + + + + + Protein flexibility or motion report + + + Protein structure report (flexibility or motion) + beta12orEarlier + Protein flexibility or motion + edam + data + Informative report on flexibility or motion of a protein structure. + Protein property (flexibility or motion) + bioinformatics + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + data + + + + + + + + Protein solvent accessibility + + data + data + Data on the solvent accessible or buried surface area of a protein structure. + beta12orEarlier + edam + bioinformatics + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. + + + + + + + + Protein surface report + + + Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. + data + beta12orEarlier + bioinformatics + edam + Protein structure report (surface) + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + data + + + + + + + + Ramachandran plot + + bioinformatics + edam + Phi/psi angle data or a Ramachandran plot of a protein structure. + beta12orEarlier + data + data + + + + + + + + Protein dipole moment + + edam + beta12orEarlier + bioinformatics + Data on the net charge distribution (dipole moment) of a protein structure. + data + data + + + + + + + + Protein distance matrix + + data + edam + A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. + data + beta12orEarlier + bioinformatics + + + + + + + + Protein contact map + + data + bioinformatics + edam + data + beta12orEarlier + An amino acid residue contact map for a protein structure. + + + + + + + + Protein residue 3D cluster + + data + data + edam + Report on clusters of contacting residues in protein structures such as a key structural residue network. + bioinformatics + beta12orEarlier + + + + + + + + Protein hydrogen bonds + + edam + data + bioinformatics + data + beta12orEarlier + Patterns of hydrogen bonding in protein structures. + + + + + + + + Protein non-canonical interactions + + + data + beta12orEarlier + edam + Non-canonical atomic interactions in protein structures. + data + Protein non-canonical interactions report + bioinformatics + + + + + + + + CATH node + + data + CATH classification node report + beta12orEarlier + bioinformatics + edam + data + Information on a node from the CATH database. + The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. + + + + + + + + SCOP node + + bioinformatics + edam + beta12orEarlier + data + Information on a node from the SCOP database. + SCOP classification node + data + + + + + + + + EMBASSY domain classification + + true + An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. + edam + bioinformatics + beta12orEarlier + data + data + beta12orEarlier + + + + + + + + + CATH class + + bioinformatics + edam + data + data + Information on a protein 'class' node from the CATH database. + beta12orEarlier + + + + + + + + CATH architecture + + data + bioinformatics + Information on a protein 'architecture' node from the CATH database. + edam + beta12orEarlier + data + + + + + + + + CATH topology + + beta12orEarlier + bioinformatics + Information on a protein 'topology' node from the CATH database. + edam + data + data + + + + + + + + CATH homologous superfamily + + Information on a protein 'homologous superfamily' node from the CATH database. + data + beta12orEarlier + data + bioinformatics + edam + + + + + + + + CATH structurally similar group + + edam + Information on a protein 'structurally similar group' node from the CATH database. + bioinformatics + beta12orEarlier + data + data + + + + + + + + CATH functional category + + data + beta12orEarlier + edam + bioinformatics + Information on a protein 'functional category' node from the CATH database. + data + + + + + + + + Protein fold recognition report + + true + beta12orEarlier + edam + data + Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. + bioinformatics + A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s). + beta12orEarlier + data + + + + + + + + + Protein-protein interaction + + + + + + + + data + data + edam + Data on protein-protein interaction(s). + bioinformatics + For example, an informative report about a specific protein complex (of multiple polypeptide chains). + Protein structure report (protein complex) + beta12orEarlier + + + + + + + + Protein-ligand interaction + + + + + + + + data + data + bioinformatics + beta12orEarlier + Data on protein-ligand (small molecule) interaction(s). + edam + + + + + + + + Protein-nucleic acid interaction + + + + + + + + Data on protein-DNA/RNA interaction(s). + beta12orEarlier + data + data + bioinformatics + edam + + + + + + + + Nucleic acid melting profile + + data + edam + beta12orEarlier + bioinformatics + data + Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating. + A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. + Nucleic acid stability profile + + + + + + + + Nucleic acid enthalpy + + data + Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + data + edam + beta12orEarlier + bioinformatics + + + + + + + + Nucleic acid entropy + + data + beta12orEarlier + data + Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + edam + bioinformatics + + + + + + + + Nucleic acid melting temperature + + true + bioinformatics + beta12orEarlier + beta12orEarlier + Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + data + edam + data + + + + + + + + + Nucleic acid stitch profile + + A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. + bioinformatics + Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + data + data + beta12orEarlier + edam + + + + + + + + DNA base pair stacking energies data + + edam + data + data + beta12orEarlier + bioinformatics + DNA base pair stacking energies data. + + + + + + + + DNA base pair twist angle data + + edam + bioinformatics + DNA base pair twist angle data. + data + beta12orEarlier + data + + + + + + + + DNA base trimer roll angles data + + data + data + edam + DNA base trimer roll angles data. + beta12orEarlier + bioinformatics + + + + + + + + Vienna RNA parameters + + true + bioinformatics + edam + beta12orEarlier + data + beta12orEarlier + RNA parameters used by the Vienna package. + data + + + + + + + + + Vienna RNA structure constraints + + true + beta12orEarlier + beta12orEarlier + data + bioinformatics + Structure constraints used by the Vienna package. + data + edam + + + + + + + + + Vienna RNA concentration data + + true + beta12orEarlier + bioinformatics + edam + data + data + RNA concentration data used by the Vienna package. + beta12orEarlier + + + + + + + + + Vienna RNA calculated energy + + true + bioinformatics + data + edam + RNA calculated energy data generated by the Vienna package. + beta12orEarlier + beta12orEarlier + data + + + + + + + + + Base pairing probability matrix dotplot + + data + data + Dotplot of RNA base pairing probability matrix. + Such as generated by the Vienna package. + beta12orEarlier + edam + bioinformatics + + + + + + + + Nucleic acid folding report + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + bioinformatics + Nucleic acid report (folding model) + A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. + beta12orEarlier + data + data + Nucleic acid report (folding) + edam + + + + + + + + Codon usage table + + + + + + + + beta12orEarlier + data + A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. + Table of codon usage data calculated from one or more nucleic acid sequences. + bioinformatics + data + edam + + + + + + + + Genetic code + + bioinformatics + edam + data + A genetic code need not include detailed codon usage information. + data + A genetic code for an organism. + beta12orEarlier + + + + + + + + Codon adaptation index + + true + data + edam + data + beta12orEarlier + bioinformatics + beta12orEarlier + CAI + A simple measure of synonymous codon usage bias often used to predict gene expression levels. + + + + + + + + + Codon usage bias plot + + data + bioinformatics + edam + A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. + data + beta12orEarlier + Synonymous codon usage statistic plot + + + + + + + + Nc statistic + + true + data + beta12orEarlier + The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons. + edam + data + bioinformatics + beta12orEarlier + + + + + + + + + Codon usage fraction difference + + beta12orEarlier + edam + The differences in codon usage fractions between two codon usage tables. + data + data + bioinformatics + + + + + + + + Pharmacogenomic annotation + + Data on the influence of genotype on drug response. + The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. + bioinformatics + beta12orEarlier + data + edam + data + + + + + + + + Disease annotation + + + + + + + + data + beta12orEarlier + bioinformatics + data + An informative report on a specific disease. + edam + + + + + + + + Gene annotation (linkage disequilibrium) + + data + beta12orEarlier + bioinformatics + data + edam + A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). + + + + + + + + Heat map + + A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. + data + bioinformatics + edam + data + beta12orEarlier + A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. + + + + + + + + Affymetrix probe sets library file + + true + bioinformatics + data + edam + beta12orEarlier + data + beta12orEarlier + CDF file + Affymetrix library file of information about which probes belong to which probe set. + + + + + + + + + Affymetrix probe sets information library file + + true + beta12orEarlier + GIN file + bioinformatics + data + beta12orEarlier + data + Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. + edam + + + + + + + + + Molecular weights standard fingerprint + + Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. + bioinformatics + data + data + edam + beta12orEarlier + + + + + + + + Pathway or network (metabolic) + + data + bioinformatics + edam + data + A report typically including a map (diagram) of a metabolic pathway. + beta12orEarlier + This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. + + + + + + + + Pathway or network (genetic information processing) + + data + A report typically including a map (diagram) of a genetic information processing pathway. + bioinformatics + data + edam + beta12orEarlier + + + + + + + + Pathway or network (environmental information processing) + + beta12orEarlier + bioinformatics + edam + A report typically including a map (diagram) of an environmental information processing pathway. + data + data + + + + + + + + Pathway or network (signal transduction) + + beta12orEarlier + edam + data + data + bioinformatics + A report typically including a map (diagram) of a signal transduction pathway. + + + + + + + + Pathway or network (cellular process) + + beta12orEarlier + data + edam + data + A report typically including a map (diagram) of a cellular process pathway. + bioinformatics + + + + + + + + Pathway or network (disease) + + data + edam + A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease. + bioinformatics + data + beta12orEarlier + + + + + + + + Pathway or network (drug structure relationship) + + edam + data + beta12orEarlier + bioinformatics + data + A report typically including a map (diagram) of drug structure relationships. + + + + + + + + Pathway or network (protein-protein interaction) + + data + beta12orEarlier + data + A report typically including a map (diagram) of a network of protein interactions. + edam + bioinformatics + + + + + + + + MIRIAM datatype + + beta12orEarlier + bioinformatics + An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. + edam + A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. + data + data + + + + + + + + E-value + + Expectation value + A simple floating point number defining the lower or upper limit of an expectation value (E-value). + beta12orEarlier + data + edam + bioinformatics + data + An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. + + + + + + + + Z-value + + A z-value might be specified as a threshold for reporting hits from database searches. + The z-value is the number of standard deviations a data value is above or below a mean value. + bioinformatics + data + edam + beta12orEarlier + data + + + + + + + + P-value + + The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true. + A z-value might be specified as a threshold for reporting hits from database searches. + data + data + beta12orEarlier + bioinformatics + edam + + + + + + + + Database version information + + + beta12orEarlier + Information on a database (or ontology) version, for example name, version number and release date. + edam + bioinformatics + Ontology version information + data + data + + + + + + + + Tool version information + + + data + data + edam + beta12orEarlier + Information on an application version, for example name, version number and release date. + bioinformatics + + + + + + + + CATH version information + + true + Information on a version of the CATH database. + edam + beta12orEarlier + data + bioinformatics + beta12orEarlier + data + + + + + + + + + Swiss-Prot to PDB mapping + + true + data + edam + beta12orEarlier + data + bioinformatics + beta12orEarlier + Cross-mapping of Swiss-Prot codes to PDB identifiers. + + + + + + + + + Sequence database cross-references + + true + bioinformatics + edam + beta12orEarlier + data + data + beta12orEarlier + Cross-references from a sequence record to other databases. + + + + + + + + + Job status + + data + Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). + bioinformatics + data + edam + beta12orEarlier + Metadata on the status of a submitted job. + + + + + + + + Job ID + + true + beta12orEarlier + 1.0 + edam + bioinformatics + The (typically numeric) unique identifier of a submitted job. + identifiers + data + identifier + + + + + + + + + Job type + + A label (text token) describing the type of job, for example interactive or non-interactive. + beta12orEarlier + bioinformatics + data + data + edam + + + + + + + + Tool log + + beta12orEarlier + edam + data + bioinformatics + A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages. + data + + + + + + + + DaliLite log file + + true + beta12orEarlier + bioinformatics + data + data + edam + DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. + beta12orEarlier + + + + + + + + + STRIDE log file + + true + edam + beta12orEarlier + beta12orEarlier + data + STRIDE log file. + data + bioinformatics + + + + + + + + + NACCESS log file + + true + data + NACCESS log file. + data + bioinformatics + beta12orEarlier + beta12orEarlier + edam + + + + + + + + + EMBOSS wordfinder log file + + true + data + edam + beta12orEarlier + beta12orEarlier + bioinformatics + EMBOSS wordfinder log file. + data + + + + + + + + + EMBOSS domainatrix log file + + true + bioinformatics + edam + data + beta12orEarlier + data + EMBOSS (EMBASSY) domainatrix application log file. + beta12orEarlier + + + + + + + + + EMBOSS sites log file + + true + EMBOSS (EMBASSY) sites application log file. + data + beta12orEarlier + edam + data + beta12orEarlier + bioinformatics + + + + + + + + + EMBOSS supermatcher error file + + true + bioinformatics + edam + beta12orEarlier + beta12orEarlier + data + EMBOSS (EMBASSY) supermatcher error file. + data + + + + + + + + + EMBOSS megamerger log file + + true + data + data + EMBOSS megamerger log file. + beta12orEarlier + beta12orEarlier + edam + bioinformatics + + + + + + + + + EMBOSS whichdb log file + + true + beta12orEarlier + data + EMBOSS megamerger log file. + bioinformatics + edam + data + beta12orEarlier + + + + + + + + + EMBOSS vectorstrip log file + + true + EMBOSS vectorstrip log file. + data + bioinformatics + data + edam + beta12orEarlier + beta12orEarlier + + + + + + + + + Username + + beta12orEarlier + identifiers + edam + data + identifier + bioinformatics + A username on a computer system. + + + + + + + + Password + + identifier + bioinformatics + data + edam + identifiers + A password on a computer system. + beta12orEarlier + + + + + + + + Email address + + identifiers + Moby:EmailAddress + A valid email address of an end-user. + Moby:Email + bioinformatics + identifier + edam + data + beta12orEarlier + + + + + + + + Person name + + bioinformatics + data + The name of a person. + identifiers + identifier + beta12orEarlier + edam + + + + + + + + Number of iterations + + edam + beta12orEarlier + bioinformatics + data + Number of iterations of an algorithm. + data + + + + + + + + Number of output entities + + data + data + beta12orEarlier + edam + Number of entities (for example database hits, sequences, alignments etc) to write to an output file. + bioinformatics + + + + + + + + Hit sort order + + true + bioinformatics + data + data + edam + beta12orEarlier + beta12orEarlier + Controls the order of hits (reported matches) in an output file from a database search. + + + + + + + + + Drug annotation + + + + + + + + data + beta12orEarlier + bioinformatics + An informative report on a specific drug. + data + edam + + + + + + + + Phylogenetic tree image + + + See also 'Phylogenetic tree' + bioinformatics + beta12orEarlier + An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information. + data + edam + data + + + + + + + + RNA secondary structure image + + beta12orEarlier + Image of RNA secondary structure, knots, pseudoknots etc. + data + bioinformatics + edam + data + + + + + + + + Protein secondary structure image + + + beta12orEarlier + Image of protein secondary structure. + data + data + edam + bioinformatics + + + + + + + + Structure image + + + Image of one or more molecular tertiary (3D) structures. + data + data + bioinformatics + beta12orEarlier + edam + + + + + + + + Sequence alignment image + + + edam + bioinformatics + Image of two or more aligned molecular sequences possibly annotated with alignment features. + data + beta12orEarlier + data + + + + + + + + Structure image (small molecule) + + + edam + beta12orEarlier + Small molecule structure image + The molecular identifier and formula are typically included. + An image of the structure of a small chemical compound. + data + data + Chemical structure image + bioinformatics + + + + + + + + Fate map + + beta12orEarlier + A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. + edam + data + data + bioinformatics + + + + + + + + Microarray spots image + + + data + edam + data + An image of spots from a microarray experiment. + beta12orEarlier + bioinformatics + + + + + + + + BioPax + + true + data + bioinformatics + data + beta12orEarlier + A term from the BioPax ontology. + beta12orEarlier + edam + + + + + + + + + GO + + true + Moby:GO_Term + Moby:GOTerm + beta12orEarlier + A term definition from The Gene Ontology (GO). + Moby:Annotated_GO_Term_With_Probability + data + Moby:Annotated_GO_Term + Gene Ontology term + beta12orEarlier + bioinformatics + data + edam + + + + + + + + + MeSH + + true + beta12orEarlier + beta12orEarlier + bioinformatics + A term from the MeSH vocabulary. + data + edam + data + + + + + + + + + HGNC + + true + bioinformatics + beta12orEarlier + edam + A term from the HGNC controlled vocabulary. + data + beta12orEarlier + data + + + + + + + + + NCBI taxonomy vocabulary + + true + data + A term from the NCBI taxonomy vocabulary. + edam + beta12orEarlier + bioinformatics + beta12orEarlier + data + + + + + + + + + Plant ontology term + + true + bioinformatics + data + edam + A term from the Plant Ontology (PO). + data + beta12orEarlier + beta12orEarlier + + + + + + + + + UMLS + + true + data + A term from the UMLS vocabulary. + edam + beta12orEarlier + beta12orEarlier + bioinformatics + data + + + + + + + + + FMA + + true + edam + data + beta12orEarlier + bioinformatics + A term from Foundational Model of Anatomy. + beta12orEarlier + data + Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. + + + + + + + + + EMAP + + true + beta12orEarlier + data + edam + beta12orEarlier + bioinformatics + A term from the EMAP mouse ontology. + data + + + + + + + + + ChEBI + + true + edam + beta12orEarlier + data + data + bioinformatics + beta12orEarlier + A term from the ChEBI ontology. + + + + + + + + + MGED + + true + data + A term from the MGED ontology. + beta12orEarlier + data + beta12orEarlier + bioinformatics + edam + + + + + + + + + myGrid + + true + beta12orEarlier + bioinformatics + A term from the myGrid ontology. + data + data + edam + beta12orEarlier + The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. + + + + + + + + + GO (biological process) + + true + Data Type is an enumerated string. + beta12orEarlier + data + A term definition for a biological process from the Gene Ontology (GO). + edam + data + bioinformatics + beta12orEarlier + + + + + + + + + GO (molecular function) + + true + beta12orEarlier + bioinformatics + Data Type is an enumerated string. + data + beta12orEarlier + edam + data + A term definition for a molecular function from the Gene Ontology (GO). + + + + + + + + + GO (cellular component) + + true + A term definition for a cellular component from the Gene Ontology (GO). + beta12orEarlier + data + Data Type is an enumerated string. + data + beta12orEarlier + bioinformatics + edam + + + + + + + + + Ontology relation type + + bioinformatics + A relation type defined in an ontology. + data + edam + beta12orEarlier + data + + + + + + + + Ontology concept definition + + The definition of a concept from an ontology. + data + data + bioinformatics + beta12orEarlier + edam + + + + + + + + Ontology concept comment + + bioinformatics + edam + A comment on a concept from an ontology. + data + beta12orEarlier + data + + + + + + + + Ontology concept reference + + true + data + edam + beta12orEarlier + data + bioinformatics + Reference for a concept from an ontology. + beta12orEarlier + + + + + + + + + doc2loc document information + + true + Information on a published article provided by the doc2loc program. + The doc2loc output includes the url, format, type and availability code of a document for every service provider. + data + edam + beta12orEarlier + data + beta12orEarlier + bioinformatics + + + + + + + + + PDB residue number + + A residue identifier (a string) from a PDB file. + edam + data + data + bioinformatics + beta12orEarlier + PDBML:PDB_residue_no + WHATIF: pdb_number + + + + + + + + Atomic coordinate + + Cartesian coordinate + edam + data + bioinformatics + beta12orEarlier + Cartesian coordinate of an atom (in a molecular structure). + data + + + + + + + + Atomic x coordinate + + Cartesian x coordinate of an atom (in a molecular structure). + beta12orEarlier + WHATIF: PDBx_Cartn_x + edam + data + bioinformatics + data + PDBML:_atom_site.Cartn_x in PDBML + Cartesian x coordinate + + + + + + + + Atomic y coordinate + + data + data + WHATIF: PDBx_Cartn_y + edam + Cartesian y coordinate of an atom (in a molecular structure). + PDBML:_atom_site.Cartn_y in PDBML + beta12orEarlier + bioinformatics + Cartesian y coordinate + + + + + + + + Atomic z coordinate + + bioinformatics + data + Cartesian z coordinate + data + edam + beta12orEarlier + Cartesian z coordinate of an atom (in a molecular structure). + WHATIF: PDBx_Cartn_z + PDBML:_atom_site.Cartn_z + + + + + + + + PDB atom name + + Identifier (a string) of a specific atom from a PDB file for a molecular structure. + bioinformatics + identifier + WHATIF: atom_type + PDBML:pdbx_PDB_atom_name + identifiers + WHATIF: alternate_atom + WHATIF: PDBx_auth_atom_id + beta12orEarlier + edam + WHATIF: PDBx_type_symbol + data + + + + + + + + Protein atom + + beta12orEarlier + data + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + data + bioinformatics + Data on a single atom from a protein structure. + CHEBI:33250 + Atom data + edam + + + + + + + + Protein residue + + Residue + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + edam + Data on a single amino acid residue position in a protein structure. + bioinformatics + data + beta12orEarlier + data + + + + + + + + Atom name + + + data + beta12orEarlier + identifier + edam + Name of an atom. + bioinformatics + identifiers + + + + + + + + PDB residue name + + identifiers + beta12orEarlier + bioinformatics + WHATIF: type + edam + identifier + data + Three-letter amino acid residue names as used in PDB files. + + + + + + + + PDB model number + + identifiers + WHATIF: model_number + edam + beta12orEarlier + bioinformatics + identifier + Identifier of a model structure from a PDB file. + Model number + PDBML:pdbx_PDB_model_num + data + + + + + + + + CATH domain report + + true + edam + bioinformatics + beta12orEarlier + data + The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. + Summary of domain classification information for a CATH domain. + data + beta13 + + + + + + + + + CATH representative domain sequences (ATOM) + + true + data + FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). + beta12orEarlier + beta12orEarlier + edam + data + bioinformatics + + + + + + + + + CATH representative domain sequences (COMBS) + + true + beta12orEarlier + beta12orEarlier + bioinformatics + FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). + data + edam + data + + + + + + + + + CATH domain sequences (ATOM) + + true + data + beta12orEarlier + data + beta12orEarlier + edam + FASTA sequence database for all CATH domains (based on PDB ATOM records). + bioinformatics + + + + + + + + + CATH domain sequences (COMBS) + + true + data + beta12orEarlier + edam + bioinformatics + beta12orEarlier + FASTA sequence database for all CATH domains (based on COMBS sequence data). + data + + + + + + + + + Sequence version information + + + edam + bioinformatics + data + Information on an molecular sequence version. + beta12orEarlier + data + + + + + + + + Score or penalty + + A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty). + beta12orEarlier + edam + bioinformatics + data + data + + + + + + + + Protein report (function) + + true + beta12orEarlier + edam + bioinformatics + Report on general functional properties of specific protein(s). + beta13 + For properties that can be mapped to a sequence, use 'Sequence report' instead. + data + data + + + + + + + + + Gene name (ASPGD) + + edam + http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS + identifier + identifiers + data + Name of a gene from Aspergillus Genome Database. + beta12orEarlier + bioinformatics + + + + + + + + Gene name (CGD) + + data + identifier + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS + bioinformatics + edam + Name of a gene from Candida Genome Database. + identifiers + + + + + + + + Gene name (dictyBase) + + Name of a gene from dictyBase database. + beta12orEarlier + edam + identifiers + bioinformatics + data + http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase + identifier + + + + + + + + Gene name (EcoGene primary) + + identifier + EcoGene primary gene name + identifiers + data + Primary name of a gene from EcoGene Database. + edam + beta12orEarlier + bioinformatics + http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G + + + + + + + + Gene name (MaizeGDB) + + beta12orEarlier + identifier + identifiers + bioinformatics + edam + Name of a gene from MaizeGDB (maize genes) database. + data + http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus + + + + + + + + Gene name (SGD) + + + data + bioinformatics + beta12orEarlier + identifier + edam + Name of a gene from Saccharomyces Genome Database. + identifiers + http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS + + + + + + + + Gene name (TGD) + + data + http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS + identifiers + Name of a gene from Tetrahymena Genome Database. + edam + bioinformatics + identifier + beta12orEarlier + + + + + + + + Gene name (CGSC) + + Symbol of a gene from E.coli Genetic Stock Center. + bioinformatics + data + identifiers + identifier + http://www.geneontology.org/doc/GO.xrf_abbs: CGSC + edam + beta12orEarlier + + + + + + + + Gene name (HGNC) + + Symbol of a gene approved by the HUGO Gene Nomenclature Committee. + HGNC gene symbol + Gene name (HUGO) + HGNC:[0-9]{1,5} + HUGO gene symbol + HGNC gene name + edam + identifier + http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene + HUGO gene name + identifiers + Official gene name + bioinformatics + HGNC symbol + HUGO symbol + beta12orEarlier + data + + + + + + + + Gene name (MGD) + + identifier + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: MGD + MGI:[0-9]+ + edam + bioinformatics + identifiers + data + Symbol of a gene from the Mouse Genome Database. + + + + + + + + Gene name (Bacillus subtilis) + + data + bioinformatics + beta12orEarlier + identifier + Symbol of a gene from Bacillus subtilis Genome Sequence Project. + identifiers + http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG + edam + + + + + + + + Gene ID (PlasmoDB) + + identifier + http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB + beta12orEarlier + bioinformatics + Identifier of a gene from PlasmoDB Plasmodium Genome Resource. + identifiers + data + edam + + + + + + + + Gene ID (EcoGene) + + data + EcoGene Accession + edam + identifiers + Identifier of a gene from EcoGene Database. + identifier + beta12orEarlier + EcoGene ID + bioinformatics + + + + + + + + Gene ID (FlyBase) + + http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase + data + http://www.geneontology.org/doc/GO.xrf_abbs: FB + Gene identifier from FlyBase database. + bioinformatics + beta12orEarlier + identifier + identifiers + edam + + + + + + + + Gene ID (GeneDB Glossina morsitans) + + true + beta12orEarlier + Gene identifier from Glossina morsitans GeneDB database. + beta13 + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans + identifier + bioinformatics + identifiers + data + edam + + + + + + + + + Gene ID (GeneDB Leishmania major) + + true + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor + bioinformatics + identifiers + Gene identifier from Leishmania major GeneDB database. + data + beta13 + identifier + edam + + + + + + + + + Gene ID (GeneDB Plasmodium falciparum) + + true + beta12orEarlier + identifiers + edam + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum + Gene identifier from Plasmodium falciparum GeneDB database. + identifier + beta13 + data + bioinformatics + + + + + + + + + Gene ID (GeneDB Schizosaccharomyces pombe) + + true + bioinformatics + identifier + edam + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe + Gene identifier from Schizosaccharomyces pombe GeneDB database. + beta13 + data + identifiers + + + + + + + + + Gene ID (GeneDB Trypanosoma brucei) + + true + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei + beta12orEarlier + identifier + edam + data + bioinformatics + beta13 + identifiers + Gene identifier from Trypanosoma brucei GeneDB database. + + + + + + + + + Gene ID (Gramene) + + Gene identifier from Gramene database. + http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE + beta12orEarlier + bioinformatics + data + identifiers + identifier + edam + http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene + + + + + + + + Gene ID (Virginia microbial) + + bioinformatics + Gene identifier from Virginia Bioinformatics Institute microbial database. + identifiers + data + edam + http://www.geneontology.org/doc/GO.xrf_abbs: VMD + identifier + http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD + beta12orEarlier + + + + + + + + Gene ID (SGN) + + beta12orEarlier + identifiers + identifier + Gene identifier from Sol Genomics Network. + edam + data + bioinformatics + http://www.geneontology.org/doc/GO.xrf_abbs: SGN + + + + + + + + Gene ID (WormBase) + + + identifier + http://www.geneontology.org/doc/GO.xrf_abbs: WormBase + Gene identifier used by WormBase database. + beta12orEarlier + bioinformatics + edam + http://www.geneontology.org/doc/GO.xrf_abbs: WB + WBGene[0-9]{8} + data + identifiers + + + + + + + + Gene synonym + + true + identifier + Any name (other than the recommended one) for a gene. + Gene name synonym + data + identifiers + bioinformatics + beta12orEarlier + edam + beta12orEarlier + + + + + + + + + ORF name + + + The name of an open reading frame attributed by a sequencing project. + identifier + edam + bioinformatics + identifiers + beta12orEarlier + data + + + + + + + + Sequence assembly component + + true + data + beta12orEarlier + bioinformatics + beta12orEarlier + A component of a larger sequence assembly. + edam + data + + + + + + + + + Chromosome annotation (aberration) + + true + edam + A report on a chromosome aberration such as abnormalities in chromosome structure. + beta12orEarlier + beta12orEarlier + bioinformatics + data + data + + + + + + + + + Clone ID + + data + identifiers + An identifier of a clone (cloned molecular sequence) from a database. + identifier + bioinformatics + beta12orEarlier + edam + + + + + + + + PDB insertion code + + edam + An insertion code (part of the residue number) for an amino acid residue from a PDB file. + data + data + PDBML:pdbx_PDB_ins_code + WHATIF: insertion_code + bioinformatics + beta12orEarlier + + + + + + + + Atomic occupancy + + The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. + beta12orEarlier + data + The fraction of an atom type present at a site in a molecular structure. + bioinformatics + edam + data + WHATIF: PDBx_occupancy + + + + + + + + Isotropic B factor + + bioinformatics + beta12orEarlier + WHATIF: PDBx_B_iso_or_equiv + data + edam + data + Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. + + + + + + + + Deletion map + + Deletion-based cytogenetic map + bioinformatics + edam + data + A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. + beta12orEarlier + A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. + data + + + + + + + + QTL map + + Quantitative trait locus map + bioinformatics + data + beta12orEarlier + data + A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. + edam + + + + + + + + Haplotype map + + data + A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. + bioinformatics + Moby:Haplotyping_Study_obj + data + edam + beta12orEarlier + + + + + + + + Map set + + data + data + Moby:GCP_CorrelatedMapSet + bioinformatics + edam + Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. + Moby:GCP_CorrelatedLinkageMapSet + beta12orEarlier + + + + + + + + Map feature + + true + Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. + beta12orEarlier + edam + Moby:MapFeature + A feature which may mapped (positioned) on a genetic or other type of map. + data + beta12orEarlier + bioinformatics + data + + + + + + + + + + + Map type + + + beta12orEarlier + data + data + edam + Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. + A designation of the type of map (genetic map, physical map, sequence map etc) or map set. + bioinformatics + + + + + + + + Protein fold name + + bioinformatics + beta12orEarlier + identifiers + edam + data + The name of a protein fold. + identifier + + + + + + + + Taxon + + Moby:BriefTaxonConcept + The name of a group of organisms belonging to the same taxonomic rank. + data + For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. + edam + Taxonomic rank + Taxonomy rank + beta12orEarlier + identifiers + Moby:PotentialTaxon + identifier + bioinformatics + + + + + + + + Organism identifier + + + + + + + + edam + data + bioinformatics + identifier + A unique identifier of a (group of) organisms. + beta12orEarlier + identifiers + + + + + + + + Genus name + + identifier + The name of a genus of organism. + edam + identifiers + bioinformatics + data + beta12orEarlier + + + + + + + + Taxonomic classification + + Moby:TaxonTCS + identifiers + Moby:TaxonScientificName + identifier + Taxonomic information + bioinformatics + Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. + Taxonomic name + Moby:iANT_organism-xml + data + The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. + edam + beta12orEarlier + Moby:GCP_Taxon + Moby:TaxonName + + + + + + + + iHOP organism ID + + identifier + data + A unique identifier for an organism used in the iHOP database. + Moby_namespace:iHOPorganism + beta12orEarlier + bioinformatics + edam + identifiers + + + + + + + + Genbank common name + + beta12orEarlier + identifier + Common name for an organism as used in the GenBank database. + edam + bioinformatics + data + identifiers + + + + + + + + NCBI taxon + + beta12orEarlier + identifier + data + edam + bioinformatics + The name of a taxon from the NCBI taxonomy database. + identifiers + + + + + + + + Synonym + + true + An alternative for a word. + data + edam + data + beta12orEarlier + Alternative name + bioinformatics + beta12orEarlier + + + + + + + + + Misspelling + + true + beta12orEarlier + bioinformatics + edam + beta12orEarlier + data + data + A common misspelling of a word. + + + + + + + + + Acronym + + true + beta12orEarlier + data + edam + data + bioinformatics + An abbreviation of a phrase or word. + beta12orEarlier + + + + + + + + + Misnomer + + true + bioinformatics + edam + beta12orEarlier + beta12orEarlier + data + A term which is likely to be misleading of its meaning. + data + + + + + + + + + Author ID + + beta12orEarlier + identifiers + Moby:Author + edam + data + identifier + Information on the authors of a published work. + bioinformatics + + + + + + + + DragonDB author identifier + + data + edam + identifiers + bioinformatics + beta12orEarlier + identifier + An identifier representing an author in the DragonDB database. + + + + + + + + Annotated URI + + + Moby:DescribedLink + data + data + bioinformatics + A URI along with annotation describing the data found at the address. + beta12orEarlier + edam + + + + + + + + UniProt keywords + + true + A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. + bioinformatics + data + beta12orEarlier + beta12orEarlier + edam + data + + + + + + + + + Gene ID (GeneFarm) + + edam + beta12orEarlier + Identifier of a gene from the GeneFarm database. + identifiers + bioinformatics + identifier + Moby_namespace:GENEFARM_GeneID + data + + + + + + + + Blattner number + + edam + data + The blattner identifier for a gene. + Moby_namespace:Blattner_number + identifiers + identifier + bioinformatics + beta12orEarlier + + + + + + + + Gene ID (MIPS Maize) + + true + bioinformatics + edam + identifiers + data + identifier + beta13 + Moby_namespace:MIPS_GE_Maize + beta12orEarlier + Identifier for genetic elements in MIPS Maize database. + MIPS genetic element identifier (Maize) + + + + + + + + + Gene ID (MIPS Medicago) + + true + bioinformatics + beta13 + identifier + beta12orEarlier + MIPS genetic element identifier (Medicago) + Identifier for genetic elements in MIPS Medicago database. + Moby_namespace:MIPS_GE_Medicago + edam + data + identifiers + + + + + + + + + Gene name (DragonDB) + + Moby_namespace:DragonDB_Gene + beta12orEarlier + bioinformatics + identifiers + data + edam + The name of an Antirrhinum Gene from the DragonDB database. + identifier + + + + + + + + Gene name (Arabidopsis) + + bioinformatics + data + beta12orEarlier + identifier + edam + A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. + identifiers + Moby_namespace:ArabidopsisGeneSymbol + + + + + + + + iHOP symbol + + + + beta12orEarlier + identifiers + bioinformatics + edam + Moby_namespace:iHOPsymbol + A unique identifier of a protein or gene used in the iHOP database. + identifier + data + + + + + + + + Gene name (GeneFarm) + + identifiers + edam + GeneFarm gene ID + Moby_namespace:GENEFARM_GeneName + bioinformatics + beta12orEarlier + identifier + data + Name of a gene from the GeneFarm database. + + + + + + + + Locus ID + + + + + + + + + edam + beta12orEarlier + identifiers + A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. + data + identifier + bioinformatics + Locus identifier + Locus name + + + + + + + + Locus ID (AGI) + + AGI identifier + identifiers + identifier + beta12orEarlier + AGI locus code + Arabidopsis gene loci number + edam + bioinformatics + http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode + Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases) + AGI ID + data + AT[1-5]G[0-9]{5} + + + + + + + + Locus ID (ASPGD) + + Identifier for loci from ASPGD (Aspergillus Genome Database). + http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID + data + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD + bioinformatics + identifier + identifiers + edam + + + + + + + + Locus ID (MGG) + + edam + identifiers + http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG + beta12orEarlier + identifier + bioinformatics + Identifier for loci from Magnaporthe grisea Database at the Broad Institute. + data + + + + + + + + Locus ID (CGD) + + http://www.geneontology.org/doc/GO.xrf_abbs: CGD + data + CGDID + bioinformatics + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: CGDID + CGD locus identifier + edam + identifiers + identifier + Identifier for loci from CGD (Candida Genome Database). + + + + + + + + Locus ID (CMR) + + http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR + Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. + data + edam + http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR + bioinformatics + beta12orEarlier + identifiers + identifier + + + + + + + + NCBI locus tag + + identifier + data + bioinformatics + Identifier for loci from NCBI database. + http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag + identifiers + edam + Locus ID (NCBI) + Moby_namespace:LocusID + beta12orEarlier + + + + + + + + Locus ID (SGD) + + + SGDID + bioinformatics + identifier + Identifier for loci from SGD (Saccharomyces Genome Database). + identifiers + data + http://www.geneontology.org/doc/GO.xrf_abbs: SGD + beta12orEarlier + edam + http://www.geneontology.org/doc/GO.xrf_abbs: SGDID + + + + + + + + Locus ID (MMP) + + bioinformatics + beta12orEarlier + identifiers + Moby_namespace:MMP_Locus + Identifier of loci from Maize Mapping Project. + identifier + edam + data + + + + + + + + Locus ID (DictyBase) + + identifier + bioinformatics + identifiers + data + Identifier of locus from DictyBase (Dictyostelium discoideum). + beta12orEarlier + edam + Moby_namespace:DDB_gene + + + + + + + + Locus ID (EntrezGene) + + Moby_namespace:EntrezGene_EntrezGeneID + identifiers + beta12orEarlier + edam + identifier + Moby_namespace:EntrezGene_ID + data + Identifier of a locus from EntrezGene database. + bioinformatics + + + + + + + + Locus ID (MaizeGDB) + + identifier + edam + identifiers + beta12orEarlier + Moby_namespace:MaizeGDB_Locus + Identifier of locus from MaizeGDB (Maize genome database). + bioinformatics + data + + + + + + + + Quantitative trait locus + + true + Moby:SO_QTL + edam + A QTL sometimes but does not necessarily correspond to a gene. + data + A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment). + data + beta12orEarlier + beta12orEarlier + QTL + bioinformatics + + + + + + + + + Gene ID (KOME) + + data + bioinformatics + edam + Moby_namespace:GeneId + beta12orEarlier + identifier + identifiers + Identifier of a gene from the KOME database. + + + + + + + + Locus ID (Tropgene) + + data + identifiers + edam + beta12orEarlier + Moby:Tropgene_locus + Identifier of a locus from the Tropgene database. + identifier + bioinformatics + + + + + + + + Alignment + + bioinformatics + data + data + beta12orEarlier + edam + An alignment of molecular sequences, structures or profiles derived from them. + + + + + + + + Atomic property + + bioinformatics + data + beta12orEarlier + edam + Data for an atom (in a molecular structure). + data + General atomic property + + + + + + + + UniProt keyword + + http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW + Moby_namespace:SP_KW + data + A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. + data + bioinformatics + edam + beta12orEarlier + + + + + + + + Ordered locus name + + true + beta12orEarlier + edam + A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. + bioinformatics + identifiers + data + identifier + beta12orEarlier + + + + + + + + + Map position + + + + PDBML:_atom_site.id + Moby:GCP_MapPoint + Moby:GCP_MapPosition + Moby:GCP_MapInterval + This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. + beta12orEarlier + Moby:Locus + Moby:MapPosition + Moby:HitPosition + Moby:GenePosition + data + A position in a map (for example a genetic map), either a single position (point) or a region / interval. + data + edam + bioinformatics + Locus + Moby:Position + + + + + + + + Amino acid property + + Amino acid data + beta12orEarlier + data + edam + data + bioinformatics + Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids. + + + + + + + + Annotation + + true + A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. + bioinformatics + beta12orEarlier + data + data + beta13 + This is a broad data type and is used a placeholder for other, more specific types. + edam + + + + + + + + + Map attribute + + + + + + + + bioinformatics + beta12orEarlier + data + An attribute of a molecular map (genetic or physical). + edam + data + + + + + + + + Vienna RNA structural data + + true + beta12orEarlier + edam + beta12orEarlier + data + data + bioinformatics + Data used by the Vienna RNA analysis package. + + + + + + + + + Sequence mask parameter + + data + Data used to replace (mask) characters in a molecular sequence. + bioinformatics + edam + data + beta12orEarlier + + + + + + + + Enzyme kinetics data + + This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + edam + Data concerning chemical reaction(s) catalysed by enzyme(s). + data + data + bioinformatics + + + + + + + + Michaelis Menten plot + + edam + beta12orEarlier + data + A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent. + data + bioinformatics + + + + + + + + Hanes Woolf plot + + A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v). + edam + data + bioinformatics + beta12orEarlier + data + + + + + + + + Experimental data + + true + Experimental measurement data + edam + data + beta13 + bioinformatics + beta12orEarlier + Raw data from or annotation on laboratory experiments. + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + data + + + + + + + + + + Genome version information + + + Information on a genome version. + data + bioinformatics + beta12orEarlier + edam + data + + + + + + + + Evidence + + beta12orEarlier + bioinformatics + data + data + edam + Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc. + + + + + + + + Sequence record lite + + data + edam + bioinformatics + A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. + data + beta12orEarlier + + + + + + + + Sequence + + + + + + + + edam + data + One or more molecular sequences, possibly with associated annotation. + data + bioinformatics + This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. + beta12orEarlier + + + + + + + + + + Sequence record lite (nucleic acid) + + + bioinformatics + edam + data + A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. + data + beta12orEarlier + + + + + + + + Sequence record lite (protein) + + + A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. + data + beta12orEarlier + edam + bioinformatics + data + + + + + + + + Report + + beta12orEarlier + data + document + data + bioinformatics + This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location + of some thing. + Document + edam + A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself. + Text + + + + + + + + + Molecular property (general) + + data + beta12orEarlier + General data for a molecule. + bioinformatics + General molecular property + data + edam + + + + + + + + Structural data + + true + edam + beta13 + Data concerning molecular structural data. + data + data + beta12orEarlier + bioinformatics + This is a broad data type and is used a placeholder for other, more specific types. + + + + + + + + + + Sequence motif (nucleic acid) + + bioinformatics + beta12orEarlier + data + data + edam + A nucleotide sequence motif. + + + + + + + + Sequence motif (protein) + + edam + An amino acid sequence motif. + bioinformatics + beta12orEarlier + data + data + + + + + + + + Search parameter + + data + data + Some simple value controlling a search operation, typically a search of a database. + beta12orEarlier + edam + bioinformatics + + + + + + + + Database hits + + edam + data + bioinformatics + A report of hits from searching a database of some type. + beta12orEarlier + data + + + + + + + + Secondary structure + + The secondary structure assignment (predicted or real) of a nucleic acid or protein. + beta12orEarlier + data + data + edam + bioinformatics + + + + + + + + Matrix + + An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences. + bioinformatics + data + This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + data + edam + + + + + + + + Alignment report + + This is a broad data type and is used a placeholder for other, more specific types. + edam + data + An informative report about a molecular alignment of some type, including alignment-derived data or metadata. + bioinformatics + beta12orEarlier + data + + + + + + + + Nucleic acid report + + data + bioinformatics + beta12orEarlier + data + edam + An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data. + + + + + + + + Structure report + + Structure-derived report + data + beta12orEarlier + bioinformatics + An informative report on general information, properties or features of one or more molecular tertiary (3D) structures. + data + edam + + + + + + + + Nucleic acid structure report + + + A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s). + data + beta12orEarlier + Nucleic acid property (structural) + bioinformatics + Nucleic acid structural property + This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. + edam + data + + + + + + + + Molecular property + + bioinformatics + data + Physicochemical property + data + edam + A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. + SO:0000400 + beta12orEarlier + + + + + + + + DNA base structural data + + + data + edam + beta12orEarlier + data + Structural data for DNA base pairs or runs of bases, such as energy or angle data. + bioinformatics + + + + + + + + Database entry version information + + + edam + data + Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on. + data + beta12orEarlier + bioinformatics + + + + + + + + Accession + + data + bioinformatics + edam + A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. + beta12orEarlier + + identifier + identifiers + + + + + + + + + Nucleic acid features (SNP) + + An SNP is an individual point mutation or substitution of a single nucleotide. + beta12orEarlier + data + edam + data + SNP annotation + Single nucleotide polymorphism + Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence. + bioinformatics + + + + + + + + Data reference + + beta12orEarlier + data + Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology. + edam + bioinformatics + A list of database accessions or identifiers are usually included. + data + + + + + + + + Job identifier + + bioinformatics + identifiers + beta12orEarlier + + edam + An identifier of a submitted job. + data + identifier + + + + + + + + Name + + + + + edam + A name of a thing, which need not necessarily uniquely identify it. + Symbolic name + bioinformatics + identifier + identifiers + data + beta12orEarlier + + + Closely related, but focusing on labeling and human readability but not on identification. + + + + + + + + + + + Type + + data + data + edam + beta12orEarlier + + A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values). + bioinformatics + + + + + + + + User ID + + edam + bioinformatics + identifier + data + beta12orEarlier + An identifier of a software end-user (typically a person). + identifiers + + + + + + + + KEGG organism code + + + edam + A three-letter code used in the KEGG databases to uniquely identify organisms. + beta12orEarlier + bioinformatics + identifier + identifiers + data + + + + + + + + Gene name (KEGG GENES) + + + edam + identifiers + Moby_namespace:GeneId + Name of an entry (gene) from the KEGG GENES database. + data + bioinformatics + identifier + [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* + KEGG GENES entry name + beta12orEarlier + + + + + + + + BioCyc ID + + + edam + identifiers + bioinformatics + beta12orEarlier + Identifier of an object from one of the BioCyc databases. + identifier + data + + + + + + + + Compound ID (BioCyc) + + + edam + beta12orEarlier + Identifier of a compound from the BioCyc chemical compounds database. + identifier + bioinformatics + BioCyc compound identifier + identifiers + data + BioCyc compound ID + + + + + + + + Reaction ID (BioCyc) + + + + + + + + + identifiers + bioinformatics + beta12orEarlier + edam + data + Identifier of a biological reaction from the BioCyc reactions database. + identifier + + + + + + + + Enzyme ID (BioCyc) + + + beta12orEarlier + BioCyc enzyme ID + edam + identifier + Identifier of an enzyme from the BioCyc enzymes database. + data + identifiers + bioinformatics + + + + + + + + Reaction ID + + + + + + + + + identifier + Identifier of a biological reaction from a database. + edam + bioinformatics + identifiers + beta12orEarlier + data + + + + + + + + Identifier (hybrid) + + edam + beta12orEarlier + This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. + An identifier that is re-used for data objects of fundamentally different types (typically served from a single database). + identifiers + data + bioinformatics + identifier + + + + + + + + Molecular property identifier + + + + + + + + identifiers + bioinformatics + Identifier of a molecular property. + edam + data + beta12orEarlier + identifier + + + + + + + + Codon usage table identifier + + + + + + + + + + + + + + data + identifier + edam + bioinformatics + beta12orEarlier + identifiers + Identifier of a codon usage table, for example a genetic code. + + + + + + + + FlyBase primary identifier + + Primary identifier of an object from the FlyBase database. + identifiers + bioinformatics + identifier + edam + data + beta12orEarlier + + + + + + + + WormBase identifier + + identifier + identifiers + Identifier of an object from the WormBase database. + beta12orEarlier + bioinformatics + data + edam + + + + + + + + WormBase wormpep ID + + + bioinformatics + beta12orEarlier + CE[0-9]{5} + identifiers + Protein identifier used by WormBase database. + edam + identifier + data + + + + + + + + Nucleic acid features (codon) + + true + beta12orEarlier + data + data + bioinformatics + An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon. + beta12orEarlier + edam + + + + + + + + + Map identifier + + + + + + + + data + identifiers + identifier + edam + bioinformatics + beta12orEarlier + An identifier of a map of a molecular sequence. + + + + + + + + Person identifier + + identifiers + beta12orEarlier + bioinformatics + edam + data + identifier + An identifier of a software end-user (typically a person). + + + + + + + + Nucleic acid identifier + + + + + + + + identifiers + bioinformatics + beta12orEarlier + edam + identifier + data + Name or other identifier of a nucleic acid molecule. + + + + + + + + Translation frame specification + + edam + data + Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). + data + bioinformatics + beta12orEarlier + + + + + + + + Genetic code identifier + + + + + + + + bioinformatics + data + identifier + identifiers + beta12orEarlier + An identifier of a genetic code. + edam + + + + + + + + Genetic code name + + + bioinformatics + identifier + identifiers + beta12orEarlier + data + Informal name for a genetic code, typically an organism name. + edam + + + + + + + + File format name + + beta12orEarlier + bioinformatics + identifiers + Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on. + edam + identifier + data + + + + + + + + Sequence profile type + + + beta12orEarlier + A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. + data + edam + bioinformatics + data + + + + + + + + Operating system name + + bioinformatics + Name of a computer operating system such as Linux, PC or Mac. + beta12orEarlier + edam + identifier + data + identifiers + + + + + + + + Mutation type + + true + bioinformatics + A type of point or block mutation, including insertion, deletion, change, duplication and moves. + beta12orEarlier + data + edam + data + beta12orEarlier + + + + + + + + + Logical operator + + data + edam + bioinformatics + identifier + A logical operator such as OR, AND, XOR, and NOT. + identifiers + beta12orEarlier + + + + + + + + Results sort order + + bioinformatics + A control of the order of data that is output, for example the order of sequences in an alignment. + edam + data + data + beta12orEarlier + Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. + + + + + + + + Toggle + + true + data + edam + beta12orEarlier + bioinformatics + A simple parameter that is a toggle (boolean value), typically a control for a modal tool. + beta12orEarlier + data + + + + + + + + + Sequence width + + true + The width of an output sequence or alignment. + beta12orEarlier + bioinformatics + data + beta12orEarlier + edam + data + + + + + + + + + Gap penalty + + A penalty for introducing or extending a gap in an alignment. + data + beta12orEarlier + data + edam + bioinformatics + + + + + + + + Nucleic acid melting temperature + + Melting temperature + data + data + A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. + bioinformatics + edam + beta12orEarlier + + + + + + + + Concentration + + data + data + The concentration of a chemical compound. + beta12orEarlier + bioinformatics + edam + + + + + + + + Window step size + + Size of the incremental 'step' a sequence window is moved over a sequence. + bioinformatics + data + beta12orEarlier + data + edam + + + + + + + + EMBOSS graph + + true + An image of a graph generated by the EMBOSS suite. + bioinformatics + beta12orEarlier + beta12orEarlier + data + data + edam + + + + + + + + + EMBOSS report + + true + edam + beta12orEarlier + data + beta12orEarlier + An application report generated by the EMBOSS suite. + bioinformatics + data + + + + + + + + + Sequence offset + + + An offset for a single-point sequence position. + data + edam + data + beta12orEarlier + bioinformatics + + + + + + + + Threshold + + edam + A value that serves as a threshold for a tool (usually to control scoring or output). + beta12orEarlier + data + data + bioinformatics + + + + + + + + Protein report (transcription factor) + + true + data + edam + An informative report on a transcription factor protein. + data + beta12orEarlier + Transcription factor binding site data + This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. + bioinformatics + beta13 + + + + + + + + + Database category name + + true + identifiers + beta12orEarlier + identifier + The name of a category of biological or bioinformatics database. + edam + bioinformatics + beta12orEarlier + data + + + + + + + + + Sequence profile name + + true + data + bioinformatics + edam + identifier + Name of a sequence profile. + beta12orEarlier + beta12orEarlier + identifiers + + + + + + + + + Color + + true + beta12orEarlier + beta12orEarlier + data + Specification of one or more colors. + data + edam + bioinformatics + + + + + + + + + Rendering parameter + + Graphics parameter + Graphical parameter + A parameter that is used to control rendering (drawing) to a device or image. + bioinformatics + data + beta12orEarlier + data + edam + + + + + + + + Sequence name + + + identifier + data + edam + bioinformatics + identifiers + Any arbitrary name of a molecular sequence. + beta12orEarlier + + + + + + + + Date + + edam + beta12orEarlier + data + A temporal date. + bioinformatics + data + + + + + + + + Word composition + + true + edam + beta12orEarlier + beta12orEarlier + data + bioinformatics + Word composition data for a molecular sequence. + data + + + + + + + + + + Fickett testcode plot + + data + beta12orEarlier + data + A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. + edam + bioinformatics + + + + + + + + Sequence similarity plot + + A plot of sequence similarities identified from word-matching or character comparison. + bioinformatics + data + beta12orEarlier + edam + data + + + + + + + + Helical wheel + + An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. + bioinformatics + edam + data + beta12orEarlier + data + + + + + + + + Helical net + + edam + An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix. + bioinformatics + data + Useful for highlighting amphipathicity and other properties. + beta12orEarlier + data + + + + + + + + Protein sequence properties plot + + true + A plot of general physicochemical properties of a protein sequence. + edam + beta12orEarlier + data + beta12orEarlier + data + bioinformatics + + + + + + + + + Protein ionization curve + + data + A plot of pK versus pH for a protein. + bioinformatics + beta12orEarlier + data + edam + + + + + + + + Sequence composition plot + + A plot of character or word composition / frequency of a molecular sequence. + beta12orEarlier + data + edam + bioinformatics + data + + + + + + + + Nucleic acid density plot + + edam + data + data + Density plot (of base composition) for a nucleotide sequence. + beta12orEarlier + bioinformatics + + + + + + + + Sequence trace image + + bioinformatics + beta12orEarlier + data + edam + Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). + data + + + + + + + + Nucleic acid features (siRNA) + + + + + + + + A report on siRNA duplexes in mRNA. + bioinformatics + data + data + beta12orEarlier + edam + + + + + + + + Sequence set (stream) + + true + data + This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. + data + beta12orEarlier + edam + bioinformatics + beta12orEarlier + A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing. + + + + + + + + + FlyBase secondary identifier + + beta12orEarlier + identifier + identifiers + bioinformatics + Secondary identifier are used to handle entries that were merged with or split from other entries in the database. + Secondary identifier of an object from the FlyBase database. + edam + data + + + + + + + + Cardinality + + true + beta12orEarlier + data + beta12orEarlier + edam + data + bioinformatics + The number of a certain thing. + + + + + + + + Exactly 1 + + true + bioinformatics + edam + A single thing. + data + data + beta12orEarlier + beta12orEarlier + + + + + + + + 1 or more + + true + beta12orEarlier + edam + bioinformatics + beta12orEarlier + One or more things. + data + data + + + + + + + + Exactly 2 + + true + data + beta12orEarlier + edam + beta12orEarlier + bioinformatics + Exactly two things. + data + + + + + + + + 2 or more + + true + data + edam + data + beta12orEarlier + bioinformatics + beta12orEarlier + Two or more things. + + + + + + + + Sequence checksum + + + Hash + edam + Hash code + A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing. + data + Hash value + bioinformatics + Hash sum + data + beta12orEarlier + + + + + + + + Protein features (chemical modification) + + Protein modification annotation + data + bioinformatics + Data on a chemical modification of a protein. + beta12orEarlier + MOD:00000 + GO:0006464 + edam + data + + + + + + + + Error + + data + data + bioinformatics + Data on an error generated by computer system or tool. + beta12orEarlier + edam + + + + + + + + Database entry metadata + + data + bioinformatics + Basic information on any arbitrary database entry. + edam + data + beta12orEarlier + + + + + + + + Gene cluster + + true + A cluster of similar genes. + beta12orEarlier + data + edam + beta13 + data + bioinformatics + + + + + + + + + Sequence record full + + SO:2000061 + A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. + data + beta12orEarlier + edam + bioinformatics + data + + + + + + + + + Plasmid identifier + + data + beta12orEarlier + identifier + An identifier of a plasmid in a database. + bioinformatics + edam + identifiers + + + + + + + + Mutation ID + + + A unique identifier of a specific mutation catalogued in a database. + beta12orEarlier + identifier + identifiers + bioinformatics + edam + data + + + + + + + + Mutation annotation (basic) + + true + data + beta12orEarlier + edam + data + beta12orEarlier + bioinformatics + Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style. + + + + + + + + + Mutation annotation (prevalence) + + true + edam + data + beta12orEarlier + An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. + bioinformatics + data + beta12orEarlier + + + + + + + + + Mutation annotation (prognostic) + + true + data + beta12orEarlier + An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study. + edam + beta12orEarlier + data + bioinformatics + + + + + + + + + Mutation annotation (functional) + + true + data + beta12orEarlier + data + beta12orEarlier + bioinformatics + edam + An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on. + + + + + + + + + Codon number + + data + data + The number of a codon, for instance, at which a mutation is located. + bioinformatics + beta12orEarlier + edam + + + + + + + + Tumor annotation + + beta12orEarlier + An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. + bioinformatics + edam + data + data + + + + + + + + Server metadata + + bioinformatics + edam + beta12orEarlier + data + Basic information about a server on the web, such as an SRS server. + data + + + + + + + + Database field name + + identifier + beta12orEarlier + data + identifiers + bioinformatics + The name of a field in a database. + edam + + + + + + + + Sequence cluster ID (SYSTERS) + + identifier + edam + bioinformatics + data + beta12orEarlier + identifiers + SYSTERS cluster ID + Unique identifier of a sequence cluster from the SYSTERS database. + + + + + + + + Ontology metadata + + + + + + + + bioinformatics + data + edam + data + Data concerning a biological ontology. + beta12orEarlier + + + + + + + + Raw SCOP domain classification + + true + Raw SCOP domain classification data files. + beta12orEarlier + These are the parsable data files provided by SCOP. + beta13 + data + bioinformatics + data + edam + + + + + + + + + Raw CATH domain classification + + true + beta12orEarlier + bioinformatics + data + beta13 + Raw CATH domain classification data files. + data + These are the parsable data files provided by CATH. + edam + + + + + + + + + Heterogen annotation + + bioinformatics + edam + data + An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. + beta12orEarlier + data + + + + + + + + Phylogenetic property values + + true + beta12orEarlier + data + data + Phylogenetic property values data. + edam + beta12orEarlier + bioinformatics + + + + + + + + + Sequence set (bootstrapped) + + A collection of sequences output from a bootstrapping (resampling) procedure. + data + bioinformatics + data + Bootstrapping is often performed in phylogenetic analysis. + beta12orEarlier + edam + + + + + + + + Phylogenetic consensus tree + + true + data + beta12orEarlier + beta12orEarlier + bioinformatics + A consensus phylogenetic tree derived from comparison of multiple trees. + edam + data + + + + + + + + + Schema + + edam + data + A data schema for organising or transforming data of some type. + data + bioinformatics + beta12orEarlier + + + + + + + + DTD + + edam + beta12orEarlier + data + bioinformatics + A DTD (document type definition). + data + + + + + + + + XML Schema + + edam + data + data + An XML Schema. + XSD + beta12orEarlier + bioinformatics + + + + + + + + Relax-NG schema + + edam + data + A relax-NG schema. + bioinformatics + data + beta12orEarlier + + + + + + + + XSLT stylesheet + + data + data + An XSLT stylesheet. + beta12orEarlier + edam + bioinformatics + + + + + + + + Data resource definition name + + + The name of a data type. + identifier + beta12orEarlier + identifiers + bioinformatics + data + edam + + + + + + + + OBO file format name + + bioinformatics + beta12orEarlier + Name of an OBO file format such as OBO-XML, plain and so on. + edam + identifiers + identifier + data + + + + + + + + Gene ID (MIPS) + + MIPS genetic element identifier + identifiers + beta12orEarlier + data + bioinformatics + Identifier for genetic elements in MIPS database. + identifier + edam + + + + + + + + Sequence identifier (protein) + + true + identifier + data + beta12orEarlier + edam + identifiers + beta12orEarlier + bioinformatics + An identifier of protein sequence(s) or protein sequence database entries. + + + + + + + + + Sequence identifier (nucleic acid) + + true + beta12orEarlier + identifiers + An identifier of nucleotide sequence(s) or nucleotide sequence database entries. + edam + beta12orEarlier + identifier + data + bioinformatics + + + + + + + + + EMBL accession + + edam + data + An accession number of an entry from the EMBL sequence database. + EMBL accession number + EMBL identifier + beta12orEarlier + EMBL ID + identifiers + bioinformatics + identifier + + + + + + + + UniProt ID + + + + + + + + edam + UniProt entry name + data + UniProt identifier + beta12orEarlier + bioinformatics + UniProtKB entry name + An identifier of a polypeptide in the UniProt database. + identifier + UniProtKB identifier + identifiers + + + + + + + + GenBank accession + + bioinformatics + GenBank identifier + identifiers + GenBank ID + GenBank accession number + beta12orEarlier + edam + data + Accession number of an entry from the GenBank sequence database. + identifier + + + + + + + + Gramene secondary identifier + + identifier + Gramene secondary ID + Secondary (internal) identifier of a Gramene database entry. + identifiers + edam + Gramene internal ID + bioinformatics + data + Gramene internal identifier + beta12orEarlier + + + + + + + + Sequence variation ID + + + bioinformatics + identifier + beta12orEarlier + identifiers + data + An identifier of an entry from a database of molecular sequence variation. + edam + + + + + + + + Gene ID + + + identifiers + identifier + beta12orEarlier + Gene accession + Gene code + bioinformatics + A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. + edam + data + + + + + + + + Gene name (AceView) + + beta12orEarlier + edam + Name of an entry (gene) from the AceView genes database. + identifier + identifiers + AceView gene name + data + bioinformatics + + + + + + + + Gene ID (ECK) + + http://www.geneontology.org/doc/GO.xrf_abbs: ECK + E. coli K-12 gene identifier + identifier + Identifier of an E. coli K-12 gene from EcoGene Database. + data + edam + bioinformatics + beta12orEarlier + ECK accession + identifiers + + + + + + + + Gene ID (HGNC) + + bioinformatics + identifier + edam + Identifier for a gene approved by the HUGO Gene Nomenclature Committee. + beta12orEarlier + data + HGNC ID + identifiers + + + + + + + + Gene name + + + beta12orEarlier + bioinformatics + identifiers + edam + data + identifier + The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol. + + + + + + + + Gene name (NCBI) + + edam + identifier + bioinformatics + Name of an entry (gene) from the NCBI genes database. + NCBI gene name + identifiers + data + beta12orEarlier + + + + + + + + SMILES string + + edam + data + beta12orEarlier + A specification of a chemical structure in SMILES format. + bioinformatics + data + + + + + + + + STRING ID + + beta12orEarlier + identifier + data + bioinformatics + Unique identifier of an entry from the STRING database of protein-protein interactions. + identifiers + edam + + + + + + + + Virus annotation + + beta12orEarlier + bioinformatics + data + data + edam + An informative report on a specific virus. + + + + + + + + Virus annotation (taxonomy) + + edam + beta12orEarlier + data + data + An informative report on the taxonomy of a specific virus. + bioinformatics + + + + + + + + Reaction ID (SABIO-RK) + + bioinformatics + data + [0-9]+ + edam + beta12orEarlier + identifier + Identifier of a biological reaction from the SABIO-RK reactions database. + identifiers + + + + + + + + Carbohydrate structure report + + data + bioinformatics + edam + beta12orEarlier + data + Annotation on or information derived from one or more specific carbohydrate 3D structure(s). + + + + + + + + GI number + + edam + identifiers + bioinformatics + Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. + A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record. + gi number + NCBI GI number + data + identifier + beta12orEarlier + + + + + + + + NCBI version + + accession.version + Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. + identifier + beta12orEarlier + An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number. + identifiers + bioinformatics + edam + NCBI accession.version + data + + + + + + + + Cell line name + + edam + data + The name of a cell line. + bioinformatics + identifier + beta12orEarlier + identifiers + + + + + + + + Cell line name (exact) + + The name of a cell line. + data + beta12orEarlier + identifier + edam + identifiers + bioinformatics + + + + + + + + Cell line name (truncated) + + data + identifiers + identifier + edam + beta12orEarlier + The name of a cell line. + bioinformatics + + + + + + + + Cell line name (no punctuation) + + identifiers + beta12orEarlier + edam + data + bioinformatics + identifier + The name of a cell line. + + + + + + + + Cell line name (assonant) + + edam + bioinformatics + beta12orEarlier + data + identifier + The name of a cell line. + identifiers + + + + + + + + Enzyme ID + + + Enzyme accession + beta12orEarlier + identifiers + A unique, persistent identifier of an enzyme. + data + identifier + bioinformatics + edam + + + + + + + + REBASE enzyme number + + edam + data + beta12orEarlier + bioinformatics + identifiers + Identifier of an enzyme from the REBASE enzymes database. + identifier + + + + + + + + DrugBank ID + + edam + bioinformatics + Unique identifier of a drug from the DrugBank database. + DB[0-9]{5} + identifier + identifiers + data + beta12orEarlier + + + + + + + + GI number (protein) + + A unique identifier assigned to NCBI protein sequence records. + Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. + bioinformatics + edam + identifier + beta12orEarlier + protein gi + identifiers + protein gi number + data + + + + + + + + Bit score + + data + beta12orEarlier + data + Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. + edam + A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system. + bioinformatics + + + + + + + + Translation phase specification + + + data + bioinformatics + Phase + Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. + edam + beta12orEarlier + data + + + + + + + + Metadata + + beta12orEarlier + data + edam + Provenance metadata + bioinformatics + This is a broad data type and is used a placeholder for other, more specific types. + data + Data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing. + + + + + + + + Ontology identifier + + + + + + + + identifiers + edam + Any arbitrary identifier of an ontology. + data + identifier + beta12orEarlier + bioinformatics + + + + + + + + Ontology concept name + + + beta12orEarlier + identifiers + identifier + bioinformatics + data + The name of a concept in an ontology. + edam + + + + + + + + Genome build identifier + + data + edam + identifiers + An identifier of a build of a particular genome. + bioinformatics + beta12orEarlier + identifier + + + + + + + + Pathway or network name + + edam + beta12orEarlier + data + identifiers + bioinformatics + identifier + The name of a biological pathway or network. + + + + + + + + Pathway ID (KEGG) + + + [a-zA-Z_0-9]{2,3}[0-9]{5} + identifier + beta12orEarlier + data + edam + identifiers + KEGG pathway ID + bioinformatics + Identifier of a pathway from the KEGG pathway database. + + + + + + + + Pathway ID (NCI-Nature) + + Identifier of a pathway from the NCI-Nature pathway database. + [a-zA-Z_0-9]+ + data + bioinformatics + identifier + identifiers + beta12orEarlier + edam + + + + + + + + Pathway ID (ConsensusPathDB) + + + Identifier of a pathway from the ConsensusPathDB pathway database. + bioinformatics + identifier + beta12orEarlier + edam + data + identifiers + + + + + + + + Sequence cluster ID (UniRef) + + edam + UniRef entry accession + bioinformatics + data + Unique identifier of an entry from the UniRef database. + identifier + beta12orEarlier + UniRef cluster id + identifiers + + + + + + + + Sequence cluster ID (UniRef100) + + Unique identifier of an entry from the UniRef100 database. + UniRef100 entry accession + identifiers + bioinformatics + UniRef100 cluster id + data + identifier + edam + beta12orEarlier + + + + + + + + Sequence cluster ID (UniRef90) + + Unique identifier of an entry from the UniRef90 database. + edam + bioinformatics + identifier + identifiers + data + UniRef90 cluster id + beta12orEarlier + UniRef90 entry accession + + + + + + + + Sequence cluster ID (UniRef50) + + identifiers + UniRef50 cluster id + identifier + data + Unique identifier of an entry from the UniRef50 database. + edam + bioinformatics + UniRef50 entry accession + beta12orEarlier + + + + + + + + Ontological data + + true + beta13 + edam + Data concerning an ontology. + This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + data + data + bioinformatics + + + + + + + + + + RNA family annotation + + bioinformatics + data + An informative report on a specific RNA family or other group of classified RNA sequences. + beta12orEarlier + edam + data + + + + + + + + RNA family identifier + + + + + + + + identifiers + Identifier of an RNA family, typically an entry from a RNA sequence classification database. + data + bioinformatics + edam + identifier + beta12orEarlier + + + + + + + + RFAM accession + + + identifier + beta12orEarlier + edam + Stable accession number of an entry (RNA family) from the RFAM database. + identifiers + bioinformatics + data + + + + + + + + Protein signature type + + + data + bioinformatics + edam + A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. + data + beta12orEarlier + + + + + + + + Domain-nucleic acid interaction + + beta12orEarlier + data + data + bioinformatics + edam + Data on protein domain-DNA/RNA interaction(s). + + + + + + + + Domain-domain interaction + + bioinformatics + data + data + beta12orEarlier + Data on protein domain-protein domain interaction(s). + edam + + + + + + + + Domain-domain interaction (indirect) + + true + data + data + Data on indirect protein domain-protein domain interaction(s). + beta12orEarlier + bioinformatics + edam + beta12orEarlier + + + + + + + + + Sequence accession (hybrid) + + + + + + + + data + beta12orEarlier + Accession number of a nucleotide or protein sequence database entry. + edam + bioinformatics + identifiers + identifier + + + + + + + + 2D PAGE data + + true + beta12orEarlier + edam + bioinformatics + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + data + Data concerning two-dimensional polygel electrophoresis. + data + beta13 + + + + + + + + + + Experiment annotation (2D PAGE) + + + + + + + + data + edam + An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel. + bioinformatics + data + beta12orEarlier + + + + + + + + Pathway or network accession + + + edam + identifier + identifiers + data + beta12orEarlier + A persistent, unique identifier of a biological pathway or network (typically a database entry). + bioinformatics + + + + + + + + Secondary structure alignment + + beta12orEarlier + bioinformatics + data + Alignment of the (1D representations of) secondary structure of two or more molecules. + edam + data + + + + + + + + ASTD ID + + + Identifier of an object from the ASTD database. + identifier + beta12orEarlier + bioinformatics + identifiers + data + edam + + + + + + + + ASTD ID (exon) + + Identifier of an exon from the ASTD database. + bioinformatics + beta12orEarlier + identifier + edam + data + identifiers + + + + + + + + ASTD ID (intron) + + edam + identifiers + Identifier of an intron from the ASTD database. + identifier + beta12orEarlier + data + bioinformatics + + + + + + + + ASTD ID (polya) + + identifier + beta12orEarlier + edam + identifiers + data + Identifier of a polyA signal from the ASTD database. + bioinformatics + + + + + + + + ASTD ID (tss) + + edam + identifier + identifiers + data + bioinformatics + beta12orEarlier + Identifier of a transcription start site from the ASTD database. + + + + + + + + 2D PAGE spot (annotated) + + bioinformatics + data + edam + data + An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. + beta12orEarlier + 2D PAGE spot annotation + + + + + + + + Spot ID + + + Unique identifier of a spot from a two-dimensional (protein) gel. + data + edam + identifiers + beta12orEarlier + identifier + bioinformatics + + + + + + + + Spot serial number + + beta12orEarlier + data + edam + bioinformatics + identifiers + Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. + identifier + + + + + + + + Spot ID (HSC-2DPAGE) + + beta12orEarlier + identifier + bioinformatics + data + edam + identifiers + Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. + + + + + + + + Protein-motif interaction + + true + data + beta12orEarlier + Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. + edam + data + beta13 + bioinformatics + + + + + + + + + Strain identifier + + identifier + data + beta12orEarlier + identifiers + Identifier of a strain of an organism variant, typically a plant, virus or bacterium. + edam + bioinformatics + + + + + + + + CABRI accession + + + edam + beta12orEarlier + data + bioinformatics + identifiers + A unique identifier of an item from the CABRI database. + identifier + + + + + + + + Experiment annotation (genotype) + + data + edam + Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. + beta12orEarlier + bioinformatics + data + + + + + + + + Genotype experiment ID + + + + + + + + + data + Identifier of an entry from a database of genotype experiment metadata. + edam + identifiers + identifier + beta12orEarlier + bioinformatics + + + + + + + + EGA accession + + Identifier of an entry from the EGA database. + beta12orEarlier + bioinformatics + identifiers + identifier + data + edam + + + + + + + + IPI protein ID + + identifier + bioinformatics + beta12orEarlier + identifiers + IPI[0-9]{8} + data + edam + Identifier of a protein entry catalogued in the International Protein Index (IPI) database. + + + + + + + + RefSeq accession (protein) + + beta12orEarlier + Accession number of a protein from the RefSeq database. + identifier + identifiers + edam + bioinformatics + data + RefSeq protein ID + + + + + + + + EPD ID + + bioinformatics + identifiers + EPD identifier + identifier + data + Identifier of an entry (promoter) from the EPD database. + edam + beta12orEarlier + + + + + + + + TAIR accession + + + Identifier of an entry from the TAIR database. + beta12orEarlier + edam + data + bioinformatics + identifiers + identifier + + + + + + + + TAIR accession (At gene) + + edam + Identifier of an Arabidopsis thaliana gene from the TAIR database. + identifiers + bioinformatics + beta12orEarlier + data + identifier + + + + + + + + UniSTS accession + + data + Identifier of an entry from the UniSTS database. + bioinformatics + edam + identifiers + beta12orEarlier + identifier + + + + + + + + UNITE accession + + edam + identifiers + bioinformatics + Identifier of an entry from the UNITE database. + data + beta12orEarlier + identifier + + + + + + + + UTR accession + + bioinformatics + data + edam + identifiers + Identifier of an entry from the UTR database. + identifier + beta12orEarlier + + + + + + + + UniParc accession + + data + UPI + UniParc ID + identifier + Accession number of a UniParc (protein sequence) database entry. + UPI[A-F0-9]{10} + identifiers + edam + bioinformatics + beta12orEarlier + + + + + + + + mFLJ/mKIAA number + + bioinformatics + identifier + data + Identifier of an entry from the Rouge or HUGE databases. + identifiers + beta12orEarlier + edam + + + + + + + + Fungi annotation + + An informative report on a specific fungus. + data + data + beta12orEarlier + edam + bioinformatics + + + + + + + + Fungi annotation (anamorph) + + bioinformatics + edam + An informative report on a specific fungus anamorph. + data + beta12orEarlier + data + + + + + + + + Nucleic acid features (exon) + + Gene features (exon) + beta12orEarlier + data + data + An informative report on an exon in a nucleotide sequences. + bioinformatics + edam + + + + + + + + Protein ID (Ensembl) + + + bioinformatics + Unique identifier for a protein from the Ensembl database. + data + Ensembl protein ID + beta12orEarlier + identifier + edam + identifiers + + + + + + + + Gene annotation (transcript) + + An informative report on a specific gene transcript, clone or EST. + edam + Gene annotation (clone or EST) + Gene transcript annotation + beta12orEarlier + bioinformatics + data + data + + + + + + + + Toxin annotation + + edam + bioinformatics + An informative report on a specific toxin. + data + data + beta12orEarlier + + + + + + + + Protein report (membrane protein) + + true + beta12orEarlier + data + bioinformatics + An informative report on a membrane protein. + data + edam + beta12orEarlier + + + + + + + + + Protein-drug interaction + + beta12orEarlier + bioinformatics + edam + data + Informative report on protein-drug interaction(s) including binding affinity data. + data + + + + + + + + Map data + + true + edam + bioinformatics + Data concerning a map of molecular sequence(s). + beta13 + This is a broad data type and is used a placeholder for other, more specific types. + data + beta12orEarlier + data + + + + + + + + + + Phylogenetic raw data + + beta12orEarlier + bioinformatics + data + edam + data + This is a broad data type and is used a placeholder for other, more specific types. + Data concerning phylogeny, typically of molecular sequences. + Phylogenetic data + + + + + + + + Protein data + + true + data + data + beta13 + edam + beta12orEarlier + bioinformatics + Data concerning one or more protein molecules. + This is a broad data type and is used a placeholder for other, more specific types. + + + + + + + + + Nucleic acid data + + true + bioinformatics + This is a broad data type and is used a placeholder for other, more specific types. + data + data + beta12orEarlier + beta13 + Data concerning one or more nucleic acid molecules. + edam + + + + + + + + + Article data + + true + beta13 + edam + bioinformatics + Data concerning the scientific literature. + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. + data + beta12orEarlier + data + + + + + + + + + + + Parameter + + + bioinformatics + data + edam + Tool parameter + + Tool-specific parameter + data + Parameter or primitive + beta12orEarlier + Typically a simple numerical or string value that controls the operation of a tool. + + + Slightly narrower in the sense of changing the characteristics of a system/function. + + + + + + + + + + + Molecular data + + true + This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + beta13 + Data concerning a specific type of molecule. + edam + bioinformatics + data + data + Molecule-specific data + + + + + + + + + Molecule report + + data + data + edam + beta12orEarlier + Molecular report + bioinformatics + An informative report on a specific molecule. + + + + + + + + Organism annotation + + bioinformatics + data + edam + beta12orEarlier + data + An informative report on a specific organism. + + + + + + + + Experiment annotation + + edam + Annotation on a wet lab experiment, such as experimental conditions. + data + data + beta12orEarlier + bioinformatics + + + + + + + + Nucleic acid features (mutation) + + data + Annotation on a mutation. + edam + Mutation annotation + data + beta12orEarlier + bioinformatics + + + + + + + + Sequence parameter + + data + data + bioinformatics + beta12orEarlier + edam + A parameter concerning calculations on molecular sequences. + + + + + + + + Sequence tag profile + + bioinformatics + data + Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed. + Sequencing-based expression profile + beta12orEarlier + edam + SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. + data + + + + + + + + Mass spectrometry data + beta12orEarlier + + Data concerning a mass spectrometry measurement. + bioinformatics + data + edam + data + + + + + + + + + Protein structure raw data + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + bioinformatics + Raw data from experimental methods for determining protein structure. + data + edam + data + beta12orEarlier + + + + + + + + Mutation identifier + + identifier + beta12orEarlier + bioinformatics + edam + data + identifiers + An identifier of a mutation. + + + + + + + + Alignment data + + true + bioinformatics + edam + This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. + data + data + beta12orEarlier + Data concerning an alignment of two or more molecular sequences, structures or derived data. + beta13 + + + + + + + + + + Data index data + + true + This is a broad data type and is used a placeholder for other, more specific types. + Database index + beta13 + bioinformatics + Data concerning an index of data. + data + edam + data + beta12orEarlier + + + + + + + + + + Amino acid name (single letter) + + identifier + identifiers + bioinformatics + edam + Single letter amino acid identifier, e.g. G. + data + beta12orEarlier + + + + + + + + Amino acid name (three letter) + + identifier + data + edam + Three letter amino acid identifier, e.g. GLY. + bioinformatics + identifiers + beta12orEarlier + + + + + + + + Amino acid name (full name) + + Full name of an amino acid, e.g. Glycine. + identifiers + bioinformatics + beta12orEarlier + edam + data + identifier + + + + + + + + Toxin identifier + + + + + + + + data + identifier + bioinformatics + Identifier of a toxin. + identifiers + edam + beta12orEarlier + + + + + + + + ArachnoServer ID + + beta12orEarlier + edam + identifier + bioinformatics + Unique identifier of a toxin from the ArachnoServer database. + identifiers + data + + + + + + + + Expressed gene list + + A simple summary of expressed genes. + edam + Gene annotation (expressed gene list) + data + bioinformatics + beta12orEarlier + data + + + + + + + + BindingDB Monomer ID + + Unique identifier of a monomer from the BindingDB database. + beta12orEarlier + identifiers + edam + identifier + bioinformatics + data + + + + + + + + GO concept name + + true + data + The name of a concept from the GO ontology. + edam + bioinformatics + beta12orEarlier + beta12orEarlier + identifiers + identifier + + + + + + + + + GO concept ID (biological process) + + An identifier of a 'biological process' concept from the the Gene Ontology. + bioinformatics + identifiers + identifier + edam + data + beta12orEarlier + [0-9]{7}|GO:[0-9]{7} + + + + + + + + GO concept ID (molecular function) + + An identifier of a 'molecular function' concept from the the Gene Ontology. + data + bioinformatics + identifier + [0-9]{7}|GO:[0-9]{7} + identifiers + beta12orEarlier + edam + + + + + + + + GO concept name (cellular component) + + true + identifier + bioinformatics + beta12orEarlier + identifiers + edam + beta12orEarlier + The name of a concept for a cellular component from the GO ontology. + data + + + + + + + + + Northern blot image + + An image arising from a Northern Blot experiment. + data + beta12orEarlier + edam + bioinformatics + data + + + + + + + + Blot ID + + + identifier + edam + data + identifiers + beta12orEarlier + Unique identifier of a blot from a Northern Blot. + bioinformatics + + + + + + + + BlotBase blot ID + + identifiers + bioinformatics + identifier + data + Unique identifier of a blot from a Northern Blot from the BlotBase database. + beta12orEarlier + edam + + + + + + + + Hierarchy + + Hierarchy annotation + bioinformatics + edam + A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation. + beta12orEarlier + data + data + + + + + + + + Hierarchy identifier + + true + bioinformatics + identifier + data + Identifier of an entry from a database of biological hierarchies. + identifiers + edam + beta12orEarlier + beta12orEarlier + + + + + + + + + Brite hierarchy ID + + edam + identifier + Identifier of an entry from the Brite database of biological hierarchies. + bioinformatics + beta12orEarlier + identifiers + data + + + + + + + + Cancer type + + true + beta12orEarlier + bioinformatics + beta12orEarlier + edam + A type (represented as a string) of cancer. + data + data + + + + + + + + + BRENDA organism ID + + bioinformatics + beta12orEarlier + data + A unique identifier for an organism used in the BRENDA database. + edam + identifier + identifiers + + + + + + + + UniGene taxon + + data + identifiers + beta12orEarlier + identifier + bioinformatics + UniGene organism abbreviation + edam + The name of a taxon using the controlled vocabulary of the UniGene database. + + + + + + + + UTRdb taxon + + bioinformatics + identifier + data + edam + The name of a taxon using the controlled vocabulary of the UTRdb database. + beta12orEarlier + identifiers + + + + + + + + Catalogue identifier + + An identifier of a catalogue of biological resources. + beta12orEarlier + identifier + identifiers + data + edam + bioinformatics + + + + + + + + CABRI catalogue name + + + bioinformatics + beta12orEarlier + identifiers + data + The name of a catalogue of biological resources from the CABRI database. + edam + identifier + + + + + + + + Secondary structure alignment metadata + + true + data + edam + data + bioinformatics + beta12orEarlier + beta12orEarlier + An informative report on protein secondary structure alignment-derived data or metadata. + + + + + + + + + Molecular interaction + + bioinformatics + Molecular interaction data + edam + beta12orEarlier + data + Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). + data + + + + + + + + Pathway or network + + + + + + + + data + Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). + edam + beta12orEarlier + bioinformatics + Network + data + + + + + + + + Small molecule data + + true + data + beta13 + edam + beta12orEarlier + Data concerning one or more small molecules. + data + This is a broad data type and is used a placeholder for other, more specific types. + bioinformatics + + + + + + + + + Genotype and phenotype data + + true + Data concerning a particular genotype, phenotype or a genotype / phenotype relation. + bioinformatics + data + data + edam + beta13 + beta12orEarlier + + + + + + + + + Microarray data + + This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 + data + edam + beta12orEarlier + Image or hybridisation data for a microarray, typically a study of gene expression. + data + Gene expression data + bioinformatics + + + + + + + + Compound ID (KEGG) + + + KEGG compound identifier + identifier + beta12orEarlier + Unique identifier of a chemical compound from the KEGG database. + edam + C[0-9]+ + KEGG compound ID + bioinformatics + data + identifiers + + + + + + + + RFAM name + + + beta12orEarlier + identifiers + edam + data + Name (not necessarily stable) an entry (RNA family) from the RFAM database. + bioinformatics + identifier + + + + + + + + Reaction ID (KEGG) + + + edam + Identifier of a biological reaction from the KEGG reactions database. + beta12orEarlier + data + identifiers + R[0-9]+ + identifier + bioinformatics + + + + + + + + Drug ID (KEGG) + + + data + identifiers + identifier + D[0-9]+ + edam + Unique identifier of a drug from the KEGG Drug database. + bioinformatics + beta12orEarlier + + + + + + + + Ensembl ID + + + identifier + identifiers + data + beta12orEarlier + edam + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. + ENS[A-Z]*[FPTG][0-9]{11} + bioinformatics + + + + + + + + ICD identifier + + + + + + + + identifier + data + bioinformatics + beta12orEarlier + identifiers + edam + [A-Z][0-9]+(\.[-[0-9]+])? + An identifier of a disease from the International Classification of Diseases (ICD) database. + + + + + + + + Sequence cluster ID (CluSTr) + + identifier + CluSTr cluster ID + identifiers + beta12orEarlier + edam + [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? + bioinformatics + CluSTr ID + Unique identifier of a sequence cluster from the CluSTr database. + data + + + + + + + + KEGG Glycan ID + + + beta12orEarlier + bioinformatics + edam + data + identifier + Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). + identifiers + G[0-9]+ + + + + + + + + TCDB ID + + data + A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins. + identifier + [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+ + TC number + edam + OBO file for regular expression. + bioinformatics + beta12orEarlier + identifiers + + + + + + + + MINT ID + + beta12orEarlier + data + edam + identifier + Unique identifier of an entry from the MINT database of protein-protein interactions. + identifiers + MINT\-[0-9]{1,5} + bioinformatics + + + + + + + + DIP ID + + data + identifiers + bioinformatics + DIP[\:\-][0-9]{3}[EN] + beta12orEarlier + edam + identifier + Unique identifier of an entry from the DIP database of protein-protein interactions. + + + + + + + + Signaling Gateway protein ID + + bioinformatics + identifier + A[0-9]{6} + data + Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. + identifiers + edam + beta12orEarlier + + + + + + + + Protein modification ID + + + Identifier of a protein modification catalogued in a database. + beta12orEarlier + bioinformatics + data + identifiers + edam + identifier + + + + + + + + RESID ID + + beta12orEarlier + edam + AA[0-9]{4} + identifier + Identifier of a protein modification catalogued in the RESID database. + bioinformatics + identifiers + data + + + + + + + + RGD ID + + + Identifier of an entry from the RGD database. + beta12orEarlier + [0-9]{4,7} + identifiers + edam + bioinformatics + data + identifier + + + + + + + + TAIR accession (protein) + + + + + + + + + beta12orEarlier + Identifier of a protein sequence from the TAIR database. + identifiers + AASequence:[0-9]{10} + data + edam + identifier + bioinformatics + + + + + + + + Compound ID (HMDB) + + identifiers + beta12orEarlier + bioinformatics + data + HMDB[0-9]{5} + Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). + identifier + HMDB ID + edam + + + + + + + + LIPID MAPS ID + + LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})? + edam + identifiers + data + bioinformatics + Identifier of an entry from the LIPID MAPS database. + LM ID + identifier + beta12orEarlier + + + + + + + + PeptideAtlas ID + + data + PAp[0-9]{8} + identifiers + edam + identifier + beta12orEarlier + PDBML:pdbx_PDB_strand_id + bioinformatics + Identifier of a peptide from the PeptideAtlas peptide databases. + + + + + + + + Molecular interaction ID + + + + + + + + + bioinformatics + beta12orEarlier + Identifier of a report of molecular interactions from a database (typically). + identifier + data + edam + identifiers + + + + + + + + BioGRID interaction ID + + A unique identifier of an interaction from the BioGRID database. + bioinformatics + beta12orEarlier + data + [0-9]+ + identifier + identifiers + edam + + + + + + + + Enzyme ID (MEROPS) + + S[0-9]{2}\.[0-9]{3} + Unique identifier of a peptidase enzyme from the MEROPS database. + beta12orEarlier + MEROPS ID + bioinformatics + edam + identifiers + identifier + data + + + + + + + + Mobile genetic element ID + + + beta12orEarlier + edam + identifier + identifiers + bioinformatics + data + An identifier of a mobile genetic element. + + + + + + + + ACLAME ID + + identifiers + An identifier of a mobile genetic element from the Aclame database. + mge:[0-9]+ + beta12orEarlier + data + edam + bioinformatics + identifier + + + + + + + + SGD ID + + + data + identifier + PWY[a-zA-Z_0-9]{2}\-[0-9]{3} + identifiers + Identifier of an entry from the Saccharomyces genome database (SGD). + beta12orEarlier + bioinformatics + edam + + + + + + + + Book ID + + + data + bioinformatics + identifiers + identifier + edam + Unique identifier of a book. + beta12orEarlier + + + + + + + + ISBN + + identifier + bioinformatics + data + edam + identifiers + The International Standard Book Number (ISBN) is for identifying printed books. + (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X) + beta12orEarlier + + + + + + + + Compound ID (3DMET) + + edam + bioinformatics + identifiers + Identifier of a metabolite from the 3DMET database. + beta12orEarlier + data + identifier + 3DMET ID + B[0-9]{5} + + + + + + + + MatrixDB interaction ID + + beta12orEarlier + edam + bioinformatics + identifier + data + A unique identifier of an interaction from the MatrixDB database. + identifiers + ([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*) + + + + + + + + cPath ID + + + edam + A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database. + beta12orEarlier + These identifiers are unique within the cPath database, however, they are not stable between releases. + identifiers + identifier + [0-9]+ + data + bioinformatics + + + + + + + + PubChem bioassay ID + + + bioinformatics + beta12orEarlier + data + identifier + edam + [0-9]+ + Identifier of an assay from the PubChem database. + identifiers + + + + + + + + PubChem identifier + + + Identifier of an entry from the PubChem database. + bioinformatics + edam + beta12orEarlier + identifier + data + identifiers + + + + + + + + Reaction ID (MACie) + + Identifier of an enzyme reaction mechanism from the MACie database. + identifier + bioinformatics + edam + MACie entry number + M[0-9]{4} + identifiers + data + beta12orEarlier + + + + + + + + Gene ID (miRBase) + + identifier + miRNA name + beta12orEarlier + miRNA identifier + MI[0-9]{7} + Identifier for a gene from the miRBase database. + identifiers + miRNA ID + data + edam + bioinformatics + + + + + + + + Gene ID (ZFIN) + + ZDB\-GENE\-[0-9]+\-[0-9]+ + identifier + edam + beta12orEarlier + bioinformatics + Identifier for a gene from the Zebrafish information network genome (ZFIN) database. + data + identifiers + + + + + + + + Reaction ID (Rhea) + + edam + data + beta12orEarlier + identifier + Identifier of an enzyme-catalysed reaction from the Rhea database. + [0-9]{5} + bioinformatics + identifiers + + + + + + + + Pathway ID (Unipathway) + + Identifier of a biological pathway from the Unipathway database. + upaid + identifier + bioinformatics + edam + beta12orEarlier + data + identifiers + UPA[0-9]{5} + + + + + + + + Compound ID (ChEMBL) + + identifier + Identifier of a small molecular from the ChEMBL database. + data + identifiers + edam + [0-9]+ + beta12orEarlier + ChEMBL ID + bioinformatics + + + + + + + + LGICdb identifier + + data + [a-zA-Z_0-9]+ + identifier + beta12orEarlier + bioinformatics + identifiers + Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. + edam + + + + + + + + Reaction kinetics ID (SABIO-RK) + + edam + identifiers + beta12orEarlier + bioinformatics + identifier + [0-9]+ + Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. + data + + + + + + + + PharmGKB ID + + + data + edam + identifier + beta12orEarlier + identifiers + PA[0-9]+ + bioinformatics + Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + + + + + + + + Pathway ID (PharmGKB) + + + beta12orEarlier + bioinformatics + PA[0-9]+ + Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + edam + identifier + identifiers + data + + + + + + + + Disease ID (PharmGKB) + + + data + edam + Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + bioinformatics + identifiers + PA[0-9]+ + identifier + beta12orEarlier + + + + + + + + Drug ID (PharmGKB) + + + bioinformatics + identifiers + identifier + Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + data + PA[0-9]+ + beta12orEarlier + edam + + + + + + + + Drug ID (TTD) + + beta12orEarlier + identifiers + Identifier of a drug from the Therapeutic Target Database (TTD). + data + edam + bioinformatics + identifier + DAP[0-9]+ + + + + + + + + Target ID (TTD) + + bioinformatics + identifier + beta12orEarlier + Identifier of a target protein from the Therapeutic Target Database (TTD). + identifiers + TTDS[0-9]+ + edam + data + + + + + + + + Cell type identifier + + edam + A unique identifier of a type or group of cells. + identifier + data + bioinformatics + identifiers + beta12orEarlier + + + + + + + + NeuronDB ID + + edam + identifiers + beta12orEarlier + identifier + A unique identifier of a neuron from the NeuronDB database. + data + [0-9]+ + bioinformatics + + + + + + + + NeuroMorpho ID + + data + edam + bioinformatics + identifiers + identifier + [a-zA-Z_0-9]+ + A unique identifier of a neuron from the NeuroMorpho database. + beta12orEarlier + + + + + + + + Compound ID (ChemIDplus) + + beta12orEarlier + [0-9]+ + ChemIDplus ID + data + edam + identifiers + Identifier of a chemical from the ChemIDplus database. + bioinformatics + identifier + + + + + + + + Pathway ID (SMPDB) + + SMP[0-9]{5} + bioinformatics + data + edam + identifier + identifiers + Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). + beta12orEarlier + + + + + + + + BioNumbers ID + + beta12orEarlier + data + bioinformatics + identifiers + identifier + edam + Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. + [0-9]+ + + + + + + + + T3DB ID + + Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. + identifier + T3D[0-9]+ + data + beta12orEarlier + identifiers + bioinformatics + edam + + + + + + + + Carbohydrate identifier + + + + + + + + + + + + + + Identifier of a carbohydrate. + bioinformatics + edam + identifiers + beta12orEarlier + data + identifier + + + + + + + + GlycomeDB ID + + identifier + identifiers + data + edam + [0-9]+ + beta12orEarlier + bioinformatics + Identifier of an entry from the GlycomeDB database. + + + + + + + + LipidBank ID + + Identifier of an entry from the LipidBank database. + identifier + edam + bioinformatics + identifiers + [a-zA-Z_0-9]+[0-9]+ + data + beta12orEarlier + + + + + + + + CDD ID + + Identifier of a conserved domain from the Conserved Domain Database. + identifier + edam + data + cd[0-9]{5} + bioinformatics + identifiers + beta12orEarlier + + + + + + + + MMDB ID + + beta12orEarlier + data + bioinformatics + identifier + identifiers + An identifier of an entry from the MMDB database. + MMDB accession + [0-9]{1,5} + edam + + + + + + + + iRefIndex ID + + [0-9]+ + beta12orEarlier + data + bioinformatics + Unique identifier of an entry from the iRefIndex database of protein-protein interactions. + identifiers + identifier + edam + + + + + + + + ModelDB ID + + edam + beta12orEarlier + identifiers + [0-9]+ + bioinformatics + Unique identifier of an entry from the ModelDB database. + identifier + data + + + + + + + + Pathway ID (DQCS) + + bioinformatics + beta12orEarlier + identifiers + Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). + data + edam + [0-9]+ + identifier + + + + + + + + Ensembl ID (Homo sapiens) + + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). + ENS([EGTP])[0-9]{11} + edam + bioinformatics + identifier + beta12orEarlier + beta12orEarlier + data + identifiers + + + + + + + + + Ensembl ID ('Bos taurus') + + true + ENSBTA([EGTP])[0-9]{11} + beta12orEarlier + identifiers + edam + bioinformatics + identifier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). + data + beta12orEarlier + + + + + + + + + Ensembl ID ('Canis familiaris') + + true + bioinformatics + edam + identifiers + identifier + beta12orEarlier + ENSCAF([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). + data + beta12orEarlier + + + + + + + + + Ensembl ID ('Cavia porcellus') + + true + beta12orEarlier + data + beta12orEarlier + identifiers + identifier + ENSCPO([EGTP])[0-9]{11} + bioinformatics + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). + edam + + + + + + + + + Ensembl ID ('Ciona intestinalis') + + true + identifier + ENSCIN([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). + beta12orEarlier + data + bioinformatics + edam + identifiers + beta12orEarlier + + + + + + + + + Ensembl ID ('Ciona savignyi') + + true + identifiers + edam + identifier + beta12orEarlier + beta12orEarlier + ENSCSAV([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). + data + bioinformatics + + + + + + + + + Ensembl ID ('Danio rerio') + + true + ENSDAR([EGTP])[0-9]{11} + beta12orEarlier + beta12orEarlier + bioinformatics + identifiers + data + edam + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). + identifier + + + + + + + + + Ensembl ID ('Dasypus novemcinctus') + + true + identifier + bioinformatics + data + beta12orEarlier + ENSDNO([EGTP])[0-9]{11} + beta12orEarlier + identifiers + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). + edam + + + + + + + + + Ensembl ID ('Echinops telfairi') + + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). + data + edam + beta12orEarlier + identifier + bioinformatics + identifiers + beta12orEarlier + ENSETE([EGTP])[0-9]{11} + + + + + + + + + Ensembl ID ('Erinaceus europaeus') + + true + beta12orEarlier + data + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). + identifier + beta12orEarlier + bioinformatics + ENSEEU([EGTP])[0-9]{11} + edam + identifiers + + + + + + + + + Ensembl ID ('Felis catus') + + true + data + edam + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). + ENSFCA([EGTP])[0-9]{11} + identifier + beta12orEarlier + identifiers + bioinformatics + + + + + + + + + Ensembl ID ('Gallus gallus') + + true + bioinformatics + beta12orEarlier + identifier + edam + data + beta12orEarlier + identifiers + ENSGAL([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). + + + + + + + + + Ensembl ID ('Gasterosteus aculeatus') + + true + edam + identifier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). + bioinformatics + beta12orEarlier + ENSGAC([EGTP])[0-9]{11} + data + identifiers + beta12orEarlier + + + + + + + + + Ensembl ID ('Homo sapiens') + + true + identifier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). + beta12orEarlier + beta12orEarlier + data + bioinformatics + edam + ENSHUM([EGTP])[0-9]{11} + identifiers + + + + + + + + + Ensembl ID ('Loxodonta africana') + + true + identifiers + ENSLAF([EGTP])[0-9]{11} + identifier + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). + beta12orEarlier + bioinformatics + data + edam + + + + + + + + + Ensembl ID ('Macaca mulatta') + + true + bioinformatics + beta12orEarlier + beta12orEarlier + ENSMMU([EGTP])[0-9]{11} + identifiers + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). + data + identifier + edam + + + + + + + + + Ensembl ID ('Monodelphis domestica') + + true + ENSMOD([EGTP])[0-9]{11} + bioinformatics + edam + beta12orEarlier + identifier + identifiers + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). + beta12orEarlier + data + + + + + + + + + Ensembl ID ('Mus musculus') + + true + edam + data + identifiers + identifier + beta12orEarlier + ENSMUS([EGTP])[0-9]{11} + beta12orEarlier + bioinformatics + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). + + + + + + + + + Ensembl ID ('Myotis lucifugus') + + true + data + identifiers + beta12orEarlier + edam + bioinformatics + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). + identifier + beta12orEarlier + ENSMLU([EGTP])[0-9]{11} + + + + + + + + + Ensembl ID ("Ornithorhynchus anatinus") + + true + identifiers + ENSOAN([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). + edam + beta12orEarlier + bioinformatics + identifier + data + beta12orEarlier + + + + + + + + + Ensembl ID ('Oryctolagus cuniculus') + + true + edam + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). + bioinformatics + beta12orEarlier + data + identifiers + beta12orEarlier + ENSOCU([EGTP])[0-9]{11} + identifier + + + + + + + + + Ensembl ID ('Oryzias latipes') + + true + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). + data + ENSORL([EGTP])[0-9]{11} + identifiers + edam + identifier + beta12orEarlier + bioinformatics + + + + + + + + + Ensembl ID ('Otolemur garnettii') + + true + bioinformatics + ENSSAR([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). + beta12orEarlier + identifiers + edam + beta12orEarlier + data + identifier + + + + + + + + + Ensembl ID ('Pan troglodytes') + + true + identifier + ENSPTR([EGTP])[0-9]{11} + data + identifiers + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). + edam + bioinformatics + beta12orEarlier + beta12orEarlier + + + + + + + + + Ensembl ID ('Rattus norvegicus') + + true + identifier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). + bioinformatics + edam + identifiers + beta12orEarlier + ENSRNO([EGTP])[0-9]{11} + beta12orEarlier + data + + + + + + + + + Ensembl ID ('Spermophilus tridecemlineatus') + + true + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). + ENSSTO([EGTP])[0-9]{11} + data + identifier + identifiers + beta12orEarlier + edam + bioinformatics + + + + + + + + + Ensembl ID ('Takifugu rubripes') + + true + edam + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). + beta12orEarlier + beta12orEarlier + identifier + ENSFRU([EGTP])[0-9]{11} + bioinformatics + identifiers + data + + + + + + + + + Ensembl ID ('Tupaia belangeri') + + true + beta12orEarlier + bioinformatics + beta12orEarlier + data + edam + identifier + identifiers + ENSTBE([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). + + + + + + + + + Ensembl ID ('Xenopus tropicalis') + + true + identifiers + ENSXET([EGTP])[0-9]{11} + edam + data + bioinformatics + beta12orEarlier + beta12orEarlier + identifier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). + + + + + + + + + CATH identifier + + + + + + + + identifier + edam + Identifier of a protein domain (or other node) from the CATH database. + identifiers + data + bioinformatics + beta12orEarlier + + + + + + + + CATH node ID (family) + + + + + + + + data + edam + 2.10.10.10 + A code number identifying a family from the CATH database. + beta12orEarlier + identifiers + identifier + bioinformatics + + + + + + + + Enzyme ID (CAZy) + + bioinformatics + CAZy ID + beta12orEarlier + Identifier of an enzyme from the CAZy enzymes database. + data + identifiers + identifier + edam + + + + + + + + Clone ID (IMAGE) + + bioinformatics + identifiers + IMAGE cloneID + I.M.A.G.E. cloneID + edam + data + beta12orEarlier + identifier + A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). + + + + + + + + GO concept ID (cellular compartment) + + beta12orEarlier + data + [0-9]{7}|GO:[0-9]{7} + edam + identifier + An identifier of a 'cellular compartment' concept from the Gene Ontology. + identifiers + bioinformatics + GO concept identifier (cellular compartment) + + + + + + + + Chromosome name (BioCyc) + + beta12orEarlier + identifier + bioinformatics + identifiers + Name of a chromosome as used in the BioCyc database. + data + edam + + + + + + + + CleanEx entry name + + bioinformatics + An identifier of a gene expression profile from the CleanEx database. + beta12orEarlier + data + identifier + edam + identifiers + + + + + + + + CleanEx dataset code + + identifiers + An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. + beta12orEarlier + edam + bioinformatics + data + identifier + + + + + + + + Genome metadata + + beta12orEarlier + data + data + edam + bioinformatics + Provenance metadata or other general information concerning a genome as a whole. + + + + + + + + Protein ID (CORUM) + + Unique identifier for a protein complex from the CORUM database. + identifier + CORUM complex ID + data + beta12orEarlier + identifiers + bioinformatics + edam + + + + + + + + CDD PSSM-ID + + bioinformatics + identifiers + Unique identifier of a position-specific scoring matrix from the CDD database. + identifier + data + edam + beta12orEarlier + + + + + + + + Protein ID (CuticleDB) + + Unique identifier for a protein from the CuticleDB database. + identifiers + edam + identifier + bioinformatics + beta12orEarlier + CuticleDB ID + data + + + + + + + + DBD ID + + beta12orEarlier + data + Identifier of a predicted transcription factor from the DBD database. + bioinformatics + identifier + edam + identifiers + + + + + + + + Oligonucleotide probe annotation + + + + + + + + edam + data + General annotation on an oligonucleotide probe. + data + beta12orEarlier + bioinformatics + + + + + + + + Oligonucleotide ID + + + data + beta12orEarlier + bioinformatics + edam + Identifier of an oligonucleotide from a database. + identifiers + identifier + + + + + + + + dbProbe ID + + bioinformatics + edam + data + identifiers + beta12orEarlier + identifier + Identifier of an oligonucleotide probe from the dbProbe database. + + + + + + + + Dinucleotide property + + Physicochemical property data for one or more dinucleotides. + data + beta12orEarlier + edam + data + bioinformatics + + + + + + + + DiProDB ID + + Identifier of an dinucleotide property from the DiProDB database. + edam + beta12orEarlier + data + identifier + identifiers + bioinformatics + + + + + + + + Protein features (disordered structure) + + + Protein structure report (disordered structure) + An informative report about disordered structure in a protein. + data + data + bioinformatics + beta12orEarlier + edam + + + + + + + + Protein ID (DisProt) + + Unique identifier for a protein from the DisProt database. + edam + identifier + identifiers + bioinformatics + beta12orEarlier + DisProt ID + data + + + + + + + + Embryo annotation + + + + + + + + beta12orEarlier + data + data + edam + bioinformatics + Annotation on an embryo or concerning embryological development. + + + + + + + + Transcript ID (Ensembl) + + + Unique identifier for a gene transcript from the Ensembl database. + beta12orEarlier + bioinformatics + edam + identifiers + data + identifier + Ensembl Transcript ID + + + + + + + + Inhibitor annotation + + edam + data + An informative report on one or more small molecules that are enzyme inhibitors. + data + beta12orEarlier + bioinformatics + + + + + + + + Promoter ID + + + Moby:GeneAccessionList + identifiers + beta12orEarlier + edam + data + bioinformatics + An identifier of a promoter of a gene that is catalogued in a database. + identifier + + + + + + + + EST accession + + data + identifiers + beta12orEarlier + Identifier of an EST sequence. + identifier + bioinformatics + edam + + + + + + + + COGEME EST ID + + Identifier of an EST sequence from the COGEME database. + bioinformatics + beta12orEarlier + identifiers + identifier + edam + data + + + + + + + + COGEME unisequence ID + + identifiers + A unisequence is a single sequence assembled from ESTs. + beta12orEarlier + Identifier of a unisequence from the COGEME database. + bioinformatics + edam + identifier + data + + + + + + + + Protein family ID (GeneFarm) + + bioinformatics + Accession number of an entry (family) from the TIGRFam database. + identifier + identifiers + beta12orEarlier + data + GeneFarm family ID + edam + + + + + + + + Family name + + edam + identifier + bioinformatics + identifiers + The name of a family of organism. + data + beta12orEarlier + + + + + + + + Genus name (virus) + + true + beta12orEarlier + edam + data + bioinformatics + beta13 + The name of a genus of viruses. + identifiers + identifier + + + + + + + + + Family name (virus) + + true + bioinformatics + data + identifiers + The name of a family of viruses. + beta13 + beta12orEarlier + edam + identifier + + + + + + + + + Database name (SwissRegulon) + + true + data + bioinformatics + beta12orEarlier + edam + identifier + The name of a SwissRegulon database. + beta13 + identifiers + + + + + + + + + Sequence feature ID (SwissRegulon) + + This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". + data + A feature identifier as used in the SwissRegulon database. + identifiers + edam + beta12orEarlier + identifier + bioinformatics + + + + + + + + FIG ID + + data + identifiers + beta12orEarlier + A unique identifier of gene in the NMPDR database. + bioinformatics + identifier + A FIG ID consists of four parts: a prefix, genome id, locus type and id number. + edam + + + + + + + + Gene ID (Xenbase) + + data + beta12orEarlier + bioinformatics + A unique identifier of gene in the Xenbase database. + identifiers + identifier + edam + + + + + + + + Gene ID (Genolist) + + bioinformatics + data + edam + identifier + A unique identifier of gene in the Genolist database. + beta12orEarlier + identifiers + + + + + + + + Gene name (Genolist) + + Name of an entry (gene) from the Genolist genes database. + data + identifier + Genolist gene name + beta12orEarlier + bioinformatics + identifiers + edam + + + + + + + + ABS ID + + bioinformatics + identifiers + edam + Identifier of an entry (promoter) from the ABS database. + beta12orEarlier + ABS identifier + identifier + data + + + + + + + + AraC-XylS ID + + identifier + beta12orEarlier + identifiers + Identifier of a transcription factor from the AraC-XylS database. + data + edam + bioinformatics + + + + + + + + Gene name (HUGO) + + true + Name of an entry (gene) from the HUGO database. + bioinformatics + edam + beta12orEarlier + beta12orEarlier + data + identifiers + identifier + + + + + + + + + Locus ID (PseudoCAP) + + Identifier of a locus from the PseudoCAP database. + identifiers + edam + bioinformatics + beta12orEarlier + identifier + data + + + + + + + + Locus ID (UTR) + + data + Identifier of a locus from the UTR database. + beta12orEarlier + edam + identifiers + bioinformatics + identifier + + + + + + + + MonosaccharideDB ID + + beta12orEarlier + identifier + identifiers + data + Unique identifier of a monosaccharide from the MonosaccharideDB database. + bioinformatics + edam + + + + + + + + Database name (CMD) + + true + edam + identifier + identifiers + beta13 + The name of a subdivision of the Collagen Mutation Database (CMD) database. + data + beta12orEarlier + bioinformatics + + + + + + + + + Database name (Osteogenesis) + + true + data + beta12orEarlier + identifiers + bioinformatics + The name of a subdivision of the Osteogenesis database. + edam + identifier + beta13 + + + + + + + + + Genome identifier + + identifier + edam + data + identifiers + beta12orEarlier + An identifier of a particular genome. + bioinformatics + + + + + + + + GenomeReviews ID + + data + An identifier of a particular genome. + bioinformatics + identifiers + edam + beta12orEarlier + identifier + + + + + + + + GlycoMap ID + + identifier + bioinformatics + data + Identifier of an entry from the GlycosciencesDB database. + beta12orEarlier + edam + [0-9]+ + identifiers + + + + + + + + Carbohydrate conformational map + + A conformational energy map of the glycosidic linkages in a carbohydrate molecule. + bioinformatics + beta12orEarlier + data + data + edam + + + + + + + + Nucleic acid features (intron) + + Gene features (intron) + beta12orEarlier + edam + bioinformatics + An informative report on an intron in a nucleotide sequences. + data + data + + + + + + + + Transcription factor name + + + beta12orEarlier + The name of a transcription factor. + identifiers + edam + data + identifier + bioinformatics + + + + + + + + TCID + + identifier + edam + bioinformatics + data + identifiers + beta12orEarlier + Identifier of a membrane transport proteins from the transport classification database (TCDB). + + + + + + + + Pfam domain name + + identifier + data + identifiers + edam + PF[0-9]{5} + bioinformatics + Name of a domain from the Pfam database. + beta12orEarlier + + + + + + + + Pfam clan ID + + Accession number of a Pfam clan. + identifier + data + edam + bioinformatics + identifiers + CL[0-9]{4} + beta12orEarlier + + + + + + + + Gene ID (VectorBase) + + edam + identifiers + data + Identifier for a gene from the VectorBase database. + bioinformatics + identifier + beta12orEarlier + VectorBase ID + + + + + + + + UTRSite ID + + beta12orEarlier + data + bioinformatics + identifiers + identifier + Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. + edam + + + + + + + + Sequence motif metadata + + + + + + + + data + bioinformatics + beta12orEarlier + Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. + data + edam + + + + + + + + Locus annotation + + true + beta12orEarlier + beta12orEarlier + Locus report + data + An informative report on a particular locus. + bioinformatics + edam + data + + + + + + + + + Protein name (UniProt) + + identifiers + edam + beta12orEarlier + data + Official name of a protein as used in the UniProt database. + identifier + bioinformatics + + + + + + + + Term ID list + + data + edam + The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. + data + beta12orEarlier + bioinformatics + One or more terms from one or more controlled vocabularies which are annotations on an entity. + + + + + + + + HAMAP ID + + data + edam + identifiers + identifier + beta12orEarlier + Name of a protein family from the HAMAP database. + bioinformatics + + + + + + + + Identifier with metadata + + data + beta12orEarlier + edam + bioinformatics + Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance. + data + + + + + + + + Gene symbol annotation + + true + beta12orEarlier + bioinformatics + data + edam + Annotation about a gene symbol. + beta12orEarlier + data + + + + + + + + + Transcript ID + + + + + + + + + identifiers + data + bioinformatics + identifier + beta12orEarlier + Identifier of a RNA transcript. + edam + + + + + + + + HIT ID + + beta12orEarlier + identifiers + edam + identifier + data + Identifier of an RNA transcript from the H-InvDB database. + bioinformatics + + + + + + + + HIX ID + + beta12orEarlier + A unique identifier of gene cluster in the H-InvDB database. + data + identifier + identifiers + edam + bioinformatics + + + + + + + + HPA antibody id + + bioinformatics + Identifier of a antibody from the HPA database. + beta12orEarlier + identifier + identifiers + edam + data + + + + + + + + IMGT/HLA ID + + identifier + edam + identifiers + beta12orEarlier + Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. + bioinformatics + data + + + + + + + + Gene ID (JCVI) + + bioinformatics + data + beta12orEarlier + edam + A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). + identifier + identifiers + + + + + + + + Kinase name + + identifiers + The name of a kinase protein. + data + bioinformatics + identifier + beta12orEarlier + edam + + + + + + + + ConsensusPathDB entity ID + + + beta12orEarlier + bioinformatics + identifiers + edam + Identifier of a physical entity from the ConsensusPathDB database. + identifier + data + + + + + + + + ConsensusPathDB entity name + + + bioinformatics + data + edam + Name of a physical entity from the ConsensusPathDB database. + identifier + beta12orEarlier + identifiers + + + + + + + + CCAP strain number + + beta12orEarlier + The number of a strain of algae and protozoa from the CCAP database. + identifiers + data + edam + identifier + bioinformatics + + + + + + + + Stock number + + + edam + bioinformatics + data + identifier + An identifier of stock from a catalogue of biological resources. + identifiers + beta12orEarlier + + + + + + + + Stock number (TAIR) + + identifier + edam + data + identifiers + A stock number from The Arabidopsis information resource (TAIR). + bioinformatics + beta12orEarlier + + + + + + + + REDIdb ID + + data + Identifier of an entry from the RNA editing database (REDIdb). + identifier + identifiers + bioinformatics + edam + beta12orEarlier + + + + + + + + SMART domain name + + edam + beta12orEarlier + identifier + Name of a domain from the SMART database. + bioinformatics + identifiers + data + + + + + + + + Protein family ID (PANTHER) + + identifiers + Panther family ID + data + bioinformatics + Accession number of an entry (family) from the PANTHER database. + beta12orEarlier + edam + identifier + + + + + + + + RNAVirusDB ID + + data + A unique identifier for a virus from the RNAVirusDB database. + edam + Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. + identifiers + identifier + beta12orEarlier + bioinformatics + + + + + + + + Virus ID + + + An accession of annotation on a (group of) viruses (catalogued in a database). + bioinformatics + beta12orEarlier + data + identifier + edam + identifiers + + + + + + + + NCBI Genome Project ID + + beta12orEarlier + edam + identifiers + identifier + bioinformatics + data + An identifier of a genome project assigned by NCBI. + + + + + + + + NCBI genome accession + + identifiers + bioinformatics + beta12orEarlier + edam + data + identifier + A unique identifier of a whole genome assigned by the NCBI. + + + + + + + + Sequence profile metadata + + + + + + + + bioinformatics + edam + data + beta12orEarlier + data + Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on. + + + + + + + + Protein ID (TopDB) + + data + identifiers + identifier + Unique identifier for a membrane protein from the TopDB database. + TopDB ID + bioinformatics + beta12orEarlier + edam + + + + + + + + Gel identifier + + data + identifier + bioinformatics + beta12orEarlier + Identifier of a two-dimensional (protein) gel. + identifiers + edam + + + + + + + + Reference map name (SWISS-2DPAGE) + + + Name of a reference map gel from the SWISS-2DPAGE database. + identifiers + identifier + data + edam + beta12orEarlier + bioinformatics + + + + + + + + Protein ID (PeroxiBase) + + Unique identifier for a peroxidase protein from the PeroxiBase database. + beta12orEarlier + bioinformatics + identifier + data + PeroxiBase ID + identifiers + edam + + + + + + + + SISYPHUS ID + + bioinformatics + Identifier of an entry from the SISYPHUS database of tertiary structure alignments. + beta12orEarlier + identifiers + edam + identifier + data + + + + + + + + ORF ID + + + Accession of an open reading frame (catalogued in a database). + bioinformatics + edam + identifiers + identifier + data + beta12orEarlier + + + + + + + + ORF identifier + + identifier + beta12orEarlier + An identifier of an open reading frame. + bioinformatics + edam + data + identifiers + + + + + + + + Linucs ID + + edam + beta12orEarlier + identifiers + Identifier of an entry from the GlycosciencesDB database. + data + identifier + bioinformatics + + + + + + + + Protein ID (LGICdb) + + identifiers + Unique identifier for a ligand-gated ion channel protein from the LGICdb database. + edam + LGICdb ID + data + bioinformatics + identifier + beta12orEarlier + + + + + + + + MaizeDB ID + + bioinformatics + data + identifiers + identifier + Identifier of an EST sequence from the MaizeDB database. + edam + beta12orEarlier + + + + + + + + Gene ID (MfunGD) + + identifier + A unique identifier of gene in the MfunGD database. + data + bioinformatics + identifiers + beta12orEarlier + edam + + + + + + + + Orpha number + + + + + + + + identifiers + An identifier of a disease from the Orpha database. + data + bioinformatics + beta12orEarlier + identifier + edam + + + + + + + + Protein ID (EcID) + + identifier + bioinformatics + Unique identifier for a protein from the EcID database. + data + beta12orEarlier + edam + identifiers + + + + + + + + Clone ID (RefSeq) + + + identifier + identifiers + edam + data + beta12orEarlier + bioinformatics + A unique identifier of a cDNA molecule catalogued in the RefSeq database. + + + + + + + + Protein ID (ConoServer) + + data + bioinformatics + Unique identifier for a cone snail toxin protein from the ConoServer database. + identifiers + beta12orEarlier + identifier + edam + + + + + + + + GeneSNP ID + + beta12orEarlier + identifier + identifiers + bioinformatics + data + edam + Identifier of a GeneSNP database entry. + + + + + + + + Lipid identifier + + + + + + + + + + + + + + bioinformatics + edam + beta12orEarlier + identifier + data + identifiers + Identifier of a lipid. + + + + + + + + Databank + + true + beta12orEarlier + edam + A flat-file (textual) data archive. + beta12orEarlier + data + bioinformatics + data + + + + + + + + Web portal + + true + beta12orEarlier + data + edam + bioinformatics + data + beta12orEarlier + A web site providing data (web pages) on a common theme to a HTTP client. + + + + + + + + Gene ID (VBASE2) + + edam + identifiers + VBASE2 ID + beta12orEarlier + identifier + bioinformatics + Identifier for a gene from the VBASE2 database. + data + + + + + + + + DPVweb ID + + bioinformatics + A unique identifier for a virus from the DPVweb database. + identifier + beta12orEarlier + edam + identifiers + data + DPVweb virus ID + + + + + + + + Pathway ID (BioSystems) + + data + edam + [0-9]+ + bioinformatics + Identifier of a pathway from the BioSystems pathway database. + beta12orEarlier + identifier + identifiers + + + + + + + + Experimental data (proteomics) + + true + bioinformatics + edam + data + beta12orEarlier + beta12orEarlier + Data concerning a proteomics experiment. + data + + + + + + + + + Abstract + + bioinformatics + data + An abstract of a scientific article. + edam + beta12orEarlier + data + + + + + + + + Lipid structure + + data + bioinformatics + 3D coordinate and associated data for a lipid structure. + data + beta12orEarlier + edam + + + + + + + + Drug structure + + bioinformatics + 3D coordinate and associated data for the (3D) structure of a drug. + data + beta12orEarlier + edam + data + + + + + + + + Toxin structure + + beta12orEarlier + data + 3D coordinate and associated data for the (3D) structure of a toxin. + bioinformatics + data + edam + + + + + + + + Position-specific scoring matrix + + + data + A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment. + edam + bioinformatics + data + beta12orEarlier + + + + + + + + Distance matrix + + data + edam + data + beta12orEarlier + bioinformatics + A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity. + + + + + + + + Structural distance matrix + + data + edam + bioinformatics + beta12orEarlier + Distances (values representing similarity) between a group of molecular structures. + data + + + + + + + + Article metadata + + + + + + + + + Bibliographic data concerning scientific article(s). + data + edam + beta12orEarlier + data + bioinformatics + + + + + + + + Ontology concept + + + + + + + + bioinformatics + data + data + A concept from a biological ontology. + This includes any fields from the concept definition such as concept name, definition, comments and so on. + beta12orEarlier + edam + + + + + + + + Codon usage bias + + data + data + beta12orEarlier + A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. + edam + bioinformatics + + + + + + + + Experiment annotation (Northern blot) + + data + bioinformatics + data + beta12orEarlier + edam + General annotation on a Northern Blot experiment. + + + + + + + + Nucleic acid features (VNTR) + + VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. + data + beta12orEarlier + edam + Variable number of tandem repeat polymorphism + bioinformatics + VNTR annotation + data + Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. + + + + + + + + Nucleic acid features (microsatellite) + + bioinformatics + beta12orEarlier + A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. + Microsatellite annotation + edam + data + Annotation on a microsatellite polymorphism in a DNA sequence. + data + + + + + + + + Nucleic acid features (RFLP) + + data + Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence. + data + edam + An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. + RFLP annotation + bioinformatics + beta12orEarlier + + + + + + + + Radiation hybrid map + + data + beta12orEarlier + RH map + edam + data + A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. + bioinformatics + The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. + + + + + + + + ID list + + edam + bioinformatics + data + beta12orEarlier + A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data. + data + + + + + + + + Phylogenetic gene frequencies data + + data + bioinformatics + data + Gene frequencies data that may be read during phylogenetic tree calculation. + beta12orEarlier + edam + + + + + + + + Sequence set (polymorphic) + + true + A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. + bioinformatics + beta12orEarlier + data + edam + beta13 + data + + + + + + + + + DRCAT resource + + data + edam + beta12orEarlier + data + An entry (resource) from the DRCAT bioinformatics resource catalogue. + bioinformatics + + + + + + + + Protein complex + + bioinformatics + edam + data + 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another. + beta12orEarlier + data + + + + + + + + Protein structural motif + + data + 3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role. + edam + bioinformatics + beta12orEarlier + data + + + + + + + + Lipid structure report + + Annotation on or information derived from one or more specific lipid 3D structure(s). + bioinformatics + data + edam + data + beta12orEarlier + + + + + + + + Secondary structure image + + Image of one or more molecular secondary structures. + edam + bioinformatics + data + data + beta12orEarlier + + + + + + + + Secondary structure report + + edam + An informative report on general information, properties or features of one or more molecular secondary structures. + bioinformatics + data + beta12orEarlier + Secondary structure-derived report + data + + + + + + + + DNA features + + true + data + beta12orEarlier + bioinformatics + DNA sequence-specific feature annotation (not in a feature table). + beta12orEarlier + data + edam + + + + + + + + + Nucleic acid features (RNA features) + + bioinformatics + RNA features + Features concerning RNA or regions of DNA that encode an RNA molecule. + beta12orEarlier + data + data + edam + + + + + + + + Plot + + true + beta12orEarlier + data + edam + bioinformatics + Biological data that is plotted as a graph of some type. + beta12orEarlier + data + + + + + + + + + Nucleic acid features (polymorphism annotation) + + beta12orEarlier + Annotation on a polymorphism. + edam + Polymorphism annotation + data + data + bioinformatics + + + + + + + + Sequence record (protein) + + + data + edam + Protein sequence record + bioinformatics + data + beta12orEarlier + A protein sequence and associated metadata. + + + + + + + + Sequence record (nucleic acid) + + + edam + data + Nucleic acid sequence record + bioinformatics + A nucleic acid sequence and associated metadata. + Nucleotide sequence record + data + beta12orEarlier + + + + + + + + Sequence record full (protein) + + + data + beta12orEarlier + data + bioinformatics + A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. + SO:2000061 + edam + + + + + + + + Sequence record full (nucleic acid) + + + data + edam + SO:2000061 + beta12orEarlier + A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. + bioinformatics + data + + + + + + + + Biological model accession + + + identifier + Accession of a mathematical model, typically an entry from a database. + beta12orEarlier + edam + identifiers + data + bioinformatics + + + + + + + + Cell type name + + + beta12orEarlier + data + bioinformatics + identifiers + The name of a type or group of cells. + edam + identifier + + + + + + + + Cell type accession + + + identifier + identifiers + Accession of a type or group of cells (catalogued in a database). + beta12orEarlier + data + bioinformatics + edam + + + + + + + + Compound accession + + + Chemical compound accession + edam + beta12orEarlier + Accession of an entry from a database of chemicals. + identifier + data + identifiers + Small molecule accession + bioinformatics + + + + + + + + Drug accession + + + data + beta12orEarlier + identifiers + edam + Accession of a drug. + identifier + bioinformatics + + + + + + + + Toxin name + + + bioinformatics + edam + data + beta12orEarlier + identifier + Name of a toxin. + identifiers + + + + + + + + Toxin accession + + + identifier + identifiers + bioinformatics + data + edam + Accession of a toxin (catalogued in a database). + beta12orEarlier + + + + + + + + Monosaccharide accession + + + bioinformatics + identifier + beta12orEarlier + data + identifiers + edam + Accession of a monosaccharide (catalogued in a database). + + + + + + + + Drug name + + + Common name of a drug. + identifiers + bioinformatics + edam + data + beta12orEarlier + identifier + + + + + + + + Carbohydrate accession + + + bioinformatics + beta12orEarlier + edam + Accession of an entry from a database of carbohydrates. + data + identifier + identifiers + + + + + + + + Molecule accession + + + bioinformatics + beta12orEarlier + data + identifiers + identifier + edam + Accession of a specific molecule (catalogued in a database). + + + + + + + + Data resource definition accession + + + Accession of a data definition (catalogued in a database). + bioinformatics + beta12orEarlier + data + edam + identifier + identifiers + + + + + + + + Genome accession + + + beta12orEarlier + An accession of a particular genome (in a database). + data + identifiers + edam + identifier + bioinformatics + + + + + + + + Map accession + + + identifiers + beta12orEarlier + edam + An accession of a map of a molecular sequence (deposited in a database). + bioinformatics + data + identifier + + + + + + + + Lipid accession + + + Accession of an entry from a database of lipids. + identifiers + data + edam + identifier + beta12orEarlier + bioinformatics + + + + + + + + Peptide ID + + + Accession of a peptide deposited in a database. + identifier + identifiers + data + bioinformatics + beta12orEarlier + edam + + + + + + + + Protein accession + + + Accession of a protein deposited in a database. + identifier + bioinformatics + data + beta12orEarlier + identifiers + edam + + + + + + + + Organism accession + + + edam + beta12orEarlier + identifier + identifiers + data + An accession of annotation on a (group of) organisms (catalogued in a database). + bioinformatics + + + + + + + + Organism name + + + identifiers + The name of an organism (or group of organisms). + data + Moby:OrganismsLongName + beta12orEarlier + edam + Moby:InfraspecificEpithet + Moby:FirstEpithet + Moby:BriefOccurrenceRecord + Moby:OccurrenceRecord + bioinformatics + Moby:OrganismsShortName + identifier + Moby:Organism_Name + + + + + + + + Protein family accession + + + edam + bioinformatics + identifiers + beta12orEarlier + Accession of a protein family (that is deposited in a database). + data + identifier + + + + + + + + Transcription factor accession + + + + beta12orEarlier + edam + identifier + bioinformatics + data + Accession of an entry from a database of transcription factors or binding sites. + identifiers + + + + + + + + Strain accession + + + + + + + + + identifier + edam + Identifier of a strain of an organism variant, typically a plant, virus or bacterium. + data + identifiers + bioinformatics + beta12orEarlier + + + + + + + + Virus identifier + + + + + + + + edam + identifiers + identifier + beta12orEarlier + An accession of annotation on a (group of) viruses (catalogued in a database). + data + bioinformatics + + + + + + + + Sequence features metadata + + data + edam + Metadata on sequence features. + data + bioinformatics + beta12orEarlier + + + + + + + + Gramene identifier + + bioinformatics + identifier + Identifier of a Gramene database entry. + data + identifiers + edam + beta12orEarlier + + + + + + + + DDBJ accession + + An identifier of an entry from the DDBJ sequence database. + identifier + bioinformatics + data + DDBJ identifier + DDBJ ID + edam + identifiers + beta12orEarlier + DDBJ accession number + + + + + + + + ConsensusPathDB identifier + + An identifier of an entity from the ConsensusPathDB database. + identifier + beta12orEarlier + data + edam + identifiers + bioinformatics + + + + + + + + Sequence data + + true + Data concerning molecular sequence(s). + bioinformatics + beta13 + edam + data + data + beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. + + + + + + + + + + Codon usage data + + true + Data concerning codon usage. + beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. + bioinformatics + data + beta13 + data + edam + + + + + + + + + + Article report + + data + Data concerning or derived from the analysis of a scientific article. + edam + bioinformatics + data + beta12orEarlier + + + + + + + + Sequence report + + edam + An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata). + bioinformatics + data + Sequence-derived report + data + beta12orEarlier + + + + + + + + Protein secondary structure report + + edam + data + data + beta12orEarlier + bioinformatics + An informative report about the properties or features of one or more protein secondary structures. + + + + + + + + Hopp and Woods plot + + data + bioinformatics + data + edam + beta12orEarlier + A Hopp and Woods plot of predicted antigenicity of a peptide or protein. + + + + + + + + Nucleic acid melting curve + + bioinformatics + beta12orEarlier + A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). + Shows the proportion of nucleic acid which are double-stranded versus temperature. + edam + data + data + + + + + + + + Nucleic acid probability profile + + data + Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature + data + bioinformatics + A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). + beta12orEarlier + edam + + + + + + + + Nucleic acid temperature profile + + data + Melting map + beta12orEarlier + edam + bioinformatics + data + Plots melting temperature versus base position. + A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). + + + + + + + + Pathway or network (gene regulation) + + + + + + + + beta12orEarlier + A report typically including a map (diagram) of a gene regulatory network. + data + data + bioinformatics + edam + + + + + + + + 2D PAGE image (annotated) + + 2D PAGE image annotation + edam + beta12orEarlier + bioinformatics + data + data + An informative report on a two-dimensional (2D PAGE) gel. + + + + + + + + Oligonucleotide probe sets annotation + + data + data + General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set. + bioinformatics + beta12orEarlier + edam + + + + + + + + Microarray image + + + + + + + + + edam + bioinformatics + An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. + data + data + Gene expression image + beta12orEarlier + + + + + + + + Image + + data + data + + edam + Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type. + beta12orEarlier + bioinformatics + + + + + + + + + Sequence image + + + bioinformatics + data + edam + beta12orEarlier + data + Image of a molecular sequence, possibly with sequence features or properties shown. + + + + + + + + Protein hydropathy data + + data + beta12orEarlier + edam + A report on protein properties concerning hydropathy. + Protein hydropathy report + data + bioinformatics + + + + + + + + Workflow data + + true + data + bioinformatics + beta12orEarlier + data + edam + Data concerning a computational workflow. + beta13 + + + + + + + + + + Workflow + + A computational workflow. + data + bioinformatics + beta12orEarlier + edam + data + + + + + + + + Secondary structure data + + true + Data concerning molecular secondary structure data. + bioinformatics + beta12orEarlier + beta13 + data + data + edam + + + + + + + + + + Raw sequence (protein) + + + edam + A raw protein sequence (string of characters). + bioinformatics + beta12orEarlier + data + data + + + + + + + + Raw sequence (nucleic acid) + + + data + A raw nucleic acid sequence. + edam + data + beta12orEarlier + bioinformatics + + + + + + + + Protein sequence + + data + data + One or more protein sequences, possibly with associated annotation. + edam + + bioinformatics + beta12orEarlier + + + + + + + + Nucleic acid sequence + + bioinformatics + beta12orEarlier + + edam + One or more nucleic acid sequences, possibly with associated annotation. + data + data + + + + + + + + Reaction data + + bioinformatics + Reaction annotation + edam + data + This is a broad data type and is used a placeholder for other, more specific types. + data + Enzyme kinetics annotation + Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. + beta12orEarlier + + + + + + + + Peptide property + + data + Data concerning small peptides. + data + Peptide data + edam + beta12orEarlier + bioinformatics + + + + + + + + Protein classification + + + + + + + + + bioinformatics + edam + beta12orEarlier + Data concerning the classification of protein sequences or structures. + data + Protein classification data + data + This is a broad data type and is used a placeholder for other, more specific types. + + + + + + + + Sequence motif data + + true + This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + beta13 + bioinformatics + Data concerning specific or conserved pattern in molecular sequences. + data + data + edam + + + + + + + + + Sequence profile data + + true + Data concerning models representing a (typically multiple) sequence alignment. + data + beta13 + This is a broad data type and is used a placeholder for other, more specific types. + bioinformatics + beta12orEarlier + data + edam + + + + + + + + + Pathway or network data + + true + beta12orEarlier + data + beta13 + data + bioinformatics + Data concerning a specific biological pathway or network. + edam + + + + + + + + + + Pathway or network report + + + + + + + + An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. + beta12orEarlier + bioinformatics + data + edam + data + + + + + + + + Nucleic acid thermodynamic data + + data + edam + data + beta12orEarlier + Nucleic acid thermodynamic property + A thermodynamic or kinetic property of a nucleic acid molecule. + Nucleic acid property (thermodynamic or kinetic) + bioinformatics + + + + + + + + Nucleic acid classification + + + + + + + + + data + data + This is a broad data type and is used a placeholder for other, more specific types. + edam + bioinformatics + Nucleic acid classification data + Data concerning the classification of nucleic acid sequences or structures. + beta12orEarlier + + + + + + + + Classification + + + + + + + + bioinformatics + data + This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. + edam + Classification data + data + Data concerning a classification of molecular sequences, structures or other entities. + beta12orEarlier + + + + + + + + Protein features (key folding sites) + + data + bioinformatics + beta12orEarlier + A report on key residues involved in protein folding. + data + edam + + + + + + + + Protein torsion angle data + + edam + data + beta12orEarlier + data + Torsion angle data for a protein structure. + bioinformatics + Torsion angle data + + + + + + + + Protein structure image + + + Structure image (protein) + edam + data + bioinformatics + beta12orEarlier + data + An image of protein structure. + + + + + + + + Phylogenetic character weights + + data + beta12orEarlier + edam + Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. + bioinformatics + data + + + + + + + + Sequence annotation track + + Genome track + Genome-browser track + Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. + Annotation track + Genomic track + data + data + edam + bioinformatics + Genome annotation track + beta12orEarlier + + + + + + + + UniProt accession + + + + + + + + UniProt accession number + identifier + bioinformatics + UniProtKB accession + Accession number of a UniProt (protein sequence) database entry. + [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9] + identifiers + TrEMBL entry accession + Swiss-Prot entry accession + data + edam + UniProt entry accession + P43353|Q7M1G0|Q9C199|A5A6J6 + beta12orEarlier + UniProtKB accession number + + + + + + + + NCBI genetic code ID + + + identifiers + identifier + Identifier of a genetic code in the NCBI list of genetic codes. + bioinformatics + data + beta12orEarlier + edam + 16 + [1-9][0-9]? + + + + + + + + Ontology concept identifier + + + + + + + + beta12orEarlier + identifier + Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. + bioinformatics + data + identifiers + edam + + + + + + + + GO concept name (biological process) + + true + beta12orEarlier + beta12orEarlier + bioinformatics + The name of a concept for a biological process from the GO ontology. + identifiers + edam + data + identifier + + + + + + + + + GO concept name (molecular function) + + true + edam + The name of a concept for a molecular function from the GO ontology. + identifier + identifiers + beta12orEarlier + bioinformatics + data + beta12orEarlier + + + + + + + + + Taxonomy + + + + + + + + Taxonomic data + data + edam + beta12orEarlier + Data concerning the classification, identification and naming of organisms. + This is a broad data type and is used a placeholder for other, more specific types. + data + bioinformatics + + + + + + + + Protein ID (EMBL/GenBank/DDBJ) + + data + identifiers + edam + This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. + EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators. + beta13 + identifier + bioinformatics + + + + + + + + Core data + + beta13 + data + data + edam + bioinformatics + A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation. + Core data entities typically have a format and may be identified by an accession number. + + + + + + + + Sequence feature identifier + + + + + + + + + Name or other identifier of molecular sequence feature(s). + data + beta13 + identifier + edam + bioinformatics + identifiers + + + + + + + + Structure identifier + + + + + + + + bioinformatics + An identifier of a molecular tertiary structure, typically an entry from a structure database. + identifiers + identifier + edam + data + beta13 + + + + + + + + Matrix identifier + + + + + + + + edam + beta13 + identifier + identifiers + An identifier of an array of numerical values, such as a comparison matrix. + bioinformatics + data + + + + + + + + Protein sequence composition + + Sequence property (protein composition) + A report (typically a table) on character or word composition / frequency of protein sequence(s). + bioinformatics + data + data + beta13 + edam + + + + + + + + Nucleic acid sequence composition + + + beta13 + A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). + bioinformatics + data + edam + Sequence property (nucleic acid composition) + data + + + + + + + + Protein domain classification node + + bioinformatics + edam + data + A node from a classification of protein structural domain(s). + beta13 + data + + + + + + + + CAS number + + edam + Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. + bioinformatics + identifier + data + CAS registry number + beta13 + identifiers + + + + + + + + ATC code + + beta13 + Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC). + edam + bioinformatics + identifier + identifiers + data + + + + + + + + UNII + + Unique Ingredient Identifier + A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA). + beta13 + identifier + bioinformatics + identifiers + data + edam + + + + + + + + Geotemporal metadata + + Basic information concerning geographical location or time. + data + data + beta13 + edam + bioinformatics + + + + + + + + System metadata + + data + data + beta13 + Metadata concerning the software, hardware or other aspects of a computer system. + edam + bioinformatics + + + + + + + + Sequence feature name + + + beta13 + edam + data + A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. + identifiers + identifier + bioinformatics + + + + + + + + Experimental measurement + + Measurement data + Raw experimental data + Measurement metadata + Experimentally measured data + Measured data + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + edam + Measurement + Experimental measurement data + bioinformatics + Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware. + data + beta13 + data + + + + + + + + Raw microarray data + + + Such data as found in Affymetrix CEL or GPR files. + data + Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. + edam + bioinformatics + beta13 + data + + + + + + + + Processed microarray data + + + + + + + + + data + edam + Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. + Gene expression report + Microarray probe set data + beta13 + Gene annotation (expression) + data + bioinformatics + Data generated from processing and analysis of probe set data from a microarray experiment. + + + + + + + + Normalised microarray data + + Gene expression data matrix + The final processed (normalised) data for a set of hybridisations in a microarray experiment. + This combines data from all hybridisations. + beta13 + edam + bioinformatics + data + Gene expression matrix + data + + + + + + + + Sample annotation + + data + bioinformatics + beta13 + This might include compound and dose in a dose response experiment. + data + Annotation on a biological sample, for example experimental factors and their values. + edam + + + + + + + + Microarray annotation + + data + beta13 + Annotation on the array itself used in a microarray experiment. + bioinformatics + edam + This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. + data + + + + + + + + Microarray protocol annotation + + Annotation on laboratory and/or data processing protocols used in an microarray experiment. + beta13 + data + data + This might describe e.g. the normalisation methods used to process the raw data. + edam + bioinformatics + + + + + + + + Microarray hybridisation data + + + + + + + + beta13 + data + Data concerning the hybridisations measured during a microarray experiment. + edam + bioinformatics + data + + + + + + + + Protein features (topological domains) + + + + + + + + bioinformatics + Summary of topological domains such as cytoplasmic regions in a protein. + beta13 + Protein topological domains + data + data + edam + + + + + + + + Sequence features (compositionally-biased regions) + + A report of regions in a molecular sequence that are biased to certain characters. + edam + data + beta13 + data + bioinformatics + + + + + + + + Protein features (sequence variants) + + data + A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. + edam + bioinformatics + beta13 + data + + + + + + + + Nucleic acid features (difference and change) + + data + edam + A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. + data + bioinformatics + beta13 + + + + + + + + Nucleic acid features (expression signal) + + data + data + edam + A report on regions within a nucleic acid sequence containing a signal that alters a biological function. + beta13 + bioinformatics + + + + + + + + Nucleic acid features (binding) + + A report on regions of a nucleic acid sequence that bind some other molecule. + This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). + data + edam + beta13 + data + bioinformatics + + + + + + + + Nucleic acid features (repeats) + + + edam + beta13 + bioinformatics + A report on repetitive elements within a nucleic acid sequence. + data + data + This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. + + + + + + + + Nucleic acid features (replication and recombination) + + data + data + This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. + bioinformatics + A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination. + edam + beta13 + + + + + + + + Nucleic acid features (structure) + + beta13 + edam + bioinformatics + data + data + A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. + + + + + + + + Protein features (repeats) + + + beta13 + data + data + edam + bioinformatics + Location of short repetitive subsequences (repeat sequences) in a protein sequence. + + + + + + + + Protein features (motifs) + + + Use this concept if another, more specific concept is not available. + edam + bioinformatics + beta13 + Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. + data + data + + + + + + + + Nucleic acid features (motifs) + + + bioinformatics + data + edam + beta13 + Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. + Use this concept if another, more specific concept is not available. + data + + + + + + + + Nucleic acid features (d-loop) + + edam + data + A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. + data + A report on displacement loops in a mitochondrial DNA sequence. + bioinformatics + beta13 + + + + + + + + Nucleic acid features (stem loop) + + A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. + bioinformatics + A report on stem loops in a DNA sequence. + data + data + beta13 + edam + + + + + + + + Nucleic acid features (mRNA features) + + edam + bioinformatics + data + beta13 + Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. + data + This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + mRNA features + + + + + + + + Nucleic acid features (signal or transit peptide) + + data + data + beta13 + bioinformatics + edam + A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. + A report on a coding sequence for a signal or transit peptide. + + + + + + + + Nucleic acid features (non-coding RNA) + + Non-coding RNA features + beta13 + Features concerning non-coding or functional RNA molecules, including tRNA and rRNA. + data + edam + bioinformatics + ncRNA features + data + + + + + + + + Nucleic acid features (transcriptional) + + beta13 + data + Features concerning transcription of DNA into RNA including the regulation of transcription. + data + edam + This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. + bioinformatics + + + + + + + + Nucleic acid features (STS) + + beta13 + A report on sequence tagged sites (STS) in nucleic acid sequences. + edam + bioinformatics + data + Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. + data + + + + + + + + Nucleic acid features (immunoglobulin gene structure) + + A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments. + edam + data + beta13 + data + bioinformatics + + + + + + + + SCOP class + + Information on a 'class' node from the SCOP database. + data + beta13 + data + bioinformatics + edam + + + + + + + + SCOP fold + + edam + data + Information on a 'fold' node from the SCOP database. + beta13 + data + bioinformatics + + + + + + + + SCOP superfamily + + bioinformatics + data + Information on a 'superfamily' node from the SCOP database. + data + beta13 + edam + + + + + + + + SCOP family + + bioinformatics + beta13 + Information on a 'family' node from the SCOP database. + data + data + edam + + + + + + + + SCOP protein + + data + bioinformatics + beta13 + Information on a 'protein' node from the SCOP database. + edam + data + + + + + + + + SCOP species + + bioinformatics + data + Information on a 'species' node from the SCOP database. + beta13 + edam + data + + + + + + + + Experiment annotation (mass spectrometry) + + General annotation on a mass spectrometry experiment. + beta13 + bioinformatics + data + edam + data + + + + + + + + Gene family annotation + + + data + data + edam + An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene. + bioinformatics + beta13 + + + + + + + + Protein image + + edam + An image of a protein. + bioinformatics + beta13 + data + data + + + + + + + + Protein alignment + + + data + edam + beta13 + data + bioinformatics + An alignment of protein sequences and/or structures. + + + + + + + + Experiment annotation (sequencing) + + + + + + + + data + data + Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. + bioinformatics + 1.0 + edam + + + + + + + + Sequence assembly report + + data + 1.1 + edam + bioinformatics + data + An informative report about a DNA sequence assembly. + + + + + + + + Genome index + + edam + An index of a genome sequence. + Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. + 1.1 + data + data + bioinformatics + + + + + + + + Experiment annotation (GWAS) + + Experiment annotation (genome-wide association study) + data + Metadata on a genome-wide association study (GWAS). + 1.1 + data + edam + bioinformatics + + + + + + + + Cytoband position + + bioinformatics + edam + data + data + Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on. + The position of a cytogenetic band in a genome. + 1.2 + + + + + + + + Cell type ontology ID + + + identifiers + identifier + bioinformatics + beta12orEarlier + CL_[0-9]{7} + edam + data + Cell type ontology concept ID. + CL ID + 1.2 + + + + + + + + Kinetic model + + Mathematical model of a network, that contains biochemical kinetics. + 1.2 + bioinformatics + data + data + edam + + + + + + + + SMILES + + + formats + bioinformatics + format + Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. + edam + beta12orEarlier + + + + + + + + + + + + InChI + + + format + bioinformatics + edam + beta12orEarlier + Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. + formats + + + + + + + + mf + + + format + The general MF query format consists of a series of valid atomic symbols, with an optional number or range. + bioinformatics + beta12orEarlier + edam + Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound. + formats + + + + + + + + inchikey + + + bioinformatics + An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. + beta12orEarlier + format + The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. + edam + formats + + + + + + + + smarts + + bioinformatics + formats + edam + beta12orEarlier + SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation. + format + + + + + + + + unambiguous pure + + + bioinformatics + formats + format + edam + Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. + beta12orEarlier + + + + + + + + nucleotide + + + Non-sequence characters may be used for example for gaps. + format + beta12orEarlier + + formats + bioinformatics + Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. + edam + + + + + + + + protein + + + beta12orEarlier + bioinformatics + Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. + format + formats + edam + + Non-sequence characters may be used for gaps and translation stop. + + + + + + + + consensus + + + formats + Alphabet for the consensus of two or more molecular sequences. + bioinformatics + edam + beta12orEarlier + format + + + + + + + + pure nucleotide + + + edam + Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. + formats + beta12orEarlier + bioinformatics + format + + + + + + + + unambiguous pure nucleotide + + + formats + Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . + bioinformatics + beta12orEarlier + edam + format + + + + + + + + dna + + format + beta12orEarlier + formats + edam + bioinformatics + Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. + + + + + + + + + rna + + + edam + Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. + bioinformatics + beta12orEarlier + formats + format + + + + + + + + unambiguous pure dna + + + formats + beta12orEarlier + format + edam + Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. + bioinformatics + + + + + + + + pure dna + + + format + beta12orEarlier + formats + edam + bioinformatics + Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. + + + + + + + + unambiguous pure rna sequence + + + bioinformatics + beta12orEarlier + Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. + formats + format + edam + + + + + + + + pure rna + + + beta12orEarlier + edam + bioinformatics + Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. + format + formats + + + + + + + + unambiguous pure protein + + + bioinformatics + Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. + format + beta12orEarlier + edam + formats + + + + + + + + pure protein + + + format + edam + formats + Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. + beta12orEarlier + bioinformatics + + + + + + + + UniGene entry format + + true + formats + edam + beta12orEarlier + format + bioinformatics + A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. + Format of an entry from UniGene. + beta12orEarlier + + + + + + + + + COG sequence cluster format + + true + edam + formats + Format of an entry from the COG database of clusters of (related) protein sequences. + bioinformatics + beta12orEarlier + format + beta12orEarlier + + + + + + + + + EMBL feature location + + + Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. + Feature location + beta12orEarlier + format + bioinformatics + edam + formats + + + + + + + + quicktandem + + + beta12orEarlier + format + edam + bioinformatics + Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). + formats + + + + + + + + Sanger inverted repeats + + + Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). + formats + edam + beta12orEarlier + format + bioinformatics + + + + + + + + EMBOSS repeat + + + formats + bioinformatics + format + beta12orEarlier + Report format for tandem repeats in a sequence (an EMBOSS report format). + edam + + + + + + + + est2genome format + + + Format of a report on exon-intron structure generated by EMBOSS est2genome. + edam + formats + bioinformatics + beta12orEarlier + format + + + + + + + + restrict format + + + bioinformatics + beta12orEarlier + edam + format + formats + Report format for restriction enzyme recognition sites used by EMBOSS restrict program. + + + + + + + + restover format + + + Report format for restriction enzyme recognition sites used by EMBOSS restover program. + beta12orEarlier + format + formats + edam + bioinformatics + + + + + + + + REBASE restriction sites + + + Report format for restriction enzyme recognition sites used by REBASE database. + format + edam + bioinformatics + formats + beta12orEarlier + + + + + + + + FASTA search results format + + + format + bioinformatics + formats + This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) + beta12orEarlier + Format of results of a sequence database search using FASTA. + edam + + + + + + + + BLAST results + + + formats + This includes score data, alignment data and summary table. + format + edam + beta12orEarlier + bioinformatics + Format of results of a sequence database search using some variant of BLAST. + + + + + + + + mspcrunch + + + Format of results of a sequence database search using some variant of MSPCrunch. + bioinformatics + formats + beta12orEarlier + format + edam + + + + + + + + Smith-Waterman format + + + formats + bioinformatics + Format of results of a sequence database search using some variant of Smith Waterman. + beta12orEarlier + format + edam + + + + + + + + dhf + + + bioinformatics + formats + format + Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. + The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. + beta12orEarlier + edam + + + + + + + + lhf + + + format + The hits are putative ligand-binding sequences and are found from a search of a sequence database. + Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. + edam + bioinformatics + formats + beta12orEarlier + + + + + + + + InterPro hits format + + + edam + bioinformatics + beta12orEarlier + Results format for searches of the InterPro database. + formats + format + + + + + + + + InterPro protein view report format + + beta12orEarlier + edam + bioinformatics + formats + The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. + Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries. + format + + + + + + + + InterPro match table format + + bioinformatics + edam + format + formats + The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. + beta12orEarlier + Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry. + + + + + + + + HMMER Dirichlet prior + + + Dirichlet distribution HMMER format. + beta12orEarlier + formats + bioinformatics + format + edam + + + + + + + + MEME Dirichlet prior + + + bioinformatics + Dirichlet distribution MEME format. + beta12orEarlier + edam + formats + format + + + + + + + + HMMER emission and transition + + + formats + bioinformatics + format + beta12orEarlier + Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. + edam + + + + + + + + prosite-pattern + + + formats + edam + beta12orEarlier + Format of a regular expression pattern from the Prosite database. + bioinformatics + format + + + + + + + + EMBOSS sequence pattern + + + beta12orEarlier + Format of an EMBOSS sequence pattern. + bioinformatics + edam + formats + format + + + + + + + + meme-motif + + + formats + bioinformatics + format + edam + beta12orEarlier + A motif in the format generated by the MEME program. + + + + + + + + prosite-profile + + + bioinformatics + beta12orEarlier + formats + format + edam + Sequence profile (sequence classifier) format used in the PROSITE database. + + + + + + + + JASPAR format + + + formats + A profile (sequence classifier) in the format used in the JASPAR database. + bioinformatics + edam + beta12orEarlier + format + + + + + + + + MEME background Markov model + + + beta12orEarlier + edam + format + formats + bioinformatics + Format of the model of random sequences used by MEME. + + + + + + + + HMMER format + + + formats + format + bioinformatics + beta12orEarlier + Format of a hidden Markov model representation used by the HMMER package. + edam + + + + + + + + HMMER-aln + + + + formats + FASTA-style format for multiple sequences aligned by HMMER package to an HMM. + edam + beta12orEarlier + format + bioinformatics + + + + + + + + DIALIGN format + + + beta12orEarlier + edam + formats + bioinformatics + Format of multiple sequences aligned by DIALIGN package. + format + + + + + + + + daf + + + formats + beta12orEarlier + bioinformatics + format + edam + EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family. + The format is clustal-like and includes annotation of domain family classification information. + + + + + + + + Sequence-MEME profile alignment + + + Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. + beta12orEarlier + bioinformatics + formats + format + edam + + + + + + + + HMMER profile alignment (sequences versus HMMs) + + + formats + beta12orEarlier + format + bioinformatics + Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. + edam + + + + + + + + HMMER profile alignment (HMM versus sequences) + + + formats + beta12orEarlier + Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. + bioinformatics + edam + format + + + + + + + + Phylip distance matrix + + + format + edam + Format of PHYLIP phylogenetic distance matrix data. + formats + beta12orEarlier + Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). + bioinformatics + + + + + + + + ClustalW dendrogram + + + formats + edam + format + Dendrogram (tree file) format generated by ClustalW. + beta12orEarlier + bioinformatics + + + + + + + + Phylip tree raw + + + formats + edam + beta12orEarlier + bioinformatics + Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. + format + + + + + + + + Phylip continuous quantitative characters + + + PHYLIP file format for continuous quantitative character data. + bioinformatics + format + beta12orEarlier + formats + edam + + + + + + + + Phylogenetic property values format + + true + format + formats + bioinformatics + beta12orEarlier + beta12orEarlier + edam + Format of phylogenetic property data. + + + + + + + + + Phylip character frequencies format + + + edam + PHYLIP file format for phylogenetics character frequency data. + format + beta12orEarlier + bioinformatics + formats + + + + + + + + Phylip discrete states format + + + bioinformatics + format + edam + formats + beta12orEarlier + Format of PHYLIP discrete states data. + + + + + + + + Phylip cliques format + + + edam + Format of PHYLIP cliques data. + bioinformatics + formats + format + beta12orEarlier + + + + + + + + Phylip tree format + + + beta12orEarlier + edam + format + formats + bioinformatics + Phylogenetic tree data format used by the PHYLIP program. + + + + + + + + TreeBASE format + + + format + The format of an entry from the TreeBASE database of phylogenetic data. + beta12orEarlier + formats + bioinformatics + edam + + + + + + + + TreeFam format + + + The format of an entry from the TreeFam database of phylogenetic data. + format + formats + edam + beta12orEarlier + bioinformatics + + + + + + + + Phylip tree distance format + + + format + formats + beta12orEarlier + bioinformatics + edam + Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package. + + + + + + + + dssp + + + Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins). + bioinformatics + edam + formats + format + The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. + beta12orEarlier + + + + + + + + hssp + + + beta12orEarlier + format + Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). + bioinformatics + formats + edam + + + + + + + + Dot-bracket format + + + Vienna RNA secondary structure format + Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server. + beta12orEarlier + Vienna RNA format + edam + formats + format + bioinformatics + + + + + + + + Vienna local RNA secondary structure format + + + beta12orEarlier + edam + bioinformatics + Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server. + formats + format + + + + + + + + PDB database entry format + + + + + + + + edam + format + Format of an entry (or part of an entry) from the PDB database. + beta12orEarlier + bioinformatics + PDB entry format + formats + + + + + + + + PDB format + + + Entry format of PDB database in PDB format. + beta12orEarlier + bioinformatics + format + PDB + edam + formats + + + + + + + + mmCIF + + + mmcif + edam + formats + beta12orEarlier + bioinformatics + Entry format of PDB database in mmCIF format. + format + + + + + + + + PDBML + + + format + beta12orEarlier + formats + edam + bioinformatics + Entry format of PDB database in PDBML (XML) format. + + + + + + + + Domainatrix 3D-1D scoring matrix format + + true + formats + bioinformatics + Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. + format + beta12orEarlier + beta12orEarlier + edam + + + + + + + + aaindex + + + beta12orEarlier + format + formats + edam + bioinformatics + Amino acid index format used by the AAindex database. + + + + + + + + IntEnz enzyme report format + + true + bioinformatics + IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. + edam + beta12orEarlier + beta12orEarlier + formats + format + Format of an entry from IntEnz (The Integrated Relational Enzyme Database). + + + + + + + + + BRENDA enzyme report format + + true + edam + beta12orEarlier + beta12orEarlier + formats + Format of an entry from the BRENDA enzyme database. + format + bioinformatics + + + + + + + + + KEGG REACTION enzyme report format + + true + beta12orEarlier + Format of an entry from the KEGG REACTION database of biochemical reactions. + format + edam + formats + bioinformatics + beta12orEarlier + + + + + + + + + KEGG ENZYME enzyme report format + + true + beta12orEarlier + edam + Format of an entry from the KEGG ENZYME database. + format + beta12orEarlier + formats + bioinformatics + + + + + + + + + REBASE proto enzyme report format + + true + format + bioinformatics + beta12orEarlier + beta12orEarlier + formats + edam + Format of an entry from the proto section of the REBASE enzyme database. + + + + + + + + + REBASE withrefm enzyme report format + + true + formats + format + Format of an entry from the withrefm section of the REBASE enzyme database. + bioinformatics + beta12orEarlier + edam + beta12orEarlier + + + + + + + + + Pcons report format + + + edam + Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. + format + beta12orEarlier + formats + Format of output of the Pcons Model Quality Assessment Program (MQAP). + bioinformatics + + + + + + + + ProQ report format + + + Format of output of the ProQ protein model quality predictor. + ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. + edam + formats + bioinformatics + beta12orEarlier + format + + + + + + + + SMART domain assignment report format + + true + beta12orEarlier + The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. + Format of SMART domain assignment data. + beta12orEarlier + format + edam + bioinformatics + formats + + + + + + + + + BIND entry format + + true + formats + edam + beta12orEarlier + beta12orEarlier + bioinformatics + format + Entry format for the BIND database of protein interaction. + + + + + + + + + IntAct entry format + + true + formats + Entry format for the IntAct database of protein interaction. + bioinformatics + beta12orEarlier + format + edam + beta12orEarlier + + + + + + + + + InterPro entry format + + true + format + This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. + beta12orEarlier + edam + formats + beta12orEarlier + Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. + bioinformatics + + + + + + + + + InterPro entry abstract format + + true + format + beta12orEarlier + Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. + formats + References are included and a functional inference is made where possible. + beta12orEarlier + edam + bioinformatics + + + + + + + + + Gene3D entry format + + true + bioinformatics + beta12orEarlier + beta12orEarlier + edam + format + formats + Entry format for the Gene3D protein secondary database. + + + + + + + + + PIRSF entry format + + true + formats + format + beta12orEarlier + bioinformatics + beta12orEarlier + Entry format for the PIRSF protein secondary database. + edam + + + + + + + + + PRINTS entry format + + true + formats + edam + Entry format for the PRINTS protein secondary database. + bioinformatics + beta12orEarlier + beta12orEarlier + format + + + + + + + + + Panther Families and HMMs entry format + + true + formats + bioinformatics + Entry format for the Panther library of protein families and subfamilies. + format + beta12orEarlier + edam + beta12orEarlier + + + + + + + + + Pfam entry format + + true + edam + beta12orEarlier + formats + format + beta12orEarlier + bioinformatics + Entry format for the Pfam protein secondary database. + + + + + + + + + SMART entry format + + true + beta12orEarlier + formats + edam + Entry format for the SMART protein secondary database. + beta12orEarlier + format + bioinformatics + + + + + + + + + Superfamily entry format + + true + format + beta12orEarlier + Entry format for the Superfamily protein secondary database. + beta12orEarlier + formats + bioinformatics + edam + + + + + + + + + TIGRFam entry format + + true + beta12orEarlier + bioinformatics + Entry format for the TIGRFam protein secondary database. + edam + formats + format + beta12orEarlier + + + + + + + + + ProDom entry format + + true + beta12orEarlier + bioinformatics + formats + format + edam + beta12orEarlier + Entry format for the ProDom protein domain classification database. + + + + + + + + + FSSP entry format + + true + beta12orEarlier + bioinformatics + Entry format for the FSSP database. + beta12orEarlier + formats + format + edam + + + + + + + + + findkm + + + A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax). + formats + bioinformatics + edam + beta12orEarlier + format + + + + + + + + Ensembl gene report format + + true + formats + beta12orEarlier + format + Entry format of Ensembl genome database. + bioinformatics + beta12orEarlier + edam + + + + + + + + + DictyBase gene report format + + true + beta12orEarlier + Entry format of DictyBase genome database. + edam + bioinformatics + beta12orEarlier + formats + format + + + + + + + + + CGD gene report format + + true + Entry format of Candida Genome database. + beta12orEarlier + format + beta12orEarlier + bioinformatics + edam + formats + + + + + + + + + DragonDB gene report format + + true + format + edam + beta12orEarlier + formats + Entry format of DragonDB genome database. + bioinformatics + beta12orEarlier + + + + + + + + + EcoCyc gene report format + + true + bioinformatics + edam + beta12orEarlier + format + beta12orEarlier + formats + Entry format of EcoCyc genome database. + + + + + + + + + FlyBase gene report format + + true + Entry format of FlyBase genome database. + bioinformatics + beta12orEarlier + beta12orEarlier + edam + formats + format + + + + + + + + + Gramene gene report format + + true + bioinformatics + edam + Entry format of Gramene genome database. + beta12orEarlier + beta12orEarlier + format + formats + + + + + + + + + KEGG GENES gene report format + + true + beta12orEarlier + formats + Entry format of KEGG GENES genome database. + beta12orEarlier + bioinformatics + edam + format + + + + + + + + + MaizeGDB gene report format + + true + format + Entry format of the Maize genetics and genomics database (MaizeGDB). + edam + bioinformatics + beta12orEarlier + beta12orEarlier + formats + + + + + + + + + MGD gene report format + + true + edam + formats + format + beta12orEarlier + beta12orEarlier + bioinformatics + Entry format of the Mouse Genome Database (MGD). + + + + + + + + + RGD gene report format + + true + beta12orEarlier + format + Entry format of the Rat Genome Database (RGD). + beta12orEarlier + edam + bioinformatics + formats + + + + + + + + + SGD gene report format + + true + beta12orEarlier + Entry format of the Saccharomyces Genome Database (SGD). + bioinformatics + format + edam + beta12orEarlier + formats + + + + + + + + + GeneDB gene report format + + true + format + beta12orEarlier + formats + beta12orEarlier + bioinformatics + edam + Entry format of the Sanger GeneDB genome database. + + + + + + + + + TAIR gene report format + + true + format + Entry format of The Arabidopsis Information Resource (TAIR) genome database. + edam + beta12orEarlier + bioinformatics + formats + beta12orEarlier + + + + + + + + + WormBase gene report format + + true + edam + formats + beta12orEarlier + beta12orEarlier + bioinformatics + format + Entry format of the WormBase genomes database. + + + + + + + + + ZFIN gene report format + + true + Entry format of the Zebrafish Information Network (ZFIN) genome database. + beta12orEarlier + formats + edam + beta12orEarlier + format + bioinformatics + + + + + + + + + TIGR gene report format + + true + bioinformatics + beta12orEarlier + beta12orEarlier + edam + formats + Entry format of the TIGR genome database. + format + + + + + + + + + dbSNP polymorphism report format + + true + format + bioinformatics + beta12orEarlier + Entry format for the dbSNP database. + formats + beta12orEarlier + edam + + + + + + + + + OMIM entry format + + true + Format of an entry from the OMIM database of genotypes and phenotypes. + edam + beta12orEarlier + beta12orEarlier + formats + bioinformatics + format + + + + + + + + + HGVbase entry format + + true + formats + beta12orEarlier + beta12orEarlier + bioinformatics + format + Format of a record from the HGVbase database of genotypes and phenotypes. + edam + + + + + + + + + HIVDB entry format + + true + edam + Format of a record from the HIVDB database of genotypes and phenotypes. + formats + format + bioinformatics + beta12orEarlier + beta12orEarlier + + + + + + + + + KEGG DISEASE entry format + + true + formats + bioinformatics + beta12orEarlier + Format of an entry from the KEGG DISEASE database. + format + edam + beta12orEarlier + + + + + + + + + Primer3 primer + + + edam + beta12orEarlier + Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program. + bioinformatics + formats + format + + + + + + + + ABI + + + formats + beta12orEarlier + edam + format + A format of raw sequence read data from an Applied Biosystems sequencing machine. + bioinformatics + + + + + + + + mira + + + formats + beta12orEarlier + bioinformatics + format + Format of MIRA sequence trace information file. + edam + + + + + + + + CAF + + + formats + beta12orEarlier + format + edam + bioinformatics + Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata. + + + + + + + + + + exp + + + edam + beta12orEarlier + formats + bioinformatics + format + Sequence assembly project file EXP format. + + + + + + + + SCF + + + bioinformatics + edam + formats + Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. + beta12orEarlier + format + + + + + + + + + + PHD + + + bioinformatics + beta12orEarlier + formats + format + PHD sequence trace format to store serialised chromatogram data (reads). + edam + + + + + + + + + + dat + + + + + + + + + beta12orEarlier + edam + Affymetrix image data file format + Format of Affymetrix data file of raw image data. + bioinformatics + formats + format + + + + + + + + cel + + + + + + + + + Format of Affymetrix data file of information about (raw) expression levels of the individual probes. + Affymetrix probe raw data format + beta12orEarlier + bioinformatics + format + edam + formats + + + + + + + + affymetrix + + + bioinformatics + format + beta12orEarlier + Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering. + edam + formats + + + + + + + + ArrayExpress entry format + + true + beta12orEarlier + format + Entry format for the ArrayExpress microarrays database. + edam + bioinformatics + formats + beta12orEarlier + + + + + + + + + affymetrix-exp + + + beta12orEarlier + edam + format + formats + Affymetrix experimental conditions data file format + Affymetrix data file format for information about experimental conditions and protocols. + bioinformatics + + + + + + + + CHP + + + + + + + + + Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. + format + edam + formats + bioinformatics + beta12orEarlier + Affymetrix probe normalised data format + + + + + + + + EMDB entry format + + true + edam + beta12orEarlier + Format of an entry from the Electron Microscopy DataBase (EMDB). + bioinformatics + formats + beta12orEarlier + format + + + + + + + + + KEGG PATHWAY entry format + + true + format + The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. + formats + beta12orEarlier + edam + bioinformatics + beta12orEarlier + + + + + + + + + MetaCyc entry format + + true + beta12orEarlier + The format of an entry from the MetaCyc metabolic pathways database. + beta12orEarlier + bioinformatics + formats + format + edam + + + + + + + + + HumanCyc entry format + + true + bioinformatics + beta12orEarlier + format + beta12orEarlier + edam + formats + The format of a report from the HumanCyc metabolic pathways database. + + + + + + + + + INOH entry format + + true + beta12orEarlier + bioinformatics + The format of an entry from the INOH signal transduction pathways database. + format + formats + edam + beta12orEarlier + + + + + + + + + PATIKA entry format + + true + edam + beta12orEarlier + format + formats + The format of an entry from the PATIKA biological pathways database. + beta12orEarlier + bioinformatics + + + + + + + + + Reactome entry format + + true + beta12orEarlier + The format of an entry from the reactome biological pathways database. + beta12orEarlier + format + formats + edam + bioinformatics + + + + + + + + + aMAZE entry format + + true + beta12orEarlier + edam + The format of an entry from the aMAZE biological pathways and molecular interactions database. + format + bioinformatics + formats + beta12orEarlier + + + + + + + + + CPDB entry format + + true + beta12orEarlier + edam + beta12orEarlier + The format of an entry from the CPDB database. + bioinformatics + format + formats + + + + + + + + + Panther Pathways entry format + + true + format + bioinformatics + The format of an entry from the Panther Pathways database. + edam + beta12orEarlier + formats + beta12orEarlier + + + + + + + + + Taverna workflow format + + + formats + bioinformatics + beta12orEarlier + format + Format of Taverna workflows. + edam + + + + + + + + BioModel mathematical model format + + true + Format of mathematical models from the BioModel database. + format + beta12orEarlier + Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. + bioinformatics + formats + edam + beta12orEarlier + + + + + + + + + KEGG LIGAND entry format + + true + format + bioinformatics + beta12orEarlier + formats + beta12orEarlier + The format of an entry from the KEGG LIGAND chemical database. + edam + + + + + + + + + KEGG COMPOUND entry format + + true + bioinformatics + beta12orEarlier + format + formats + The format of an entry from the KEGG COMPOUND database. + beta12orEarlier + edam + + + + + + + + + KEGG PLANT entry format + + true + edam + The format of an entry from the KEGG PLANT database. + bioinformatics + beta12orEarlier + format + beta12orEarlier + formats + + + + + + + + + KEGG GLYCAN entry format + + true + beta12orEarlier + edam + bioinformatics + The format of an entry from the KEGG GLYCAN database. + formats + beta12orEarlier + format + + + + + + + + + PubChem entry format + + true + edam + bioinformatics + beta12orEarlier + formats + beta12orEarlier + format + The format of an entry from PubChem. + + + + + + + + + ChemSpider entry format + + true + edam + bioinformatics + beta12orEarlier + The format of an entry from a database of chemical structures and property predictions. + formats + format + beta12orEarlier + + + + + + + + + ChEBI entry format + + true + ChEBI includes an ontological classification defining relations between entities or classes of entities. + The format of an entry from Chemical Entities of Biological Interest (ChEBI). + formats + beta12orEarlier + edam + bioinformatics + beta12orEarlier + format + + + + + + + + + MSDchem ligand dictionary entry format + + true + beta12orEarlier + bioinformatics + formats + beta12orEarlier + The format of an entry from the MSDchem ligand dictionary. + edam + format + + + + + + + + + HET group dictionary entry format + + + bioinformatics + beta12orEarlier + format + formats + edam + The format of an entry from the HET group dictionary (HET groups from PDB files). + + + + + + + + KEGG DRUG entry format + + true + formats + beta12orEarlier + beta12orEarlier + format + edam + bioinformatics + The format of an entry from the KEGG DRUG database. + + + + + + + + + PubMed citation + + + formats + Format of bibliographic reference as used by the PubMed database. + bioinformatics + beta12orEarlier + edam + format + + + + + + + + Medline Display Format + + + format + edam + bioinformatics + Bibliographic reference information including citation information is included + formats + Format for abstracts of scientific articles from the Medline database. + beta12orEarlier + + + + + + + + CiteXplore-core + + + edam + formats + CiteXplore 'core' citation format including title, journal, authors and abstract. + format + beta12orEarlier + bioinformatics + + + + + + + + CiteXplore-all + + + edam + beta12orEarlier + formats + bioinformatics + format + CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. + + + + + + + + pmc + + + formats + format + Article format of the PubMed Central database. + edam + beta12orEarlier + bioinformatics + + + + + + + + iHOP text mining abstract format + + + format + iHOP abstract format. + bioinformatics + edam + formats + beta12orEarlier + + + + + + + + Oscar3 + + + edam + bioinformatics + beta12orEarlier + formats + Text mining abstract format from the Oscar 3 application. + format + Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. + + + + + + + + PDB atom record format + + true + Format of an ATOM record (describing data for an individual atom) from a PDB file. + format + beta12orEarlier + bioinformatics + formats + edam + beta13 + + + + + + + + + CATH chain report format + + true + beta12orEarlier + Format of CATH domain classification information for a polypeptide chain. + beta12orEarlier + edam + The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. + format + formats + bioinformatics + + + + + + + + + CATH PDB report format + + true + The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. + Format of CATH domain classification information for a protein PDB file. + beta12orEarlier + formats + bioinformatics + format + edam + beta12orEarlier + + + + + + + + + NCBI gene report format + + true + formats + beta12orEarlier + beta12orEarlier + Entry (gene) format of the NCBI database. + bioinformatics + format + edam + + + + + + + + + GeneIlluminator gene report format + + true + Moby:GI_Gene + beta12orEarlier + bioinformatics + format + edam + formats + beta12orEarlier + This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. + Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service. + + + + + + + + + BacMap gene card format + + true + format + edam + beta12orEarlier + Moby:BacMapGeneCard + beta12orEarlier + formats + bioinformatics + Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database. + + + + + + + + + ColiCard report format + + true + beta12orEarlier + beta12orEarlier + formats + bioinformatics + Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). + format + Moby:ColiCard + edam + + + + + + + + + PlasMapper TextMap + + + Map of a plasmid (circular DNA) in PlasMapper TextMap format. + bioinformatics + beta12orEarlier + format + edam + formats + + + + + + + + newick + + + Phylogenetic tree Newick (text) format. + format + formats + beta12orEarlier + bioinformatics + edam + + + + + + + + TreeCon format + + + Phylogenetic tree TreeCon (text) format. + bioinformatics + beta12orEarlier + edam + format + formats + + + + + + + + Nexus format + + + formats + beta12orEarlier + format + Phylogenetic tree Nexus (text) format. + edam + bioinformatics + + + + + + + + beta12orEarlier + formats + bioinformatics + edam + format + + + + + Format + A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. + The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. + Exchange format + Data format + Data model + File format + + + + + + + + + + + + + + + + + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) + Data model + + + + + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + File format + + + + + Closely related concept focusing on the specification of a data format. + + + + + + GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials. + + + + + + Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format. + + + + + + BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format. + + + + + + Format can be a quality of a data record. + + + + + + + + + + + Atomic data format + + true + format + bioinformatics + edam + Data format for an individual atom. + formats + beta13 + beta12orEarlier + + + + + + + + + Sequence record format + + + + + + + + formats + beta12orEarlier + edam + Data format for a molecular sequence record. + bioinformatics + format + + + + + + + + Sequence feature annotation format + + + + + + + + bioinformatics + Data format for molecular sequence feature information. + edam + formats + beta12orEarlier + format + + + + + + + + Alignment format + + + + + + + + beta12orEarlier + Data format for molecular sequence alignment information. + edam + formats + format + bioinformatics + + + + + + + + acedb + + format + formats + ACEDB sequence format. + beta12orEarlier + bioinformatics + edam + + + + + + + + clustal sequence format + + true + beta12orEarlier + formats + edam + Clustalw output format. + beta12orEarlier + bioinformatics + format + + + + + + + + + codata + + + beta12orEarlier + format + Codata entry format. + bioinformatics + formats + edam + + + + + + + + dbid + + bioinformatics + formats + format + edam + beta12orEarlier + Fasta format variant with database name before ID. + + + + + + + + EMBL format + + + bioinformatics + EMBL + EMBL sequence format + EMBL entry format. + beta12orEarlier + edam + formats + format + + + + + + + + Staden experiment format + + + formats + edam + beta12orEarlier + format + Staden experiment file format. + bioinformatics + + + + + + + + FASTA format + + + FASTA sequence format + beta12orEarlier + format + FASTA format including NCBI-style IDs. + edam + formats + FASTA + bioinformatics + + + + + + + + FASTQ + + formats + beta12orEarlier + edam + bioinformatics + format + FASTQ short read format ignoring quality scores. + + + + + + + + FASTQ-illumina + + format + formats + beta12orEarlier + bioinformatics + FASTQ Illumina 1.3 short read format. + edam + + + + + + + + FASTQ-sanger + + beta12orEarlier + formats + edam + bioinformatics + format + FASTQ short read format with phred quality. + + + + + + + + FASTQ-solexa + + beta12orEarlier + formats + edam + bioinformatics + format + FASTQ Solexa/Illumina 1.0 short read format. + + + + + + + + fitch program + + + edam + beta12orEarlier + formats + Fitch program format. + bioinformatics + format + + + + + + + + gcg + + + formats + edam + format + bioinformatics + beta12orEarlier + GCG sequence format. + + + + + + + + GenBank format + + + format + bioinformatics + formats + Genbank entry format. + beta12orEarlier + edam + + + + + + + + genpept + + Genpept protein entry format. + format + Currently identical to refseqp format + edam + bioinformatics + beta12orEarlier + formats + + + + + + + + GFF2-seq + + + bioinformatics + format + beta12orEarlier + formats + GFF feature file format with sequence in the header. + edam + + + + + + + + GFF3-seq + + + formats + edam + beta12orEarlier + GFF3 feature file format with sequence. + bioinformatics + format + + + + + + + + giFASTA format + + beta12orEarlier + bioinformatics + format + formats + FASTA sequence format including NCBI-style GIs. + edam + + + + + + + + hennig86 + + + edam + Hennig86 output sequence format. + bioinformatics + beta12orEarlier + format + formats + + + + + + + + ig + + + beta12orEarlier + format + formats + bioinformatics + Intelligenetics sequence format. + edam + + + + + + + + igstrict + + + format + Intelligenetics sequence format (strict version). + beta12orEarlier + formats + edam + bioinformatics + + + + + + + + jackknifer + + + formats + format + beta12orEarlier + bioinformatics + edam + Jackknifer interleaved and non-interleaved sequence format. + + + + + + + + mase format + + + Mase program sequence format. + edam + beta12orEarlier + bioinformatics + format + formats + + + + + + + + mega-seq + + + format + Mega interleaved and non-interleaved sequence format. + edam + beta12orEarlier + formats + bioinformatics + + + + + + + + msf + + + + edam + format + formats + GCG MSF (multiple sequence file) file format. + beta12orEarlier + bioinformatics + + + + + + + + nbrf + + + bioinformatics + edam + formats + beta12orEarlier + format + NBRF/PIR entry sequence format. + + + + + + + + nexus-seq + + + + edam + bioinformatics + formats + Nexus/paup interleaved sequence format. + format + beta12orEarlier + + + + + + + + pdbatom + + + + PDB sequence format (ATOM lines). + bioinformatics + beta12orEarlier + formats + format + pdb format in EMBOSS. + edam + + + + + + + + pdbatomnuc + + + + formats + format + pdbnuc format in EMBOSS. + beta12orEarlier + PDB nucleotide sequence format (ATOM lines). + bioinformatics + edam + + + + + + + + pdbseqresnuc + + + + edam + beta12orEarlier + PDB nucleotide sequence format (SEQRES lines). + format + formats + bioinformatics + pdbnucseq format in EMBOSS. + + + + + + + + pdbseqres + + + + bioinformatics + edam + pdbseq format in EMBOSS. + beta12orEarlier + PDB sequence format (SEQRES lines). + format + formats + + + + + + + + Pearson format + + Plain old FASTA sequence format (unspecified format for IDs). + edam + bioinformatics + format + beta12orEarlier + formats + + + + + + + + phylip sequence format + + true + bioinformatics + beta12orEarlier + formats + beta12orEarlier + Phylip interleaved sequence format. + edam + format + + + + + + + + + phylipnon sequence format + + true + bioinformatics + formats + edam + beta12orEarlier + beta12orEarlier + Phylip non-interleaved sequence format. + format + + + + + + + + + raw + + + format + Raw sequence format with no non-sequence characters. + beta12orEarlier + bioinformatics + formats + edam + + + + + + + + refseqp + + + Currently identical to genpept format + bioinformatics + format + formats + edam + Refseq protein entry sequence format. + beta12orEarlier + + + + + + + + selex sequence format + + true + Selex sequence format. + edam + beta12orEarlier + beta12orEarlier + format + formats + bioinformatics + + + + + + + + + Staden format + + + edam + beta12orEarlier + Staden suite sequence format. + formats + bioinformatics + format + + + + + + + + + + + + Stockholm format + + + formats + Stockholm multiple sequence alignment format (used by Pfam and Rfam). + edam + format + bioinformatics + beta12orEarlier + + + + + + + + + + strider format + + + formats + beta12orEarlier + DNA strider output sequence format. + edam + format + bioinformatics + + + + + + + + UniProtKB format + + beta12orEarlier + UniProtKB entry sequence format. + formats + format + bioinformatics + edam + + + + + + + + plain text format (unformatted) + + + formats + Plain text sequence format (essentially unformatted). + beta12orEarlier + edam + format + bioinformatics + + + + + + + + treecon sequence format + + true + Treecon output sequence format. + edam + bioinformatics + format + beta12orEarlier + beta12orEarlier + formats + + + + + + + + + ASN.1 sequence format + + + format + bioinformatics + beta12orEarlier + NCBI ASN.1-based sequence format. + formats + edam + + + + + + + + DAS format + + + formats + edam + bioinformatics + beta12orEarlier + format + DAS sequence (XML) format (any type). + das sequence format + + + + + + + + dasdna + + + format + formats + bioinformatics + The use of this format is deprecated. + edam + DAS sequence (XML) format (nucleotide-only). + beta12orEarlier + + + + + + + + debug-seq + + + format + edam + bioinformatics + beta12orEarlier + EMBOSS debugging trace sequence format of full internal data content. + formats + + + + + + + + jackknifernon + + + bioinformatics + format + Jackknifer output sequence non-interleaved format. + beta12orEarlier + edam + formats + + + + + + + + meganon sequence format + + true + formats + edam + bioinformatics + Mega non-interleaved output sequence format. + format + beta12orEarlier + beta12orEarlier + + + + + + + + + NCBI format + + beta12orEarlier + There are several variants of this. + bioinformatics + NCBI FASTA sequence format with NCBI-style IDs. + edam + formats + format + + + + + + + + nexusnon + + + + bioinformatics + beta12orEarlier + edam + Nexus/paup non-interleaved sequence format. + formats + format + + + + + + + + GFF2 + + format + formats + edam + General Feature Format (GFF) of sequence features. + bioinformatics + beta12orEarlier + + + + + + + + + + GFF3 + + Generic Feature Format version 3 (GFF3) of sequence features. + format + formats + beta12orEarlier + bioinformatics + edam + + + + + + + + + + pir + + + format + beta12orEarlier + formats + PIR feature format. + bioinformatics + edam + + + + + + + + swiss feature + + true + bioinformatics + beta12orEarlier + edam + beta12orEarlier + format + Swiss-Prot feature format. + formats + + + + + + + + + DASGFF + + + edam + format + beta12orEarlier + DASGFF feature + bioinformatics + formats + DAS GFF (XML) feature format. + das feature + + + + + + + + debug-feat + + + bioinformatics + format + edam + formats + beta12orEarlier + EMBOSS debugging trace feature format of full internal data content. + + + + + + + + EMBL feature + + true + beta12orEarlier + edam + format + formats + bioinformatics + beta12orEarlier + EMBL feature format. + + + + + + + + + GenBank feature + + true + bioinformatics + edam + beta12orEarlier + format + Genbank feature format. + beta12orEarlier + formats + + + + + + + + + ClustalW format + + + bioinformatics + ClustalW format for (aligned) sequences. + formats + format + beta12orEarlier + edam + + + + + + + + debug + + + beta12orEarlier + formats + edam + format + bioinformatics + EMBOSS alignment format for debugging trace of full internal data content. + + + + + + + + FASTA-aln + + + edam + Fasta format for (aligned) sequences. + bioinformatics + format + beta12orEarlier + formats + + + + + + + + markx0 + + Pearson MARKX0 alignment format. + beta12orEarlier + format + formats + edam + bioinformatics + + + + + + + + markx1 + + edam + beta12orEarlier + bioinformatics + format + Pearson MARKX1 alignment format. + formats + + + + + + + + markx10 + + bioinformatics + format + formats + Pearson MARKX10 alignment format. + beta12orEarlier + edam + + + + + + + + markx2 + + format + bioinformatics + Pearson MARKX2 alignment format. + beta12orEarlier + formats + edam + + + + + + + + markx3 + + Pearson MARKX3 alignment format. + format + formats + beta12orEarlier + edam + bioinformatics + + + + + + + + match + + + edam + beta12orEarlier + bioinformatics + format + formats + Alignment format for start and end of matches between sequence pairs. + + + + + + + + mega + + format + beta12orEarlier + formats + Mega format for (typically aligned) sequences. + bioinformatics + edam + + + + + + + + meganon + + beta12orEarlier + Mega non-interleaved format for (typically aligned) sequences. + format + formats + bioinformatics + edam + + + + + + + + msf alignment format + + true + bioinformatics + formats + MSF format for (aligned) sequences. + beta12orEarlier + edam + format + beta12orEarlier + + + + + + + + + nexus alignment format + + true + edam + format + formats + beta12orEarlier + beta12orEarlier + bioinformatics + Nexus/paup format for (aligned) sequences. + + + + + + + + + nexusnon alignment format + + true + format + edam + beta12orEarlier + Nexus/paup non-interleaved format for (aligned) sequences. + bioinformatics + formats + beta12orEarlier + + + + + + + + + pair + + format + bioinformatics + beta12orEarlier + formats + EMBOSS simple sequence pair alignment format. + edam + + + + + + + + Phylip format + + formats + bioinformatics + edam + Phylip format for (aligned) sequences. + beta12orEarlier + format + + + + + + + + Phylipnon + + formats + bioinformatics + Phylip non-interleaved format for (aligned) sequences. + beta12orEarlier + edam + format + + + + + + + + scores format + + + edam + formats + Alignment format for score values for pairs of sequences. + beta12orEarlier + bioinformatics + format + + + + + + + + selex + + + + SELEX format for (aligned) sequences. + formats + beta12orEarlier + edam + format + bioinformatics + + + + + + + + EMBOSS simple format + + + formats + edam + beta12orEarlier + format + bioinformatics + EMBOSS simple multiple alignment format. + + + + + + + + srs format + + + Simple multiple sequence (alignment) format for SRS. + formats + bioinformatics + format + beta12orEarlier + edam + + + + + + + + srspair + + + bioinformatics + edam + formats + format + Simple sequence pair (alignment) format for SRS. + beta12orEarlier + + + + + + + + T-Coffee format + + + bioinformatics + beta12orEarlier + formats + T-Coffee program alignment format. + edam + format + + + + + + + + TreeCon-seq + + + + beta12orEarlier + formats + Treecon format for (aligned) sequences. + edam + format + bioinformatics + + + + + + + + Phylogenetic tree format + + + + + + + + bioinformatics + beta12orEarlier + Data format for a phylogenetic tree. + format + formats + edam + + + + + + + + Biological pathway or network format + + + + + + + + Data format for a biological pathway or network. + bioinformatics + format + formats + edam + beta12orEarlier + + + + + + + + Sequence-profile alignment format + + + + + + + + format + bioinformatics + Data format for a sequence-profile alignment. + edam + beta12orEarlier + formats + + + + + + + + Sequence-profile alignment (HMM) format + + true + Data format for a sequence-HMM profile alignment. + formats + bioinformatics + beta12orEarlier + edam + format + beta12orEarlier + + + + + + + + + Amino acid index format + + + + + + + + bioinformatics + beta12orEarlier + edam + formats + format + Data format for an amino acid index. + + + + + + + + Article format + + + + + + + + formats + format + Data format for a full-text scientific article. + bioinformatics + edam + Literature format + beta12orEarlier + + + + + + + + Text mining report format + + + + + + + + formats + Data format for an abstract (report) from text mining. + format + beta12orEarlier + edam + bioinformatics + + + + + + + + Enzyme kinetics report format + + + + + + + + bioinformatics + edam + format + formats + beta12orEarlier + Data format for reports on enzyme kinetics. + + + + + + + + Small molecule report format + + + + + + + + format + Format of a report on a chemical compound. + bioinformatics + Chemical compound annotation format + edam + formats + beta12orEarlier + + + + + + + + Gene annotation format + + + + + + + + bioinformatics + format + formats + beta12orEarlier + Format of a report on a particular locus, gene, gene system or groups of genes. + edam + + + + + + + + Workflow format + + + + + + + + formats + Format of a workflow. + beta12orEarlier + edam + format + bioinformatics + + + + + + + + Tertiary structure format + + edam + Data format for a molecular tertiary structure. + beta12orEarlier + formats + bioinformatics + format + + + + + + + + Biological model format + + true + formats + edam + 1.2 + beta12orEarlier + bioinformatics + format + Data format for a biological model. + + + + + + + + + + Chemical formula format + + + + + + + + bioinformatics + edam + format + formats + Text format of a chemical formula. + beta12orEarlier + + + + + + + + Phylogenetic character data format + + + + + + + + bioinformatics + Format of raw (unplotted) phylogenetic data. + format + formats + edam + beta12orEarlier + + + + + + + + Phylogenetic continuous quantitative character format + + + + + + + + beta12orEarlier + edam + Format of phylogenetic continuous quantitative character data. + bioinformatics + formats + format + + + + + + + + Phylogenetic discrete states format + + + + + + + + edam + format + beta12orEarlier + bioinformatics + Format of phylogenetic discrete states data. + formats + + + + + + + + Phylogenetic tree report (cliques) format + + + + + + + + format + beta12orEarlier + bioinformatics + Format of phylogenetic cliques data. + formats + edam + + + + + + + + Phylogenetic tree report (invariants) format + + + + + + + + formats + format + Format of phylogenetic invariants data. + edam + bioinformatics + beta12orEarlier + + + + + + + + Electron microscopy model format + + true + bioinformatics + Annotation format for electron microscopy models. + format + beta12orEarlier + beta12orEarlier + formats + edam + + + + + + + + + Phylogenetic tree report (tree distances) format + + + + + + + + edam + bioinformatics + formats + beta12orEarlier + format + Format for phylogenetic tree distance data. + + + + + + + + Polymorphism report format + + true + formats + format + 1.0 + Format for sequence polymorphism data. + bioinformatics + beta12orEarlier + edam + + + + + + + + Protein family report format + + + + + + + + formats + edam + format + bioinformatics + beta12orEarlier + Format for reports on a protein family. + + + + + + + + Molecular interaction format + + + + + + + + Format for molecular interaction data. + bioinformatics + beta12orEarlier + edam + format + formats + + + + + + + + Sequence assembly format + + + + + + + + Format for sequence assembly data. + bioinformatics + formats + beta12orEarlier + format + edam + + + + + + + + Microarray experiment data format + + + + + + + + Format for microarray experimental data. + beta12orEarlier + formats + edam + format + bioinformatics + + + + + + + + Sequence trace format + + + + + + + + format + beta12orEarlier + edam + formats + bioinformatics + Format for sequence trace data (i.e. including base call information). + + + + + + + + Gene expression report format + + + + + + + + beta12orEarlier + bioinformatics + edam + Format for a report on gene expression. + format + formats + + + + + + + + Genotype and phenotype annotation format + + true + bioinformatics + beta12orEarlier + format + edam + Format of a report on genotype / phenotype information. + beta12orEarlier + formats + + + + + + + + + Map format + + + + + + + + bioinformatics + format + beta12orEarlier + formats + edam + Format of a map of (typically one) molecular sequence annotated with features. + + + + + + + + Nucleic acid features (primers) format + + + + + + + + formats + Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. + format + edam + beta12orEarlier + bioinformatics + + + + + + + + Protein report format + + + + + + + + beta12orEarlier + format + formats + bioinformatics + edam + Format of a report of general information about a specific protein. + + + + + + + + Protein report (enzyme) format + + true + bioinformatics + format + edam + beta12orEarlier + beta12orEarlier + Format of a report of general information about a specific enzyme. + formats + + + + + + + + + 3D-1D scoring matrix format + + + + + + + + formats + Format of a matrix of 3D-1D scores (amino acid environment probabilities). + beta12orEarlier + format + edam + bioinformatics + + + + + + + + Protein structure report (quality evaluation) format + + + + + + + + edam + formats + beta12orEarlier + Format of a report on the quality of a protein three-dimensional model. + bioinformatics + format + + + + + + + + Database hits (sequence) format + + + + + + + + beta12orEarlier + formats + format + Format of a report on sequence hits and associated data from searching a sequence database. + bioinformatics + edam + + + + + + + + Sequence distance matrix format + + + + + + + + Format of a matrix of genetic distances between molecular sequences. + beta12orEarlier + bioinformatics + format + edam + formats + + + + + + + + Sequence motif format + + + + + + + + beta12orEarlier + format + Format of a sequence motif. + edam + bioinformatics + formats + + + + + + + + Sequence profile format + + + + + + + + edam + formats + bioinformatics + beta12orEarlier + Format of a sequence profile. + format + + + + + + + + Hidden Markov model format + + + + + + + + bioinformatics + Format of a hidden Markov model. + edam + formats + format + beta12orEarlier + + + + + + + + Dirichlet distribution format + + + + + + + + format + formats + bioinformatics + beta12orEarlier + edam + Data format of a dirichlet distribution. + + + + + + + + HMM emission and transition counts format + + + + + + + + beta12orEarlier + format + edam + formats + bioinformatics + Data format for the emission and transition counts of a hidden Markov model. + + + + + + + + RNA secondary structure format + + + + + + + + Format for secondary structure (predicted or real) of an RNA molecule. + edam + format + bioinformatics + beta12orEarlier + formats + + + + + + + + Protein secondary structure format + + + + + + + + beta12orEarlier + format + Format for secondary structure (predicted or real) of a protein molecule. + edam + formats + bioinformatics + + + + + + + + Sequence range format + + + + + + + + format + formats + edam + bioinformatics + Format used to specify range(s) of sequence positions. + beta12orEarlier + + + + + + + + pure + + + bioinformatics + beta12orEarlier + formats + edam + Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. + format + + + + + + + + unpure + + + formats + edam + bioinformatics + beta12orEarlier + Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. + format + + + + + + + + unambiguous sequence + + + formats + format + bioinformatics + beta12orEarlier + edam + Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. + + + + + + + + ambiguous + + + edam + formats + format + Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. + beta12orEarlier + bioinformatics + + + + + + + + Sequence features (repeats) format + + + + + + + + Format used for map of repeats in molecular (typically nucleotide) sequences. + format + bioinformatics + edam + beta12orEarlier + formats + + + + + + + + Nucleic acid features (restriction sites) format + + + + + + + + Format used for report on restriction enzyme recognition sites in nucleotide sequences. + bioinformatics + formats + format + beta12orEarlier + edam + + + + + + + + Gene features (coding region) format + + + + + + + + formats + Format used for report on coding regions in nucleotide sequences. + beta12orEarlier + format + bioinformatics + edam + + + + + + + + Sequence cluster format + + + + + + + + format + edam + Format used for clusters of molecular sequences. + bioinformatics + formats + beta12orEarlier + + + + + + + + Sequence cluster format (protein) + + beta12orEarlier + Format used for clusters of protein sequences. + bioinformatics + edam + format + formats + + + + + + + + Sequence cluster format (nucleic acid) + + beta12orEarlier + edam + format + bioinformatics + formats + Format used for clusters of nucleotide sequences. + + + + + + + + Gene cluster format + + true + formats + Format used for clusters of genes. + edam + format + beta12orEarlier + beta13 + bioinformatics + + + + + + + + + EMBL-like (text) + + + A text format resembling EMBL entry format. + bioinformatics + edam + formats + beta12orEarlier + format + This concept may be used for the many non-standard EMBL-like text formats. + + + + + + + + FASTQ-like format (text) + + + beta12orEarlier + formats + This concept may be used for non-standard FASTQ short read-like formats. + format + bioinformatics + A text format resembling FASTQ short read format. + edam + + + + + + + + EMBLXML + + edam + formats + beta12orEarlier + bioinformatics + format + XML format for EMBL entries. + + + + + + + + cdsxml + + bioinformatics + format + beta12orEarlier + edam + XML format for EMBL entries. + formats + + + + + + + + insdxml + + formats + format + XML format for EMBL entries. + edam + bioinformatics + beta12orEarlier + + + + + + + + geneseq + + format + edam + beta12orEarlier + Geneseq sequence format. + formats + bioinformatics + + + + + + + + UniProt-like (text) + + + bioinformatics + format + formats + edam + beta12orEarlier + A text sequence format resembling uniprotkb entry format. + + + + + + + + UniProt format + + formats + UniProt entry sequence format. + format + beta12orEarlier + bioinformatics + edam + + + + + + + + ipi + + formats + bioinformatics + format + ipi sequence format. + edam + beta12orEarlier + + + + + + + + medline + + + format + beta12orEarlier + bioinformatics + formats + Abstract format used by MedLine database. + edam + + + + + + + + Ontology format + + + + + + + + edam + bioinformatics + beta12orEarlier + format + Format used for ontologies. + formats + + + + + + + + OBO format + + A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. + bioinformatics + format + beta12orEarlier + edam + formats + + + + + + + + OWL format + + + + formats + A serialisation format conforming to the Web Ontology Language (OWL) model. + beta12orEarlier + edam + bioinformatics + format + + + + + + + + FASTA-like (text) + + + edam + beta12orEarlier + This concept may also be used for the many non-standard FASTA-like formats. + formats + bioinformatics + A text format resembling FASTA format. + format + + + + + + + + + Sequence record full format + + + + + + + + bioinformatics + format + edam + formats + Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. + beta12orEarlier + + + + + + + + Sequence record lite format + + + + + + + + Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment. + bioinformatics + format + edam + formats + beta12orEarlier + + + + + + + + EMBL format (XML) + + formats + edam + format + bioinformatics + This is a placeholder for other more specific concepts. It should not normally be used for annotation. + An XML format for EMBL entries. + beta12orEarlier + + + + + + + + GenBank-like format (text) + + + beta12orEarlier + edam + This concept may be used for the non-standard GenBank-like text formats. + bioinformatics + formats + A text format resembling GenBank entry (plain text) format. + format + + + + + + + + Sequence feature table format (text) + + bioinformatics + format + beta12orEarlier + Text format for a sequence feature table. + edam + formats + + + + + + + + Strain data format + + true + format + 1.0 + beta12orEarlier + formats + edam + bioinformatics + Format of a report on organism strain data / cell line. + + + + + + + + CIP strain data format + + true + formats + beta12orEarlier + edam + beta12orEarlier + bioinformatics + format + Format for a report of strain data as used for CIP database entries. + + + + + + + + + phylip property values + + true + formats + beta12orEarlier + beta12orEarlier + edam + PHYLIP file format for phylogenetic property data. + bioinformatics + format + + + + + + + + + STRING entry format (HTML) + + true + formats + Entry format (HTML) for the STRING database of protein interaction. + beta12orEarlier + format + edam + beta12orEarlier + bioinformatics + + + + + + + + + STRING entry format (XML) + + + format + beta12orEarlier + formats + edam + Entry format (XML) for the STRING database of protein interaction. + bioinformatics + + + + + + + + GFF + + + bioinformatics + beta12orEarlier + GFF feature format (of indeterminate version). + formats + format + edam + + + + + + + + GTF + + edam + beta12orEarlier + bioinformatics + Gene Transfer Format (GTF), a restricted version of GFF. + format + formats + + + + + + + + + + + FASTA-HTML + + + format + bioinformatics + formats + beta12orEarlier + FASTA format wrapped in HTML elements. + edam + + + + + + + + EMBL-HTML + + + beta12orEarlier + formats + format + edam + bioinformatics + EMBL entry format wrapped in HTML elements. + + + + + + + + BioCyc enzyme report format + + true + bioinformatics + formats + format + edam + Format of an entry from the BioCyc enzyme database. + beta12orEarlier + beta12orEarlier + + + + + + + + + ENZYME enzyme report format + + true + formats + format + beta12orEarlier + beta12orEarlier + Format of an entry from the Enzyme nomenclature database (ENZYME). + bioinformatics + edam + + + + + + + + + PseudoCAP gene report format + + true + Format of a report on a gene from the PseudoCAP database. + edam + beta12orEarlier + format + beta12orEarlier + formats + bioinformatics + + + + + + + + + GeneCards gene report format + + true + bioinformatics + edam + beta12orEarlier + format + beta12orEarlier + Format of a report on a gene from the GeneCards database. + formats + + + + + + + + + beta12orEarlier + formats + edam + bioinformatics + format + Textual format + Textual format. + Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). + + Tabular format + Plain text + + + + + Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. + Tabular format + + + + + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + + + + + + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + + + + + + + + + + + beta12orEarlier + formats + edam + bioinformatics + format + HTML + HTML format. + + + + + + + + Hypertext Markup Language + + + + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + + + + + + + + + + + beta12orEarlier + formats + edam + bioinformatics + format + XML + eXtensible Markup Language (XML) format. + Data in XML format can be serialised into text, or binary format. + + Extensible Markup Language + + + + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + + + + + + + + + + + Binary format + + edam + formats + bioinformatics + Binary format. + beta12orEarlier + Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. + format + + + + + + + + URI format + + true + bioinformatics + format + beta12orEarlier + Typical textual representation of a URI. + formats + edam + beta13 + + + + + + + + + NCI-Nature pathway entry format + + true + beta12orEarlier + format + The format of an entry from the NCI-Nature pathways database. + bioinformatics + beta12orEarlier + formats + edam + + + + + + + + + Format (typed) + + edam + A broad class of format distinguished by the scientific nature of the data that is identified. + format + beta12orEarlier + This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. + bioinformatics + formats + + + + + + + + BioXSD + + + + + + + + + + + + + + + + + + + + + + + + BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). + formats + bioinformatics + beta12orEarlier + format + BioXSD XML format + edam + + + + + + + + + + RDF format + + + + A serialisation format conforming to the Resource Description Framework (RDF) model. + + beta12orEarlier + bioinformatics + format + edam + formats + + + + + + + + + GenBank-HTML + + + Genbank entry format wrapped in HTML elements. + bioinformatics + beta12orEarlier + edam + formats + format + + + + + + + + Protein features (domains) format + + true + formats + Format of a report on protein features (domain composition). + bioinformatics + beta12orEarlier + beta12orEarlier + format + edam + + + + + + + + + EMBL-like format + + edam + formats + This concept may be used for the many non-standard EMBL-like formats. + A format resembling EMBL entry (plain text) format. + bioinformatics + format + beta12orEarlier + + + + + + + + FASTQ-like format + + bioinformatics + beta12orEarlier + This concept may be used for non-standard FASTQ short read-like formats. + formats + format + A format resembling FASTQ short read format. + edam + + + + + + + + FASTA-like + + format + edam + A format resembling FASTA format. + formats + beta12orEarlier + bioinformatics + This concept may be used for the many non-standard FASTA-like formats. + + + + + + + + uniprotkb-like format + + + A sequence format resembling uniprotkb entry format. + beta12orEarlier + format + edam + formats + bioinformatics + + + + + + + + Sequence feature table format + + + + + + + + edam + beta12orEarlier + format + Format for a sequence feature table. + bioinformatics + formats + + + + + + + + OBO + + + OBO ontology text format. + format + formats + bioinformatics + edam + beta12orEarlier + + + + + + + + OBO-XML + + + edam + OBO ontology XML format. + bioinformatics + formats + beta12orEarlier + format + + + + + + + + Sequence record format (text) + + formats + bioinformatics + format + beta12orEarlier + edam + Data format for a molecular sequence record. + + + + + + + + Sequence record format (XML) + + format + bioinformatics + Data format for a molecular sequence record. + edam + formats + beta12orEarlier + + + + + + + + Sequence feature table format (XML) + + formats + bioinformatics + beta12orEarlier + format + XML format for a sequence feature table. + edam + + + + + + + + Alignment format (text) + + beta12orEarlier + bioinformatics + edam + format + formats + Text format for molecular sequence alignment information. + + + + + + + + Alignment format (XML) + + beta12orEarlier + bioinformatics + edam + formats + XML format for molecular sequence alignment information. + format + + + + + + + + Phylogenetic tree format (text) + + formats + bioinformatics + Text format for a phylogenetic tree. + beta12orEarlier + edam + format + + + + + + + + Phylogenetic tree format (XML) + + formats + format + XML format for a phylogenetic tree. + edam + beta12orEarlier + bioinformatics + + + + + + + + EMBL-like (XML) + + + edam + beta12orEarlier + formats + format + This concept may be used for the any non-standard EMBL-like XML formats. + bioinformatics + An XML format resembling EMBL entry format. + + + + + + + + GenBank-like format + + bioinformatics + This concept may be used for the non-standard GenBank-like formats. + edam + formats + format + beta12orEarlier + A format resembling GenBank entry (plain text) format. + + + + + + + + STRING entry format + + true + bioinformatics + formats + beta12orEarlier + Entry format for the STRING database of protein interaction. + format + edam + beta12orEarlier + + + + + + + + + Sequence assembly format (text) + + Text format for sequence assembly data. + bioinformatics + edam + format + beta12orEarlier + formats + + + + + + + + Amino acid identifier format + + true + beta12orEarlier + bioinformatics + Text format (representation) of amino acid residues. + format + beta13 + edam + formats + + + + + + + + + completely unambiguous + + + formats + Alphabet for a molecular sequence without any unknown positions or ambiguity characters. + format + edam + beta12orEarlier + bioinformatics + + + + + + + + completely unambiguous pure + + + Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters. + edam + bioinformatics + format + beta12orEarlier + formats + + + + + + + + completely unambiguous pure nucleotide + + + edam + format + beta12orEarlier + Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters . + bioinformatics + formats + + + + + + + + completely unambiguous pure dna + + + Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters. + formats + bioinformatics + edam + format + beta12orEarlier + + + + + + + + completely unambiguous pure rna sequence + + + formats + format + beta12orEarlier + Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters. + edam + bioinformatics + + + + + + + + Raw sequence format + + + + + + + + Format of a raw molecular sequence (i.e. the alphabet used). + beta12orEarlier + formats + edam + format + bioinformatics + + + + + + + + + BAM + + + + BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. + beta12orEarlier + format + formats + edam + bioinformatics + + + + + + + + + + SAM + + + + edam + Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. + beta12orEarlier + The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. + format + formats + bioinformatics + + + + + + + + + + SBML + + + formats + beta12orEarlier + edam + format + Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation. + bioinformatics + + + + + + + + + + completely unambiguous pure protein + + + edam + formats + format + Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters. + beta12orEarlier + bioinformatics + + + + + + + + Bibliographic reference format + + + + + + + + + + + + + + bioinformatics + formats + beta12orEarlier + edam + Format of a bibliographic reference. + format + + + + + + + + Sequence annotation track format + + + + + + + + bioinformatics + formats + edam + beta12orEarlier + Format of a sequence annotation track. + format + + + + + + + + Alignment format (pair only) + + + + + + + + format + Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. + formats + bioinformatics + edam + beta12orEarlier + + + + + + + + Sequence variation annotation format + + + + + + + + bioinformatics + edam + beta12orEarlier + Format of sequence variation annotation. + formats + format + + + + + + + + markx0 variant + + + format + formats + edam + beta12orEarlier + Some variant of Pearson MARKX alignment format. + bioinformatics + + + + + + + + mega variant + + + + beta12orEarlier + edam + Some variant of Mega format for (typically aligned) sequences. + bioinformatics + format + formats + + + + + + + + Phylip format variant + + + + bioinformatics + Some variant of Phylip format for (aligned) sequences. + format + edam + formats + beta12orEarlier + + + + + + + + AB1 + + + format + AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). + AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. + bioinformatics + formats + edam + beta12orEarlier + + + + + + + + ACE + + + format + edam + bioinformatics + beta12orEarlier + ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards). + formats + + + + + + + + + + BED + + + BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). + Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser. + edam + bioinformatics + beta12orEarlier + format + formats + + + + + + + + + + bigBed + + + bigBed format for large sequence annotation tracks, similar to textual BED format. + format + beta12orEarlier + bioinformatics + formats + edam + + + + + + + + + + WIG + + + edam + bioinformatics + Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser. + format + beta12orEarlier + formats + + + + + + + + + + bigWig + + + formats + format + beta12orEarlier + bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. + edam + bioinformatics + + + + + + + + + + PSL + + + + beta12orEarlier + formats + edam + bioinformatics + format + PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. + + + + + + + + + + MAF + + + + beta12orEarlier + format + Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. + formats + edam + Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. + bioinformatics + + + + + + + + + + 2bit + + + format + edam + 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. + formats + bioinformatics + beta12orEarlier + + + + + + + + + + + .nib + + + formats + format + beta12orEarlier + .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. + bioinformatics + edam + + + + + + + + + + genePred + + + bioinformatics + beta12orEarlier + edam + formats + format + genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. + genePred table format for gene prediction tracks. + + + + + + + + + + pgSnp + + + edam + beta12orEarlier + bioinformatics + formats + format + Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser. + + + + + + + + + + axt + + + axt format of alignments, typically produced from BLASTZ. + format + beta12orEarlier + edam + formats + bioinformatics + + + + + + + + + + LAV + + + beta12orEarlier + format + LAV format of alignments generated by BLASTZ and LASTZ. + bioinformatics + formats + edam + + + + + + + + + + Pileup + + + bioinformatics + beta12orEarlier + format + formats + Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s). + edam + + + + + + + + + + VCF + + + Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). + bioinformatics + beta12orEarlier + edam + formats + format + + + + + + + + + + SRF + + + edam + beta12orEarlier + formats + bioinformatics + Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. + format + + + + + + + + + + ZTR + + + edam + format + formats + ZTR format for storing chromatogram data from DNA sequencing instruments. + beta12orEarlier + bioinformatics + + + + + + + + + + GVF + + + edam + beta12orEarlier + formats + format + bioinformatics + Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. + + + + + + + + + + BCF + + + edam + format + BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). + bioinformatics + beta12orEarlier + formats + + + + + + + + + Matrix format + + + + + + + + beta13 + formats + format + Format of a matrix (array) of numerical values. + bioinformatics + edam + + + + + + + + Protein domain classification format + + + + + + + + bioinformatics + beta13 + formats + edam + Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). + format + + + + + + + + Raw SCOP domain classification format + + edam + These are the parsable data files provided by SCOP. + beta13 + format + formats + Format of raw SCOP domain classification data files. + bioinformatics + + + + + + + + Raw CATH domain classification format + + bioinformatics + edam + format + Format of raw CATH domain classification data files. + beta13 + These are the parsable data files provided by CATH. + formats + + + + + + + + CATH domain report format + + bioinformatics + The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. + format + beta13 + Format of summary of domain classification information for a CATH domain. + edam + formats + + + + + + + + SBRML + + + format + 1.0 + bioinformatics + formats + edam + Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. + + + + + + + + + + BioPAX + + + edam + format + formats + 1.0 + BioPAX is an exchange format for pathway data, with its data model defined in OWL. + bioinformatics + + + + + + + + + + EBI Application Result XML + + + + bioinformatics + edam + format + 1.0 + EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. + formats + + + + + + + + + + PSI MI XML (MIF) + + + edam + XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. + formats + bioinformatics + MIF + 1.0 + format + + + + + + + + + + phyloXML + + + formats + 1.0 + bioinformatics + edam + format + phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data. + + + + + + + + + + NeXML + + + formats + bioinformatics + NeXML is a standardised XML format for rich phyloinformatic data. + edam + 1.0 + format + + + + + + + + + + MAGE-ML + + + + formats + 1.0 + MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). + format + bioinformatics + edam + + + + + + + + + + MAGE-TAB + + + + MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). + formats + 1.0 + bioinformatics + edam + format + + + + + + + + + + GCDML + + + + + + + + + bioinformatics + GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). + format + edam + 1.0 + formats + + + + + + + + + + GTrack + + + GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG). + bioinformatics + format + edam + formats + 1.0 + + + + + + + + + + Biological pathway or network report format + + + + + + + + edam + formats + bioinformatics + format + beta12orEarlier + Data format for a report of information derived from a biological pathway or network. + + + + + + + + Experiment annotation format + + format + edam + bioinformatics + formats + Data format for annotation on a laboratory experiment. + beta12orEarlier + + + + + + + + Cytoband format + + + + + + + + + format + formats + edam + 1.2 + Reflects a UCSC Browser DB table. + Cytoband format for chromosome cytobands. + bioinformatics + + + + + + + + + + CopasiML + + + + formats + CopasiML, the native format of COPASI. + bioinformatics + edam + format + 1.2 + + + + + + + + + + CellML + + + 1.2 + formats + bioinformatics + edam + CellML, the format for mathematical models of biological and other networks. + format + + + + + + + + + + 1.2 + formats + edam + bioinformatics + format + PSI MI TAB (MITAB) + Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. + + + + + + + + + + + + 1.2 + formats + edam + bioinformatics + format + PSI-PAR + Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema. + + + + + + + + + + + 1.2 + formats + edam + bioinformatics + format + mzML + mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. + mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. + + + + + + + + + + + + 1.2 + formats + bioinformatics + edam + format + Mass spectrometry data format + Format for mass spectrometry data. + + + + + + + + + + + + + + + 1.2 + formats + edam + bioinformatics + format + TraML + TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. + + + + + + + + + + + + 1.2 + formats + edam + bioinformatics + format + mzIdentML + mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines. + + + + + + + + + + + + 1.2 + formats + edam + bioinformatics + format + mzQuantML + mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics. + + + + + + + + + + + + 1.2 + formats + edam + bioinformatics + format + GelML + GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. + + + + + + + + + + + + + + + + + + 1.2 + formats + edam + bioinformatics + format + spML + spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. + + + + + + + + + + + + + + + + + + OWL Functional Syntax + + + + A human-readable encoding for the Web Ontology Language (OWL). + 1.2 + bioinformatics + format + edam + formats + + + + + + + + Manchester OWL Syntax + + + + A syntax for writing OWL class expressions. + This format was influenced by the OWL Abstract Syntax and the DL style syntax. + 1.2 + bioinformatics + format + edam + formats + + + + + + + + KRSS2 Syntax + + + A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". + This format is used in Protege 4. + 1.2 + bioinformatics + format + + edam + formats + + + + + + + + Turtle + + + + The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs. + The SPARQL Query Language incorporates a very similar syntax. + 1.2 + bioinformatics + format + edam + formats + + + + + + + + N-Triples + + + + A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. + N-Triples should not be confused with Notation 3 which is a superset of Turtle. + 1.2 + bioinformatics + format + edam + formats + + + + + + + + Notation3 + + + + A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. + N3 + bioinformatics + format + edam + formats + + + + + + + + RDF/XML + + + + + Resource Description Framework (RDF) XML format. + RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. + 1.2 + bioinformatics + format + RDF + edam + formats + + + + + + + + + OWL/XML + + + + + formats + OWL ontology XML serialisation format. + 1.2 + OWL + edam + bioinformatics + format + + + + + + + + beta12orEarlier + operations + edam + bioinformatics + operation + + Operation + A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. + Function + Computational operation + Computational procedure + Computational method + Computational subroutine + Function (programming) + Lambda abstraction + Mathematical operation + Mathematical function + Process + Computational tool + + + + + + + + + sumo:Function + + + + + + + + + + + + + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Function + + + + + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Process + + + + + Computational tool provides one or more operations. + Computational tool + + + + + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'. + + + + + + However, operation is not a GFO 'Concept' present only in someone's mind. + + + + + + GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. + + + + + + BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s). + + + + + + Function, including an operation, can be a quality/property of e.g. a computational tool. + + + + + + Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool. + + + + + + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. + + + + + + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. + + + + + + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. + + + + + + However, one may think that an operation is not a process. + + + + + + However, one may think that an operation is not a process and not a physical entity. + + + + + + Method may in addition focus on how to achieve the result, not just on what to achieve as with operation. + + + + + + + + + + + Search and retrieval + + + + + + + + + + + + + + bioinformatics + operations + operation + Database retrieval + Search or query a data resource and retrieve entries and / or annotation. + beta12orEarlier + edam + + + + + + + + Data retrieval (database cross-reference) + + true + beta13 + operation + operations + Search database to retrieve all relevant references to a particular entity or entry. + beta12orEarlier + edam + bioinformatics + + + + + + + + + Annotation + + + + + + + + + + + + + + bioinformatics + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. + This is a broad concept and is used a placeholder for other, more specific concepts. + edam + beta12orEarlier + operation + operations + + + + + + + + Data indexing + + + + + + + + Database indexing + bioinformatics + operations + edam + Generate an index of (typically a file of) biological data. + beta12orEarlier + operation + + + + + + + + Data index analysis + + + + + + + + + + + + + + edam + beta12orEarlier + Analyse an index of biological data. + bioinformatics + operation + operations + Database index analysis + + + + + + + + Annotation retrieval (sequence) + + true + beta12orEarlier + Retrieve basic information about a molecular sequence. + operations + bioinformatics + edam + beta12orEarlier + operation + + + + + + + + + Sequence generation + + edam + Generate a molecular sequence by some means. + beta12orEarlier + operation + operations + bioinformatics + + + + + + + + Sequence editing + + + operation + operations + beta12orEarlier + bioinformatics + edam + Edit or change a molecular sequence, either randomly or specifically. + + + + + + + + Sequence merging + + operations + Sequence splicing + operation + Merge two or more (typically overlapping) molecular sequences. + beta12orEarlier + edam + bioinformatics + + + + + + + + Sequence conversion + + operation + beta12orEarlier + operations + bioinformatics + edam + Convert a molecular sequence from one type to another. + + + + + + + + Sequence complexity calculation + + + + + + + + + + + + + + operations + edam + Calculate sequence complexity, for example to find low-complexity regions in sequences. + operation + beta12orEarlier + bioinformatics + + + + + + + + Sequence ambiguity calculation + + + + + + + + + + + + + + beta12orEarlier + operations + Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. + bioinformatics + operation + edam + + + + + + + + Sequence composition calculation + + + + + + + + + + + + + + edam + Calculate character or word composition or frequency of a molecular sequence. + operations + bioinformatics + beta12orEarlier + operation + + + + + + + + Repeat sequence analysis + + + + + + + + Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. + edam + beta12orEarlier + Find and/or analyse repeat sequences in (typically nucleotide) sequences. + operation + operations + bioinformatics + + + + + + + + Sequence motif discovery + + + + + + + + + beta12orEarlier + edam + operations + Motif discovery + Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). + operation + bioinformatics + Motifs and patterns might be conserved or over-represented (occur with improbable frequency). + + + + + + + + Sequence motif recognition + + + + + + + + + bioinformatics + Sequence motif detection + operation + Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). + edam + beta12orEarlier + operations + Motif detection + Motif recognition + + + + + + + + Sequence motif comparison + + + + + + + + + Find motifs shared by molecular sequences. + beta12orEarlier + operations + edam + operation + bioinformatics + + + + + + + + Transcription regulatory sequence analysis + + true + beta12orEarlier + operation + edam + Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. + beta13 + For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. + bioinformatics + operations + + + + + + + + + Conserved transcription regulatory sequence identification + + + + + + + + + operation + Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites). + beta12orEarlier + bioinformatics + operations + edam + For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. + + + + + + + + Protein property calculation (from structure) + + + + + + + + + + + + + + + + operations + This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. + bioinformatics + Protein structural property calculation + operation + edam + beta12orEarlier + Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure. + + + + + + + + Protein flexibility and motion analysis + + + + + + + + + bioinformatics + Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. + Analyse flexibility and motion in protein structure. + operations + beta12orEarlier + operation + edam + + + + + + + + Protein structural motif recognition + + + + + + + + + + + + + + Protein structural feature identification + beta12orEarlier + operations + operation + This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. + Identify or screen for 3D structural motifs in protein structure(s). + bioinformatics + edam + + + + + + + + Protein domain recognition + + + + + + + + + + + + + + Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). + bioinformatics + edam + operations + beta12orEarlier + operation + + + + + + + + Protein architecture analysis + + + + + + + + Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). + operations + operation + beta12orEarlier + bioinformatics + edam + + + + + + + + Residue interaction calculation + + + + + + + + + + + + + + operation + WHATIF: SymShellOneXML + WHATIF: SymShellFiveXML + Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s). + bioinformatics + WHATIF:ListContactsNormal + beta12orEarlier + operations + WHATIF:ListSideChainContactsNormal + WHATIF:ListSideChainContactsRelaxed + edam + WHATIF: SymShellTwoXML + WHATIF:ListContactsRelaxed + WHATIF: SymShellTenXML + + + + + + + + Torsion angle calculation + + + + + + + + operation + bioinformatics + Calculate, visualise or analyse phi/psi angles of a protein structure. + beta12orEarlier + operations + edam + + + + + + + + Protein property calculation + + + + + + + + + + + + + + + + + + + + + Protein property rendering + operation + beta12orEarlier + This includes methods to render and visualise the properties of a protein sequence. + operations + bioinformatics + edam + Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. + + + + + + + + Peptide immunogenicity prediction + + + + + + + + + + + + + + + edam + bioinformatics + operations + operation + Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. + This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. + beta12orEarlier + + + + + + + + Feature prediction + + + + + + + + + + + + + + + SO:0000110 + bioinformatics + beta12orEarlier + Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. + operation + edam + operations + Sequence feature detection + + + + + + + + Data retrieval (feature table) + + true + operations + operation + beta12orEarlier + bioinformatics + edam + Extract a sequence feature table from a sequence database entry. + beta13 + + + + + + + + + Feature table query + + + + + + + + + + + + + + + + + + + + beta12orEarlier + edam + operations + Query the features (in a feature table) of molecular sequence(s). + bioinformatics + operation + + + + + + + + Feature comparison + + + + + + + + + + + + + + + edam + Feature table comparison + operations + operation + Compare the feature tables of two or more molecular sequences. + Sequence feature comparison + beta12orEarlier + bioinformatics + + + + + + + + Data retrieval (sequence alignment) + + true + Display basic information about a sequence alignment. + beta13 + operations + beta12orEarlier + edam + operation + bioinformatics + + + + + + + + + Sequence alignment analysis + + + + + + + + + + + + + + + + beta12orEarlier + operation + bioinformatics + Analyse a molecular sequence alignment. + operations + edam + + + + + + + + Sequence alignment comparison + + + bioinformatics + edam + operation + See also 'Sequence profile alignment'. + beta12orEarlier + Compare (typically by aligning) two molecular sequence alignments. + operations + + + + + + + + Sequence alignment conversion + + operation + Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). + edam + beta12orEarlier + operations + bioinformatics + + + + + + + + Nucleic acid property processing + + true + edam + bioinformatics + beta13 + Process (read and / or write) physicochemical property data of nucleic acids. + beta12orEarlier + operations + operation + + + + + + + + + Nucleic acid property calculation + + + + + + + + edam + Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence. + operation + beta12orEarlier + operations + bioinformatics + + + + + + + + Splice transcript prediction + + + + + + + + operations + Predict splicing alternatives or transcript isoforms from analysis of sequence data. + operation + beta12orEarlier + bioinformatics + edam + + + + + + + + Frameshift error detection + + + + + + + + + operation + Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. + edam + operations + bioinformatics + Detect frameshift errors in DNA sequences (from sequencing projects). + beta12orEarlier + + + + + + + + Vector sequence detection + + + operation + edam + Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences. + operations + bioinformatics + beta12orEarlier + + + + + + + + Protein secondary structure prediction + + + + + + + + + + + + + + + + beta12orEarlier + edam + Predict secondary structure of protein sequences. + operations + Secondary structure prediction (protein) + operation + bioinformatics + Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. + + + + + + + + Protein super-secondary structure prediction + + + + + + + + bioinformatics + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. + Predict super-secondary structure of protein sequence(s). + operations + edam + operation + beta12orEarlier + + + + + + + + Transmembrane protein prediction + + + + + + + + + edam + beta12orEarlier + bioinformatics + operation + Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. + operations + + + + + + + + Transmembrane protein analysis + + + + + + + + + + + + + + bioinformatics + operation + operations + Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). + Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions. + beta12orEarlier + edam + + + + + + + + Structure prediction + + + + + + + + + + + + + + + edam + beta12orEarlier + bioinformatics + operation + Predict tertiary structure of a molecular (biopolymer) sequence. + operations + + + + + + + + Residue interaction prediction + + + + + + + + + Methods usually involve multiple sequence alignment analysis. + beta12orEarlier + Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences. + operation + operations + edam + bioinformatics + + + + + + + + Protein interaction raw data analysis + + + + + + + + + + + + + + beta12orEarlier + bioinformatics + operation + edam + operations + Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. + + + + + + + + Protein-protein interaction prediction (from protein sequence) + + + Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. + operations + operation + bioinformatics + edam + beta12orEarlier + + + + + + + + Protein-protein interaction prediction (from protein structure) + + + bioinformatics + Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. + beta12orEarlier + operations + edam + operation + + + + + + + + Protein interaction network analysis + + + + + + + + + + + + + + + + edam + operation + beta12orEarlier + Analyse a network of protein interactions. + operations + bioinformatics + + + + + + + + Protein interaction network comparison + + + + + + + + + operation + Compare two or more networks of protein interactions. + edam + operations + beta12orEarlier + bioinformatics + + + + + + + + RNA secondary structure prediction + + + + + + + + + + + + + + + beta12orEarlier + Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc). + bioinformatics + operations + Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). + operation + edam + + + + + + + + Nucleic acid folding analysis + + + + + + + + + + + + + + + operation + Nucleic acid folding + bioinformatics + operations + Nucleic acid folding modelling + Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. + edam + beta12orEarlier + + + + + + + + Data retrieval (restriction enzyme annotation) + + true + Retrieve information on restriction enzymes or restriction enzyme sites. + bioinformatics + edam + beta12orEarlier + operations + Restriction enzyme information retrieval + beta13 + operation + + + + + + + + + Genetic marker identification + + true + edam + operations + beta13 + bioinformatics + A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. + Identify genetic markers in DNA sequences. + operation + beta12orEarlier + + + + + + + + + Genetic mapping + + + + + + + + + + + + + + operation + Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. + bioinformatics + Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. + Genetic map generation + edam + Linkage mapping + beta12orEarlier + operations + + + + + + + + Linkage analysis + + + + + + + + + + + + + + edam + For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. + beta12orEarlier + bioinformatics + Analyse genetic linkage. + operation + operations + + + + + + + + Codon usage table generation + + + + + + + + operations + edam + operation + beta12orEarlier + bioinformatics + Calculate codon usage statistics and create a codon usage table. + + + + + + + + Codon usage table comparison + + + Compare two or more codon usage tables. + bioinformatics + edam + operation + beta12orEarlier + operations + + + + + + + + Codon usage analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + edam + synon: Codon usage table analysis + operation + Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences. + bioinformatics + operations + synon: Codon usage data analysis + beta12orEarlier + + + + + + + + Base position variability plotting + + + + + + + + + + + + + + bioinformatics + beta12orEarlier + Identify and plot third base position variability in a nucleotide sequence. + operation + operations + edam + + + + + + + + Sequence word comparison + + + + + + + + beta12orEarlier + bioinformatics + edam + operations + Find exact character or word matches between molecular sequences without full sequence alignment. + operation + + + + + + + + Sequence distance matrix generation + + + + + + + + + + + + + + bioinformatics + Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. + operations + edam + beta12orEarlier + operation + Phylogenetic distance matrix generation + + + + + + + + Sequence redundancy removal + + + + + + + + + + + + + + operation + Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. + edam + operations + bioinformatics + beta12orEarlier + + + + + + + + Sequence clustering + + + + + + + + + + Sequence cluster generation + Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences. + beta12orEarlier + bioinformatics + operations + edam + operation + The clusters may be output or used internally for some other purpose. + + + + + + + + Sequence alignment construction + + + + + + + + + + + + + + + + + Sequence alignment computation + operation + operations + Sequence alignment + bioinformatics + Sequence alignment generation + edam + Align (identify equivalent sites within) molecular sequences. + beta12orEarlier + + + + + + + + Hybrid sequence alignment construction + + true + Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). + edam + operation + Hybrid sequence alignment + operations + beta13 + beta12orEarlier + bioinformatics + + + + + + + + + Structure-based sequence alignment construction + + + + + + + + Align molecular sequences using sequence and structural information. + bioinformatics + beta12orEarlier + operation + operations + edam + Structure-based sequence alignment + + + + + + + + Structure alignment construction + + + + + + + + + + + operations + bioinformatics + Structure alignment + edam + beta12orEarlier + Align (superimpose) molecular tertiary structures. + operation + + + + + + + + Sequence profile generation + + + + + + + + + + + + + + + operation + beta12orEarlier + Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. + operations + bioinformatics + edam + + + + + + + + Structural (3D) profile generation + + + + + + + + + + + + + + + + + + + + + + operation + edam + beta12orEarlier + Generate some type of structural (3D) profile or template from a structure or structure alignment. + operations + Structural profile generation + bioinformatics + + + + + + + + Sequence profile alignment construction + + + + + + + + + + + + + + + Align sequence profiles (representing sequence alignments). + beta12orEarlier + See also 'Sequence alignment comparison'. + bioinformatics + operation + Sequence profile alignment + edam + operations + + + + + + + + Structural (3D) profile alignment construction + + + + + + + + + + + + + + + + + + + + + bioinformatics + Structural (3D) profile alignment + Align structural (3D) profiles or templates (representing structures or structure alignments). + Structural profile alignment + operation + edam + beta12orEarlier + operations + + + + + + + + Sequence-profile alignment construction + + + + + + + + + + + + + + + + operation + A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. + operations + Sequence-profile alignment + Align molecular sequence(s) to sequence profile(s). + beta12orEarlier + bioinformatics + edam + + + + + + + + Sequence-3D profile alignment construction + + + + + + + + + + + + + + + + + + + + + + Sequence-3D profile alignment + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). + operations + edam + bioinformatics + beta12orEarlier + operation + + + + + + + + Protein threading + + + + + + + + + + + + + + + + + + + + + + + + + + + Sequence-structure alignment + Align molecular sequence to structure in 3D space (threading). + beta12orEarlier + edam + Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. + operation + operations + bioinformatics + + + + + + + + Protein fold recognition + + + + + + + + + + + + + + + + bioinformatics + edam + Protein fold prediction + operation + Recognize (predict and identify) known protein structural domains or folds in protein sequence(s). + Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. + Protein domain prediction + operations + beta12orEarlier + + + + + + + + Data retrieval (metadata and documentation) + + + + + + + + operation + operations + This includes documentation, general information and other metadata on entities such as databases, database entries and tools. + beta12orEarlier + Data retrieval (metadata) + Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described. + bioinformatics + Data retrieval (documentation) + edam + + + + + + + + Literature search + + + + + + + + + + + + + + bioinformatics + edam + operation + operations + Query the biomedical and informatics literature. + beta12orEarlier + + + + + + + + Text mining + + + + + + + + + + + + + + + + + + + + Process and analyse text (typically the biomedical and informatics literature) to extract information from it. + edam + Text data mining + operations + beta12orEarlier + operation + bioinformatics + + + + + + + + Virtual PCR + + + + + + + + Perform in-silico (virtual) PCR. + operation + operations + edam + bioinformatics + beta12orEarlier + + + + + + + + PCR primer design + + + + + + + + + + + + + + + + + + + + operations + bioinformatics + Design or predict oligonucleotide primers for PCR and DNA amplification etc. + edam + Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. + PCR primer prediction + beta12orEarlier + operation + + + + + + + + Microarray probe design + + + + + + + + + + + + + + + + + + + + + + + + + + + operation + Microarray probe prediction + edam + bioinformatics + beta12orEarlier + operations + Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. + + + + + + + + Sequence assembly + + + + + + + + + + + + + + + + Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence. + bioinformatics + edam + operation + operations + For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. + beta12orEarlier + + + + + + + + Microarray data standardization and normalization + + + + + + + + + + + + + + + edam + This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. + operations + Standardize or normalize microarray data. + operation + bioinformatics + beta12orEarlier + + + + + + + + Sequencing-based expression profile data processing + + true + operations + beta12orEarlier + beta12orEarlier + bioinformatics + operation + edam + Process (read and / or write) SAGE, MPSS or SBS experimental data. + + + + + + + + + Gene expression profile clustering + + + + + + + + edam + Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles. + beta12orEarlier + operation + operations + bioinformatics + + + + + + + + Gene expression profile generation + + + + + + + + Gene expression profiling + beta12orEarlier + Generate a gene expression profile or pattern, for example from microarray data. + edam + operations + Expression profiling + bioinformatics + operation + + + + + + + + Gene expression profile comparison + + + + + + + + + Compare gene expression profiles or patterns. + operation + beta12orEarlier + edam + operations + bioinformatics + + + + + + + + Functional profiling + + true + operation + beta12orEarlier + bioinformatics + operations + Interpret (in functional terms) and annotate gene expression data. + beta12orEarlier + edam + + + + + + + + + EST and cDNA sequence analysis + + true + bioinformatics + operation + For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. + beta12orEarlier + beta12orEarlier + edam + operations + Analyse EST or cDNA sequences. + + + + + + + + + Structural genomics target selection + + true + operations + bioinformatics + beta12orEarlier + operation + Methods will typically navigate a graph of protein families of known structure. + Identify and select targets for protein structural determination. + edam + beta12orEarlier + + + + + + + + + Protein secondary structure assignment + + + + + + + + + + + + + + + bioinformatics + edam + Assign secondary structure from protein coordinate or experimental data. + operation + beta12orEarlier + operations + + + + + + + + Protein structure assignment + + + + + + + + + + + + + + edam + operation + operations + Assign a protein tertiary structure (3D coordinates) from raw experimental data. + beta12orEarlier + bioinformatics + + + + + + + + Protein model evaluation + + + + + + + + + + + + + + + + + + + + + + + + + + + beta12orEarlier + operations + WHATIF: UseFileDB + operation + Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. + edam + bioinformatics + Evaluate the quality or correctness a protein three-dimensional model. + + + + + + + + Protein model refinement + + + WHATIF: CorrectedPDBasXML + operation + bioinformatics + edam + The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. + operations + beta12orEarlier + Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc. + + + + + + + + Phylogenetic tree construction + + + + + + + + + + + + + + + + Phylogenetic tree generation + edam + beta12orEarlier + Construct a phylogenetic tree. + Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. + bioinformatics + operations + Phylogenetic tree construction + operation + + + + + + + + Phylogenetic tree analysis + + + + + + + + + + + + + + bioinformatics + edam + operation + operations + Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. + beta12orEarlier + + + + + + + + Phylogenetic tree comparison + + + operations + operation + For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. + Compare two or more phylogenetic trees. + beta12orEarlier + bioinformatics + edam + + + + + + + + Phylogenetic tree editing + + + + + + + + + + + + + + + edam + operation + Edit a phylogenetic tree. + beta12orEarlier + bioinformatics + operations + + + + + + + + Phylogenetic footprinting / shadowing + + + + + + + + operation + Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing). + beta12orEarlier + bioinformatics + operations + edam + A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. + + + + + + + + Protein folding simulation + + edam + Simulate the folding of a protein. + beta12orEarlier + bioinformatics + operations + operation + + + + + + + + Protein folding pathway prediction + + + edam + operations + beta12orEarlier + bioinformatics + operation + Predict the folding pathway(s) or non-native structural intermediates of a protein. + + + + + + + + Protein SNP mapping + + + + + + + + + + + + + + bioinformatics + edam + Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). + operations + operation + beta12orEarlier + + + + + + + + Protein modelling (mutation) + + + + + + + + + + + + + + + operations + beta12orEarlier + operation + Methods might predict silent or pathological mutations. + edam + Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function. + Protein mutation modelling + bioinformatics + + + + + + + + Immunogen design + + true + edam + operation + beta12orEarlier + beta12orEarlier + Design molecules that elicit an immune response (immunogens). + operations + bioinformatics + + + + + + + + + Zinc finger protein domain prediction and optimisation + + + + + + + + + + + + + + + edam + operations + beta12orEarlier + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). + bioinformatics + operation + + + + + + + + Enzyme kinetics calculation + + + + + + + + + + + + + + operation + Calculate Km, Vmax and derived data for an enzyme reaction. + edam + beta12orEarlier + operations + bioinformatics + + + + + + + + File reformatting + + edam + operation + operations + Reformat a file of data (or equivalent entity in memory). + beta12orEarlier + bioinformatics + + + + + + + + File validation + + + bioinformatics + operation + operations + beta12orEarlier + edam + Test and validate the format and content of a data file. + + + + + + + + Plotting and rendering + + + + + + + + + + + + + + + + + + + + operation + edam + Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. + Visualisation + bioinformatics + operations + beta12orEarlier + + + + + + + + Sequence database search + + + + + + + + + + + + + + + operations + beta12orEarlier + operation + bioinformatics + This excludes direct retrieval methods (e.g. the dbfetch program). + edam + Search a sequence database by sequence comparison and retrieve similar sequences. + + + + + + + + Structure database search + + + + + + + + + + + + + + + operation + bioinformatics + beta12orEarlier + operations + Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data. + edam + + + + + + + + Protein secondary database search + + + + + + + + + + + + + + + edam + operations + Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. + beta12orEarlier + Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). + operation + bioinformatics + Protein sequence classification + + + + + + + + Motif database search + + + + + + + + + + + + + + + + operations + bioinformatics + Screen a sequence against a motif or pattern database. + beta12orEarlier + edam + operation + + + + + + + + Sequence profile database search + + + + + + + + + + operations + Search a database of sequence profiles with a query sequence. + operation + bioinformatics + edam + beta12orEarlier + + + + + + + + Transmembrane protein database search + + true + edam + operation + bioinformatics + beta12orEarlier + operations + Search a database of transmembrane proteins, for example for sequence or structural similarities. + beta12orEarlier + + + + + + + + + Sequence retrieval (by code) + + edam + beta12orEarlier + operations + operation + bioinformatics + Query a database and retrieve sequences with a given entry code or accession number. + + + + + + + + Sequence retrieval (by keyword) + + edam + beta12orEarlier + bioinformatics + operations + operation + Query a database and retrieve sequences containing a given keyword. + + + + + + + + Sequence database search (by sequence) + + + + beta12orEarlier + Search a sequence database and retrieve sequences that are similar to a query sequence. + operations + bioinformatics + Sequence similarity search + edam + operation + + + + + + + + Sequence database search (by motif or pattern) + + + + + + + + + + + + + + + operation + operations + bioinformatics + edam + beta12orEarlier + Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. + + + + + + + + Sequence database search (by amino acid composition) + + + + + + + + + + + + + + beta12orEarlier + operation + operations + Search a sequence database and retrieve sequences of a given amino acid composition. + edam + bioinformatics + + + + + + + + Sequence database search (by physicochemical property) + + operation + beta12orEarlier + Search a sequence database and retrieve sequences with a specified physicochemical property. + operations + edam + bioinformatics + + + + + + + + Sequence database search (by sequence using word-based methods) + + + operation + bioinformatics + Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. + operations + Sequence similarity search (word-based methods) + Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. + edam + beta12orEarlier + + + + + + + + Sequence database search (by sequence using profile-based methods) + + + operations + This includes tools based on PSI-BLAST. + beta12orEarlier + bioinformatics + Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. + Sequence similarity search (profile-based methods) + edam + operation + + + + + + + + Sequence database search (by sequence using local alignment-based methods) + + + + + + + + + This includes tools based on the Smith-Waterman algorithm or FASTA. + Sequence similarity search (local alignment-based methods) + operation + beta12orEarlier + bioinformatics + operations + Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. + edam + + + + + + + + Sequence database search (by sequence using global alignment-based methods) + + + + + + + + + edam + bioinformatics + Sequence similarity search (global alignment-based methods) + beta12orEarlier + operations + Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. + This includes tools based on the Needleman and Wunsch algorithm. + operation + + + + + + + + Sequence database search (by sequence for primer sequences) + + + + + + + + edam + Sequence similarity search (primer sequences) + operation + operations + STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. + bioinformatics + Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. + beta12orEarlier + + + + + + + + Sequence database search (by molecular weight) + + + + + + + + + + + + + + + + + + + + beta12orEarlier + edam + Peptide mass fingerprinting + bioinformatics + operations + Protein fingerprinting + operation + Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry. + + + + + + + + Sequence database search (by isoelectric point) + + + + + + + + bioinformatics + edam + operation + Search sequence(s) or a sequence database for sequences of a given isoelectric point. + operations + beta12orEarlier + + + + + + + + Structure retrieval (by code) + + beta12orEarlier + operation + bioinformatics + Query a tertiary structure database and retrieve entries with a given entry code or accession number. + operations + edam + + + + + + + + Structure retrieval (by keyword) + + beta12orEarlier + operation + operations + Query a tertiary structure database and retrieve entries containing a given keyword. + edam + bioinformatics + + + + + + + + Structure database search (by sequence) + + + + operation + Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. + operations + bioinformatics + Structure retrieval by sequence + edam + beta12orEarlier + + + + + + + + Structure database search (by structure) + + + + + + + + operation + Structural similarity search + operations + Structure retrieval by structure + bioinformatics + edam + Search a tertiary structure database and retrieve structures that are similar to a query structure. + beta12orEarlier + + + + + + + + Sequence annotation + + + + + + + + + + + + + + Annotate a molecular sequence record with terms from a controlled vocabulary. + edam + beta12orEarlier + operations + bioinformatics + operation + + + + + + + + Genome annotation + + Annotate a genome sequence with terms from a controlled vocabulary. + operations + bioinformatics + beta12orEarlier + edam + operation + + + + + + + + Nucleic acid sequence reverse and complement + + Generate the reverse and / or complement of a nucleotide sequence. + operation + beta12orEarlier + operations + edam + bioinformatics + + + + + + + + Random sequence generation + + beta12orEarlier + operations + operation + bioinformatics + Generate a random sequence, for example, with a specific character composition. + edam + + + + + + + + Nucleic acid restriction digest + + + + + + + + + + + + + + + operations + edam + Generate digest fragments for a nucleotide sequence containing restriction sites. + bioinformatics + operation + beta12orEarlier + + + + + + + + Protein sequence cleavage + + + + + + + + + + + + + + + edam + Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. + bioinformatics + beta12orEarlier + operations + operation + + + + + + + + Sequence mutation and randomization + + operations + edam + operation + bioinformatics + Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. + beta12orEarlier + + + + + + + + Sequence masking + + + + + + + + bioinformatics + operations + beta12orEarlier + edam + operation + For example, SNPs or repeats in a DNA sequence might be masked. + Mask characters in a molecular sequence (replacing those characters with a mask character). + + + + + + + + Sequence cutting + + operation + beta12orEarlier + operations + edam + bioinformatics + Cut (remove) characters or a region from a molecular sequence. + + + + + + + + Restriction site creation + + + + + + + + beta12orEarlier + operation + bioinformatics + edam + Create (or remove) restriction sites in sequences, for example using silent mutations. + operations + + + + + + + + DNA translation + + + + + + + + operation + Translate a DNA sequence into protein. + operations + beta12orEarlier + edam + bioinformatics + + + + + + + + DNA transcription + + + + + + + + Transcribe a nucleotide sequence into mRNA sequence(s). + operation + edam + beta12orEarlier + bioinformatics + operations + + + + + + + + Sequence composition calculation (nucleic acid) + + + beta12orEarlier + operations + edam + bioinformatics + Calculate base frequency or word composition of a nucleotide sequence. + operation + + + + + + + + Sequence composition calculation (protein) + + + bioinformatics + beta12orEarlier + Calculate amino acid frequency or word composition of a protein sequence. + edam + operation + operations + + + + + + + + Repeat sequence detection + + + + + + + + + operations + Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. + bioinformatics + operation + edam + beta12orEarlier + + + + + + + + Repeat sequence organisation analysis + + + Analyse repeat sequence organization such as periodicity. + beta12orEarlier + edam + operations + bioinformatics + operation + + + + + + + + Protein hydropathy calculation (from structure) + + + edam + beta12orEarlier + operations + Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. + bioinformatics + operation + + + + + + + + Protein solvent accessibility calculation + + + + + + + + + + + + + + Calculate solvent accessible or buried surface areas in protein structures. + bioinformatics + edam + operation + beta12orEarlier + operations + + + + + + + + Protein hydropathy cluster calculation + + + operation + Identify clusters of hydrophobic or charged residues in a protein structure. + bioinformatics + beta12orEarlier + operations + edam + + + + + + + + Protein dipole moment calculation + + + + + + + + edam + Calculate whether a protein structure has an unusually large net charge (dipole moment). + bioinformatics + operation + beta12orEarlier + operations + + + + + + + + Protein surface and interior calculation + + + + + + + + + + + + + + Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc. + bioinformatics + beta12orEarlier + edam + operations + operation + + + + + + + + Binding site prediction (from structure) + + + edam + operation + Ligand-binding and active site prediction (from structure) + bioinformatics + beta12orEarlier + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. + operations + + + + + + + + Protein-nucleic acid binding site analysis + + + + + + + + + + + + + + beta12orEarlier + edam + operation + operations + bioinformatics + Analyse RNA or DNA-binding sites in protein structure. + + + + + + + + Protein peeling + + + + + + + + edam + operation + bioinformatics + Decompose a structure into compact or globular fragments (protein peeling). + operations + beta12orEarlier + + + + + + + + Protein distance matrix calculation + + + + + + + + operations + edam + Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. + operation + bioinformatics + beta12orEarlier + + + + + + + + Protein contact map calculation + + + + + + + + operations + Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. + operation + bioinformatics + edam + beta12orEarlier + + + + + + + + Protein residue cluster calculation + + + + + + + + beta12orEarlier + edam + Calculate clusters of contacting residues in protein structures. + operations + Cluster of contacting residues might be key structural residues. + operation + bioinformatics + + + + + + + + Hydrogen bond calculation + + + + + + + + Identify potential hydrogen bonds between amino acids and other groups. + operations + edam + WHATIF:ShowHydrogenBonds + operation + WHATIF:ShowHydrogenBondsM + bioinformatics + beta12orEarlier + The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. + WHATIF:HasHydrogenBonds + + + + + + + + Residue non-canonical interaction detection + + + + + + + + + Calculate non-canonical atomic interactions in protein structures. + bioinformatics + operations + beta12orEarlier + edam + operation + + + + + + + + Ramachandran plot calculation + + + + + + + + bioinformatics + operations + operation + beta12orEarlier + Calculate a Ramachandran plot of a protein structure. + edam + + + + + + + + Ramachandran plot evaluation + + + + + + + + + + + + + + operation + Analyse (typically to validate) a Ramachandran plot of a protein structure. + edam + operations + beta12orEarlier + bioinformatics + + + + + + + + Protein molecular weight calculation + + + + + + + + + + + + + + operations + beta12orEarlier + edam + Calculate the molecular weight of a protein sequence or fragments. + operation + bioinformatics + + + + + + + + Protein extinction coefficient calculation + + + + + + + + Predict extinction coefficients or optical density of a protein sequence. + operations + operation + edam + bioinformatics + beta12orEarlier + + + + + + + + Protein pH-dependent property calculation + + + + + + + + + + + + + + beta12orEarlier + Calculate pH-dependent properties from pKa calculations of a protein sequence. + operation + bioinformatics + edam + operations + + + + + + + + Protein hydropathy calculation (from sequence) + + edam + beta12orEarlier + operations + Hydropathy calculation on a protein sequence. + operation + bioinformatics + + + + + + + + Protein titration curve plotting + + + + + + + + bioinformatics + Plot a protein titration curve. + edam + operation + operations + beta12orEarlier + + + + + + + + Protein isoelectric point calculation + + + + + + + + operations + Calculate isoelectric point of a protein sequence. + bioinformatics + beta12orEarlier + operation + edam + + + + + + + + Protein hydrogen exchange rate calculation + + + + + + + + operation + beta12orEarlier + bioinformatics + operations + edam + Estimate hydrogen exchange rate of a protein sequence. + + + + + + + + Protein hydrophobic region calculation + + beta12orEarlier + Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. + edam + bioinformatics + operations + operation + + + + + + + + Protein aliphatic index calculation + + + + + + + + edam + bioinformatics + operations + Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. + beta12orEarlier + operation + + + + + + + + Protein hydrophobic moment plotting + + + + + + + + operations + edam + Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. + operation + bioinformatics + Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. + beta12orEarlier + + + + + + + + Protein globularity prediction + + + + + + + + edam + operation + operations + bioinformatics + beta12orEarlier + Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc. + + + + + + + + Protein solubility prediction + + + + + + + + edam + operation + operations + bioinformatics + beta12orEarlier + Predict the solubility or atomic solvation energy of a protein sequence. + + + + + + + + Protein crystallizability prediction + + + + + + + + operations + Predict crystallizability of a protein sequence. + operation + edam + beta12orEarlier + bioinformatics + + + + + + + + Protein signal peptide detection (eukaryotes) + + Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins. + operation + operations + bioinformatics + edam + beta12orEarlier + + + + + + + + Protein signal peptide detection (bacteria) + + beta12orEarlier + Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins. + operations + bioinformatics + operation + edam + + + + + + + + MHC peptide immunogenicity prediction + + beta12orEarlier + bioinformatics + operation + operations + edam + Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. + + + + + + + + Protein feature prediction (from sequence) + + + edam + bioinformatics + Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. + operation + Sequence feature detection (protein) + beta12orEarlier + Methods typically involve scanning for known motifs, patterns and regular expressions. + operations + + + + + + + + Nucleic acid feature prediction + + + + + + + + + + + + + + + + + operation + edam + operations + beta12orEarlier + bioinformatics + Methods typically involve scanning for known motifs, patterns and regular expressions. + Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions. + Sequence feature detection (nucleic acid) + + + + + + + + Epitope mapping + + + + + + + + + + + + + + + operation + beta12orEarlier + Epitope mapping is commonly done during vaccine design. + operations + Predict antigenic determinant sites (epitopes) in protein sequences. + edam + bioinformatics + + + + + + + + Protein post-translation modification site prediction + + + + + + + + + + + + + + Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. + operations + operation + Predict post-translation modification sites in protein sequences. + beta12orEarlier + edam + bioinformatics + + + + + + + + Protein signal peptide detection + + + + + + + + + + + + + + + operations + beta12orEarlier + bioinformatics + operation + Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. + Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. + edam + + + + + + + + Binding site prediction (from sequence) + + + operations + beta12orEarlier + edam + Ligand-binding and active site prediction (from sequence) + Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. + bioinformatics + operation + + + + + + + + Protein-nucleic acid binding prediction + + + + + + + + operation + bioinformatics + Predict RNA and DNA-binding binding sites in protein sequences. + operations + beta12orEarlier + edam + + + + + + + + Protein folding site prediction + + + + + + + + + beta12orEarlier + Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization. + operations + bioinformatics + operation + edam + + + + + + + + Protein cleavage site prediction + + + + + + + + + + + + + + operation + Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. + beta12orEarlier + operations + bioinformatics + edam + + + + + + + + Epitope mapping (MHC Class I) + + operation + beta12orEarlier + Predict epitopes that bind to MHC class I molecules. + edam + operations + bioinformatics + + + + + + + + Epitope mapping (MHC Class II) + + bioinformatics + operations + beta12orEarlier + operation + edam + Predict epitopes that bind to MHC class II molecules. + + + + + + + + Whole gene prediction + + operation + edam + Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. + operations + bioinformatics + beta12orEarlier + + + + + + + + Gene component prediction + + operations + Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences. + bioinformatics + beta12orEarlier + edam + Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. + operation + + + + + + + + Transposon prediction + + + + + + + + edam + bioinformatics + Detect or predict transposons, retrotransposons / retrotransposition signatures etc. + operations + operation + beta12orEarlier + + + + + + + + PolyA signal detection + + + + + + + + beta12orEarlier + bioinformatics + operation + edam + operations + Detect polyA signals in nucleotide sequences. + + + + + + + + Quadruplex formation site detection + + + + + + + + + + + + + + Quadruplex structure prediction + beta12orEarlier + edam + operation + Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. + operations + Detect quadruplex-forming motifs in nucleotide sequences. + bioinformatics + + + + + + + + CpG island and isochore detection + + + + + + + + + + + + + + CpG island and isochores rendering + operations + beta12orEarlier + operation + CpG island and isochores detection + Find CpG rich regions in a nucleotide sequence or isochores in genome sequences. + An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. + bioinformatics + edam + + + + + + + + Restriction site recognition + + + + + + + + + + + + + + Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. + beta12orEarlier + edam + operations + bioinformatics + operation + + + + + + + + Nucleosome formation or exclusion sequence prediction + + + + + + + + Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. + beta12orEarlier + edam + operation + bioinformatics + operations + + + + + + + + Splice site prediction + + + + + + + + + + + + + + operation + Methods might require a pre-mRNA or genomic DNA sequence. + Identify, predict or analyse splice sites in nucleotide sequences. + edam + bioinformatics + operations + beta12orEarlier + + + + + + + + Integrated gene prediction + + operation + bioinformatics + beta12orEarlier + Predict whole gene structure using a combination of multiple methods to achieve better predictions. + edam + operations + + + + + + + + Operon prediction + + operations + bioinformatics + operation + beta12orEarlier + Find operons (operators, promoters and genes) in bacteria genes. + edam + + + + + + + + Coding region prediction + + + + + + + + beta12orEarlier + bioinformatics + operations + operation + Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. + edam + + + + + + + + Selenocysteine insertion sequence (SECIS) prediction + + + + + + + + edam + beta12orEarlier + SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. + Predict selenocysteine insertion sequence (SECIS) in a DNA sequence. + operation + operations + bioinformatics + + + + + + + + Transcription regulatory element prediction + + + + + + + + + + + + + + This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. + operation + beta12orEarlier + operations + edam + bioinformatics + Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences. + + + + + + + + Translation initiation site prediction + + + + + + + + bioinformatics + edam + operation + operations + Predict translation initiation sites, possibly by searching a database of sites. + beta12orEarlier + + + + + + + + Promoter prediction + + + + + + + + edam + beta12orEarlier + operations + Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. + bioinformatics + Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences. + operation + + + + + + + + Transcription regulatory element prediction (DNA-cis) + + Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences. + edam + Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. + operation + beta12orEarlier + operations + bioinformatics + + + + + + + + Transcription regulatory element prediction (RNA-cis) + + beta12orEarlier + operation + operations + bioinformatics + edam + Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences. + Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. + + + + + + + + Transcription regulatory element prediction (trans) + + + + + + + + operation + Functional RNA identification + bioinformatics + operations + Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets. + Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. + edam + beta12orEarlier + + + + + + + + Matrix/scaffold attachment site prediction + + + + + + + + beta12orEarlier + operation + Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. + operations + bioinformatics + edam + MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. + + + + + + + + Transcription factor binding site prediction + + + + + + + + bioinformatics + Identify or predict transcription factor binding sites in DNA sequences. + operation + operations + beta12orEarlier + edam + + + + + + + + Exonic splicing enhancer prediction + + + + + + + + + + + + + + edam + beta12orEarlier + bioinformatics + operations + operation + Identify or predict exonic splicing enhancers (ESE) in exons. + An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. + + + + + + + + Sequence alignment quality evaluation + + + beta12orEarlier + operations + edam + Evaluate molecular sequence alignment accuracy. + operation + bioinformatics + Evaluation might be purely sequence-based or use structural information. + + + + + + + + Sequence alignment analysis (conservation) + + + + + + + + operations + operation + Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. + edam + bioinformatics + beta12orEarlier + Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. + + + + + + + + Sequence alignment analysis (site correlation) + + + + + + + + bioinformatics + beta12orEarlier + operations + edam + operation + This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. + Analyse correlations between sites in a molecular sequence alignment. + + + + + + + + Sequence alignment analysis (chimeric sequence detection) + + + operation + Detects chimeric sequences (chimeras) from a sequence alignment. + edam + operations + bioinformatics + A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. + beta12orEarlier + + + + + + + + Sequence alignment analysis (recombination detection) + + operations + bioinformatics + Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. + Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. + operation + beta12orEarlier + edam + + + + + + + + Sequence alignment analysis (indel detection) + + Identify insertion, deletion and duplication events from a sequence alignment. + Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. + bioinformatics + operations + beta12orEarlier + operation + edam + + + + + + + + Nucleosome formation potential prediction + + true + operation + operations + beta12orEarlier + Predict nucleosome formation potential of DNA sequences. + edam + beta12orEarlier + bioinformatics + + + + + + + + + Nucleic acid thermodynamic property calculation + + + + + + + + beta12orEarlier + operations + edam + Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy. + operation + bioinformatics + + + + + + + + Nucleic acid melting profile plotting + + + + + + + + operation + operations + bioinformatics + A melting profile is used to visualise and analyse partly melted DNA conformations. + beta12orEarlier + Calculate and plot a DNA or DNA/RNA melting profile. + edam + + + + + + + + Nucleic acid stitch profile plotting + + + + + + + + edam + Calculate and plot a DNA or DNA/RNA stitch profile. + operations + bioinformatics + beta12orEarlier + operation + A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. + + + + + + + + Nucleic acid melting curve plotting + + + + + + + + bioinformatics + edam + Calculate and plot a DNA or DNA/RNA melting curve. + beta12orEarlier + operations + operation + + + + + + + + Nucleic acid probability profile plotting + + + + + + + + Calculate and plot a DNA or DNA/RNA probability profile. + edam + bioinformatics + operation + operations + beta12orEarlier + + + + + + + + Nucleic acid temperature profile plotting + + + + + + + + operations + bioinformatics + edam + beta12orEarlier + operation + Calculate and plot a DNA or DNA/RNA temperature profile. + + + + + + + + Nucleic acid curvature calculation + + + + + + + + + + + + + + bioinformatics + operation + This includes properties such as. + beta12orEarlier + edam + Calculate curvature and flexibility / stiffness of a nucleotide sequence. + operations + + + + + + + + microRNA detection + + + + + + + + beta12orEarlier + Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence. + edam + bioinformatics + operation + operations + + + + + + + + tRNA gene prediction + + + + + + + + edam + beta12orEarlier + operations + operation + Identify or predict tRNA genes in genomic sequences (tRNA). + bioinformatics + + + + + + + + siRNA binding specificity prediction + + + + + + + + edam + operations + operation + beta12orEarlier + Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. + bioinformatics + + + + + + + + Protein secondary structure prediction (integrated) + + beta12orEarlier + bioinformatics + operations + operation + edam + Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. + + + + + + + + Protein secondary structure prediction (helices) + + Predict helical secondary structure of protein sequences. + beta12orEarlier + bioinformatics + operations + operation + edam + + + + + + + + Protein secondary structure prediction (turns) + + beta12orEarlier + operations + edam + Predict turn structure (for example beta hairpin turns) of protein sequences. + bioinformatics + operation + + + + + + + + Protein secondary structure prediction (coils) + + edam + bioinformatics + Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences. + operations + operation + beta12orEarlier + + + + + + + + Protein secondary structure prediction (disulfide bonds) + + Predict cysteine bonding state and disulfide bond partners in protein sequences. + edam + operation + operations + beta12orEarlier + bioinformatics + + + + + + + + GPCR prediction + + + Predict G protein-coupled receptors (GPCR). + edam + G protein-coupled receptor (GPCR) prediction + beta12orEarlier + bioinformatics + operations + operation + + + + + + + + GPCR analysis + + + + + + + + + + + + + + operation + G protein-coupled receptor (GPCR) analysis + bioinformatics + beta12orEarlier + operations + Analyse G-protein coupled receptor proteins (GPCRs). + edam + + + + + + + + Protein structure prediction + + + + + + + + + + + + + + + + + Predict tertiary structure (backbone and side-chain conformation) of protein sequences. + operation + operations + edam + bioinformatics + beta12orEarlier + + + + + + + + Nucleic acid structure prediction + + + + + + + + + + + + + + + + + operations + Methods might identify thermodynamically stable or evolutionarily conserved structures. + operation + bioinformatics + Predict tertiary structure of DNA or RNA. + beta12orEarlier + edam + + + + + + + + Ab initio structure prediction + + + + + + + + bioinformatics + beta12orEarlier + edam + operation + Predict tertiary structure of protein sequence(s) without homologs of known structure. + operations + + + + + + + + Protein modelling + + + + + + + + + + Protein structure comparative modelling + Homology structure modelling + The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. + Homology modelling + bioinformatics + Build a three-dimensional protein model based on known (for example homologs) structures. + beta12orEarlier + operation + Comparative modelling + edam + operations + + + + + + + + Protein docking + + + + + + + + + + + + + + + + + + + + + edam + bioinformatics + This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. + operation + beta12orEarlier + Model the structure of a protein in complex with a small molecule or another macromolecule. + operations + + + + + + + + Protein modelling (backbone) + + operations + edam + beta12orEarlier + Methods might require a preliminary C(alpha) trace. + operation + Model protein backbone conformation. + bioinformatics + + + + + + + + Protein modelling (side chains) + + Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc. + bioinformatics + edam + operation + Methods might use a residue rotamer library. + operations + beta12orEarlier + + + + + + + + Protein modelling (loops) + + Model loop conformation in protein structures. + edam + operations + bioinformatics + operation + beta12orEarlier + + + + + + + + Protein-ligand docking + + + + + + + + + + + + + + edam + bioinformatics + Virtual ligand screening + Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. + operations + beta12orEarlier + Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. + operation + + + + + + + + Structured RNA prediction and optimisation + + + + + + + + + + + + + + + operations + bioinformatics + Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. + edam + beta12orEarlier + RNA inverse folding + operation + Nucleic acid folding family identification + + + + + + + + SNP detection + + + + + + + + + + edam + operations + operation + bioinformatics + This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. + beta12orEarlier + Single nucleotide polymorphism detection + Find single nucleotide polymorphisms (SNPs) between sequences. + + + + + + + + Radiation Hybrid Mapping + + + + + + + + operations + operation + beta12orEarlier + Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers. + bioinformatics + edam + + + + + + + + Functional mapping + + true + beta12orEarlier + operations + This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + beta12orEarlier + operation + edam + Map the genetic architecture of dynamic complex traits. + bioinformatics + + + + + + + + + Haplotype inference + + + + + + + + Haplotype mapping + bioinformatics + Haplotype reconstruction + edam + Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). + beta12orEarlier + Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. + operation + operations + + + + + + + + Linkage disequilibrium calculation + + + + + + + + Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). + operations + operation + Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. + edam + bioinformatics + beta12orEarlier + + + + + + + + Genetic code prediction + + + + + + + + + operations + bioinformatics + Predict genetic code from analysis of codon usage data. + edam + beta12orEarlier + operation + + + + + + + + Dotplot plotting + + + + + + + + + bioinformatics + operations + edam + Draw a dotplot of sequence similarities identified from word-matching or character comparison. + beta12orEarlier + operation + + + + + + + + Pairwise sequence alignment construction + + + + + + + + bioinformatics + beta12orEarlier + edam + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Pairwise sequence alignment + Align exactly two molecular sequences. + operations + operation + + + + + + + + Multiple sequence alignment construction + + beta12orEarlier + Multiple sequence alignment + operations + This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. + Align two or more molecular sequences. + edam + bioinformatics + operation + + + + + + + + Pairwise sequence alignment construction (local) + + Local alignment methods identify regions of local similarity. + bioinformatics + operations + operation + Pairwise sequence alignment (local) + Locally align exactly two molecular sequences. + Local pairwise sequence alignment construction + beta12orEarlier + edam + + + + + + + + Pairwise sequence alignment construction (global) + + operations + Pairwise sequence alignment (global) + bioinformatics + beta12orEarlier + Global alignment methods identify similarity across the entire length of the sequences. + Globally align exactly two molecular sequences. + operation + Global pairwise sequence alignment construction + edam + + + + + + + + Multiple sequence alignment construction (local) + + Locally align two or more molecular sequences. + operation + edam + Local alignment methods identify regions of local similarity. + beta12orEarlier + bioinformatics + Local multiple sequence alignment construction + operations + Multiple sequence alignment (local) + + + + + + + + Multiple sequence alignment construction (global) + + edam + Global alignment methods identify similarity across the entire length of the sequences. + Globally align two or more molecular sequences. + operations + beta12orEarlier + Multiple sequence alignment (global) + Global multiple sequence alignment construction + operation + bioinformatics + + + + + + + + Multiple sequence alignment construction (constrained) + + operation + Constrained multiple sequence alignment construction + Multiple sequence alignment (constrained) + edam + bioinformatics + operations + Align two or more molecular sequences with user-defined constraints. + beta12orEarlier + + + + + + + + Multiple sequence alignment construction (consensus) + + operation + Multiple sequence alignment (consensus) + Align two or more molecular sequences using multiple methods to achieve higher quality. + beta12orEarlier + Consensus multiple sequence alignment construction + bioinformatics + operations + edam + + + + + + + + Multiple sequence alignment construction (phylogenetic tree-based) + + + + + + + + Multiple sequence alignment (phylogenetic tree-based) + operations + bioinformatics + Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. + beta12orEarlier + Phylogenetic tree-based multiple sequence alignment construction + This is supposed to give a more biologically meaningful alignment than standard alignments. + operation + edam + + + + + + + + Secondary structure alignment construction + + + + + + + + + + + + + + + + Align molecular secondary structure (represented as a 1D string). + edam + beta12orEarlier + operations + Secondary structure alignment + operation + bioinformatics + + + + + + + + Protein secondary structure alignment construction + + + + + + + + + Secondary structure alignment (protein) + bioinformatics + Align protein secondary structures. + operation + Protein secondary structure alignment + beta12orEarlier + edam + operations + + + + + + + + RNA secondary structure alignment construction + + + + + + + + + + + + + + + operation + beta12orEarlier + Secondary structure alignment (RNA) + bioinformatics + edam + Align RNA secondary structures. + RNA secondary structure alignment + operations + + + + + + + + Pairwise structure alignment construction + + Align (superimpose) exactly two molecular tertiary structures. + bioinformatics + Pairwise structure alignment + operation + operations + edam + beta12orEarlier + + + + + + + + Multiple structure alignment construction + + Multiple structure alignment + beta12orEarlier + operations + edam + This includes methods that use an existing alignment. + bioinformatics + operation + Align (superimpose) two or more molecular tertiary structures. + + + + + + + + Structure alignment (protein) + + true + operation + Align protein tertiary structures. + edam + operations + beta12orEarlier + bioinformatics + beta13 + + + + + + + + + Structure alignment (RNA) + + true + beta12orEarlier + operation + Align RNA tertiary structures. + edam + bioinformatics + operations + beta13 + + + + + + + + + Pairwise structure alignment construction (local) + + edam + bioinformatics + operations + operation + beta12orEarlier + Local pairwise structure alignment construction + Local alignment methods identify regions of local similarity, common substructures etc. + Pairwise structure alignment (local) + Locally align (superimpose) exactly two molecular tertiary structures. + + + + + + + + Pairwise structure alignment construction (global) + + Pairwise structure alignment (global) + Globally align (superimpose) exactly two molecular tertiary structures. + operations + edam + beta12orEarlier + bioinformatics + operation + Global alignment methods identify similarity across the entire structures. + Global pairwise structure alignment construction + + + + + + + + Multiple structure alignment construction (local) + + Multiple structure alignment (local) + edam + Locally align (superimpose) two or more molecular tertiary structures. + beta12orEarlier + operations + Local alignment methods identify regions of local similarity, common substructures etc. + bioinformatics + Local multiple structure alignment construction + operation + + + + + + + + Multiple structure alignment construction (global) + + Globally align (superimpose) two or more molecular tertiary structures. + Global multiple structure alignment construction + Global alignment methods identify similarity across the entire structures. + operation + edam + beta12orEarlier + bioinformatics + Multiple structure alignment (global) + operations + + + + + + + + Sequence profile alignment construction (pairwise) + + Align exactly two molecular profiles. + beta12orEarlier + operations + Sequence profile alignment (pairwise) + bioinformatics + operation + Pairwise sequence profile alignment construction + edam + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + + + + + + + + Sequence profile alignment construction (multiple) + + Sequence profile alignment (multiple) + bioinformatics + Multiple sequence profile alignment construction + beta12orEarlier + operation + edam + Align two or more molecular profiles. + operations + + + + + + + + Structural (3D) profile alignment construction (pairwise) + + beta12orEarlier + bioinformatics + Structural (3D) profile alignment (pairwise) + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + operations + operation + Align exactly two molecular Structural (3D) profiles. + edam + Pairwise structural (3D) profile alignment construction + + + + + + + + Structural (3D) profile alignment construction (multiple) + + bioinformatics + Structural (3D) profile alignment (multiple) + edam + beta12orEarlier + Multiple structural (3D) profile alignment construction + operations + Align two or more molecular 3D profiles. + operation + + + + + + + + Data retrieval (tool metadata) + + + + + + + + Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. + Data retrieval (tool annotation) + Tool information retrieval + beta12orEarlier + operations + edam + bioinformatics + operation + + + + + + + + Data retrieval (database metadata) + + + + + + + + edam + operations + beta12orEarlier + Database information retrieval + Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. + Data retrieval (database annotation) + operation + bioinformatics + + + + + + + + PCR primer design (for large scale sequencing) + + + + + + + + bioinformatics + operation + operations + beta12orEarlier + edam + Predict primers for large scale sequencing. + + + + + + + + PCR primer design (for genotyping polymorphisms) + + operations + edam + operation + Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). + beta12orEarlier + bioinformatics + + + + + + + + PCR primer design (for gene transcription profiling) + + + + + + + + operation + edam + bioinformatics + beta12orEarlier + operations + Predict primers for gene transcription profiling. + + + + + + + + PCR primer design (for conserved primers) + + bioinformatics + operations + Predict primers that are conserved across multiple genomes or species. + beta12orEarlier + operation + edam + + + + + + + + PCR primer design (based on gene structure) + + + + + + + + operation + beta12orEarlier + bioinformatics + operations + Predict primers based on gene structure, promoters, exon-exon junctions etc. + edam + + + + + + + + PCR primer design (for methylation PCRs) + + operations + Predict primers for methylation PCRs. + bioinformatics + edam + beta12orEarlier + operation + + + + + + + + Sequence assembly (mapping assembly) + + edam + The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. + bioinformatics + beta12orEarlier + Sequence assembly by combining fragments using an existing backbone sequence. + operation + operations + + + + + + + + Sequence assembly (de-novo assembly) + + beta12orEarlier + De-novo assemblers are much slower and more memory intensive than mapping assemblers. + operations + bioinformatics + Sequence assembly by combining fragments into a new, previously unknown sequence. + edam + operation + + + + + + + + Sequence assembly (genome assembly) + + edam + bioinformatics + operation + beta12orEarlier + Sequence assembly capable on a very large scale such as assembly of whole genomes. + operations + + + + + + + + Sequence assembly (EST assembly) + + Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. + operations + Sequence assembly for EST sequences (transcribed mRNA). + bioinformatics + beta12orEarlier + edam + operation + + + + + + + + Tag mapping + + + + + + + + bioinformatics + beta12orEarlier + Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. + edam + Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts. + operation + operations + Tag to gene assignment + + + + + + + + SAGE data processing + + true + operation + bioinformatics + edam + Serial analysis of gene expression data processing + Process (read and / or write) serial analysis of gene expression (SAGE) data. + operations + beta12orEarlier + beta12orEarlier + + + + + + + + + MPSS data processing + + true + operations + beta12orEarlier + edam + bioinformatics + Massively parallel signature sequencing data processing + beta12orEarlier + operation + Process (read and / or write) massively parallel signature sequencing (MPSS) data. + + + + + + + + + SBS data processing + + true + bioinformatics + operations + edam + operation + Process (read and / or write) sequencing by synthesis (SBS) data. + beta12orEarlier + beta12orEarlier + Sequencing by synthesis data processing + + + + + + + + + Heat map generation + + + + + + + + Generate a heat map of gene expression from microarray data. + The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. + beta12orEarlier + operations + bioinformatics + operation + edam + + + + + + + + Gene expression profile analysis + + + + + + + + edam + operation + Analyse one or more gene expression profiles, typically to interpret them in functional terms. + bioinformatics + beta12orEarlier + operations + Functional profiling + + + + + + + + Gene expression profile pathway mapping + + + + + + + + + operations + Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway. + beta12orEarlier + edam + operation + bioinformatics + + + + + + + + Protein secondary structure assignment (from coordinate data) + + + bioinformatics + Assign secondary structure from protein coordinate data. + beta12orEarlier + operation + operations + edam + + + + + + + + Protein secondary structure assignment (from CD data) + + + + + + + + operation + operations + edam + bioinformatics + beta12orEarlier + Assign secondary structure from circular dichroism (CD) spectroscopic data. + + + + + + + + Protein structure assignment (from X-ray crystallographic data) + + + + + + + + operations + beta12orEarlier + bioinformatics + operation + edam + Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. + + + + + + + + Protein structure assignment (from NMR data) + + + + + + + + operation + operations + edam + Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. + bioinformatics + beta12orEarlier + + + + + + + + Phylogenetic tree construction (data centric) + + Construct a phylogenetic tree from a specific type of data. + operations + beta12orEarlier + operation + bioinformatics + edam + + + + + + + + Phylogenetic tree construction (method centric) + + operation + operations + beta12orEarlier + Construct a phylogenetic tree using a specific method. + edam + bioinformatics + + + + + + + + Phylogenetic tree construction (from molecular sequences) + + + Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. + operations + bioinformatics + operation + beta12orEarlier + Phylogenetic tree construction from molecular sequences. + edam + + + + + + + + Phylogenetic tree construction (from continuous quantitative characters) + + + + + + + + operation + Phylogenetic tree construction from continuous quantitative character data. + bioinformatics + beta12orEarlier + operations + edam + + + + + + + + Phylogenetic tree construction (from gene frequencies) + + + + + + + + + + + + + + beta12orEarlier + Phylogenetic tree construction from gene frequency data. + bioinformatics + operation + edam + operations + + + + + + + + Phylogenetic tree construction (from polymorphism data) + + + + + + + + bioinformatics + operation + beta12orEarlier + operations + Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data. + edam + + + + + + + + Phylogenetic species tree construction + + beta12orEarlier + Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison. + bioinformatics + edam + operations + operation + + + + + + + + Phylogenetic tree construction (parsimony methods) + + beta12orEarlier + operation + This includes evolutionary parsimony (invariants) methods. + Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment. + operations + bioinformatics + edam + + + + + + + + Phylogenetic tree construction (minimum distance methods) + + Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances. + edam + beta12orEarlier + bioinformatics + operations + This includes neighbor joining (NJ) clustering method. + operation + + + + + + + + Phylogenetic tree construction (maximum likelihood and Bayesian methods) + + edam + beta12orEarlier + operations + operation + bioinformatics + Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. + Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. + + + + + + + + Phylogenetic tree construction (quartet methods) + + Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. + operation + edam + operations + beta12orEarlier + bioinformatics + + + + + + + + Phylogenetic tree construction (AI methods) + + beta12orEarlier + operation + edam + operations + Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms. + bioinformatics + + + + + + + + Sequence alignment analysis (phylogenetic modelling) + + + + + + + + + + + + + + + bioinformatics + beta12orEarlier + operations + edam + Identify a plausible model of DNA substitution that explains a DNA sequence alignment. + operation + + + + + + + + Phylogenetic tree analysis (shape) + + + + + + + + beta12orEarlier + Analyse the shape (topology) of a phylogenetic tree. + bioinformatics + edam + operation + Phylogenetic tree topology analysis + operations + + + + + + + + Phylogenetic tree bootstrapping + + + + + + + + + operations + bioinformatics + operation + beta12orEarlier + Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. + edam + + + + + + + + Phylogenetic tree analysis (gene family prediction) + + + + + + + + + + + + + + beta12orEarlier + edam + bioinformatics + operation + operations + Predict families of genes and gene function based on their position in a phylogenetic tree. + + + + + + + + Phylogenetic tree analysis (natural selection) + + bioinformatics + Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive). + Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. + edam + operations + operation + beta12orEarlier + + + + + + + + Phylogenetic tree construction (consensus) + + + edam + operations + bioinformatics + beta12orEarlier + Methods typically test for topological similarity between trees using for example a congruence index. + operation + Compare two or more phylogenetic trees to produce a consensus tree. + + + + + + + + Phylogenetic sub/super tree detection + + Compare two or more phylogenetic trees to detect subtrees or supertrees. + beta12orEarlier + bioinformatics + edam + operation + operations + + + + + + + + Phylogenetic tree distances calculation + + + + + + + + operations + bioinformatics + edam + operation + Compare two or more phylogenetic trees to calculate distances between trees. + beta12orEarlier + + + + + + + + Phylogenetic tree annotation + + + operation + Annotate a phylogenetic tree with terms from a controlled vocabulary. + operations + bioinformatics + edam + beta12orEarlier + + + + + + + + + Peptide immunogen prediction and optimisation + + + + + + + + + + + + + + + + + + + + + Predict and optimise peptide ligands that elicit an immunological response. + beta12orEarlier + operations + edam + bioinformatics + operation + + + + + + + + DNA vaccine prediction and optimisation + + + + + + + + + + + + + + + edam + operation + bioinformatics + beta12orEarlier + operations + Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. + + + + + + + + Sequence reformatting + + + operations + bioinformatics + operation + edam + Reformat (a file or other report of) molecular sequence(s). + beta12orEarlier + + + + + + + + Sequence alignment reformatting + + + operation + beta12orEarlier + Reformat (a file or other report of) molecular sequence alignment(s). + operations + bioinformatics + edam + + + + + + + + Codon usage table reformatting + + + + + + + + + + + + + + + edam + beta12orEarlier + operations + bioinformatics + Reformat a codon usage table. + operation + + + + + + + + Sequence rendering + + + + + + + + + + + + + + + edam + operations + beta12orEarlier + bioinformatics + operation + Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. + + + + + + + + Sequence alignment rendering + + + + + + + + + + + + + + + Visualise, format or print a molecular sequence alignment. + bioinformatics + operations + operation + beta12orEarlier + edam + + + + + + + + Sequence cluster rendering + + + + + + + + + Visualise, format or render sequence clusters. + operation + bioinformatics + edam + operations + beta12orEarlier + + + + + + + + Phylogenetic tree rendering + + + + + + + + + operation + operations + bioinformatics + edam + beta12orEarlier + Visualise or plot a phylogenetic tree. + + + + + + + + RNA secondary structure rendering + + + + + + + + + beta12orEarlier + Visualise RNA secondary structure, knots, pseudoknots etc. + operation + edam + bioinformatics + operations + + + + + + + + Protein secondary structure rendering + + + + + + + + + bioinformatics + operations + edam + beta12orEarlier + Render and visualise protein secondary structure. + operation + + + + + + + + Structure rendering + + + + + + + + + + + + + + + Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. + beta12orEarlier + bioinformatics + operation + edam + operations + + + + + + + + Microarray data rendering + + + + + + + + + + + + + + + operations + beta12orEarlier + bioinformatics + edam + Visualise microarray data. + operation + + + + + + + + Protein interaction network rendering + + + + + + + + + edam + bioinformatics + Identify and analyse networks of protein interactions. + operation + beta12orEarlier + operations + + + + + + + + Map rendering + + + + + + + + + edam + operation + operations + Render and visualise a DNA map. + DNA map rendering + bioinformatics + beta12orEarlier + + + + + + + + Sequence motif rendering + + true + beta12orEarlier + edam + beta12orEarlier + bioinformatics + Render a sequence with motifs. + operations + operation + + + + + + + + + Restriction map rendering + + + + + + + + + beta12orEarlier + operation + bioinformatics + operations + edam + Visualise restriction maps in DNA sequences. + + + + + + + + DNA linear map rendering + + true + operation + bioinformatics + edam + Draw a linear maps of DNA. + operations + beta12orEarlier + beta12orEarlier + + + + + + + + + DNA circular map rendering + + Draw a circular maps of DNA, for example a plasmid map. + bioinformatics + edam + operations + beta12orEarlier + operation + + + + + + + + Operon rendering + + + + + + + + beta12orEarlier + bioinformatics + edam + operation + operations + Visualise operon structure etc. + + + + + + + + Nucleic acid folding family identification + + true + operation + bioinformatics + beta12orEarlier + Identify folding families of related RNAs. + edam + beta12orEarlier + operations + + + + + + + + + Nucleic acid folding energy calculation + + edam + operations + Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. + bioinformatics + beta12orEarlier + operation + + + + + + + + Annotation retrieval + + true + beta12orEarlier + edam + operations + Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. + operation + Retrieve existing annotation (or documentation), typically annotation on a database entity. + beta12orEarlier + bioinformatics + + + + + + + + + Protein function prediction + + + + + + + + + operation + For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. + beta12orEarlier + edam + operations + Predict general functional properties of a protein. + bioinformatics + + + + + + + + Protein function comparison + + + + + + + + + bioinformatics + beta12orEarlier + edam + operation + Compare the functional properties of two or more proteins. + operations + + + + + + + + Sequence submission + + + + + + + + + + + + + + operation + beta12orEarlier + edam + bioinformatics + Submit a molecular sequence to a database. + operations + + + + + + + + Gene regulatory network analysis + + + + + + + + + Analyse a known network of gene regulation. + operations + bioinformatics + edam + operation + beta12orEarlier + + + + + + + + Data loading + + + + + + + + operation + Data submission + edam + beta12orEarlier + Prepare or load a user-specified data file so that it is available for use. + Database submission + operations + bioinformatics + WHATIF:UploadPDB + + + + + + + + Sequence retrieval + + + + + + + + + beta12orEarlier + operation + operations + This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. + edam + bioinformatics + Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. + Data retrieval (sequences) + + + + + + + + Structure retrieval + + + + + + + + + operation + Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation. + edam + WHATIF:EchoPDB + operations + bioinformatics + This includes direct retrieval methods but not those that perform calculations on the sequence or structure. + WHATIF:DownloadPDB + beta12orEarlier + + + + + + + + Surface rendering + + + edam + A dot has three coordinates (x,y,z) and (typically) a color. + bioinformatics + beta12orEarlier + operation + Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. + WHATIF:GetSurfaceDots + operations + + + + + + + + Protein atom surface calculation (accessible) + + Calculate the solvent accessibility ('accessible surface') for each atom in a structure. + WHATIF:AtomAccessibilitySolvent + operation + WHATIF:AtomAccessibilitySolventPlus + beta12orEarlier + Waters are not considered. + edam + bioinformatics + operations + + + + + + + + Protein atom surface calculation (accessible molecular) + + operation + Waters are not considered. + operations + WHATIF:AtomAccessibilityMolecularPlus + WHATIF:AtomAccessibilityMolecular + edam + Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. + bioinformatics + beta12orEarlier + + + + + + + + Protein residue surface calculation (accessible) + + Calculate the solvent accessibility ('accessible surface') for each residue in a structure. + beta12orEarlier + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + operations + bioinformatics + WHATIF:ResidueAccessibilitySolvent + edam + operation + + + + + + + + Protein residue surface calculation (vacuum accessible) + + beta12orEarlier + edam + operations + WHATIF:ResidueAccessibilityVacuum + operation + bioinformatics + Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + + + + + + + + Protein residue surface calculation (accessible molecular) + + beta12orEarlier + edam + bioinformatics + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + operations + Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. + WHATIF:ResidueAccessibilityMolecular + operation + + + + + + + + Protein residue surface calculation (vacuum molecular) + + operations + WHATIF:ResidueAccessibilityVacuumMolecular + Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. + beta12orEarlier + edam + operation + bioinformatics + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + + + + + + + + Protein surface calculation (accessible molecular) + + Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. + WHATIF:TotAccessibilityMolecular + beta12orEarlier + operations + edam + operation + bioinformatics + + + + + + + + Protein surface calculation (accessible) + + operations + bioinformatics + operation + Calculate the solvent accessibility ('accessible surface') for a structure as a whole. + beta12orEarlier + WHATIF:TotAccessibilitySolvent + edam + + + + + + + + Backbone torsion angle calculation + + Calculate for each residue in a protein structure all its backbone torsion angles. + WHATIF:ResidueTorsionsBB + beta12orEarlier + operations + edam + bioinformatics + operation + + + + + + + + Full torsion angle calculation + + WHATIF:ResidueTorsions + Calculate for each residue in a protein structure all its torsion angles. + beta12orEarlier + operation + bioinformatics + operations + edam + + + + + + + + Cysteine torsion angle calculation + + edam + operation + operations + Calculate for each cysteine (bridge) all its torsion angles. + WHATIF:CysteineTorsions + bioinformatics + beta12orEarlier + + + + + + + + Tau angle calculation + + operation + For each amino acid in a protein structure calculate the backbone angle tau. + bioinformatics + Tau is the backbone angle N-Calpha-C (angle over the C-alpha). + beta12orEarlier + edam + WHATIF:ShowTauAngle + operations + + + + + + + + Cysteine bridge detection + + operation + beta12orEarlier + bioinformatics + Detect cysteine bridges (from coordinate data) in a protein structure. + WHATIF:ShowCysteineBridge + edam + operations + + + + + + + + Free cysteine detection + + WHATIF:ShowCysteineFree + bioinformatics + operations + Detect free cysteines in a protein structure. + beta12orEarlier + A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. + operation + edam + + + + + + + + Metal-bound cysteine detection + + Detect cysteines that are bound to metal in a protein structure. + operation + operations + WHATIF:ShowCysteineMetal + edam + bioinformatics + beta12orEarlier + + + + + + + + Residue contact calculation (residue-nucleic acid) + + + + operations + bioinformatics + edam + Calculate protein residue contacts with nucleic acids in a structure. + WHATIF:ShowProteiNucleicContacts + WHATIF:HasNucleicContacts + operation + beta12orEarlier + + + + + + + + Residue contact calculation (residue-metal) + + + edam + WHATIF:HasMetalContactsPlus + operation + WHATIF:HasMetalContacts + bioinformatics + operations + Calculate protein residue contacts with metal in a structure. + beta12orEarlier + + + + + + + + Residue contact calculation (residue-negative ion) + + WHATIF:HasNegativeIonContacts + beta12orEarlier + bioinformatics + WHATIF:HasNegativeIonContactsPlus + edam + operations + Calculate ion contacts in a structure (all ions for all side chain atoms). + operation + + + + + + + + Residue bump detection + + Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance. + operation + operations + edam + bioinformatics + beta12orEarlier + WHATIF:ShowBumps + + + + + + + + Residue symmetry contact calculation + + bioinformatics + operations + operation + beta12orEarlier + A symmetry contact is a contact between two atoms in different asymmetric unit. + WHATIF:SymmetryContact + edam + Calculate the number of symmetry contacts made by residues in a protein structure. + + + + + + + + Residue contact calculation (residue-ligand) + + + WHATIF:ShowDrugContacts + WHATIF:ShowDrugContactsShort + bioinformatics + beta12orEarlier + WHATIF:ShowLigandContacts + operation + Calculate contacts between residues and ligands in a protein structure. + operations + edam + + + + + + + + Salt bridge calculation + + WHATIF:HasSaltBridgePlus + operation + edam + operations + Calculate (and possibly score) salt bridges in a protein structure. + bioinformatics + WHATIF:ShowSaltBridgesH + WHATIF:HasSaltBridge + beta12orEarlier + WHATIF:ShowSaltBridges + Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. + + + + + + + + Rotamer likelihood prediction + + bioinformatics + beta12orEarlier + WHATIF:ShowLikelyRotamers100 + WHATIF:ShowLikelyRotamers200 + WHATIF:ShowLikelyRotamers300 + WHATIF:ShowLikelyRotamers400 + operation + WHATIF:ShowLikelyRotamers700 + Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. + WHATIF:ShowLikelyRotamers900 + operations + WHATIF:ShowLikelyRotamers800 + WHATIF:ShowLikelyRotamers600 + Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. + WHATIF:ShowLikelyRotamers500 + WHATIF:ShowLikelyRotamers + edam + + + + + + + + Proline mutation value calculation + + beta12orEarlier + operation + WHATIF:ProlineMutationValue + edam + Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein. + operations + bioinformatics + + + + + + + + Residue packing validation + + bioinformatics + operations + edam + Identify poorly packed residues in protein structures. + WHATIF: PackingQuality + operation + beta12orEarlier + + + + + + + + Dihedral angle validation + + WHATIF: ImproperQualityMax + edam + operation + beta12orEarlier + bioinformatics + Identify for each residue in a protein structure any improper dihedral (phi/psi) angles. + WHATIF: ImproperQualitySum + operations + + + + + + + + PDB file sequence retrieval + + true + beta12orEarlier + edam + bioinformatics + WHATIF: PDB_sequence + operations + beta12orEarlier + operation + Extract a molecular sequence from a PDB file. + + + + + + + + + HET group detection + + A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. + beta12orEarlier + Identify HET groups in PDB files. + WHATIF: HETGroupNames + bioinformatics + operation + edam + operations + + + + + + + + DSSP secondary structure assignment + + true + operations + beta12orEarlier + edam + Determine for residue the DSSP determined secondary structure in three-state (HSC). + operation + bioinformatics + WHATIF: ResidueDSSP + beta12orEarlier + + + + + + + + + Structure reformatting + + + bioinformatics + WHATIF: PDBasXML + operation + beta12orEarlier + Reformat (a file or other report of) tertiary structure data. + edam + operations + + + + + + + + Protein cysteine and disulfide bond assignment + + + + + + + + beta12orEarlier + operations + bioinformatics + Assign cysteine bonding state and disulfide bond partners in protein structures. + edam + operation + + + + + + + + Residue validation + + The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). + WHATIF: UseResidueDB + operation + beta12orEarlier + Identify poor quality amino acid positions in protein structures. + operations + edam + bioinformatics + + + + + + + + Structure retrieval (water) + + operation + Query a tertiary structure database and retrieve water molecules. + bioinformatics + WHATIF:MovedWaterPDB + operations + edam + beta12orEarlier + + + + + + + + siRNA duplex prediction + + + + + + + + + + + + + + operations + edam + Identify or predict siRNA duplexes in RNA. + beta12orEarlier + operation + bioinformatics + + + + + + + + Sequence alignment refinement + + + beta12orEarlier + edam + Refine an existing sequence alignment. + operations + bioinformatics + operation + + + + + + + + Listfile processing + + + beta12orEarlier + Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). + bioinformatics + operation + operations + edam + + + + + + + + Sequence file processing + + + beta12orEarlier + edam + operations + operation + bioinformatics + Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences. + + + + + + + + Sequence alignment file processing + + + + Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. + operation + edam + operations + bioinformatics + beta12orEarlier + + + + + + + + Small molecule data processing + + true + operation + edam + Process (read and / or write) physicochemical property data for small molecules. + operations + beta12orEarlier + bioinformatics + beta13 + + + + + + + + + Data retrieval (ontology annotation) + + true + beta12orEarlier + bioinformatics + operation + Ontology information retrieval + operations + edam + Search and retrieve documentation on a bioinformatics ontology. + beta13 + + + + + + + + + Data retrieval (ontology concept) + + true + bioinformatics + operation + beta13 + beta12orEarlier + Query an ontology and retrieve concepts or relations. + operations + Ontology retrieval + edam + + + + + + + + + Representative sequence identification + + + + + + + + bioinformatics + beta12orEarlier + operation + operations + edam + Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences. + + + + + + + + Structure file processing + + + bioinformatics + operations + beta12orEarlier + edam + Perform basic (non-analytical) operations on a file of molecular tertiary structural data. + operation + + + + + + + + Data retrieval (sequence profile) + + true + beta13 + This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. + bioinformatics + operation + edam + beta12orEarlier + operations + Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. + + + + + + + + + Statistical calculation + + true + edam + beta12orEarlier + beta12orEarlier + operations + bioinformatics + Perform a statistical data operation of some type, e.g. calibration or validation. + operation + + + + + + + + + 3D-1D scoring matrix generation + + + + + + + + + + + + + + + Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. + operation + operations + bioinformatics + A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. + beta12orEarlier + edam + + + + + + + + Transmembrane protein rendering + + + + + + + + + + + + + + + operations + beta12orEarlier + bioinformatics + operation + Visualise transmembrane proteins, typically the transmembrane regions within a sequence. + edam + + + + + + + + Demonstration + + true + beta13 + bioinformatics + edam + operation + operations + An operation performing purely illustrative (pedagogical) purposes. + beta12orEarlier + + + + + + + + Data retrieval (pathway or network) + + true + beta13 + Query a biological pathways database and retrieve annotation on one or more pathways. + operation + bioinformatics + operations + beta12orEarlier + edam + + + + + + + + + Data retrieval (identifier) + + true + edam + beta13 + bioinformatics + Query a database and retrieve one or more data identifiers. + beta12orEarlier + operation + operations + + + + + + + + + Nucleic acid density plotting + + edam + operation + operations + Calculate a density plot (of base composition) for a nucleotide sequence. + bioinformatics + beta12orEarlier + + + + + + + + Sequence analysis + + + + + + + + + + + + + + + + + + + + operations + edam + operation + bioinformatics + Sequence analysis (general) + beta12orEarlier + Analyse one or more known molecular sequences. + + + + + + + + Sequence motif processing + + + + + + + + + + operation + edam + beta12orEarlier + Process (read and / or write) molecular sequence motifs. + operations + bioinformatics + + + + + + + + Protein interaction data processing + + + + + + + + + operations + bioinformatics + beta12orEarlier + edam + Process (read and / or write) protein interaction data. + operation + + + + + + + + Protein structure analysis + + + + + + + + + + + + + + + operation + bioinformatics + beta12orEarlier + Structure analysis (protein) + Analyse protein tertiary structural data. + edam + operations + + + + + + + + Annotation processing + + true + operation + operations + bioinformatics + Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. + edam + beta12orEarlier + beta12orEarlier + + + + + + + + + Sequence feature analysis + + true + beta12orEarlier + operation + Analyse features in molecular sequences. + operations + bioinformatics + beta12orEarlier + edam + + + + + + + + + File processing + + + + + + + + + + Data file processing + operations + File handling + bioinformatics + edam + operation + Report handling + beta12orEarlier + Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations. + + + + + + + + Gene expression analysis + + true + beta12orEarlier + bioinformatics + operations + Analyse gene expression and regulation data. + beta12orEarlier + edam + operation + + + + + + + + + Structural (3D) profile processing + + + + + + + + + operations + operation + edam + bioinformatics + Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. + beta12orEarlier + + + + + + + + Data index processing + + + Process (read and / or write) an index of (typically a file of) biological data. + operations + operation + Database index processing + bioinformatics + beta12orEarlier + edam + + + + + + + + Sequence profile processing + + + + + + + + + + bioinformatics + Process (read and / or write) some type of sequence profile. + beta12orEarlier + edam + operation + operations + + + + + + + + Protein function analysis + + + + + + + + edam + operations + beta12orEarlier + Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report. + This is a broad concept and is used a placeholder for other, more specific concepts. + operation + bioinformatics + + + + + + + + Protein folding analysis + + + + + + + + + + + + + + + beta12orEarlier + edam + operation + Protein folding modelling + Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report. + This is a broad concept and is used a placeholder for other, more specific concepts. + bioinformatics + operations + + + + + + + + Protein secondary structure analysis + + + + + + + + + + + + + + + operation + edam + Analyse known protein secondary structure data. + operations + bioinformatics + Secondary structure analysis (protein) + beta12orEarlier + + + + + + + + Physicochemical property data processing + + true + bioinformatics + operation + beta12orEarlier + Process (read and / or write) data on the physicochemical property of a molecule. + operations + beta13 + edam + + + + + + + + + Primer and probe design + + + + + + + + + bioinformatics + operations + Primer and probe prediction + Predict oligonucleotide primers or probes. + operation + beta12orEarlier + edam + + + + + + + + Analysis and processing + + + operation + Process (read and / or write) data of a specific type, for example applying analytical methods. + beta12orEarlier + edam + bioinformatics + Calculation + operations + Computation + + + + + + + + Database search + + + + + + + + + Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. + Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. + operations + bioinformatics + operation + beta12orEarlier + edam + + + + + + + + Data retrieval + + + + + + + + Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords. + edam + operations + beta12orEarlier + operation + bioinformatics + Information retrieval + + + + + + + + Prediction, detection and recognition + + operations + edam + Predict, recognise, detect or identify some properties of a biomolecule. + bioinformatics + beta12orEarlier + operation + + + + + + + + Comparison + + Compare two or more things to identify similarities. + edam + bioinformatics + operation + operations + beta12orEarlier + + + + + + + + Optimisation and refinement + + operation + bioinformatics + edam + Refine or optimise some data model. + beta12orEarlier + operations + + + + + + + + Modelling and simulation + + + + + + + + Model or simulate some biological entity or system. + edam + operation + operations + beta12orEarlier + bioinformatics + + + + + + + + Data handling + + true + beta12orEarlier + operation + operations + Perform basic operations on some data or a database. + bioinformatics + beta12orEarlier + edam + + + + + + + + + Evaluation and validation + + edam + Validate or standardise some data. + Validation and standardisation + bioinformatics + operation + operations + beta12orEarlier + + + + + + + + Mapping and assembly + + + + + + + + + + + + + + operations + Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. + operation + bioinformatics + beta12orEarlier + edam + This is a broad concept and is used a placeholder for other, more specific concepts. + + + + + + + + Design + + true + edam + Design a biological entity (typically a molecular sequence or structure) with specific properties. + beta13 + operation + operations + beta12orEarlier + bioinformatics + + + + + + + + + Microarray data processing + + true + operation + bioinformatics + operations + beta12orEarlier + edam + Process (read and / or write) microarray data. + beta12orEarlier + + + + + + + + + Codon usage table processing + + + beta12orEarlier + bioinformatics + operations + Process (read and / or write) a codon usage table. + operation + edam + + + + + + + + Data retrieval (codon usage table) + + true + beta13 + edam + bioinformatics + beta12orEarlier + Retrieve a codon usage table and / or associated annotation. + operations + operation + + + + + + + + + Gene expression profile processing + + + beta12orEarlier + operations + Process (read and / or write) a gene expression profile. + bioinformatics + operation + edam + + + + + + + + Gene expression profile annotation + + + + + + + + + Annotate a gene expression profile with concepts from an ontology of gene functions. + operation + bioinformatics + beta12orEarlier + operations + edam + + + + + + + + Gene regulatory network prediction + + + + + + + + + beta12orEarlier + operation + Predict a network of gene regulation. + edam + operations + bioinformatics + + + + + + + + Pathway or network processing + + + + + + + + + operation + bioinformatics + operations + edam + beta12orEarlier + Generate, analyse or handle a biological pathway or network. + + + + + + + + RNA secondary structure processing + + + + + + + + + + + + + + + + + operations + bioinformatics + edam + Process (read and / or write) RNA secondary structure data. + operation + beta12orEarlier + + + + + + + + Structure processing (RNA) + + true + bioinformatics + operations + edam + beta13 + beta12orEarlier + Process (read and / or write) RNA tertiary structure data. + operation + + + + + + + + + RNA structure prediction + + + + + + + + Predict RNA tertiary structure. + beta12orEarlier + bioinformatics + edam + operation + operations + + + + + + + + DNA structure prediction + + + + + + + + bioinformatics + beta12orEarlier + Predict DNA tertiary structure. + operation + edam + operations + + + + + + + + Phylogenetic tree processing + + + + + + + + + edam + Process (read and / or write) a phylogenetic tree. + beta12orEarlier + operations + bioinformatics + operation + + + + + + + + Protein secondary structure processing + + + + + + + + + + + beta12orEarlier + operations + edam + bioinformatics + operation + Process (read and / or write) protein secondary structure data. + + + + + + + + Protein interaction network processing + + + + + + + + + + edam + operation + Process (read and / or write) a network of protein interactions. + bioinformatics + beta12orEarlier + operations + + + + + + + + Sequence processing + + + bioinformatics + edam + beta12orEarlier + operation + Process (read and / or write) one or more molecular sequences and associated annotation. + operations + Sequence processing (general) + + + + + + + + Sequence processing (protein) + + + + edam + bioinformatics + operation + beta12orEarlier + Process (read and / or write) a protein sequence and associated annotation. + operations + + + + + + + + Sequence processing (nucleic acid) + + + + operations + operation + bioinformatics + beta12orEarlier + edam + Process (read and / or write) a nucleotide sequence and associated annotation. + + + + + + + + Sequence comparison + + + + + + + + + + + + + + + + + + + + + beta12orEarlier + edam + operations + bioinformatics + Compare two or more molecular sequences. + operation + + + + + + + + Sequence cluster processing + + + + + + + + + operation + bioinformatics + beta12orEarlier + edam + operations + Process (read and / or write) a sequence cluster. + + + + + + + + Feature table processing + + + + + + + + + + + + + + + + + + + + + + + + + + operations + beta12orEarlier + operation + edam + bioinformatics + Process (read and / or write) a sequence feature table. + + + + + + + + Gene and gene component prediction + + + + + + + + + + + + + + Gene finding + bioinformatics + operations + beta12orEarlier + operation + edam + Detect, predict and identify genes or components of genes in DNA sequences. + + + + + + + + GPCR classification + + + + + + + + + edam + Classify G-protein coupled receptors (GPCRs) into families and subfamilies. + beta12orEarlier + operations + bioinformatics + operation + G protein-coupled receptor (GPCR) classification + + + + + + + + GPCR coupling selectivity prediction + + + + + + + + + + operation + edam + operations + beta12orEarlier + bioinformatics + Predict G-protein coupled receptor (GPCR) coupling selectivity. + + + + + + + + Structure processing (protein) + + + + + + + + + + Process (read and / or write) a protein tertiary structure. + beta12orEarlier + operations + operation + bioinformatics + edam + + + + + + + + Protein atom surface calculation + + operation + edam + operations + beta12orEarlier + Calculate the solvent accessibility for each atom in a structure. + bioinformatics + Waters are not considered. + + + + + + + + Protein residue surface calculation + + operation + Calculate the solvent accessibility for each residue in a structure. + edam + operations + beta12orEarlier + bioinformatics + + + + + + + + Protein surface calculation + + operations + edam + beta12orEarlier + Calculate the solvent accessibility of a structure as a whole. + operation + bioinformatics + + + + + + + + Sequence alignment processing + + + + + + + + + edam + operations + beta12orEarlier + bioinformatics + Process (read and / or write) a molecular sequence alignment. + operation + + + + + + + + Protein-protein interaction prediction + + + + + + + + + + + + + + bioinformatics + operations + beta12orEarlier + edam + Identify or predict protein-protein interactions, interfaces, binding sites etc. + operation + + + + + + + + Structure processing + + + beta12orEarlier + Process (read and / or write) a molecular tertiary structure. + operation + edam + bioinformatics + operations + + + + + + + + Map annotation + + + + + + + + + + + + + + + edam + bioinformatics + Annotate a DNA map of some type with terms from a controlled vocabulary. + operations + operation + beta12orEarlier + + + + + + + + Data retrieval (protein annotation) + + true + operation + Protein information retrieval + edam + beta12orEarlier + bioinformatics + operations + beta13 + Retrieve information on a protein. + + + + + + + + + Data retrieval (phylogenetic tree) + + true + operations + Retrieve a phylogenetic tree from a data resource. + bioinformatics + operation + beta13 + edam + beta12orEarlier + + + + + + + + + Data retrieval (protein interaction annotation) + + true + operation + edam + operations + beta12orEarlier + bioinformatics + beta13 + Retrieve information on a protein interaction. + + + + + + + + + Data retrieval (protein family annotation) + + true + operation + operations + Retrieve information on a protein family. + edam + beta12orEarlier + bioinformatics + beta13 + Protein family information retrieval + + + + + + + + + Data retrieval (RNA family annotation) + + true + beta13 + beta12orEarlier + operations + RNA family information retrieval + operation + Retrieve information on an RNA family. + edam + bioinformatics + + + + + + + + + Data retrieval (gene annotation) + + true + bioinformatics + beta13 + Retrieve information on a specific gene. + Gene information retrieval + beta12orEarlier + operations + edam + operation + + + + + + + + + Data retrieval (genotype and phenotype annotation) + + true + bioinformatics + operations + Retrieve information on a specific genotype or phenotype. + beta13 + beta12orEarlier + Genotype and phenotype information retrieval + edam + operation + + + + + + + + + Protein architecture comparison + + + + + + + + + beta12orEarlier + operation + bioinformatics + Compare the architecture of two or more protein structures. + operations + edam + + + + + + + + Protein architecture recognition + + + + + + + + + + operation + Identify the architecture of a protein structure. + edam + operations + bioinformatics + beta12orEarlier + + + + + + + + Molecular dynamics simulation + + + + + + + + + + + + + + + + + + + + + + edam + Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. + bioinformatics + operation + operations + beta12orEarlier + + + + + + + + Nucleic acid sequence analysis + + + + + + + + + + + + + + + operations + edam + bioinformatics + Sequence analysis (nucleic acid) + beta12orEarlier + operation + Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). + + + + + + + + Protein sequence analysis + + + + + + + + + + + + + + + operations + beta12orEarlier + Sequence analysis (protein) + operation + edam + Analyse a protein sequence (using methods that are only applicable to protein sequences). + bioinformatics + + + + + + + + Structure analysis + + + + + + + + + + + + + + + + + + + + operations + Analyse known molecular tertiary structures. + operation + edam + bioinformatics + beta12orEarlier + + + + + + + + Nucleic acid structure analysis + + + + + + + + + + + + + + + operations + operation + edam + bioinformatics + beta12orEarlier + Analyse nucleic acid tertiary structural data. + + + + + + + + Secondary structure processing + + + + + + + + + beta12orEarlier + operations + edam + Process (read and / or write) a molecular secondary structure. + bioinformatics + operation + + + + + + + + Structure comparison + + + + + + + + + Compare two or more molecular tertiary structures. + operation + bioinformatics + operations + beta12orEarlier + edam + + + + + + + + Helical wheel rendering + + + + + + + + Render a helical wheel representation of protein secondary structure. + operation + operations + beta12orEarlier + bioinformatics + edam + + + + + + + + Topology diagram rendering + + + + + + + + bioinformatics + operations + edam + Render a topology diagram of protein secondary structure. + beta12orEarlier + operation + + + + + + + + Protein structure comparison + + + + + + + + + + + + + + + + Compare protein tertiary structures. + beta12orEarlier + operations + Methods might identify structural neighbors, find structural similarities or define a structural core. + Structure comparison (protein) + operation + edam + bioinformatics + + + + + + + + Protein secondary structure comparison + + + + + + + + + + edam + bioinformatics + operation + Compare protein secondary structures. + beta12orEarlier + Protein secondary structure + Secondary structure comparison (protein) + operations + + + + + + + + Protein subcellular localization prediction + + + + + + + + + bioinformatics + Predict the subcellular localization of a protein sequence. + The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. + beta12orEarlier + operations + Protein targeting prediction + edam + operation + + + + + + + + Residue contact calculation (residue-residue) + + operation + Calculate contacts between residues in a protein structure. + operations + bioinformatics + edam + beta12orEarlier + + + + + + + + Hydrogen bond calculation (inter-residue) + + + beta12orEarlier + operations + bioinformatics + Identify potential hydrogen bonds between amino acid residues. + operation + edam + + + + + + + + Protein interaction prediction + + + + + + + + + edam + beta12orEarlier + operations + operation + bioinformatics + Predict the interactions of proteins with other molecules. + + + + + + + + Codon usage data processing + + true + edam + operation + bioinformatics + operations + Process (read and / or write) codon usage data. + beta13 + beta12orEarlier + + + + + + + + + Gene expression data processing + + + + + + + + + + + + + + + + Process (read and / or write) gene expression (typically microarray) data. + bioinformatics + operations + Microarray data processing + beta12orEarlier + operation + edam + Gene expression (microarray) data processing + + + + + + + + Gene regulatory network processing + + + + + + + + + + operations + bioinformatics + Process (read and / or write) a network of gene regulation. + operation + beta12orEarlier + edam + + + + + + + + Pathway or network analysis + + + + + + + + + + + + + + beta12orEarlier + Network analysis + edam + Analyse a known biological pathway or network. + bioinformatics + operations + Pathway analysis + operation + + + + + + + + Sequencing-based expression profile data analysis + + true + operations + beta12orEarlier + operation + beta12orEarlier + Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. + edam + bioinformatics + + + + + + + + + Splicing analysis + + + + + + + + + + + + + + + + operations + beta12orEarlier + Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences. + operation + edam + Splicing modelling + bioinformatics + + + + + + + + Microarray raw data analysis + + true + bioinformatics + operations + Analyse raw microarray data. + beta12orEarlier + beta12orEarlier + edam + operation + + + + + + + + + Nucleic acid data processing + + + + + + + + + beta12orEarlier + Process (read and / or write) nucleic acid sequence or structural data. + operation + operations + edam + bioinformatics + + + + + + + + Protein data processing + + + + + + + + + operation + operations + beta12orEarlier + edam + bioinformatics + Process (read and / or write) protein sequence or structural data. + + + + + + + + Sequence data processing + + true + operation + edam + beta13 + beta12orEarlier + Process (read and / or write) molecular sequence data. + operations + bioinformatics + + + + + + + + + Structural data processing + + true + operations + edam + beta12orEarlier + operation + bioinformatics + beta13 + Process (read and / or write) molecular structural data. + + + + + + + + + Text processing + + + edam + Process (read and / or write) text. + operations + beta12orEarlier + operation + bioinformatics + + + + + + + + Sequence alignment analysis (protein) + + + + + + + + + + + + + + + + operation + edam + operations + beta12orEarlier + bioinformatics + Analyse a protein sequence alignment, typically to detect features or make predictions. + + + + + + + + Sequence alignment analysis (nucleic acid) + + + + + + + + + + + + + + + + Analyse a protein sequence alignment, typically to detect features or make predictions. + operations + beta12orEarlier + edam + bioinformatics + operation + + + + + + + + Nucleic acid sequence comparison + + + + operation + beta12orEarlier + Compare two or more nucleic acid sequences. + operations + bioinformatics + Sequence comparison (nucleic acid) + edam + + + + + + + + Protein sequence comparison + + + + operations + operation + Compare two or more protein sequences. + bioinformatics + Sequence comparison (protein) + edam + beta12orEarlier + + + + + + + + DNA back-translation + + + + + + + + Back-translate a protein sequence into DNA. + operation + beta12orEarlier + operations + edam + bioinformatics + + + + + + + + Sequence editing (nucleic acid) + + + beta12orEarlier + bioinformatics + Edit or change a nucleic acid sequence, either randomly or specifically. + operations + edam + operation + + + + + + + + Sequence editing (protein) + + + beta12orEarlier + operation + edam + operations + Edit or change a protein sequence, either randomly or specifically. + bioinformatics + + + + + + + + Sequence generation (nucleic acid) + + + + + + + + + operations + bioinformatics + operation + beta12orEarlier + Generate a nucleic acid sequence by some means. + edam + + + + + + + + Sequence generation (protein) + + + + + + + + + edam + operation + bioinformatics + operations + beta12orEarlier + Generate a protein sequence by some means. + + + + + + + + Sequence rendering (nucleic acid) + + + + + + + + + Visualise, format or render a nucleic acid sequence. + beta12orEarlier + edam + Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. + operations + operation + bioinformatics + + + + + + + + Sequence rendering (protein) + + + Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. + edam + operation + bioinformatics + Visualise, format or render a protein sequence. + beta12orEarlier + operations + + + + + + + + Nucleic acid structure comparison + + + + operation + bioinformatics + operations + edam + Structure comparison (nucleic acid) + beta12orEarlier + Compare nucleic acid tertiary structures. + + + + + + + + Structure processing (nucleic acid) + + + + + + + + + + + bioinformatics + operation + Process (read and / or write) nucleic acid tertiary structure data. + edam + beta12orEarlier + operations + + + + + + + + DNA mapping + + + + + + + + + + edam + Generate a map of a DNA sequence annotated with positional or non-positional features of some type. + beta12orEarlier + bioinformatics + operation + operations + + + + + + + + Map data processing + + + + + + + + + operations + Process (read and / or write) a DNA map of some type. + bioinformatics + beta12orEarlier + edam + DNA map data processing + operation + + + + + + + + Protein hydropathy calculation + + + + + + + + + + + + + + operations + Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). + operation + bioinformatics + edam + beta12orEarlier + + + + + + + + Binding site prediction + + + + + + + + + + + + + + + + + + + + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. + operations + edam + bioinformatics + beta12orEarlier + operation + Ligand-binding and active site prediction + + + + + + + + Sequence tagged site (STS) mapping + + + + + + + + An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. + bioinformatics + Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). + edam + beta12orEarlier + Sequence mapping + operations + operation + + + + + + + + Alignment construction + + + + + + + + beta12orEarlier + Alignment + bioinformatics + edam + operations + operation + Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. + + + + + + + + Protein fragment weight comparison + + + Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data. + beta12orEarlier + edam + bioinformatics + operation + operations + + + + + + + + Protein property comparison + + + + + + + + beta12orEarlier + Compare the physicochemical properties of two or more proteins (or reference data). + bioinformatics + operations + operation + edam + + + + + + + + Secondary structure comparison + + + + + + + + + + + + + + + + + + + + operation + beta12orEarlier + Compare two or more molecular secondary structures. + edam + bioinformatics + operations + + + + + + + + Hopp and Woods plotting + + edam + bioinformatics + operations + Generate a Hopp and Woods plot of antigenicity of a protein. + beta12orEarlier + operation + + + + + + + + Microarray cluster textual view rendering + + edam + operations + bioinformatics + operation + Visualise gene clusters with gene names. + beta12orEarlier + + + + + + + + Microarray wave graph rendering + + edam + Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis. + This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. + bioinformatics + operations + operation + beta12orEarlier + Microarray cluster temporal graph rendering + + + + + + + + Microarray dendrograph rendering + + operations + Microarray view rendering + Microarray checks view rendering + operation + edam + beta12orEarlier + Generate a dendrograph of raw, preprocessed or clustered microarray data. + bioinformatics + + + + + + + + Microarray proximity map rendering + + bioinformatics + operations + Generate a plot of distances (distance matrix) between genes. + operation + edam + Microarray distance map rendering + beta12orEarlier + + + + + + + + Microarray tree or dendrogram view rendering + + Microarray matrix tree plot rendering + Microarray 2-way dendrogram rendering + edam + operations + Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression. + beta12orEarlier + operation + bioinformatics + + + + + + + + Microarray principal component rendering + + Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values. + edam + bioinformatics + operations + beta12orEarlier + operation + + + + + + + + Microarray scatter plot rendering + + operations + operation + edam + beta12orEarlier + bioinformatics + Generate a scatter plot of microarray data, typically after principal component analysis. + + + + + + + + Whole microarray graph view rendering + + beta12orEarlier + edam + bioinformatics + Visualise gene expression data where each band (or line graph) corresponds to a sample. + operations + operation + + + + + + + + Microarray tree-map rendering + + operation + Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. + operations + beta12orEarlier + edam + bioinformatics + + + + + + + + Microarray Box-Whisker plot rendering + + bioinformatics + edam + operation + Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles. + operations + beta12orEarlier + + + + + + + + Physical mapping + + + + + + + + + + + + + + operation + operations + edam + bioinformatics + Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. + beta12orEarlier + + + + + + + + Analysis + + true + beta12orEarlier + edam + beta12orEarlier + For non-analytical operations, see the 'Processing' branch. + bioinformatics + operations + operation + Apply analytical methods to existing data of a specific type. + + + + + + + + + Alignment analysis + + + + + + + + + + + + + + Analyse an existing alignment of two or more molecular sequences, structures or derived data. + operation + operations + beta12orEarlier + edam + bioinformatics + + + + + + + + Article analysis + + + + + + + + + + + + + + + + + + + + beta12orEarlier + bioinformatics + operations + operation + edam + Analyse a body of scientific text (typically a full text article from a scientific journal.) + + + + + + + + Molecular interaction analysis + + true + bioinformatics + beta13 + edam + operation + operations + beta12orEarlier + Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. + + + + + + + + Protein interaction analysis + + + + + + + + + Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. + operations + edam + operation + bioinformatics + beta12orEarlier + + + + + + + + Residue contact calculation + + bioinformatics + edam + Calculate contacts between residues and some other group in a protein structure. + beta12orEarlier + operations + operation + + + + + + + + Alignment processing + + + beta12orEarlier + edam + Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. + operation + bioinformatics + operations + + + + + + + + Structure alignment processing + + + + + + + + + + edam + bioinformatics + beta12orEarlier + Process (read and / or write) a molecular tertiary (3D) structure alignment. + operations + operation + + + + + + + + Codon usage bias calculation + + + + + + + + operations + edam + beta12orEarlier + bioinformatics + Calculate codon usage bias. + operation + + + + + + + + Codon usage bias plotting + + + + + + + + bioinformatics + operation + edam + operations + Generate a codon usage bias plot. + beta12orEarlier + + + + + + + + Codon usage fraction calculation + + + + + + + + operations + edam + bioinformatics + beta12orEarlier + Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc. + operation + + + + + + + + Classification + + + + + + + + operations + Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. + bioinformatics + edam + beta12orEarlier + operation + + + + + + + + Molecular interaction data processing + + true + Process (read and / or write) molecular interaction data. + edam + bioinformatics + operation + operations + beta12orEarlier + beta13 + + + + + + + + Sequence classification + + + operation + bioinformatics + Assign molecular sequence(s) to a group or category. + edam + operations + beta12orEarlier + + + + + + + + Structure classification + + + operations + edam + bioinformatics + beta12orEarlier + Assign molecular structure(s) to a group or category. + operation + + + + + + + + Protein comparison + + beta12orEarlier + edam + bioinformatics + operation + Compare two or more proteins (or some aspect) to identify similarities. + operations + + + + + + + + Nucleic acid comparison + + Compare two or more nucleic acids to identify similarities. + beta12orEarlier + operation + bioinformatics + operations + edam + + + + + + + + Prediction, detection and recognition (protein) + + operations + Predict, recognise, detect or identify some properties of proteins. + bioinformatics + beta12orEarlier + operation + edam + + + + + + + + Prediction, detection and recognition (nucleic acid) + + Predict, recognise, detect or identify some properties of nucleic acids. + edam + operation + operations + bioinformatics + beta12orEarlier + + + + + + + + Structure editing + + + + + + + + + beta13 + Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. + edam + operations + bioinformatics + operation + + + + + + + + Sequence alignment editing + + + operation + bioinformatics + operations + beta13 + edam + Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically. + + + + + + + + Pathway or network rendering + + + + + + + + + + beta13 + bioinformatics + operations + operation + edam + Render (visualise) a biological pathway or network. + + + + + + + + Protein function prediction (from sequence) + + + + + + + + + + Predict general (non-positional) functional properties of a protein from analysing its sequence. + For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. + edam + operation + bioinformatics + operations + beta13 + + + + + + + + Protein site detection + + + bioinformatics + beta13 + operations + edam + name: Sequence motif recognition (protein) + Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. + operation + + + + + + + + Protein property calculation (from sequence) + + + edam + bioinformatics + operations + operation + Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. + beta13 + + + + + + + + Protein feature prediction (from structure) + + + Predict, recognise and identify positional features in proteins from analysing protein structure. + operations + operation + beta13 + bioinformatics + edam + + + + + + + + Protein feature prediction + + + + + + + + + + + + + + + + operations + operation + edam + beta13 + Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. + bioinformatics + + + + + + + + Sequence screening + + bioinformatics + beta13 + Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. + edam + operations + operation + + + + + + + + Protein interaction network prediction + + + + + + + + operations + Predict a network of protein interactions. + edam + bioinformatics + operation + beta13 + + + + + + + + Nucleic acid design + + operations + Design (or predict) nucleic acid sequences with specific chemical or physical properties. + bioinformatics + beta13 + edam + operation + + + + + + + + Editing + + Edit, convert or otherwise change a data entity, either randomly or specifically. + bioinformatics + edam + operation + beta13 + operations + + + + + + + + Sequence assembly evaluation + + + + + + + + + + + + + + + + + + + + + + bioinformatics + edam + operations + 1.1 + Evaluate a DNA sequence assembly, typically for purposes of quality control. + operation + + + + + + + + Genome alignment construction + + Genome alignment + 1.1 + edam + operations + Align two or more (tpyically huge) molecular sequences that represent genomes. + bioinformatics + operation + + + + + + + + Localized reassembly + + operation + 1.1 + operations + bioinformatics + Reconstruction of a sequence assembly in a localised area. + edam + + + + + + + + Sequence assembly rendering + + Assembly visualisation + edam + operations + 1.1 + bioinformatics + operation + Render and visualise a DNA sequence assembly. + Assembly rendering + Sequence assembly visualisation + + + + + + + + Base-calling + + + + + + + + Base calling + operation + operations + 1.1 + Phred base calling + Phred base-calling + bioinformatics + Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. + edam + + + + + + + + Bisulfite mapping + + Bisulfite sequence alignment + The mapping of methylation sites in a DNA (genome) sequence. + bioinformatics + Bisulfite sequence mapping + operations + edam + operation + Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. + 1.1 + + + + + + + + Sequence contamination filtering + + + + + + + + Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. + operations + operation + beta12orEarlier + bioinformatics + edam + + + + + + + + Trim ends + + bioinformatics + For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. + operation + operations + 1.1 + Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. + edam + + + + + + + + Trim vector + + operations + edam + 1.1 + operation + bioinformatics + Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. + + + + + + + + Trim to reference + + operation + Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. + bioinformatics + edam + 1.1 + operations + + + + + + + + Sequence trimming + + bioinformatics + operations + edam + Cut (remove) the end from a molecular sequence. + operation + 1.1 + + + + + + + + Genome feature comparison + + 1.1 + Compare the features of two genome sequences. + Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. + bioinformatics + operation + edam + operations + + + + + + + + Sequencing error detection + + + + + + + + beta12orEarlier + Short-read error correction + operation + Detect errors in DNA sequences generated from sequencing projects). + operations + edam + bioinformatics + Short read error correction + + + + + + + + Genotyping + + edam + Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. + Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. + operations + 1.1 + bioinformatics + operation + + + + + + + + Genetic variation analysis + + + + + + + + Genetic variation annotation + edam + operation + bioinformatics + 1.1 + Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. + Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. + Sequence variation analysis + operations + + + + + + + + Oligonucleotide alignment construction + + operation + operations + Short sequence read mapping + Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. + Short read alignment + 1.1 + Read alignment + Oligonucleotide alignment + The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. + edam + Short read mapping + bioinformatics + Read mapping + Oligonucleotide mapping + Short oligonucleotide alignment + + + + + + + + Split read mapping + + operations + operation + 1.1 + edam + bioinformatics + A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. + + + + + + + + DNA barcoding + + Sample barcoding + operation + 1.1 + edam + operations + bioinformatics + Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. + + + + + + + + SNP calling + + bioinformatics + edam + operation + 1.1 + Operations usually score confidence in the prediction or some other statistical measure of evidence. + operations + Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism. + + + + + + + + Mutation detection + + operations + bioinformatics + edam + 1.1 + operation + Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware. + Polymorphism detection + + + + + + + + Chromatogram visualisation + + edam + operations + 1.1 + operation + Chromatogram viewing + Visualise, format or render an image of a Chromatogram. + bioinformatics + + + + + + + + Methylation analysis + + bioinformatics + Determine cytosine methylation states in nucleic acid sequences. + 1.1 + edam + operation + operations + + + + + + + + Methylation calling + + bioinformatics + Determine cytosine methylation status of specific positions in a nucleic acid sequences. + edam + operations + 1.1 + operation + + + + + + + + Methylation level analysis (global) + + operations + Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay. + bioinformatics + operation + edam + Global methylation analysis + 1.1 + + + + + + + + Methylation level analysis (gene-specific) + + bioinformatics + operation + operations + Many different techniques are available for this. + Measure the level of methyl cytosines in specific genes. + edam + 1.1 + Gene-specific methylation analysis + + + + + + + + Genome rendering + + Genome browsing + bioinformatics + Genome viewing + operation + edam + Genome visualisation + Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. + 1.1 + operations + Genome visualization + + + + + + + + Genome comparison + + bioinformatics + Genomic region matching + 1.1 + edam + operations + operation + Compare the sequence or features of two or more genomes, for example, to find matching regions. + + + + + + + + Genome indexing + + + + + + + + 1.1 + bioinformatics + Generate an index of a genome sequence. + operations + Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. + operation + edam + + + + + + + + Genome indexing (Burrows-Wheeler) + + operations + operation + 1.1 + Generate an index of a genome sequence using the Burrows-Wheeler algorithm. + edam + bioinformatics + The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. + + + + + + + + Genome indexing (suffix arrays) + + bioinformatics + operations + A suffix array consists of the lexicographically sorted list of suffixes of a genome. + operation + edam + suffix arrays + Generate an index of a genome sequence using a suffix arrays algorithm. + 1.1 + + + + + + + + Spectrum analysis + + Mass spectrum analysis + operation + Analyse a spectrum from a mass spectrometry (or other) experiment. + edam + bioinformatics + 1.1 + Spectral analysis + operations + + + + + + + + Peak detection + + + + + + + + operation + operations + edam + Identify peaks in a spectrum from a mass spectrometry experiment. + bioinformatics + Peak finding + 1.1 + + + + + + + + Scaffolding + + + + operation + Scaffold may be positioned along a chromosome physical map to create a "golden path". + 1.1 + edam + operations + bioinformatics + Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps. + Scaffold construction + + + + + + + + Scaffold gap completion + + + + bioinformatics + Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. + operations + 1.1 + operation + Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences. + edam + + + + + + + + Sequencing quality control + + + bioinformatics + operations + operation + Sequencing QC + Raw sequence data quality control. + edam + Analyse raw sequence data from a sequencing pipeline and identify problems. + 1.1 + + + + + + + + Read pre-processing + + 1.1 + operations + Pre-process sequence reads to ensure (or improve) quality and reliability. + operation + bioinformatics + This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. + edam + Sequence read pre-processing + + + + + + + + Species frequency estimation + + + + + + + + 1.1 + Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples. + operations + bioinformatics + operation + edam + + + + + + + + Peak calling + + 1.1 + Protein binding peak detection + Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. + bioinformatics + Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). + edam + operations + operation + + + + + + + + Differential expression analysis + + operations + operation + 1.1 + Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. + edam + Differentially expressed gene identification + bioinformatics + Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. + + + + + + + + Gene set testing + + edam + Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc. + bioinformatics + Gene sets can be defined beforehand by biological function, chromosome locations and so on. + operations + 1.1 + operation + + + + + + + + Variant classification + + + operations + edam + Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) + operation + bioinformatics + 1.1 + Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins. + + + + + + + + Variant prioritization + + edam + bioinformatics + 1.1 + operation + operations + Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. + Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. + + + + + + + + Variant mapping + + bioinformatics + operations + Variant calling + Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. + edam + Methods often utilise a database of aligned reads. + operation + 1.1 + + + + + + + + Structural variation discovery + + operations + Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. + bioinformatics + operation + 1.1 + edam + Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s). + + + + + + + + Exome analysis + + Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. + Exome sequencing is considered a cheap alternative to whole genome sequencing. + bioinformatics + Targeted exome capture + 1.1 + edam + Exome sequence analysis + operation + operations + + + + + + + + Read depth analysis + + Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications. + 1.1 + operations + bioinformatics + operation + edam + + + + + + + + Gene expression QTL analysis + + + + + + + + operation + operations + bioinformatics + 1.1 + edam + expression quantitative trait loci profiling + expression QTL profiling + Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes. + eQTL profiling + + + + + + + + Copy number estimation + + operation + Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. + bioinformatics + edam + 1.1 + operations + Transcript copy number estimation + Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). + + + + + + + + Primer removal + + + bioinformatics + Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). + operations + operation + 1.2 + edam + + + + + + + + Transcriptome assembly + + + + + + + + + + + + + + + + Infer a transcriptome sequence by analysis of short sequence reads. + bioinformatics + edam + operation + operations + 1.2 + + + + + + + + Transcriptome assembly (de novo) + + Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. + de novo transcriptome assembly + bioinformatics + edam + operation + operations + 1.2 + + + + + + + + Transcriptome assembly (mapping) + + Infer a transcriptome sequence by mapping short reads to a reference genome. + bioinformatics + edam + operation + operations + 1.2 + + + + + + + + beta12orEarlier + topics + edam + bioinformatics + topic + + + + Topic + A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. + + + sumo:FieldOfStudy + + + + + + + + + GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated. + + + + + + GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. + + + + + + BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the topic. + + + + + + Topic can be a quality of an entity. + + + + + + + + + + + Nucleic acid analysis + + edam + beta12orEarlier + bioinformatics + topic + topics + Nucleic acid informatics + Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis. + Nucleic acid bioinformatics + Nucleic acids + + + + + + + + + + Protein analysis + + beta12orEarlier + Processing and analysis of protein data, typically molecular sequence and structural data. + bioinformatics + Protein bioinformatics + edam + Proteins + topic + Protein informatics + topics + + + + + + + + + Metabolites + + + beta12orEarlier + Topic concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. + bioinformatics + This concept excludes macromolecules such as proteins and nucleic acids. + topics + topic + edam + + + + + + + + Sequence analysis + + Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles. + bioinformatics + topic + BioCatalogue:Sequence Analysis + topics + Sequences + edam + beta12orEarlier + + + + + + + + + Structure analysis + + beta12orEarlier + topics + This includes related concepts such as structural properties, alignments and structural motifs. + edam + Structural bioinformatics + topic + bioinformatics + Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids. + Computation structural biology + + + + + + + + + Structure prediction + + bioinformatics + topic + edam + beta12orEarlier + Topic concerning the prediction of molecular (secondary or tertiary) structure. + topics + + + + + + + + Alignment + + true + edam + Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). + beta12orEarlier + beta12orEarlier + topic + topics + bioinformatics + + + + + + + + + + + Phylogenetics + + Phylogenetic simulation + bioinformatics + BioCatalogue:Phylogeny + edam + This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data. + BioCatalogue:Statistical Robustness + topics + Phylogenetic clocks, dating and stratigraphy + Topic concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc. + topic + beta12orEarlier + + + + + + + + + Functional genomics + + Topic concerning the study of gene or protein functions and their interactions. + bioinformatics + topics + edam + topic + beta12orEarlier + + + + + + + + Ontology + + topics + BioCatalogue:Ontology Lookup + bioinformatics + This includes the annotation of entities (typically biological database entries) with concepts from a controlled vocabulary. + Applied ontology + beta12orEarlier + Topic concerning ontologies, controlled vocabularies, structured glossary or other related resource. + Ontologies + topic + edam + BioCatalogue:Ontology + + + + + + + + Data search and retrieval + + Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information. + BioCatalogue:Structure Retrieval + BioCatalogue:Image Retrieval + bioinformatics + edam + BioCatalogue:Sequence Retrieval + BioCatalogue:Data Retrieval + BioCatalogue:Identifier Retrieval + topic + This includes, for example, search, query and retrieval of molecular sequences and associated data. + topics + Data retrieval + beta12orEarlier + + + + + + + + Data handling + + Topic for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation. + beta12orEarlier + topics + edam + topic + bioinformatics + Data types, processing and visualisation + + + + + + + + + Data visualisation + + edam + bioinformatics + Data rendering and visualisation + Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data. + beta12orEarlier + topic + Data rendering + Data plotting + topics + + + + + + + + Nucleic acid thermodynamics + + Nucleic acid properties + DNA melting + edam + topic + This includes the study of thermal and conformational properties including DNA or DNA/RNA denaturation (melting). + Topic concerning the study of the thermodynamic properties of a nucleic acid. + topics + Nucleic acid denaturation + beta12orEarlier + bioinformatics + Nucleic acid physicochemistry + + + + + + + + Nucleic acid structure analysis + + + bioinformatics + edam + The processing and analysis of nucleic acid (secondary or tertiary) structural data. + topic + topics + beta12orEarlier + + + + + + + + RNA + + Topic concerning RNA sequences and structures. + topic + edam + bioinformatics + topics + beta12orEarlier + + + + + + + + Nucleic acid restriction + + + topics + bioinformatics + topic + edam + Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. + beta12orEarlier + + + + + + + + Mapping + + topic + edam + beta12orEarlier + topics + Topic concerning the mapping of complete (typically nucleotide) sequences. + bioinformatics + + + + + + + + Codon usage analysis + + bioinformatics + topic + edam + topics + Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on. + beta12orEarlier + + + + + + + + Translation + + Topic concerning the translation of mRNA into protein. + bioinformatics + beta12orEarlier + topic + edam + topics + + + + + + + + Gene finding + + BioCatalogue:Gene Prediction + bioinformatics + edam + Gene discovery + Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. + This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. + Gene prediction + topics + beta12orEarlier + topic + + + + + + + + Transcription + + BioCatalogue:Transcription Factors + bioinformatics + beta12orEarlier + topic + Topic concerning the transcription of DNA into mRNA. + edam + topics + + + + + + + + Promoters + + true + topic + edam + Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). + BioCatalogue:Promoter Prediction + beta13 + topics + bioinformatics + beta12orEarlier + + + + + + + + + Nucleic acid folding + + true + beta12orEarlier + edam + Topic concerning the folding (in 3D space) of nucleic acid molecules. + topic + bioinformatics + beta12orEarlier + topics + + + + + + + + + Gene structure and RNA splicing + + + topics + This includes splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. + RNA splicing + topic + Gene structure + beta12orEarlier + bioinformatics + edam + Topic concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons). + + + + + + + + Proteomics + + BioCatalogue:Proteomics + Protein expression + Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues). + bioinformatics + edam + Topic concerning the study of whole proteomes of organisms. + beta12orEarlier + topic + topics + + + + + + + + + Structural genomics + + + edam + beta12orEarlier + BioCatalogue:Structural Genomics + topic + topics + bioinformatics + Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. + + + + + + + + Protein properties + + topics + beta12orEarlier + Protein physicochemistry + Topic for the study of the physical and biochemical properties of peptides and proteins. + topic + edam + bioinformatics + + + + + + + + Protein interactions + + + topics + BioCatalogue:Protein Interaction + Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. + edam + beta12orEarlier + bioinformatics + This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. + topic + + + + + + + + Protein folding and stability + + bioinformatics + edam + beta12orEarlier + topic + topics + Topic concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation. + + + + + + + + Two-dimensional gel electrophoresis + + true + topics + beta12orEarlier + bioinformatics + beta13 + Topic concerning two-dimensional gel electrophoresis image and related data. + topic + edam + + + + + + + + + Mass spectrometry + + true + topic + topics + beta13 + Topic concerning mass spectrometry and related data. + beta12orEarlier + edam + bioinformatics + + + + + + + + + Protein microarrays + + true + beta13 + edam + beta12orEarlier + bioinformatics + topics + topic + Topic concerning protein microarray data. + + + + + + + + + + Protein hydropathy + + topic + bioinformatics + topics + beta12orEarlier + Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein. + edam + + + + + + + + Protein targeting and localization + + + edam + beta12orEarlier + topic + topics + bioinformatics + Topic for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. + + + + + + + + Protein cleavage sites and proteolysis + + bioinformatics + topic + edam + topics + beta12orEarlier + Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. + + + + + + + + Protein structure comparison + + true + beta12orEarlier + topics + Use this concept for methods that are exclusively for protein structure. + beta12orEarlier + bioinformatics + topic + Topic concerning the comparison of two or more protein structures. + edam + + + + + + + + + + Protein residue interaction analysis + + beta12orEarlier + bioinformatics + Protein residue interactions + topic + topics + The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. + edam + + + + + + + + Protein-protein interactions + + Topic concerning protein-protein interactions, protein complexes, protein functional coupling etc. + beta12orEarlier + bioinformatics + edam + topics + topic + + + + + + + + Protein-ligand interactions + + bioinformatics + topic + edam + topics + Topic concerning protein-ligand (small molecule) interactions. + BioCatalogue:Ligand Interaction + beta12orEarlier + + + + + + + + Protein-nucleic acid interactions + + topics + bioinformatics + topic + Topic concerning protein-DNA/RNA interactions. + edam + beta12orEarlier + + + + + + + + Protein design + + bioinformatics + topic + Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. + topics + beta12orEarlier + edam + + + + + + + + G protein-coupled receptors (GPCR) + + true + beta12orEarlier + beta12orEarlier + Topic concerning G-protein coupled receptors (GPCRs). + bioinformatics + topic + edam + topics + + + + + + + + + Carbohydrates + + edam + Topic concerning carbohydrates, typically including structural information. + topics + bioinformatics + beta12orEarlier + topic + + + + + + + + Lipids + + edam + topics + Topic concerning lipids and their structures. + beta12orEarlier + bioinformatics + topic + + + + + + + + Small molecules + + Topic concerning small molecules of biological significance, typically including structural information. + edam + topic + beta12orEarlier + CHEBI:23367 + bioinformatics + Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. + topics + + + + + + + + Sequence editing + + true + beta12orEarlier + Edit, convert or otherwise change a molecular sequence, either randomly or specifically. + edam + beta12orEarlier + bioinformatics + topic + topics + + + + + + + + + + Sequence composition analysis + + topic + topics + bioinformatics + beta12orEarlier + Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats. + edam + + + + + + + + Sequence motifs + + Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. + bioinformatics + topic + topics + Motifs + edam + beta12orEarlier + + + + + + + + Sequence comparison + + topic + bioinformatics + topics + BioCatalogue:Nucleotide Sequence Similarity + The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. + Topic concerning the comparison of two or more molecular sequences. + edam + beta12orEarlier + BioCatalogue:Protein Sequence Similarity + + + + + + + + Sequence sites and features + + beta12orEarlier + bioinformatics + topic + edam + topics + Topic concerning the positional features, such as functional and other key sites, in molecular sequences. + + + + + + + + Sequence database search + + true + beta12orEarlier + topic + edam + The query is a sequence-based entity such as another sequence, a motif or profile. + beta12orEarlier + Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). + topics + bioinformatics + + + + + + + + + Sequence clustering + + Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities. + topics + bioinformatics + topic + beta12orEarlier + edam + This includes systems that generate, process and analyse sequence clusters. + + + + + + + + Protein structural motifs and surfaces + + topic + topics + Protein surfaces + bioinformatics + beta12orEarlier + Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. + This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. + Structural motifs + Protein structural features + Protein structural motifs + edam + + + + + + + + Structural (3D) profiles + + Structural profiles + edam + bioinformatics + beta12orEarlier + topics + The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment. + topic + + + + + + + + Protein structure prediction + + + BioCatalogue:Protein Structure Prediction + edam + topic + topics + Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. + beta12orEarlier + bioinformatics + + + + + + + + Nucleic acid structure prediction + + + topic + BioCatalogue:Nucleotide Structure Prediction + BioCatalogue:Nucleotide Tertiary Structure + Nucleic acid folding + Topic concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure. + bioinformatics + edam + BioCatalogue:Nucleotide Secondary Structure + beta12orEarlier + topics + RNA/DNA structure prediction + + + + + + + + Ab initio structure prediction + + beta12orEarlier + bioinformatics + de novo protein structure prediction + edam + Topic for the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. + topics + topic + + + + + + + + Homology modelling + + topics + beta12orEarlier + topic + edam + Topic for the modelling of the three-dimensional structure of a protein using known sequence and structural data. + bioinformatics + Comparative modelling + + + + + + + + Molecular dynamics + + bioinformatics + beta12orEarlier + Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. + Molecular flexibility + edam + Molecular motions + topics + This includes resources concerning flexibility and motion in protein and other molecular structures. + topic + + + + + + + + Molecular docking + + Topic for modelling the structure of proteins in complex with small molecules or other macromolecules. + topics + bioinformatics + edam + topic + beta12orEarlier + + + + + + + + Protein secondary structure prediction + + + topic + beta12orEarlier + edam + Topic concerning the prediction of secondary or supersecondary structure of protein sequences. + topics + bioinformatics + BioCatalogue:Protein Secondary Structure + + + + + + + + Protein tertiary structure prediction + + + Topic concerning the prediction of tertiary structure of protein sequences. + beta12orEarlier + bioinformatics + edam + BioCatalogue:Protein Tertiary Structure + topic + topics + + + + + + + + Protein fold recognition + + topic + beta12orEarlier + bioinformatics + Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). + edam + topics + + + + + + + + Sequence alignment + + + bioinformatics + BioCatalogue:Protein Multiple Alignment + Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). + topic + BioCatalogue:Protein Pairwise Alignment + edam + beta12orEarlier + This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. + BioCatalogue:Nucleotide Multiple Alignment + BioCatalogue:Protein Sequence Alignment + topics + BioCatalogue:Nucleotide Pairwise Alignment + BioCatalogue:Nucleotide Sequence Alignment + + + + + + + + + Structure alignment + + + beta12orEarlier + This includes the generation, storage, analysis, rendering etc. of structure alignments. + edam + topics + bioinformatics + topic + Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). + Structure alignment generation + + + + + + + + Threading + + edam + beta12orEarlier + Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). + topics + bioinformatics + topic + Sequence-structure alignment + + + + + + + + Sequence profiles and HMMs + + Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. + beta12orEarlier + bioinformatics + Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment. + topics + edam + topic + + + + + + + + Phylogeny reconstruction + + topic + BioCatalogue:Tree Inference + topics + Currently too specific for the topic sub-ontology (but might be unobsoleted). + Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. + BioCatalogue:Evolutionary Distance Measurements + bioinformatics + beta12orEarlier + edam + + + + + + + + Phylogenomics + + + topics + edam + topic + Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. + bioinformatics + beta12orEarlier + + + + + + + + Virtual PCR + + true + Topic concerning simulated polymerase chain reaction (PCR). + topic + edam + topics + PCR + beta12orEarlier + bioinformatics + beta13 + Polymerase chain reaction + + + + + + + + + Sequence assembly + + bioinformatics + Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. + beta12orEarlier + topic + edam + topics + + + + + + + + Genetic variation + + + + Mutation and polymorphism + edam + bioinformatics + DNA variation + topics + beta12orEarlier + Topic concerning DNA sequence variation (mutation and polymorphism) data. + topic + + + + + + + + + Microarrays + + beta12orEarlier + topics + Topic concerning microarrays, for example, to process microarray data or design probes and experiments. + DNA microarrays + edam + topic + BioCatalogue:Microarrays + bioinformatics + + + + + + + + + Pharmacoinformatics + + topic + Computational pharmacology + bioinformatics + edam + Topic for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on. + beta12orEarlier + topics + + + + + + + + Transcriptomics + + + Gene expression resources + Gene expression profiling + Expression profiling + edam + Topic concerning primarily raw or processed gene (mRNA) expression (typically microarray) data, including the analysis of gene expression levels, by identifying, quantifying or comparing mRNA transcripts and the interpretation (in functional terms) of gene expression data. + Gene expression analysis + bioinformatics + http://edamontology.org/topic_0197 + topics + topic + beta12orEarlier + This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein. + + + + + + + + + Gene regulation + + Gene regulation resources + bioinformatics + beta12orEarlier + topic + edam + Topic concerning primarily the regulation of gene expression. + topics + + + + + + + + Pharmacogenomics + + + bioinformatics + Pharmacogenetics + topic + topics + Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. + edam + beta12orEarlier + + + + + + + + Drug design + + edam + bioinformatics + beta12orEarlier + topic + This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. + Topic concerning the design of drugs or potential drug compounds. + topics + + + + + + + + Fish + + edam + The resource may be specific to a fish, a group of fish or all fish. + topics + Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation. + bioinformatics + beta12orEarlier + topic + + + + + + + + Flies + + Fly + edam + topics + beta12orEarlier + topic + bioinformatics + Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation. + The resource may be specific to a fly, a group of flies or all flies. + + + + + + + + Mice or rats + + Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation. + topics + Mouse or rat + beta12orEarlier + topic + edam + bioinformatics + The resource may be specific to a group of mice / rats or all mice / rats. + + + + + + + + Worms + + beta12orEarlier + topics + Worm + bioinformatics + The resource may be specific to a worm, a group of worms or all worms. + edam + Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation. + topic + + + + + + + + Literature analysis + + topic + topics + BioCatalogue: Document Discovery + BioCatalogue: Literature retrieval + beta12orEarlier + The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. + bioinformatics + Literature search and analysis + Literature sources + edam + + + + + + + + Text mining + + BioCatalogue:Document Clustering + BioCatalogue:Document Similarity + edam + Text data mining + topic + BioCatalogue:Text Mining + beta12orEarlier + Topic concerning the analysis of the biomedical and informatics literature. + bioinformatics + topics + BioCatalogue:Named Entity Recognition + + + + + + + + Annotation + + edam + Ontology annotation + Topic for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary. + bioinformatics + BioCatalogue:Ontology Annotation + topics + BioCatalogue:Genome Annotation + beta12orEarlier + topic + + + + + + + + Data processing and validation + + topic + beta12orEarlier + Data file handling + Report processing + topics + Report handling + bioinformatics + This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. + edam + Topic concerning basic manipulations of files or reports of generic biological data. + File handling + + + + + + + + Sequence annotation + + true + edam + Annotate a molecular sequence. + bioinformatics + topics + beta12orEarlier + topic + beta12orEarlier + + + + + + + + + Genome annotation + + true + topic + topics + Annotate a genome. + beta12orEarlier + beta12orEarlier + bioinformatics + BioCatalogue:Genome Annotation + edam + + + + + + + + + + NMR + + true + Topic concerning raw NMR data. + edam + topic + bioinformatics + beta13 + topics + beta12orEarlier + + + + + + + + + Sequence classification + + Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. + topics + Topic concerning the classification of molecular sequences based on some measure of their similarity. + beta12orEarlier + topic + edam + bioinformatics + + + + + + + + Protein classification + + + + bioinformatics + beta12orEarlier + topic + edam + Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. + topics + + + + + + + + Sequence motif or profile + + true + beta12orEarlier + Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. + edam + This includes comparison, discovery, recognition etc. of sequence motifs. + topics + bioinformatics + topic + beta12orEarlier + + + + + + + + + + Protein modifications + + + edam + MOD:00000 + topic + bioinformatics + EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) + topics + GO:0006464 + beta12orEarlier + Topic concerning protein chemical modifications, e.g. post-translational modifications. + Protein post-translational modification + + + + + + + + Pathways, networks and models + + + Topic concerning biological pathways, networks and other models, including their construction and analysis. + BioCatalogue:Pathways + Network or pathway analysis + edam + http://edamontology.org/topic_3076 + beta13 + bioinformatics + BioCatalogue:Pathway Retrieval + topic + topics + + + + + + + + Informatics + + true + bioinformatics + topic + beta12orEarlier + beta12orEarlier + A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area. + edam + topics + + + + + + + + + Literature data resources + + + beta12orEarlier + topics + topic + edam + Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. + bioinformatics + + + + + + + + Laboratory resources + + topic + Topic concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. + beta12orEarlier + topics + edam + bioinformatics + + + + + + + + Cell culture resources + + beta12orEarlier + topics + Topic concerning general cell culture or data on a specific cell lines. + edam + topic + bioinformatics + + + + + + + + Ecoinformatics + + Topic concerning the application of information technology to the ecological and environmental sciences. + Computational ecology + edam + beta12orEarlier + bioinformatics + topic + topics + Ecological informatics + + + + + + + + + Electron microscopy + + true + edam + Topic concerning electron microscopy data. + bioinformatics + beta12orEarlier + topics + beta13 + topic + + + + + + + + + Cell cycle + + true + topic + beta12orEarlier + topics + edam + Topic concerning the cell cycle including key genes and proteins. + beta13 + bioinformatics + + + + + + + + + Peptides and amino acids + + bioinformatics + topics + edam + Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides. + topic + beta12orEarlier + + + + + + + + Organelle genes and proteins + + beta12orEarlier + bioinformatics + topics + edam + Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). + topic + + + + + + + + Ribosomal genes and proteins + + Ribosome genes and proteins + topic + bioinformatics + topics + Topic concerning ribosomes, typically of ribosome-related genes and proteins. + beta12orEarlier + edam + + + + + + + + Scents + + true + beta13 + edam + beta12orEarlier + topic + A database about scents. + topics + bioinformatics + + + + + + + + + Drugs and targets + + + topic + edam + topics + beta12orEarlier + Topic concerning the structures of drugs, drug target, their interactions and binding affinities. + bioinformatics + + + + + + + + Genome, proteome and model organisms + + + + topic + General information on or more organisms, genomes (including molecular sequences and map, genes and annotation) and proteomes may be included. + topics + beta12orEarlier + Genome map + edam + bioinformatics + Topic concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms. + + + + + + + + Genomics + + BioCatalogue:Functional Genomics + beta12orEarlier + Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. + bioinformatics + topic + topics + BioCatalogue:Genomics + edam + + + + + + + + + Genes, gene family or system + + + bioinformatics + topics + edam + topic + Topic concerning particular gene(s), gene system or groups of genes. + beta12orEarlier + + + + + + + + Chromosomes + + edam + Topic concerning chromosomes. + beta12orEarlier + bioinformatics + topics + topic + + + + + + + + Genotype and phenotype + + bioinformatics + beta12orEarlier + topics + edam + Genotyping + Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. + Genotype and phenotype resources + topic + + + + + + + + Gene expression and microarray + + true + topic + beta12orEarlier + bioinformatics + edam + topics + beta12orEarlier + Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. + + + + + + + + + + Probes and primers + + + edam + beta12orEarlier + bioinformatics + topics + Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). + topic + + + + + + + + + Disease resources + + beta12orEarlier + Topic concerning diseases. + topics + edam + bioinformatics + topic + + + + + + + + Specific protein resources + + topic + beta12orEarlier + topics + Specific protein + edam + Topic concerning a particular protein, protein family or other group of proteins. + bioinformatics + + + + + + + + Taxonomy + + bioinformatics + topic + Topic concerning organism classification, identification and naming. + topics + beta12orEarlier + edam + + + + + + + + Protein sequence analysis + + + topic + topics + BioCatalogue:Protein Sequence Analysis + Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. + edam + beta12orEarlier + bioinformatics + + + + + + + + Nucleic acid sequence analysis + + + topic + topics + edam + bioinformatics + Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles. + BioCatalogue:Nucleotide Sequence Analysis + beta12orEarlier + + + + + + + + Repeat sequences + + + Repeat sequence + edam + topics + beta12orEarlier + bioinformatics + topic + BioCatalogue:Repeats + Topic concerning the repetitive nature of molecular sequences. + + + + + + + + Low complexity sequences + + + edam + topics + beta12orEarlier + bioinformatics + Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity. + topic + + + + + + + + Proteome + + true + edam + bioinformatics + beta13 + topics + beta12orEarlier + Topic concerning a specific proteome including protein sequences and annotation. + topic + + + + + + + + + DNA + + + The DNA sequences might be coding or non-coding sequences. + bioinformatics + topics + edam + topic + Topic concerning DNA sequences and structure, including processes such as methylation and replication. + beta12orEarlier + DNA analysis + + + + + + + + mRNA, EST or cDNA database + + beta12orEarlier + edam + mRNA, EST or cDNA + topics + Transcriptome database + Topic concerning data resources for messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences. + topic + Transcriptome + bioinformatics + + + + + + + + Functional and non-coding RNA + + bioinformatics + topic + beta12orEarlier + edam + Non-coding RNA + For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). + Topic concerning functional or non-coding RNA sequences. + Functional RNA + topics + + + + + + + + rRNA + + topics + bioinformatics + Topic concerning one or more ribosomal RNA (rRNA) sequences. + beta12orEarlier + edam + topic + + + + + + + + tRNA + + topic + bioinformatics + Topic concerning one or more transfer RNA (tRNA) sequences. + edam + beta12orEarlier + topics + + + + + + + + Protein secondary structure + + topics + This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. + bioinformatics + topic + Topic concerning protein secondary structure or secondary structure alignments. + edam + Protein secondary structure analysis + beta12orEarlier + + + + + + + + RNA structure and alignment + + beta12orEarlier + Topic concerning RNA secondary or tertiary structure and alignments. + RNA alignment + edam + topics + RNA structure alignment + bioinformatics + topic + RNA structure + + + + + + + + Protein tertiary structure + + topics + beta12orEarlier + Protein tertiary structure analysis + Topic concerning protein tertiary structures. + edam + topic + bioinformatics + + + + + + + + Nucleic acid classification + + + + topics + beta12orEarlier + topic + bioinformatics + Topic concerning nucleic acid classification (typically sequence classification). + edam + + + + + + + + Protein families + + + Topic concerning primarily proteins that have been classified as members of a protein family (or other grouping). + A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. + beta12orEarlier + topics + Protein sequence classification + Protein secondary + topic + edam + bioinformatics + + + + + + + + Protein domains and folds + + + topic + BioCatalogue:Domains + topics + edam + bioinformatics + Topic concerning protein tertiary structural domains and folds. + beta12orEarlier + + + + + + + + Nucleic acid sequence alignment + + + bioinformatics + topic + Topic concerning nucleotide sequence alignments. + edam + beta12orEarlier + topics + + + + + + + + Protein sequence alignment + + + topics + topic + A sequence profile typically represents a sequence alignment. + Topic concerning protein sequence alignments. + bioinformatics + edam + beta12orEarlier + + + + + + + + Nucleic acid sites and features + + + Nucleic acid functional sites + topics + Topic concerning positional features such as functional sites in nucleotide sequences. + bioinformatics + topic + Nucleic acid features + edam + beta12orEarlier + + + + + + + + Protein sites and features + + + edam + Protein functional sites + topic + topics + Topic concerning positional features such as functional sites in protein sequences. + beta12orEarlier + Protein sequence features + bioinformatics + + + + + + + + Transcription factors and regulatory sites + + + + + + + Topic concerning transcription factors; proteins that bind to DNA and control transcription of DNA to mRNA, either promoting (as an activator) or blocking (as a repressor) the binding to DNA of RNA polymerase, and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. + This includes promoters, enhancers, silencers and boundary elements / insulators. This includes sequence and structural information, binding profiles etc, and may also include the transcription factor binding site in DNA. + beta12orEarlier + Transcriptional regulatory sites + bioinformatics + Transcription factor and binding site + Transcription factors + edam + topic + topics + + + + + + + + Phosphorylation sites + + true + beta12orEarlier + Topic concerning protein phosphorylation and phosphorylation sites in protein sequences. + edam + topic + topics + bioinformatics + 1.0 + + + + + + + + + + Metabolic pathways + + + topic + Topic concerning metabolic pathways. + edam + bioinformatics + beta12orEarlier + topics + + + + + + + + Signaling pathways + + topic + beta12orEarlier + Topic concerning signaling pathways. + topics + edam + bioinformatics + + + + + + + + Protein and peptide identification + + + + beta12orEarlier + Peptide identification and proteolysis + edam + bioinformatics + Proteomics data resources + Topic concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays. + Proteomics data + This includes the results of any methods that separate, characterize and identify expressed proteins. + topics + topic + + + + + + + + Workflows + + true + topics + 1.0 + bioinformatics + beta12orEarlier + Topic concerning biological or biomedical analytical workflows or pipelines. + topic + edam + + + + + + + + Data types and objects + + true + topics + 1.0 + beta12orEarlier + topic + bioinformatics + Topic concerning structuring data into basic types and (computational) objects. + edam + + + + + + + + + Biological models + + beta12orEarlier + topics + Topic concerning mathematical or other models of biological processes. + bioinformatics + topic + This includes databases of models and methods to construct or analyse a model. + edam + BioCatalogue:Model Creation + + + + + + + + Mitochondrial genes and proteins + + Mitochondria genes and proteins + topic + topics + Topic concerning mitochondria, typically of mitochondrial genes and proteins. + bioinformatics + beta12orEarlier + edam + + + + + + + + Plants + + bioinformatics + topics + beta12orEarlier + Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. + topic + edam + The resource may be specific to a plant, a group of plants or all plants. + Plant + + + + + + + + Viruses + + bioinformatics + The resource may be specific to a virus, a group of viruses or all viruses. + topics + beta12orEarlier + Virus + Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. + edam + topic + + + + + + + + Fungi + + topics + Fungal + The resource may be specific to a fungus, a group of fungi or all fungi. + bioinformatics + Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. + edam + topic + beta12orEarlier + + + + + + + + Pathogens + + Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. + edam + bioinformatics + The resource may be specific to a pathogen, a group of pathogens or all pathogens. + beta12orEarlier + topics + topic + Pathogen + + + + + + + + Arabidopsis + + topic + beta12orEarlier + bioinformatics + Topic concerning Arabidopsis-specific data. + topics + edam + + + + + + + + Rice + + beta12orEarlier + Topic concerning rice-specific data. + topics + edam + bioinformatics + topic + + + + + + + + Genetic mapping and linkage + + Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. + Genetic linkage + topics + topic + edam + bioinformatics + beta12orEarlier + Linkage mapping + + + + + + + + Comparative genomics + + BioCatalogue:Comparative Genomics + bioinformatics + topic + edam + beta12orEarlier + topics + Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. + + + + + + + + Mobile genetic elements + + edam + bioinformatics + Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. + beta12orEarlier + topic + topics + + + + + + + + Human disease + + true + Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease. + bioinformatics + edam + beta12orEarlier + topic + topics + beta13 + + + + + + + + + Immunoinformatics + + Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. + edam + beta12orEarlier + topics + bioinformatics + Computational immunology + topic + + + + + + + + + + Membrane proteins + + Topic concerning a protein or region of a protein that spans a membrane. + topics + bioinformatics + Transmembrane proteins + topic + beta12orEarlier + edam + + + + + + + + Enzymes and reactions + + topics + bioinformatics + edam + beta12orEarlier + topic + Topic concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. + + + + + + + + Structure comparison + + beta12orEarlier + bioinformatics + Topic concerning the comparison of two or more molecular structures. + topics + This might involve comparison of secondary or tertiary (3D) structural information. + edam + topic + + + + + + + + Protein function analysis + + beta12orEarlier + edam + Topic for the study of protein function. + bioinformatics + topics + topic + + + + + + + + Prokaryotes and archae + + Prokaryote and archae + Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. + beta12orEarlier + topic + topics + bioinformatics + edam + The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. + + + + + + + + Protein databases + + + topics + Protein data resources + Topic concerning protein data resources. + beta12orEarlier + topic + bioinformatics + edam + + + + + + + + Structure determination + + Raw structural data analysis + Structure assignment + topics + Structural determination + edam + Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, including the assignment or modelling of molecular structure from such data. + beta12orEarlier + topic + Structural assignment + bioinformatics + + + + + + + + Cell biology resources + + Topic concerning cells, such as key genes and proteins involved in the cell cycle. + bioinformatics + edam + topic + topics + beta12orEarlier + + + + + + + + Classification + + true + edam + topics + Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. + beta12orEarlier + bioinformatics + topic + beta13 + + + + + + + + + Lipoproteins + + topic + topics + beta12orEarlier + Topic concerning lipoproteins (protein-lipid assemblies). + bioinformatics + edam + + + + + + + + Phylogeny visualisation + + true + bioinformatics + edam + topics + beta12orEarlier + beta12orEarlier + topic + BioCatalogue:Tree Display + Visualise a phylogeny, for example, render a phylogenetic tree. + + + + + + + + + Chemoinformatics + + edam + bioinformatics + Chemical informatics + BioCatalogue:Chemoinformatics + topic + Computational chemistry + topics + beta12orEarlier + Cheminformatics + Topic for the application of information technology to chemistry. + + + + + + + + Systems biology + + BioCatalogue:Systems Biology + topic + edam + bioinformatics + topics + Topic concerning the holistic modelling and analysis of biological systems and the interactions therein. + beta12orEarlier + + + + + + + + + + Biostatistics + + Topic for the application of statistical methods to biological problems. + beta12orEarlier + BioCatalogue:Biostatistics + Biometry + bioinformatics + topics + topic + Biometrics + edam + + + + + + + + + + Structure database search + + true + edam + Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). + topic + beta12orEarlier + beta12orEarlier + bioinformatics + topics + The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. + + + + + + + + + Molecular modelling + + + edam + Topic for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. + beta12orEarlier + topics + bioinformatics + topic + + + + + + + + Protein function prediction + + Topic concerning the prediction of functional properties of a protein. + bioinformatics + topics + topic + BioCatalogue:Function Prediction + edam + beta12orEarlier + + + + + + + + SNPs + + A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. + Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. + edam + bioinformatics + beta12orEarlier + topics + topic + + + + + + + + Transmembrane protein prediction + + true + topics + beta12orEarlier + beta12orEarlier + Predict transmembrane domains and topology in protein sequences. + topic + bioinformatics + edam + + + + + + + + + + Nucleic acid structure comparison + + true + beta12orEarlier + beta12orEarlier + topic + Use this concept for methods that are exclusively for nucleic acid structures. + topics + Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. + edam + bioinformatics + + + + + + + + + + Cancer + + Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer. + topics + edam + beta12orEarlier + Cancer resources + topic + bioinformatics + + + + + + + + Toxins and targets + + + beta12orEarlier + topic + Topic concerning structural and associated data for toxic chemical substances. + topics + bioinformatics + edam + + + + + + + + Tool topic + + true + beta12orEarlier + edam + topic + bioinformatics + A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. + topics + beta12orEarlier + + + + + + + + + Study topic + + true + beta12orEarlier + bioinformatics + edam + topic + topics + beta12orEarlier + A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. + + + + + + + + + Nomenclature + + topics + bioinformatics + beta12orEarlier + Topic concerning biological nomenclature (naming), symbols and terminology. + edam + topic + + + + + + + + Disease genes and proteins + + + edam + beta12orEarlier + Topic concerning the genes, gene variations and proteins involved in one or more specific diseases. + topic + bioinformatics + topics + + + + + + + + Protein structure analysis + + + + + Topic concerning protein secondary or tertiary structural data and/or associated annotation. + edam + beta12orEarlier + http://edamontology.org/topic_3040 + Protein structure + topics + bioinformatics + topic + + + + + + + + Humans + + bioinformatics + edam + topic + The resource may be specific to a human, a group of humans or all humans. + Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. + Human + topics + beta12orEarlier + + + + + + + + Gene resources + + + Gene database + Informatics resource (typically a database) primarily focussed on genes. + edam + bioinformatics + topic + beta12orEarlier + topics + Gene resource + + + + + + + + Yeast + + edam + topics + topic + beta12orEarlier + Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. + bioinformatics + + + + + + + + Eukaryotes + + beta12orEarlier + edam + The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. + Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. + topic + Eukaryote + topics + bioinformatics + + + + + + + + Invertebrates + + Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. + topics + bioinformatics + beta12orEarlier + The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. + edam + topic + + + + + + + + Vertebrates + + beta12orEarlier + Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. + topics + topic + bioinformatics + edam + The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. + Vertebrate + + + + + + + + Unicellular eukaryotes + + bioinformatics + Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. + Unicellular eukaryote + topics + The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. + beta12orEarlier + topic + edam + + + + + + + + Protein structure alignment + + + topics + beta12orEarlier + Topic concerning protein secondary or tertiary structure alignments. + edam + topic + bioinformatics + + + + + + + + X-ray crystallography + + true + bioinformatics + topics + edam + beta12orEarlier + topic + Topic concerning X-ray crystallography data. + beta13 + + + + + + + + + Ontologies, nomenclature and classification + + topics + beta12orEarlier + Topic concerning conceptualisation, categorisation and naming, or that help to identify, group, or name things in a structured way according to some schema based on observable relationships. + topic + edam + bioinformatics + + + + + + + + + Immunity genes, immunoproteins and antigens + + + edam + topics + beta12orEarlier + bioinformatics + This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." + Immunoproteins and immunopeptides + topic + Topic concerning immunity-related genes, proteins and their ligands. + + + + + + + + Molecules + + true + edam + beta12orEarlier + beta12orEarlier + Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. + topics + topic + CHEBI:23367 + bioinformatics + + + + + + + + Toxicoinformatics + + Computational toxicology + topic + Topic concerning the adverse effects of chemical substances on living organisms. + beta12orEarlier + edam + bioinformatics + topics + + + + + + + + High-throughput sequencing + + true + topics + beta12orEarlier + beta13 + edam + bioinformatics + Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. + topic + Next-generation sequencing + + + + + + + + + Structural clustering + + beta12orEarlier + topics + topic + bioinformatics + Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. + Structure classification + edam + + + + + + + + Gene regulatory networks + + + topic + beta12orEarlier + topics + edam + bioinformatics + Topic concerning gene regulatory networks. + + + + + + + + Disease (specific) + + true + topic + edam + bioinformatics + beta12orEarlier + topics + Informatics resources dedicated to one or more specific diseases (not diseases in general). + beta12orEarlier + + + + + + + + + Nucleic acid design + + bioinformatics + topics + topic + edam + beta12orEarlier + Topic for the design of nucleic acid sequences with specific conformations. + + + + + + + + Primer or probe design + + beta13 + bioinformatics + Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes. + edam + topics + topic + + + + + + + + Structure databases + + + topic + Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. + Structure data resources + bioinformatics + edam + topics + beta13 + + + + + + + + Nucleic acid structure + + edam + topics + bioinformatics + Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. + beta13 + topic + + + + + + + + Sequence databases + + + edam + bioinformatics + Sequence data resources + topics + beta13 + Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles. + Sequence data resource + Sequence data + topic + + + + + + + + Nucleic acid sequences + + topic + topics + bioinformatics + edam + Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + beta13 + + + + + + + + Protein sequences + + + edam + beta13 + topic + topics + BioCatalogue:Protein Sequence Analysis + bioinformatics + Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + + + + + + + + Protein interaction networks + + + Topic concerning protein-protein interaction networks. + edam + topic + topics + beta13 + bioinformatics + + + + + + + + Molecular biology reference + + topic + bioinformatics + BioCatalogue: Document Discovery + topics + BioCatalogue: Literature retrieval + Topic concerning general molecular biology information extracted from the literature. + edam + beta13 + + + + + + + + Mammals + + bioinformatics + topics + Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. + beta13 + topic + edam + + + + + + + + Biodiversity + + topics + Biodiversity data resources + Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet. + Biodiversity data resource + topic + bioinformatics + beta13 + edam + + + + + + + + + Sequence clusters and classification + + beta13 + Sequence clusters + topic + Sequence families + Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity. + edam + topics + bioinformatics + This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. + + + + + + + + Genetics + + bioinformatics + beta13 + edam + Genetics data resources + topic + topics + Topic concerning the study of genes, genetic variation and heredity in living organisms. + + + + + + + + + Quantitative genetics + + Topic concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight). + topics + edam + bioinformatics + topic + beta13 + + + + + + + + Population genetics + + topics + topic + beta13 + Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. + edam + bioinformatics + + + + + + + + Regulatory RNA + + beta13 + bioinformatics + Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). + edam + topic + topics + Micro RNAs are short single stranded RNA molecules that regulate gene expression. + + + + + + + + Documentation and help + + bioinformatics + beta13 + topics + Topic concerning documentation and getting help. + topic + edam + + + + + + + + Genetic organisation + + topics + bioinformatics + edam + beta13 + Topic concerning the structural and functional organisation of genes and other genetic elements. + topic + + + + + + + + Medical informatics resources + + Health and disease + beta13 + Topic for the application of information technology to health, disease and biomedicine. + Healthcare informatics + Biomedical informatics + edam + Clinical informatics + Health informatics + bioinformatics + topics + topic + + + + + + + + Developmental biology resources + + beta13 + bioinformatics + topic + edam + Topic concerning how organisms grow and develop. + topics + + + + + + + + Embryology resources + + topic + Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. + topics + beta13 + edam + bioinformatics + + + + + + + + Anatomy resources + + topics + topic + Topic concerning the structures of living organisms. + beta13 + bioinformatics + edam + + + + + + + + Literature and reference + + bioinformatics + edam + Topic concerning the scientific literature, reference information and documentation. + topics + topic + beta13 + + + + + + + + + Biological science resources + + topics + Phenotype resource + bioinformatics + topic + edam + Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. + beta13 + + + + + + + + Biological data resources + + Biological data resource + topics + bioinformatics + Biological databases + topic + beta13 + edam + A topic concerning primarily a specific type of bioinformatics data, typically the broad category of content of a digital archives of biological data, including databanks, databases proper, web portals and other data resources. + + + + + + + + + Sequence feature detection + + edam + beta13 + topics + Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences. + topic + bioinformatics + + + + + + + + + Nucleic acid feature detection + + + edam + beta13 + topic + Topic concerning the detection of positional features such as functional sites in nucleotide sequences. + bioinformatics + topics + + + + + + + + Protein feature detection + + + topic + edam + bioinformatics + topics + Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites. + beta13 + + + + + + + + Biological system modelling + + Topic for modelling biological systems in mathematical terms. + beta13 + topics + BioCatalogue:Model Execution + bioinformatics + topic + BioCatalogue:Model Analysis + edam + + + + + + + + Data acquisition and deposition + + Topic concerning the acquisition and deposition of biological data. + edam + Database submission + beta13 + bioinformatics + topics + topic + + + + + + + + Gene and protein resources + + + topic + topics + Genes and proteins resources + bioinformatics + Topic concerning specific genes and their encoded proteins or a related group of such genes and proteins. + beta13 + edam + + + + + + + + Sequencing + + topics + bioinformatics + 1.1 + topic + Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. + edam + + + + + + + + + ChIP-seq + + + Chip-sequencing + 1.1 + Chip seq + Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. + bioinformatics + topics + edam + Chip sequencing + topic + + + + + + + + RNA-Seq + + + This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. + WTSS + topics + A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. + Small RNA-Seq + edam + bioinformatics + 1.1 + topic + Whole transcriptome shotgun sequencing + RNA-seq + Small RNA-seq + + + + + + + + DNA methylation + + topic + 1.1 + bioinformatics + topics + edam + Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. + + + + + + + + + Metabolomics + + Topic concerning the study of metabolites and the chemical processes they are involved in, especially the systematic study of the chemical fingerprints of specific cellular processes. + bioinformatics + 1.1 + topic + edam + topics + + + + + + + + + Epigenomics + + A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. + bioinformatics + topics + edam + 1.1 + Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. + topic + Epigenetics + + + + + + + + + Metagenomics + + + 1.1 + edam + Topic concerning the study of genetic material recovered from environmental samples. + bioinformatics + topic + Environmental genomics + Ecogenomics + topics + Community genomics + + + + + + + + + Structural variation + + + Genomic structural variation + edam + bioinformatics + Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. + 1.1 + topic + topics + + + + + + + + DNA packaging + + + topic + Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. + topics + edam + beta12orEarlier + bioinformatics + + + + + + + + + DNA-Seq + + topics + DNA-seq + edam + bioinformatics + A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. + 1.1 + topic + + + + + + + + RNA-Seq alignment + + topics + beta12orEarlier + topic + bioinformatics + RNA-seq alignment + Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. + edam + + + + + + + + ChIP-on-chip + + + ChIP-chip + 1.1 + Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. + edam + topics + topic + bioinformatics + + + + + + + + Obsolete concept (EDAM) + + + true + An obsolete concept (redefined in EDAM). + Needed for conversion to the OBO format. + 1.2 / http://www.geneontology.org/formats/oboInOwl + + + + + +