From ec4637752a71ecb4914f8e1a680f3bcd820e4521 Mon Sep 17 00:00:00 2001 From: matuskalas Date: Tue, 1 Nov 2016 03:41:35 +0100 Subject: [PATCH] History of releases: 1.0 --- releases/EDAM.obo | 28680 +++++++++++++++++++++++++++------------------------- 1 file changed, 14625 insertions(+), 14055 deletions(-) diff --git a/releases/EDAM.obo b/releases/EDAM.obo index 665b1ef..730d5ef 100644 --- a/releases/EDAM.obo +++ b/releases/EDAM.obo @@ -1,860 +1,505 @@ format-version: 1.2 -date: 15:01:2011 15:01 -data-version: Beta13 -subsetdef: topic "Topic" -subsetdef: data "Data" -subsetdef: format "Format" -subsetdef: identifier "Identifier" -subsetdef: operation "Operation" -! Use for mapping to "global" id space(s) e.g.: -! idspace: EDAM http://purl.org/edam/ "EDAM concepts" -! NEXT term number is 0003155 -! xref: WHATIF: CorrectedPDBasXML -! xref:http://www.geneontology.org/doc/GO.xrf_abbs: FB -! xref:Moby:GI_Gene ! xref: Moby_namespace:iHOPorganism -! xref: SO:0000348 -! xref: BioCatalogue:Protein Multiple Alignment -! xref: GO:0006464 ! protein modification process -! regex: Regular expression for validating a "data<-identifier" value. -! spec: URL of format specification for a "format" term -! seealso: Ontology concept ID of concept in external ontology for 'fine-grained' annotation -! {cardinality=1, minCardinality=1, maxCardinality=1} +data-version: 1.0 +date: 13:01:2012 18:00 ! Always GMT (UTC) or British Summer Time +saved-by: Matus Kalas +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" +default-relationship-id-prefix: EDAM +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. +remark: NB.! This is a version for the NCBO BioPortal with all attribute modifiers commented out (due to a current 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_1.0.obo (version 1.0). + + + + + + + + ! ! Relations ! -[Typedef] -id: has_topic -name: has_topic -def: "'Data' or 'Operation' is within the scope of a 'Topic'." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: is_topic_of -domain: EDAM:0000004 ! Operation -domain: EDAM:0000006 ! Data -range: EDAM:0000003 ! Topic -! Note: second 'domain' line is not visible in OBOEdit [Typedef] id: has_input -name: has_input -def: "An 'Operation' consumes a certain type of 'Data'." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true +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 -domain: EDAM:0000004 ! Operation -range: EDAM:0000006 ! Data +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: has_output -name: has_output -def: "An 'Operation' produces a certain type of 'Data'." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: is_output_of -domain: EDAM:0000004 ! Operation -range: EDAM:0000006 ! Data +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_format -name: has_format -def: "'Data' has a certain 'Format'." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: is_format_of -domain: EDAM:0000006 ! Data -range: EDAM:0001915 ! Format +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: has_identifier -name: has_identifier -def: "'Data' is identified by an 'Identifier'." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: is_identifier_of -domain: EDAM:0000006 ! Data -range: EDAM:0000842 ! Identifier +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. -! For annotating tools [Typedef] -id: has_operation -name: has_operation -def: "A tool has an 'Operation'." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -range: EDAM:0000004 ! Operation +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_format_of -name: is_format_of -def: "A data 'Format' is a format of a certain type of 'Data'." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: has_format -domain: EDAM:0001915 ! Format -range: EDAM:0000006 ! Data +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: is_identifier_of -name: is_identifier_of -def: "A data 'Identifier' is an identifier of a certain type of 'Data'." [EDAM:EBI] -is_anti_symmetric: true +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_transitive: true -inverse_of: has_identifier -domain: EDAM:0000842 ! Identifier -range: EDAM:0000006 ! Data +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_topic_of -name: is_topic_of -def: "'Topic' is_topic_of 'Data' or 'Operation'." [EDAM:EBI] -is_anti_symmetric: true +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_transitive: true -inverse_of: has_topic -domain: EDAM:0000003 ! Topic -range: EDAM:0000003 ! Topic +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: is_input_of -name: is_input_of -def: "'Data' is an input of an 'Operation'." [EDAM:EBI] -is_anti_symmetric: true +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_transitive: true -inverse_of: has_input -domain: EDAM:0000006 ! Data -range: EDAM:0000004 ! Operation +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_output_of -name: is_output_of -def: "'Data' is an output of an 'Operation'." [EDAM:EBI] -is_anti_symmetric: true +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_transitive: true -inverse_of: has_output -domain: EDAM:0000006 ! Data -range: EDAM:0000004 ! Operation - - +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: regex -name: regex -is_metadata_tag: true +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: spec -name: spec -is_metadata_tag: true +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. -[Typedef] -id: seealso -name: seealso -is_metadata_tag: true -! -! Top-level terms (sub-ontologies) -! - -[Term] -id: EDAM:0000003 -name: Topic -namespace: topic -def: "A broad category within bioinformatics that covers one or (typically) a combination of fields of study, types of data, processing, analysis or technology." [EDAM:EBI "EMBRACE definition"] -subset: topic - -[Term] -id: EDAM:0000004 -name: Operation -namespace: operation -def: "A function or process performed by a tool; what is done, but not (typically) how or in what context." [EDAM:EBI "EMBRACE definition"] -subset: operation - -[Term] -id: EDAM:0000006 -name: Data -namespace: data -alt_id: EDAM:0003030 -def: "A type of data in common use in bioinformatics." [EDAM:EBI "EMBRACE definition"] -subset: data - - -[Term] -id: EDAM:0003031 -name: Core data -namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: Core data entities typically have a format and may be identified by an accession number. -subset: data -is_a: EDAM:0000006 ! Data - - -[Term] -id: EDAM:0001915 -name: Format -namespace: format -def: "A specific layout for encoding a specific type of data in a computer file or memory." [EDAM:EBI "EMBRACE definition"] -subset: format - -[Term] -id: EDAM:0000842 -name: Identifier -namespace: identifier -alt_id: EDAM:0002860 -alt_id: EDAM:0002861 -alt_id: EDAM:0002926 -def: "A short numerical or textual label that identifies (typically uniquely) something such as data, a resource or a biological entity." [EDAM:EBI "EMBRACE definition"] -comment: This term is used for datatypes with the sole purpose of identification. It is not used for datatypes which contain other fields not related to identification. Identifiers typically are enumerated string (a string with one of a limited set of values) or are strings that are conformant to a regular expression. An ID is not necessarily stable or persistent over time, for example between different versions of a database. -subset: identifier -is_a: EDAM:0000006 ! Data - - -[Term] -id: EDAM:0000002 -name: Biological entity -namespace: entity -def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things or an observable phenomenon or occurrence." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true ! -! Biological entity +! Concept metadata tags, modifiers, and qualifiers ! -[Term] -id: EDAM:0000008 -name: Undefined -namespace: entity -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0002199 -name: Physical entity -namespace: entity -def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000012 -name: Phenomenon -namespace: entity -def: "An observable biological occurrence or event with a physical basis." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000009 -name: Discrete entity -namespace: entity -def: "Any biological thing with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000010 -name: Entity feature -namespace: entity -def: "A physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000011 -name: Entity collection -namespace: entity -def: "A collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000013 -name: Molecular entity -namespace: entity -def: "Any atom, molecule or molecular complex with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0000883 ! Structure -is_obsolete: true - -[Term] -id: EDAM:0000014 -name: Atom -namespace: entity -def: "The basic unit of matter consisting of negatively charged electrons bound by electromagnetic force to a nucleus of protons and neutrons." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000015 -name: Small molecule -namespace: entity -def: "Any small molecule." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000016 -name: Biopolymer -namespace: entity -def: "A single organic macromolecule made up of monomeric units." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0002044 ! Sequence -is_obsolete: true - -[Term] -id: EDAM:0000017 -name: Molecular complex -namespace: entity -def: "Two or more whole molecules in association with one another." [EDAM:EBI "EMBRACE definition"] -synonym: "Molecular assembly" EXACT [] -is_obsolete: true - -[Term] -id: EDAM:0000018 -name: Biomonomer -namespace: entity -def: "A small organic molecule that can chemically bond to other monomers to form a biopolymer." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000019 -name: Ligand -namespace: entity -def: "A molecule that can bind and form a complex with a biopolymer, typically a protein." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000020 -name: Drug -namespace: entity -def: "A substance that changes the normal functioning of an organism." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0002577 -name: Toxin -namespace: entity -def: "A poisonous substance produced by living cells or organisms." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000021 -name: Amino acid -namespace: entity -def: "The building block of proteins, an alpha amino acid consists of a carbon atom (C-alpha) attached to a hydrogen atom, an amino group, a carboxylate group and one of (typically) 20 common R-groups (side-chain)." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000022 -name: Nucleotide -namespace: entity -def: "The building block of nucleic acids, a nucleotide consists of a nucleobase (nitrogenous base, either a purine or pyrimidine), a five-carbon sugar (either ribose or 2'-deoxyribose), and one to three phosphate groups." [EDAM:EBI "EMBRACE definition"] -synonym: "Base" EXACT [] -xref: SO:0001236 -is_obsolete: true - -[Term] -id: EDAM:0000023 -name: Monosaccharide -namespace: entity -def: "The building block of polysaccharides, a monosaccharide is an aldehyde or ketone with hydroxyl groups." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000024 -name: Nucleic acid -namespace: entity -def: "An organic polymer of nucleotide monomers in an unbranched chain, bound together by covalent bonds." [EDAM:EBI "EMBRACE definition"] -synonym: "Polynucleotide chain" EXACT [] -synonym: "Polynucleotide" EXACT [] -xref: SO:0000348 -! relationship: has_attribute EDAM:0001207 ! Nucleotide sequence -! relationship: has_attribute EDAM:0001459 ! Nucleic acid structure -is_obsolete: true - -[Term] -id: EDAM:0000025 -name: Polypeptide -namespace: entity -def: "An organic polymer of alpha amino acid residues in an unbranched chain, bound together by peptide bonds." [EDAM:EBI "EMBRACE definition"] -synonym: "Polypeptide chain" EXACT [] -! relationship: has_attribute EDAM:0001208 ! Protein sequence -! relationship: has_attribute EDAM:0001460 ! Protein structure -is_obsolete: true - -[Term] -id: EDAM:0000026 -name: Polysaccharide -namespace: entity -def: "An organic polymer of either mono- or di-saccharide subunits in an unbranched chain, bound together by glycosidic bonds." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000027 -name: Oligonucleotide -namespace: entity -def: "An organic polymer of nucleotide monomers in a short (typically less than 30 subunits) unbranched chain, bound together by covalent bonds." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0001207 ! Nucleotide sequence -is_obsolete: true - -[Term] -id: EDAM:0000028 -name: DNA -namespace: entity -def: "A deoxyribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] -xref: SO:0000352 -! relationship: has_attribute EDAM:0001212 ! DNA sequence -! relationship: has_attribute EDAM:0001464 ! DNA structure -is_obsolete: true - -[Term] -id: EDAM:0000029 -name: RNA -namespace: entity -def: "A ribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] -xref: SO:0000356 -! relationship: has_attribute EDAM:0001213 ! RNA sequence -! relationship: has_attribute EDAM:0001465 ! RNA structure -is_obsolete: true - -[Term] -id: EDAM:0000030 -name: Mobile genetic element -namespace: entity -def: "A DNA molecule that can move around within a genome." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0002010 -name: cDNA -namespace: entity -def: "A deoxyribonucleic acid molecule synthesises by reverse transcriptase from an RNA template." [EDAM:EBI "EMBRACE definition"] -xref: SO:0000756 -! relationship: has_attribute EDAM:0001212 ! DNA sequence -! relationship: has_attribute EDAM:0001464 ! DNA structure -is_obsolete: true - -[Term] -id: EDAM:0000031 -name: Transposon -namespace: entity -def: "A DNA sequence that can undergo transposition or move to different positions in the genome of a single cell." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000032 -name: Plasmid -namespace: entity -def: "A DNA molecule existing outside a chromosome and capable of independent replication." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000033 -name: Retrotransposon -namespace: entity -def: "A DNA element that can amplify itself in a genome, by copying itself to RNA then back to DNA using a reverse transcriptase." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000034 -name: Insertion sequence -namespace: entity -def: "A DNA sequence that is smaller than most other transposable elements and which codes only for proteins involved in transposition." [EDAM:EBI "EMBRACE definition"] -synonym: "Insertion sequence element" EXACT [] -synonym: "IS element" EXACT [] -is_obsolete: true - -[Term] -id: EDAM:0000035 -name: tRNA -namespace: entity -def: "Transfer RNA (tRNA) is a small ribonucleic acid molecule that binds a specific amino acid." [EDAM:EBI "EMBRACE definition"] -comment: The amino acid is transferred to a nascent polypeptide chain during protein synthesis at the ribosome. -synonym: "Transfer RNA" EXACT [] -! relationship: has_attribute EDAM:0001213 ! RNA sequence -is_obsolete: true - -[Term] -id: EDAM:0000036 -name: Peptide -namespace: entity -def: "An organic polymer of alpha amino acid residues in a short unbranched chain. Peptides typically have fewer than 50 subunits and can be made synthetically." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0001208 ! Protein sequence -is_obsolete: true - -[Term] -id: EDAM:0000037 -name: Protein -namespace: entity -def: "One or more polypeptide chains in a stable conformation." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0001460 ! Protein structure -is_obsolete: true - -[Term] -id: EDAM:0000038 -name: Uncomplexed protein -namespace: entity -def: "A single polypeptide chain in a stable conformation." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0001460 ! Protein structure -is_obsolete: true - -[Term] -id: EDAM:0000039 -name: Enzyme -namespace: entity -def: "Enzyme." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0001460 ! Protein structure -is_obsolete: true - -[Term] -id: EDAM:0000040 -name: Transmembrane protein -namespace: entity -def: "A transmembrane protein molecule." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0001460 ! Protein structure -is_obsolete: true - -[Term] -id: EDAM:0000041 -name: Transcription factor -namespace: entity -def: "A protein that, upon binding a cis-regulatory DNA element, regulates (enhances or represses) transcription." [EDAM:EBI "EMBRACE definition"] -synonym: "Sequence-specific DNA binding factor" EXACT [] -! relationship: has_attribute EDAM:0001460 ! Protein structure -is_obsolete: true - -[Term] -id: EDAM:0000042 -name: Restriction enzyme -namespace: entity -def: "An enzyme that cuts DNA at specific nucleotide subsequence(s) (restriction sites)." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0001460 ! Protein structure -is_obsolete: true - -[Term] -id: EDAM:0000043 -name: RNA/DNA hybrid -namespace: entity -def: "A hybrid (complementary base-paired) molecule of DNA and RNA." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true +[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 -[Term] -id: EDAM:0000044 -name: Protein-protein complex -namespace: entity -def: "A protein comprising two or more polypeptide chain subunits in a stable association." [EDAM:EBI "EMBRACE definition"] -! synonym: "Protein complex" EXACT [] -! relationship: has_attribute EDAM:0001460 ! Protein structure -is_obsolete: 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 -[Term] -id: EDAM:0000045 -name: Protein-ligand complex -namespace: entity -def: "A protein-ligand (small molecule) complex." [EDAM:EBI "EMBRACE definition"] -is_obsolete: 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 -[Term] -id: EDAM:0000046 -name: Protein-nucleic acid complex -namespace: entity -def: "A protein-DNA/RNA complex." [EDAM:EBI "EMBRACE definition"] -is_obsolete: 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 -[Term] -id: EDAM:0000047 -name: Protein complex -namespace: entity -def: "A protein comprising two or more polypeptide chain subunits in a stable association." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -! consider: EDAM:0000044 ! Protein-protein complex +[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 -[Term] -id: EDAM:0001851 -name: Chromosome -namespace: entity -def: "A nucleic acid molecule which controls its own replication via the action of proteins at replication start sites." [EDAM:EBI "EMBRACE definition"] -xref: SO:0000340 -is_obsolete: 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 -[Term] -id: EDAM:0001749 -name: Atom group -namespace: entity -def: "A group of two or more atoms from a molecular structure." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true +[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 -[Term] -id: EDAM:0000048 -name: Nucleic acid feature -namespace: entity -def: "A feature of a nucleic acid molecule that can be mapped to a specific region(s) in its molecular sequence." [EDAM:EBI "EMBRACE definition"] -is_obsolete: 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 -[Term] -id: EDAM:0000049 -name: Protein feature -namespace: entity -def: "A feature of a protein molecule that can be mapped to a specific region(s) in its molecular sequence." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0001854 -name: Binding site -namespace: entity -def: "A region of a molecular surface involved in interactions with other molecules." [EDAM:EBI "EMBRACE definition"] -xref: SO:0000409 -is_obsolete: true -[Term] -id: EDAM:0001750 -name: Atom pair -namespace: entity -def: "A pair (exactly 2) atoms from a molecular structure." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000050 -name: Codon -namespace: entity -def: "Three nucleotides encoding typically a single, specific amino acid." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000051 -name: Gene -namespace: entity -def: "The hereditary unit, corresponding to the genomic sequence(s) encoding one or more functional products." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000052 -name: Operon -namespace: entity -def: "A functional unit of DNA including an operator, a common promoter, and one or more structural genes under common control." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000053 -name: Protein-coding region -namespace: entity -def: "The portion of a gene's DNA or RNA that is composed of exons and encodes a protein product." [EDAM:EBI "EMBRACE definition"] -synonym: "Coding region" EXACT [] -is_obsolete: true -[Term] -id: EDAM:0000054 -name: Transcription regulatory element -namespace: entity -def: "A region of DNA involved in transcription regulation." [EDAM:EBI "EMBRACE definition"] -synonym: "Gene regulatory element" EXACT [] -is_obsolete: true -[Term] -id: EDAM:0000055 -name: Restriction site -namespace: entity -def: "A restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000056 -name: Scaffold / matrix attachment site -namespace: entity -def: "Regions of DNA sequence in eukaryotic chromosomes where the nuclear matrix attaches." [EDAM:EBI "EMBRACE definition"] -synonym: "Matrix attachment region" EXACT [] -is_obsolete: true -[Term] -id: EDAM:0000057 -name: Splice site -namespace: entity -def: "A site in a transcribed RNA sequence at which RNA splicing occurs (introns are removed and exons are joined)." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0001909 -name: Allele -namespace: entity -def: "An alternative form of a gene that can exist at a single locus." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000058 -name: Gene cis-regulatory element -namespace: entity -def: "A DNA element that can bind a transcription factor to regulate (enhance or repress) the expression (transcription) of genes located on the same strand." [EDAM:EBI "EMBRACE definition"] -synonym: "Cis-element" EXACT [] -is_obsolete: true - -[Term] -id: EDAM:0000059 -name: Gene trans-regulatory element -namespace: entity -def: "A DNA element that encodes a transcription factor which regulates gene(s) distant from the gene from which they were transcribed." [EDAM:EBI "EMBRACE definition"] -synonym: "Trans-element" EXACT [] -is_obsolete: true +! +! Top-level concepts (sub-ontologies) +! [Term] -id: EDAM:0000060 -name: Promoter -namespace: entity -def: "The DNA element where transcription is initiated." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true +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 [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 [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 [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 [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 [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:0000061 -name: Enhancer -namespace: entity -def: "An element that can bind a transcription factor to enhance transcription." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true [Term] -id: EDAM:0000062 -name: Silencer -namespace: entity -def: "An element that can bind a transcription factor to repress transcription." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true +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 [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 [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:0000063 -name: Response element -namespace: entity -def: "An element within or near the promoter that can bind certain transcription factors, for example a hormone receptor complex." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true [Term] -id: EDAM:0000064 -name: Protein residue -namespace: entity -def: "A single amino acid position in a protein, bound to one (C or N-terminal positions) or two other residues by covalent (peptide) bonds." [EDAM:EBI "EMBRACE definition"] -synonym: "Residue" EXACT [] -is_obsolete: true +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 [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 [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:0001751 -name: Protein residue group -namespace: entity -def: "A group of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] -synonym: "Residue group" EXACT [] -is_obsolete: true -[Term] -id: EDAM:0000065 -name: Protein domain -namespace: entity -def: "A region of a protein (typically a region of a single polypeptide chain) forming a distinct, compact conformation. Domains show some independence in terms of evolution, folding, structure or function and (typically) reoccur in other proteins." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0001468 ! Protein domain -is_obsolete: true -[Term] -id: EDAM:0001752 -name: Protein residue pair -namespace: entity -def: "A pair of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] -synonym: "Residue pair" EXACT [] -is_obsolete: true -[Term] -id: EDAM:0001753 -name: Protein residue group (continuous) -namespace: entity -def: "A group of continuous (adjacent) amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] -synonym: "Residue group (continuous)" EXACT [] -is_obsolete: true -[Term] -id: EDAM:0001754 -name: Protein residue group (discontinuous) -namespace: entity -def: "A group of discontinuous amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] -comment: One or more residues in the group are discontinuous (non-adjacent). -synonym: "Residue group (discontinuous)" EXACT [] -is_obsolete: true [Term] -id: EDAM:0000066 -name: Genome -namespace: entity -def: "An organisms total complement of DNA or RNA (some viruses) and therefore its hereditary information. A genome includes genes and non-coding regions." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true - -[Term] -id: EDAM:0000067 -name: Proteome -namespace: entity -def: "An organisms total complement of expressed proteins. More specifically, those proteins expressed in a cell, tissue or the whole organism under defined conditions at a specific time." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true +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:0000068 -name: Nucleosome -namespace: entity -def: "The repeating structural unit of eukaryotic chromatin, which is folded successively into chromosomes." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000069 -name: Taxonomic rank -namespace: entity -def: "One of the major taxonomic ranks of life." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000070 -name: Kingdom -namespace: entity -def: "A kingdom or organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0001871 -name: Genus -namespace: entity -def: "A genus of organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000071 -name: Species -namespace: entity -def: "A species or organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true [Term] -id: EDAM:0000072 -name: Strain -namespace: entity -def: "A strain or prokaryotic organisms." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true +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 -[Term] -id: EDAM:0000073 -name: Metabolic pathway -namespace: entity -def: "A group of related chemical (enzyme catalysed) reactions occurring within a cell." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000074 -name: Mutation -namespace: entity -def: "A change to the nucleotide sequence of an organism's genome." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -[Term] -id: EDAM:0000075 -name: Single-nucleotide polymorphism -namespace: entity -def: "A single nucleotide variation in the genome of members of a species, or between paired chromosomes of an individual." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true @@ -865,186 +510,178 @@ is_obsolete: true ! [Term] -id: EDAM:0000076 -name: Undefined -namespace: topic -alt_id: EDAM:0000580 -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true - -[Term] -id: EDAM:0002807 +id: EDAM_topic:2807 name: Tool topic namespace: topic -def: "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000003 ! 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:0002809 +id: EDAM_topic:2809 name: Study topic namespace: topic -def: "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000003 ! 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:0003071 +id: EDAM_topic:3071 !{since=beta13} name: Biological data resources namespace: topic -alt_id: EDAM:0002808 -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." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Biological databases" EXACT [] -synonym: "Biological data resource" EXACT [] -is_a: EDAM:0000003 ! 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:0000077 +id: EDAM_topic:0077 name: Nucleic acid analysis namespace: topic -alt_id: EDAM:0003046 -def: "Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Nucleic acids" EXACT [] -synonym: "Nucleic acid informatics" EXACT [] -synonym: "Nucleic acid bioinformatics" EXACT [] -is_a: EDAM:0000003 ! 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:0002839 +id: EDAM_topic:2839 name: Molecules namespace: topic -def: "Resources concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true +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:0000078 +id: EDAM_topic:0078 name: Protein analysis namespace: topic -alt_id: EDAM:0000586 -def: "Processing and analysis of protein data, typically molecular sequence and structural data." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Protein informatics" EXACT [] -synonym: "Protein bioinformatics" EXACT [] -synonym: "Proteins" EXACT [] -is_a: EDAM:0000003 ! 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:0002225 +id: EDAM_topic:2225 name: Protein databases namespace: topic -def: "Data resources concerning proteins." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Protein data resources" EXACT [] -is_a: EDAM:0003071 ! Biological data resources -is_a: EDAM:0000078 ! Protein analysis +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:0000079 +id: EDAM_topic:0079 name: Metabolites namespace: topic -def: "Informatics resources (typically structural data) concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0000154 ! Small molecules +is_a: EDAM_topic:0154 ! Small molecules [Term] -id: EDAM:0000080 +id: EDAM_topic:0080 name: Sequence analysis namespace: topic -alt_id: EDAM:0002228 -alt_id: EDAM:0000584 -def: "Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Sequences" EXACT [] +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:0000003 ! Topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM:0003041 +id: EDAM_topic:3041 !{since=beta13} name: Sequence databases namespace: topic -def: "Data resources concerning molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Sequence data" EXACT [] -synonym: "Sequence data resource" EXACT [] -synonym: "Sequence data resources" EXACT [] -is_a: EDAM:0003071 ! Biological data resources -is_a: EDAM:0000080 ! Sequence analysis +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:0000081 +id: EDAM_topic:0081 name: Structure analysis namespace: topic -alt_id: EDAM:0000693 -alt_id: EDAM:0002827 -alt_id: EDAM:0000585 -def: "Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Structural bioinformatics" EXACT [] -synonym: "Computation structural biology" EXACT [] -is_a: EDAM:0000003 ! Topic +synonym: "Structural bioinformatics" EXACT [http://edamontology.org] +synonym: "Computation structural biology" EXACT [http://edamontology.org] +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM:0003038 +id: EDAM_topic:3038 !{since=beta13} name: Structure databases namespace: topic -alt_id: EDAM:0003059 -def: "Data resources concerning molecular secondary or tertiary (3D) structural information, typically of proteins and nucleic acids." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Structure data resources" EXACT [] -is_a: EDAM:0003071 ! Biological data resources -is_a: EDAM:0000081 ! Structure analysis +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:0000082 +id: EDAM_topic:0082 name: Structure prediction namespace: topic -alt_id: EDAM:0000171 -def: "Resources concerning the prediction of molecular (secondary or tertiary) structure." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000081 ! Structure analysis +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:0000083 +id: EDAM_topic:0083 name: Alignment namespace: topic -def: "Resources concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000182 ! Sequence alignment -consider: EDAM:0000183 ! Structure alignment -consider: EDAM:0000184 ! Threading +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:0000084 -alt_id: EDAM:0000192 -alt_id: EDAM:0000193 +id: EDAM_topic:0084 +! alt_id: EDAM_topic:0192 +! alt_id: EDAM_topic:0193 name: Phylogenetics namespace: topic -alt_id: EDAM:0000636 -def: "Resources concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic xref: BioCatalogue:Phylogeny xref: BioCatalogue:Statistical Robustness -synonym: "Phylogenetic simulation" EXACT [] -synonym: "Phylogenetic clocks, dating and stratigraphy" EXACT [] -is_a: EDAM:0000003 ! Topic +synonym: "Phylogenetic simulation" EXACT [http://edamontology.org] +synonym: "Phylogenetic clocks, dating and stratigraphy" EXACT [http://edamontology.org] +is_a: EDAM_topic:0003 ! Topic @@ -1054,2464 +691,2508 @@ is_a: EDAM:0000003 ! Topic [Term] -id: EDAM:0000200 -alt_id: EDAM:0000206 +id: EDAM_topic:0200 +! alt_id: EDAM_topic:0206 name: Microarrays namespace: topic -def: "Informatics resources concerning microarrays, for example, to process microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"] -subset: topic +subset: topics +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 [] -is_a: EDAM:0000607 ! Laboratory resources +synonym: "DNA microarrays" EXACT [http://edamontology.org] +is_a: EDAM_topic:0607 ! Laboratory resources [Term] -id: EDAM:0000121 +id: EDAM_topic:0121 name: Proteomics namespace: topic -alt_id: EDAM:0000764 -def: "Informatics resources concerning the study of whole proteomes of organisms." [EDAM:EBI "EMBRACE definition"] +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). -subset: topic -synonym: "Protein expression" EXACT [] +synonym: "Protein expression" EXACT [http://edamontology.org] xref: BioCatalogue:Proteomics -is_a: EDAM:0000003 ! Topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM:0000085 +id: EDAM_topic:0085 name: Functional genomics namespace: topic -def: "Informatics resources concerning the study of gene or protein functions and their interactions." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000622 ! Genomics +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:0000122 +id: EDAM_topic:0122 name: Structural genomics namespace: topic -def: "Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002226 ! Structure determination -is_a: EDAM:0000622 ! Genomics +is_a: EDAM_topic:2226 ! Structure determination +is_a: EDAM_topic:0622 ! Genomics [Term] -id: EDAM:0003061 +id: EDAM_topic:3061 !{since=beta13} name: Documentation and help namespace: topic -def: "Resources concerning documentation and getting help." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003068 ! Literature and reference +subset: topics +def: "Topic concerning documentation and getting help." [http://edamontology.org] +is_a: EDAM_topic:3068 ! Literature and reference [Term] -id: EDAM:0003047 +id: EDAM_topic:3047 !{since=beta13} name: Molecular biology reference namespace: topic -def: "Resources concerning general molecular biology information extracted from the literature." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000606 ! Literature data resources +is_a: EDAM_topic:0606 ! Literature data resources [Term] -id: EDAM:0000089 -name: Ontologies +id: EDAM_topic:0089 +name: Ontology namespace: topic -alt_id: EDAM:0002255 -def: "Resources concerning ontologies of biological or bioinformatics concepts (terms and relations), controlled vocabularies, structured glossary or other related resource." [EDAM:EBI "EMBRACE definition"] -comment: This includes the annotation of entities (typically biological database entries) with terms from a controlled vocabulary. -subset: topic -synonym: "Ontology" EXACT [] +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:0002829 ! Ontologies, nomenclature and classification +is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] -id: EDAM:0000090 -alt_id: EDAM:0000155 -alt_id: EDAM:0002274 -alt_id: EDAM:0000165 +id: EDAM_topic:0090 +! alt_id: EDAM_topic:0155 +! alt_id: EDAM_topic:2274 +! alt_id: EDAM_topic:0165 name: Data search and retrieval namespace: topic -def: "Resources concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [EDAM:EBI "EMBRACE definition"] +subset: topics +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. -subset: topic -synonym: "Data retrieval" EXACT [] +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:0000091 ! Data handling +is_a: EDAM_topic:0091 ! Data handling [Term] -id: EDAM:0000091 +id: EDAM_topic:0091 name: Data handling namespace: topic -alt_id: EDAM:0002282 -def: "Resources for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Data types, processing and visualisation" EXACT [] -is_a: EDAM:0000003 ! 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:0000092 +id: EDAM_topic:0092 name: Data visualisation namespace: topic -def: "Resources for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Data rendering and visualisation" EXACT [] -synonym: "Data rendering" EXACT [] -synonym: "Data plotting" EXACT [] -is_a: EDAM:0000091 ! Data handling +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:0002258 +id: EDAM_topic:2258 name: Chemoinformatics namespace: topic -def: "Informatics resources for the application of information technology to chemistry." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Cheminformatics" EXACT [] -synonym: "Chemical informatics" EXACT [] -synonym: "Computational chemistry" EXACT [] +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:0000003 ! Topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM:0002269 +id: EDAM_topic:2269 name: Biostatistics namespace: topic -def: "Informatics resources for the application of statistical methods to biological problems." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Biometry" EXACT [] -synonym: "Biometrics" EXACT [] +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:0000091 ! Data handling +is_a: EDAM_topic:0091 ! Data handling [Term] -id: EDAM:0003077 -alt_id: EDAM:0001779 +id: EDAM_topic:3077 !{since=beta13} +! alt_id: EDAM_topic:1779 name: Data acquisition and deposition namespace: topic -def: "Resources concerning the acquisition and deposition of biological data." [EDAM:EBI "EMBRACE definition"] -synonym: "Database submission" EXACT [] -subset: topic -is_a: EDAM:0000091 ! Data handling +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:0000094 +id: EDAM_topic:0094 name: Nucleic acid thermodynamics namespace: topic -alt_id: EDAM:0000614 -alt_id: EDAM:0000104 -def: "Informatics resources concerning the study of the thermodynamic properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"] +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). -subset: topic -synonym: "Nucleic acid physicochemistry" EXACT [] -synonym: "Nucleic acid properties" EXACT [] -synonym: "Nucleic acid denaturation" EXACT [] -synonym: "DNA melting" EXACT [] -is_a: EDAM:0000640 ! Nucleic acid sequence analysis +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:0000097 +id: EDAM_topic:0097 name: Nucleic acid structure analysis namespace: topic -alt_id: EDAM:0000699 -alt_id: EDAM:0000106 -def: "The processing and analysis of nucleic acid (secondary or tertiary) structural data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000081 ! Structure analysis -is_a: EDAM:0000077 ! Nucleic acid analysis +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:0003039 +id: EDAM_topic:3039 !{since=beta13} name: Nucleic acid structure namespace: topic -alt_id: EDAM:0002833 -def: "Data resources concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003038 ! Structure databases +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:0000099 +id: EDAM_topic:0099 name: RNA namespace: topic -alt_id: EDAM:0000653 -def: "Informatics resources concerning RNA sequences and structures." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003042 ! Nucleic acid sequences +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:0000100 +id: EDAM_topic:0100 name: Nucleic acid restriction namespace: topic -def: "Informatics resources for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000640 ! Nucleic acid sequence analysis -is_a: EDAM:0000821 ! Enzymes and reactions +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:0000107 +id: EDAM_topic:0107 name: Codon usage analysis namespace: topic -def: "Resources concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000110 ! Transcription +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:0000109 +id: EDAM_topic:0109 name: Gene finding namespace: topic -def: "Resources that aim to identify, predict, model or analyse genes or gene structure in DNA sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Gene prediction" EXACT [] +synonym: "Gene prediction" EXACT [http://edamontology.org] xref: BioCatalogue:Gene Prediction -is_a: EDAM:0003073 ! Nucleic acid feature detection +is_a: EDAM_topic:3073 ! Nucleic acid feature detection [Term] -id: EDAM:0000110 +id: EDAM_topic:0110 name: Transcription namespace: topic -def: "Informatics resources concerning the transcription of DNA into mRNA." [EDAM:EBI "EMBRACE definition"] -subset: topic +subset: topics +def: "Topic concerning the transcription of DNA into mRNA." [http://edamontology.org] xref: BioCatalogue:Transcription Factors -is_a: EDAM:0000640 ! Nucleic acid sequence analysis +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM:0000108 +id: EDAM_topic:0108 name: Translation namespace: topic -def: "Informatics resources concerning the translation of mRNA into protein." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000640 ! Nucleic acid sequence analysis +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:0000111 +id: EDAM_topic:0111 name: Promoters namespace: topic -def: "Informatics resources concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0000749 ! Transcription factors and regulatory sites +is_obsolete: true !{since=beta13} +consider: EDAM_topic:0749 ! Transcription factors and regulatory sites [Term] -id: EDAM:0000112 +id: EDAM_topic:0112 name: Nucleic acid folding namespace: topic -def: "Informatics resources concerning the folding (in 3D space) of nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000173 ! Nucleic acid structure prediction +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:0000114 +id: EDAM_topic:0114 name: Gene structure and RNA splicing namespace: topic -alt_id: EDAM:0000750 -def: "Informatics resources concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "RNA splicing" EXACT [] -synonym: "Gene structure" EXACT [] -is_a: EDAM:0003062 ! Genetic organisation -is_a: EDAM:0000747 ! Nucleic acid sites and features +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:0000123 +id: EDAM_topic:0123 name: Protein properties namespace: topic -alt_id: EDAM:0000615 -def: "Informatics resources for the study of the physical and biochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Protein physicochemistry" EXACT [] -is_a: EDAM:0000639 ! Protein sequence analysis +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:0001775 +id: EDAM_topic:1775 name: Protein function analysis namespace: topic -alt_id: EDAM:0003057 -def: "Informatics resources for the study of protein function." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000078 ! Protein analysis +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:0000128 +id: EDAM_topic:0128 name: Protein interactions namespace: topic -alt_id: EDAM:0000587 -def: "Informatics resources concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." [EDAM:EBI "EMBRACE definition"] -subset: 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] xref: BioCatalogue:Protein Interaction -is_a: EDAM:0001775 ! Protein function analysis -is_a: EDAM:0002225 ! Protein databases +is_a: EDAM_topic:1775 ! Protein function analysis +is_a: EDAM_topic:2225 ! Protein databases [Term] -id: EDAM:0000130 +id: EDAM_topic:0130 name: Protein folding and stability namespace: topic -def: "Informatics resources concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002814 ! Protein structure analysis +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:0002232 +id: EDAM_topic:2232 name: Lipoproteins namespace: topic -def: "Informatics resources concerning lipoproteins (protein-lipid assemblies)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000635 ! Specific protein resources +subset: topics +def: "Topic concerning lipoproteins (protein-lipid assemblies)." [http://edamontology.org] +is_a: EDAM_topic:0635 ! Specific protein resources [Term] -id: EDAM:0000137 +id: EDAM_topic:0137 name: Protein hydropathy namespace: topic -def: "Informatics resources for the study of the hydrophobic, hydrophilic and charge properties of a protein." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000123 ! Protein properties +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:0000140 +id: EDAM_topic:0140 name: Protein targeting and localization namespace: topic -alt_id: EDAM:0000588 -def: "Informatics resources for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002276 ! Protein function prediction -is_a: EDAM:0002225 ! Protein databases +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:0000143 +id: EDAM_topic:0143 name: Protein structure comparison namespace: topic -def: "Resources concerning the comparison of two or more protein structures." [EDAM:EBI "EMBRACE definition"] -comment: Use this term for methods that are exclusively for protein structure. -subset: topic -is_obsolete: true -consider: EDAM:0000698 ! Protein tertiary structure -consider: EDAM:0001770 ! Structure comparison +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:0002280 +id: EDAM_topic:2280 name: Nucleic acid structure comparison namespace: topic -def: "Resources concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [EDAM:EBI "EMBRACE definition"] -comment: Use this term for methods that are exclusively for nucleic acid structures. -subset: topic -is_obsolete: true -consider: EDAM:0000097 ! Nucleic acid structure analysis -consider: EDAM:0001770 ! Structure comparison +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:0000144 +id: EDAM_topic:0144 name: Protein residue interaction analysis namespace: topic -def: "The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Protein residue interactions" EXACT [] -is_a: EDAM:0002814 ! Protein structure analysis +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:0002276 +id: EDAM_topic:2276 name: Protein function prediction namespace: topic -def: "Resources concerning the prediction of functional properties of a protein." [EDAM:EBI "EMBRACE definition"] -subset: topic +subset: topics +def: "Topic concerning the prediction of functional properties of a protein." [http://edamontology.org] xref: BioCatalogue:Function Prediction -is_a: EDAM:0001775 ! Protein function analysis +is_a: EDAM_topic:1775 ! Protein function analysis [Term] -id: EDAM:0000147 +id: EDAM_topic:0147 name: Protein-protein interactions namespace: topic -alt_id: EDAM:0000719 -def: "Informatics resources concerning protein-protein interactions, protein complexes, protein functional coupling etc." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000128 ! Protein interactions +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:0000148 +id: EDAM_topic:0148 name: Protein-ligand interactions namespace: topic -alt_id: EDAM:0000717 -def: "Informatics resources concerning protein-ligand (small molecule) interactions." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000128 ! Protein interactions +is_a: EDAM_topic:0128 ! Protein interactions [Term] -id: EDAM:0000149 +id: EDAM_topic:0149 name: Protein-nucleic acid interactions namespace: topic -alt_id: EDAM:0000718 -def: "Informatics resources concerning protein-DNA/RNA interactions." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000128 ! Protein interactions +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:0000150 +id: EDAM_topic:0150 name: Protein design namespace: topic -def: "Informatics resources concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000172 ! Protein structure prediction +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:0000151 +id: EDAM_topic:0151 name: G protein-coupled receptors (GPCR) namespace: topic -def: "Resources concerning G-protein coupled receptors (GPCRs)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000820 ! Membrane proteins +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:0002278 +id: EDAM_topic:2278 name: Transmembrane protein prediction namespace: topic -def: "Predict transmembrane domains and topology in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000820 ! Membrane proteins -consider: EDAM:0000178 ! Protein secondary structure prediction +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:0000152 +id: EDAM_topic:0152 name: Carbohydrates namespace: topic -alt_id: EDAM:0000695 -def: "Informatics resources concerning carbohydrates, typically including structural information." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003038 ! Structure databases +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:0000153 +id: EDAM_topic:0153 name: Lipids namespace: topic -alt_id: EDAM:0002624 -def: "Informatics resources concerning lipids and their structures." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003038 ! Structure databases +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:0000154 +id: EDAM_topic:0154 name: Small molecules namespace: topic -alt_id: EDAM:0000696 -def: "Informatics resources concerning small molecules of biological significance, typically including structural information." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0003038 ! Structure databases +synonym: "molecular entity" RELATED [CHEBI:23367] +is_a: EDAM_topic:3038 ! Structure databases [Term] -id: EDAM:0000156 +id: EDAM_topic:0156 name: Sequence editing namespace: topic -def: "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000080 ! Sequence analysis -consider: EDAM:0000091 ! Data handling +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:0000157 +id: EDAM_topic:0157 name: Sequence composition analysis namespace: topic -def: "Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000080 ! Sequence analysis +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:0000158 -alt_id: EDAM:0000161 -alt_id: EDAM:0000162 +id: EDAM_topic:0158 +! alt_id: EDAM_topic:0161 +! alt_id: EDAM_topic:0162 name: Sequence motifs namespace: topic -def: "Resources concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Motifs" EXACT [] -is_a: EDAM:0000594 ! Sequence classification +subset: topics +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:0000188 +id: EDAM_topic:0188 name: Sequence profiles and HMMs namespace: topic -alt_id: EDAM:0000744 -alt_id: EDAM:0000746 -alt_id: EDAM:0001763 -def: "Resources concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0000594 ! Sequence classification +is_a: EDAM_topic:0594 ! Sequence classification [Term] -id: EDAM:0000159 -alt_id: EDAM:0002260 -alt_id: EDAM:0002261 +id: EDAM_topic:0159 +! alt_id: EDAM_topic:2260 +! alt_id: EDAM_topic:2261 name: Sequence comparison namespace: topic -def: "Resources concerning the comparison of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic xref: BioCatalogue:Protein Sequence Similarity xref: BioCatalogue:Nucleotide Sequence Similarity -is_a: EDAM:0000080 ! Sequence analysis +is_a: EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM:0000160 +id: EDAM_topic:0160 name: Sequence sites and features namespace: topic -alt_id: EDAM:0000600 -def: "Data resources concerning the positional features, such as functional and other key sites, in molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003041 ! Sequence databases +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:0003072 +id: EDAM_topic:3072 !{since=beta13} name: Sequence feature detection namespace: topic -def: "Resources concerning the detection of the positional features, such as functional and other key sites, in molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000080 ! Sequence analysis +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:0000163 +id: EDAM_topic:0163 name: Sequence database search namespace: topic -def: "Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence)." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_obsolete: true -consider: EDAM:0000159 ! Sequence comparison +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_topic:0159 ! Sequence comparison [Term] -id: EDAM:0003052 +id: EDAM_topic:3052 !{since=beta13} name: Sequence clusters and classification namespace: topic -def: "Data resources concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Sequence clusters" EXACT [] -synonym: "Sequence families" EXACT [] -is_a: EDAM:0003041 ! Sequence databases +synonym: "Sequence clusters" EXACT [http://edamontology.org] +synonym: "Sequence families" EXACT [http://edamontology.org] +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM:0000164 +id: EDAM_topic:0164 name: Sequence clustering namespace: topic -def: "Resources concerning the comparison and grouping together of molecular sequences on the basis of their similarities." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0000159 ! Sequence comparison +is_a: EDAM_topic:0159 ! Sequence comparison [Term] -id: EDAM:0000594 +id: EDAM_topic:0594 name: Sequence classification namespace: topic -def: "Resources concerning the classification of molecular sequences based on some measure of their similarity." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0000080 ! Sequence analysis +is_a: EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM:0000166 +id: EDAM_topic:0166 name: Protein structural motifs and surfaces namespace: topic -alt_id: EDAM:0000139 -alt_id: EDAM:0000170 -alt_id: EDAM:0000146 -alt_id: EDAM:0000589 -def: "Resources 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." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Protein structural features" EXACT [] -synonym: "Protein surfaces" EXACT [] -synonym: "Protein structural motifs" EXACT [] -synonym: "Structural motifs" EXACT [] -is_a: EDAM:0000698 ! Protein tertiary structure +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:0000167 +id: EDAM_topic:0167 name: Structural (3D) profiles namespace: topic -alt_id: EDAM:0000599 -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." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Structural profiles" EXACT [] -is_a: EDAM:0001770 ! Structure comparison +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:0001770 -alt_id: EDAM:0000168 -alt_id: EDAM:0000169 +id: EDAM_topic:1770 +! alt_id: EDAM_topic:0168 +! alt_id: EDAM_topic:0169 name: Structure comparison namespace: topic -def: "Resources concerning the comparison of two or more molecular structures." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0000081 ! Structure analysis +is_a: EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM:0002844 +id: EDAM_topic:2844 name: Structural clustering namespace: topic -def: "Resources concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Structure classification" EXACT [] -is_a: EDAM:0001770 ! Structure comparison +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:0002271 +id: EDAM_topic:2271 name: Structure database search namespace: topic -def: "Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure)." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_obsolete: true -consider: EDAM:0001770 ! Structure comparison +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_topic:1770 ! Structure comparison [Term] -id: EDAM:0000172 +id: EDAM_topic:0172 name: Protein structure prediction namespace: topic -def: "Resources concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000082 ! Structure prediction -is_a: EDAM:0002814 ! Protein structure analysis +is_a: EDAM_topic:0082 ! Structure prediction +is_a: EDAM_topic:2814 ! Protein structure analysis [Term] -id: EDAM:0000173 +id: EDAM_topic:0173 name: Nucleic acid structure prediction namespace: topic -alt_id: EDAM:0000181 -def: "Resources concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Nucleic acid folding" EXACT [] -synonym: "RNA/DNA structure prediction" EXACT [] +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:0000082 ! Structure prediction -is_a: EDAM:0000097 ! Nucleic acid structure analysis +is_a: EDAM_topic:0082 ! Structure prediction +is_a: EDAM_topic:0097 ! Nucleic acid structure analysis [Term] -id: EDAM:0002953 +id: EDAM_topic:2953 name: Nucleic acid design namespace: topic -def: "Resources for the design of nucleic acid sequences with specific conformations." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000077 ! Nucleic acid analysis +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:0000174 +id: EDAM_topic:0174 name: Ab initio structure prediction namespace: topic -def: "Resources 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." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "de novo protein structure prediction" EXACT [] -is_a: EDAM:0000082 ! Structure prediction +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:0002275 +id: EDAM_topic:2275 name: Molecular modelling namespace: topic -def: "Resources for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. " [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000082 ! Structure prediction -is_a: EDAM:0000172 ! Protein structure prediction +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:0000175 +id: EDAM_topic:0175 name: Homology modelling namespace: topic -def: "Resources for the modelling of the three-dimensional structure of a protein using known sequence and structural data." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Comparative modelling" EXACT [] -is_a: EDAM:0002275 ! Molecular modelling +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:0000176 -alt_id: EDAM:0000145 +id: EDAM_topic:0176 +! alt_id: EDAM_topic:0145 name: Molecular dynamics namespace: topic -def: "Resources concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Molecular motions" EXACT [] -synonym: "Molecular flexibility" EXACT [] -is_a: EDAM:0002275 ! Molecular modelling +synonym: "Molecular motions" EXACT [http://edamontology.org] +synonym: "Molecular flexibility" EXACT [http://edamontology.org] +is_a: EDAM_topic:2275 ! Molecular modelling [Term] -id: EDAM:0000177 +id: EDAM_topic:0177 name: Molecular docking namespace: topic -def: "Resources for modelling the structure of proteins in complex with small molecules or other macromolecules." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002275 ! Molecular modelling +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:0000178 +id: EDAM_topic:0178 name: Protein secondary structure prediction namespace: topic -def: "Resources concerning the prediction of secondary or supersecondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000172 ! Protein structure prediction +is_a: EDAM_topic:0172 ! Protein structure prediction [Term] -id: EDAM:0000179 +id: EDAM_topic:0179 name: Protein tertiary structure prediction namespace: topic -def: "Resources concerning the prediction of tertiary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000172 ! Protein structure prediction +is_a: EDAM_topic:0172 ! Protein structure prediction [Term] -id: EDAM:0000180 +id: EDAM_topic:0180 name: Protein fold recognition namespace: topic -def: "Resources concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000172 ! Protein structure prediction +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:0000182 +id: EDAM_topic:0182 name: Sequence alignment namespace: topic -alt_id: EDAM:0002283 -alt_id: EDAM:0000185 -alt_id: EDAM:0000186 -alt_id: EDAM:0000187 -alt_id: EDAM:0000596 -alt_id: EDAM:0000189 -def: "Resources concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic 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:0000159 ! Sequence comparison -is_a: EDAM:0003041 ! Sequence databases +is_a: EDAM_topic:0159 ! Sequence comparison +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM:0000183 -alt_id: EDAM:0002272 -alt_id: EDAM:0002273 +id: EDAM_topic:0183 +! alt_id: EDAM_topic:2272 +! alt_id: EDAM_topic:2273 name: Structure alignment namespace: topic -alt_id: EDAM:0000597 -alt_id: EDAM:0000190 -def: "Resources concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Structure alignment generation" EXACT [] -is_a: EDAM:0001770 ! Structure comparison -is_a: EDAM:0003038 ! Structure databases +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:0000184 +id: EDAM_topic:0184 name: Threading namespace: topic -def: "Resources concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Sequence-structure alignment" EXACT [] -is_a: EDAM:0000180 ! Protein fold recognition +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:0000191 +id: EDAM_topic:0191 name: Phylogeny reconstruction namespace: topic -def: "Resources concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -comment: Currently too specific for the topic branch (but might be unobsoleted). -subset: 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:0000084 ! Phylogenetics +is_a: EDAM_topic:0084 ! Phylogenetics [Term] -id: EDAM:0002257 +id: EDAM_topic:2257 name: Phylogeny visualisation namespace: topic -def: "Visualise a phylogeny, for example, render a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: topic +subset: topics +def: "Visualise a phylogeny, for example, render a phylogenetic tree." [http://edamontology.org] xref: BioCatalogue:Tree Display -is_obsolete: true -consider: EDAM:0000084 ! Phylogenetics +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_topic:0084 ! Phylogenetics [Term] -id: EDAM:0000194 +id: EDAM_topic:0194 name: Phylogenomics namespace: topic -def: "Resources 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." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000084 ! Phylogenetics -is_a: EDAM:0000622 ! Genomics +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:0002842 +id: EDAM_topic:2842 name: High-throughput sequencing namespace: topic -def: "Informatics resources concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Next-generation sequencing" EXACT [] -is_obsolete: true -consider: EDAM:0000102 ! Sequencing and mapping +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:0102 ! Sequencing and mapping [Term] -id: EDAM:0000195 +id: EDAM_topic:0195 name: Virtual PCR namespace: topic -def: "Informatics resources concerning simulated polymerase chain reaction (PCR)." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "PCR" EXACT [] -synonym: "Polymerase chain reaction" EXACT [] -is_obsolete: true -consider: EDAM:0000077 ! Nucleic acid analysis +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:0000196 +id: EDAM_topic:0196 name: Sequence assembly namespace: topic -def: "Resources concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000102 ! Sequencing and mapping +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:0102 ! Sequencing and mapping [Term] -id: EDAM:0000133 +id: EDAM_topic:0133 name: Two-dimensional gel electrophoresis namespace: topic -alt_id: EDAM:0000765 -def: "Resources concerning two-dimensional gel electrophoresis image and related data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000121 ! Proteomics +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:0000134 +id: EDAM_topic:0134 name: Mass spectrometry namespace: topic -alt_id: EDAM:0000766 -def: "Resources concerning mass spectrometry and related data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000121 ! Proteomics +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:0000135 +id: EDAM_topic:0135 name: Protein microarrays namespace: topic -def: "Resources concerning protein microarray data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000121 ! Proteomics -consider: EDAM:0000200 ! Microarrays +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:0000102 +id: EDAM_topic:0102 name: Sequencing and mapping namespace: topic -def: "Informatics resources concerning the determination and mapping of complete (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000640 ! Nucleic acid sequence analysis +subset: topics +def: "Topic concerning the determination and mapping of complete (typically nucleotide) sequences." [http://edamontology.org] +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM:0000197 +id: EDAM_topic:0197 name: Gene expression resources namespace: topic -def: "Data resources concerning primarily raw or processed gene expression (typically microarray) data." [EDAM:EBI "EMBRACE definition"] +subset: topics +def: "Topic concerning primarily raw or processed gene expression (typically microarray) 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. -subset: topic -is_a: EDAM:0002816 ! Gene resources -is_a: EDAM:0000203 ! Transcriptomics +is_a: EDAM_topic:2816 ! Gene resources +is_a: EDAM_topic:0203 ! Transcriptomics [Term] -id: EDAM:0003062 +id: EDAM_topic:3062 !{since=beta13} name: Genetic organisation namespace: topic -def: "Data resources concerning the structural and functional organisation of genes and other genetic elements." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002816 ! Gene resources +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:0000204 +id: EDAM_topic:0204 name: Gene regulation resources namespace: topic -alt_id: EDAM:0003049 -alt_id: EDAM:0000631 -def: "Data resources concerning primarily the regulation of gene expression." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002816 ! Gene resources +subset: topics +! alt_id: EDAM_topic:3049 +! alt_id: EDAM_topic:0631 +def: "Topic concerning primarily the regulation of gene expression." [http://edamontology.org] +is_a: EDAM_topic:2816 ! Gene resources [Term] -id: EDAM:0000199 +id: EDAM_topic:0199 name: Genetic variation namespace: topic -alt_id: EDAM:0000626 -def: "Resources concerning DNA sequence variation (mutation and polymorphism) data." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Mutation and polymorphism" EXACT [] -synonym: "DNA variation" EXACT [] -is_a: EDAM:0000625 ! Genotype and phenotype resources -is_a: EDAM:0003041 ! Sequence databases -is_a: EDAM:0000640 ! Nucleic acid sequence analysis +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 resources +is_a: EDAM_topic:3041 ! Sequence databases +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM:0000202 +id: EDAM_topic:0202 name: Pharmacoinformatics namespace: topic -def: "Informatics resources for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Computational pharmacology" EXACT [] -is_a: EDAM:0002258 ! Chemoinformatics +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:0000203 +id: EDAM_topic:0203 name: Transcriptomics namespace: topic -def: "Informatics resources concerning the analysis of mRNA expression levels, by identifying, quantifying or comparing mRNA transcripts or interpreting (in functional terms) gene expression data." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Gene expression profiling" EXACT [] -synonym: "Expression profiling" EXACT [] -is_a: EDAM:0000003 ! Topic +subset: topics +def: "Topic concerning the analysis of mRNA expression levels, by identifying, quantifying or comparing mRNA transcripts or interpreting (in functional terms) gene expression data." [http://edamontology.org] +synonym: "Gene expression profiling" EXACT [http://edamontology.org] +synonym: "Expression profiling" EXACT [http://edamontology.org] +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM:0002277 +id: EDAM_topic:2277 name: SNPs namespace: topic -def: "Resources concerning single nucleotide polymorphisms (SNP) and associated data." [EDAM:EBI "EMBRACE definition"] +subset: topics +def: "Topic concerning single nucleotide polymorphisms (SNP) and associated data." [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. -subset: topic -is_a: EDAM:0000199 ! Genetic variation +is_a: EDAM_topic:0199 ! Genetic variation [Term] -id: EDAM:0000208 +id: EDAM_topic:0208 name: Pharmacogenomics namespace: topic -def: "Informatics resources concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Pharmacogenetics" EXACT [] -is_a: EDAM:0000202 ! Pharmacoinformatics -is_a: EDAM:0000622 ! Genomics +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:0000209 +id: EDAM_topic:0209 name: Drug design namespace: topic -def: "Informatics resources concerning the design of drugs or potential drug compounds." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0000202 ! Pharmacoinformatics +is_a: EDAM_topic:0202 ! Pharmacoinformatics [Term] -id: EDAM:0000210 +id: EDAM_topic:0210 name: Fish namespace: topic -def: "Informatics resources concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0002820 ! Vertebrates +is_a: EDAM_topic:2820 ! Vertebrates [Term] -id: EDAM:0000211 +id: EDAM_topic:0211 name: Flies namespace: topic -def: "Informatics resources concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Fly" EXACT [] -is_a: EDAM:0002819 ! Invertebrates +synonym: "Fly" EXACT [http://edamontology.org] +is_a: EDAM_topic:2819 ! Invertebrates [Term] -id: EDAM:0003048 +id: EDAM_topic:3048 !{since=beta13} name: Mammals namespace: topic -def: "Informatics resources concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002820 ! Vertebrates +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:0000213 +id: EDAM_topic:0213 name: Mice or rats namespace: topic -def: "Informatics resources concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Mouse or rat" EXACT [] -is_a: EDAM:0003048 ! Mammals +synonym: "Mouse or rat" EXACT [http://edamontology.org] +is_a: EDAM_topic:3048 ! Mammals [Term] -id: EDAM:0000215 +id: EDAM_topic:0215 name: Worms namespace: topic -def: "Informatics resources concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Worm" EXACT [] -is_a: EDAM:0002819 ! Invertebrates +synonym: "Worm" EXACT [http://edamontology.org] +is_a: EDAM_topic:2819 ! Invertebrates [Term] -id: EDAM:0000217 +id: EDAM_topic:0217 name: Literature analysis namespace: topic -alt_id: EDAM:0000088 -alt_id: EDAM:0003058 -def: "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." [EDAM:EBI "EMBRACE definition"] -subset: 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 [] -synonym: "Literature sources" EXACT [] -is_a: EDAM:0003068 ! Literature and reference +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:0000606 +id: EDAM_topic:0606 name: Literature data resources namespace: topic -def: "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003068 ! Literature and reference -is_a: EDAM:0003071 ! Biological data resources +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:0003068 +id: EDAM_topic:3068 !{since=beta13} name: Literature and reference namespace: topic -def: "Informatics resources concerning the scientific literature, reference information and documentation." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000003 ! 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:0000218 +id: EDAM_topic:0218 name: Text mining namespace: topic -def: "Resources concerning the analysis of the biomedical and informatics literature." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Text data mining" EXACT [] +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:0000217 ! Literature analysis +is_a: EDAM_topic:0217 ! Literature analysis [Term] -id: EDAM:0000219 -alt_id: EDAM:0002256 +id: EDAM_topic:0219 +! alt_id: EDAM_topic:2256 name: Annotation namespace: topic -def: "Resources for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Ontology annotation" EXACT [] +subset: topics +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:0002829 ! Ontologies, nomenclature and classification +is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] -id: EDAM:0000221 +id: EDAM_topic:0221 name: Sequence annotation namespace: topic -def: "Annotate a molecular sequence." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000219 ! Annotation +subset: topics +def: "Annotate a molecular sequence." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_topic:0219 ! Annotation [Term] -id: EDAM:0000222 +id: EDAM_topic:0222 name: Genome annotation namespace: topic -def: "Annotate a genome." [EDAM:EBI "EMBRACE definition"] -subset: topic +subset: topics +def: "Annotate a genome." [http://edamontology.org] xref: BioCatalogue:Genome Annotation -is_obsolete: true -consider: EDAM:0000219 ! Annotation -consider: EDAM:0000621 ! Genome, proteome and model organisms +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_topic:0219 ! Annotation +consider: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] -id: EDAM:0002230 +id: EDAM_topic:2230 name: Classification namespace: topic -def: "Resources that help to identify, group, or name things in a structured way according to some schema based on observable relationships." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0002829 ! Ontologies, nomenclature and classification +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:0002829 +id: EDAM_topic:2829 name: Ontologies, nomenclature and classification namespace: topic -def: "Informatics resources 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." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000003 ! 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:0002811 +id: EDAM_topic:2811 name: Nomenclature namespace: topic -alt_id: EDAM:0000619 -def: "Informatics resources concerning biological nomenclature (naming), symbols and terminology." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002829 ! Ontologies, nomenclature and classification +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:0002229 +id: EDAM_topic:2229 name: Cell biology resources namespace: topic -def: "Informatics resources concerning cells, such as key genes and proteins involved in the cell cycle." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003070 ! Biological science resources +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:0003064 +id: EDAM_topic:3064 !{since=beta13} name: Developmental biology resources namespace: topic -def: "Informatics resources concerning how organisms grow and develop." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003070 ! Biological science resources +subset: topics +def: "Topic concerning how organisms grow and develop." [http://edamontology.org] +is_a: EDAM_topic:3070 ! Biological science resources [Term] -id: EDAM:0003067 +id: EDAM_topic:3067 !{since=beta13} name: Anatomy resources namespace: topic -def: "Informatics resources concerning the structures of living organisms." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003070 ! Biological science resources +subset: topics +def: "Topic concerning the structures of living organisms." [http://edamontology.org] +is_a: EDAM_topic:3070 ! Biological science resources [Term] -id: EDAM:0003065 +id: EDAM_topic:3065 !{since=beta13} name: Embryology resources namespace: topic -def: "Informatics resources concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003064 ! Developmental biology resources +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:0003053 +id: EDAM_topic:3053 !{since=beta13} name: Genetics namespace: topic -alt_id: EDAM:0002227 -def: "Informatics resources concerning the study of genes, genetic variation and heredity in living organisms." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Genetics data resources" EXACT [] -is_a: EDAM:0000003 ! 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:0002226 +id: EDAM_topic:2226 name: Structure determination namespace: topic -alt_id: EDAM:0000136 -def: "Informatics resources 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." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Structural determination" EXACT [] -synonym: "Structural assignment" EXACT [] -synonym: "Structure assignment" EXACT [] -synonym: "Raw structural data analysis" EXACT [] -is_a: EDAM:0000081 ! Structure analysis +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:0000595 +id: EDAM_topic:0595 name: Protein classification namespace: topic -alt_id: EDAM:0000129 -def: "Resources concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000078 ! Protein analysis -is_a: EDAM:0002829 ! Ontologies, nomenclature and classification -is_a: EDAM:0000594 ! Sequence classification +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:0000598 +id: EDAM_topic:0598 name: Sequence motif or profile namespace: topic -def: "Resources concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_obsolete: true -consider: EDAM:0000158 ! Sequence motifs -consider: EDAM:0000188 ! Sequence profiles and HMMs +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_topic:0158 ! Sequence motifs +consider: EDAM_topic:0188 ! Sequence profiles and HMMs [Term] -id: EDAM:0000601 +id: EDAM_topic:0601 name: Protein modifications namespace: topic -alt_id: EDAM:0000142 -def: "Informatics resources concerning protein chemical modifications, e.g. post-translational modifications." [EDAM:EBI "EMBRACE definition"] -comment: EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of term GO:0006464) and/or the Protein Modifications ontology (children of term MOD:00000) -subset: topic -xref: GO:0006464 ! protein modification process -synonym: "Protein post-translation modification" EXACT [] -is_a: EDAM:0000123 ! Protein properties -is_a: EDAM:0002225 ! Protein databases -seealso: GO:0006464 ! protein modification process -seealso: MOD:00000 ! protein modification - -[Term] -id: EDAM:0000602 +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 -alt_id: EDAM:0000198 -alt_id: EDAM:0000755 -def: "Data resources concerning biological pathways, networks and other models." [EDAM:EBI "EMBRACE definition"] -subset: topic +subset: topics +! alt_id: EDAM_topic:0198 +! alt_id: EDAM_topic:0755 +def: "Topic concerning biological pathways, networks and other models." [http://edamontology.org] xref: BioCatalogue:Pathways xref: BioCatalogue:Pathway Retrieval -is_a: EDAM:0002259 ! Systems biology -is_a: EDAM:0003071 ! Biological data resources +is_a: EDAM_topic:2259 ! Systems biology +is_a: EDAM_topic:3071 ! Biological data resources [Term] -id: EDAM:0003075 +id: EDAM_topic:3075 !{since=beta13} name: Biological system modelling namespace: topic -def: "Resources for modelling biological systems in mathematical terms." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002259 ! Systems biology +is_a: EDAM_topic:2259 ! Systems biology [Term] -id: EDAM:0003076 +id: EDAM_topic:3076 !{since=beta13} name: Network or pathway analysis namespace: topic -def: "The processing (including construction) and analysis of biological networks and pathways." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002259 ! Systems biology +subset: topics +def: "The processing (including construction) and analysis of biological networks and pathways." [http://edamontology.org] +is_a: EDAM_topic:2259 ! Systems biology [Term] -id: EDAM:0002259 +id: EDAM_topic:2259 name: Systems biology namespace: topic -def: "Informatics resources concerning the holistic modelling and analysis of biological systems and the interactions therein." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000003 ! Topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM:0000605 +id: EDAM_topic:0605 name: Informatics namespace: topic -alt_id: EDAM:0002841 -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." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000091 ! Data handling +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:0000607 +id: EDAM_topic:0607 name: Laboratory resources namespace: topic -def: "Data resources concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003071 ! Biological data resources +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:0000608 +id: EDAM_topic:0608 name: Cell culture resources namespace: topic -def: "Informatics resources concerning general cell culture or data on a specific cell lines." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000607 ! Laboratory resources +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:0000610 +id: EDAM_topic:0610 name: Ecoinformatics namespace: topic -def: "Informatics resources concerning the application of information technology to the ecological and environmental sciences." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Computational ecology" EXACT [] -synonym: "Ecological informatics" EXACT [] -is_a: EDAM:0000003 ! 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:0003063 +id: EDAM_topic:3063 !{since=beta13} name: Medical informatics resources namespace: topic -alt_id: EDAM:0000087 -def: "Informatics resources for the application of information technology to health, disease and biomedicine." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Health and disease" EXACT [] -synonym: "Healthcare informatics" EXACT [] -synonym: "Health informatics" EXACT [] -synonym: "Clinical informatics" EXACT [] -synonym: "Biomedical informatics" EXACT [] -is_a: EDAM:0000607 ! Laboratory resources +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:0003050 +id: EDAM_topic:3050 !{since=beta13} name: Biodiversity namespace: topic -def: "Informatics resources concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Biodiversity data resource" EXACT [] -synonym: "Biodiversity data resources" EXACT [] -is_a: EDAM:0000610 ! Ecoinformatics +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:0002840 +id: EDAM_topic:2840 name: Toxicoinformatics namespace: topic -def: "Informatics resources concerning the adverse effects of chemical substances on living organisms." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Computational toxicology" EXACT [] -is_a: EDAM:0002258 ! Chemoinformatics +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:0002661 +id: EDAM_topic:2661 name: Toxins and targets namespace: topic -def: "Informatics resources concerning structural and associated data for toxic chemical substances." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002840 ! Toxicoinformatics -is_a: EDAM:0000154 ! Small molecules +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:0000611 +id: EDAM_topic:0611 name: Electron microscopy namespace: topic -def: "Informatics resources concerning electron microscopy data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0002226 ! Structure determination +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:0002828 +id: EDAM_topic:2828 name: X-ray crystallography namespace: topic -def: "Resources concerning X-ray crystallography data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0002226 ! Structure determination +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:0000593 +id: EDAM_topic:0593 name: NMR namespace: topic -def: "Resources concerning raw NMR data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0002226 ! Structure determination +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:0000612 +id: EDAM_topic:0612 name: Cell cycle namespace: topic -alt_id: EDAM:0000609 -def: "Resources concerning the cell cycle including key genes and proteins." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0002229 ! Cell biology resources +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:0000613 +id: EDAM_topic:0613 name: Peptides and amino acids namespace: topic -alt_id: EDAM:0000604 -def: "Informatics resources concerning the physicochemical, biochemical or structural properties of amino acids or peptides." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000154 ! Small molecules +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:0000616 +id: EDAM_topic:0616 name: Organelle genes and proteins namespace: topic -def: "Informatics resources concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003078 ! Gene and protein resources +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:0000617 +id: EDAM_topic:0617 name: Ribosomal genes and proteins namespace: topic -def: "Informatics resources concerning ribosomes, typically of ribosome-related genes and proteins." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Ribosome genes and proteins" EXACT [] -is_a: EDAM:0000616 ! Organelle genes and proteins +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:0000621 +id: EDAM_topic:0621 name: Genome, proteome and model organisms namespace: topic -alt_id: EDAM:0000086 -alt_id: EDAM:0000591 -alt_id: EDAM:0000643 -alt_id: EDAM:0000800 -alt_id: EDAM:0000795 -def: "Informatics resources concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Genome map" EXACT [] -is_a: EDAM:0000622 ! Genomics -is_a: EDAM:0000121 ! Proteomics -is_a: EDAM:0000625 ! Genotype and phenotype resources +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 resources [Term] -id: EDAM:0000622 +id: EDAM_topic:0622 name: Genomics namespace: topic -alt_id: EDAM:0000093 -alt_id: EDAM:0000794 -def: "Informatics resources concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000003 ! Topic +is_a: EDAM_topic:0003 ! Topic [Term] -id: EDAM:0002816 +id: EDAM_topic:2816 name: Gene resources namespace: topic -alt_id: EDAM:0000630 -def: "Informatics resource (typically a database) primarily focussed on genes." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Gene database" EXACT [] -synonym: "Gene resource" EXACT [] -is_a: EDAM:0003071 ! Biological data resources -is_a: EDAM:0003053 ! Genetics +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] -id: EDAM:0003054 -name: Molecular genetics -namespace: topic -def: "Resources concerning the structure and function of genes at a molecular level." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0003053 ! 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:0003055 +id: EDAM_topic:3055 !{since=beta13} name: Quantitative genetics namespace: topic -def: "Resources concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003053 ! Genetics +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:0003056 +id: EDAM_topic:3056 !{since=beta13} name: Population genetics namespace: topic -def: "Resources 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:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003053 ! Genetics +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:0000623 +id: EDAM_topic:0623 name: Genes, gene family or system namespace: topic -def: "Data resources concerning particular gene(s), gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003052 ! Sequence clusters and classification -is_a: EDAM:0002816 ! Gene resources +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:0000624 +id: EDAM_topic:0624 name: Chromosomes namespace: topic -def: "Informatics resources concerning chromosomes." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003062 ! Genetic organisation +subset: topics +def: "Topic concerning chromosomes." [http://edamontology.org] +is_a: EDAM_topic:3062 ! Genetic organisation [Term] -id: EDAM:0000625 +id: EDAM_topic:0625 name: Genotype and phenotype resources namespace: topic -alt_id: EDAM:0002231 -def: "Informatics resources 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." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002816 ! Gene resources +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] +is_a: EDAM_topic:2816 ! Gene resources [Term] -id: EDAM:0003078 +id: EDAM_topic:3078 !{since=beta13} name: Gene and protein resources namespace: topic -def: "Data resources concerning specific genes and their encoded proteins or a related group of such genes and proteins." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Genes and proteins resources" EXACT [] -is_a: EDAM:0000635 ! Specific protein resources -is_a: EDAM:0000623 ! Genes, gene family or system +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:0003070 +id: EDAM_topic:3070 !{since=beta13} name: Biological science resources namespace: topic -alt_id: EDAM:0003066 -def: "Informatics resources concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Phenotype resource" EXACT [] -is_a: EDAM:0003071 ! Biological data resources +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:0000629 +id: EDAM_topic:0629 name: Gene expression and microarray namespace: topic -def: "Resources concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000197 ! Gene expression resources -consider: EDAM:0000200 ! Microarrays +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:0197 ! Gene expression resources +consider: EDAM_topic:0200 ! Microarrays [Term] -id: EDAM:0000634 +id: EDAM_topic:0634 name: Disease resources namespace: topic -def: "Informatics resources concerning diseases." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000625 ! Genotype and phenotype resources +subset: topics +def: "Topic concerning diseases." [http://edamontology.org] +is_a: EDAM_topic:0625 ! Genotype and phenotype resources [Term] -id: EDAM:0002813 +id: EDAM_topic:2813 name: Disease genes and proteins namespace: topic -alt_id: EDAM:0000819 -def: "Informatics resources concerning the genes, gene variations and proteins involved in one or more specific diseases." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000634 ! Disease resources -is_a: EDAM:0003078 ! Gene and protein resources +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:0000635 +id: EDAM_topic:0635 name: Specific protein resources namespace: topic -def: "Informatics resources concerning a particular protein, protein family or other group of proteins." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Specific protein" EXACT [] -is_a: EDAM:0002225 ! Protein databases +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:0000637 +id: EDAM_topic:0637 name: Taxonomy namespace: topic -def: "Informatics resources concerning organism classification, identification and naming." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002829 ! Ontologies, nomenclature and classification +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:0000639 +id: EDAM_topic:0639 name: Protein sequence analysis namespace: topic -alt_id: EDAM:0000125 -def: "Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000080 ! Sequence analysis -is_a: EDAM:0000078 ! Protein analysis +is_a: EDAM_topic:0080 ! Sequence analysis +is_a: EDAM_topic:0078 ! Protein analysis [Term] -id: EDAM:0003043 +id: EDAM_topic:3043 !{since=beta13} name: Protein sequences namespace: topic -def: "Data resources concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] -subset: 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:0003041 ! Sequence databases -is_a: EDAM:0002225 ! Protein databases +is_a: EDAM_topic:3041 ! Sequence databases +is_a: EDAM_topic:2225 ! Protein databases [Term] -id: EDAM:0000640 +id: EDAM_topic:0640 name: Nucleic acid sequence analysis namespace: topic -alt_id: EDAM:0000096 -def: "Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000080 ! Sequence analysis -is_a: EDAM:0000077 ! Nucleic acid analysis +is_a: EDAM_topic:0080 ! Sequence analysis +is_a: EDAM_topic:0077 ! Nucleic acid analysis [Term] -id: EDAM:0003042 +id: EDAM_topic:3042 !{since=beta13} name: Nucleic acid sequences namespace: topic -def: "Data resources concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003041 ! Sequence databases +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:0000641 +id: EDAM_topic:0641 name: Repeat sequences namespace: topic -alt_id: EDAM:0002262 -def: "Resources concerning the repetitive nature of molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Repeat sequence" EXACT [] +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:0000157 ! Sequence composition analysis -is_a: EDAM:0003041 ! Sequence databases +is_a: EDAM_topic:0157 ! Sequence composition analysis +is_a: EDAM_topic:3041 ! Sequence databases [Term] -id: EDAM:0000642 +id: EDAM_topic:0642 name: Low complexity sequences namespace: topic -alt_id: EDAM:0002263 -def: "Resources concerning the (character) complexity of molecular sequences, particularly regions of low complexity." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000157 ! Sequence composition analysis -is_a: EDAM:0003041 ! Sequence databases +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:0000644 +id: EDAM_topic:0644 name: Proteome namespace: topic -def: "Resources concerning a specific proteome including protein sequences and annotation." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000080 ! Sequence analysis +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." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0003041 ! Sequence database +! [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:0000654 +id: EDAM_topic:0654 name: DNA namespace: topic -alt_id: EDAM:0000098 -alt_id: EDAM:0000666 -alt_id: EDAM:0000627 -alt_id: EDAM:0000628 -def: "Resources concerning DNA sequences and structure, including processes such as methylation and replication." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0003042 ! Nucleic acid sequences +is_a: EDAM_topic:3042 ! Nucleic acid sequences [Term] -id: EDAM:0000655 +id: EDAM_topic:0655 name: mRNA, EST or cDNA namespace: topic -alt_id: EDAM:0000205 -def: "Resources concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Transcriptome" EXACT [] -is_a: EDAM:0000099 ! RNA +subset: topics +! alt_id: EDAM_topic:0205 +def: "Topic concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [http://edamontology.org] +synonym: "Transcriptome" EXACT [http://edamontology.org] +is_a: EDAM_topic:0099 ! RNA [Term] -id: EDAM:0000659 +id: EDAM_topic:0659 name: Functional RNA namespace: topic -alt_id: EDAM:0000113 -alt_id: EDAM:0000119 -alt_id: EDAM:0000664 -alt_id: EDAM:0000665 -alt_id: EDAM:0000120 -def: "Resources concerning functional or non-coding RNA sequences." [EDAM:EBI "EMBRACE definition"] +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). -subset: topic -is_a: EDAM:0000099 ! RNA +is_a: EDAM_topic:0099 ! RNA [Term] -id: EDAM:0003060 +id: EDAM_topic:3060 !{since=beta13} name: Regulatory RNA namespace: topic -alt_id: EDAM:0000661 -alt_id: EDAM:0000662 -alt_id: EDAM:0000117 -alt_id: EDAM:0000118 -def: "Resources concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA)." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0000659 ! Functional RNA +is_a: EDAM_topic:0659 ! Functional RNA [Term] -id: EDAM:0000660 +id: EDAM_topic:0660 name: rRNA namespace: topic -alt_id: EDAM:0000116 -def: "Resources concerning one or more ribosomal RNA (rRNA) sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000659 ! Functional RNA +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 RNA [Term] -id: EDAM:0000663 +id: EDAM_topic:0663 name: tRNA namespace: topic -alt_id: EDAM:0000115 -def: "Resources concerning one or more transfer RNA (tRNA) sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000659 ! Functional RNA +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 RNA [Term] -id: EDAM:0002814 +id: EDAM_topic:2814 name: Protein structure analysis namespace: topic -alt_id: EDAM:0000126 -alt_id: EDAM:0000590 -def: "Resources concerning protein secondary or tertiary structural data and/or associated annotation." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000078 ! Protein analysis -is_a: EDAM:0000081 ! Structure analysis +subset: topics +! alt_id: EDAM_topic:0126 +! alt_id: EDAM_topic:0590 +def: "Topic concerning protein secondary or tertiary structural data and/or associated annotation." [http://edamontology.org] +is_a: EDAM_topic:0078 ! Protein analysis +is_a: EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM:0003040 +id: EDAM_topic:3040 !{since=beta13} name: Protein structure namespace: topic -def: "Data resources concerning protein secondary or tertiary structural data and/or associated annotation." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003038 ! Structure databases -is_a: EDAM:0002225 ! Protein databases +subset: topics +def: "Topic concerning protein secondary or tertiary structural data and/or associated annotation." [http://edamontology.org] +is_a: EDAM_topic:3038 ! Structure databases +is_a: EDAM_topic:2225 ! Protein databases [Term] -id: EDAM:0000694 +id: EDAM_topic:0694 name: Protein secondary structure namespace: topic -alt_id: EDAM:0002124 -def: "Data resources concerning protein secondary structure or secondary structure alignments." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Protein secondary structure analysis" EXACT [] -is_a: EDAM:0003040 ! Protein structure +synonym: "Protein secondary structure analysis" EXACT [http://edamontology.org] +is_a: EDAM_topic:3040 ! Protein structure [Term] -id: EDAM:0000698 +id: EDAM_topic:0698 name: Protein tertiary structure namespace: topic -alt_id: EDAM:0002125 -def: "Data resources concerning protein tertiary structures." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003040 ! Protein structure +subset: topics +! alt_id: EDAM_topic:2125 +def: "Topic concerning protein tertiary structures." [http://edamontology.org] +is_a: EDAM_topic:3040 ! Protein structure [Term] -id: EDAM:0000697 +id: EDAM_topic:0697 name: RNA structure and alignment namespace: topic -def: "Resources concerning RNA secondary or tertiary structure and alignments." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "RNA structure" EXACT [] -synonym: "RNA structure alignment" EXACT [] -synonym: "RNA alignment" EXACT [] -is_a: EDAM:0000183 ! Structure alignment +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:0002826 +id: EDAM_topic:2826 name: Protein structure alignment namespace: topic -def: "Resources concerning protein secondary or tertiary structure alignments." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000183 ! Structure alignment -is_a: EDAM:0002814 ! Protein structure analysis +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:0000620 +id: EDAM_topic:0620 name: Drugs and targets namespace: topic -def: "Informatics resources concerning the structures of drugs, drug target, their interactions and binding affinities." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000154 ! Small molecules -is_a: EDAM:0000202 ! Pharmacoinformatics +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:0000618 +id: EDAM_topic:0618 name: Scents namespace: topic -def: "A database about scents." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000154 ! Small molecules +subset: topics +def: "A database about scents." [http://edamontology.org] +is_obsolete: true !{since=beta13} +consider: EDAM_topic:0154 ! Small molecules [Term] -id: EDAM:0000722 +id: EDAM_topic:0722 name: Nucleic acid classification namespace: topic -def: "Resources concerning nucleic acid classification (typically sequence classification)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002829 ! Ontologies, nomenclature and classification -is_a: EDAM:0000077 ! Nucleic acid analysis -is_a: EDAM:0000594 ! Sequence classification +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: "Resources concerning protein structural classifications." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0001770 ! Structure comparison -consider: EDAM:0000736 ! Protein domains and folds +! [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:0000724 +id: EDAM_topic:0724 name: Protein families namespace: topic -def: "Data resources concerning primarily proteins that have been classified as members of a protein family (or other grouping)." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Protein sequence classification" EXACT [] -synonym: "Protein secondary" EXACT [] -is_a: EDAM:0003052 ! Sequence clusters and classification -is_a: EDAM:0002225 ! Protein databases +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:0000736 +id: EDAM_topic:0736 name: Protein domains and folds namespace: topic -alt_id: EDAM:0000703 -alt_id: EDAM:0000700 -alt_id: EDAM:0000127 -def: "Resources concerning protein tertiary structural domains and folds." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000698 ! Protein tertiary structure -is_a: EDAM:0000724 ! Protein families +is_a: EDAM_topic:0698 ! Protein tertiary structure +is_a: EDAM_topic:0724 ! Protein families [Term] -id: EDAM:0000740 +id: EDAM_topic:0740 name: Nucleic acid sequence alignment namespace: topic -def: "Resources concerning nucleotide sequence alignments." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000182 ! Sequence alignment -is_a: EDAM:0000640 ! Nucleic acid sequence analysis +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:0000741 +id: EDAM_topic:0741 name: Protein sequence alignment namespace: topic -def: "Resources concerning protein sequence alignments." [EDAM:EBI "EMBRACE definition"] +subset: topics +def: "Topic concerning protein sequence alignments." [http://edamontology.org] comment: A sequence profile typically represents a sequence alignment. -subset: topic -is_a: EDAM:0000182 ! Sequence alignment -is_a: EDAM:0000639 ! Protein sequence analysis +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: "Resources concerning nucleotide sequence motifs, or sequence profiles derived from an nucleic acid sequence alignment." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000158 ! Sequence motifs +! [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: "Resources concerning protein sequence motifs, or sequence profiles derived from an protein sequence alignment." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000158 ! 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:0000747 +id: EDAM_topic:0747 name: Nucleic acid sites and features namespace: topic -alt_id: EDAM:0000105 -alt_id: EDAM:0000095 -def: "Data resources concerning positional features such as functional sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Nucleic acid functional sites" EXACT [] -synonym: "Nucleic acid features" EXACT [] -is_a: EDAM:0000160 ! Sequence sites and features -is_a: EDAM:0003042 ! Nucleic acid sequences +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:0003073 +id: EDAM_topic:3073 !{since=beta13} name: Nucleic acid feature detection namespace: topic -def: "Resources concerning the detection of positional features such as functional sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000640 ! Nucleic acid sequence analysis -is_a: EDAM:0003072 ! Sequence feature detection +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:0000748 +id: EDAM_topic:0748 name: Protein sites and features namespace: topic -alt_id: EDAM:0000124 -alt_id: EDAM:0000138 -def: "Data resources concerning positional features such as functional sites in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Protein functional sites" EXACT [] -synonym: "Protein sequence features" EXACT [] -is_a: EDAM:0000160 ! Sequence sites and features -is_a: EDAM:0003043 ! Protein sequences +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:0003074 +id: EDAM_topic:3074 !{since=beta13} name: Protein feature detection namespace: topic -def: "Resources concerning the detection, identification and analysis of positional protein sequence features, such as functional sites." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000639 ! Protein sequence analysis -is_a: EDAM:0003072 ! Sequence feature detection +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:0000749 +id: EDAM_topic:0749 name: Transcription factors and regulatory sites namespace: topic -alt_id: EDAM:0000811 -def: "Resources 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." [EDAM:EBI "EMBRACE definition"] +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 [] -synonym: "Transcription factors" EXACT [] -synonym: "Transcription factor and binding site" EXACT [] -is_a: EDAM:0000204 ! Gene regulation resources -is_a: EDAM:0000110 ! Transcription -is_a: EDAM:0000635 ! Specific protein resources -is_a: EDAM:0000747 ! Nucleic acid sites and features -is_a: EDAM:0003062 ! Genetic organisation -is_a: EDAM:0003073 ! Nucleic acid feature detection +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 resources +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:0000751 +id: EDAM_topic:0751 name: Phosphorylation sites namespace: topic -def: "Resources concerning protein phosphorylation and phosphorylation sites in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000601 ! Protein modifications -is_a: EDAM:0000748 ! Protein sites and features - +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:0000753 +id: EDAM_topic:0753 name: Metabolic pathways namespace: topic -def: "Informatics resources concerning metabolic pathways." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000602 ! Pathways, networks and models +subset: topics +def: "Topic concerning metabolic pathways." [http://edamontology.org] +is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM:0000754 +id: EDAM_topic:0754 name: Signaling pathways namespace: topic -def: "Informatics resources concerning signaling pathways." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000602 ! Pathways, networks and models +subset: topics +def: "Topic concerning signaling pathways." [http://edamontology.org] +is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM:0003044 +id: EDAM_topic:3044 !{since=beta13} name: Protein interaction networks namespace: topic -def: "Informatics resources concerning protein-protein interaction networks." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000602 ! Pathways, networks and models -is_a: EDAM:0000147 ! Protein-protein interactions +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:0000771 +id: EDAM_topic:0771 name: Biological models namespace: topic -alt_id: EDAM:0002267 -alt_id: EDAM:0002268 -def: "Informatics resources concerning mathematical or other models of biological processes." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic xref: BioCatalogue:Model Creation -is_a: EDAM:0000602 ! Pathways, networks and models +is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM:0002846 +id: EDAM_topic:2846 name: Gene regulatory networks namespace: topic -def: "Informatics resources concerning gene regulatory networks." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000602 ! Pathways, networks and models -is_a: EDAM:0000204 ! Gene regulation resources +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 resources [Term] -id: EDAM:0000767 +id: EDAM_topic:0767 name: Protein and peptide identification namespace: topic -alt_id: EDAM:0000603 -def: "Informatics resources concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Peptide identification and proteolysis" EXACT [] -synonym: "Proteomics data" EXACT [] -synonym: "Proteomics data resources" EXACT [] -is_a: EDAM:0000121 ! Proteomics -is_a: EDAM:0000639 ! Protein sequence analysis -is_a: EDAM:0002225 ! Protein databases +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:0000141 +id: EDAM_topic:0141 name: Protein cleavage sites and proteolysis namespace: topic -def: "Resources concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000639 ! Protein sequence analysis +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:0000769 +id: EDAM_topic:0769 name: Workflows namespace: topic -def: "Resources concerning biological or biomedical analytical workflows or pipelines." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000091 ! Data handling +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:0000220 +id: EDAM_topic:0220 name: Data processing and validation namespace: topic -alt_id: EDAM:0002286 -alt_id: EDAM:0002270 -alt_id: EDAM:0002834 -def: "Resources concerning basic manipulations of files or reports of generic biological data." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Report handling" EXACT [] -synonym: "File handling" EXACT [] -synonym: "Data file handling" EXACT [] -synonym: "Report processing" EXACT [] -is_a: EDAM:0000091 ! Data handling +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:0000770 +id: EDAM_topic:0770 name: Data types and objects namespace: topic -def: "Resources concerning structuring data into basic types and (computational) objects." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000091 ! Data handling +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:0000632 +id: EDAM_topic:0632 name: Probes and primers namespace: topic -alt_id: EDAM:0000207 -def: "Resources concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000607 ! Laboratory resources -is_a: EDAM:0003041 ! Sequence databases +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:0003032 +id: EDAM_topic:3032 !{since=beta13} name: Primer or probe design namespace: topic -def: "Informatics resources concerning the design of primers for PCR and DNA amplification or the design of molecular probes." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000080 ! Sequence analysis +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:0000779 +id: EDAM_topic:0779 name: Mitochondrial genes and proteins namespace: topic -def: "Informatics resources concerning mitochondria, typically of mitochondrial genes and proteins." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Mitochondria genes and proteins" EXACT [] -is_a: EDAM:0000616 ! Organelle genes and proteins +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:0002818 +id: EDAM_topic:2818 name: Eukaryotes namespace: topic -alt_id: EDAM:0000669 -def: "Informatics resources concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Eukaryote" EXACT [] -is_a: EDAM:0000621 ! Genome, proteome and model organisms +synonym: "Eukaryote" EXACT [http://edamontology.org] +is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] -id: EDAM:0002821 +id: EDAM_topic:2821 name: Unicellular eukaryotes namespace: topic -alt_id: EDAM:0000675 -def: "Informatics resources concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Unicellular eukaryote" EXACT [] -is_a: EDAM:0002818 ! Eukaryotes +synonym: "Unicellular eukaryote" EXACT [http://edamontology.org] +is_a: EDAM_topic:2818 ! Eukaryotes + [Term] -id: EDAM:0002819 +id: EDAM_topic:2819 name: Invertebrates namespace: topic -alt_id: EDAM:0000678 -def: "Informatics resources concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -is_a: EDAM:0002818 ! Eukaryotes +is_a: EDAM_topic:2818 ! Eukaryotes [Term] -id: EDAM:0002820 +id: EDAM_topic:2820 name: Vertebrates namespace: topic -alt_id: EDAM:0000679 -def: "Informatics resources concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Vertebrate" EXACT [] -is_a: EDAM:0002818 ! Eukaryotes +synonym: "Vertebrate" EXACT [http://edamontology.org] +is_a: EDAM_topic:2818 ! Eukaryotes [Term] -id: EDAM:0002815 +id: EDAM_topic:2815 name: Humans namespace: topic -alt_id: EDAM:0000692 -alt_id: EDAM:0000687 -def: "Informatics resources concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Human" EXACT [] -is_a: EDAM:0003048 ! Mammals +synonym: "Human" EXACT [http://edamontology.org] +is_a: EDAM_topic:3048 ! Mammals [Term] -id: EDAM:0000780 +id: EDAM_topic:0780 name: Plants namespace: topic -alt_id: EDAM:0000677 -alt_id: EDAM:0000785 -alt_id: EDAM:0000784 -alt_id: EDAM:0000214 -def: "Informatics resources concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Plant" EXACT [] -is_a: EDAM:0002818 ! Eukaryotes +synonym: "Plant" EXACT [http://edamontology.org] +is_a: EDAM_topic:2818 ! Eukaryotes [Term] -id: EDAM:0000781 +id: EDAM_topic:0781 name: Viruses namespace: topic -alt_id: EDAM:0000790 -alt_id: EDAM:0000671 -alt_id: EDAM:0000791 -def: "Informatics resources concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Virus" EXACT [] -is_a: EDAM:0000621 ! Genome, proteome and model organisms +synonym: "Virus" EXACT [http://edamontology.org] +is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] -id: EDAM:0000782 +id: EDAM_topic:0782 name: Fungi namespace: topic -alt_id: EDAM:0000792 -alt_id: EDAM:0000793 -alt_id: EDAM:0000676 -def: "Informatics resources concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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 [] -subset: topic -is_a: EDAM:0002818 ! Eukaryotes +synonym: "Fungal" EXACT [http://edamontology.org] +is_a: EDAM_topic:2818 ! Eukaryotes [Term] -id: EDAM:0000783 +id: EDAM_topic:0783 name: Pathogens namespace: topic -def: "Informatics resources concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Pathogen" EXACT [] -is_a: EDAM:0000621 ! Genome, proteome and model organisms +synonym: "Pathogen" EXACT [http://edamontology.org] +is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] -id: EDAM:0001811 +id: EDAM_topic:1811 name: Prokaryotes and archae namespace: topic -alt_id: EDAM:0000691 -alt_id: EDAM:0000670 -alt_id: EDAM:0000212 -def: "Informatics resources concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: topic -synonym: "Prokaryote and archae" EXACT [] -is_a: EDAM:0000621 ! Genome, proteome and model organisms +synonym: "Prokaryote and archae" EXACT [http://edamontology.org] +is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] -id: EDAM:0000786 +id: EDAM_topic:0786 name: Arabidopsis namespace: topic -def: "Informatics resources concerning Arabidopsis-specific data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000780 ! Plants +subset: topics +def: "Topic concerning Arabidopsis-specific data." [http://edamontology.org] +is_a: EDAM_topic:0780 ! Plants [Term] -id: EDAM:0000787 +id: EDAM_topic:0787 name: Rice namespace: topic -def: "Informatics resources concerning rice-specific data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000780 ! Plants +subset: topics +def: "Topic concerning rice-specific data." [http://edamontology.org] +is_a: EDAM_topic:0780 ! Plants [Term] -id: EDAM:0002817 +id: EDAM_topic:2817 name: Yeast namespace: topic -alt_id: EDAM:0000682 -alt_id: EDAM:0000216 -def: "Informatics resources concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000782 ! Fungi +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:0000796 +id: EDAM_topic:0796 name: Genetic mapping and linkage namespace: topic -alt_id: EDAM:0000103 -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." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Genetic linkage" EXACT [] -synonym: "Linkage mapping" EXACT [] -is_a: EDAM:0000102 ! Sequencing and mapping -relationship: has_topic EDAM:0003053 ! Genetics +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 ! Sequencing and mapping +relationship: has_topic EDAM_topic:3053 ! Genetics [Term] -id: EDAM:0000797 +id: EDAM_topic:0797 name: Comparative genomics namespace: topic -alt_id: EDAM:0000101 -def: "Informatics resources for the study (typically comparison) of the structure or function of multiple genomes." [EDAM:EBI "EMBRACE definition"] -subset: topic +subset: topics +! alt_id: EDAM_topic:0101 +def: "Topic for the study (typically comparison) of the structure or function of multiple genomes." [http://edamontology.org] xref: BioCatalogue:Comparative Genomics -is_a: EDAM:0000622 ! Genomics +is_a: EDAM_topic:0622 ! Genomics [Term] -id: EDAM:0000798 +id: EDAM_topic:0798 name: Mobile genetic elements namespace: topic -def: "Resources concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0003062 ! Genetic organisation +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:0000801 -name: Human genes -namespace: resources -def: "Resources concerning human genes." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000623 ! Genes, gene family or system +! [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:0000803 +id: EDAM_topic:0803 name: Human disease namespace: topic -def: "Resources concerning human diseases, typically describing the genes, mutations and proteins implicated in disease." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000634 ! Disease resources +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:0000804 +id: EDAM_topic:0804 name: Immunoinformatics namespace: topic -alt_id: EDAM:0000201 -alt_id: EDAM:0000633 -def: "Informatics resources for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Computational immunology" EXACT [] -is_a: EDAM:0000003 ! Topics +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 ! Topics [Term] -id: EDAM:0002830 +id: EDAM_topic:2830 name: Immunity genes, immunoproteins and antigens namespace: topic -def: "Informatics resources concerning immunity-related genes, proteins and their ligands." [EDAM:EBI "EMBRACE definition"] +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." -subset: topic -synonym: "Immunoproteins and immunopeptides" EXACT [] -is_a: EDAM:0000804 ! Immunoinformatics -is_a: EDAM:0003078 ! Gene and protein resources +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:0002847 +id: EDAM_topic:2847 name: Disease (specific) namespace: topic -def: "Informatics resources dedicated to one or more specific diseases (not diseases in general)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000634 ! Disease resources +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:0002640 +id: EDAM_topic:2640 name: Cancer resources namespace: topic -alt_id: EDAM:0000805 -def: "Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000634 ! Disease resources +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] +is_a: EDAM_topic:0634 ! Disease resources [Term] -id: EDAM:0000820 +id: EDAM_topic:0820 name: Membrane proteins namespace: topic -alt_id: EDAM:0000131 -def: "Informatics resources concerning a protein or region of a protein that spans a membrane." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Transmembrane proteins" EXACT [] -is_a: EDAM:0000635 ! Specific protein resources +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:0000821 +id: EDAM_topic:0821 name: Enzymes and reactions namespace: topic -alt_id: EDAM:0000132 -def: "Informatics resources concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000635 ! Specific protein resources +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 + + + + + + + + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + + + + + ! @@ -3520,2765 +3201,2769 @@ is_a: EDAM:0000635 ! Specific protein resources [Term] -id: EDAM:0000223 -name: Undefined -namespace: operation -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true - - -[Term] -id: EDAM:0002945 +id: EDAM_operation:2945 name: Analysis namespace: operation -def: "Apply analytical methods to existing data of a specific type." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_obsolete: true -consider: EDAM:0002420 ! Analysis and processing +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_operation:2420 ! Analysis and processing [Term] -id: EDAM:0002420 +id: EDAM_operation:2420 name: Analysis and processing namespace: operation -def: "Process (read and / or write) data of a specific type, for example applying analytical methods." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Calculation" EXACT [] -synonym: "Computation" EXACT [] -is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000006 ! Data {minCardinality=0} -relationship: has_output EDAM:0000006 ! Data {minCardinality=0} +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 ! Data ! !{min_cardinality=0} +relationship: has_output EDAM_data:0006 ! Data ! !{min_cardinality=0} [Term] -id: EDAM:0002423 +id: EDAM_operation:2423 name: Prediction, detection and recognition namespace: operation -def: "Predict, recognise, detect or identify some properties of a biomolecule." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000004 ! 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:0003023 +id: EDAM_operation:3023 name: Prediction, detection and recognition (protein) namespace: operation -def: "Predict, recognise, detect or identify some properties of proteins." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002423 ! Prediction, detection and recognition +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:0003024 +id: EDAM_operation:3024 name: Prediction, detection and recognition (nucleic acid) namespace: operation -def: "Predict, recognise, detect or identify some properties of nucleic acids." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002423 ! Prediction, detection and recognition +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:0002946 +id: EDAM_operation:2946 name: Alignment analysis namespace: operation -def: "Analyse an existing alignment of two or more molecular sequences, structures or derived data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002951 ! Alignment processing -relationship: has_input EDAM:0001916 ! Alignment {minCardinality=1} ! Extends cardinality constraint on parent. -relationship: has_output EDAM:0002083 ! Alignment report {minCardinality=1} +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:0002947 +id: EDAM_operation:2947 name: Article analysis namespace: operation -def: "Analyse a body of scientific text (typically a full text article from a scientific journal.)" [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002505 ! Text processing -relationship: has_input EDAM:0000971 ! Article {minCardinality=1} -relationship: has_output EDAM:0002954 ! Article report -relationship: has_topic EDAM:0000217 ! Literature analysis +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:0002993 +id: EDAM_operation:2993 name: Molecular interaction data processing namespace: operation -def: "Process (read and / or write) molecular interaction data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true +subset: operations +def: "Process (read and / or write) molecular interaction data." [http://edamontology.org] +is_obsolete: true !{since=beta13} [Term] -id: EDAM:0002948 +id: EDAM_operation:2948 name: Molecular interaction analysis namespace: operation -def: "Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true +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:0002949 +id: EDAM_operation:2949 name: Protein interaction analysis namespace: operation -def: "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002405 ! Protein interaction data processing -relationship: has_output EDAM:0000906 ! Protein report (interaction) {minCardinality=1} -relationship: has_topic EDAM:0000128 ! Protein interactions +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 report (interaction) +relationship: has_topic EDAM_topic:0128 ! Protein interactions [Term] -id: EDAM:0003096 +id: EDAM_operation:3096 !{since=beta13} name: Editing namespace: operation -def: "Edit, convert or otherwise change a data entity, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000004 ! 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:0002928 -name: Alignment +id: EDAM_operation:2928 +name: Alignment construction namespace: operation -def: "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000004 ! Operation -is_a: EDAM:0002951 ! Alignment processing -relationship: has_output EDAM:0001916 ! Alignment {minCardinality=1} +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:0004 ! Operation +is_a: EDAM_operation:2951 ! Alignment processing +relationship: has_output EDAM_data:1916 !{min_cardinality=1} ! Alignment [Term] -id: EDAM:0002424 +id: EDAM_operation:2424 name: Comparison namespace: operation -def: "Compare two or more things to identify similarities." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000004 ! Operation +subset: operations +def: "Compare two or more things to identify similarities." [http://edamontology.org] +is_a: EDAM_operation:0004 ! Operation [Term] -id: EDAM:0002997 +id: EDAM_operation:2997 name: Protein comparison namespace: operation -def: "Compare two or more proteins (or some aspect) to identify similarities." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002424 ! Comparison +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:0002998 +id: EDAM_operation:2998 name: Nucleic acid comparison namespace: operation -def: "Compare two or more nucleic acids to identify similarities." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002424 ! Comparison +subset: operations +def: "Compare two or more nucleic acids to identify similarities." [http://edamontology.org] +is_a: EDAM_operation:2424 ! Comparison [Term] -id: EDAM:0002990 +id: EDAM_operation:2990 name: Classification namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000004 ! Operation -relationship: has_output EDAM:0002987 ! Classification {minCardinality=1} +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:0002995 +id: EDAM_operation:2995 name: Sequence classification namespace: operation -def: "Assign molecular sequence(s) to a group or category." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002990 ! Classification -is_a: EDAM:0002403 ! Sequence analysis +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:0003093 +id: EDAM_operation:3093 !{since=beta13} name: Sequence screening namespace: operation -def: "Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002995 ! Sequence classification +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:0002996 +id: EDAM_operation:2996 name: Structure classification namespace: operation -def: "Assign molecular structure(s) to a group or category." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002990 ! Classification -is_a: EDAM:0002480 ! Structure analysis +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:0002425 +id: EDAM_operation:2425 name: Optimisation and refinement namespace: operation -def: "Refine or optimise some data model." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000004 ! Operation +subset: operations +def: "Refine or optimise some data model." [http://edamontology.org] +is_a: EDAM_operation:0004 ! Operation [Term] -id: EDAM:0002426 +id: EDAM_operation:2426 name: Modelling and simulation namespace: operation -def: "Model or simulate some biological entity or system." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000004 ! Operation -relationship: has_topic EDAM:0002275 ! Molecular modelling +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:0002427 +id: EDAM_operation:2427 name: Data handling namespace: operation -def: "Perform basic operations on some data or a database." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002420 ! Analysis and processing +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:0002428 -name: Validation and standardisation +id: EDAM_operation:2428 +name: Evaluation and validation namespace: operation -def: "Validate or standardise some data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000004 ! 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:0002429 +id: EDAM_operation:2429 name: Mapping and assembly namespace: operation -def: "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad concept and is used a placeholder for other, more specific terms. -subset: operation -is_a: EDAM:0000004 ! Operation -relationship: has_topic EDAM:0000102 ! Sequencing and mapping +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 ! Sequencing and mapping [Term] -id: EDAM:0002430 +id: EDAM_operation:2430 name: Design namespace: operation -def: "Design a biological entity (typically a molecular sequence or structure) with specific properties." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) +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:0002238 +id: EDAM_operation:2238 name: Statistical calculation namespace: operation -def: "Perform a statistical data operation of some type, e.g. calibration or validation." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000004 ! 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:0000224 +id: EDAM_operation:0224 name: Search and retrieval namespace: operation -def: "Search or query a data resource and retrieve entries and / or annotation." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Database retrieval" EXACT [] -is_a: EDAM:0000004 ! Operation -relationship: has_output EDAM:0000006 ! Data {minCardinality=0} -relationship: has_topic EDAM:0000090 ! Data search and retrieval +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 ! Data ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0090 ! Data search and retrieval [Term] -id: EDAM:0002501 +id: EDAM_operation:2501 name: Nucleic acid data processing namespace: operation -def: "Process (read and / or write) nucleic acid sequence or structural data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002084 ! Nucleic acid report {minCardinality=0} -relationship: has_output EDAM:0002084 ! Nucleic acid report {minCardinality=0} -relationship: has_topic EDAM:0000077 ! Nucleic acid analysis +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 ! Nucleic acid report ! !{min_cardinality=0} +relationship: has_output EDAM_data:2084 ! Nucleic acid report ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] -id: EDAM:0002502 +id: EDAM_operation:2502 name: Protein data processing namespace: operation -def: "Process (read and / or write) protein sequence or structural data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0000896 ! Protein report {minCardinality=0} -relationship: has_output EDAM:0000896 ! Protein report {minCardinality=0} -relationship: has_topic EDAM:0000078 ! Protein analysis +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 ! Protein report ! !{min_cardinality=0} +relationship: has_output EDAM_data:0896 ! Protein report ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0078 ! Protein analysis [Term] -id: EDAM:0002407 +id: EDAM_operation:2407 name: Annotation processing namespace: operation -def: "Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002951 +id: EDAM_operation:2951 name: Alignment processing namespace: operation -def: "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0001916 ! Alignment {minCardinality=0} -relationship: has_output EDAM:0001916 ! Alignment {minCardinality=0} +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 ! Alignment ! !{min_cardinality=0} +relationship: has_output EDAM_data:1916 ! Alignment ! !{min_cardinality=0} [Term] -id: EDAM:0002412 +id: EDAM_operation:2412 name: Data index processing namespace: operation -def: "Process (read and / or write) an index of (typically a file of) biological data." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Database index processing" EXACT [] -is_a: EDAM:0002409 ! File processing -relationship: has_input EDAM:0000955 ! Data index {minCardinality=0} -relationship: has_output EDAM:0000955 ! Data index {minCardinality=0} -relationship: has_topic EDAM:0000220 ! Data processing and validation +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 ! Data index ! !{min_cardinality=0} +relationship: has_output EDAM_data:0955 ! Data index ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] -id: EDAM:0002504 +id: EDAM_operation:2504 name: Structural data processing namespace: operation -def: "Process (read and / or write) molecular structural data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002465 ! Structure processing +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:0002403 +id: EDAM_operation:2403 name: Sequence analysis namespace: operation -alt_id: EDAM:0002477 -def: "Analyse one or more known molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Sequence analysis (general)" EXACT [] -is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} -relationship: has_output EDAM:0002955 ! Sequence report {minCardinality=1} -relationship: has_topic EDAM:0000080 ! Sequence analysis +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:0002408 +id: EDAM_operation:2408 name: Sequence feature analysis namespace: operation -def: "Analyse features in molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000253 ! Sequence feature detection +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:0002404 +id: EDAM_operation:2404 name: Sequence motif processing namespace: operation -def: "Process (read and / or write) molecular sequence motifs." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0001353 ! Sequence motif {minCardinality=0} -relationship: has_output EDAM:0001353 ! Sequence motif {minCardinality=0} -relationship: has_topic EDAM:0000158 ! Sequence motifs +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 ! Sequence motif ! !{min_cardinality=0} +relationship: has_output EDAM_data:1353 ! Sequence motif ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] -id: EDAM:0002417 +id: EDAM_operation:2417 name: Physicochemical property data processing namespace: operation -def: "Process (read and / or write) data on the physicochemical property of a molecule." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002420 ! Analysis and processing +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:0002414 +id: EDAM_operation:2414 name: Protein function analysis namespace: operation -def: "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad concept and is used a placeholder for other, more specific terms. -subset: operation -is_a: EDAM:0002502 ! Protein data processing -relationship: has_output EDAM:0000896 ! Protein report +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:0000258 +id: EDAM_operation:0258 name: Sequence alignment analysis namespace: operation -def: "Analyse a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002463 ! Sequence alignment processing -is_a: EDAM:0002946 ! Alignment analysis -relationship: has_input EDAM:0000292 ! Sequence alignment {minCardinality=1} ! Extends cardinality constraint on parent. -relationship: has_output EDAM:0000867 ! Sequence alignment report {minCardinality=1} -relationship: has_topic EDAM:0000182 ! Sequence alignment +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:0002506 +id: EDAM_operation:2506 name: Sequence alignment analysis (protein) namespace: operation -def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000258 ! Sequence alignment analysis -is_a: EDAM:0002502 ! Protein data processing -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_input EDAM:0001384 ! Sequence alignment (protein) {minCardinality=1} -relationship: has_topic EDAM:0000741 ! Protein sequence alignment +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:0002507 +id: EDAM_operation:2507 name: Sequence alignment analysis (nucleic acid) namespace: operation -def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000258 ! Sequence alignment analysis -is_a: EDAM:0002501 ! Nucleic acid data processing -is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_input EDAM:0001383 ! Sequence alignment (nucleic acid) {minCardinality=1} -relationship: has_topic EDAM:0000740 ! Nucleic acid sequence alignment +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:0002416 +id: EDAM_operation:2416 name: Protein secondary structure analysis namespace: operation -def: "Analyse known protein secondary structure data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002444 ! Protein secondary structure processing -synonym: "Secondary structure analysis (protein)" EXACT [] -relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} -relationship: has_output EDAM:0002956 ! Protein secondary structure report -relationship: has_topic EDAM:0000694 ! Protein secondary structure +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:0000270 +id: EDAM_operation:0270 name: Transmembrane protein analysis namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -comment: Use this (or child) term 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: operation -is_a: EDAM:0002502 ! Protein data processing -relationship: has_output EDAM:0001456 ! Protein features (membrane regions) -relationship: has_topic EDAM:0000820 ! Membrane proteins +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:0002476 +id: EDAM_operation:2476 name: Molecular dynamics simulation namespace: operation -def: "Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002423 ! Prediction, detection and recognition -is_a: EDAM:0002480 ! Structure analysis -is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_output EDAM:0000883 ! Structure -relationship: has_topic EDAM:0000082 ! Structure prediction -relationship: has_topic EDAM:0000176 ! Molecular dynamics +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:0000271 +id: EDAM_operation:0271 name: Structure prediction namespace: operation -def: "Predict tertiary structure of a molecular (biopolymer) sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002423 ! Prediction, detection and recognition -is_a: EDAM:0002465 ! Structure processing -relationship: has_output EDAM:0000883 ! Structure -relationship: has_topic EDAM:0000082 ! Structure prediction +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:0002405 +id: EDAM_operation:2405 name: Protein interaction data processing namespace: operation -def: "Process (read and / or write) protein interaction data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000906 ! Protein report (interaction) {minCardinality=0} -relationship: has_output EDAM:0000906 ! Protein report (interaction) {minCardinality=0} -relationship: has_topic EDAM:0000128 ! Protein interactions +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 ! Protein report (interaction) ! !{min_cardinality=0} +relationship: has_output EDAM_data:0906 ! Protein report (interaction) ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0128 ! Protein interactions [Term] -id: EDAM:0002521 +id: EDAM_operation:2521 name: Map data processing namespace: operation -def: "Process (read and / or write) a DNA map of some type." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "DNA map data processing" EXACT [] -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0001274 ! Map {minCardinality=0} -relationship: has_output EDAM:0001274 ! Map {minCardinality=0} -relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage +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 ! Map ! !{min_cardinality=0} +relationship: has_output EDAM_data:1274 ! Map ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] -id: EDAM:0002520 +id: EDAM_operation:2520 name: DNA mapping namespace: operation -def: "Generate a map of a DNA sequence annotated with positional or non-positional features of some type." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002521 ! Map data processing -is_a: EDAM:0002429 ! Mapping and assembly -relationship: has_output EDAM:0001274 ! Map {minCardinality=1} -relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage +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:0000282 +id: EDAM_operation:0282 name: Genetic mapping namespace: operation -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Genetic map generation" EXACT [] -synonym: "Linkage mapping" EXACT [] -is_a: EDAM:0002520 ! DNA mapping -relationship: has_output EDAM:0001278 ! Genetic map {minCardinality=1} -relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage +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:0002944 +id: EDAM_operation:2944 name: Physical mapping namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002520 ! DNA mapping -relationship: has_output EDAM:0001280 ! Physical map {minCardinality=1} -relationship: has_topic EDAM:0000102 ! Sequencing and mapping +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 ! Sequencing and mapping [Term] -id: EDAM:0002871 +id: EDAM_operation:2871 name: Sequence tagged site (STS) mapping namespace: operation -def: "Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Sequence mapping" EXACT [] -is_a: EDAM:0002944 ! Physical mapping -relationship: has_output EDAM:0001279 ! Sequence map {minCardinality=1} +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:0000283 +id: EDAM_operation:0283 name: Linkage analysis namespace: operation -def: "Analyse genetic linkage." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002478 ! Nucleic acid sequence analysis -relationship: has_output EDAM:0000927 ! Gene annotation (linkage) -relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage +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:0002493 +id: EDAM_operation:2493 name: Codon usage data processing namespace: operation -def: "Process (read and / or write) codon usage data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000286 ! Codon usage analysis +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:0002503 +id: EDAM_operation:2503 name: Sequence data processing namespace: operation -def: "Process (read and / or write) molecular sequence data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002446 ! Sequence processing +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:0002463 +id: EDAM_operation:2463 name: Sequence alignment processing namespace: operation -def: "Process (read and / or write) a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002951 ! Alignment processing -relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=0} -relationship: has_output EDAM:0000863 ! Sequence alignment {minCardinality=0} -relationship: has_topic EDAM:0000182 ! Sequence alignment +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 ! Sequence alignment ! !{min_cardinality=0} +relationship: has_output EDAM_data:0863 ! Sequence alignment ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] -id: EDAM:0002952 +id: EDAM_operation:2952 name: Structure alignment processing namespace: operation -def: "Process (read and / or write) a molecular tertiary (3D) structure alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002951 ! Alignment processing -relationship: has_input EDAM:0000886 ! Structure alignment {minCardinality=0} -relationship: has_output EDAM:0000886 ! Structure alignment {minCardinality=0} -relationship: has_topic EDAM:0000183 ! Structure alignment +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 ! Structure alignment ! !{min_cardinality=0} +relationship: has_output EDAM_data:0886 ! Structure alignment ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] -id: EDAM:0000292 -name: Sequence alignment +id: EDAM_operation:0292 +name: Sequence alignment construction namespace: operation -def: "Align (identify equivalent sites within) molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Sequence alignment generation" EXACT [] -is_a: EDAM:0002463 ! Sequence alignment processing -is_a: EDAM:0002451 ! Sequence comparison -is_a: EDAM:0002928 ! Alignment -relationship: has_output EDAM:0000863 ! Sequence alignment {minCardinality=1} -relationship: has_topic EDAM:0000182 ! Sequence alignment +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 !{min_cardinality=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:0000293 -name: Hybrid sequence alignment +id: EDAM_operation:0293 +name: Hybrid sequence alignment construction namespace: operation -def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000292 ! Sequence alignment +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 [Term] -id: EDAM:0000294 -name: Structure-based sequence alignment +id: EDAM_operation:0294 +name: Structure-based sequence alignment construction namespace: operation -def: "Align molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000292 ! Sequence alignment -relationship: has_topic EDAM:0000182 ! Sequence alignment +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:0002480 +id: EDAM_operation:2480 name: Structure analysis namespace: operation -alt_id: EDAM:0002431 -def: "Analyse known molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002465 ! Structure processing -relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} -relationship: has_output EDAM:0002085 ! Structure report {minCardinality=1} -relationship: has_topic EDAM:0000081 ! Structure analysis +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:0002931 +id: EDAM_operation:2931 name: Secondary structure comparison namespace: operation -def: "Compare two or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002424 ! Comparison -relationship: has_input EDAM:0002081 ! Secondary structure {minCardinality=2} -relationship: has_output EDAM:0002881 ! Secondary structure report {minCardinality=1} -relationship: has_topic EDAM:0001770 ! Structure comparison +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:0002483 +id: EDAM_operation:2483 name: Structure comparison namespace: operation -def: "Compare two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002424 ! Comparison -is_a: EDAM:0002480 ! Structure analysis -relationship: has_topic EDAM:0001770 ! Structure comparison +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:0000295 -name: Structure alignment +id: EDAM_operation:0295 +name: Structure alignment construction namespace: operation -def: "Align (superimpose) molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002928 ! Alignment -is_a: EDAM:0002483 ! Structure comparison -is_a: EDAM:0002952 ! Structure alignment processing -relationship: has_output EDAM:0000886 ! Structure alignment {minCardinality=1} -relationship: has_topic EDAM:0000183 ! Structure alignment +subset: operations +def: "Align (superimpose) molecular tertiary structures." [http://edamontology.org] +synonym: "Structure alignment" EXACT [http://edamontology.org] +is_a: EDAM_operation:2928 ! Alignment +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:0002413 +id: EDAM_operation:2413 name: Sequence profile processing namespace: operation -def: "Process (read and / or write) some type of sequence profile." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0001354 ! Sequence profile {minCardinality=0} -relationship: has_output EDAM:0001354 ! Sequence profile {minCardinality=0} -relationship: has_topic EDAM:0000188 ! Sequence profiles and HMMs +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 ! Sequence profile ! !{min_cardinality=0} +relationship: has_output EDAM_data:1354 ! Sequence profile ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] -id: EDAM:0002411 +id: EDAM_operation:2411 name: Structural (3D) profile processing namespace: operation -def: "Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=0} -relationship: has_output EDAM:0000889 ! Structural (3D) profile {minCardinality=0} -relationship: has_topic EDAM:0000167 ! Structural (3D) profiles +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 ! Structural (3D) profile ! !{min_cardinality=0} +relationship: has_output EDAM_data:0889 ! Structural (3D) profile ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] -id: EDAM:0000303 +id: EDAM_operation:0303 name: Protein fold recognition namespace: operation -def: "Recognize (predict and identify) known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Protein domain prediction" EXACT [] -synonym: "Protein fold prediction" EXACT [] -is_a: EDAM:0000414 ! Protein feature detection (from sequence) -is_a: EDAM:0000474 ! Protein structure prediction -is_a: EDAM:0002997 ! Protein comparison -relationship: has_output EDAM:0000901 ! Protein features (domains) {minCardinality=1} -relationship: has_topic EDAM:0000184 ! Threading +synonym: "Protein domain prediction" EXACT [http://edamontology.org] +synonym: "Protein fold prediction" EXACT [http://edamontology.org] +is_a: EDAM_operation:0414 ! Protein feature detection (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:0002246 +id: EDAM_operation:2246 name: Demonstration namespace: operation -def: "An operation performing purely illustrative (pedagogical) purposes." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true +subset: operations +def: "An operation performing purely illustrative (pedagogical) purposes." [http://edamontology.org] +is_obsolete: true !{since=beta13} [Term] -id: EDAM:0002505 +id: EDAM_operation:2505 name: Text processing namespace: operation -def: "Process (read and / or write) text." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002048 ! Report {minCardinality=0} -relationship: has_output EDAM:0002048 ! Report {minCardinality=0} +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 ! Report ! !{min_cardinality=0} +relationship: has_output EDAM_data:2048 ! Report ! !{min_cardinality=0} [Term] -id: EDAM:0000306 +id: EDAM_operation:0306 name: Text mining namespace: operation -def: "Process and analyse text (typically the biomedical and informatics literature) to extract information from it." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Text data mining" EXACT [] -is_a: EDAM:0002947 ! Article analysis -relationship: has_input EDAM:0002048 ! Report {minCardinality=0} -relationship: has_output EDAM:0000972 ! Text mining report -relationship: has_topic EDAM:0000218 ! Text mining +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 ! Report ! !{min_cardinality=0} +relationship: has_output EDAM_data:0972 ! Text mining report +relationship: has_topic EDAM_topic:0218 ! Text mining [Term] -id: EDAM:0002419 +id: EDAM_operation:2419 name: Primer and probe design namespace: operation -def: "Predict oligonucleotide primers or probes." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003095 ! Nucleic acid design -is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -synonym: "Primer and probe prediction" EXACT [] -relationship: has_topic EDAM:0003032 ! Primer or probe design +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:0000310 +id: EDAM_operation:0310 name: Sequence assembly namespace: operation -def: "Assemble fragments of a DNA sequence to reconstruct the original sequence." [EDAM:EBI "EMBRACE definition"] +subset: operations +def: "Assemble fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] comment: Typically, contigs (for example ESTs and genomic DNA fragments) are aligned and merged, depending on the detected fragment overlaps. Annotation of the assembled sequence might be generated. -subset: operation -is_a: EDAM:0002429 ! Mapping and assembly -is_a: EDAM:0002446 ! Sequence processing -is_a: EDAM:0002478 ! Nucleic acid sequence analysis -relationship: has_output EDAM:0000925 ! Sequence assembly -relationship: has_topic EDAM:0000196 ! Sequence assembly +is_a: EDAM_operation:2429 ! Mapping and assembly +is_a: EDAM_operation:2446 ! Sequence processing +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:0002432 +id: EDAM_operation:2432 name: Microarray data processing namespace: operation -def: "Process (read and / or write) microarray data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002495 ! Gene expression data processing +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:0002495 +id: EDAM_operation:2495 name: Gene expression data processing namespace: operation -def: "Process (read and / or write) gene expression (typically microarray) data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -synonym: "Gene expression (microarray) data processing" EXACT [] -synonym: "Microarray data processing" EXACT [] -relationship: has_input EDAM:0003117 ! Microarray hybridisation data {minCardinality=0} -relationship: has_output EDAM:0003117 ! Microarray hybridisation data {minCardinality=0} -relationship: has_topic EDAM:0000197 ! Gene expression resources -relationship: has_topic EDAM:0000200 ! Microarrays +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 ! Microarray hybridisation data ! !{min_cardinality=0} +relationship: has_output EDAM_data:3117 ! Microarray hybridisation data ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0197 ! Gene expression resources +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] -id: EDAM:0002500 +id: EDAM_operation:2500 name: Microarray raw data analysis namespace: operation -def: "Analyse raw microarray data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002495 ! Gene expression data processing +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:0000311 +id: EDAM_operation:0311 name: Microarray data standardization and normalization namespace: operation -def: "Standardize or normalize microarray data." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002495 ! Gene expression data processing -is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_input EDAM:0003117 ! Microarray hybridisation data {minCardinality=1} -relationship: has_output EDAM:0003117 ! Microarray hybridisation data {minCardinality=1} +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:0000318 +id: EDAM_operation:0318 name: Structural genomics target selection namespace: operation -def: "Identify and select targets for protein structural determination." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_obsolete: true -consider: EDAM:0002406 ! Protein structure analysis +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_operation:2406 ! Protein structure analysis [Term] -id: EDAM:0002406 +id: EDAM_operation:2406 name: Protein structure analysis namespace: operation -alt_id: EDAM:0002458 -def: "Analyse protein tertiary structural data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002480 ! Structure analysis -is_a: EDAM:0002459 ! Structure processing (protein) -synonym: "Structure analysis (protein)" EXACT [] -relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=1} -relationship: has_output EDAM:0000897 ! Protein property +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:0002481 +id: EDAM_operation:2481 name: Nucleic acid structure analysis namespace: operation -alt_id: EDAM:0002418 -def: "Analyse nucleic acid tertiary structural data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002480 ! Structure analysis -is_a: EDAM:0002519 ! Structure processing (nucleic acid) -relationship: has_input EDAM:0001459 ! Nucleic acid structure {minCardinality=1} -relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=1} +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:0000324 +id: EDAM_operation:0324 name: Phylogenetic tree analysis namespace: operation -def: "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002443 ! Phylogenetic tree processing -relationship: has_input EDAM:0000872 ! Phylogenetic tree {minCardinality=1} -relationship: has_output EDAM:0001438 ! Phylogenetic tree report {minCardinality=1} +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:0002438 +id: EDAM_operation:2438 name: Pathway or network processing namespace: operation -def: "Generate, analyse or handle a biological pathway or network." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002600 ! Pathway or network {minCardinality=0} -relationship: has_output EDAM:0002600 ! Pathway or network {minCardinality=0} -relationship: has_topic EDAM:0000602 ! Pathways, networks and models +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 ! Pathway or network ! !{min_cardinality=0} +relationship: has_output EDAM_data:2600 ! Pathway or network ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] -id: EDAM:0003083 +id: EDAM_operation:3083 !{since=beta13} name: Pathway or network rendering namespace: operation -def: "Render (visualise) a biological pathway or network." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002438 ! Pathway or network processing -is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0002600 ! Pathway or network {minCardinality=1} -relationship: has_topic EDAM:0000602 ! Pathways, networks and models +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:0002497 +id: EDAM_operation:2497 name: Pathway or network analysis namespace: operation -def: "Analyse a known biological pathway or network." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002438 ! Pathway or network processing -relationship: has_input EDAM:0002600 ! Pathway or network {minCardinality=1} -relationship: has_output EDAM:0002984 ! Pathway or network report {minCardinality=1} +subset: operations +def: "Analyse a known biological pathway or network." [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:0002415 +id: EDAM_operation:2415 name: Protein folding analysis namespace: operation -def: "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad concept and is used a placeholder for other, more specific terms. -subset: operation -synonym: "Protein folding modelling" EXACT [] -is_a: EDAM:0002502 ! Protein data processing -is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_output EDAM:0000903 ! Protein folding report {minCardinality=1} -relationship: has_topic EDAM:0000130 ! Protein folding and stability +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:0000331 +id: EDAM_operation:0331 name: Protein modelling (mutation) namespace: operation -def: "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000477 ! Protein modelling -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -synonym: "Protein mutation modelling" EXACT [] -relationship: has_topic EDAM:0000130 ! Protein folding and stability -relationship: has_topic EDAM:0000199 ! Genetic variation +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:0000332 +id: EDAM_operation:0332 name: Immunogen design namespace: operation -def: "Design molecules that elicit an immune response (immunogens)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000559 ! Peptide immunogen prediction and optimisation +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:0002409 +id: EDAM_operation:2409 name: File processing namespace: operation -def: "Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Report handling" EXACT [] -synonym: "File handling" EXACT [] -synonym: "Data file processing" EXACT [] -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0000006 ! Data {minCardinality=0} -relationship: has_output EDAM:0000006 ! Data {minCardinality=0} -relationship: has_topic EDAM:0000220 ! Data processing and validation +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 ! Data ! !{min_cardinality=0} +relationship: has_output EDAM_data:0006 ! Data ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] -id: EDAM:0000337 +id: EDAM_operation:0337 name: Plotting and rendering namespace: operation -def: "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Visualisation" EXACT [] -is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000006 ! Data {minCardinality=1} -relationship: has_output EDAM:0002968 ! Image {minCardinality=0} -relationship: has_topic EDAM:0000092 ! Data visualisation +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 ! Image ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0092 ! Data visualisation [Term] -id: EDAM:0002121 +id: EDAM_operation:2121 name: Sequence file processing namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002446 ! Sequence processing -is_a: EDAM:0002409 ! File processing +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:0003081 +id: EDAM_operation:3081 !{since=beta13} name: Sequence alignment editing namespace: operation -def: "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002122 ! Sequence alignment file processing -is_a: EDAM:0003096 ! Editing +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:0002122 +id: EDAM_operation:2122 name: Sequence alignment file processing namespace: operation -def: "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002409 ! File processing -is_a: EDAM:0002463 ! Sequence alignment processing -relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=1} -relationship: has_output EDAM:0000863 ! Sequence alignment {minCardinality=1} +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:0003080 +id: EDAM_operation:3080 !{since=beta13} name: Structure editing namespace: operation -def: "Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002234 ! Structure file processing -is_a: EDAM:0003096 ! Editing -relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} +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:0002234 +id: EDAM_operation:2234 name: Structure file processing namespace: operation -def: "Perform basic (non-analytical) operations on a file of molecular tertiary structural data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002409 ! File processing -is_a: EDAM:0002465 ! Structure processing +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:0002120 +id: EDAM_operation:2120 name: Listfile processing namespace: operation -def: "Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002409 ! File processing -relationship: has_input EDAM:0001111 ! EMBOSS listfile -relationship: has_output EDAM:0001111 ! EMBOSS listfile +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:0001812 +id: EDAM_operation:1812 name: Data loading namespace: operation -def: "Prepare or load a user-specified data file so that it is available for use." [EDAM:EBI "EMBRACE definition"] -subset: operation +subset: operations +def: "Prepare or load a user-specified data file so that it is available for use." [http://edamontology.org] xref: WHATIF:UploadPDB -is_a: EDAM:0002409 ! File processing -relationship: has_input EDAM:0000842 ! Identifier {minCardinality=1} +is_a: EDAM_operation:2409 ! File processing +relationship: has_input EDAM_data:0842 !{min_cardinality=1} ! Identifier [Term] -id: EDAM:0000335 +id: EDAM_operation:0335 name: File reformatting namespace: operation -def: "Reformat a file of data (or equivalent entity in memory)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002409 ! File processing +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:0000336 +id: EDAM_operation:0336 name: File validation namespace: operation -def: "Test and validate the format and content of a data file." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002409 ! File processing -is_a: EDAM:0002428 ! Validation and standardisation +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:0002421 +id: EDAM_operation:2421 name: Database search namespace: operation -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000224 ! Search and retrieval -is_a: EDAM:0002424 ! Comparison -relationship: has_output EDAM:0002080 ! Database hits {cardinality=0} +is_a: EDAM_operation:0224 ! Search and retrieval +is_a: EDAM_operation:2424 ! Comparison +relationship: has_output EDAM_data:2080 ! Database hits ! !{min_cardinality=0} [Term] -id: EDAM:0002422 +id: EDAM_operation:2422 name: Data retrieval namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000224 ! Search and retrieval -relationship: has_input EDAM:0000842 ! Identifier {minCardinality=1} +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:0000343 +id: EDAM_operation:0343 name: Transmembrane protein database search namespace: operation -def: "Search a database of transmembrane proteins, for example for sequence or structural similarities." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002421 ! Database search +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:0000304 +id: EDAM_operation:0304 name: Data retrieval (metadata and documentation) namespace: operation -def: "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Data retrieval (documentation)" EXACT [] -synonym: "Data retrieval (metadata)" EXACT [] -relationship: has_output EDAM:0002337 ! Metadata {minCardinality=1} -is_a: EDAM:0002422 ! Data retrieval +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:0000225 +id: EDAM_operation:0225 name: Data retrieval (database cross-reference) namespace: operation -def: "Search database to retrieve all relevant references to a particular entity or entry." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0001813 +id: EDAM_operation:1813 name: Sequence retrieval namespace: operation -def: "Query a sequence data resource (typically a database) and retrieve sequences and / or annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Data retrieval (sequences)" EXACT [] -is_a: EDAM:0002422 ! Data retrieval -is_a: EDAM:0002446 ! Sequence processing -relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} +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 ! Sequence ! !{min_cardinality=0} [Term] -id: EDAM:0001814 +id: EDAM_operation:1814 name: Structure retrieval namespace: operation -def: "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation xref: WHATIF:DownloadPDB xref: WHATIF:EchoPDB -is_a: EDAM:0002422 ! Data retrieval -is_a: EDAM:0002465 ! Structure processing -relationship: has_output EDAM:0000883 ! Structure {minCardinality=0} +is_a: EDAM_operation:2422 ! Data retrieval +is_a: EDAM_operation:2465 ! Structure processing +relationship: has_output EDAM_data:0883 ! Structure ! !{min_cardinality=0} [Term] -id: EDAM:0002237 +id: EDAM_operation:2237 name: Data retrieval (sequence profile) namespace: operation -def: "Query a profile data resource and retrieve one or more profile(s) and / or associated annotation." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +is_obsolete: true !{since=beta13} +consider: EDAM_operation:2422 ! Data retrieval [Term] -id: EDAM:0002434 +id: EDAM_operation:2434 name: Data retrieval (codon usage table) namespace: operation -def: "Retrieve a codon usage table and / or associated annotation." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002264 +id: EDAM_operation:2264 name: Data retrieval (pathway or network) namespace: operation -def: "Query a biological pathways database and retrieve annotation on one or more pathways." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002265 +id: EDAM_operation:2265 name: Data retrieval (identifier) namespace: operation -def: "Query a database and retrieve one or more data identifiers." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002224 +id: EDAM_operation:2224 name: Data retrieval (ontology concept) namespace: operation -def: "Query an ontology and retrieve concepts or relations." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Ontology retrieval" EXACT [] -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002222 +id: EDAM_operation:2222 name: Data retrieval (ontology annotation) namespace: operation -def: "Search and retrieve documentation on a bioinformatics ontology." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Ontology information retrieval" EXACT [] -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002468 +id: EDAM_operation:2468 name: Data retrieval (phylogenetic tree) namespace: operation -def: "Retrieve a phylogenetic tree from a data resource." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0000257 +id: EDAM_operation:0257 name: Data retrieval (sequence alignment) namespace: operation -def: "Display basic information about a sequence alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002473 +id: EDAM_operation:2473 name: Data retrieval (genotype and phenotype annotation) namespace: operation -def: "Retrieve information on a specific genotype or phenotype." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Genotype and phenotype information retrieval" EXACT [] -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002472 +id: EDAM_operation:2472 name: Data retrieval (gene annotation) namespace: operation -def: "Retrieve information on a specific gene." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Gene information retrieval" EXACT [] -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002471 +id: EDAM_operation:2471 name: Data retrieval (RNA family annotation) namespace: operation -def: "Retrieve information on an RNA family." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "RNA family information retrieval" EXACT [] -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002470 +id: EDAM_operation:2470 name: Data retrieval (protein family annotation) namespace: operation -def: "Retrieve information on a protein family." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Protein family information retrieval" EXACT [] -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002469 +id: EDAM_operation:2469 name: Data retrieval (protein interaction annotation) namespace: operation -def: "Retrieve information on a protein interaction." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0002467 +id: EDAM_operation:2467 name: Data retrieval (protein annotation) namespace: operation -def: "Retrieve information on a protein." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Protein information retrieval" EXACT [] -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0000280 +id: EDAM_operation:0280 name: Data retrieval (restriction enzyme annotation) namespace: operation -def: "Retrieve information on restriction enzymes or restriction enzyme sites." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Restriction enzyme information retrieval" EXACT [] -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0000515 +id: EDAM_operation:0515 name: Data retrieval (tool metadata) namespace: operation -def: "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Tool information retrieval" EXACT [] -synonym: "Data retrieval (tool annotation)" EXACT [] -is_a: EDAM:0000304 ! Data retrieval (metadata and documentation) -relationship: has_output EDAM:0000958 ! Tool metadata {minCardinality=0} +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 ! Tool metadata ! !{min_cardinality=0} [Term] -id: EDAM:0000516 +id: EDAM_operation:0516 name: Data retrieval (database metadata) namespace: operation -def: "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Database information retrieval" EXACT [] -synonym: "Data retrieval (database annotation)" EXACT [] -is_a: EDAM:0000304 ! Data retrieval (metadata and documentation) -relationship: has_output EDAM:0000957 ! Database metadata {minCardinality=0} +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 ! Database metadata ! !{min_cardinality=0} [Term] -id: EDAM:0000344 +id: EDAM_operation:0344 name: Sequence retrieval (by code) namespace: operation -def: "Query a database and retrieve sequences with a given entry code or accession number." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0001813 ! Sequence retrieval +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:0000345 +id: EDAM_operation:0345 name: Sequence retrieval (by keyword) namespace: operation -def: "Query a database and retrieve sequences containing a given keyword." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0001813 ! Sequence retrieval +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:0001845 +id: EDAM_operation:1845 name: PDB file sequence retrieval namespace: operation -def: "Extract a molecular sequence from a PDB file." [EDAM:WHATIF "EMBRACE definition"] -subset: operation +subset: operations +def: "Extract a molecular sequence from a PDB file." [http://edamontology.org, WHATIF] xref: WHATIF: PDB_sequence -is_obsolete: true -consider: EDAM:0000344 ! Sequence retrieval (by code) +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_operation:0344 ! Sequence retrieval (by code) [Term] -id: EDAM:0000305 +id: EDAM_operation:0305 name: Literature search namespace: operation -def: "Query the biomedical and informatics literature." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002421 ! Database search -relationship: has_output EDAM:0000970 ! Bibliographic reference {minCardinality=0} -relationship: has_topic EDAM:0000217 ! Literature analysis +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 ! Bibliographic reference ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0217 ! Literature analysis [Term] -id: EDAM:0000338 +id: EDAM_operation:0338 name: Sequence database search namespace: operation -def: "Search a sequence database by sequence comparison and retrieve similar sequences." [EDAM:EBI "EMBRACE definition"] +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). -subset: operation -is_a: EDAM:0002421 ! Database search -is_a: EDAM:0002403 ! Sequence analysis -relationship: has_output EDAM:0000857 ! Database hits (sequence) {minCardinality=0} -relationship: has_topic EDAM:0000159 ! Sequence comparison +is_a: EDAM_operation:2421 ! Database search +is_a: EDAM_operation:2403 ! Sequence analysis +relationship: has_output EDAM_data:0857 ! Database hits (sequence) ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0159 ! Sequence comparison [Term] -id: EDAM:0000339 +id: EDAM_operation:0339 name: Structure database search namespace: operation -def: "Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002421 ! Database search -is_a: EDAM:0002996 ! Structure classification -relationship: has_output EDAM:0000885 ! Database hits (structure) {minCardinality=0} -relationship: has_topic EDAM:0000081 ! Structure analysis +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 ! Database hits (structure) ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM:0000340 +id: EDAM_operation:0340 name: Protein secondary database search namespace: operation -def: "Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group." [EDAM:EBI "EMBRACE definition"] +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.). -subset: operation -synonym: "Protein sequence classification" EXACT [] -is_a: EDAM:0002421 ! Database search -is_a: EDAM:0003093 ! Sequence screening -relationship: has_output EDAM:0000858 ! Database hits (secondary) {minCardinality=0} -relationship: has_topic EDAM:0000595 ! Protein classification +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 ! Database hits (secondary) ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0595 ! Protein classification [Term] -id: EDAM:0000341 +id: EDAM_operation:0341 name: Motif database search namespace: operation -def: "Screen a sequence against a motif or pattern database." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002421 ! Database search -is_a: EDAM:0000239 ! Sequence motif recognition -is_a: EDAM:0003093 ! Sequence screening -relationship: has_output EDAM:0001298 ! Sequence features (motifs) {minCardinality=0} -relationship: has_topic EDAM:0000158 ! Sequence motifs +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 ! Sequence features (motifs) ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] -id: EDAM:0000342 +id: EDAM_operation:0342 name: Sequence profile database search namespace: operation -def: "Search a database of sequence profiles with a query sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002421 ! Database search -is_a: EDAM:0000300 ! Sequence-profile alignment -is_a: EDAM:0003093 ! Sequence screening -relationship: has_output EDAM:0001298 ! Sequence features (motifs) +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 +is_a: EDAM_operation:3093 ! Sequence screening +relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM:0000346 +id: EDAM_operation:0346 name: Sequence database search (by sequence) namespace: operation -def: "Search a sequence database and retrieve sequences that are similar to a query sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Sequence similarity search" EXACT [] -is_a: EDAM:0000338 ! Sequence database search -is_a: EDAM:0003093 ! Sequence screening -is_a: EDAM:0002451 ! Sequence comparison +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:0000347 +id: EDAM_operation:0347 name: Sequence database search (by motif or pattern) namespace: operation -def: "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000338 ! Sequence database search -is_a: EDAM:0000239 ! Sequence motif recognition -relationship: has_input EDAM:0001353 ! Sequence motif {minCardinality=1} -relationship: has_topic EDAM:0000158 ! Sequence motifs +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:0000348 +id: EDAM_operation:0348 name: Sequence database search (by amino acid composition) namespace: operation -def: "Search a sequence database and retrieve sequences of a given amino acid composition." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000338 ! Sequence database search -relationship: has_input EDAM:0001267 ! Amino acid frequencies -relationship: has_topic EDAM:0000157 ! Sequence composition analysis +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:0000349 +id: EDAM_operation:0349 name: Sequence database search (by physicochemical property) namespace: operation -def: "Search a sequence database and retrieve sequences with a specified physicochemical property." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000338 ! Sequence database search +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:0000350 +id: EDAM_operation:0350 name: Sequence database search (by sequence using word-based methods) namespace: operation -def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Sequence similarity search (word-based methods)" EXACT [] -is_a: EDAM:0000346 ! Sequence database search (by sequence) -is_a: EDAM:0000288 ! Sequence word comparison +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:0000351 +id: EDAM_operation:0351 name: Sequence database search (by sequence using profile-based methods) namespace: operation -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Sequence similarity search (profile-based methods)" EXACT [] -is_a: EDAM:0000346 ! Sequence database search (by sequence) -is_a: EDAM:0000300 ! Sequence-profile alignment +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 [Term] -id: EDAM:0000352 +id: EDAM_operation:0352 name: Sequence database search (by sequence using local alignment-based methods) namespace: operation -def: "Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Sequence similarity search (local alignment-based methods) " EXACT [] -is_a: EDAM:0000346 ! Sequence database search (by sequence) -is_a: EDAM:0000493 ! Pairwise sequence alignment (local) -relationship: has_topic EDAM:0000182 ! Sequence alignment +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 (local) +relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] -id: EDAM:0000353 +id: EDAM_operation:0353 name: Sequence database search (by sequence using global alignment-based methods) namespace: operation -def: "Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Sequence similarity search (global alignment-based methods)" EXACT [] -is_a: EDAM:0000346 ! Sequence database search (by sequence) -is_a: EDAM:0000494 ! Pairwise sequence alignment (global) -relationship: has_topic EDAM:0000182 ! Sequence alignment +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 (global) +relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] -id: EDAM:0000354 +id: EDAM_operation:0354 name: Sequence database search (by sequence for primer sequences) namespace: operation -def: "Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Sequence similarity search (primer sequences)" EXACT [] -is_a: EDAM:0000346 ! Sequence database search (by sequence) -relationship: has_topic EDAM:0003032 ! Primer or probe design +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:0000355 +id: EDAM_operation:0355 name: Sequence database search (by molecular weight) namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Protein fingerprinting" EXACT [] -synonym: "Peptide mass fingerprinting" EXACT [] -is_a: EDAM:0000349 ! Sequence database search (by physicochemical property) -relationship: has_input EDAM:0000944 ! Peptide mass fingerprint -relationship: has_topic EDAM:0000123 ! Protein properties -relationship: has_topic EDAM:0000767 ! Protein and peptide identification +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:0000356 +id: EDAM_operation:0356 name: Sequence database search (by isoelectric point) namespace: operation -def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000349 ! Sequence database search (by physicochemical property) -relationship: has_topic EDAM:0000123 ! Protein properties +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:0000357 +id: EDAM_operation:0357 name: Structure retrieval (by code) namespace: operation -def: "Query a tertiary structure database and retrieve entries with a given entry code or accession number." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0001814 ! Structure retrieval +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:0000358 +id: EDAM_operation:0358 name: Structure retrieval (by keyword) namespace: operation -def: "Query a tertiary structure database and retrieve entries containing a given keyword." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0001814 ! Structure retrieval +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:0001914 +id: EDAM_operation:1914 name: Structure retrieval (water) namespace: operation -def: "Query a tertiary structure database and retrieve water molecules." [EDAM:EBI "EMBRACE definition"] -subset: operation +subset: operations +def: "Query a tertiary structure database and retrieve water molecules." [http://edamontology.org] xref: WHATIF:MovedWaterPDB -is_a: EDAM:0001814 ! Structure retrieval +is_a: EDAM_operation:1814 ! Structure retrieval [Term] -id: EDAM:0000359 +id: EDAM_operation:0359 name: Structure database search (by sequence) namespace: operation -def: "Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Structure retrieval by sequence" EXACT [] -is_a: EDAM:0000339 ! Structure database search -is_a: EDAM:0002451 ! Sequence comparison -is_a: EDAM:0003093 ! Sequence screening +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:0000360 +id: EDAM_operation:0360 name: Structure database search (by structure) namespace: operation -def: "Search a tertiary structure database and retrieve structures that are similar to a query structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Structure retrieval by structure" EXACT [] -synonym: "Structural similarity search" EXACT [] -is_a: EDAM:0000339 ! Structure database search -relationship: has_topic EDAM:0001770 ! Structure comparison -relationship: has_topic EDAM:0001770 ! Structure comparison +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:0000226 +id: EDAM_operation:0226 name: Annotation namespace: operation -def: "Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad concept and is used a placeholder for other, more specific terms. -subset: operation -is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000582 ! Ontology -relationship: has_topic EDAM:0000089 ! Ontologies +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 ! Ontologies [Term] -id: EDAM:0001774 +id: EDAM_operation:1774 name: Annotation retrieval namespace: operation -def: "Retrieve existing annotation (or documentation), typically annotation on a database entity." [EDAM:EBI "EMBRACE definition"] -comment: Use this terms for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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:0000361 +id: EDAM_operation:0361 name: Sequence annotation namespace: operation -def: "Annotate a molecular sequence record with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000226 ! Annotation -relationship: has_input EDAM:0000849 ! Sequence record {minCardinality=1} -relationship: has_output EDAM:0000849 ! Sequence record {minCardinality=1} +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:0000362 +id: EDAM_operation:0362 name: Genome annotation namespace: operation -def: "Annotate a genome sequence with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000361 ! Sequence annotation +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:0002466 +id: EDAM_operation:2466 name: Map annotation namespace: operation -def: "Annotate a DNA map of some type with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000226 ! Annotation -is_a: EDAM:0002521 ! Map data processing -relationship: has_input EDAM:0001274 ! Map {minCardinality=1} -relationship: has_output EDAM:0001274 ! Map {minCardinality=1} +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:0000227 +id: EDAM_operation:0227 name: Data indexing namespace: operation -def: "Generate an index of (typically a file of) biological data." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Database indexing" EXACT [] -is_a: EDAM:0002412 ! Data index processing -relationship: has_output EDAM:0000955 ! Data index +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:0000228 +id: EDAM_operation:0228 name: Data index analysis namespace: operation -def: "Analyse an index of biological data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002412 ! Data index processing -is_a: EDAM:0002412 ! Data index processing -synonym: "Database index analysis" EXACT [] -relationship: has_input EDAM:0000955 ! Data index {minCardinality=1} -relationship: has_output EDAM:0000956 ! Data index report {minCardinality=1} +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:0002478 +id: EDAM_operation:2478 name: Nucleic acid sequence analysis namespace: operation -def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002403 ! Sequence analysis -is_a: EDAM:0002448 ! Sequence processing (nucleic acid) -relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=1} -relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis +subset: operations +def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [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:0003095 +id: EDAM_operation:3095 !{since=beta13} name: Nucleic acid design namespace: operation -def: "Design (or predict) nucleic acid sequences with specific chemical or physical properties." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002478 ! Nucleic acid sequence analysis +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:0002479 +id: EDAM_operation:2479 name: Protein sequence analysis namespace: operation -def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002403 ! Sequence analysis -is_a: EDAM:0002447 ! Sequence processing (protein) -synonym: "Sequence analysis (protein)" EXACT [] -relationship: has_input EDAM:0002976 ! Protein sequence {minCardinality=1} -relationship: has_topic EDAM:0000639 ! Protein sequence analysis +subset: operations +def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [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:0002446 +id: EDAM_operation:2446 name: Sequence processing namespace: operation -alt_id: EDAM:0002449 -def: "Process (read and / or write) one or more molecular sequences and associated annotation." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Sequence processing (general)" EXACT [] -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002044 ! Sequence {minCardinality=0} -relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} -relationship: has_topic EDAM:0000080 ! Sequence analysis +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 ! Sequence ! !{min_cardinality=0} +relationship: has_output EDAM_data:2044 ! Sequence ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] -id: EDAM:0002447 +id: EDAM_operation:2447 name: Sequence processing (protein) namespace: operation -def: "Process (read and / or write) a protein sequence and associated annotation." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002446 ! Sequence processing -is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0002976 ! Protein sequence {minCardinality=0} -relationship: has_output EDAM:0002976 ! Protein sequence {minCardinality=0} +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 ! Protein sequence ! !{min_cardinality=0} +relationship: has_output EDAM_data:2976 ! Protein sequence ! !{min_cardinality=0} [Term] -id: EDAM:0002448 +id: EDAM_operation:2448 name: Sequence processing (nucleic acid) namespace: operation -def: "Process (read and / or write) a nucleotide sequence and associated annotation." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002446 ! Sequence processing -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=0} -relationship: has_output EDAM:0002977 ! Nucleic acid sequence {minCardinality=0} +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 ! Nucleic acid sequence ! !{min_cardinality=0} +relationship: has_output EDAM_data:2977 ! Nucleic acid sequence ! !{min_cardinality=0} [Term] -id: EDAM:0000229 +id: EDAM_operation:0229 name: Annotation retrieval (sequence) namespace: operation -def: "Retrieve basic information about a molecular sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0001813 ! Sequence retrieval +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:0000230 +id: EDAM_operation:0230 name: Sequence generation namespace: operation -def: "Generate a molecular sequence by some means." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002121 ! Sequence file processing +subset: operations +def: "Generate a molecular sequence by some means." [http://edamontology.org] +is_a: EDAM_operation:2121 ! Sequence file processing [Term] -id: EDAM:0002513 +id: EDAM_operation:2513 name: Sequence generation (nucleic acid) namespace: operation -def: "Generate a nucleic acid sequence by some means." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000230 ! Sequence generation -is_a: EDAM:0002448 ! Sequence processing (nucleic acid) -relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis +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:0002514 +id: EDAM_operation:2514 name: Sequence generation (protein) namespace: operation -def: "Generate a protein sequence by some means." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000230 ! Sequence generation -is_a: EDAM:0002447 ! Sequence processing (protein) -relationship: has_topic EDAM:0000639 ! Protein sequence analysis +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:0000231 +id: EDAM_operation:0231 name: Sequence editing namespace: operation -def: "Edit or change a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002121 ! Sequence file processing -is_a: EDAM:0003096 ! Editing +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:0002511 +id: EDAM_operation:2511 name: Sequence editing (nucleic acid) namespace: operation -def: "Edit or change a nucleic acid sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000231 ! Sequence editing -is_a: EDAM:0002448 ! Sequence processing (nucleic acid) +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:0002512 +id: EDAM_operation:2512 name: Sequence editing (protein) namespace: operation -def: "Edit or change a protein sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000231 ! Sequence editing -is_a: EDAM:0002447 ! Sequence processing (protein) +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:0000232 +id: EDAM_operation:0232 name: Sequence merging namespace: operation -def: "Merge two or more (typically overlapping) molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Sequence splicing" EXACT [] -is_a: EDAM:0000231 ! Sequence editing +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:0000233 +id: EDAM_operation:0233 name: Sequence conversion namespace: operation -def: "Convert a molecular sequence from one type to another." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000231 ! Sequence editing +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:0001780 +id: EDAM_operation:1780 name: Sequence submission namespace: operation -def: "Submit a molecular sequence to a database." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} -relationship: has_topic EDAM:0000091 ! Data handling +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:0091 ! Data handling [Term] -id: EDAM:0000234 +id: EDAM_operation:0234 name: Sequence complexity calculation namespace: operation -alt_id: EDAM:0000373 -alt_id: EDAM:0000374 -def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000236 ! Sequence composition calculation -relationship: has_output EDAM:0001259 ! Sequence complexity {minCardinality=1} -relationship: has_topic EDAM:0000642 ! Low complexity sequences +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:0000235 +id: EDAM_operation:0235 name: Sequence ambiguity calculation namespace: operation -alt_id: EDAM:0000375 -alt_id: EDAM:0000376 -def: "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000236 ! Sequence composition calculation -relationship: has_output EDAM:0001260 ! Sequence ambiguity {minCardinality=1} -relationship: has_topic EDAM:0000157 ! Sequence composition analysis +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:0000291 +id: EDAM_operation:0291 name: Sequence clustering namespace: operation -def: "Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Sequence cluster generation" EXACT [] -is_a: EDAM:0002451 ! Sequence comparison -is_a: EDAM:0002452 ! Sequence cluster processing -is_a: EDAM:0002995 ! Sequence classification -relationship: has_output EDAM:0001235 ! Sequence cluster {minCardinality=0} +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 ! Sequence cluster ! !{min_cardinality=0} [Term] -id: EDAM:0000236 +id: EDAM_operation:0236 name: Sequence composition calculation namespace: operation -def: "Calculate character or word composition or frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002403 ! Sequence analysis -relationship: has_output EDAM:0001261 ! Sequence composition -relationship: has_topic EDAM:0000157 ! Sequence composition analysis -relationship: has_topic EDAM:0000157 ! Sequence composition analysis +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:0000237 +id: EDAM_operation:0237 name: Repeat sequence analysis namespace: operation -def: "Find and/or analyse repeat sequences in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002403 ! Sequence analysis -relationship: has_topic EDAM:0000641 ! Repeat sequences +is_a: EDAM_operation:2403 ! Sequence analysis +relationship: has_topic EDAM_topic:0641 ! Repeat sequences [Term] -id: EDAM:0000290 +id: EDAM_operation:0290 name: Sequence redundancy removal namespace: operation -def: "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000291 ! Sequence clustering -relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} -relationship: has_topic EDAM:0000164 ! Sequence clustering +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 ! Sequence ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] -id: EDAM:0002451 +id: EDAM_operation:2451 name: Sequence comparison namespace: operation -def: "Compare two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002403 ! Sequence analysis -is_a: EDAM:0002424 ! Comparison -relationship: has_input EDAM:0002044 ! Sequence {minCardinality=2} -relationship: has_output EDAM:0002955 ! Sequence report -relationship: has_topic EDAM:0000159 ! Sequence comparison +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:0002508 +id: EDAM_operation:2508 name: Nucleic acid sequence comparison namespace: operation -def: "Compare two or more nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Sequence comparison (nucleic acid)" EXACT [] -is_a: EDAM:0002451 ! Sequence comparison -is_a: EDAM:0002478 ! Nucleic acid sequence analysis -is_a: EDAM:0002998 ! Nucleic acid comparison +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:0002509 +id: EDAM_operation:2509 name: Protein sequence comparison namespace: operation -def: "Compare two or more protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Sequence comparison (protein)" EXACT [] -is_a: EDAM:0002451 ! Sequence comparison -is_a: EDAM:0002479 ! Protein sequence analysis -is_a: EDAM:0002997 ! Protein comparison +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:0000288 +id: EDAM_operation:0288 name: Sequence word comparison namespace: operation -def: "Find exact character or word matches between molecular sequences without full sequence alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002451 ! Sequence comparison -relationship: has_output EDAM:0000861 ! Sequence alignment (words) {minCardinality=1} +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:0000289 +id: EDAM_operation:0289 name: Sequence distance matrix generation namespace: operation -def: "Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Phylogenetic distance matrix generation" EXACT [] -is_a: EDAM:0002451 ! Sequence comparison -relationship: has_output EDAM:0000870 ! Sequence distance matrix -relationship: has_topic EDAM:0000084 ! Phylogenetics +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:0000266 +id: EDAM_operation:0266 name: Vector sequence detection namespace: operation -def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002508 ! Nucleic acid sequence comparison -is_a: EDAM:0000415 ! Nucleic acid feature detection +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 detection [Term] -id: EDAM:0002233 +id: EDAM_operation:2233 name: Representative sequence identification namespace: operation -def: "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000291 ! Sequence clustering -relationship: has_topic EDAM:0000164 ! Sequence clustering +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:0000317 +id: EDAM_operation:0317 name: EST and cDNA sequence analysis namespace: operation -def: "Analyse EST or cDNA sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_obsolete: true -consider: EDAM:0002403 ! Sequence analysis +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_operation:2403 ! Sequence analysis [Term] -id: EDAM:0000265 +id: EDAM_operation:0265 name: Frameshift error detection namespace: operation -def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002508 ! Nucleic acid sequence comparison -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_topic EDAM:0000102 ! Sequencing and mapping +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison +is_a: EDAM_operation:0415 ! Nucleic acid feature detection +relationship: has_topic EDAM_topic:0102 ! Sequencing and mapping [Term] -id: EDAM:0000241 +id: EDAM_operation:0241 name: Transcription regulatory sequence analysis namespace: operation -def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_obsolete: true -consider: EDAM:0000438 ! Transcription regulatory element prediction +is_obsolete: true !{since=beta13} +consider: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] -id: EDAM:0000281 +id: EDAM_operation:0281 name: Genetic marker identification namespace: operation -def: "Identify genetic markers in DNA sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_obsolete: true -consider: EDAM:0000415 ! Nucleic acid feature detection +is_obsolete: true !{since=beta13} +consider: EDAM_operation:0415 ! Nucleic acid feature detection [Term] -id: EDAM:0000363 +id: EDAM_operation:0363 name: Nucleic acid sequence reverse and complement namespace: operation -def: "Generate the reverse and / or complement of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002513 ! Sequence generation (nucleic acid) +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:0000364 +id: EDAM_operation:0364 name: Random sequence generation namespace: operation -def: "Generate a random sequence, for example, with a specific character composition." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000230 ! Sequence generation +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:0000365 +id: EDAM_operation:0365 name: Nucleic acid restriction digest namespace: operation -def: "Generate digest fragments for a nucleotide sequence containing restriction sites." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002513 ! Sequence generation (nucleic acid) -is_a: EDAM:0000262 ! Nucleic acid property calculation -relationship: has_output EDAM:0001239 ! Restriction digest -relationship: has_topic EDAM:0000100 ! Nucleic acid restriction +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:0000366 +id: EDAM_operation:0366 name: Protein sequence cleavage namespace: operation -def: "Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002514 ! Sequence generation (protein) -is_a: EDAM:0003088 ! Protein property calculation (from sequence) -relationship: has_output EDAM:0001238 ! Proteolytic digest -relationship: has_topic EDAM:0000767 ! Protein and peptide identification +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:0000367 +id: EDAM_operation:0367 name: Sequence mutation and randomization namespace: operation -def: "Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000231 ! Sequence editing +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:0000368 +id: EDAM_operation:0368 name: Sequence masking namespace: operation -def: "Mask characters in a molecular sequence (replacing those characters with a mask character)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000231 ! Sequence editing -relationship: has_input EDAM:0000851 ! Sequence mask character {minCardinality=1} +is_a: EDAM_operation:0231 ! Sequence editing +relationship: has_input EDAM_data:0851 !{min_cardinality=1} ! Sequence mask character [Term] -id: EDAM:0000369 +id: EDAM_operation:0369 name: Sequence cutting namespace: operation -def: "Cut (remove) characters or a region from a molecular sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000231 ! Sequence editing +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:0000370 +id: EDAM_operation:0370 name: Restriction site creation namespace: operation -def: "Create (or remove) restriction sites in sequences, for example using silent mutations." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002511 ! Sequence editing (nucleic acid) -relationship: has_topic EDAM:0000100 ! Nucleic acid restriction +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:0000371 +id: EDAM_operation:0371 name: DNA translation namespace: operation -def: "Translate a DNA sequence into protein." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000233 ! Sequence conversion -relationship: has_topic EDAM:0000108 ! Translation +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:0000372 +id: EDAM_operation:0372 name: DNA transcription namespace: operation -def: "Transcribe a nucleotide sequence into mRNA sequence(s)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000233 ! Sequence conversion -relationship: has_topic EDAM:0000110 ! Transcription +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:0002510 +id: EDAM_operation:2510 name: DNA back-translation namespace: operation -def: "Back-translate a protein sequence into DNA." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000233 ! Sequence conversion -relationship: has_topic EDAM:0000108 ! Translation +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:0000377 +id: EDAM_operation:0377 name: Sequence composition calculation (nucleic acid) namespace: operation -def: "Calculate base frequency or word composition of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000236 ! Sequence composition calculation -is_a: EDAM:0000262 ! Nucleic acid property calculation +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:0000378 +id: EDAM_operation:0378 name: Sequence composition calculation (protein) namespace: operation -def: "Calculate amino acid frequency or word composition of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000236 ! Sequence composition calculation -is_a: EDAM:0003088 ! Protein property calculation (from sequence) +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:0002284 +id: EDAM_operation:2284 name: Nucleic acid density plotting namespace: operation -def: "Calculate a density plot (of base composition) for a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000377 ! Sequence composition calculation (nucleic acid) +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:0000379 +id: EDAM_operation:0379 name: Repeat sequence detection namespace: operation -alt_id: EDAM:0002450 -def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000237 ! Repeat sequence analysis -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0001299 ! Sequence features (repeats) +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 detection +relationship: has_output EDAM_data:1299 ! Sequence features (repeats) [Term] -id: EDAM:0000380 +id: EDAM_operation:0380 name: Repeat sequence organisation analysis namespace: operation -def: "Analyse repeat sequence organization such as periodicity." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000237 ! Repeat sequence analysis -is_a: EDAM:0000236 ! Sequence composition calculation +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:0000490 +id: EDAM_operation:0490 name: Dotplot plotting namespace: operation -def: "Draw a dotplot of sequence similarities identified from word-matching or character comparison." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000288 ! Sequence word comparison -is_a: EDAM:0000565 ! Sequence alignment rendering -relationship: has_output EDAM:0000862 ! Dotplot {minCardinality=1} +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:0000242 +id: EDAM_operation:0242 name: Conserved transcription regulatory sequence identification namespace: operation -def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000438 ! Transcription regulatory element prediction -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0001315 ! Gene features (TFBS) +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction +is_a: EDAM_operation:0415 ! Nucleic acid feature detection +relationship: has_output EDAM_data:1315 ! Gene features (TFBS) [Term] -id: EDAM:0000238 +id: EDAM_operation:0238 name: Sequence motif discovery namespace: operation -def: "Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery)." [EDAM:EBI "EMBRACE definition"] +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). -subset: operation -synonym: "Motif discovery" EXACT [] -is_a: EDAM:0000253 ! Sequence feature detection -is_a: EDAM:0002404 ! Sequence motif processing -relationship: has_output EDAM:0001298 ! Sequence features (motifs) +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:0000239 +id: EDAM_operation:0239 name: Sequence motif recognition namespace: operation -def: "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Sequence motif detection" EXACT [] -is_a: EDAM:0002404 ! Sequence motif processing -is_a: EDAM:0000253 ! Sequence feature detection -relationship: has_output EDAM:0001298 ! Sequence features (motifs) +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] +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:0000240 +id: EDAM_operation:0240 name: Sequence motif comparison namespace: operation -def: "Find motifs shared by molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002451 ! Sequence comparison -is_a: EDAM:0002404 ! Sequence motif processing -relationship: has_output EDAM:0001298 ! Sequence features (motifs) +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:0002123 +id: EDAM_operation:2123 name: Small molecule data processing namespace: operation -def: "Process (read and / or write) physicochemical property data for small molecules." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002420 ! Analysis and processing +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:0000250 +id: EDAM_operation:0250 name: Protein property calculation namespace: operation -alt_id: EDAM:0002933 -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Protein property rendering" EXACT [] -is_a: EDAM:0002502 ! Protein data processing -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_input EDAM:0000897 ! Protein property {minCardinality=0} -relationship: has_output EDAM:0000897 ! Protein property {minCardinality=0} -relationship: has_topic EDAM:0000123 ! Protein properties +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 ! Protein property ! !{min_cardinality=0} +relationship: has_output EDAM_data:0897 ! Protein property ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0123 ! Protein properties [Term] -id: EDAM:0003088 +id: EDAM_operation:3088 !{since=beta13} name: Protein property calculation (from sequence) namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000250 ! Protein property calculation -is_a: EDAM:0002479 ! Protein sequence analysis +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:0000261 +id: EDAM_operation:0261 name: Nucleic acid property processing namespace: operation -def: "Process (read and / or write) physicochemical property data of nucleic acids." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000262 ! Nucleic acid property calculation +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:0000334 +id: EDAM_operation:0334 name: Enzyme kinetics calculation namespace: operation -def: "Calculate Km, Vmax and derived data for an enzyme reaction." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003088 ! Protein property calculation (from sequence) -relationship: has_output EDAM:0002024 ! Enzyme kinetics data {minCardinality=1} -relationship: has_topic EDAM:0000821 ! Enzymes and reactions +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:0000398 +id: EDAM_operation:0398 name: Protein molecular weight calculation namespace: operation -def: "Calculate the molecular weight of a protein sequence or fragments." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003088 ! Protein property calculation (from sequence) -relationship: has_output EDAM:0001519 ! Peptide molecular weights {minCardinality=1} -relationship: has_topic EDAM:0000767 ! Protein and peptide identification +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:0002930 +id: EDAM_operation:2930 name: Protein property comparison namespace: operation -def: "Compare the physicochemical properties of two or more proteins (or reference data)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002997 ! Protein comparison -relationship: has_output EDAM:0000897 ! Protein property {minCardinality=1} +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:0002929 +id: EDAM_operation:2929 name: Protein fragment weight comparison namespace: operation -def: "Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000398 ! Protein molecular weight calculation -is_a: EDAM:0002930 ! Protein property comparison +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:0000399 +id: EDAM_operation:0399 name: Protein extinction coefficient calculation namespace: operation -def: "Predict extinction coefficients or optical density of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003088 ! Protein property calculation (from sequence) -relationship: has_output EDAM:0001531 ! Protein extinction coefficient {minCardinality=1} +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:0000400 +id: EDAM_operation:0400 name: Protein pH-dependent property calculation namespace: operation -def: "Calculate pH-dependent properties from pKa calculations of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003088 ! Protein property calculation (from sequence) -relationship: has_output EDAM:0000897 ! Protein property -relationship: has_topic EDAM:0000137 ! Protein hydropathy +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:0000401 +id: EDAM_operation:0401 name: Protein hydropathy calculation (from sequence) namespace: operation -def: "Hydropathy calculation on a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002574 ! Protein hydropathy calculation +subset: operations +def: "Hydropathy calculation on a protein sequence." [http://edamontology.org] +is_a: EDAM_operation:2574 ! Protein hydropathy calculation [Term] -id: EDAM:0000252 +id: EDAM_operation:0252 name: Peptide immunogenicity prediction namespace: operation -def: "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002492 ! Protein interaction prediction -is_a: EDAM:0003088 ! Protein property calculation (from sequence) -relationship: has_output EDAM:0001534 ! Peptide immunogenicity {minCardinality=1} -relationship: has_topic EDAM:0000804 ! Immunoinformatics +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 +relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] -id: EDAM:0002932 +id: EDAM_operation:2932 name: Hopp and Woods plotting namespace: operation -def: "Generate a Hopp and Woods plot of antigenicity of a protein." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000252 ! Peptide immunogenicity prediction +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:0000402 +id: EDAM_operation:0402 name: Protein titration curve plotting namespace: operation -def: "Plot a protein titration curve." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000400 ! Protein pH-dependent property calculation -relationship: has_output EDAM:0001527 ! Protein titration curve {minCardinality=1} +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:0000403 +id: EDAM_operation:0403 name: Protein isoelectric point calculation namespace: operation -def: "Calculate isoelectric point of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000400 ! Protein pH-dependent property calculation -relationship: has_output EDAM:0001528 ! Protein isoelectric point {minCardinality=1} +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:0000404 +id: EDAM_operation:0404 name: Protein hydrogen exchange rate calculation namespace: operation -def: "Estimate hydrogen exchange rate of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000400 ! Protein pH-dependent property calculation -relationship: has_output EDAM:0001530 ! Protein hydrogen exchange rate {minCardinality=1} +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:0000405 +id: EDAM_operation:0405 name: Protein hydrophobic region calculation namespace: operation -def: "Calculate hydrophobic or hydrophilic / charged regions of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) +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:0000406 +id: EDAM_operation:0406 name: Protein aliphatic index calculation namespace: operation -def: "Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM:0001521 ! Protein aliphatic index {minCardinality=1} +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:0000407 +id: EDAM_operation:0407 name: Protein hydrophobic moment plotting namespace: operation -def: "Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM:0001520 ! Peptide hydrophobic moment {minCardinality=1} +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:0000408 +id: EDAM_operation:0408 name: Protein globularity prediction namespace: operation -def: "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM:0001526 ! Protein globularity {minCardinality=1} +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:0000409 +id: EDAM_operation:0409 name: Protein solubility prediction namespace: operation -def: "Predict the solubility or atomic solvation energy of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM:0001524 ! Protein solubility {minCardinality=1} +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:0000410 +id: EDAM_operation:0410 name: Protein crystallizability prediction namespace: operation -def: "Predict crystallizability of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -relationship: has_output EDAM:0001525 ! Protein crystallizability {minCardinality=1} +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:0000455 +id: EDAM_operation:0455 name: Nucleic acid thermodynamic property calculation namespace: operation -def: "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000262 ! Nucleic acid property calculation -relationship: has_output EDAM:0002985 ! Nucleic acid thermodynamic data {minCardinality=1} +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:0000456 +id: EDAM_operation:0456 name: Nucleic acid melting profile plotting namespace: operation -def: "Calculate and plot a DNA or DNA/RNA melting profile." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000262 ! Nucleic acid property calculation -relationship: has_output EDAM:0001583 ! Nucleic acid melting profile {minCardinality=1} +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:0000262 +id: EDAM_operation:0262 name: Nucleic acid property calculation namespace: operation -def: "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002478 ! Nucleic acid sequence analysis -relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=1} +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:0002439 +id: EDAM_operation:2439 name: RNA secondary structure processing namespace: operation -def: "Process (read and / or write) RNA secondary structure data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002482 ! Secondary structure processing -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000880 ! RNA secondary structure {minCardinality=0} -relationship: has_output EDAM:0000880 ! RNA secondary structure {minCardinality=0} -relationship: has_topic EDAM:0000097 ! Nucleic acid structure analysis -relationship: has_topic EDAM:0000697 ! RNA structure and alignment +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 ! RNA secondary structure ! !{min_cardinality=0} +relationship: has_output EDAM_data:0880 ! RNA secondary structure ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis +relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] -id: EDAM:0002519 +id: EDAM_operation:2519 name: Structure processing (nucleic acid) namespace: operation -def: "Process (read and / or write) nucleic acid tertiary structure data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002465 ! Structure processing -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0001459 ! Nucleic acid structure {minCardinality=0} -relationship: has_output EDAM:0001459 ! Nucleic acid structure {minCardinality=0} -relationship: has_topic EDAM:0000097 ! Nucleic acid structure analysis +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 ! Nucleic acid structure ! !{min_cardinality=0} +relationship: has_output EDAM_data:1459 ! Nucleic acid structure ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis [Term] -id: EDAM:0002440 +id: EDAM_operation:2440 name: Structure processing (RNA) namespace: operation -def: "Process (read and / or write) RNA tertiary structure data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002519 ! Structure processing (nucleic acid) +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:0000278 +id: EDAM_operation:0278 name: RNA secondary structure prediction namespace: operation -def: "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." [EDAM:EBI "EMBRACE definition"] +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). -subset: operation -is_a: EDAM:0002439 ! RNA secondary structure processing -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0000880 ! RNA secondary structure {minCardinality=1} -relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction +is_a: EDAM_operation:2439 ! RNA secondary structure processing +is_a: EDAM_operation:0415 ! Nucleic acid feature detection +relationship: has_output EDAM_data:0880 !{min_cardinality=1} ! RNA secondary structure +relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] -id: EDAM:0002441 +id: EDAM_operation:2441 name: RNA structure prediction namespace: operation -def: "Predict RNA tertiary structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000475 ! Nucleic acid structure prediction -relationship: has_output EDAM:0001465 ! RNA structure {minCardinality=1} +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:0002442 +id: EDAM_operation:2442 name: DNA structure prediction namespace: operation -def: "Predict DNA tertiary structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000475 ! Nucleic acid structure prediction -relationship: has_output EDAM:0001464 ! DNA structure {minCardinality=1} +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:0000279 +id: EDAM_operation:0279 name: Nucleic acid folding analysis namespace: operation -def: "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002426 ! Modelling and simulation -is_a: EDAM:0002501 ! Nucleic acid data processing -synonym: "Nucleic acid folding" EXACT [] -synonym: "Nucleic acid folding modelling" EXACT [] -relationship: has_output EDAM:0001596 ! Nucleic acid folding report -relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction +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:0000461 +id: EDAM_operation:0461 name: Nucleic acid curvature calculation namespace: operation -def: "Calculate curvature and flexibility / stiffness of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] +subset: operations +def: "Calculate curvature and flexibility / stiffness of a nucleotide sequence." [http://edamontology.org] comment: This includes properties such as. -subset: operation -is_a: EDAM:0000262 ! Nucleic acid property calculation -relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=1} -relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis +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 [Term] -id: EDAM:0001768 +id: EDAM_operation:1768 name: Nucleic acid folding family identification namespace: operation -def: "Identify folding families of related RNAs." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000483 ! Structured RNA prediction and optimisation +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 [Term] -id: EDAM:0001769 +id: EDAM_operation:1769 name: Nucleic acid folding energy calculation namespace: operation -def: "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000279 ! Nucleic acid folding analysis +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 [Term] -id: EDAM:0001777 +id: EDAM_operation:1777 name: Protein function prediction namespace: operation -def: "Predict general functional properties of a protein." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002414 ! Protein function analysis -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_topic EDAM:0002276 ! Protein function prediction +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:0003084 +id: EDAM_operation:3084 !{since=beta13} name: Protein function prediction (from sequence) namespace: operation -def: "Predict general (non-positional) functional properties of a protein from analysing its sequence." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0001777 ! Protein function prediction -is_a: EDAM:0002479 ! Protein sequence analysis -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_topic EDAM:0002276 ! Protein function prediction +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:0001778 +id: EDAM_operation:1778 name: Protein function comparison namespace: operation -def: "Compare the functional properties of two or more proteins." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002414 ! Protein function analysis -is_a: EDAM:0002997 ! Protein comparison -relationship: has_topic EDAM:0001775 ! Protein function analysis +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 [Term] -id: EDAM:0000413 +id: EDAM_operation:0413 name: MHC peptide immunogenicity prediction namespace: operation -def: "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000252 ! Peptide immunogenicity prediction +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 [Term] -id: EDAM:0000253 -name: Sequence feature detection +id: EDAM_operation:0253 +name: Feature prediction namespace: operation -def: "Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002403 ! Sequence analysis -is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_output EDAM:0001255 ! Sequence features {minCardinality=1} -relationship: has_topic EDAM:0003072 ! Sequence feature detection +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 ! Feature prediction [Term] -id: EDAM:0002453 +id: EDAM_operation:2453 name: Feature table processing namespace: operation -def: "Process (read and / or write) a sequence feature table." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0001270 ! Sequence feature table {minCardinality=0} -relationship: has_input EDAM:0002201 ! Sequence record full {minCardinality=0} -relationship: has_output EDAM:0001255 ! Sequence features {minCardinality=0} -relationship: has_topic EDAM:0000160 ! Sequence sites and features +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 ! Sequence feature table ! !{min_cardinality=0} +relationship: has_input EDAM_data:2201 ! Sequence record full ! !{min_cardinality=0} +relationship: has_output EDAM_data:1255 ! Sequence features ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0160 ! Sequence sites and features [Term] -id: EDAM:0000254 +id: EDAM_operation:0254 name: Data retrieval (feature table) namespace: operation -def: "Extract a sequence feature table from a sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002422 ! Data retrieval +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 [Term] -id: EDAM:0000255 +id: EDAM_operation:0255 name: Feature table query namespace: operation -def: "Query the features (in a feature table) of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002453 ! Feature table processing -relationship: has_input EDAM:0001270 ! Sequence feature table {minCardinality=0} -relationship: has_input EDAM:0002201 ! Sequence record full {minCardinality=0} -relationship: has_output EDAM:0001255 ! Sequence features +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 ! Sequence feature table ! !{min_cardinality=0} +relationship: has_input EDAM_data:2201 ! Sequence record full ! !{min_cardinality=0} +relationship: has_output EDAM_data:1255 ! Sequence features [Term] -id: EDAM:0000256 +id: EDAM_operation:0256 name: Feature table comparison namespace: operation -def: "Compare the feature tables of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002453 ! Feature table processing -is_a: EDAM:0002424 ! Comparison -relationship: has_input EDAM:0001270 ! Sequence feature table {minCardinality=0} -relationship: has_input EDAM:0002201 ! Sequence record full {minCardinality=0} +subset: operations +def: "Compare the feature tables of two or more molecular sequences." [http://edamontology.org] +is_a: EDAM_operation:2453 ! Feature table processing +is_a: EDAM_operation:2424 ! Comparison +relationship: has_input EDAM_data:1270 ! Sequence feature table ! !{min_cardinality=0} +relationship: has_input EDAM_data:2201 ! Sequence record full ! !{min_cardinality=0} [Term] -id: EDAM:0003092 -name: Protein feature detection +id: EDAM_operation:3092 !{since=beta13} +name: Protein feature prediction namespace: operation -def: "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002502 ! Protein data processing -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0001277 ! Protein features {minCardinality=1} -relationship: has_topic EDAM:0003074 ! Protein feature detection +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 [Term] -id: EDAM:0000414 -name: Protein feature detection (from sequence) +id: EDAM_operation:0414 +name: Protein feature prediction (from sequence) namespace: operation -def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Sequence feature detection (protein)" EXACT [] -is_a: EDAM:0003092 ! Protein feature detection -is_a: EDAM:0000253 ! Sequence feature detection -is_a: EDAM:0002479 ! Protein sequence analysis +synonym: "Sequence feature detection (protein)" EXACT [http://edamontology.org] +is_a: EDAM_operation:3092 ! Protein feature detection +! is_a: EDAM_operation:0253 ! Feature prediction +is_a: EDAM_operation:2479 ! Protein sequence analysis [Term] -id: EDAM:0003090 -name: Protein feature detection (from structure) +id: EDAM_operation:3090 !{since=beta13} +name: Protein feature prediction (from structure) namespace: operation -def: "Predict, recognise and identify positional features in proteins from analysing protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003092 ! Protein feature detection -is_a: EDAM:0002406 ! Protein structure analysis +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 detection +is_a: EDAM_operation:2406 ! Protein structure analysis [Term] -id: EDAM:0003087 +id: EDAM_operation:3087 !{since=beta13} name: Protein site detection namespace: operation -alt_id: EDAM:0000382 -def: "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "name: Sequence motif recognition (protein)" EXACT [] -is_a: EDAM:0000414 ! Protein feature detection (from sequence) -is_a: EDAM:0000239 ! Sequence motif recognition +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 detection (from sequence) +is_a: EDAM_operation:0239 ! Sequence motif recognition [Term] -id: EDAM:0000415 -name: Nucleic acid feature detection +id: EDAM_operation:0415 +name: Nucleic acid feature prediction namespace: operation -alt_id: EDAM:0000381 -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Sequence feature detection (nucleic acid)" EXACT [] -is_a: EDAM:0000239 ! Sequence motif recognition -is_a: EDAM:0002478 ! Nucleic acid sequence analysis -is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM:0001276 ! Nucleic acid features {minCardinality=1} -relationship: has_topic EDAM:0003073 ! Nucleic acid feature detection +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 @@ -6289,826 +5974,826 @@ relationship: has_topic EDAM:0003073 ! Nucleic acid feature detection [Term] -id: EDAM:0000416 +id: EDAM_operation:0416 name: Epitope mapping namespace: operation -def: "Predict antigenic determinant sites (epitopes) in protein sequences." [EDAM:EBI "EMBRACE definition"] +subset: operations +def: "Predict antigenic determinant sites (epitopes) in protein sequences." [http://edamontology.org] comment: Epitope mapping is commonly done during vaccine design. -subset: operation -is_a: EDAM:0003087 ! Protein site detection -is_a: EDAM:0002429 ! Mapping and assembly -relationship: has_output EDAM:0001326 ! Protein features (binding sites) -relationship: has_topic EDAM:0000804 ! Immunoinformatics +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 [Term] -id: EDAM:0000417 +id: EDAM_operation:0417 name: Protein post-translation modification site prediction namespace: operation -def: "Predict post-translation modification sites in protein sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0003087 ! Protein site detection -relationship: has_output EDAM:0001324 ! Protein features (post-translation modifications) -relationship: has_topic EDAM:0000601 ! Protein modifications +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:0002489 +id: EDAM_operation:2489 name: Protein subcellular localization prediction namespace: operation -def: "Predict the subcellular localization of a protein sequence." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Protein targeting prediction" EXACT [] -is_a: EDAM:0003084 ! Protein function prediction (from sequence) -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_topic EDAM:0000140 ! Protein targeting and localization +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 [Term] -id: EDAM:0000418 +id: EDAM_operation:0418 name: Protein signal peptide detection namespace: operation -def: "Detect or predict signal peptides and signal peptide cleavage sites in protein sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0003087 ! Protein site detection -is_a: EDAM:0002489 ! Protein subcellular localization prediction -relationship: has_output EDAM:0001322 ! Protein features (signal peptides) -relationship: has_topic EDAM:0000140 ! Protein targeting and localization +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 [Term] -id: EDAM:0000419 +id: EDAM_operation:0419 name: Binding site prediction (from sequence) namespace: operation -def: "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Ligand-binding and active site prediction (from sequence)" EXACT [] -is_a: EDAM:0003087 ! Protein site detection -is_a: EDAM:0002575 ! Binding site prediction +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 [Term] -id: EDAM:0000420 +id: EDAM_operation:0420 name: Protein-nucleic acid binding prediction namespace: operation -def: "Predict RNA and DNA-binding binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000419 ! Binding site prediction (from sequence) -relationship: has_output EDAM:0001326 ! Protein features (binding sites) {minCardinality=0} +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 ! Protein features (binding sites) ! !{min_cardinality=0} [Term] -id: EDAM:0000421 +id: EDAM_operation:0421 name: Protein folding site prediction namespace: operation -def: "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003087 ! Protein site detection -is_a: EDAM:0002415 ! Protein folding analysis -relationship: has_output EDAM:0002989 ! Protein features (key folding sites) {minCardinality=1} +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) [Term] -id: EDAM:0000422 +id: EDAM_operation:0422 name: Protein cleavage site prediction namespace: operation -def: "Detect or predict cleavage sites (enzymatic or chemical) in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003087 ! Protein site detection -relationship: has_output EDAM:0001323 ! Protein features (cleavage sites) -relationship: has_topic EDAM:0000767 ! Protein and peptide identification +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 [Term] -id: EDAM:0000423 +id: EDAM_operation:0423 name: Epitope mapping (MHC Class I) namespace: operation -def: "Predict epitopes that bind to MHC class I molecules." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000416 ! Epitope mapping +subset: operations +def: "Predict epitopes that bind to MHC class I molecules." [http://edamontology.org] +is_a: EDAM_operation:0416 ! Epitope mapping [Term] -id: EDAM:0000424 +id: EDAM_operation:0424 name: Epitope mapping (MHC Class II) namespace: operation -def: "Predict epitopes that bind to MHC class II molecules." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000416 ! Epitope mapping +subset: operations +def: "Predict epitopes that bind to MHC class II molecules." [http://edamontology.org] +is_a: EDAM_operation:0416 ! Epitope mapping [Term] -id: EDAM:0000411 +id: EDAM_operation:0411 name: Protein signal peptide detection (eukaryotes) namespace: operation -def: "Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000418 ! Protein signal peptide detection +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 [Term] -id: EDAM:0000412 +id: EDAM_operation:0412 name: Protein signal peptide detection (bacteria) namespace: operation -def: "Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000418 ! Protein signal peptide detection +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 [Term] -id: EDAM:0002454 +id: EDAM_operation:2454 name: Gene and gene component prediction namespace: operation -def: "Detect, predict and identify genes or components of genes in DNA sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Gene finding" EXACT [] -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0001300 ! Nucleic acid features (gene structure) -relationship: has_topic EDAM:0000109 ! Gene finding +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 detection +relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene structure) +relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] -id: EDAM:0000425 +id: EDAM_operation:0425 name: Whole gene prediction namespace: operation -def: "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002454 ! Gene and gene component prediction +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 [Term] -id: EDAM:0000426 +id: EDAM_operation:0426 name: Gene component prediction namespace: operation -def: "Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002454 ! Gene and gene component prediction +is_a: EDAM_operation:2454 ! Gene and gene component prediction [Term] -id: EDAM:0000427 +id: EDAM_operation:0427 name: Transposon prediction namespace: operation -def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0001301 ! Nucleic acid features (mobile genetic elements) +subset: operations +def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [http://edamontology.org] +is_a: EDAM_operation:0415 ! Nucleic acid feature detection +relationship: has_output EDAM_data:1301 ! Nucleic acid features (mobile genetic elements) [Term] -id: EDAM:0000428 +id: EDAM_operation:0428 name: PolyA signal detection namespace: operation -def: "Detect polyA signals in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0001302 ! Nucleic acid features (PolyA signal or site) +subset: operations +def: "Detect polyA signals in nucleotide sequences." [http://edamontology.org] +is_a: EDAM_operation:0415 ! Nucleic acid feature detection +relationship: has_output EDAM_data:1302 ! Nucleic acid features (PolyA signal or site) [Term] -id: EDAM:0000429 +id: EDAM_operation:0429 name: Quadruplex formation site detection namespace: operation -alt_id: EDAM:0002455 -def: "Detect quadruplex-forming motifs in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000415 ! Nucleic acid feature detection -synonym: "Quadruplex structure prediction" EXACT [] -relationship: has_output EDAM:0001303 ! Nucleic acid features (quadruplexes) -relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction +is_a: EDAM_operation:0415 ! Nucleic acid feature detection +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 [Term] -id: EDAM:0000430 +id: EDAM_operation:0430 name: CpG island and isochore detection namespace: operation -alt_id: EDAM:0000576 -def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "CpG island and isochores detection" EXACT [] -synonym: "CpG island and isochores rendering" EXACT [] -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0001304 ! Nucleic acid features (CpG island and isochore) -relationship: has_topic EDAM:0000157 ! Sequence composition analysis +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 detection +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:0000431 +id: EDAM_operation:0431 name: Restriction site recognition namespace: operation -def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0001305 ! Nucleic acid features (restriction sites) -relationship: has_topic EDAM:0000100 ! Nucleic acid restriction +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 detection +relationship: has_output EDAM_data:1305 ! Nucleic acid features (restriction sites) +relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] -id: EDAM:0000433 +id: EDAM_operation:0433 name: Splice site prediction namespace: operation -def: "Identify, predict or analyse splice sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0001307 ! Nucleic acid features (splice sites) -relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing +is_a: EDAM_operation:0415 ! Nucleic acid feature detection +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:0000453 +id: EDAM_operation:0453 name: Nucleosome formation potential prediction namespace: operation -def: "Predict nucleosome formation potential of DNA sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000432 ! Nucleosome formation or exclusion sequence prediction +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 [Term] -id: EDAM:0000432 +id: EDAM_operation:0432 name: Nucleosome formation or exclusion sequence prediction namespace: operation -def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000415 ! Nucleic acid feature detection -relationship: has_output EDAM:0001306 ! Nucleic acid features (nucleosome exclusion sequences) +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 detection +relationship: has_output EDAM_data:1306 ! Nucleic acid features (nucleosome exclusion sequences) [Term] -id: EDAM:0000434 +id: EDAM_operation:0434 name: Integrated gene prediction namespace: operation -def: "Predict whole gene structure using a combination of multiple methods to achieve better predictions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000425 ! Whole gene prediction +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 [Term] -id: EDAM:0000435 +id: EDAM_operation:0435 name: Operon prediction namespace: operation -def: "Find operons (operators, promoters and genes) in bacteria genes." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000425 ! Whole gene prediction +subset: operations +def: "Find operons (operators, promoters and genes) in bacteria genes." [http://edamontology.org] +is_a: EDAM_operation:0425 ! Whole gene prediction [Term] -id: EDAM:0000464 +id: EDAM_operation:0464 name: tRNA gene prediction namespace: operation -def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000425 ! Whole gene prediction -relationship: has_topic EDAM:0000663 ! tRNA +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 [Term] -id: EDAM:0000436 +id: EDAM_operation:0436 name: Coding region prediction namespace: operation -def: "Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000426 ! Gene component prediction -relationship: has_output EDAM:0001313 ! Nucleic acid features (coding sequence) +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) [Term] -id: EDAM:0000437 +id: EDAM_operation:0437 name: Selenocysteine insertion sequence (SECIS) prediction namespace: operation -def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000426 ! Gene component prediction -relationship: has_output EDAM:0001300 ! Nucleic acid features (gene structure) +is_a: EDAM_operation:0426 ! Gene component prediction +relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene structure) [Term] -id: EDAM:0000438 +id: EDAM_operation:0438 name: Transcription regulatory element prediction namespace: operation -def: "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000426 ! Gene component prediction -relationship: has_topic EDAM:0000110 ! Transcription -relationship: has_topic EDAM:0000749 ! Transcription factors and regulatory sites +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:0000439 +id: EDAM_operation:0439 name: Translation initiation site prediction namespace: operation -def: "Predict translation initiation sites, possibly by searching a database of sites." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000436 ! Coding region prediction -relationship: has_topic EDAM:0000108 ! Translation +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 [Term] -id: EDAM:0000440 +id: EDAM_operation:0440 name: Promoter prediction namespace: operation -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000438 ! Transcription regulatory element prediction -relationship: has_output EDAM:0001312 ! Gene features (promoter) +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction +relationship: has_output EDAM_data:1312 ! Gene features (promoter) [Term] -id: EDAM:0000441 +id: EDAM_operation:0441 name: Transcription regulatory element prediction (DNA-cis) namespace: operation -def: "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000438 ! Transcription regulatory element prediction +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] -id: EDAM:0000442 +id: EDAM_operation:0442 name: Transcription regulatory element prediction (RNA-cis) namespace: operation -def: "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000438 ! Transcription regulatory element prediction +is_a: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] -id: EDAM:0000443 +id: EDAM_operation:0443 name: Transcription regulatory element prediction (trans) namespace: operation -def: "Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Functional RNA identification" EXACT [] -is_a: EDAM:0000438 ! Transcription regulatory element prediction -relationship: has_topic EDAM:0003060 ! Regulatory RNA +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 [Term] -id: EDAM:0000444 +id: EDAM_operation:0444 name: Matrix/scaffold attachment site prediction namespace: operation -def: "Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000438 ! Transcription regulatory element prediction -relationship: has_output EDAM:0001308 ! Nucleic acid features (matrix/scaffold attachment sites) +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:0000445 +id: EDAM_operation:0445 name: Transcription factor binding site prediction namespace: operation -def: "Identify or predict transcription factor binding sites in DNA sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000440 ! Promoter prediction -relationship: has_output EDAM:0001315 ! Gene features (TFBS) +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) [Term] -id: EDAM:0000446 +id: EDAM_operation:0446 name: Exonic splicing enhancer prediction namespace: operation -def: "Identify or predict exonic splicing enhancers (ESE) in exons." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000440 ! Promoter prediction -relationship: has_output EDAM:0002397 ! Nucleic acid features (exon) -relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing +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:0002008 +id: EDAM_operation:2008 name: siRNA duplex prediction namespace: operation -def: "Identify or predict siRNA duplexes in RNA." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) -relationship: has_output EDAM:0002169 ! Nucleic acid features (siRNA) -relationship: has_topic EDAM:0003060 ! Regulatory RNA +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 [Term] -id: EDAM:0000465 +id: EDAM_operation:0465 name: siRNA binding specificity prediction namespace: operation -def: "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) -relationship: has_topic EDAM:0003060 ! Regulatory RNA +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 [Term] -id: EDAM:0000463 +id: EDAM_operation:0463 name: microRNA detection namespace: operation -def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) -relationship: has_output EDAM:0001310 ! Nucleic acid features (microRNA) +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) [Term] -id: EDAM:0000259 +id: EDAM_operation:0259 name: Sequence alignment comparison namespace: operation -def: "Compare (typically by aligning) two molecular sequence alignments." [EDAM:EBI "EMBRACE definition"] +subset: operations +def: "Compare (typically by aligning) two molecular sequence alignments." [http://edamontology.org] comment: See also 'Sequence profile alignment'. -subset: operation -is_a: EDAM:0000258 ! Sequence alignment analysis -is_a: EDAM:0002424 ! Comparison +is_a: EDAM_operation:0258 ! Sequence alignment analysis +is_a: EDAM_operation:2424 ! Comparison [Term] -id: EDAM:0000260 +id: EDAM_operation:0260 name: Sequence alignment conversion namespace: operation -def: "Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003081 ! Sequence alignment editing +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 [Term] -id: EDAM:0000447 +id: EDAM_operation:0447 name: Sequence alignment quality evaluation namespace: operation -def: "Evaluate molecular sequence alignment accuracy." [EDAM:EBI "EMBRACE definition"] +subset: operations +def: "Evaluate molecular sequence alignment accuracy." [http://edamontology.org] comment: Evaluation might be purely sequence-based or use structural information. -subset: operation -is_a: EDAM:0002428 ! Validation and standardisation -is_a: EDAM:0000258 ! Sequence alignment analysis +is_a: EDAM_operation:2428 ! Evaluation and validation +is_a: EDAM_operation:0258 ! Sequence alignment analysis [Term] -id: EDAM:0000448 +id: EDAM_operation:0448 name: Sequence alignment analysis (conservation) namespace: operation -def: "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." [EDAM:EBI "EMBRACE definition"] -comment: Use this term 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: operation -is_a: EDAM:0000258 ! Sequence alignment analysis -relationship: has_output EDAM:0001415 ! Sequence alignment report (site conservation) +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) [Term] -id: EDAM:0000449 +id: EDAM_operation:0449 name: Sequence alignment analysis (site correlation) namespace: operation -def: "Analyse correlations between sites in a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000258 ! Sequence alignment analysis -relationship: has_output EDAM:0001416 ! Sequence alignment report (site correlation) +is_a: EDAM_operation:0258 ! Sequence alignment analysis +relationship: has_output EDAM_data:1416 ! Sequence alignment report (site correlation) [Term] -id: EDAM:0000450 +id: EDAM_operation:0450 name: Sequence alignment analysis (chimeric sequence detection) namespace: operation -def: "Detects chimeric sequences (chimeras) from a sequence alignment." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) -relationship: has_topic EDAM:0000077 ! Nucleic acid analysis +is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) +relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] -id: EDAM:0000451 +id: EDAM_operation:0451 name: Sequence alignment analysis (recombination detection) namespace: operation -def: "Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) +is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] -id: EDAM:0000452 +id: EDAM_operation:0452 name: Sequence alignment analysis (indel detection) namespace: operation -def: "Identify insertion, deletion and duplication events from a sequence alignment." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) +is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] -id: EDAM:0000457 +id: EDAM_operation:0457 name: Nucleic acid stitch profile plotting namespace: operation -def: "Calculate and plot a DNA or DNA/RNA stitch profile." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000456 ! Nucleic acid melting profile plotting -relationship: has_output EDAM:0001587 ! Nucleic acid stitch profile +is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting +relationship: has_output EDAM_data:1587 ! Nucleic acid stitch profile [Term] -id: EDAM:0000458 +id: EDAM_operation:0458 name: Nucleic acid melting curve plotting namespace: operation -def: "Calculate and plot a DNA or DNA/RNA melting curve." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000456 ! Nucleic acid melting profile plotting -relationship: has_output EDAM:0002958 ! Nucleic acid melting curve +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 [Term] -id: EDAM:0000459 +id: EDAM_operation:0459 name: Nucleic acid probability profile plotting namespace: operation -def: "Calculate and plot a DNA or DNA/RNA probability profile." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000456 ! Nucleic acid melting profile plotting -relationship: has_output EDAM:0002959 ! Nucleic acid probability profile +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 [Term] -id: EDAM:0000460 +id: EDAM_operation:0460 name: Nucleic acid temperature profile plotting namespace: operation -def: "Calculate and plot a DNA or DNA/RNA temperature profile." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000456 ! Nucleic acid melting profile plotting -relationship: has_output EDAM:0002960 ! Nucleic acid temperature profile +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 [Term] -id: EDAM:0002444 +id: EDAM_operation:2444 name: Protein secondary structure processing namespace: operation -def: "Process (read and / or write) protein secondary structure data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002482 ! Secondary structure processing -is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=0} -relationship: has_output EDAM:0000876 ! Protein features (secondary structure) {minCardinality=0} -relationship: has_topic EDAM:0000694 ! Protein secondary structure +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 ! Protein features (secondary structure) ! !{min_cardinality=0} +relationship: has_output EDAM_data:0876 ! Protein features (secondary structure) ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0694 ! Protein secondary structure [Term] -id: EDAM:0000319 +id: EDAM_operation:0319 name: Protein secondary structure assignment namespace: operation -def: "Assign secondary structure from protein coordinate or experimental data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002444 ! Protein secondary structure processing -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} -relationship: has_topic EDAM:0002226 ! Structure determination +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 [Term] -id: EDAM:0000267 +id: EDAM_operation:0267 name: Protein secondary structure prediction namespace: operation -def: "Predict secondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Secondary structure prediction (protein)" EXACT [] -is_a: EDAM:0002444 ! Protein secondary structure processing -is_a: EDAM:0000414 ! Protein feature detection (from sequence) -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} -relationship: has_topic EDAM:0000178 ! Protein secondary structure prediction +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 detection (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 [Term] -id: EDAM:0000268 +id: EDAM_operation:0268 name: Protein super-secondary structure prediction namespace: operation -def: "Predict super-secondary structure of protein sequence(s)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_output EDAM:0000877 ! Protein features (super-secondary) +is_a: EDAM_operation:0267 ! Protein secondary structure prediction +relationship: has_output EDAM_data:0877 ! Protein features (super-secondary) [Term] -id: EDAM:0000534 +id: EDAM_operation:0534 name: Protein secondary structure assignment (from coordinate data) namespace: operation -def: "Assign secondary structure from protein coordinate data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000319 ! Protein secondary structure assignment -is_a: EDAM:0003090 ! Protein feature detection (from structure) +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 detection (from structure) [Term] -id: EDAM:0000535 +id: EDAM_operation:0535 name: Protein secondary structure assignment (from CD data) namespace: operation -def: "Assign secondary structure from circular dichroism (CD) spectroscopic data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000319 ! Protein secondary structure assignment -relationship: has_input EDAM:0000939 ! Protein circular dichroism (CD) spectroscopic data +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 [Term] -id: EDAM:0001847 +id: EDAM_operation:1847 name: DSSP secondary structure assignment namespace: operation -def: "Determine for residue the DSSP determined secondary structure in three-state (HSC)." [EDAM:WHATIF "EMBRACE definition"] -subset: 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 -consider: EDAM:0000534 ! Protein secondary structure assignment (from coordinate data) +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data) [Term] -id: EDAM:0000467 +id: EDAM_operation:0467 name: Protein secondary structure prediction (integrated) namespace: operation -def: "Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000267 ! Protein secondary structure prediction +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 [Term] -id: EDAM:0000468 +id: EDAM_operation:0468 name: Protein secondary structure prediction (helices) namespace: operation -def: "Predict helical secondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000267 ! Protein secondary structure prediction +subset: operations +def: "Predict helical secondary structure of protein sequences." [http://edamontology.org] +is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] -id: EDAM:0000469 +id: EDAM_operation:0469 name: Protein secondary structure prediction (turns) namespace: operation -def: "Predict turn structure (for example beta hairpin turns) of protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000267 ! Protein secondary structure prediction +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 [Term] -id: EDAM:0000470 +id: EDAM_operation:0470 name: Protein secondary structure prediction (coils) namespace: operation -def: "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000267 ! Protein secondary structure prediction +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 [Term] -id: EDAM:0000471 +id: EDAM_operation:0471 name: Protein secondary structure prediction (disulfide bonds) namespace: operation -def: "Predict cysteine bonding state and disulfide bond partners in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000267 ! Protein secondary structure prediction +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 [Term] -id: EDAM:0000269 +id: EDAM_operation:0269 name: Transmembrane protein prediction namespace: operation -def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000270 ! Transmembrane protein analysis -is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_output EDAM:0001456 ! Protein features (membrane regions) {minCardinality=1} +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) [Term] -id: EDAM:0002456 +id: EDAM_operation:2456 name: GPCR classification namespace: operation -def: "Classify G-protein coupled receptors (GPCRs) into families and subfamilies." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "G protein-coupled receptor (GPCR) classification" EXACT [] -is_a: EDAM:0000473 ! GPCR analysis -is_a: EDAM:0002995 ! Sequence classification -relationship: has_output EDAM:0000907 ! Protein family {minCardinality=1} +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 [Term] -id: EDAM:0002457 +id: EDAM_operation:2457 name: GPCR coupling selectivity prediction namespace: operation -def: "Predict G-protein coupled receptor (GPCR) coupling selectivity." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000473 ! GPCR analysis -is_a: EDAM:0002492 ! Protein interaction prediction -is_a: EDAM:0003088 ! Protein property calculation (from sequence) -relationship: has_output EDAM:0000896 ! Protein report {minCardinality=1} +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 [Term] -id: EDAM:0000473 +id: EDAM_operation:0473 name: GPCR analysis namespace: operation -def: "Analyse G-protein coupled receptor proteins (GPCRs)." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "G protein-coupled receptor (GPCR) analysis" EXACT [] -is_a: EDAM:0000270 ! Transmembrane protein analysis -relationship: has_output EDAM:0001456 ! Protein features (membrane regions) -relationship: has_topic EDAM:0000820 ! Membrane proteins +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 [Term] -id: EDAM:0000472 +id: EDAM_operation:0472 name: GPCR prediction namespace: operation -def: "Predict G protein-coupled receptors (GPCR)." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "G protein-coupled receptor (GPCR) prediction" EXACT [] -is_a: EDAM:0000269 ! Transmembrane protein prediction -is_a: EDAM:0000473 ! GPCR analysis +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 [Term] -id: EDAM:0000474 +id: EDAM_operation:0474 name: Protein structure prediction namespace: operation -def: "Predict tertiary structure (backbone and side-chain conformation) of protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000271 ! Structure prediction -is_a: EDAM:0002459 ! Structure processing (protein) -is_a: EDAM:0002479 ! Protein sequence analysis -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0001460 ! Protein structure {minCardinality=1} -relationship: has_topic EDAM:0000179 ! Protein tertiary structure prediction +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 [Term] -id: EDAM:0000475 +id: EDAM_operation:0475 name: Nucleic acid structure prediction namespace: operation -def: "Predict tertiary structure of DNA or RNA." [EDAM:EBI "EMBRACE definition"] +subset: operations +def: "Predict tertiary structure of DNA or RNA." [http://edamontology.org] comment: Methods might identify thermodynamically stable or evolutionarily conserved structures. -subset: operation -is_a: EDAM:0000271 ! Structure prediction -is_a: EDAM:0002519 ! Structure processing (nucleic acid) -is_a: EDAM:0002478 ! Nucleic acid sequence analysis -is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM:0001459 ! Nucleic acid structure {minCardinality=1} -relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction +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 [Term] -id: EDAM:0000476 +id: EDAM_operation:0476 name: Ab initio structure prediction namespace: operation -def: "Predict tertiary structure of protein sequence(s) without homologs of known structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000474 ! Protein structure prediction -relationship: has_topic EDAM:0000174 ! Ab initio structure prediction +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 [Term] -id: EDAM:0000477 +id: EDAM_operation:0477 name: Protein modelling namespace: operation -def: "Build a three-dimensional protein model based on known (for example homologs) structures." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Comparative modelling" EXACT [] -synonym: "Homology modelling" EXACT [] -synonym: "Homology structure modelling" EXACT [] -synonym: "Protein structure comparative modelling" EXACT [] -is_a: EDAM:0002406 ! Protein structure analysis -is_a: EDAM:0000474 ! Protein structure prediction -is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_topic EDAM:0000175 ! Homology modelling +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 [Term] -id: EDAM:0000478 +id: EDAM_operation:0478 name: Protein docking namespace: operation -def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000477 ! Protein modelling -is_a: EDAM:0002492 ! Protein interaction prediction -relationship: has_output EDAM:0001461 ! Protein-ligand complex {minCardinality=0} -relationship: has_output EDAM:0002877 ! Protein complex {minCardinality=0} -relationship: has_topic EDAM:0000177 ! Molecular docking +is_a: EDAM_operation:0477 ! Protein modelling +is_a: EDAM_operation:2492 ! Protein interaction prediction +relationship: has_output EDAM_data:1461 ! Protein-ligand complex ! !{min_cardinality=0} +relationship: has_output EDAM_data:2877 ! Protein complex ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0177 ! Molecular docking [Term] -id: EDAM:0000302 +id: EDAM_operation:0302 name: Protein threading namespace: operation -def: "Align molecular sequence to structure in 3D space (threading)." [EDAM:EBI "EMBRACE definition"] -comment: Use this term 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: operation -synonym: "Sequence-structure alignment" EXACT [] -is_a: EDAM:0000303 ! Protein fold recognition -is_a: EDAM:0002928 ! Alignment -relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=1} -relationship: has_output EDAM:0000893 ! Sequence-structure alignment {minCardinality=1} -relationship: has_topic EDAM:0000175 ! Homology modelling -relationship: has_topic EDAM:0000184 ! Threading +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 +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 [Term] -id: EDAM:0000479 +id: EDAM_operation:0479 name: Protein modelling (backbone) namespace: operation -def: "Model protein backbone conformation." [EDAM:EBI "EMBRACE definition"] +subset: operations +def: "Model protein backbone conformation." [http://edamontology.org] comment: Methods might require a preliminary C(alpha) trace. -subset: operation -is_a: EDAM:0000477 ! Protein modelling +is_a: EDAM_operation:0477 ! Protein modelling [Term] -id: EDAM:0000480 +id: EDAM_operation:0480 name: Protein modelling (side chains) namespace: operation -def: "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000477 ! Protein modelling +is_a: EDAM_operation:0477 ! Protein modelling [Term] -id: EDAM:0000481 +id: EDAM_operation:0481 name: Protein modelling (loops) namespace: operation -def: "Model loop conformation in protein structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000477 ! Protein modelling +subset: operations +def: "Model loop conformation in protein structures." [http://edamontology.org] +is_a: EDAM_operation:0477 ! Protein modelling [Term] -id: EDAM:0001841 +id: EDAM_operation:1841 name: Rotamer likelihood prediction namespace: operation -def: "Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure." [EDAM:WHATIF "EMBRACE definition"] +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. -subset: operation xref: WHATIF:ShowLikelyRotamers xref: WHATIF:ShowLikelyRotamers100 xref: WHATIF:ShowLikelyRotamers200 @@ -7119,1184 +6804,1235 @@ xref: WHATIF:ShowLikelyRotamers600 xref: WHATIF:ShowLikelyRotamers700 xref: WHATIF:ShowLikelyRotamers800 xref: WHATIF:ShowLikelyRotamers900 -is_a: EDAM:0000480 ! Protein modelling (side chains) +is_a: EDAM_operation:0480 ! Protein modelling (side chains) [Term] -id: EDAM:0000482 +id: EDAM_operation:0482 name: Protein-ligand docking namespace: operation -def: "Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Virtual ligand screening" EXACT [] -is_a: EDAM:0000478 ! Protein docking -relationship: has_output EDAM:0001461 ! Protein-ligand complex {minCardinality=1} -relationship: has_topic EDAM:0000148 ! Protein-ligand interactions +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 [Term] -id: EDAM:0000483 +id: EDAM_operation:0483 name: Structured RNA prediction and optimisation namespace: operation -def: "Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "RNA inverse folding" EXACT [] -synonym: "Nucleic acid folding family identification" EXACT [] -is_a: EDAM:0003095 ! Nucleic acid design -is_a: EDAM:0002425 ! Optimisation and refinement -relationship: has_output EDAM:0001234 ! Sequence set (nucleic acid) -relationship: has_topic EDAM:0002953 ! Nucleic acid design +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 [Term] -id: EDAM:0000273 +id: EDAM_operation:0273 name: Protein interaction raw data analysis namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002949 ! Protein interaction analysis -relationship: has_input EDAM:0000905 ! Protein interaction raw data -relationship: has_topic EDAM:0000147 ! Protein-protein interactions +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 [Term] -id: EDAM:0002492 +id: EDAM_operation:2492 name: Protein interaction prediction namespace: operation -def: "Predict the interactions of proteins with other molecules." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002405 ! Protein interaction data processing -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0000906 ! Protein report (interaction) {minCardinality=1} +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 report (interaction) [Term] -id: EDAM:0002464 +id: EDAM_operation:2464 name: Protein-protein interaction prediction namespace: operation -def: "Identify or predict protein-protein interactions, interfaces, binding sites etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002492 ! Protein interaction prediction -relationship: has_output EDAM:0001565 ! Protein-protein interaction {minCardinality=1} -relationship: has_topic EDAM:0000147 ! Protein-protein interactions +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 [Term] -id: EDAM:0000274 +id: EDAM_operation:0274 name: Protein-protein interaction prediction (from protein sequence) namespace: operation -def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002464 ! Protein-protein interaction prediction -is_a: EDAM:0003084 ! Protein function prediction (from sequence) +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) [Term] -id: EDAM:0000275 +id: EDAM_operation:0275 name: Protein-protein interaction prediction (from protein structure) namespace: operation -def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002464 ! Protein-protein interaction prediction -is_a: EDAM:0003090 ! Protein feature detection (from structure) +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 detection (from structure) [Term] -id: EDAM:0002445 +id: EDAM_operation:2445 name: Protein interaction network processing namespace: operation -def: "Process (read and / or write) a network of protein interactions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002405 ! Protein interaction data processing -is_a: EDAM:0002438 ! Pathway or network processing -relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=0} -relationship: has_output EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=0} -relationship: has_topic EDAM:0003044 ! Protein interaction networks +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 ! Pathway or network (protein-protein interaction) ! !{min_cardinality=0} +relationship: has_output EDAM_data:1663 ! Pathway or network (protein-protein interaction) ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:3044 ! Protein interaction networks [Term] -id: EDAM:0000333 +id: EDAM_operation:0333 name: Zinc finger protein domain prediction and optimisation namespace: operation -def: "Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000420 ! Protein-nucleic acid binding prediction -is_a: EDAM:0002425 ! Optimisation and refinement -relationship: has_output EDAM:0001567 ! Protein-nucleic acid interaction -relationship: has_topic EDAM:0000150 ! Protein design +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 [Term] -id: EDAM:0000276 +id: EDAM_operation:0276 name: Protein interaction network analysis namespace: operation -def: "Analyse a network of protein interactions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002445 ! Protein interaction network processing -is_a: EDAM:0002949 ! Protein interaction analysis -is_a: EDAM:0002497 ! Pathway or network analysis -relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=1} -relationship: has_output EDAM:0002984 ! Pathway or network report +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 [Term] -id: EDAM:0000277 +id: EDAM_operation:0277 name: Protein interaction network comparison namespace: operation -def: "Compare two or more networks of protein interactions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000276 ! Protein interaction network analysis -is_a: EDAM:0001778 ! Protein function comparison -relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=2} +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) [Term] -id: EDAM:0000484 +id: EDAM_operation:0484 name: SNP detection namespace: operation -def: "Find single nucleotide polymorphisms (SNPs) between sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Single nucleotide polymorphism detection" EXACT [] -is_a: EDAM:0002508 ! Nucleic acid sequence comparison -is_a: EDAM:0002508 ! Nucleic acid sequence comparison -relationship: has_output EDAM:0002885 ! Nucleic acid features (polymorphism annotation) +synonym: "Single nucleotide polymorphism detection" EXACT [http://edamontology.org] +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison +relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] -id: EDAM:0000485 +id: EDAM_operation:0485 name: Radiation Hybrid Mapping namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002944 ! Physical mapping -relationship: has_output EDAM:0002870 ! Radiation hybrid map {minCardinality=1} +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 [Term] -id: EDAM:0000486 +id: EDAM_operation:0486 name: Functional mapping namespace: operation -def: "Map the genetic architecture of dynamic complex traits." [EDAM:EBI "EMBRACE definition"] +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). -subset: operation -is_obsolete: true -consider: EDAM:0000282 ! Genetic mapping +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_operation:0282 ! Genetic mapping [Term] -id: EDAM:0000487 +id: EDAM_operation:0487 name: Haplotype inference namespace: operation -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." [EDAM:EBI "EMBRACE definition"] +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. 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: operation -synonym: "Haplotype mapping" EXACT [] -is_a: EDAM:0000283 ! Linkage analysis -relationship: has_output EDAM:0001863 ! Haplotype map {minCardinality=1} +synonym: "Haplotype mapping" EXACT [http://edamontology.org] +is_a: EDAM_operation:0283 ! Linkage analysis +relationship: has_output EDAM_data:1863 !{min_cardinality=1} ! Haplotype map [Term] -id: EDAM:0000488 +id: EDAM_operation:0488 name: Linkage disequilibrium calculation namespace: operation -def: "Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000283 ! Linkage analysis -relationship: has_output EDAM:0001634 ! Gene annotation (linkage disequilibrium) {minCardinality=1} +is_a: EDAM_operation:0283 ! Linkage analysis +relationship: has_output EDAM_data:1634 !{min_cardinality=1} ! Gene annotation (linkage disequilibrium) [Term] -id: EDAM:0000286 +id: EDAM_operation:0286 name: Codon usage analysis namespace: operation -alt_id: EDAM:0002494 -def: "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "synon: Codon usage table analysis" EXACT [] -synonym: "synon: Codon usage data analysis" EXACT [] -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=0} -relationship: has_input EDAM:0001597 ! Codon usage table {minCardinality=0} -relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=0} -relationship: has_output EDAM:0000914 ! Codon usage report {minCardinality=0} -relationship: has_topic EDAM:0000107 ! Codon usage analysis +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 ! Nucleic acid sequence ! !{min_cardinality=0} +relationship: has_input EDAM_data:1597 ! Codon usage table ! !{min_cardinality=0} +relationship: has_output EDAM_data:1597 ! Codon usage table ! !{min_cardinality=0} +relationship: has_output EDAM_data:0914 ! Codon usage report ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] -id: EDAM:0002433 +id: EDAM_operation:2433 name: Codon usage table processing namespace: operation -def: "Process (read and / or write) a codon usage table." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000286 ! Codon usage analysis -relationship: has_input EDAM:0001597 ! Codon usage table {minCardinality=0} -relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=0} +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 ! Codon usage table ! !{min_cardinality=0} +relationship: has_output EDAM_data:1597 ! Codon usage table ! !{min_cardinality=0} [Term] -id: EDAM:0000287 +id: EDAM_operation:0287 name: Base position variability plotting namespace: operation -def: "Identify and plot third base position variability in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000286 ! Codon usage analysis -relationship: has_output EDAM:0001263 ! Sequence composition (base position variability) {minCardinality=1} -relationship: has_topic EDAM:0000109 ! Gene finding +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 [Term] -id: EDAM:0000489 +id: EDAM_operation:0489 name: Genetic code prediction namespace: operation -def: "Predict genetic code from analysis of codon usage data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000286 ! Codon usage analysis -is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM:0001598 ! Genetic code {minCardinality=1} +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 [Term] -id: EDAM:0002962 +id: EDAM_operation:2962 name: Codon usage bias calculation namespace: operation -def: "Calculate codon usage bias." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000286 ! Codon usage analysis -relationship: has_output EDAM:0002865 ! Codon usage bias {minCardinality=1} +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 [Term] -id: EDAM:0002963 +id: EDAM_operation:2963 name: Codon usage bias plotting namespace: operation -def: "Generate a codon usage bias plot." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002962 ! Codon usage bias calculation -relationship: has_output EDAM:0001600 ! Codon usage bias plot {minCardinality=1} +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 [Term] -id: EDAM:0002964 +id: EDAM_operation:2964 name: Codon usage fraction calculation namespace: operation -def: "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000286 ! Codon usage analysis -relationship: has_output EDAM:0001602 ! Codon usage fraction difference {minCardinality=1} +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 [Term] -id: EDAM:0000284 +id: EDAM_operation:0284 name: Codon usage table generation namespace: operation -def: "Calculate codon usage statistics and create a codon usage table." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002433 ! Codon usage table processing -relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=1} +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 [Term] -id: EDAM:0000285 +id: EDAM_operation:0285 name: Codon usage table comparison namespace: operation -def: "Compare two or more codon usage tables." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002433 ! Codon usage table processing -is_a: EDAM:0002998 ! Nucleic acid comparison +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 [Term] -id: EDAM:0000491 -name: Pairwise sequence alignment +id: EDAM_operation:0491 +name: Pairwise sequence alignment construction namespace: operation -def: "Align exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000292 ! Sequence alignment -relationship: has_output EDAM:0001381 ! Sequence alignment (pair) {minCardinality=1} +is_a: EDAM_operation:0292 ! Sequence alignment construction +relationship: has_output EDAM_data:1381 !{min_cardinality=1} ! Sequence alignment (pair) [Term] -id: EDAM:0000492 -name: Multiple sequence alignment +id: EDAM_operation:0492 +name: Multiple sequence alignment construction namespace: operation -def: "Align two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000292 ! Sequence alignment +is_a: EDAM_operation:0292 ! Sequence alignment construction [Term] -id: EDAM:0002089 +id: EDAM_operation:2089 name: Sequence alignment refinement namespace: operation -def: "Refine an existing sequence alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000258 ! Sequence alignment analysis -is_a: EDAM:0002425 ! Optimisation and refinement +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 [Term] -id: EDAM:0000493 -name: Pairwise sequence alignment (local) +id: EDAM_operation:0493 +name: Pairwise sequence alignment construction (local) namespace: operation -def: "Locally align exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000491 ! Pairwise sequence alignment +synonym: "Local pairwise sequence alignment construction" EXACT [http.//edamontology.org] +is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction [Term] -id: EDAM:0000494 -name: Pairwise sequence alignment (global) +id: EDAM_operation:0494 +name: Pairwise sequence alignment construction (global) namespace: operation -def: "Globally align exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000491 ! Pairwise sequence alignment +synonym: "Global pairwise sequence alignment construction" EXACT [http://edamontology.org] +is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction [Term] -id: EDAM:0000495 -name: Multiple sequence alignment (local) +id: EDAM_operation:0495 +name: Multiple sequence alignment construction (local) namespace: operation -def: "Locally align two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000492 ! Multiple sequence alignment +synonym: "Local multiple sequence alignment construction" EXACT [http.//edamontology.org] +is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] -id: EDAM:0000496 -name: Multiple sequence alignment (global) +id: EDAM_operation:0496 +name: Multiple sequence alignment construction (global) namespace: operation -def: "Globally align two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000492 ! Multiple sequence alignment +synonym: "Global multiple sequence alignment construction" EXACT [http.//edamontology.org] +is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] -id: EDAM:0000497 -name: Multiple sequence alignment (constrained) +id: EDAM_operation:0497 +name: Multiple sequence alignment construction (constrained) namespace: operation -def: "Align two or more molecular sequences with user-defined constraints." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000492 ! Multiple sequence alignment +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 [Term] -id: EDAM:0000498 -name: Multiple sequence alignment (consensus) +id: EDAM_operation:0498 +name: Multiple sequence alignment construction (consensus) namespace: operation -def: "Align two or more molecular sequences using multiple methods to achieve higher quality." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000492 ! Multiple sequence alignment +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 [Term] -id: EDAM:0000499 -name: Multiple sequence alignment (phylogenetic tree-based) +id: EDAM_operation:0499 +name: Multiple sequence alignment construction (phylogenetic tree-based) namespace: operation -def: "Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000492 ! Multiple sequence alignment -relationship: has_topic EDAM:0000084 ! Phylogenetics +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 [Term] -id: EDAM:0000500 -name: Secondary structure alignment +id: EDAM_operation:0500 +name: Secondary structure alignment construction namespace: operation -def: "Align molecular secondary structure (represented as a 1D string)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002482 ! Secondary structure processing -is_a: EDAM:0002931 ! Secondary structure comparison -is_a: EDAM:0000294 ! Structure-based sequence alignment -relationship: has_output EDAM:0002366 ! Secondary structure alignment {minCardinality=1} -relationship: has_topic EDAM:0000182 ! Sequence alignment +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 [Term] -id: EDAM:0000501 -name: Protein secondary structure alignment +id: EDAM_operation:0501 +name: Protein secondary structure alignment construction namespace: operation -def: "Align protein secondary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000500 ! Secondary structure alignment -is_a: EDAM:0002488 ! Protein secondary structure comparison -synonym: "Secondary structure alignment (protein)" EXACT [] -relationship: has_output EDAM:0000878 ! Secondary structure alignment (protein) {minCardinality=1} +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) [Term] -id: EDAM:0000502 -name: RNA secondary structure alignment +id: EDAM_operation:0502 +name: RNA secondary structure alignment construction namespace: operation -def: "Align RNA secondary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002439 ! RNA secondary structure processing -is_a: EDAM:0000500 ! Secondary structure alignment -synonym: "Secondary structure alignment (RNA)" EXACT [] -relationship: has_input EDAM:0000880 ! RNA secondary structure {minCardinality=2} -relationship: has_output EDAM:0000881 ! Secondary structure alignment (RNA) {minCardinality=1} +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 +relationship: has_output EDAM_data:0881 !{min_cardinality=1} ! Secondary structure alignment (RNA) [Term] -id: EDAM:0000503 -name: Pairwise structure alignment +id: EDAM_operation:0503 +name: Pairwise structure alignment construction namespace: operation -def: "Align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000295 ! Structure alignment +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 [Term] -id: EDAM:0000504 -name: Multiple structure alignment +id: EDAM_operation:0504 +name: Multiple structure alignment construction namespace: operation -def: "Align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000295 ! Structure alignment +is_a: EDAM_operation:0295 ! Structure alignment construction [Term] -id: EDAM:0002488 +id: EDAM_operation:2488 name: Protein secondary structure comparison namespace: operation -def: "Compare protein secondary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002416 ! Protein secondary structure analysis -is_a: EDAM:0002931 ! Secondary structure comparison -is_a: EDAM:0002997 ! Protein comparison -synonym: "Secondary structure comparison (protein)" EXACT [] -relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=2} +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) [Term] -id: EDAM:0002487 +id: EDAM_operation:2487 name: Protein structure comparison namespace: operation -def: "Compare protein tertiary structures." [EDAM:EBI "EMBRACE definition"] +subset: operations +def: "Compare protein tertiary structures." [http://edamontology.org] comment: Methods might identify structural neighbors, find structural similarities or define a structural core. -subset: operation -is_a: EDAM:0002459 ! Structure processing (protein) -is_a: EDAM:0002483 ! Structure comparison -is_a: EDAM:0002997 ! Protein comparison -synonym: "Structure comparison (protein)" EXACT [] -relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=2} -relationship: has_output EDAM:0000897 ! Protein property +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 [Term] -id: EDAM:0002518 +id: EDAM_operation:2518 name: Nucleic acid structure comparison namespace: operation -def: "Compare nucleic acid tertiary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Structure comparison (nucleic acid)" EXACT [] -is_a: EDAM:0002483 ! Structure comparison -is_a: EDAM:0002481 ! Nucleic acid structure analysis -is_a: EDAM:0002998 ! Nucleic acid comparison +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 [Term] -id: EDAM:0000505 +id: EDAM_operation:0505 name: Structure alignment (protein) namespace: operation -def: "Align protein tertiary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000295 ! Structure alignment +subset: operations +def: "Align protein tertiary structures." [http://edamontology.org] +is_obsolete: true !{since=beta13} +consider: EDAM_operation:0295 ! Structure alignment [Term] -id: EDAM:0000506 +id: EDAM_operation:0506 name: Structure alignment (RNA) namespace: operation -def: "Align RNA tertiary structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000295 ! Structure alignment +subset: operations +def: "Align RNA tertiary structures." [http://edamontology.org] +is_obsolete: true !{since=beta13} +consider: EDAM_operation:0295 ! Structure alignment [Term] -id: EDAM:0000507 -name: Pairwise structure alignment (local) +id: EDAM_operation:0507 +name: Pairwise structure alignment construction (local) namespace: operation -def: "Locally align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000503 ! Pairwise structure alignment +synonym: "Local pairwise structure alignment construction" EXACT [http://edamontology.org] +is_a: EDAM_operation:0503 ! Pairwise structure alignment construction [Term] -id: EDAM:0000508 -name: Pairwise structure alignment (global) +id: EDAM_operation:0508 +name: Pairwise structure alignment construction (global) namespace: operation -def: "Globally align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000503 ! Pairwise structure alignment +synonym: "Global pairwise structure alignment construction" EXACT [http://edamontology.org] +is_a: EDAM_operation:0503 ! Pairwise structure alignment construction [Term] -id: EDAM:0000509 -name: Multiple structure alignment (local) +id: EDAM_operation:0509 +name: Multiple structure alignment construction (local) namespace: operation -def: "Locally align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000504 ! Multiple structure alignment +synonym: "Local multiple structure alignment construction" EXACT [http://edamontology.org] +is_a: EDAM_operation:0504 ! Multiple structure alignment construction [Term] -id: EDAM:0000510 -name: Multiple structure alignment (global) +id: EDAM_operation:0510 +name: Multiple structure alignment construction (global) namespace: operation -def: "Globally align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000504 ! Multiple structure alignment +synonym: "Global multiple structure alignment construction" EXACT [http://edamontology.org] +is_a: EDAM_operation:0504 ! Multiple structure alignment construction [Term] -id: EDAM:0000296 +id: EDAM_operation:0296 name: Sequence profile generation namespace: operation -def: "Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002413 ! Sequence profile processing -is_a: EDAM:0002463 ! Sequence alignment processing -relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=1} -relationship: has_output EDAM:0001354 ! Sequence profile {minCardinality=1} +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 [Term] -id: EDAM:0000298 -name: Sequence profile alignment +id: EDAM_operation:0298 +name: Sequence profile alignment construction namespace: operation -def: "Align sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] +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'. -subset: operation -is_a: EDAM:0002413 ! Sequence profile processing -is_a: EDAM:0002928 ! Alignment -relationship: has_input EDAM:0001354 ! Sequence profile {minCardinality=2} -relationship: has_output EDAM:0000868 ! Sequence profile alignment {minCardinality=1} +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 [Term] -id: EDAM:0000300 -name: Sequence-profile alignment +id: EDAM_operation:0300 +name: Sequence-profile alignment construction namespace: operation -def: "Align molecular sequence(s) to sequence profile(s)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002413 ! Sequence profile processing -is_a: EDAM:0002403 ! Sequence analysis -is_a: EDAM:0002928 ! Alignment -relationship: has_input EDAM:0001354 ! Sequence profile {minCardinality=1} -relationship: has_output EDAM:0000869 ! Sequence-profile alignment {minCardinality=1} +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 [Term] -id: EDAM:0000511 -name: Sequence profile alignment (pairwise) +id: EDAM_operation:0511 +name: Sequence profile alignment construction (pairwise) namespace: operation -def: "Align exactly two molecular profiles." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000298 ! Sequence profile alignment +synonym: "Pairwise sequence profile alignment construction" EXACT [http://edamontology.org] +is_a: EDAM_operation:0298 ! Sequence profile alignment construction [Term] -id: EDAM:0000512 -name: Sequence profile alignment (multiple) +id: EDAM_operation:0512 +name: Sequence profile alignment construction (multiple) namespace: operation -def: "Align two or more molecular profiles." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000298 ! Sequence profile alignment +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 [Term] -id: EDAM:0000297 +id: EDAM_operation:0297 name: Structural (3D) profile generation namespace: operation -def: "Generate some type of structural (3D) profile or template from a structure or structure alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Structural profile generation" EXACT [] -is_a: EDAM:0002411 ! Structural (3D) profile processing -is_a: EDAM:0002952 ! Structure alignment processing -is_a: EDAM:0002465 ! Structure processing -relationship: has_input EDAM:0000886 ! Structure alignment {minCardinality=1} -relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} -relationship: has_output EDAM:0000889 ! Structural (3D) profile {minCardinality=1} - -[Term] -id: EDAM:0000299 -name: Structural (3D) profile alignment -namespace: operation -def: "Align structural (3D) profiles or templates (representing structures or structure alignments)." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Structural profile alignment" EXACT [] -is_a: EDAM:0002411 ! Structural (3D) profile processing -is_a: EDAM:0002928 ! Alignment -relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=2} -relationship: has_output EDAM:0000890 ! Structural (3D) profile alignment {minCardinality=1} -relationship: has_topic EDAM:0000183 ! Structure alignment - -[Term] -id: EDAM:0000513 -name: Structural (3D) profile alignment (pairwise) -namespace: operation -def: "Align exactly two molecular Structural (3D) profiles." [EDAM:EBI "EMBRACE definition"] +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 + +[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 + +[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. -subset: operation -is_a: EDAM:0000299 ! Structural (3D) profile alignment +synonym: "Pairwise structural (3D) profile alignment construction" EXACT [http://edamontology.org] +is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction [Term] -id: EDAM:0000514 -name: Structural (3D) profile alignment (multiple) +id: EDAM_operation:0514 +name: Structural (3D) profile alignment construction (multiple) namespace: operation -def: "Align two or more molecular 3D profiles." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000299 ! Structural (3D) profile alignment +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 [Term] -id: EDAM:0000301 -name: Sequence-3D profile alignment +id: EDAM_operation:0301 +name: Sequence-3D profile alignment construction namespace: operation -def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000303 ! Protein fold recognition -is_a: EDAM:0002928 ! Alignment -is_a: EDAM:0002403 ! Sequence analysis -relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=2} -relationship: has_output EDAM:0000891 ! Sequence-3D profile alignment {minCardinality=1} -relationship: has_topic EDAM:0000184 ! Threading +is_a: EDAM_operation:0303 ! Protein fold recognition +is_a: EDAM_operation:2928 ! Alignment +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 [Term] -id: EDAM:0000308 +id: EDAM_operation:0308 name: PCR primer design namespace: operation -def: "Design or predict oligonucleotide primers for PCR and DNA amplification etc." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "PCR primer prediction" EXACT [] -is_a: EDAM:0002419 ! Primer and probe design -relationship: has_input EDAM:0002977 ! Nucleic acid sequence -relationship: has_output EDAM:0001240 ! PCR primers {minCardinality=0} -relationship: has_topic EDAM:0003032 ! Primer or probe design +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 ! PCR primers ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] -id: EDAM:0000309 +id: EDAM_operation:0309 name: Microarray probe design namespace: operation -def: "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Microarray probe prediction" EXACT [] -is_a: EDAM:0002419 ! Primer and probe design -is_a: EDAM:0002425 ! Optimisation and refinement -relationship: has_input EDAM:0002977 ! Nucleic acid sequence -relationship: has_output EDAM:0002717 ! Oligonucleotide probe annotation {minCardinality=1} -relationship: has_topic EDAM:0000200 ! Microarrays -relationship: has_topic EDAM:0003032 ! Primer or probe design +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 [Term] -id: EDAM:0000307 +id: EDAM_operation:0307 name: Virtual PCR namespace: operation -def: "Perform in-silico (virtual) PCR." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002478 ! Nucleic acid sequence analysis -relationship: has_topic EDAM:0000077 ! Nucleic acid analysis +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 [Term] -id: EDAM:0000517 +id: EDAM_operation:0517 name: PCR primer design (for large scale sequencing) namespace: operation -def: "Predict primers for large scale sequencing." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000308 ! PCR primer design -relationship: has_topic EDAM:0000102 ! Sequencing and mapping +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:0102 ! Sequencing and mapping [Term] -id: EDAM:0000518 +id: EDAM_operation:0518 name: PCR primer design (for genotyping polymorphisms) namespace: operation -def: "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000308 ! PCR primer design +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 [Term] -id: EDAM:0000519 +id: EDAM_operation:0519 name: PCR primer design (for gene transcription profiling) namespace: operation -def: "Predict primers for gene transcription profiling." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000308 ! PCR primer design -relationship: has_topic EDAM:0000203 ! Transcriptomics +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 [Term] -id: EDAM:0000520 +id: EDAM_operation:0520 name: PCR primer design (for conserved primers) namespace: operation -def: "Predict primers that are conserved across multiple genomes or species." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000308 ! PCR primer design +subset: operations +def: "Predict primers that are conserved across multiple genomes or species." [http://edamontology.org] +is_a: EDAM_operation:0308 ! PCR primer design [Term] -id: EDAM:0000521 +id: EDAM_operation:0521 name: PCR primer design (based on gene structure) namespace: operation -def: "Predict primers based on gene structure, promoters, exon-exon junctions etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000308 ! PCR primer design -relationship: has_topic EDAM:0000109 ! Gene finding +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 [Term] -id: EDAM:0000522 +id: EDAM_operation:0522 name: PCR primer design (for methylation PCRs) namespace: operation -def: "Predict primers for methylation PCRs." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000308 ! PCR primer design +subset: operations +def: "Predict primers for methylation PCRs." [http://edamontology.org] +is_a: EDAM_operation:0308 ! PCR primer design [Term] -id: EDAM:0000523 +id: EDAM_operation:0523 name: Sequence assembly (mapping assembly) namespace: operation -def: "Sequence assembly by combining fragments using an existing backbone sequence." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000310 ! Sequence assembly +is_a: EDAM_operation:0310 ! Sequence assembly [Term] -id: EDAM:0000524 +id: EDAM_operation:0524 name: Sequence assembly (de-novo assembly) namespace: operation -def: "Sequence assembly by combining fragments into a new, previously unknown sequence." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000310 ! Sequence assembly +is_a: EDAM_operation:0310 ! Sequence assembly [Term] -id: EDAM:0000525 +id: EDAM_operation:0525 name: Sequence assembly (genome assembly) namespace: operation -def: "Sequence assembly capable on a very large scale such as assembly of whole genomes." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000310 ! Sequence assembly +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 [Term] -id: EDAM:0000526 +id: EDAM_operation:0526 name: Sequence assembly (EST assembly) namespace: operation -def: "Sequence assembly for EST sequences (transcribed mRNA)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000310 ! Sequence assembly +is_a: EDAM_operation:0310 ! Sequence assembly [Term] -id: EDAM:0002410 +id: EDAM_operation:2410 name: Gene expression analysis namespace: operation -def: "Analyse gene expression and regulation data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002495 ! Gene expression data processing +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 [Term] -id: EDAM:0002435 +id: EDAM_operation:2435 name: Gene expression profile processing namespace: operation -def: "Process (read and / or write) a gene expression profile." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002495 ! Gene expression data processing -relationship: has_input EDAM:0000928 ! Gene expression profile {minCardinality=0} -relationship: has_output EDAM:0000928 ! Gene expression profile {minCardinality=0} -relationship: has_topic EDAM:0000203 ! Transcriptomics -relationship: has_topic EDAM:0000200 ! Microarrays +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 ! Gene expression profile ! !{min_cardinality=0} +relationship: has_output EDAM_data:0928 ! Gene expression profile ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0203 ! Transcriptomics +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] -id: EDAM:0000312 +id: EDAM_operation:0312 name: Sequencing-based expression profile data processing namespace: operation -def: "Process (read and / or write) SAGE, MPSS or SBS experimental data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002495 ! Gene expression data processing +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 [Term] -id: EDAM:0002498 +id: EDAM_operation:2498 name: Sequencing-based expression profile data analysis namespace: operation -def: "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002495 ! Gene expression data processing +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 [Term] -id: EDAM:0002496 +id: EDAM_operation:2496 name: Gene regulatory network processing namespace: operation -def: "Process (read and / or write) a network of gene regulation." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002438 ! Pathway or network processing -relationship: has_input EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=0} -relationship: has_output EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=0} -relationship: has_topic EDAM:0000197 ! Gene expression resources -relationship: has_topic EDAM:0002846 ! Gene regulatory networks +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 ! Pathway or network (gene regulation) ! !{min_cardinality=0} +relationship: has_output EDAM_data:2961 ! Pathway or network (gene regulation) ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0197 ! Gene expression resources +relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks [Term] -id: EDAM:0001781 +id: EDAM_operation:1781 name: Gene regulatory network analysis namespace: operation -def: "Analyse a known network of gene regulation." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002496 ! Gene regulatory network processing -is_a: EDAM:0002497 ! Pathway or network analysis -relationship: has_input EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=1} +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) [Term] -id: EDAM:0002437 +id: EDAM_operation:2437 name: Gene regulatory network prediction namespace: operation -def: "Predict a network of gene regulation." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002496 ! Gene regulatory network processing -is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=1} +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) [Term] -id: EDAM:0003094 +id: EDAM_operation:3094 !{since=beta13} name: Protein interaction network prediction namespace: operation -def: "Predict a network of protein interactions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002445 ! Protein interaction network processing -relationship: has_output EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=1} +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) [Term] -id: EDAM:0000316 +id: EDAM_operation:0316 name: Functional profiling namespace: operation -def: "Interpret (in functional terms) and annotate gene expression data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000532 ! Gene expression profile analysis +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 [Term] -id: EDAM:0000264 +id: EDAM_operation:0264 name: Splice transcript prediction namespace: operation -def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002499 ! Splicing modelling -relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing +subset: operations +def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [http://edamontology.org] +is_a: EDAM_operation:2499 ! Splicing modelling +relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] -id: EDAM:0002499 +id: EDAM_operation:2499 name: Splicing analysis namespace: operation -def: "Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Splicing modelling" EXACT [] -is_a: EDAM:0002508 ! Nucleic acid sequence comparison -is_a: EDAM:0002426 ! Modelling and simulation -is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM:0001307 ! Nucleic acid features (splice sites) {minCardinality=1} -relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing +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 [Term] -id: EDAM:0000313 +id: EDAM_operation:0313 name: Gene expression profile clustering namespace: operation -def: "Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000315 ! Gene expression profile comparison -relationship: has_output EDAM:0003111 ! Processed microarray data +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 [Term] -id: EDAM:0000314 +id: EDAM_operation:0314 name: Gene expression profile generation namespace: operation -def: "Generate a gene expression profile or pattern, for example from microarray data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002435 ! Gene expression profile processing -relationship: has_output EDAM:0000928 ! Gene expression profile {minCardinality=1} +subset: operations +def: "Generate a gene expression profile or pattern, for example from microarray data." [http://edamontology.org] +is_a: EDAM_operation:2435 ! Gene expression profile processing +relationship: has_output EDAM_data:0928 !{min_cardinality=1} ! Gene expression profile [Term] -id: EDAM:0000315 +id: EDAM_operation:0315 name: Gene expression profile comparison namespace: operation -def: "Compare gene expression profiles or patterns." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000532 ! Gene expression profile analysis -is_a: EDAM:0002998 ! Nucleic acid comparison -relationship: has_output EDAM:0003111 ! Processed microarray data +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 [Term] -id: EDAM:0002436 +id: EDAM_operation:2436 name: Gene expression profile annotation namespace: operation -def: "Annotate a gene expression profile with terms from an ontology of gene functions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000532 ! Gene expression profile analysis -is_a: EDAM:0000226 ! Annotation -relationship: has_output EDAM:0000928 ! Gene expression profile {minCardinality=1} +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 [Term] -id: EDAM:0000532 +id: EDAM_operation:0532 name: Gene expression profile analysis namespace: operation -def: "Analyse one or more gene expression profiles, typically to interpret them in functional terms." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Functional profiling" EXACT [] -is_a: EDAM:0002435 ! Gene expression profile processing -relationship: has_input EDAM:0000928 ! Gene expression profile {minCardinality=1} +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 [Term] -id: EDAM:0000533 +id: EDAM_operation:0533 name: Gene expression profile pathway mapping namespace: operation -def: "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000532 ! Gene expression profile analysis -is_a: EDAM:0002497 ! Pathway or network analysis -relationship: has_output EDAM:0002984 ! Pathway or network report +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 [Term] -id: EDAM:0000527 +id: EDAM_operation:0527 name: Tag mapping namespace: operation -def: "Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology terms." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Tag to gene assignment" EXACT [] -is_a: EDAM:0002436 ! Gene expression profile annotation -relationship: has_output EDAM:0000936 ! Sequence tag profile (with gene assignment) {minCardinality=0} +synonym: "Tag to gene assignment" EXACT [http://edamontology.org] +is_a: EDAM_operation:2436 ! Gene expression profile annotation +relationship: has_output EDAM_data:0936 ! Sequence tag profile (with gene assignment) ! !{min_cardinality=0} [Term] -id: EDAM:0000528 +id: EDAM_operation:0528 name: SAGE data processing namespace: operation -def: "Process (read and / or write) serial analysis of gene expression (SAGE) data." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Serial analysis of gene expression data processing" EXACT [] -is_obsolete: true -consider: EDAM:0002495 ! Gene expression data processing +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 [Term] -id: EDAM:0000529 +id: EDAM_operation:0529 name: MPSS data processing namespace: operation -def: "Process (read and / or write) massively parallel signature sequencing (MPSS) data." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Massively parallel signature sequencing data processing" EXACT [] -is_obsolete: true -consider: EDAM:0002495 ! Gene expression data processing +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 [Term] -id: EDAM:0000530 +id: EDAM_operation:0530 name: SBS data processing namespace: operation -def: "Process (read and / or write) sequencing by synthesis (SBS) data." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Sequencing by synthesis data processing" EXACT [] -is_obsolete: true -consider: EDAM:0002495 ! Gene expression data processing +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 [Term] -id: EDAM:0000531 +id: EDAM_operation:0531 name: Heat map generation namespace: operation -def: "Generate a heat map of gene expression from microarray data." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000571 ! Microarray data rendering -relationship: has_output EDAM:0001636 ! Heat map {minCardinality=1} +is_a: EDAM_operation:0571 ! Microarray data rendering +relationship: has_output EDAM_data:1636 !{min_cardinality=1} ! Heat map [Term] -id: EDAM:0002934 +id: EDAM_operation:2934 name: Microarray cluster textual view rendering -def: "Visualise gene clusters with gene names." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000571 ! Microarray data rendering +namespace: operation +subset: operations +def: "Visualise gene clusters with gene names." [http://edamontology.org] +is_a: EDAM_operation:0571 ! Microarray data rendering [Term] -id: EDAM:0002935 +id: EDAM_operation:2935 name: Microarray wave graph rendering namespace: operation -synonym: "Microarray cluster temporal graph rendering" EXACT [] -def: "Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000571 ! Microarray data rendering +is_a: EDAM_operation:0571 ! Microarray data rendering [Term] -id: EDAM:0002936 +id: EDAM_operation:2936 name: Microarray dendrograph rendering -synonym: "Microarray checks view rendering" EXACT [] -synonym: "Microarray view rendering" EXACT [] -def: "Generate a dendrograph of raw, preprocessed or clustered microarray data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000571 ! Microarray data 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 [Term] -id: EDAM:0002937 +id: EDAM_operation:2937 name: Microarray proximity map rendering -synonym: "Microarray distance map rendering" EXACT [] -def: "Generate a plot of distances (distance matrix) between genes." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000571 ! Microarray data 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 [Term] -id: EDAM:0002938 +id: EDAM_operation:2938 name: Microarray tree or dendrogram view rendering -synonym: "Microarray matrix tree plot rendering" EXACT [] -synonym: "Microarray 2-way dendrogram rendering" EXACT [] -def: "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000571 ! Microarray data 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 [Term] -id: EDAM:0002939 +id: EDAM_operation:2939 name: Microarray principal component rendering -def: "Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000571 ! Microarray data 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 [Term] -id: EDAM:0002940 +id: EDAM_operation:2940 name: Microarray scatter plot rendering -def: "Generate a scatter plot of microarray data, typically after principal component analysis." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000571 ! Microarray data 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 [Term] -id: EDAM:0002941 +id: EDAM_operation:2941 name: Whole microarray graph view rendering -def: "Visualise gene expression data where each band (or line graph) corresponds to a sample." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000571 ! Microarray data 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 [Term] -id: EDAM:0002942 +id: EDAM_operation:2942 name: Microarray tree-map rendering -def: "Visualise gene expression data after hierarchical clustering for representing hierarchical relationships." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000571 ! Microarray data 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 [Term] -id: EDAM:0002943 +id: EDAM_operation:2943 name: Microarray Box-Whisker plot rendering -def: "Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000571 ! Microarray data 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 [Term] -id: EDAM:0002459 +id: EDAM_operation:2459 name: Structure processing (protein) namespace: operation -def: "Process (read and / or write) a protein tertiary structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002465 ! Structure processing -is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=0} -relationship: has_output EDAM:0001460 ! Protein structure {minCardinality=0} -relationship: has_topic EDAM:0000698 ! Protein tertiary structure +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 ! Protein structure ! !{min_cardinality=0} +relationship: has_output EDAM_data:1460 ! Protein structure ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure [Term] -id: EDAM:0000243 +id: EDAM_operation:0243 name: Protein property calculation (from structure) namespace: operation -alt_id: EDAM:0003089 -def: "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0002406 ! Protein structure analysis -is_a: EDAM:0000250 ! Protein property calculation -synonym: "Protein structural property calculation" EXACT [] -relationship: has_output EDAM:0000897 ! Protein property {minCardinality=0} -relationship: has_topic EDAM:0000123 ! Protein properties -relationship: has_topic EDAM:0002814 ! Protein structure analysis +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 ! Protein property ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0123 ! Protein properties +relationship: has_topic EDAM_topic:2814 ! Protein structure analysis [Term] -id: EDAM:0000244 +id: EDAM_operation:0244 name: Protein flexibility and motion analysis namespace: operation -def: "Analyse flexibility and motion in protein structure." [EDAM:EBI "EMBRACE definition"] -comment: Use this term 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: operation -is_a: EDAM:0000243 ! Protein property calculation (from structure) -is_a: EDAM:0002476 ! Molecular dynamics simulation -relationship: has_output EDAM:0001541 ! Protein flexibility or motion report {minCardinality=1} +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 [Term] -id: EDAM:0000245 +id: EDAM_operation:0245 name: Protein structural motif recognition namespace: operation -def: "Identify or screen for 3D structural motifs in protein structure(s)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Protein structural feature identification" EXACT [] -is_a: EDAM:0003090 ! Protein feature detection (from structure) -relationship: has_output EDAM:0000899 ! Protein features (3D motif) {minCardinality=1} -relationship: has_topic EDAM:0000166 ! Protein structural motifs and surfaces +synonym: "Protein structural feature identification" EXACT [http://edamontology.org] +is_a: EDAM_operation:3090 ! Protein feature detection (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 [Term] -id: EDAM:0000246 +id: EDAM_operation:0246 name: Protein domain recognition namespace: operation -def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003090 ! Protein feature detection (from structure) -relationship: has_output EDAM:0000901 ! Protein features (domains) {minCardinality=1} -relationship: has_topic EDAM:0000736 ! Protein domains and folds +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 detection (from structure) +relationship: has_output EDAM_data:0901 !{min_cardinality=1} ! Protein features (domains) +relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] -id: EDAM:0000247 +id: EDAM_operation:0247 name: Protein architecture analysis namespace: operation -def: "Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002406 ! Protein structure analysis -relationship: has_output EDAM:0000902 ! Protein architecture report {minCardinality=1} +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 [Term] -id: EDAM:0002474 +id: EDAM_operation:2474 name: Protein architecture comparison namespace: operation -def: "Compare the architecture of two or more protein structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000247 ! Protein architecture analysis -is_a: EDAM:0002488 ! Protein secondary structure comparison -relationship: has_output EDAM:0000902 ! Protein architecture report {minCardinality=1} +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 [Term] -id: EDAM:0002475 +id: EDAM_operation:2475 name: Protein architecture recognition namespace: operation -def: "Identify the architecture of a protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000247 ! Protein architecture analysis -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -is_a: EDAM:0002996 ! Structure classification -relationship: has_output EDAM:0000902 ! Protein architecture report {minCardinality=1} +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 [Term] -id: EDAM:0000248 +id: EDAM_operation:0248 name: Residue interaction calculation namespace: operation -def: "Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s)." [EDAM:EBI "EMBRACE definition"] -subset: 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 @@ -8305,2381 +8041,2405 @@ xref: WHATIF: SymShellOneXML xref: WHATIF: SymShellTwoXML xref: WHATIF: SymShellFiveXML xref: WHATIF: SymShellTenXML -is_a: EDAM:0000243 ! Protein property calculation (from structure) -relationship: has_output EDAM:0001540 ! Protein residue interactions {minCardinality=1} -relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis +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 [Term] -id: EDAM:0000272 +id: EDAM_operation:0272 name: Residue interaction prediction namespace: operation -def: "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000243 ! Protein property calculation (from structure) -is_a: EDAM:0002506 ! Sequence alignment analysis (protein) -relationship: has_topic EDAM:0000144 ! Protein residue interaction 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 [Term] -id: EDAM:0000249 +id: EDAM_operation:0249 name: Torsion angle calculation namespace: operation -def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000243 ! Protein property calculation (from structure) -relationship: has_output EDAM:0002991 ! Protein torsion angle data +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 [Term] -id: EDAM:0000320 +id: EDAM_operation:0320 name: Protein structure assignment namespace: operation -def: "Assign a protein tertiary structure (3D coordinates) from raw experimental data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002459 ! Structure processing (protein) -relationship: has_output EDAM:0001460 ! Protein structure {minCardinality=1} -relationship: has_topic EDAM:0002226 ! Structure determination +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 [Term] -id: EDAM:0000321 +id: EDAM_operation:0321 name: Protein model evaluation namespace: operation -def: "Evaluate the quality or correctness a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation xref: WHATIF: UseFileDB -is_a: EDAM:0000477 ! Protein modelling -is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_output EDAM:0001539 ! Protein structural quality report {minCardinality=1} -relationship: has_topic EDAM:0002275 ! Molecular modelling -relationship: has_topic EDAM:0000175 ! Homology modelling -relationship: has_topic EDAM:0000179 ! Protein tertiary structure prediction +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 [Term] -id: EDAM:0000322 +id: EDAM_operation:0322 name: Protein model refinement namespace: operation -def: "Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation xref: WHATIF: CorrectedPDBasXML -is_a: EDAM:0000321 ! Protein model evaluation -is_a: EDAM:0002425 ! Optimisation and refinement +is_a: EDAM_operation:0321 ! Protein model evaluation +is_a: EDAM_operation:2425 ! Optimisation and refinement [Term] -id: EDAM:0002239 +id: EDAM_operation:2239 name: 3D-1D scoring matrix generation namespace: operation -def: "Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000243 ! Protein property calculation (from structure) -is_a: EDAM:0003088 ! Protein property calculation (from sequence) -relationship: has_output EDAM:0001499 ! 3D-1D scoring matrix {minCardinality=1} -relationship: has_topic EDAM:0000167 ! Structural (3D) profiles +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 [Term] -id: EDAM:0002574 +id: EDAM_operation:2574 name: Protein hydropathy calculation namespace: operation -def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000250 ! Protein property calculation -relationship: has_output EDAM:0002970 ! Protein hydropathy data {minCardinality=1} -relationship: has_topic EDAM:0000137 ! Protein hydropathy +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 [Term] -id: EDAM:0000383 +id: EDAM_operation:0383 name: Protein hydropathy calculation (from structure) namespace: operation -def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002574 ! Protein hydropathy calculation -is_a: EDAM:0000243 ! Protein property calculation (from structure) +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) [Term] -id: EDAM:0000384 +id: EDAM_operation:0384 name: Protein solvent accessibility calculation namespace: operation -def: "Calculate solvent accessible or buried surface areas in protein structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000243 ! Protein property calculation (from structure) -relationship: has_output EDAM:0001542 ! Protein solvent accessibility -relationship: has_topic EDAM:0000137 ! Protein hydropathy +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 [Term] -id: EDAM:0001850 +id: EDAM_operation:1850 name: Protein cysteine and disulfide bond assignment namespace: operation -def: "Assign cysteine bonding state and disulfide bond partners in protein structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000534 ! Protein secondary structure assignment (from coordinate data) -relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis +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 [Term] -id: EDAM:0000385 +id: EDAM_operation:0385 name: Protein hydropathy cluster calculation namespace: operation -def: "Identify clusters of hydrophobic or charged residues in a protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000383 ! Protein hydropathy calculation (from structure) -is_a: EDAM:0000393 ! Protein residue cluster calculation +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 [Term] -id: EDAM:0000386 +id: EDAM_operation:0386 name: Protein dipole moment calculation namespace: operation -def: "Calculate whether a protein structure has an unusually large net charge (dipole moment)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003088 ! Protein property calculation (from sequence) -relationship: has_output EDAM:0001545 ! Protein dipole moment {minCardinality=1} +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 [Term] -id: EDAM:0000387 +id: EDAM_operation:0387 name: Protein surface and interior calculation namespace: operation -def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000384 ! Protein solvent accessibility calculation -relationship: has_output EDAM:0001543 ! Protein surface report {minCardinality=1} -relationship: has_topic EDAM:0000166 ! Protein structural motifs and surfaces +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 [Term] -id: EDAM:0001816 +id: EDAM_operation:1816 name: Surface rendering namespace: operation -def: "Calculate the positions of dots that are homogeneously distributed over the surface of a molecule." [EDAM:WHATIF "EMBRACE definition"] +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. -subset: operation xref: WHATIF:GetSurfaceDots -is_a: EDAM:0002462 ! Protein surface calculation -is_a: EDAM:0000570 ! Structure rendering +is_a: EDAM_operation:2462 ! Protein surface calculation +is_a: EDAM_operation:0570 ! Structure rendering [Term] -id: EDAM:0002460 +id: EDAM_operation:2460 name: Protein atom surface calculation namespace: operation -def: "Calculate the solvent accessibility for each atom in a structure." [EDAM:WHATIF "EMBRACE definition"] +subset: operations +def: "Calculate the solvent accessibility for each atom in a structure." [http://edamontology.org, WHATIF] comment: Waters are not considered. -subset: operation -is_a: EDAM:0000387 ! Protein surface and interior calculation +is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] -id: EDAM:0001817 +id: EDAM_operation:1817 name: Protein atom surface calculation (accessible) namespace: operation -def: "Calculate the solvent accessibility ('accessible surface') for each atom in a structure." [EDAM:WHATIF "EMBRACE definition"] +subset: operations +def: "Calculate the solvent accessibility ('accessible surface') for each atom in a structure." [http://edamontology.org, WHATIF] comment: Waters are not considered. -subset: operation xref: WHATIF:AtomAccessibilitySolvent xref: WHATIF:AtomAccessibilitySolventPlus -is_a: EDAM:0002460 ! Protein atom surface calculation +is_a: EDAM_operation:2460 ! Protein atom surface calculation [Term] -id: EDAM:0001818 +id: EDAM_operation:1818 name: Protein atom surface calculation (accessible molecular) namespace: operation -def: "Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure." [EDAM:WHATIF "EMBRACE definition"] +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. -subset: operation xref: WHATIF:AtomAccessibilityMolecular xref: WHATIF:AtomAccessibilityMolecularPlus -is_a: EDAM:0002460 ! Protein atom surface calculation +is_a: EDAM_operation:2460 ! Protein atom surface calculation [Term] -id: EDAM:0002461 +id: EDAM_operation:2461 name: Protein residue surface calculation namespace: operation -def: "Calculate the solvent accessibility for each residue in a structure." [EDAM:WHATIF "EMBRACE definition"] -subset: operation -is_a: EDAM:0000387 ! Protein surface and interior calculation +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 [Term] -id: EDAM:0001819 +id: EDAM_operation:1819 name: Protein residue surface calculation (accessible) namespace: operation -def: "Calculate the solvent accessibility ('accessible surface') for each residue in a structure." [EDAM:WHATIF "EMBRACE definition"] +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). -subset: operation xref: WHATIF:ResidueAccessibilitySolvent -is_a: EDAM:0002461 ! Protein residue surface calculation +is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] -id: EDAM:0001820 +id: EDAM_operation:1820 name: Protein residue surface calculation (vacuum accessible) namespace: operation -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." [EDAM:WHATIF "EMBRACE definition"] +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). -subset: operation xref: WHATIF:ResidueAccessibilityVacuum -is_a: EDAM:0002461 ! Protein residue surface calculation +is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] -id: EDAM:0001821 +id: EDAM_operation:1821 name: Protein residue surface calculation (accessible molecular) namespace: operation -def: "Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure." [EDAM:WHATIF "EMBRACE definition"] +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). -subset: operation xref: WHATIF:ResidueAccessibilityMolecular -is_a: EDAM:0002461 ! Protein residue surface calculation +is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] -id: EDAM:0001822 +id: EDAM_operation:1822 name: Protein residue surface calculation (vacuum molecular) namespace: operation -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." [EDAM:WHATIF "EMBRACE definition"] +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). -subset: operation xref: WHATIF:ResidueAccessibilityVacuumMolecular -is_a: EDAM:0002461 ! Protein residue surface calculation +is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] -id: EDAM:0002462 +id: EDAM_operation:2462 name: Protein surface calculation namespace: operation -def: "Calculate the solvent accessibility of a structure as a whole." [EDAM:WHATIF "EMBRACE definition"] -subset: operation -is_a: EDAM:0000387 ! Protein surface and interior calculation +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 [Term] -id: EDAM:0001823 +id: EDAM_operation:1823 name: Protein surface calculation (accessible molecular) namespace: operation -def: "Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0002462 ! Protein surface calculation +is_a: EDAM_operation:2462 ! Protein surface calculation [Term] -id: EDAM:0001824 +id: EDAM_operation:1824 name: Protein surface calculation (accessible) namespace: operation -def: "Calculate the solvent accessibility ('accessible surface') for a structure as a whole." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0002462 ! Protein surface calculation +is_a: EDAM_operation:2462 ! Protein surface calculation [Term] -id: EDAM:0001829 +id: EDAM_operation:1829 name: Cysteine bridge detection namespace: operation -def: "Detect cysteine bridges (from coordinate data) in a protein structure." [EDAM:WHATIF "EMBRACE definition"] -subset: operation +subset: operations +def: "Detect cysteine bridges (from coordinate data) in a protein structure." [http://edamontology.org, WHATIF] xref: WHATIF:ShowCysteineBridge -is_a: EDAM:0001850 ! Protein cysteine and disulfide bond assignment +is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] -id: EDAM:0001830 +id: EDAM_operation:1830 name: Free cysteine detection namespace: operation -def: "Detect free cysteines in a protein structure." [EDAM:WHATIF "EMBRACE definition"] +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. -subset: operation xref: WHATIF:ShowCysteineFree -is_a: EDAM:0001850 ! Protein cysteine and disulfide bond assignment +is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] -id: EDAM:0001831 +id: EDAM_operation:1831 name: Metal-bound cysteine detection namespace: operation -def: "Detect cysteines that are bound to metal in a protein structure." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0001850 ! Protein cysteine and disulfide bond assignment +is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] -id: EDAM:0002575 +id: EDAM_operation:2575 name: Binding site prediction namespace: operation -def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Ligand-binding and active site prediction" EXACT [] -is_a: EDAM:0002492 ! Protein interaction prediction -relationship: has_output EDAM:0001325 ! Protein features (active sites) {minCardinality=0} -relationship: has_output EDAM:0001326 ! Protein features (binding sites) {minCardinality=0} -relationship: has_topic EDAM:0000148 ! Protein-ligand interactions +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 ! Protein features (active sites) ! !{min_cardinality=0} +relationship: has_output EDAM_data:1326 ! Protein features (binding sites) ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] -id: EDAM:0000388 +id: EDAM_operation:0388 name: Binding site prediction (from structure) namespace: operation -def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Ligand-binding and active site prediction (from structure)" EXACT [] -is_a: EDAM:0000245 ! Protein structural motif recognition -is_a: EDAM:0002575 ! Binding site prediction +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 [Term] -id: EDAM:0000389 +id: EDAM_operation:0389 name: Protein-nucleic acid binding site analysis namespace: operation -def: "Analyse RNA or DNA-binding sites in protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002949 ! Protein interaction analysis -relationship: has_input EDAM:0001567 ! Protein-nucleic acid interaction -relationship: has_topic EDAM:0000149 ! Protein-nucleic acid interactions +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 [Term] -id: EDAM:0000390 +id: EDAM_operation:0390 name: Protein peeling namespace: operation -def: "Decompose a structure into compact or globular fragments (protein peeling)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000246 ! Protein domain recognition -relationship: has_output EDAM:0000901 ! Protein features (domains) {minCardinality=1} +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) [Term] -id: EDAM:0000391 +id: EDAM_operation:0391 name: Protein distance matrix calculation namespace: operation -def: "Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000248 ! Residue interaction calculation -relationship: has_output EDAM:0001546 ! Protein distance matrix {minCardinality=1} +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 [Term] -id: EDAM:0000394 +id: EDAM_operation:0394 name: Hydrogen bond calculation namespace: operation -def: "Identify potential hydrogen bonds between amino acids and other groups." [EDAM:WHATIF "EMBRACE definition"] +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. -subset: operation xref: WHATIF:ShowHydrogenBondsM xref: WHATIF:ShowHydrogenBonds xref: WHATIF:ShowHydrogenBonds xref: WHATIF:HasHydrogenBonds -is_a: EDAM:0000248 ! Residue interaction calculation -relationship: has_output EDAM:0001549 ! Protein hydrogen bonds {minCardinality=1} +is_a: EDAM_operation:0248 ! Residue interaction calculation +relationship: has_output EDAM_data:1549 !{min_cardinality=1} ! Protein hydrogen bonds [Term] -id: EDAM:0002491 +id: EDAM_operation:2491 name: Hydrogen bond calculation (inter-residue) namespace: operation -def: "Identify potential hydrogen bonds between amino acid residues." [EDAM:WHATIF "EMBRACE definition"] -subset: operation -is_a: EDAM:0000394 ! Hydrogen bond calculation -is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) +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) [Term] -id: EDAM:0001839 +id: EDAM_operation:1839 name: Salt bridge calculation namespace: operation -def: "Calculate (and possibly score) salt bridges in a protein structure." [EDAM:WHATIF "EMBRACE definition"] +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. -subset: operation xref: WHATIF:HasSaltBridge xref: WHATIF:HasSaltBridgePlus xref: WHATIF:ShowSaltBridges xref: WHATIF:ShowSaltBridgesH -is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) +is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] -id: EDAM:0001846 +id: EDAM_operation:1846 name: HET group detection namespace: operation -def: "Identify HET groups in PDB files." [EDAM:WHATIF "EMBRACE definition"] +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. -subset: operation xref: WHATIF: HETGroupNames -is_a: EDAM:0001838 ! Residue contact calculation (residue-ligand) +is_a: EDAM_operation:1838 ! Residue contact calculation (residue-ligand) [Term] -id: EDAM:0002950 -alt_id: EDAM:0001833 +id: EDAM_operation:2950 +! alt_id: EDAM_operation:1833 name: Residue contact calculation namespace: operation -def: "Calculate contacts between residues and some other group in a protein structure." [EDAM:WHATIF "EMBRACE definition"] -subset: operation -is_a: EDAM:0000248 ! Residue interaction calculation +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 [Term] -id: EDAM:0001838 +id: EDAM_operation:1838 name: Residue contact calculation (residue-ligand) namespace: operation -def: "Calculate contacts between residues and ligands in a protein structure." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0002950 ! Residue contact calculation -is_a: EDAM:0000388 ! Binding site prediction (from structure) +is_a: EDAM_operation:2950 ! Residue contact calculation +is_a: EDAM_operation:0388 ! Binding site prediction (from structure) [Term] -id: EDAM:0002490 +id: EDAM_operation:2490 name: Residue contact calculation (residue-residue) namespace: operation -def: "Calculate contacts between residues in a protein structure." [EDAM:WHATIF "EMBRACE definition"] -subset: operation -is_a: EDAM:0002950 ! Residue contact calculation +subset: operations +def: "Calculate contacts between residues in a protein structure." [http://edamontology.org, WHATIF] +is_a: EDAM_operation:2950 ! Residue contact calculation [Term] -id: EDAM:0000392 +id: EDAM_operation:0392 name: Protein contact map calculation namespace: operation -def: "Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) -relationship: has_output EDAM:0001547 ! Protein contact map {minCardinality=1} +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 [Term] -id: EDAM:0000393 +id: EDAM_operation:0393 name: Protein residue cluster calculation namespace: operation -def: "Calculate clusters of contacting residues in protein structures." [EDAM:EBI "EMBRACE definition"] +subset: operations +def: "Calculate clusters of contacting residues in protein structures." [http://edamontology.org] comment: Cluster of contacting residues might be key structural residues. -subset: operation -is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) -relationship: has_output EDAM:0001548 ! Protein residue 3D cluster {minCardinality=1} +is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) +relationship: has_output EDAM_data:1548 !{min_cardinality=1} ! Protein residue 3D cluster [Term] -id: EDAM:0001832 +id: EDAM_operation:1832 name: Residue contact calculation (residue-nucleic acid) namespace: operation -def: "Calculate protein residue contacts with nucleic acids in a structure." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0002950 ! Residue contact calculation -is_a: EDAM:0000389 ! Protein-nucleic acid binding site data analysis -is_a: EDAM:0000245 ! Protein structural motif recognition +is_a: EDAM_operation:2950 ! Residue contact calculation +is_a: EDAM_operation:0389 ! Protein-nucleic acid binding site data analysis +is_a: EDAM_operation:0245 ! Protein structural motif recognition [Term] -id: EDAM:0001834 +id: EDAM_operation:1834 name: Residue contact calculation (residue-metal) namespace: operation -def: "Calculate protein residue contacts with metal in a structure." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0002950 ! Residue contact calculation -is_a: EDAM:0000388 ! Binding site prediction (from structure) +is_a: EDAM_operation:2950 ! Residue contact calculation +is_a: EDAM_operation:0388 ! Binding site prediction (from structure) [Term] -id: EDAM:0001835 +id: EDAM_operation:1835 name: Residue contact calculation (residue-negative ion) namespace: operation -def: "Calculate ion contacts in a structure (all ions for all side chain atoms)." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0002950 ! Residue contact calculation +is_a: EDAM_operation:2950 ! Residue contact calculation [Term] -id: EDAM:0001837 +id: EDAM_operation:1837 name: Residue symmetry contact calculation namespace: operation -def: "Calculate the number of symmetry contacts made by residues in a protein structure." [EDAM:WHATIF "EMBRACE definition"] +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. -subset: operation xref: WHATIF:SymmetryContact -is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) +is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] -id: EDAM:0000396 +id: EDAM_operation:0396 name: Ramachandran plot calculation namespace: operation -def: "Calculate a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000249 ! Torsion angle calculation -relationship: has_output EDAM:0001544 ! Ramachandran plot {minCardinality=1} +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 [Term] -id: EDAM:0000397 +id: EDAM_operation:0397 name: Ramachandran plot evaluation namespace: operation -def: "Analyse (typically to validate) a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0001844 ! Dihedral angle validation -relationship: has_input EDAM:0001544 ! Ramachandran plot {minCardinality=1} -relationship: has_output EDAM:0001539 ! Protein structural quality report +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 [Term] -id: EDAM:0001825 +id: EDAM_operation:1825 name: Backbone torsion angle calculation namespace: operation -def: "Calculate for each residue in a protein structure all its backbone torsion angles." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0000249 ! Torsion angle calculation +is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] -id: EDAM:0001826 +id: EDAM_operation:1826 name: Full torsion angle calculation namespace: operation -def: "Calculate for each residue in a protein structure all its torsion angles." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0000249 ! Torsion angle calculation +is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] -id: EDAM:0001827 +id: EDAM_operation:1827 name: Cysteine torsion angle calculation namespace: operation -def: "Calculate for each cysteine (bridge) all its torsion angles." [EDAM:WHATIF "EMBRACE definition"] -subset: operation +subset: operations +def: "Calculate for each cysteine (bridge) all its torsion angles." [http://edamontology.org, WHATIF] xref: WHATIF:CysteineTorsions -is_a: EDAM:0000249 ! Torsion angle calculation +is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] -id: EDAM:0001828 +id: EDAM_operation:1828 name: Tau angle calculation namespace: operation -def: "For each amino acid in a protein structure calculate the backbone angle tau." [EDAM:WHATIF "EMBRACE definition"] +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). -subset: operation xref: WHATIF:ShowTauAngle -is_a: EDAM:0000249 ! Torsion angle calculation +is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] -id: EDAM:0000536 +id: EDAM_operation:0536 name: Protein structure assignment (from X-ray crystallographic data) namespace: operation -def: "Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000320 ! Protein structure assignment -relationship: has_input EDAM:0000937 ! Protein X-ray crystallographic data {minCardinality=1} +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 [Term] -id: EDAM:0000537 +id: EDAM_operation:0537 name: Protein structure assignment (from NMR data) namespace: operation -def: "Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000320 ! Protein structure assignment -relationship: has_input EDAM:0000938 ! Protein NMR data {minCardinality=1} +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 [Term] -id: EDAM:0000395 +id: EDAM_operation:0395 name: Residue non-canonical interaction detection namespace: operation -def: "Calculate non-canonical atomic interactions in protein structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000248 ! Residue interaction calculation -is_a: EDAM:0000321 ! Protein model evaluation -relationship: has_output EDAM:0001550 ! Protein non-canonical interactions {minCardinality=1} +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 [Term] -id: EDAM:0001913 +id: EDAM_operation:1913 name: Residue validation namespace: operation -def: "Identify poor quality amino acid positions in protein structures." [EDAM:WHATIF "EMBRACE definition"] +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). -subset: operation xref: WHATIF: UseResidueDB -is_a: EDAM:0000321 ! Protein model evaluation +is_a: EDAM_operation:0321 ! Protein model evaluation [Term] -id: EDAM:0001843 +id: EDAM_operation:1843 name: Residue packing validation namespace: operation -def: "Identify poorly packed residues in protein structures." [EDAM:WHATIF "EMBRACE definition"] -subset: operation +subset: operations +def: "Identify poorly packed residues in protein structures." [http://edamontology.org, WHATIF] xref: WHATIF: PackingQuality -is_a: EDAM:0000395 ! Residue non-canonical interaction detection +is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection [Term] -id: EDAM:0001844 +id: EDAM_operation:1844 name: Dihedral angle validation namespace: operation -def: "Identify for each residue in a protein structure any improper dihedral (phi/psi) angles." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0000321 ! Protein model evaluation +is_a: EDAM_operation:0321 ! Protein model evaluation [Term] -id: EDAM:0001836 +id: EDAM_operation:1836 name: Residue bump detection namespace: operation -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." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0000395 ! Residue non-canonical interaction detection +is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection [Term] -id: EDAM:0002443 +id: EDAM_operation:2443 name: Phylogenetic tree processing namespace: operation -def: "Process (read and / or write) a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0000872 ! Phylogenetic tree {minCardinality=0} -relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=0} -relationship: has_topic EDAM:0000084 ! Phylogenetics +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 ! Phylogenetic tree ! !{min_cardinality=0} +relationship: has_output EDAM_data:0872 ! Phylogenetic tree ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] -id: EDAM:0000550 +id: EDAM_operation:0550 name: Sequence alignment analysis (phylogenetic modelling) namespace: operation -def: "Identify a plausible model of DNA substitution that explains a DNA sequence alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) -is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_output EDAM:0001439 ! DNA substitution model -relationship: has_topic EDAM:0000084 ! Phylogenetics +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 [Term] -id: EDAM:0000554 +id: EDAM_operation:0554 name: Phylogenetic tree analysis (natural selection) namespace: operation -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)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000324 ! Phylogenetic tree analysis +is_a: EDAM_operation:0324 ! Phylogenetic tree analysis [Term] -id: EDAM:0000323 +id: EDAM_operation:0323 name: Phylogenetic tree construction namespace: operation -def: "Construct a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -synonym: "Phylogenetic tree generation" EXACT [] -is_a: EDAM:0002443 ! Phylogenetic tree processing -is_a: EDAM:0002995 ! Sequence classification -relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=1} -relationship: has_topic EDAM:0000080 ! Sequence analysis -relationship: has_topic EDAM:0000084 ! Phylogenetics +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 [Term] -id: EDAM:0000325 +id: EDAM_operation:0325 name: Phylogenetic tree comparison namespace: operation -def: "Compare two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000324 ! Phylogenetic tree analysis -is_a: EDAM:0002424 ! Comparison +is_a: EDAM_operation:0324 ! Phylogenetic tree analysis +is_a: EDAM_operation:2424 ! Comparison [Term] -id: EDAM:0000326 +id: EDAM_operation:0326 name: Phylogenetic tree editing namespace: operation -def: "Edit a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002443 ! Phylogenetic tree processing -is_a: EDAM:0003096 ! Editing -relationship: has_input EDAM:0000872 ! Phylogenetic tree {minCardinality=1} -relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=1} +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 [Term] -id: EDAM:0000551 +id: EDAM_operation:0551 name: Phylogenetic tree analysis (shape) namespace: operation -def: "Analyse the shape (topology) of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "Phylogenetic tree topology analysis" EXACT [] -is_a: EDAM:0000324 ! Phylogenetic tree analysis -relationship: has_output EDAM:0001440 ! Phylogenetic tree report (tree shape) {minCardinality=1} +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) [Term] -id: EDAM:0000552 +id: EDAM_operation:0552 name: Phylogenetic tree bootstrapping namespace: operation -def: "Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000324 ! Phylogenetic tree analysis -is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_output EDAM:0001441 ! Phylogenetic tree report (tree evaluation) {minCardinality=1} +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) [Term] -id: EDAM:0000553 +id: EDAM_operation:0553 name: Phylogenetic tree analysis (gene family prediction) namespace: operation -def: "Predict families of genes and gene function based on their position in a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000324 ! Phylogenetic tree analysis -relationship: has_output EDAM:0000916 ! Gene annotation -relationship: has_topic EDAM:0000194 ! Phylogenomics +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 [Term] -id: EDAM:0000538 +id: EDAM_operation:0538 name: Phylogenetic tree construction (data centric) namespace: operation -def: "Construct a phylogenetic tree from a specific type of data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000323 ! Phylogenetic tree construction +subset: operations +def: "Construct a phylogenetic tree from a specific type of data." [http://edamontology.org] +is_a: EDAM_operation:0323 ! Phylogenetic tree construction [Term] -id: EDAM:0000539 +id: EDAM_operation:0539 name: Phylogenetic tree construction (method centric) namespace: operation -def: "Construct a phylogenetic tree using a specific method." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000323 ! Phylogenetic tree construction +subset: operations +def: "Construct a phylogenetic tree using a specific method." [http://edamontology.org] +is_a: EDAM_operation:0323 ! Phylogenetic tree construction [Term] -id: EDAM:0000540 +id: EDAM_operation:0540 name: Phylogenetic tree construction (from molecular sequences) namespace: operation -def: "Phylogenetic tree construction from molecular sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) -is_a: EDAM:0002403 ! Sequence analysis +is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) +is_a: EDAM_operation:2403 ! Sequence analysis [Term] -id: EDAM:0000541 +id: EDAM_operation:0541 name: Phylogenetic tree construction (from continuous quantitative characters) namespace: operation -def: "Phylogenetic tree construction from continuous quantitative character data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) -relationship: has_input EDAM:0001426 ! Phylogenetic continuous quantitative data {minCardinality=1} +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 [Term] -id: EDAM:0000542 +id: EDAM_operation:0542 name: Phylogenetic tree construction (from gene frequencies) namespace: operation -def: "Phylogenetic tree construction from gene frequency data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) -relationship: has_input EDAM:0002873 ! Phylogenetic gene frequencies data {minCardinality=1} -relationship: has_topic EDAM:0000197 ! Gene expression resources +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:0197 ! Gene expression resources [Term] -id: EDAM:0000543 +id: EDAM_operation:0543 name: Phylogenetic tree construction (from polymorphism data) namespace: operation -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." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) -relationship: has_topic EDAM:0000199 ! Genetic variation +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 [Term] -id: EDAM:0000544 +id: EDAM_operation:0544 name: Phylogenetic species tree construction namespace: operation -def: "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000540 ! Phylogenetic tree construction (from molecular sequences) +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) [Term] -id: EDAM:0000327 +id: EDAM_operation:0327 name: Phylogenetic footprinting / shadowing namespace: operation -def: "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing)." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000540 ! Phylogenetic tree construction (from molecular sequences) -relationship: has_topic EDAM:0000194 ! Phylogenomics +is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences) +relationship: has_topic EDAM_topic:0194 ! Phylogenomics [Term] -id: EDAM:0000545 +id: EDAM_operation:0545 name: Phylogenetic tree construction (parsimony methods) namespace: operation -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) +is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] -id: EDAM:0000546 +id: EDAM_operation:0546 name: Phylogenetic tree construction (minimum distance methods) namespace: operation -def: "Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) +is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] -id: EDAM:0000547 +id: EDAM_operation:0547 name: Phylogenetic tree construction (maximum likelihood and Bayesian methods) namespace: operation -def: "Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) +is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] -id: EDAM:0000548 +id: EDAM_operation:0548 name: Phylogenetic tree construction (quartet methods) namespace: operation -def: "Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) +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) [Term] -id: EDAM:0000549 +id: EDAM_operation:0549 name: Phylogenetic tree construction (AI methods) namespace: operation -def: "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) +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) [Term] -id: EDAM:0000555 +id: EDAM_operation:0555 name: Phylogenetic tree construction (consensus) namespace: operation -def: "Compare two or more phylogenetic trees to produce a consensus tree." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000325 ! Phylogenetic tree comparison -is_a: EDAM:0000323 ! Phylogenetic tree construction +is_a: EDAM_operation:0325 ! Phylogenetic tree comparison +is_a: EDAM_operation:0323 ! Phylogenetic tree construction [Term] -id: EDAM:0000556 +id: EDAM_operation:0556 name: Phylogenetic sub/super tree detection namespace: operation -def: "Compare two or more phylogenetic trees to detect subtrees or supertrees." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000325 ! Phylogenetic tree comparison +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 [Term] -id: EDAM:0000557 +id: EDAM_operation:0557 name: Phylogenetic tree distances calculation namespace: operation -def: "Compare two or more phylogenetic trees to calculate distances between trees." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000325 ! Phylogenetic tree comparison -relationship: has_output EDAM:0001442 ! Phylogenetic tree report (tree distances) {minCardinality=1} +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) [Term] -id: EDAM:0000558 +id: EDAM_operation:0558 name: Phylogenetic tree annotation namespace: operation -def: "Annotate a phylogenetic tree with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000326 ! Phylogenetic tree editing -is_a: EDAM:0000226 ! Annotation +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 [Term] -id: EDAM:0000328 +id: EDAM_operation:0328 name: Protein folding simulation namespace: operation -def: "Simulate the folding of a protein." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002415 ! Protein folding analysis +subset: operations +def: "Simulate the folding of a protein." [http://edamontology.org] +is_a: EDAM_operation:2415 ! Protein folding analysis [Term] -id: EDAM:0000329 +id: EDAM_operation:0329 name: Protein folding pathway prediction namespace: operation -def: "Predict the folding pathway(s) or non-native structural intermediates of a protein." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002415 ! Protein folding analysis -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) +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) [Term] -id: EDAM:0001842 +id: EDAM_operation:1842 name: Proline mutation value calculation namespace: operation -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." [EDAM:WHATIF "EMBRACE definition"] -subset: 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:0000331 ! Protein modelling (mutation) +is_a: EDAM_operation:0331 ! Protein modelling (mutation) [Term] -id: EDAM:0000330 +id: EDAM_operation:0330 name: Protein SNP mapping namespace: operation -def: "Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000331 ! Protein modelling (mutation) -relationship: has_output EDAM:0002885 ! Nucleic acid features (polymorphism annotation) -relationship: has_topic EDAM:0002277 ! SNPs +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 [Term] -id: EDAM:0000559 +id: EDAM_operation:0559 name: Peptide immunogen prediction and optimisation namespace: operation -def: "Predict and optimise peptide ligands that elicit an immunological response." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000252 ! Peptide immunogenicity prediction -is_a: EDAM:0002425 ! Optimisation and refinement -relationship: has_output EDAM:0001460 ! Protein structure -relationship: has_topic EDAM:0000150 ! Protein design -relationship: has_topic EDAM:0000804 ! Immunoinformatics +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 [Term] -id: EDAM:0000560 +id: EDAM_operation:0560 name: DNA vaccine prediction and optimisation namespace: operation -def: "Predict or optimise DNA to elicit (via DNA vaccination) an immunological response." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003095 ! Nucleic acid design -is_a: EDAM:0002425 ! Optimisation and refinement -relationship: has_topic EDAM:0000804 ! Immunoinformatics -relationship: has_topic EDAM:0002953 ! Nucleic acid design +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 [Term] -id: EDAM:0000561 +id: EDAM_operation:0561 name: Sequence reformatting namespace: operation -def: "Reformat (a file or other report of) molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000335 ! File reformatting -is_a: EDAM:0002121 ! Sequence file processing +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 [Term] -id: EDAM:0000562 +id: EDAM_operation:0562 name: Sequence alignment reformatting namespace: operation -def: "Reformat (a file or other report of) molecular sequence alignment(s)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000335 ! File reformatting -is_a: EDAM:0002122 ! Sequence alignment editing +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 editing [Term] -id: EDAM:0000563 +id: EDAM_operation:0563 name: Codon usage table reformatting namespace: operation -def: "Reformat a codon usage table." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000335 ! File reformatting -is_a: EDAM:0002433 ! Codon usage table processing -relationship: has_input EDAM:0001597 ! Codon usage table {minCardinality=1} -relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=1} +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 [Term] -id: EDAM:0001848 +id: EDAM_operation:1848 name: Structure reformatting namespace: operation -def: "Reformat (a file or other report of) tertiary structure data." [EDAM:WHATIF "EMBRACE definition"] -subset: operation +subset: operations +def: "Reformat (a file or other report of) tertiary structure data." [http://edamontology.org, WHATIF] xref: WHATIF: PDBasXML -is_a: EDAM:0002234 ! Structure file processing -is_a: EDAM:0000335 ! File reformatting +is_a: EDAM_operation:2234 ! Structure file processing +is_a: EDAM_operation:0335 ! File reformatting [Term] -id: EDAM:0000564 +id: EDAM_operation:0564 name: Sequence rendering namespace: operation -def: "Visualise, format or render a molecular sequence, possibly with sequence features or properties shown." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000337 ! Plotting and rendering -is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} -relationship: has_output EDAM:0002969 ! Sequence image {minCardinality=1} +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 [Term] -id: EDAM:0002515 +id: EDAM_operation:2515 name: Sequence rendering (nucleic acid) namespace: operation -def: "Visualise, format or render a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000564 ! Sequence rendering -is_a: EDAM:0002448 ! Sequence processing (nucleic acid) -relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis +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:0002516 +id: EDAM_operation:2516 name: Sequence rendering (protein) namespace: operation -def: "Visualise, format or render a protein sequence." [EDAM:EBI "EMBRACE definition"] +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. -subset: operation -is_a: EDAM:0000564 ! Sequence rendering -is_a: EDAM:0002447 ! Sequence processing (protein) +is_a: EDAM_operation:0564 ! Sequence rendering +is_a: EDAM_operation:2447 ! Sequence processing (protein) [Term] -id: EDAM:0000565 +id: EDAM_operation:0565 name: Sequence alignment rendering namespace: operation -def: "Visualise, format or print a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000337 ! Plotting and rendering -is_a: EDAM:0002463 ! Sequence alignment processing -relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=1} -relationship: has_output EDAM:0001711 ! Sequence alignment image {minCardinality=1} +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 [Term] -id: EDAM:0002452 +id: EDAM_operation:2452 name: Sequence cluster processing namespace: operation -def: "Process (read and / or write) a sequence cluster." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0001235 ! Sequence cluster {minCardinality=0} -relationship: has_output EDAM:0001235 ! Sequence cluster {minCardinality=0} -relationship: has_topic EDAM:0000164 ! Sequence clustering +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 ! Sequence cluster ! !{min_cardinality=0} +relationship: has_output EDAM_data:1235 ! Sequence cluster ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] -id: EDAM:0000566 +id: EDAM_operation:0566 name: Sequence cluster rendering namespace: operation -def: "Visualise, format or render sequence clusters." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000337 ! Plotting and rendering -is_a: EDAM:0002452 ! Sequence cluster processing -relationship: has_input EDAM:0001235 ! Sequence cluster {minCardinality=1} +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 [Term] -id: EDAM:0000567 +id: EDAM_operation:0567 name: Phylogenetic tree rendering namespace: operation -def: "Visualise or plot a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002443 ! Phylogenetic tree processing -is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=1} +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 [Term] -id: EDAM:0000568 +id: EDAM_operation:0568 name: RNA secondary structure rendering namespace: operation -def: "Visualise RNA secondary structure, knots, pseudoknots etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000337 ! Plotting and rendering -is_a: EDAM:0002439 ! RNA secondary structure processing -relationship: has_input EDAM:0000880 ! RNA secondary structure {minCardinality=1} +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 [Term] -id: EDAM:0000569 +id: EDAM_operation:0569 name: Protein secondary structure rendering namespace: operation -def: "Render and visualise protein secondary structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000337 ! Plotting and rendering -is_a: EDAM:0002444 ! Protein secondary structure processing -relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} +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) [Term] -id: EDAM:0002485 +id: EDAM_operation:2485 name: Helical wheel rendering namespace: operation -def: "Render a helical wheel representation of protein secondary structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000569 ! Protein secondary structure rendering -relationship: has_output EDAM:0002162 ! Helical wheel {minCardinality=1} +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 [Term] -id: EDAM:0002486 +id: EDAM_operation:2486 name: Topology diagram rendering namespace: operation -def: "Render a topology diagram of protein secondary structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000569 ! Protein secondary structure rendering -relationship: has_output EDAM:0002992 ! Protein structure image +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 [Term] -id: EDAM:0002241 +id: EDAM_operation:2241 name: Transmembrane protein rendering namespace: operation -def: "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000569 ! Protein secondary structure rendering -is_a: EDAM:0000270 ! Transmembrane protein analysis -relationship: has_input EDAM:0001456 ! Protein features (membrane regions) {minCardinality=1} -relationship: has_output EDAM:0002992 ! Protein structure image +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 [Term] -id: EDAM:0002482 +id: EDAM_operation:2482 name: Secondary structure processing namespace: operation -def: "Process (read and / or write) a molecular secondary structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002081 ! Secondary structure {minCardinality=0} -relationship: has_output EDAM:0002081 ! Secondary structure {minCardinality=0} -relationship: has_topic EDAM:0000081 ! Structure analysis +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 ! Secondary structure ! !{min_cardinality=0} +relationship: has_output EDAM_data:2081 ! Secondary structure ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM:0002465 +id: EDAM_operation:2465 name: Structure processing namespace: operation -alt_id: EDAM:0002484 -def: "Process (read and / or write) a molecular tertiary structure." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0000883 ! Structure {minCardinality=0} -relationship: has_output EDAM:0000883 ! Structure {minCardinality=0} -relationship: has_topic EDAM:0000081 ! Structure analysis +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 ! Structure ! !{min_cardinality=0} +relationship: has_output EDAM_data:0883 ! Structure ! !{min_cardinality=0} +relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] -id: EDAM:0000570 +id: EDAM_operation:0570 name: Structure rendering namespace: operation -def: "Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000337 ! Plotting and rendering -is_a: EDAM:0002465 ! Structure processing -relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} -relationship: has_output EDAM:0001710 ! Structure image +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 [Term] -id: EDAM:0000571 +id: EDAM_operation:0571 name: Microarray data rendering namespace: operation -def: "Visualise microarray data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000337 ! Plotting and rendering -is_a: EDAM:0002435 ! Gene expression profile processing -relationship: has_input EDAM:0003117 ! Microarray hybridisation data {minCardinality=1} -relationship: has_output EDAM:0002967 ! Microarray image {minCardinality=1} +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 [Term] -id: EDAM:0000572 +id: EDAM_operation:0572 name: Protein interaction network rendering namespace: operation -def: "Identify and analyse networks of protein interactions." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0003083 ! Pathway or network rendering -is_a: EDAM:0002445 ! Protein interaction network processing -relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=1} +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) [Term] -id: EDAM:0000573 +id: EDAM_operation:0573 name: Map rendering namespace: operation -def: "Render and visualise a DNA map." [EDAM:EBI "EMBRACE definition"] -subset: operation -synonym: "DNA map rendering" EXACT [] -is_a: EDAM:0002515 ! Sequence rendering (nucleic acid) -is_a: EDAM:0002521 ! Map data processing -relationship: has_input EDAM:0001274 ! Map {minCardinality=1} +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 [Term] -id: EDAM:0000574 +id: EDAM_operation:0574 name: Sequence motif rendering namespace: operation -def: "Render a sequence with motifs." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000564 ! Sequence rendering +subset: operations +def: "Render a sequence with motifs." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_operation:0564 ! Sequence rendering [Term] -id: EDAM:0000577 +id: EDAM_operation:0577 name: DNA linear map rendering namespace: operation -def: "Draw a linear maps of DNA." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000573 ! Map rendering +subset: operations +def: "Draw a linear maps of DNA." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_operation:0573 ! Map rendering [Term] -id: EDAM:0000578 +id: EDAM_operation:0578 name: DNA circular map rendering namespace: operation -def: "Draw a circular maps of DNA, for example a plasmid map." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000573 ! Map rendering +subset: operations +def: "Draw a circular maps of DNA, for example a plasmid map." [http://edamontology.org] +is_a: EDAM_operation:0573 ! Map rendering [Term] -id: EDAM:0000579 +id: EDAM_operation:0579 name: Operon rendering namespace: operation -def: "Visualise operon structure etc." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000573 ! Map rendering -relationship: has_topic EDAM:0000109 ! Gene finding +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 [Term] -id: EDAM:0000575 +id: EDAM_operation:0575 name: Restriction map rendering namespace: operation -def: "Visualise restriction maps in DNA sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000573 ! Map rendering -is_a: EDAM:0000431 ! Restriction site recognition -relationship: has_output EDAM:0001289 ! Restriction map +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 + + + + + + + + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + + + + + + + +! +! Data +! [Term] -id: EDAM:0000005 +id: EDAM_data:0005 name: Resource type namespace: data -def: "A type of computational resource used in bioinformatics." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +def: "A type of computational resource used in bioinformatics." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} [Term] -id: EDAM:0002831 +id: EDAM_data:2831 name: Databank namespace: data -def: "A flat-file (textual) data archive." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +def: "A flat-file (textual) data archive." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} [Term] -id: EDAM:0002832 +id: EDAM_data:2832 name: Web portal namespace: data -def: "A web site providing data (web pages) on a common theme to a HTTP client." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +def: "A web site providing data (web pages) on a common theme to a HTTP client." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} [Term] -id: EDAM:0000581 +id: EDAM_data:0581 name: Database namespace: data -def: "A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +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} [Term] -id: EDAM:0000007 +id: EDAM_data:0007 name: Tool namespace: data -def: "A bioinformatics package or tool, e.g. a standalone application or web service." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +def: "A bioinformatics package or tool, e.g. a standalone application or web service." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} [Term] -id: EDAM:0001884 +id: EDAM_data:1884 name: UniProt keywords namespace: data -def: "A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology +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 [Term] -id: EDAM:0000831 +id: EDAM_data:0831 name: MeSH vocabulary namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology +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 [Term] -id: EDAM:0000832 +id: EDAM_data:0832 name: HGNC vocabulary namespace: data -def: "Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology +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 [Term] -id: EDAM:0000835 +id: EDAM_data:0835 name: UMLS vocabulary namespace: data -def: "Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology - - - -! -! 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 [Term] -id: EDAM:0000841 -name: Undefined -namespace: data -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true - - - -[Term] -id: EDAM:0002100 +id: EDAM_data:2100 name: Type namespace: data -alt_id: EDAM:0002864 -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)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter +! 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 [Term] -id: EDAM:0001866 +id: EDAM_data:1866 name: Map type namespace: data -def: "A designation of the type of map (genetic map, physical map, sequence map etc) or map set." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0002100 ! Type -is_a: EDAM:0002019 ! Map attribute +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 [Term] -id: EDAM:0001094 +id: EDAM_data:1094 name: Sequence type namespace: data -def: "A label (text token) describing a type of molecular sequence." [EDAM:EBI "EMBRACE definition"] -comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). subset: data -is_a: EDAM:0002100 ! Type -is_a: EDAM:0002534 ! Sequence parameter -relationship: is_identifier_of EDAM:0002044 ! Sequence -relationship: is_identifier_of EDAM:0000849 ! Sequence record +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 [Term] -id: EDAM:0002132 +id: EDAM_data:2132 name: Mutation type namespace: data -def: "A type of point or block mutation, including insertion, deletion, change, duplication and moves." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002100 ! Type +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 [Term] -id: EDAM:0000985 +id: EDAM_data:0985 name: Molecule type namespace: data -def: "A label (text token) describing the type a molecule." [EDAM:EBI "EMBRACE definition"] -comment: For example, 'Protein', 'DNA', 'RNA' etc. subset: data -is_a: EDAM:0002100 ! Type +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 [Term] -id: EDAM:0001122 +id: EDAM_data:1122 name: Phylogenetic tree type namespace: data -def: "A label (text token) describing the type of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -comment: For example 'nj', 'upgmp' etc. subset: data -is_a: EDAM:0002100 ! Type -relationship: is_identifier_of EDAM:0000872 ! Phylogenetic tree +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 [Term] -id: EDAM:0002592 +id: EDAM_data:2592 name: Cancer type namespace: data -def: "A type (represented as a string) of cancer." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002100 ! Type +def: "A type (represented as a string) of cancer." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2100 ! Type [Term] -id: EDAM:0002524 +id: EDAM_data:2524 name: Protein data namespace: data -def: "Data concerning one or more protein molecules." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0000896 ! Protein report +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 [Term] -id: EDAM:0002525 +id: EDAM_data:2525 name: Nucleic acid data namespace: data -def: "Data concerning one or more nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0002084 ! Nucleic acid report +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 [Term] -id: EDAM:0002248 +id: EDAM_data:2248 name: Schema namespace: data -def: "A data schema for organising or transforming data of some type." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data +def: "A data schema for organising or transforming data of some type." [http://edamontology.org] +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM:0000843 +id: EDAM_data:0843 name: Database entry namespace: data -def: "An entry (retrievable via URL) from a biological database." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000006 ! Data +def: "An entry (retrievable via URL) from a biological database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0006 ! Data [Term] -id: EDAM:0002767 +id: EDAM_data:2767 name: Identifier with metadata namespace: data -def: "Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000842 ! Identifier +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 [Term] -id: EDAM:0002768 +id: EDAM_data:2768 name: Gene symbol annotation namespace: data -def: "Annotation about a gene symbol." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002767 ! Identifier with metadata +def: "Annotation about a gene symbol." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2767 ! Identifier with metadata [Term] -id: EDAM:0002087 +id: EDAM_data:2087 name: Molecular property namespace: data -def: "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Physicochemical property" EXACT [] -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0001917 +id: EDAM_data:1917 name: Atomic property namespace: data -def: "Data for an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "General atomic property" EXACT [] -is_a: EDAM:0002087 ! Molecular property +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 [Term] -id: EDAM:0002050 +id: EDAM_data:2050 name: Molecular property (general) namespace: data -def: "General data for a molecule." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "General molecular property" EXACT [] -is_a: EDAM:0002087 ! Molecular property +def: "General data for a molecule." [http://edamontology.org] +synonym: "General molecular property" EXACT [http://edamontology.org] +is_a: EDAM_data:2087 ! Molecular property [Term] -id: EDAM:0002925 +id: EDAM_data:2925 name: Sequence data namespace: data -def: "Data concerning molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0002044 ! Sequence -consider: EDAM:0002955 ! Sequence report +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 [Term] -id: EDAM:0002044 +id: EDAM_data:2044 name: Sequence namespace: data -def: "One or more molecular sequences, possibly with associated annotation." [EDAM:EBI "EMBRACE definition"] -comment: This term is a placeholder of terms 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: data -relationship: has_topic EDAM:0000080 ! Sequence analysis -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0002976 +id: EDAM_data:2976 name: Protein sequence namespace: data -def: "One or more protein sequences, possibly with associated annotation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002044 ! Sequence +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 [Term] -id: EDAM:0002977 +id: EDAM_data:2977 name: Nucleic acid sequence namespace: data -def: "One or more nucleic acid sequences, possibly with associated annotation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002044 ! Sequence +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 [Term] -id: EDAM:0002955 +id: EDAM_data:2955 name: Sequence report namespace: 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)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence-derived report" EXACT [] -is_a: EDAM:0002048 ! Report +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 [Term] -id: EDAM:0000855 +id: EDAM_data:0855 name: Sequence metadata namespace: data -def: "Basic or general information concerning molecular sequences." [EDAM:EBI "EMBRACE definition"] -comment: This is used for such things as a report including the sequence identifier, type and length. subset: data -is_a: EDAM:0001254 ! Sequence property -is_a: EDAM:0002955 ! Sequence report -is_a: EDAM:0002337 ! Metadata +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 [Term] -id: EDAM:0002522 +id: EDAM_data:2522 name: Map data namespace: data -def: "Data concerning a map of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0001274 ! Map -consider: EDAM:0002019 ! Map attribute +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 [Term] -id: EDAM:0001274 +id: EDAM_data:1274 name: Map namespace: data -def: "A map of (typically one) DNA sequence annotated with positional or non-positional features." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "DNA map" EXACT [] -relationship: has_topic EDAM:0000102 ! Sequencing and mapping -is_a: EDAM:0003031 ! Core 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 ! Sequencing and mapping +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM:0001864 +id: EDAM_data:1864 name: Map set namespace: data -def: "Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped." [EDAM:EBI "EMBRACE definition"] 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:0002019 ! Map attribute +is_a: EDAM_data:2019 ! Map attribute [Term] -id: EDAM:0002019 +id: EDAM_data:2019 name: Map attribute namespace: data -def: "An attribute of a molecular map (genetic or physical)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Metadata -relationship: has_topic EDAM:0000102 ! Sequencing and mapping +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 ! Sequencing and mapping [Term] -id: EDAM:0002080 +id: EDAM_data:2080 name: Database hits namespace: data -def: "A report of hits from searching a database of some type." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002093 ! Data reference +def: "A report of hits from searching a database of some type." [http://edamontology.org] +is_a: EDAM_data:2093 ! Data reference [Term] -id: EDAM:0000860 +id: EDAM_data:0860 name: Sequence signature namespace: data -def: "A classifier of sequences such as a sequence motif, profile or other diagnostic element." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001353 ! Sequence motif -consider: EDAM:0001354 ! Sequence profile +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 [Term] -id: EDAM:0002981 +id: EDAM_data:2981 name: Sequence motif data namespace: data -def: "Data concerning specific or conserved pattern in molecular sequences." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0001353 ! Sequence motif +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 [Term] -id: EDAM:0001353 +id: EDAM_data:1353 name: Sequence motif namespace: data -def: "Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000158 ! Sequence motifs +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 [Term] -id: EDAM:0002762 +id: EDAM_data:2762 name: Sequence motif metadata namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Metadata -relationship: has_topic EDAM:0000158 ! Sequence motifs +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 [Term] -id: EDAM:0002982 +id: EDAM_data:2982 name: Sequence profile data namespace: data -def: "Data concerning models representing a (typically multiple) sequence alignment." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0001354 ! Sequence profile +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 [Term] -id: EDAM:0001354 +id: EDAM_data:1354 name: Sequence profile namespace: data -def: "Some type of statistical model representing a (typically multiple) sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000188 ! Sequence profiles and HMMs +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 [Term] -id: EDAM:0002788 +id: EDAM_data:2788 name: Sequence profile metadata namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Metadata -relationship: has_topic EDAM:0000188 ! Sequence profiles and HMMs +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 [Term] -id: EDAM:0001355 +id: EDAM_data:1355 name: Protein signature namespace: data -def: "An entry (sequence classifier and associated data) from the InterPro database." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "InterPro entry" EXACT [] -is_a: EDAM:0000907 ! Protein family +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 [Term] -id: EDAM:0002161 +id: EDAM_data:2161 name: Sequence similarity plot namespace: data -def: "A plot of sequence similarities identified from word-matching or character comparison." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000867 ! Sequence alignment report +def: "A plot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] +is_a: EDAM_data:0867 ! Sequence alignment report [Term] -id: EDAM:0000862 +id: EDAM_data:0862 name: Dotplot namespace: data -def: "A dotplot of sequence similarities identified from word-matching or character comparison." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002161 ! Sequence similarity plot +def: "A dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] +is_a: EDAM_data:2161 ! Sequence similarity plot [Term] -id: EDAM:0002539 +id: EDAM_data:2539 name: Alignment data namespace: data -def: "Data concerning an alignment of two or more molecular sequences, structures or derived data." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0001916 ! Alignment -consider: EDAM:0002083 ! Alignment report +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 [Term] -id: EDAM:0001916 +id: EDAM_data:1916 name: Alignment namespace: data -def: "An alignment of molecular sequences, structures or profiles derived from them." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data +def: "An alignment of molecular sequences, structures or profiles derived from them." [http://edamontology.org] +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM:0002083 +id: EDAM_data:2083 name: Alignment report namespace: data -def: "An informative report about a molecular alignment of some type, including alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002048 ! Report +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 [Term] -id: EDAM:0002711 +id: EDAM_data:2711 name: Genome metadata namespace: data -def: "Provenance metadata or other general information concerning a genome as a whole." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000855 ! Sequence metadata +def: "Provenance metadata or other general information concerning a genome as a whole." [http://edamontology.org] +is_a: EDAM_data:0855 ! Sequence metadata [Term] -id: EDAM:0000867 +id: EDAM_data:0867 name: Sequence alignment report namespace: data -def: "An informative report of molecular sequence alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002083 ! Alignment report +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 [Term] -id: EDAM:0002598 +id: EDAM_data:2598 name: Secondary structure alignment metadata namespace: data -def: "An informative report on protein secondary structure alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002083 ! Alignment report +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 [Term] -id: EDAM:0000879 +id: EDAM_data:0879 name: Secondary structure alignment metadata (protein) namespace: data -def: "An informative report on protein secondary structure alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002083 ! Alignment report +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 [Term] -id: EDAM:0000882 +id: EDAM_data:0882 name: Secondary structure alignment metadata (RNA) namespace: data -def: "An informative report of RNA secondary structure alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002083 ! Alignment report +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 [Term] -id: EDAM:0002082 +id: EDAM_data:2082 name: Matrix namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0002855 +id: EDAM_data:2855 name: Distance matrix namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002082 ! Matrix +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 [Term] -id: EDAM:0000870 +id: EDAM_data:0870 name: Sequence distance matrix namespace: data -def: "A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation." [EDAM:EBI "EMBRACE definition"] -comment: Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. subset: data -synonym: "Phylogenetic distance matrix" EXACT [] +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:0002855 ! Distance matrix +is_a: EDAM_data:2855 ! Distance matrix [Term] -id: EDAM:0002856 +id: EDAM_data:2856 name: Structural distance matrix namespace: data -def: "Distances (values representing similarity) between a group of molecular structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002855 ! Distance matrix +def: "Distances (values representing similarity) between a group of molecular structures." [http://edamontology.org] +is_a: EDAM_data:2855 ! Distance matrix -! Phylogenetic character data! Also molecular sequences, microsatellites), polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments [Term] -id: EDAM:0002523 +id: EDAM_data:2523 name: Phylogenetic raw data namespace: data -def: "Data concerning phylogeny, typically of molecular sequences." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -synonym: "Phylogenetic data" EXACT [] -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0000871 +id: EDAM_data:0871 name: Phylogenetic character data namespace: data -def: "Data from which a phylogenetic tree may be generated." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002523 ! Phylogenetic raw 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 [Term] -id: EDAM:0000872 +id: EDAM_data:0872 name: Phylogenetic tree namespace: 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." [EDAM:EBI "EMBRACE definition"] -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: 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:0000084 ! Phylogenetics -is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM_topic:0084 ! Phylogenetics +is_a: EDAM_data:3031 ! Core data [Term] -id: EDAM:0001438 +id: EDAM_data:1438 name: Phylogenetic tree report namespace: data -alt_id: EDAM:0000873 -def: "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -synonym: "Phylogenetic tree-derived report" EXACT [] -is_a: EDAM:0002048 ! Report +! 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] +synonym "Tree" RELATED [http://www.evolutionaryontology.org/cdao.owl#Tree] +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM:0000874 +id: EDAM_data:0874 name: Comparison matrix namespace: data -def: "Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Substitution matrix" EXACT [] -is_a: EDAM:0002082 ! Matrix +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 [Term] -id: EDAM:0002053 +id: EDAM_data:2053 name: Structural data namespace: data -def: "Data concerning molecular structural data." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0000883 ! Structure -consider: EDAM:0002085 ! Structure report +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 data +consider: EDAM_data:2085 ! Structure report [Term] -id: EDAM:0002085 +id: EDAM_data:2085 name: Structure report namespace: data -def: "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Structure-derived report" EXACT [] -is_a: EDAM:0002048 ! Report +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 [Term] -id: EDAM:0002973 +id: EDAM_data:2973 name: Secondary structure data namespace: data -def: "Data concerning molecular secondary structure data." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002081 ! Secondary structure -consider: EDAM:0002881 ! Secondary structure report +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 [Term] -id: EDAM:0002881 +id: EDAM_data:2881 name: Secondary structure report namespace: data -def: "An informative report on general information, properties or features of one or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Secondary structure-derived report" EXACT [] -is_a: EDAM:0002048 ! Report +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 [Term] -id: EDAM:0002956 +id: EDAM_data:2956 name: Protein secondary structure report namespace: data -def: "An informative report about the properties or features of one or more protein secondary structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002881 ! Secondary structure report +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 [Term] -id: EDAM:0001494 +id: EDAM_data:1494 name: Structural transformation matrix namespace: data -def: "Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002082 ! Matrix +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 [Term] -id: EDAM:0000887 +id: EDAM_data:0887 name: Structure alignment report namespace: data -def: "An informative report on molecular tertiary structure alignment-derived data." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002083 ! Alignment report +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 [Term] -id: EDAM:0000889 +id: EDAM_data:0889 name: Structural (3D) profile namespace: data -def: "Some type of structural (3D) profile or template (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "3D profile" EXACT [] -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000167 ! Structural (3D) profiles +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 [Term] -id: EDAM:0000892 +id: EDAM_data:0892 name: Protein sequence-structure scoring matrix namespace: data -def: "Matrix of values used for scoring sequence-structure compatibility." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002082 ! Matrix +def: "Matrix of values used for scoring sequence-structure compatibility." [http://edamontology.org] +is_a: EDAM_data:2082 ! Matrix [Term] -id: EDAM:0002528 +id: EDAM_data:2528 name: Molecular data namespace: data -def: "Data concerning a specific type of molecule." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -synonym: "Molecule-specific data" EXACT [] -is_obsolete: true -consider: EDAM:0002529 ! Molecule report +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 [Term] -id: EDAM:0002599 +id: EDAM_data:2599 name: Molecular interaction namespace: data -def: "Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Molecular interaction data" EXACT [] -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0002601 +id: EDAM_data:2601 name: Small molecule data namespace: data -def: "Data concerning one or more small molecules." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0000962 ! Small molecule annotation +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 [Term] -id: EDAM:0002016 +id: EDAM_data:2016 name: Amino acid property namespace: data -def: "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Amino acid data" EXACT [] -is_a: EDAM:0002087 ! Molecular property +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 [Term] -id: EDAM:0002979 +id: EDAM_data:2979 name: Peptide property namespace: data -def: "Data concerning small peptides." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Peptide data" EXACT [] -is_a: EDAM:0002087 ! Molecular property +def: "Data concerning small peptides." [http://edamontology.org] +synonym: "Peptide data" EXACT [http://edamontology.org] +is_a: EDAM_data:2087 ! Molecular property [Term] -id: EDAM:0000895 +id: EDAM_data:0895 name: Peptide annotation namespace: data -def: "An informative report about a specific peptide." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule annotation -is_a: EDAM:0002979 ! Peptide property -relationship: has_topic EDAM:0000613 ! Peptides and amino acids +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 [Term] -id: EDAM:0002399 +id: EDAM_data:2399 name: Gene annotation (transcript) namespace: data -alt_id: EDAM:0002703 -def: "An informative report on a specific gene transcript, clone or EST." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene transcript annotation" EXACT [] -synonym: "Gene annotation (clone or EST)" EXACT [] -is_a: EDAM:0000916 ! Gene annotation +! 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 [Term] -id: EDAM:0000896 +id: EDAM_data:0896 name: Protein report namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene product annotation" EXACT [] -is_a: EDAM:0002529 ! Molecule report -relationship: has_topic EDAM:0000078 ! Protein analysis +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 [Term] -id: EDAM:0000897 +id: EDAM_data:0897 name: Protein property namespace: data -def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Protein physicochemical property" EXACT [] -is_a: EDAM:0000896 ! Protein report -is_a: EDAM:0002087 ! Molecular property +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 [Term] -id: EDAM:0001537 +id: EDAM_data:1537 name: Protein structure report namespace: data -def: "Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains." [EDAM:EBI "EMBRACE definition"] subset: data -alt_id: EDAM:0000898 -alt_id: EDAM:0001538 -alt_id: EDAM:0002377 -synonym: "Protein structure report (domain)" EXACT [] -synonym: "Protein structure-derived report" EXACT [] -synonym: "Protein structural property" EXACT [] -synonym: "Protein report (structure)" EXACT [] -synonym: "Protein property (structural)" EXACT [] -is_a: EDAM:0000896 ! Protein report -is_a: EDAM:0002085 ! Structure report +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] -id: EDAM:0003151 -name: Protein property (physicochemical) -namespace: data -def: "A report of primarily non-positional data describing intrinsic physicochemical properties of a protein molecule." [EDAM:EBI "EMBRACE definition"] -subset: data -synonym: "Protein physicochemical property" EXACT [] -is_obsolete: true -consider: EDAM:0000897 ! Protein property +! [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] -id: EDAM:0003152 -name: Protein property (sequence) -namespace: data -def: "A non-positional property of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: data -synonym: "Protein sequence property" EXACT [] -is_obsolete: true -consider: EDAM:0000897 ! 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 [Term] -id: EDAM:0002313 +id: EDAM_data:2313 name: Carbohydrate structure report namespace: data -def: "Annotation on or information derived from one or more specific carbohydrate 3D structure(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002085 ! Structure report +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 [Term] -id: EDAM:0002879 +id: EDAM_data:2879 name: Lipid structure report namespace: data -def: "Annotation on or information derived from one or more specific lipid 3D structure(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002085 ! Structure report +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 [Term] -id: EDAM:0002987 +id: EDAM_data:2987 name: Classification namespace: data -def: "Data concerning a classification of molecular sequences, structures or other entities." [EDAM:EBI "EMBRACE definition"] -comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. subset: data -synonym: "Classification data" EXACT [] -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0002829 ! Ontologies, nomenclature and classification +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 [Term] -id: EDAM:0003028 +id: EDAM_data:3028 name: Taxonomy namespace: data -def: "Data concerning the classification, identification and naming of organisms." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -synonym: "Taxonomic data" EXACT [] -is_a: EDAM:0002987 ! Classification -relationship: has_topic EDAM:0000637 ! Taxonomy +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 [Term] -id: EDAM:0002986 +id: EDAM_data:2986 name: Nucleic acid classification namespace: data -def: "Data concerning the classification of nucleic acid sequences or structures." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -synonym: "Nucleic acid classification data" EXACT [] -is_a: EDAM:0002084 ! Nucleic acid report -is_a: EDAM:0002987 ! Classification -relationship: has_topic EDAM:0000722 ! Nucleic acid classification +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 [Term] -id: EDAM:0002980 +id: EDAM_data:2980 name: Protein classification namespace: data -def: "Data concerning the classification of protein sequences or structures." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -synonym: "Protein classification data" EXACT [] -is_a: EDAM:0000896 ! Protein report -is_a: EDAM:0002987 ! Classification -relationship: has_topic EDAM:0000595 ! Protein classification +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 [Term] -id: EDAM:0000900 +id: EDAM_data:0900 name: Protein domain classification namespace: data -def: "Data concerning the classification of the sequences and/or structures of protein structural domain(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002980 ! Protein classification -relationship: has_topic EDAM:0000736 ! Protein domains and folds +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 [Term] -id: EDAM:0003101 +id: EDAM_data:3101 !{since=beta13} name: Protein domain classification node namespace: data -def: "A node from a classification of protein structural domain(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000900 ! Protein domain classification +def: "A node from a classification of protein structural domain(s)." [http://edamontology.org] +is_a: EDAM_data:0900 ! Protein domain classification [Term] -id: EDAM:0000906 +id: EDAM_data:0906 name: Protein interaction namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein report (interaction)" EXACT [] -is_a: EDAM:0002599 ! Molecular interaction -is_a: EDAM:0000896 ! Protein report -relationship: has_topic EDAM:0000128 ! Protein interactions +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 [Term] -id: EDAM:0000907 +id: EDAM_data:0907 name: Protein family namespace: data -def: "An informative report on a specific protein family or other group of classified proteins." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein family annotation" EXACT [] -is_a: EDAM:0002980 ! Protein classification -relationship: has_topic EDAM:0000724 ! Protein families +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 [Term] -id: EDAM:0002354 +id: EDAM_data:2354 name: RNA family annotation namespace: data -def: "An informative report on a specific RNA family or other group of classified RNA sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002986 ! Nucleic acid classification +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 [Term] -id: EDAM:0002978 +id: EDAM_data:2978 name: Reaction data namespace: data -alt_id: EDAM:0000908 -def: "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. -synonym: "Reaction annotation" EXACT [] -synonym: "Enzyme kinetics annotation" EXACT [] subset: data -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0002024 +id: EDAM_data:2024 name: Enzyme kinetics data namespace: data -def: "Data concerning chemical reaction(s) catalysed by enzyme(s)." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002978 ! Reaction 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 [Term] -id: EDAM:0000911 +id: EDAM_data:0911 name: Nucleotide base annotation namespace: data -def: "An informative report about a specific nucleotide base." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule annotation +def: "An informative report about a specific nucleotide base." [http://edamontology.org] +is_a: EDAM_data:0962 ! Small molecule annotation [Term] -id: EDAM:0002116 +id: EDAM_data:2116 name: Nucleic acid features (codon) namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0002084 +id: EDAM_data:2084 name: Nucleic acid report namespace: data -def: "An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002529 ! Molecule report +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 [Term] -id: EDAM:0000912 +id: EDAM_data:0912 name: Nucleic acid property namespace: data -def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Nucleic acid physicochemical property" EXACT [] -is_a: EDAM:0002084 ! Nucleic acid report -is_a: EDAM:0002087 ! Molecular property +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 [Term] -id: EDAM:0002086 +id: EDAM_data:2086 name: Nucleic acid structure report namespace: data -alt_id: EDAM:0000913 -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)." [EDAM:EBI "EMBRACE definition"] -comment: This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. subset: data -synonym: "Nucleic acid structural property" EXACT [] -synonym: "Nucleic acid property (structural)" EXACT [] -is_a: EDAM:0000912 ! Nucleic acid property -is_a: EDAM:0002085 ! Structure report +! 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 [Term] -id: EDAM:0002927 +id: EDAM_data:2927 name: Codon usage data namespace: data -def: "Data concerning codon usage." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0001597 ! Codon usage table -consider: EDAM:0000914 ! Codon usage report +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 [Term] -id: EDAM:0001597 +id: EDAM_data:1597 name: Codon usage table namespace: data -def: "Table of codon usage data calculated from one or more nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000107 ! Codon usage analysis +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 [Term] -id: EDAM:0000914 +id: EDAM_data:0914 name: Codon usage report namespace: data -def: "Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002048 ! Report -relationship: has_topic EDAM:0000107 ! Codon usage analysis +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 [Term] -id: EDAM:0002603 +id: EDAM_data:2603 name: Microarray data namespace: data -alt_id: EDAM:0002541 -def: "Image or hybridisation data for a microarray, typically a study of gene expression." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. See also EDAM:0000931 ! Experiment annotation (microarray) subset: data -synonym: "Gene expression data" EXACT [] -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0003110 +id: EDAM_data:3110 !{since=beta13} name: Raw microarray data namespace: data -def: "Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment." [EDAM:EBI "EMBRACE definition"] -comment: Such data as found in Affymetrix CEL or GPR files. subset: data -is_a: EDAM:0003117 ! Microarray hybridisation data -is_a: EDAM:0003108 ! Experimental measurement +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 [Term] -id: EDAM:0003111 +id: EDAM_data:3111 !{since=beta13} name: Processed microarray data namespace: data -alt_id: EDAM:0000929 -def: "Data generated from processing and analysis of probe set data from a microarray experiment." [EDAM:EBI "EMBRACE definition"] -comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. subset: data -synonym: "Microarray probe set data" EXACT [] -synonym: "Gene expression report" EXACT [] -synonym: "Gene annotation (expression)" EXACT [] -is_a: EDAM:0003117 ! Microarray hybridisation data -is_a: EDAM:0000928 ! Gene expression profile -relationship: has_topic EDAM:0000197 ! Gene expression resources +! 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:0197 ! Gene expression resources [Term] -id: EDAM:0003117 +id: EDAM_data:3117 !{since=beta13} name: Microarray hybridisation data namespace: data -def: "Data concerning the hybridisations measured during a microarray experiment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002603 ! Microarray data -relationship: has_topic EDAM:0000197 ! Gene expression resources +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:0197 ! Gene expression resources [Term] -id: EDAM:0003112 +id: EDAM_data:3112 !{since=beta13} name: Normalised microarray data namespace: data -def: "The final processed (normalised) data for a set of hybridisations in a microarray experiment." [EDAM:EBI "EMBRACE definition"] -comment: This combines data from all hybridisations. subset: data -synonym: "Gene expression matrix" EXACT [] -synonym: "Gene expression data matrix" EXACT [] -is_a: EDAM:0003117 ! Microarray hybridisation 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 [Term] -id: EDAM:0003113 +id: EDAM_data:3113 !{since=beta13} name: Sample annotation namespace: data -def: "Annotation on a biological sample, for example experimental factors and their values." [EDAM:EBI "EMBRACE definition"] -comment: This might include compound and dose in a dose response experiment. subset: data -is_a: EDAM:0000931 ! Experiment annotation (microarray) +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) @@ -10687,1783 +10447,1795 @@ is_a: EDAM:0000931 ! Experiment annotation (microarray) [Term] -id: EDAM:0003115 +id: EDAM_data:3115 !{since=beta13} name: Microarray annotation namespace: data -def: "Annotation on the array itself used in a microarray experiment." [EDAM:EBI "EMBRACE definition"] -comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. subset: data -is_a: EDAM:0000931 ! Experiment annotation (microarray) +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) [Term] -id: EDAM:0003116 +id: EDAM_data:3116 !{since=beta13} name: Microarray protocol annotation namespace: data -def: "Annotation on laboratory and/or data processing protocols used in an microarray experiment." [EDAM:EBI "EMBRACE definition"] -comment: This might describe e.g. the normalisation methods used to process the raw data. subset: data -is_a: EDAM:0000931 ! Experiment annotation (microarray) +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) [Term] -id: EDAM:0002763 +id: EDAM_data:2763 name: Locus annotation namespace: data -def: "An informative report on a particular locus." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Locus report" EXACT [] -is_obsolete: true -consider: EDAM:0000916 ! Gene annotation +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 [Term] -id: EDAM:0000916 +id: EDAM_data:0916 name: Gene annotation namespace: data -alt_id: EDAM:0002394 -alt_id: EDAM:0002361 -def: "An informative report on a particular locus, gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Gene report" EXACT [] -synonym: "Gene annotation (functional)" EXACT [] +! 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:0001276 ! Nucleic acid features -relationship: has_topic EDAM:0000623 ! Genes, gene family or system +is_a: EDAM_data:1276 ! Nucleic acid features +relationship: has_topic EDAM_topic:0623 ! Genes, gene family or system [Term] -id: EDAM:0003148 +id: EDAM_data:3148 !{since=beta13} name: Gene family annotation namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002986 ! Nucleic acid classification -is_a: EDAM:0000916 ! Gene annotation +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 [Term] -id: EDAM:0000918 +id: EDAM_data:0918 name: Nucleic acid features (variation) namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence variation annotation" EXACT [] -is_a: EDAM:0003122 ! Nucleic acid features (difference and change) -relationship: has_topic EDAM:0000199 ! Genetic variation +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 [Term] -id: EDAM:0000919 +id: EDAM_data:0919 name: Gene annotation (chromosome) namespace: data -def: "An informative report on a specific chromosome." [EDAM:EBI "EMBRACE definition"] -comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. subset: data -is_a: EDAM:0000916 ! Gene annotation -relationship: has_topic EDAM:0000624 ! Chromosomes +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 [Term] -id: EDAM:0002602 +id: EDAM_data:2602 name: Genotype and phenotype data namespace: data -def: "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000920 ! Genotype/phenotype annotation +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 [Term] -id: EDAM:0000920 +id: EDAM_data:0920 name: Genotype/phenotype annotation namespace: data -alt_id: EDAM:0002890 -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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002048 ! Report +! 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 [Term] -id: EDAM:0002531 +id: EDAM_data:2531 name: Experiment annotation namespace: data -def: "Annotation on a wet lab experiment, such as experimental conditions." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002048 ! Report +def: "Annotation on a wet lab experiment, such as experimental conditions." [http://edamontology.org] +is_a: EDAM_data:2048 ! Report -[Term] -id: EDAM:0003109 -name: Experimental measurement annotation -namespace: data -def: "Annotation on the result of a wet lab experiment." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0003108 ! Experimental measurement -consider: EDAM:0002531 ! Experiment annotation +! [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 [Term] -id: EDAM:0002381 +id: EDAM_data:2381 name: Experiment annotation (genotype) namespace: data -def: "Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002531 ! Experiment annotation +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 [Term] -id: EDAM:0000925 +id: EDAM_data:0925 name: Sequence assembly namespace: data -def: "An assembly of fragments of a (typically genomic) DNA sequence." [EDAM:EBI "EMBRACE definition"] -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: data -xref: SO:0001248 -is_a: EDAM:0001234 ! Sequence set (nucleic acid) +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) [Term] -id: EDAM:0002028 +id: EDAM_data:2028 name: Experimental data namespace: data -def: "Raw data from or annotation on laboratory experiments." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Experimental measurement data" EXACT [] -is_obsolete: true -consider: EDAM:0003108 ! Experimental measurement -consider: EDAM:0002531 ! Experiment annotation +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 [Term] -id: EDAM:0003108 +id: EDAM_data:3108 !{since=beta13} name: Experimental measurement namespace: data -def: "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Raw experimental data" EXACT [] -synonym: "Experimental measurement data" EXACT [] -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0002042 +id: EDAM_data:2042 name: Evidence namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter +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 [Term] -id: EDAM:0000941 +id: EDAM_data:0941 name: Electron microscopy model namespace: data -def: "Annotation on a structural 3D model (volume map) from electron microscopy." [EDAM:EBI "EMBRACE definition"] -comment: This might include the location in the model of the known features of a particular macromolecule. subset: data -is_a: EDAM:0000940 ! Electron microscopy volume map -relationship: has_topic EDAM:0002226 ! Structure determination +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 [Term] -id: EDAM:0002971 +id: EDAM_data:2971 name: Workflow data namespace: data -def: "Data concerning a computational workflow." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000949 ! Workflow metadata -consider: EDAM:0002972 ! Workflow +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 [Term] -id: EDAM:0000949 +id: EDAM_data:0949 name: Workflow metadata namespace: data -def: "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Metadata -relationship: has_topic EDAM:0000769 ! Workflows +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 [Term] -id: EDAM:0002972 +id: EDAM_data:2972 name: Workflow namespace: data -def: "A computational workflow." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000769 ! Workflows +def: "A computational workflow." [http://edamontology.org] +is_a: EDAM_data:3031 ! Core data +! relationship: has_topic EDAM_topic:0769 ! Workflows [Term] -id: EDAM:0000950 +id: EDAM_data:0950 name: Biological model namespace: data -def: "A biological model which can be represented in mathematical terms." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000771 ! Biological models +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 [Term] -id: EDAM:0002983 +id: EDAM_data:2983 name: Pathway or network data namespace: data -def: "Data concerning a specific biological pathway or network." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002600 ! Pathway or network -consider: EDAM:0002984 ! Pathway or network report +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 [Term] -id: EDAM:0002984 +id: EDAM_data:2984 name: Pathway or network report namespace: data -def: "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002048 ! Report -relationship: has_topic EDAM:0000602 ! Pathways, networks and models +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 [Term] -id: EDAM:0002600 +id: EDAM_data:2600 name: Pathway or network namespace: data -def: "Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000602 ! Pathways, networks and models +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 [Term] -id: EDAM:0001883 +id: EDAM_data:1883 name: Annotated URI namespace: data -def: "A URI along with annotation describing the data found at the address." [EDAM:EBI "EMBRACE definition"] subset: data +def: "A URI along with annotation describing the data found at the address." [http://edamontology.org] xref: Moby:DescribedLink -is_a: EDAM:0002337 ! Metadata -is_a: EDAM:0002093 ! Data reference +is_a: EDAM_data:2337 ! Metadata +is_a: EDAM_data:2093 ! Data reference [Term] -id: EDAM:0000954 +id: EDAM_data:0954 name: Database cross-mapping namespace: data -def: "A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0002093 ! Data reference +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 [Term] -id: EDAM:0002872 +id: EDAM_data:2872 name: ID list namespace: data -def: "A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002093 ! Data reference +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 [Term] -id: EDAM:0002765 +id: EDAM_data:2765 name: Term ID list namespace: data -def: "One or more terms from one or more controlled vocabularies which are annotations on an entity." [EDAM:EBI "EMBRACE definition"] -comment: The terms 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: data -is_a: EDAM:0002872 ! ID list +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 [Term] -id: EDAM:0001111 +id: EDAM_data:1111 name: EMBOSS listfile namespace: data -def: "List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002872 ! ID list +def: "List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile)." [http://edamontology.org] +is_a: EDAM_data:2872 ! ID list [Term] -id: EDAM:0002093 +id: EDAM_data:2093 name: Data reference namespace: data -def: "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology." [EDAM:EBI "EMBRACE definition"] -comment: A list of database accessions or identifiers are usually included. subset: data -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0002540 +id: EDAM_data:2540 name: Data index data namespace: data -def: "Data concerning an index of data." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -synonym: "Database index" EXACT [] -is_obsolete: true -consider: EDAM:0000955 ! Data index -consider: EDAM:0000956 ! Data index report +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 [Term] -id: EDAM:0000955 +id: EDAM_data:0955 name: Data index namespace: data -def: "An index of data of biological relevance." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000220 ! Data processing and validation +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 [Term] -id: EDAM:0000956 +id: EDAM_data:0956 name: Data index report namespace: data -def: "A report of an analysis of an index of biological data." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Database index annotation" EXACT [] -is_a: EDAM:0002048 ! Report -relationship: has_topic EDAM:0000220 ! Data processing and validation +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 [Term] -id: EDAM:0002048 +id: EDAM_data:2048 name: Report namespace: data -alt_id: EDAM:0000969 -alt_id: EDAM:0003037 -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." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Text" EXACT [] -synonym: "Textual data" EXACT [] -synonym: "Document" EXACT [] -is_a: EDAM:0000006 ! 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 [Term] -id: EDAM:0001772 +id: EDAM_data:1772 name: Score or penalty namespace: data -alt_id: EDAM:0002138 -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)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter +! 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 [Term] -id: EDAM:0002529 +id: EDAM_data:2529 name: Molecule report namespace: data -def: "An informative report on a specific molecule." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Molecular report" EXACT [] -is_a: EDAM:0002048 ! Report +def: "An informative report on a specific molecule." [http://edamontology.org] +synonym: "Molecular report" EXACT [http://edamontology.org] +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM:0000962 +id: EDAM_data:0962 name: Small molecule annotation namespace: data -def: "An informative report on a specific chemical compound." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Chemical compound annotation" EXACT [] -synonym: "Small molecule report" EXACT [] -is_a: EDAM:0002085 ! Structure report -is_a: EDAM:0002529 ! Molecule report -relationship: has_topic EDAM:0000154 ! Small molecules +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] +synonym: "molecular entity" RELATED [CHEBI:23367] +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:0000963 +id: EDAM_data:0963 name: Cell line annotation namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Organism strain data" EXACT [] -is_a: EDAM:0002530 ! Organism annotation +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 [Term] -id: EDAM:0002530 +id: EDAM_data:2530 name: Organism annotation namespace: data -def: "An informative report on a specific organism." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002048 ! Report +def: "An informative report on a specific organism." [http://edamontology.org] +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM:0002307 +id: EDAM_data:2307 name: Virus annotation namespace: data -def: "An informative report on a specific virus." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002530 ! Organism annotation +def: "An informative report on a specific virus." [http://edamontology.org] +is_a: EDAM_data:2530 ! Organism annotation [Term] -id: EDAM:0002395 +id: EDAM_data:2395 name: Fungi annotation namespace: data -def: "An informative report on a specific fungus." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002530 ! Organism annotation +def: "An informative report on a specific fungus." [http://edamontology.org] +is_a: EDAM_data:2530 ! Organism annotation [Term] -id: EDAM:0000964 +id: EDAM_data:0964 name: Scent annotation namespace: data -def: "An informative report about a specific scent." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule annotation +def: "An informative report about a specific scent." [http://edamontology.org] +is_a: EDAM_data:0962 ! Small molecule annotation [Term] -id: EDAM:0002968 +id: EDAM_data:2968 name: Image namespace: data -alt_id: EDAM:0000965 -def: "Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0002884 +id: EDAM_data:2884 name: Plot namespace: data -def: "Biological data that is plotted as a graph of some type." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002968 ! Image +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 [Term] -id: EDAM:0002353 +id: EDAM_data:2353 name: Ontological data namespace: data -def: "Data concerning an ontology." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0002223 ! Ontology metadata -consider: EDAM:0000582 ! Ontology +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 [Term] -id: EDAM:0002849 +id: EDAM_data:2849 name: Abstract namespace: data -def: "An abstract of a scientific article." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002857 ! Article metadata +def: "An abstract of a scientific article." [http://edamontology.org] +is_a: EDAM_data:2857 ! Article metadata [Term] -id: EDAM:0000970 +id: EDAM_data:0970 name: Bibliographic reference namespace: data -def: "Bibliographic data that uniquely identifies a scientific article, book or other published material." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Reference" EXACT [] -synonym: "Citation" EXACT [] +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:0002857 ! Article metadata -is_a: EDAM:0002093 ! Data reference +is_a: EDAM_data:2857 ! Article metadata +is_a: EDAM_data:2093 ! Data reference [Term] -id: EDAM:0002526 +id: EDAM_data:2526 name: Article data namespace: data -def: "Data concerning the scientific literature." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0000971 ! Article +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 [Term] -id: EDAM:0000971 +id: EDAM_data:0971 name: Article namespace: data -def: "A body of scientific text, typically a full text article from a scientific journal." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0003068 ! Literature data resources +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 data resources [Term] -id: EDAM:0002857 +id: EDAM_data:2857 name: Article metadata namespace: data -def: "Bibliographic data concerning scientific article(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002954 ! Article report -is_a: EDAM:0002337 ! Metadata -relationship: has_topic EDAM:0003068 ! Literature data resources +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 data resources [Term] -id: EDAM:0002954 +id: EDAM_data:2954 name: Article report namespace: data -def: "Data concerning or derived from the analysis of a scientific article." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002048 ! Report +def: "Data concerning or derived from the analysis of a scientific article." [http://edamontology.org] +is_a: EDAM_data:2048 ! Report [Term] -id: EDAM:0000972 +id: EDAM_data:0972 name: Text mining report namespace: data -def: "An abstract of the results of text mining." [EDAM:EBI "EMBRACE definition"] -comment: A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. subset: data -is_a: EDAM:0002954 ! Article report +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 [Term] -id: EDAM:0002143 +id: EDAM_data:2143 name: EMBOSS report namespace: data -def: "An application report generated by the EMBOSS suite." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002048 ! Report +def: "An application report generated by the EMBOSS suite." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2048 ! Report [Term] -id: EDAM:0002176 +id: EDAM_data:2176 name: Cardinality namespace: data -def: "The number of a certain thing." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +def: "The number of a certain thing." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} [Term] -id: EDAM:0002527 +id: EDAM_data:2527 name: Parameter namespace: data -alt_id: EDAM:0002029 -alt_id: EDAM:0001773 -alt_id: EDAM:0000961 -def: "Typically a simple numerical or string value that controls the operation of a tool." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Parameter or primitive" EXACT [] -synonym: "Tool parameter" EXACT [] -synonym: "Tool-specific parameter" EXACT [] -synonym: "Generic parameter" EXACT [] -is_a: EDAM:0000006 ! 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 [Term] -id: EDAM:0002190 +id: EDAM_data:2190 name: Sequence checksum namespace: data -def: "A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Hash code" EXACT [] -synonym: "Hash sum" EXACT [] -synonym: "Hash" EXACT [] -synonym: "Hash value" EXACT [] -is_a: EDAM:0002534 ! Sequence parameter -is_a: EDAM:0000855 ! Sequence metadata +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 [Term] -id: EDAM:0002192 +id: EDAM_data:2192 name: Error namespace: data -def: "Data on an error generated by computer system or tool." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000959 ! Job metadata +def: "Data on an error generated by computer system or tool." [http://edamontology.org] +is_a: EDAM_data:0959 ! Job metadata [Term] -id: EDAM:0002249 +id: EDAM_data:2249 name: DTD namespace: data -def: "A DTD (document type definition)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002248 ! Schema +def: "A DTD (document type definition)." [http://edamontology.org] +is_a: EDAM_data:2248 ! Schema [Term] -id: EDAM:0002250 -name: XSD schema +id: EDAM_data:2250 +name: XML Schema namespace: data -def: "An XSD schema." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002248 ! Schema +def: "An XML Schema." [http://edamontology.org] +synonym: "XSD" EXACT [http://edamontology.org] +is_a: EDAM_data:2248 ! Schema [Term] -id: EDAM:0002251 +id: EDAM_data:2251 name: Relax-NG schema namespace: data -def: "A relax-NG schema." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002248 ! Schema +def: "A relax-NG schema." [http://edamontology.org] +is_a: EDAM_data:2248 ! Schema [Term] -id: EDAM:0002252 +id: EDAM_data:2252 name: XSLT stylesheet namespace: data -def: "An XSLT stylesheet." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002248 ! Schema +def: "An XSLT stylesheet." [http://edamontology.org] +is_a: EDAM_data:2248 ! Schema [Term] -id: EDAM:0001743 +id: EDAM_data:1743 name: Atomic coordinate namespace: data -def: "Cartesian coordinate of an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Cartesian coordinate" EXACT [] -is_a: EDAM:0001917 ! Atomic property +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 [Term] -id: EDAM:0001857 +id: EDAM_data:1857 name: Atomic occupancy namespace: data -def: "The fraction of an atom type present at a site in a molecular structure." [EDAM:EBI "EMBRACE definition"] -comment: The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. 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:0001917 ! Atomic property +is_a: EDAM_data:1917 ! Atomic property [Term] -id: EDAM:0001858 +id: EDAM_data:1858 name: Isotropic B factor namespace: data -def: "Isotropic B factor (atomic displacement parameter) for an atom from a PDB file." [EDAM:EBI "EMBRACE definition"] 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:0001917 ! Atomic property +is_a: EDAM_data:1917 ! Atomic property [Term] -id: EDAM:0001744 +id: EDAM_data:1744 name: Atomic x coordinate namespace: data -def: "Cartesian x coordinate of an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Cartesian x coordinate" EXACT [] +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:0001743 ! Atomic coordinate +is_a: EDAM_data:1743 ! Atomic coordinate ! _atom_site.Cartn_x in PDBML [Term] -id: EDAM:0001745 +id: EDAM_data:1745 name: Atomic y coordinate namespace: data -def: "Cartesian y coordinate of an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Cartesian y coordinate" EXACT [] +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:0001743 ! Atomic coordinate +is_a: EDAM_data:1743 ! Atomic coordinate ! _atom_site.Cartn_y in PDBML [Term] -id: EDAM:0001746 +id: EDAM_data:1746 name: Atomic z coordinate namespace: data -def: "Cartesian z coordinate of an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Cartesian z coordinate" EXACT [] +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:0001743 ! Atomic coordinate +is_a: EDAM_data:1743 ! Atomic coordinate ! _atom_site.Cartn_z in PDBML [Term] -id: EDAM:0000844 +id: EDAM_data:0844 name: Molecular mass namespace: data -def: "Mass of a molecule." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002050 ! Molecular property (general) +def: "Mass of a molecule." [http://edamontology.org] +is_a: EDAM_data:2050 ! Molecular property (general) [Term] -id: EDAM:0000845 +id: EDAM_data:0845 name: Molecular charge namespace: data -def: "Net charge of a molecule." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002050 ! Molecular property (general) +def: "Net charge of a molecule." [http://edamontology.org] +is_a: EDAM_data:2050 ! Molecular property (general) ! pdbx_formal_charge in PDBML [Term] -id: EDAM:0000846 +id: EDAM_data:0846 name: Chemical formula namespace: data -def: "A specification of a chemical structure." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Chemical structure specification" EXACT [] -is_a: EDAM:0002050 ! Molecular property (general) +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) [Term] -id: EDAM:0000847 +id: EDAM_data:0847 name: QSAR descriptor namespace: data -def: "A QSAR quantitative descriptor (name-value pair) of chemical structure." [EDAM:EBI "EMBRACE definition"] -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. subset: data -is_a: EDAM:0002050 ! Molecular property (general) +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) [Term] -id: EDAM:0002301 +id: EDAM_data:2301 name: SMILES string namespace: data -def: "A specification of a chemical structure in SMILES format." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000846 ! Chemical formula +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. [Term] -id: EDAM:0001201 +id: EDAM_data:1201 name: QSAR descriptor (constitutional) namespace: data -def: "A QSAR constitutional descriptor." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "QSAR constitutional descriptor" EXACT [] -is_a: EDAM:0000847 ! QSAR descriptor +def: "A QSAR constitutional descriptor." [http://edamontology.org] +synonym: "QSAR constitutional descriptor" EXACT [http://edamontology.org] +is_a: EDAM_data:0847 ! QSAR descriptor [Term] -id: EDAM:0001202 +id: EDAM_data:1202 name: QSAR descriptor (electronic) namespace: data -def: "A QSAR electronic descriptor." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "QSAR electronic descriptor" EXACT [] -is_a: EDAM:0000847 ! QSAR descriptor +def: "A QSAR electronic descriptor." [http://edamontology.org] +synonym: "QSAR electronic descriptor" EXACT [http://edamontology.org] +is_a: EDAM_data:0847 ! QSAR descriptor [Term] -id: EDAM:0001203 +id: EDAM_data:1203 name: QSAR descriptor (geometrical) namespace: data -def: "A QSAR geometrical descriptor." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "QSAR geometrical descriptor" EXACT [] -is_a: EDAM:0000847 ! QSAR descriptor +def: "A QSAR geometrical descriptor." [http://edamontology.org] +synonym: "QSAR geometrical descriptor" EXACT [http://edamontology.org] +is_a: EDAM_data:0847 ! QSAR descriptor [Term] -id: EDAM:0001204 +id: EDAM_data:1204 name: QSAR descriptor (topological) namespace: data -def: "A QSAR topological descriptor." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "QSAR topological descriptor" EXACT [] -is_a: EDAM:0000847 ! QSAR descriptor +def: "A QSAR topological descriptor." [http://edamontology.org] +synonym: "QSAR topological descriptor" EXACT [http://edamontology.org] +is_a: EDAM_data:0847 ! QSAR descriptor [Term] -id: EDAM:0001205 +id: EDAM_data:1205 name: QSAR descriptor (molecular) namespace: data -def: "A QSAR molecular descriptor." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "QSAR molecular descriptor" EXACT [] -is_a: EDAM:0000847 ! QSAR descriptor +def: "A QSAR molecular descriptor." [http://edamontology.org] +synonym: "QSAR molecular descriptor" EXACT [http://edamontology.org] +is_a: EDAM_data:0847 ! QSAR descriptor [Term] -id: EDAM:0000848 +id: EDAM_data:0848 name: Raw sequence namespace: data -def: "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] -comment: Non-sequence characters may be used for example for gaps and translation stop. subset: data -is_a: EDAM:0002044 ! Sequence +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 [Term] -id: EDAM:0002201 +id: EDAM_data:2201 name: Sequence record full namespace: data -def: "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] 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:0000849 ! Sequence record +is_a: EDAM_data:0849 ! Sequence record [Term] -id: EDAM:0002888 +id: EDAM_data:2888 name: Sequence record full (protein) namespace: data -def: "A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] 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:0002201 ! Sequence record full -is_a: EDAM:0002886 ! Sequence record (protein) +is_a: EDAM_data:2201 ! Sequence record full +is_a: EDAM_data:2886 ! Sequence record (protein) [Term] -id: EDAM:0002889 +id: EDAM_data:2889 name: Sequence record full (nucleic acid) namespace: 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." [EDAM:EBI "EMBRACE definition"] 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:0002201 ! Sequence record full -is_a: EDAM:0002887 ! Sequence record (nucleic acid) +is_a: EDAM_data:2201 ! Sequence record full +is_a: EDAM_data:2887 ! Sequence record (nucleic acid) [Term] -id: EDAM:0000849 +id: EDAM_data:0849 name: Sequence record namespace: data -alt_id: EDAM:0001220 -alt_id: EDAM:0001224 -alt_id: EDAM:0001225 -alt_id: EDAM:0001226 -alt_id: EDAM:0001227 -alt_id: EDAM:0001229 -alt_id: EDAM:0001230 -alt_id: EDAM:0001231 -alt_id: EDAM:0001232 -def: "A molecular sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002044 ! Sequence +! 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 [Term] -id: EDAM:0002886 +id: EDAM_data:2886 name: Sequence record (protein) namespace: data -alt_id: EDAM:0001222 -def: "A protein sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein sequence record" EXACT [] -is_a: EDAM:0000849 ! Sequence record -is_a: EDAM:0002976 ! Protein sequence +! 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 [Term] -id: EDAM:0002887 +id: EDAM_data:2887 name: Sequence record (nucleic acid) namespace: data -alt_id: EDAM:0001221 -def: "A nucleic acid sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Nucleic acid sequence record" EXACT [] -synonym: "Nucleotide sequence record" EXACT [] -is_a: EDAM:0000849 ! Sequence record -is_a: EDAM:0002977 ! Nucleic acid sequence +! 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 [Term] -id: EDAM:0000850 +id: EDAM_data:0850 name: Sequence set namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for arbitrary sequence sets and associated data arising from processing. subset: data -is_a: EDAM:0002955 ! Sequence report +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 [Term] -id: EDAM:0002974 +id: EDAM_data:2974 name: Raw sequence (protein) namespace: data -def: "A raw protein sequence (string of characters)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000848 ! Raw sequence -is_a: EDAM:0002976 ! Protein sequence +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 [Term] -id: EDAM:0002975 +id: EDAM_data:2975 name: Raw sequence (nucleic acid) namespace: data -def: "A raw nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000848 ! Raw sequence -is_a: EDAM:0002977 ! Nucleic acid sequence +def: "A raw nucleic acid sequence." [http://edamontology.org] +is_a: EDAM_data:0848 ! Raw sequence +is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] -id: EDAM:0002046 +id: EDAM_data:2046 name: Sequence record lite (nucleic acid) namespace: data -def: "A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002043 ! Sequence record lite -is_a: EDAM:0002887 ! Sequence record (nucleic acid) +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) [Term] -id: EDAM:0002047 +id: EDAM_data:2047 name: Sequence record lite (protein) namespace: data -def: "A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002043 ! Sequence record lite -is_a: EDAM:0002886 ! Sequence record (protein) +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) [Term] -id: EDAM:0002043 +id: EDAM_data:2043 name: Sequence record lite namespace: data -alt_id: EDAM:0001223 -def: "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000849 ! Sequence record +! 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 [Term] -id: EDAM:0002173 +id: EDAM_data:2173 name: Sequence set (stream) namespace: data -def: "A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for sequence sets that are expected to be read and processed a single sequence at a time. subset: data -is_obsolete: true -consider: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0002245 +id: EDAM_data:2245 name: Sequence set (bootstrapped) namespace: data -def: "A collection of sequences output from a bootstrapping (resampling) procedure." [EDAM:EBI "EMBRACE definition"] -comment: Bootstrapping is often performed in phylogenetic analysis. subset: data -is_a: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001233 +id: EDAM_data:1233 name: Sequence set (protein) namespace: data -def: "Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001234 +id: EDAM_data:1234 name: Sequence set (nucleic acid) namespace: data -def: "Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000850 ! Sequence set -is_a: EDAM:0002977 ! Nucleic acid sequence +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 [Term] -id: EDAM:0001235 +id: EDAM_data:1235 name: Sequence cluster namespace: data -def: "A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information." [EDAM:EBI "EMBRACE definition"] -comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information. subset: data -is_a: EDAM:0000850 ! Sequence set -relationship: has_topic EDAM:0003052 ! Sequence clusters and classification -relationship: has_topic EDAM:0000724 ! Protein families +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 [Term] -id: EDAM:0001236 +id: EDAM_data:1236 name: Psiblast checkpoint file namespace: data -def: "A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration." [EDAM:EBI "EMBRACE definition"] -comment: A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. subset: data -is_obsolete: true -consider: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001237 +id: EDAM_data:1237 name: HMMER synthetic sequences set namespace: data -def: "Sequences generated by HMMER package in FASTA-style format." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000850 ! Sequence set +def: "Sequences generated by HMMER package in FASTA-style format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0850 ! Sequence set [Term] -id: EDAM:0001238 +id: EDAM_data:1238 name: Proteolytic digest namespace: data -def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001233 ! Sequence set (protein) -relationship: has_topic EDAM:0000767 ! Protein and peptide identification +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 [Term] -id: EDAM:0001766 +id: EDAM_data:1766 name: CATH domain sequences (ATOM) namespace: data -def: "FASTA sequence database for all CATH domains (based on PDB ATOM records)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001767 +id: EDAM_data:1767 name: CATH domain sequences (COMBS) namespace: data -def: "FASTA sequence database for all CATH domains (based on COMBS sequence data)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001239 +id: EDAM_data:1239 name: Restriction digest namespace: data -def: "Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease." [EDAM:EBI "EMBRACE definition"] 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:0001234 ! Sequence set (nucleic acid) +is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] -id: EDAM:0002874 +id: EDAM_data:2874 name: Sequence set (polymorphic) namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001234 ! Sequence set (nucleic acid) +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) [Term] -id: EDAM:0001240 +id: EDAM_data:1240 name: PCR primers namespace: data -def: "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001234 ! Sequence set (nucleic acid) +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) [Term] -id: EDAM:0001241 +id: EDAM_data:1241 name: vectorstrip cloning vector definition file namespace: data -def: "File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001242 +id: EDAM_data:1242 name: Primer3 internal oligo mishybridizing library namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001243 +id: EDAM_data:1243 name: Primer3 mispriming library file namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001244 +id: EDAM_data:1244 name: primersearch primer pairs sequence record namespace: data -def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001245 +id: EDAM_data:1245 name: Sequence cluster (protein) namespace: data -def: "A cluster of protein sequences." [EDAM:EBI "EMBRACE definition"] -comment: The sequences are typically related, for example a family of sequences. subset: data -synonym: "Protein sequence cluster" EXACT [] -is_a: EDAM:0001233 ! Sequence set (protein) -is_a: EDAM:0001235 ! Sequence cluster +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 [Term] -id: EDAM:0001246 +id: EDAM_data:1246 name: Sequence cluster (nucleic acid) namespace: data -def: "A cluster of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -comment: The sequences are typically related, for example a family of sequences. subset: data -synonym: "Nucleotide sequence cluster" EXACT [] -is_a: EDAM:0001234 ! Sequence set (nucleic acid) -is_a: EDAM:0001235 ! Sequence cluster +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 [Term] -id: EDAM:0001764 +id: EDAM_data:1764 name: CATH representative domain sequences (ATOM) namespace: data -def: "FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001235 ! Sequence cluster +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 [Term] -id: EDAM:0001765 +id: EDAM_data:1765 name: CATH representative domain sequences (COMBS) namespace: data -def: "FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001235 ! Sequence cluster +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 [Term] -id: EDAM:0002198 +id: EDAM_data:2198 name: Gene cluster namespace: data -def: "A cluster of similar genes." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001246 ! Sequence cluster (nucleic acid) +def: "A cluster of similar genes." [http://edamontology.org] +is_obsolete: true !{since=beta13} +consider: EDAM_data:1246 ! Sequence cluster (nucleic acid) [Term] -id: EDAM:0001253 +id: EDAM_data:1253 name: Sequence information report namespace: data -def: "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002043 ! Sequence record lite -consider: EDAM:0000855 ! Sequence metadata +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 [Term] -id: EDAM:0001254 +id: EDAM_data:1254 name: Sequence property namespace: data -def: "An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence properties report" EXACT [] -is_a: EDAM:0002955 ! Sequence report +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 [Term] -id: EDAM:0001255 -name: Sequence features +id: EDAM_data:1255 +name: Feature record namespace: data -alt_id: EDAM:0001271 -alt_id: EDAM:0001275 -def: "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Sequence features report" EXACT [] -synonym: "General sequence features" EXACT [] -is_a: EDAM:0002955 ! Sequence report +! 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 [Term] -id: EDAM:0002914 +id: EDAM_data:2914 name: Sequence features metadata namespace: data -def: "Metadata on sequence features." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000855 ! Sequence metadata +def: "Metadata on sequence features." [http://edamontology.org] +is_a: EDAM_data:0855 ! Sequence metadata [Term] -id: EDAM:0001020 +id: EDAM_data:1020 name: Sequence feature key namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. subset: data -synonym: "Sequence feature type" EXACT [] -synonym: "Sequence feature method" EXACT [] -is_a: EDAM:0002914 ! Sequence feature metadata +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 feature metadata [Term] -id: EDAM:0001021 +id: EDAM_data:1021 name: Sequence feature qualifier namespace: data -def: "Typically one of the EMBL or Swiss-Prot feature qualifiers." [EDAM:EBI "EMBRACE definition"] -comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location. subset: data -is_a: EDAM:0002914 ! Sequence feature metadata +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 feature metadata [Term] -id: EDAM:0001022 +id: EDAM_data:1022 name: Sequence feature label namespace: data -def: "Typically an EMBL or Swiss-Prot feature label." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Sequence feature name" EXACT [] -is_a: EDAM:0002914 ! Sequence feature metadata +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 feature metadata [Term] -id: EDAM:0001278 +id: EDAM_data:1278 name: Genetic map namespace: 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." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Linkage map" EXACT [] +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:0001274 ! Map -relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage +is_a: EDAM_data:1274 ! Map +relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] -id: EDAM:0001283 +id: EDAM_data:1283 name: Cytogenetic map namespace: data -alt_id: EDAM:0001287 -def: "A map showing banding patterns derived from direct observation of a stained chromosome." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Cytologic map" EXACT [] -synonym: "Cytogenic map" EXACT [] -synonym: "Chromosome map" EXACT [] -is_a: EDAM:0001280 ! Physical map +! 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 [Term] -id: EDAM:0002870 +id: EDAM_data:2870 name: Radiation hybrid map namespace: data -def: "A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "RH map" EXACT [] -is_a: EDAM:0001280 ! Physical map +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 [Term] -id: EDAM:0001279 +id: EDAM_data:1279 name: Sequence map namespace: data -def: "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001280 ! Physical map +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 [Term] -id: EDAM:0001280 +id: EDAM_data:1280 name: Physical map namespace: 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." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001274 ! Map +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 [Term] -id: EDAM:0001284 +id: EDAM_data:1284 name: DNA transduction map namespace: data -def: "A gene map showing distances between loci based on relative cotransduction frequencies." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001278 ! Genetic map +def: "A gene map showing distances between loci based on relative cotransduction frequencies." [http://edamontology.org] +is_a: EDAM_data:1278 ! Genetic map [Term] -id: EDAM:0001860 +id: EDAM_data:1860 name: QTL map namespace: data -def: "A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Quantitative trait locus map" EXACT [] -is_a: EDAM:0001278 ! Genetic map +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 [Term] -id: EDAM:0001859 +id: EDAM_data:1859 name: Deletion map namespace: data -def: "A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Deletion-based cytogenetic map" EXACT [] -is_a: EDAM:0001283 ! Cytogenetic map +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 [Term] -id: EDAM:0001863 +id: EDAM_data:1863 name: Haplotype map namespace: data -def: "A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation." [EDAM:EBI "EMBRACE definition"] 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:0001278 ! Genetic map +is_a: EDAM_data:1278 ! Genetic map [Term] -id: EDAM:0001285 +id: EDAM_data:1285 name: Gene map namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001279 ! Sequence map +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 [Term] -id: EDAM:0001286 +id: EDAM_data:1286 name: Plasmid map namespace: data -def: "Sequence map of a plasmid (circular DNA)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001279 ! Sequence map +def: "Sequence map of a plasmid (circular DNA)." [http://edamontology.org] +is_a: EDAM_data:1279 ! Sequence map [Term] -id: EDAM:0001288 +id: EDAM_data:1288 name: Genome map namespace: data -def: "Sequence map of a whole genome." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001279 ! Sequence map +def: "Sequence map of a whole genome." [http://edamontology.org] +is_a: EDAM_data:1279 ! Sequence map [Term] -id: EDAM:0001865 +id: EDAM_data:1865 name: Map feature namespace: data -def: "A feature which may mapped (positioned) on a genetic or other type of map." [EDAM:EBI "EMBRACE definition"] -comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. 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 -consider: EDAM:0001255 ! Sequence features -consider: EDAM:0002019 ! Map attribute -consider: EDAM:0001276 ! Nucleic acid features +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1255 ! Sequence features +consider: EDAM_data:2019 ! Map attribute +consider: EDAM_data:1276 ! Nucleic acid features [Term] -id: EDAM:0001257 +id: EDAM_data:1257 name: Sequence property (protein) namespace: data -def: "A report of general sequence properties derived from protein sequence data." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000897 ! Protein property +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 [Term] -id: EDAM:0001258 +id: EDAM_data:1258 name: Sequence property (nucleic acid) namespace: data -def: "A report of general sequence properties derived from nucleotide sequence data." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000912 ! Nucleic acid property +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 [Term] -id: EDAM:0001259 +id: EDAM_data:1259 name: Sequence complexity namespace: data -def: "A report on sequence complexity, for example low-complexity or repeat regions in sequences." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence property (complexity)" EXACT [] -is_a: EDAM:0001254 ! Sequence property +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 [Term] -id: EDAM:0001260 +id: EDAM_data:1260 name: Sequence ambiguity namespace: data -def: "A report on ambiguity in molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence property (ambiguity)" EXACT [] -is_a: EDAM:0001254 ! Sequence property +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 [Term] -id: EDAM:0001261 +id: EDAM_data:1261 name: Sequence composition namespace: data -def: "A report (typically a table) on character or word composition / frequency of a molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence property (composition)" EXACT [] -is_a: EDAM:0001254 ! Sequence property +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 [Term] -id: EDAM:0003119 +id: EDAM_data:3119 !{since=beta13} name: Sequence features (compositionally-biased regions) namespace: data -def: "A report of regions in a molecular sequence that are biased to certain characters." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001261 ! Sequence composition +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 [Term] -id: EDAM:0003085 +id: EDAM_data:3085 !{since=beta13} name: Protein sequence composition namespace: data -def: "A report (typically a table) on character or word composition / frequency of protein sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence property (protein composition)" EXACT [] -is_a: EDAM:0001261 ! Sequence composition +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 [Term] -id: EDAM:0003086 +id: EDAM_data:3086 !{since=beta13} name: Nucleic acid sequence composition namespace: data -def: "A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence property (nucleic acid composition)" EXACT [] -is_a: EDAM:0001261 ! Sequence composition -is_a: EDAM:0000912 ! Nucleic acid property +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 [Term] -id: EDAM:0001262 +id: EDAM_data:1262 name: Peptide molecular weight hits namespace: data -def: "A report on peptide fragments of certain molecular weight(s) in one or more protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001233 ! Sequence set (protein) +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) [Term] -id: EDAM:0001263 +id: EDAM_data:1263 name: Sequence composition (base position variability) namespace: data -def: "Report on or plot of third base position variability in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003086 ! Nucleic acid sequence composition +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 [Term] -id: EDAM:0002157 +id: EDAM_data:2157 name: Word composition namespace: data -def: "Word composition data for a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001268 ! Amino acid word frequencies -consider: EDAM:0001266 ! Sequence composition (base words) +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) [Term] -id: EDAM:0001264 +id: EDAM_data:1264 name: Sequence composition table namespace: data -def: "A table of character or word composition / frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001261 ! Sequence composition +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 [Term] -id: EDAM:0002166 +id: EDAM_data:2166 name: Sequence composition plot namespace: data -def: "A plot of character or word composition / frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001261 ! Sequence composition +def: "A plot of character or word composition / frequency of a molecular sequence." [http://edamontology.org] +is_a: EDAM_data:1261 ! Sequence composition [Term] -id: EDAM:0001265 +id: EDAM_data:1265 name: Sequence composition (base frequencies) namespace: data -def: "A table of base frequencies of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003086 ! Nucleic acid sequence composition +def: "A table of base frequencies of a nucleotide sequence." [http://edamontology.org] +is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] -id: EDAM:0001267 +id: EDAM_data:1267 name: Amino acid frequencies namespace: data -def: "A table of amino acid frequencies of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence composition (amino acid frequencies)" EXACT [] -is_a: EDAM:0003085 ! Protein sequence composition +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 [Term] -id: EDAM:0001266 +id: EDAM_data:1266 name: Sequence composition (base words) namespace: data -def: "A table of word composition of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003086 ! Nucleic acid sequence composition +def: "A table of word composition of a nucleotide sequence." [http://edamontology.org] +is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] -id: EDAM:0001268 +id: EDAM_data:1268 name: Amino acid word frequencies namespace: data -def: "A table of amino acid word composition of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence composition (amino acid words)" EXACT [] -is_a: EDAM:0003085 ! Protein sequence composition +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 [Term] -id: EDAM:0001269 +id: EDAM_data:1269 name: DAS sequence feature annotation namespace: data -def: "Annotation of a molecular sequence in DAS format." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001978 ! DASGFF feature +def: "Annotation of a molecular sequence in DAS format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1978 ! DASGFF [Term] -id: EDAM:0003002 +id: EDAM_data:3002 name: Sequence annotation track namespace: data -def: "Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Annotation track" EXACT [] -synonym: "Genome track" EXACT [] -synonym: "Genomic track" EXACT [] -synonym: "Genome-browser track" EXACT [] -synonym: "Genome annotation track" EXACT [] -is_a: EDAM:0001255 ! Sequence features +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 ! Sequence features [Term] -id: EDAM:0001270 +id: EDAM_data:1270 name: Sequence feature table namespace: data -def: "Annotation of positional sequence features, organized into a standard feature table." [EDAM:EBI "EMBRACE definition"] -synonym: "Feature table" EXACT [] -is_a: EDAM:0001255 ! Sequence feature annotation +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 ! Sequence feature annotation [Term] -id: EDAM:0001276 +id: EDAM_data:1276 name: Nucleic acid features namespace: data -alt_id: EDAM:0001273 -def: "Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence)." [EDAM:EBI "EMBRACE definition"] -comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. subset: data -synonym: "Nucleic acid feature table" EXACT [] -synonym: "Feature table (nucleic acid)" EXACT [] -is_a: EDAM:0002084 ! Nucleic acid report -is_a: EDAM:0001255 ! Sequence features +! 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 ! Sequence features [Term] -id: EDAM:0003139 +id: EDAM_data:3139 !{since=beta13} name: Nucleic acid features (STS) namespace: data -def: "A report on sequence tagged sites (STS) in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0003122 +id: EDAM_data:3122 !{since=beta13} name: Nucleic acid features (difference and change) namespace: data -def: "A report on features in a nucleic acid sequence that indicate changes to or differences between sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0003123 +id: EDAM_data:3123 !{since=beta13} name: Nucleic acid features (expression signal) namespace: data -def: "A report on regions within a nucleic acid sequence containing a signal that alters a biological function." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0003125 +id: EDAM_data:3125 !{since=beta13} name: Nucleic acid features (binding) namespace: data -def: "A report on regions of a nucleic acid sequence that bind some other molecule." [EDAM:EBI "EMBRACE definition"] -comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). subset: data -is_a: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0003126 +id: EDAM_data:3126 !{since=beta13} name: Nucleic acid features (repeats) namespace: data -def: "A report on repetitive elements within a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001299 ! Sequence features (repeats) -is_a: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0003127 +id: EDAM_data:3127 !{since=beta13} name: Nucleic acid features (replication and recombination) namespace: data -def: "A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0003128 +id: EDAM_data:3128 !{since=beta13} name: Nucleic acid features (structure) namespace: data -def: "A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0003132 +id: EDAM_data:3132 !{since=beta13} name: Nucleic acid features (d-loop) namespace: data -def: "A report on displacement loops in a mitochondrial DNA sequence." [EDAM:EBI "EMBRACE definition"] -comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. subset: data -is_a: EDAM:0003128 ! Nucleic acid features (structure) +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) [Term] -id: EDAM:0003133 +id: EDAM_data:3133 !{since=beta13} name: Nucleic acid features (stem loop) namespace: data -def: "A report on stem loops in a DNA sequence." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0003128 ! Nucleic acid features (structure) +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) [Term] -id: EDAM:0002882 +id: EDAM_data:2882 name: DNA features namespace: data -def: "DNA sequence-specific feature annotation (not in a feature table)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0002883 +id: EDAM_data:2883 name: Nucleic acid features (RNA features) namespace: data -def: "Features concerning RNA or regions of DNA that encode an RNA molecule." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "RNA features" EXACT [] -is_a: EDAM:0001300 ! Nucleic acid features (gene structure) +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 structure) [Term] -id: EDAM:0003134 +id: EDAM_data:3134 !{since=beta13} name: Nucleic acid features (mRNA features) namespace: data -def: "Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules." [EDAM:EBI "EMBRACE definition"] -comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). subset: data -synonym: "mRNA features" EXACT [] -is_a: EDAM:0002883 ! Nucleic acid features (RNA features) +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) [Term] -id: EDAM:0003137 +id: EDAM_data:3137 !{since=beta13} name: Nucleic acid features (non-coding RNA) namespace: data -def: "Features concerning non-coding or functional RNA molecules, including tRNA and rRNA." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "ncRNA features" EXACT [] -synonym: "Non-coding RNA features" EXACT [] -is_a: EDAM:0002883 ! Nucleic acid features (RNA features) +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) [Term] -id: EDAM:0003138 +id: EDAM_data:3138 !{since=beta13} name: Nucleic acid features (transcriptional) namespace: data -def: "Features concerning transcription of DNA into RNA including the regulation of transcription." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0002883 ! Nucleic acid features (RNA features) +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) [Term] -id: EDAM:0001277 +id: EDAM_data:1277 name: Protein features namespace: data -alt_id: EDAM:0001272 -def: "Protein sequence-specific feature annotation (positional features of a protein sequence)." [EDAM:EBI "EMBRACE definition"] -comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. subset: data -synonym: "Feature table (protein)" EXACT [] -synonym: "Protein feature table" EXACT [] -is_a: EDAM:0001255 ! Sequence features -is_a: EDAM:0000896 ! Protein report +! 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 ! Sequence features +is_a: EDAM_data:0896 ! Protein report [Term] -id: EDAM:0001256 +id: EDAM_data:1256 name: Sequence features (comparative) namespace: data -def: "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0001255 ! Sequence features +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 ! Sequence features [Term] -id: EDAM:0001298 +id: EDAM_data:1298 name: Sequence features (motifs) namespace: data -def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." [EDAM:EBI "EMBRACE definition"] -comment: Use this term if another, more specific term is not available. subset: data -is_a: EDAM:0001255 ! Sequence features +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 ! Sequence features [Term] -id: EDAM:0003130 +id: EDAM_data:3130 !{since=beta13} name: Protein features (motifs) namespace: data -def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." [EDAM:EBI "EMBRACE definition"] -comment: Use this term if another, more specific term is not available. subset: data -is_a: EDAM:0001277 ! Protein features -is_a: EDAM:0001298 ! Sequence features (motifs) +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) [Term] -id: EDAM:0003131 +id: EDAM_data:3131 !{since=beta13} name: Nucleic acid features (motifs) namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: Use this term if another, more specific term is not available. subset: data -is_a: EDAM:0001276 ! Nucleic acid features -is_a: EDAM:0001298 ! Sequence features (motifs) +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) [Term] -id: EDAM:0000858 +id: EDAM_data:0858 name: Database hits (secondary) namespace: data -def: "A report of hits from a search of a protein secondary or domain database." [EDAM:EBI "EMBRACE definition"] -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 terms under 'Protein features'. subset: data -is_a: EDAM:0002080 ! Database hits +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 [Term] -id: EDAM:0000901 +id: EDAM_data:0901 name: Protein features (domains) namespace: data -def: "Summary of structural domains or 3D folds in a protein or polypeptide chain." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Protein domain assignment" EXACT [] -synonym: "Protein structural domains" EXACT [] -is_a: EDAM:0001277 ! Protein features -relationship: has_topic EDAM:0000736 ! Protein domains and folds +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 [Term] -id: EDAM:0003118 +id: EDAM_data:3118 !{since=beta13} name: Protein features (topological domains) namespace: data -def: "Summary of topological domains such as cytoplasmic regions in a protein." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein topological domains" EXACT [] -is_a: EDAM:0001277 ! Protein features -relationship: has_topic EDAM:0000736 ! Protein domains and folds +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 @@ -12471,152 +12243,152 @@ relationship: has_topic EDAM:0000736 ! Protein domains and folds [Term] -id: EDAM:0001299 +id: EDAM_data:1299 name: Sequence features (repeats) namespace: data -alt_id: EDAM:0001282 -def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] -comment: The report might include derived data map such as classification, annotation, organization, periodicity etc. subset: data -synonym: "Repeat sequence map" EXACT [] -is_a: EDAM:0001255 ! Sequence features +! 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 ! Sequence features [Term] -id: EDAM:0003129 +id: EDAM_data:3129 !{since=beta13} name: Protein features (repeats) namespace: data -def: "Location of short repetitive subsequences (repeat sequences) in a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001299 ! Sequence features (repeats) -is_a: EDAM:0001277 ! Protein features +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 [Term] -id: EDAM:0001281 +id: EDAM_data:1281 name: Sequence signature map namespace: data -def: "Image of a sequence with matches to signatures, motifs or profiles." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001298 ! Sequence features (motifs) +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) [Term] -id: EDAM:0001290 +id: EDAM_data:1290 name: InterPro compact match image namespace: data -def: "Image showing matches between protein sequence(s) and InterPro Entries." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0001298 ! Sequence features (motifs) +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) [Term] -id: EDAM:0001291 +id: EDAM_data:1291 name: InterPro detailed match image namespace: data -def: "Image showing detailed information on matches between protein sequence(s) and InterPro Entries." [EDAM:EBI "EMBRACE definition"] -comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. subset: data -is_obsolete: true -consider: EDAM:0001298 ! Sequence features (motifs) +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) [Term] -id: EDAM:0001292 +id: EDAM_data:1292 name: InterPro architecture image namespace: data -def: "Image showing the architecture of InterPro domains in a protein sequence." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0001298 ! Sequence features (motifs) +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) [Term] -id: EDAM:0001293 +id: EDAM_data:1293 name: SMART protein schematic namespace: data -def: "SMART protein schematic in PNG format." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001298 ! Sequence features (motifs) +def: "SMART protein schematic in PNG format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1298 ! Sequence features (motifs) [Term] -id: EDAM:0001294 +id: EDAM_data:1294 name: GlobPlot domain image namespace: data -def: "Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001298 ! Sequence features (motifs) +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) [Term] -id: EDAM:0001564 +id: EDAM_data:1564 name: Protein fold recognition report namespace: data -def: "A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0000901 ! Protein features (domains) +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) [Term] -id: EDAM:0001300 +id: EDAM_data:1300 name: Nucleic acid features (gene and transcript structure) namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene annotation (structure)" EXACT [] -is_a: EDAM:0000916 ! Gene annotation -is_a: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0003140 +id: EDAM_data:3140 !{since=beta13} name: Nucleic acid features (immunoglobulin gene structure) namespace: data -def: "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001300 ! Nucleic acid features (gene structure) +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 structure) [Term] -id: EDAM:0001301 +id: EDAM_data:1301 name: Nucleic acid features (mobile genetic elements) namespace: data -def: "A report on a region of a nucleic acid sequence containin mobile genetic elements." [EDAM:EBI "EMBRACE definition"] -comment: This includes transposons, Plasmids, Bacteriophage elements and Group II introns. subset: data -synonym: "Nucleic acid features (transposons)" EXACT [] -is_a: EDAM:0001276 ! Nucleic acid features +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 [Term] -id: EDAM:0001302 +id: EDAM_data:1302 name: Nucleic acid features (PolyA signal or site) namespace: data -def: "A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "PolyA signal" EXACT [] -synonym: "PolyA site" EXACT [] -is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) +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) [Term] -id: EDAM:0003135 +id: EDAM_data:3135 !{since=beta13} name: Nucleic acid features (signal or transit peptide) namespace: data -def: "A report on a coding sequence for a signal or transit peptide." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) +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) @@ -12625,4078 +12397,4106 @@ is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) [Term] -id: EDAM:0001303 +id: EDAM_data:1303 name: Nucleic acid features (quadruplexes) namespace: data -def: "A report on quadruplex-forming motifs in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003128 ! Nucleic acid features (structure) +def: "A report on quadruplex-forming motifs in a nucleotide sequence." [http://edamontology.org] +is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] -id: EDAM:0001304 +id: EDAM_data:1304 name: Nucleic acid features (CpG island and isochore) namespace: data -def: "A report or plot of CpG rich regions (isochores) in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003138 ! Nucleic acid features (transcriptional) +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) [Term] -id: EDAM:0001305 +id: EDAM_data:1305 name: Nucleic acid features (restriction sites) namespace: data -def: "Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003125 ! Nucleic acid features (binding) +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) [Term] -id: EDAM:0001306 +id: EDAM_data:1306 name: Nucleic acid features (nucleosome exclusion sequences) namespace: data -def: "A report on nucleosome formation potential or exclusion sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003127 ! Nucleic acid features (replication and recombination) +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) [Term] -id: EDAM:0001307 +id: EDAM_data:1307 name: Nucleic acid features (splice sites) namespace: data -alt_id: EDAM:0000915 -def: "A report on splice sites in a nucleotide sequence or alternative RNA splicing events." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Nucleic acid report (RNA splice model)" EXACT [] -synonym: "Nucleic acid report (RNA splicing)" EXACT [] -is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) +! 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) [Term] -id: EDAM:0001308 +id: EDAM_data:1308 name: Nucleic acid features (matrix/scaffold attachment sites) namespace: data -def: "A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003138 ! Nucleic acid features (transcriptional) +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) [Term] -id: EDAM:0001309 +id: EDAM_data:1309 name: Gene features (exonic splicing enhancer) namespace: data -def: "A report on exonic splicing enhancers (ESE) in an exon." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002397 ! Nucleic acid features (exon) +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) [Term] -id: EDAM:0001310 +id: EDAM_data:1310 name: Nucleic acid features (microRNA) namespace: data -def: "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003137 ! Nucleic acid features (non-coding RNA) -relationship: has_topic EDAM:0003060 ! Regulatory RNA +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 [Term] -id: EDAM:0002169 +id: EDAM_data:2169 name: Nucleic acid features (siRNA) namespace: data -def: "A report on siRNA duplexes in mRNA." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003137 ! Nucleic acid features (non-coding RNA) -relationship: has_topic EDAM:0003060 ! Regulatory RNA +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 [Term] -id: EDAM:0000922 +id: EDAM_data:0922 name: Nucleic acid features (primers) namespace: data -def: "Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003127 ! Nucleic acid features (replication and recombination) -relationship: has_topic EDAM:0000632 ! Probes and primers +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 [Term] -id: EDAM:0001311 +id: EDAM_data:1311 name: Nucleic acid features (operon) namespace: data -def: "A report on operons (operators, promoters and genes) from a bacterial genome." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Gene features (operon)" EXACT [] -is_a: EDAM:0001300 ! Nucleic acid features (gene structure) +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 structure) [Term] -id: EDAM:0001312 +id: EDAM_data:1312 name: Gene features (promoter) namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003138 ! Nucleic acid features (transcriptional) +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) [Term] -id: EDAM:0001313 +id: EDAM_data:1313 name: Nucleic acid features (coding sequence) namespace: data -alt_id: EDAM:0001317 -def: "A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene features (coding sequence)" EXACT [] -synonym: "Gene features (coding region)" EXACT [] -synonym: "Gene annotation (translation)" EXACT [] -is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) +! 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) [Term] -id: EDAM:0001314 +id: EDAM_data:1314 name: Gene features (SECIS element) namespace: data -def: "A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001300 ! Nucleic acid features (gene structure) +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 structure) [Term] -id: EDAM:0001315 +id: EDAM_data:1315 name: Gene features (TFBS) namespace: data -def: "A report on the transcription factor binding sites (TFBS) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001312 ! Gene features (promoter) -is_a: EDAM:0003125 ! Nucleic acid features (binding) -relationship: has_topic EDAM:0000749 ! Transcription factors and regulatory sites +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 [Term] -id: EDAM:0002397 +id: EDAM_data:2397 name: Nucleic acid features (exon) namespace: data -def: "An informative report on an exon in a nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene features (exon)" EXACT [] -is_a: EDAM:0001313 ! Nucleic acid features (coding sequence) +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) [Term] -id: EDAM:0002754 +id: EDAM_data:2754 name: Nucleic acid features (intron) namespace: data -def: "An informative report on an intron in a nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene features (intron)" EXACT [] -is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) +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) [Term] -id: EDAM:0002160 +id: EDAM_data:2160 name: Fickett testcode plot namespace: data -def: "A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001313 ! Nucleic acid features (coding sequence) +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) [Term] -id: EDAM:0001289 +id: EDAM_data:1289 name: Restriction map namespace: data -def: "Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001305 ! Nucleic acid features (restriction sites) -is_a: EDAM:0001279 ! Sequence map -is_a: EDAM:0002969 ! Sequence image +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 [Term] -id: EDAM:0001321 +id: EDAM_data:1321 name: Protein features (sites) namespace: data -def: "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites." [EDAM:EBI "EMBRACE definition"] -comment: Use this term for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. subset: data -is_obsolete: true -consider: EDAM:0001277 ! Protein features +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 [Term] -id: EDAM:0001322 +id: EDAM_data:1322 name: Protein features (signal peptides) namespace: data -def: "A report on the location of signal peptides or signal peptide cleavage sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001277 ! Protein features +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 [Term] -id: EDAM:0003120 +id: EDAM_data:3120 !{since=beta13} name: Protein features (sequence variants) namespace: data -def: "A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001277 ! Protein features +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 [Term] -id: EDAM:0001323 +id: EDAM_data:1323 name: Protein features (cleavage sites) namespace: data -def: "A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001277 ! Protein features -relationship: has_topic EDAM:0000767 ! Protein and peptide identification +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 [Term] -id: EDAM:0001324 +id: EDAM_data:1324 name: Protein features (post-translation modifications) namespace: data -def: "A report on post-translation modifications in a protein sequence, typically describing the specific sites involved." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein features (post-translation modification sites)" EXACT [] -synonym: "Post-translation modification" EXACT [] -is_a: EDAM:0001277 ! Protein features +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] +synonym: "protein modification" RELATED [MOD:00000] +synonym: "protein modification process" RELATED [GO:0006464] +is_a: EDAM_data:1277 ! Protein features [Term] -id: EDAM:0001325 +id: EDAM_data:1325 name: Protein features (active sites) namespace: data -def: "A report on catalytic residues (active site) of an enzyme." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Enzyme active site" EXACT [] -is_a: EDAM:0001277 ! Protein features +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 [Term] -id: EDAM:0001326 +id: EDAM_data:1326 name: Protein features (binding sites) namespace: data -def: "A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001277 ! Protein features +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 [Term] -id: EDAM:0002989 +id: EDAM_data:2989 name: Protein features (key folding sites) namespace: data -def: "A report on key residues involved in protein folding." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001277 ! Protein features +def: "A report on key residues involved in protein folding." [http://edamontology.org] +is_a: EDAM_data:1277 ! Protein features [Term] -id: EDAM:0001327 +id: EDAM_data:1327 name: Protein features (epitopes) namespace: data -def: "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data." [EDAM:EBI "EMBRACE definition"] -comment: Epitope mapping is commonly done during vaccine design. subset: data -is_obsolete: true -consider: EDAM:0001326 ! Protein features (binding sites) +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) [Term] -id: EDAM:0001328 +id: EDAM_data:1328 name: Protein features (nucleic acid binding sites) namespace: data -def: "A report on RNA and DNA-binding proteins and binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001277 ! Protein features +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 [Term] -id: EDAM:0001329 +id: EDAM_data:1329 name: MHC Class I epitopes report namespace: data -def: "A report on epitopes that bind to MHC class I molecules." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001326 ! Protein features (binding sites) +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) [Term] -id: EDAM:0001330 +id: EDAM_data:1330 name: MHC Class II epitopes report namespace: data -def: "A report on predicted epitopes that bind to MHC class II molecules." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001326 ! Protein features (binding sites) +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) [Term] -id: EDAM:0001331 +id: EDAM_data:1331 name: Protein features (PEST sites) namespace: data -def: "A report or plot of PEST sites in a protein sequence." [EDAM:EBI "EMBRACE definition"] -comment: 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. subset: data -is_obsolete: true -consider: EDAM:0001323 ! Protein features (cleavage sites) +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) [Term] -id: EDAM:0000857 +id: EDAM_data:0857 name: Database hits (sequence) namespace: 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." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0002080 ! Database hits +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 [Term] -id: EDAM:0000885 +id: EDAM_data:0885 name: Database hits (structure) namespace: data -def: "Results (hits) from searching a database of tertiary structure." [EDAM:EBI "EMBRACE definition"] -comment: This includes alignment and score data. subset: data -is_a: EDAM:0002080 ! Database hits +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 [Term] -id: EDAM:0001338 +id: EDAM_data:1338 name: Sequence database hits scores list namespace: data -def: "Scores from a sequence database search (for example a BLAST search)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000857 ! Database hits (sequence) +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) [Term] -id: EDAM:0001339 +id: EDAM_data:1339 name: Sequence database hits alignments list namespace: data -def: "Alignments from a sequence database search (for example a BLAST search)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000857 ! Database hits (sequence) +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) [Term] -id: EDAM:0001340 +id: EDAM_data:1340 name: Sequence database hits evaluation data namespace: data -def: "A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000857 ! Database hits (sequence) +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) [Term] -id: EDAM:0001358 +id: EDAM_data:1358 name: Prosite nucleotide pattern namespace: data -def: "A nucleotide regular expression pattern from the Prosite database." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001353 ! Sequence motif +def: "A nucleotide regular expression pattern from the Prosite database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1353 ! Sequence motif [Term] -id: EDAM:0001359 +id: EDAM_data:1359 name: Prosite protein pattern namespace: data -def: "A protein regular expression pattern from the Prosite database." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001353 ! Sequence motif +def: "A protein regular expression pattern from the Prosite database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1353 ! Sequence motif [Term] -id: EDAM:0001352 +id: EDAM_data:1352 name: Regular expression namespace: data -def: "Regular expression pattern." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter +def: "Regular expression pattern." [http://edamontology.org] +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0002070 +id: EDAM_data:2070 name: Sequence motif (nucleic acid) namespace: data -def: "A nucleotide sequence motif." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001353 ! Sequence motif +def: "A nucleotide sequence motif." [http://edamontology.org] +is_a: EDAM_data:1353 ! Sequence motif [Term] -id: EDAM:0002071 +id: EDAM_data:2071 name: Sequence motif (protein) namespace: data -def: "An amino acid sequence motif." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001353 ! Sequence motif +def: "An amino acid sequence motif." [http://edamontology.org] +is_a: EDAM_data:1353 ! Sequence motif [Term] -id: EDAM:0002854 +id: EDAM_data:2854 name: Position-specific scoring matrix namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001354 ! Sequence profile -is_a: EDAM:0002082 ! Matrix +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 [Term] -id: EDAM:0001361 +id: EDAM_data:1361 name: Position frequency matrix namespace: data -def: "A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "PFM" EXACT [] -is_a: EDAM:0002854 ! Position-specific scoring matrix +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 [Term] -id: EDAM:0001362 +id: EDAM_data:1362 name: Position weight matrix namespace: data -def: "A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position." [EDAM:EBI "EMBRACE definition"] -comment: Contributions of individual sequences to the matrix might be uneven (weighted). subset: data -synonym: "PWM" EXACT [] -is_a: EDAM:0002854 ! Position-specific scoring matrix +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 [Term] -id: EDAM:0001363 +id: EDAM_data:1363 name: Information content matrix namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "ICM" EXACT [] -is_a: EDAM:0002854 ! Position-specific scoring matrix +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 [Term] -id: EDAM:0001364 +id: EDAM_data:1364 name: Hidden Markov model namespace: data -def: "A hidden Markov model representation of a set or alignment of sequences." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "HMM" EXACT [] -is_a: EDAM:0001354 ! Sequence profile +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 [Term] -id: EDAM:0001365 +id: EDAM_data:1365 name: Fingerprint namespace: data -def: "One or more fingerprints (sequence classifiers) as used in the PRINTS database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002854 ! Position-specific scoring matrix +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 [Term] -id: EDAM:0001368 +id: EDAM_data:1368 name: Domainatrix signature namespace: data -def: "A protein signature of the type used in the EMBASSY Signature package." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001354 ! Sequence profile +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 [Term] -id: EDAM:0001371 +id: EDAM_data:1371 name: HMMER NULL hidden Markov model namespace: data -def: "NULL hidden Markov model representation used by the HMMER package." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001364 ! Hidden Markov model +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 [Term] -id: EDAM:0001372 +id: EDAM_data:1372 name: Protein family signature namespace: data -def: "A protein family signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001355 ! Protein signature +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 [Term] -id: EDAM:0001373 +id: EDAM_data:1373 name: Protein domain signature namespace: data -def: "A protein domain signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] -comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries. subset: data -is_a: EDAM:0001355 ! Protein signature +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 [Term] -id: EDAM:0001374 +id: EDAM_data:1374 name: Protein region signature namespace: data -def: "A protein region signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] -comment: A protein region signature defines a region which cannot be described as a protein family or domain signature. subset: data -is_a: EDAM:0001355 ! Protein signature +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 [Term] -id: EDAM:0001375 +id: EDAM_data:1375 name: Protein repeat signature namespace: data -def: "A protein repeat signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001355 ! Protein signature +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 [Term] -id: EDAM:0001376 +id: EDAM_data:1376 name: Protein site signature namespace: data -def: "A protein site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] -comment: A protein site signature is a classifier for a specific site in a protein. subset: data -is_a: EDAM:0001355 ! Protein signature +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 [Term] -id: EDAM:0001377 +id: EDAM_data:1377 name: Protein conserved site signature namespace: data -def: "A protein conserved site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001376 ! Protein site signature +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 [Term] -id: EDAM:0001378 +id: EDAM_data:1378 name: Protein active site signature namespace: data -def: "A protein active site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001376 ! Protein site signature +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 [Term] -id: EDAM:0001379 +id: EDAM_data:1379 name: Protein binding site signature namespace: data -def: "A protein binding site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001376 ! Protein site signature +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 [Term] -id: EDAM:0001380 +id: EDAM_data:1380 name: Protein post-translational modification signature namespace: data -def: "A protein post-translational modification signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001376 ! Protein site signature +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 [Term] -id: EDAM:0000861 +id: EDAM_data:0861 name: Sequence alignment (words) namespace: data -def: "Alignment of exact matches between subsequences (words) within two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence word alignment" EXACT [] -is_a: EDAM:0000863 ! Sequence alignment +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 [Term] -id: EDAM:0000863 +id: EDAM_data:0863 name: Sequence alignment namespace: data -def: "Alignment of multiple molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001916 ! Alignment -relationship: has_topic EDAM:0000182 ! Sequence alignment +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 [Term] -id: EDAM:0000868 +id: EDAM_data:0868 name: Sequence profile alignment namespace: data -def: "A profile-profile alignment (each profile typically representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001916 ! Alignment +def: "A profile-profile alignment (each profile typically representing a sequence alignment)." [http://edamontology.org] +is_a: EDAM_data:1916 ! Alignment [Term] -id: EDAM:0000869 +id: EDAM_data:0869 name: Sequence-profile alignment namespace: data -def: "Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001916 ! Alignment +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 [Term] -id: EDAM:0002366 +id: EDAM_data:2366 name: Secondary structure alignment namespace: data -def: "Alignment of the (1D representations of) secondary structure of two or more molecules." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001916 ! Alignment +def: "Alignment of the (1D representations of) secondary structure of two or more molecules." [http://edamontology.org] +is_a: EDAM_data:1916 ! Alignment [Term] -id: EDAM:0000878 +id: EDAM_data:0878 name: Secondary structure alignment (protein) namespace: data -def: "Alignment of the (1D representations of) secondary structure of two or more proteins." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002366 ! Secondary structure alignment -is_a: EDAM:0003154 ! Protein alignment +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 [Term] -id: EDAM:0000881 +id: EDAM_data:0881 name: Secondary structure alignment (RNA) namespace: data -def: "Alignment of the (1D representations of) secondary structure of two or more RNA molecules." [EDAM:EBI "EMBRACE definition"] 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:0002366 ! Secondary structure alignment +is_a: EDAM_data:2366 ! Secondary structure alignment [Term] -id: EDAM:0000886 +id: EDAM_data:0886 name: Structure alignment namespace: data -def: "Alignment (superimposition) of molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001916 ! Alignment -relationship: has_topic EDAM:0000183 ! Structure alignment +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 data +relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] -id: EDAM:0000890 +id: EDAM_data:0890 name: Structural (3D) profile alignment namespace: data -def: "A 3D profile-3D profile alignment (each profile representing structures or a structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Structural profile alignment" EXACT [] -is_a: EDAM:0001916 ! Alignment +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 [Term] -id: EDAM:0000891 +id: EDAM_data:0891 name: Sequence-3D profile alignment namespace: data -def: "An alignment of a sequence to a 3D profile (representing structures or a structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence-structural profile alignment" EXACT [] -is_a: EDAM:0000893 ! Sequence-structure alignment +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 [Term] -id: EDAM:0000893 +id: EDAM_data:0893 name: Sequence-structure alignment namespace: data -def: "An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s))." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001916 ! Alignment +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 [Term] -id: EDAM:0001381 +id: EDAM_data:1381 name: Sequence alignment (pair) namespace: data -def: "Alignment of exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000863 ! Sequence alignment +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 [Term] -id: EDAM:0001382 +id: EDAM_data:1382 name: Sequence alignment (multiple) namespace: data -def: "Alignment of more than two molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000863 ! Sequence alignment +def: "Alignment of more than two molecular sequences." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM:0001383 +id: EDAM_data:1383 name: Sequence alignment (nucleic acid) namespace: data -def: "Alignment of multiple nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000863 ! Sequence alignment -is_a: EDAM:0002084 ! Nucleic acid report +def: "Alignment of multiple nucleotide sequences." [http://edamontology.org] +is_a: EDAM_data:0863 ! Sequence alignment +is_a: EDAM_data:2084 ! Nucleic acid report [Term] -id: EDAM:0001384 +id: EDAM_data:1384 name: Sequence alignment (protein) namespace: data -def: "Alignment of multiple protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000863 ! Sequence alignment -is_a: EDAM:0003154 ! Protein alignment +def: "Alignment of multiple protein sequences." [http://edamontology.org] +is_a: EDAM_data:0863 ! Sequence alignment +is_a: EDAM_data:3154 ! Protein alignment [Term] -id: EDAM:0001385 +id: EDAM_data:1385 name: Sequence alignment (hybrid) namespace: data -def: "Alignment of multiple molecular sequences of different types." [EDAM:EBI "EMBRACE definition"] -comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. subset: data -is_a: EDAM:0000863 ! Sequence alignment +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 [Term] -id: EDAM:0001386 +id: EDAM_data:1386 name: Sequence alignment (nucleic acid pair) namespace: data -def: "Alignment of exactly two nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001381 ! Sequence alignment (pair) -is_a: EDAM:0001383 ! Sequence alignment (nucleic acid) +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) [Term] -id: EDAM:0001387 +id: EDAM_data:1387 name: Sequence alignment (protein pair) namespace: data -def: "Alignment of exactly two protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001381 ! Sequence alignment (pair) -is_a: EDAM:0001384 ! Sequence alignment (protein) +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) [Term] -id: EDAM:0001389 +id: EDAM_data:1389 name: Multiple nucleotide sequence alignment namespace: data -def: "Alignment of more than two nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000863 ! Sequence alignment +def: "Alignment of more than two nucleotide sequences." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM:0001390 +id: EDAM_data:1390 name: Multiple protein sequence alignment namespace: data -def: "Alignment of more than two protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000863 ! Sequence alignment +def: "Alignment of more than two protein sequences." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0863 ! Sequence alignment [Term] -id: EDAM:0001388 +id: EDAM_data:1388 name: Hybrid sequence alignment (pair) namespace: data -def: "Alignment of exactly two molecular sequences of different types." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001385 ! Sequence alignment (hybrid) +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) [Term] -id: EDAM:0001417 +id: EDAM_data:1417 name: Sequence-profile alignment (Domainatrix signature) namespace: data -def: "Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000869 ! Sequence-profile alignment +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 [Term] -id: EDAM:0001418 +id: EDAM_data:1418 name: Sequence-profile alignment (HMM) namespace: data -def: "Alignment of molecular sequence(s) to a hidden Markov model(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000869 ! Sequence-profile alignment +def: "Alignment of molecular sequence(s) to a hidden Markov model(s)." [http://edamontology.org] +is_a: EDAM_data:0869 ! Sequence-profile alignment [Term] -id: EDAM:0001420 +id: EDAM_data:1420 name: Sequence-profile alignment (fingerprint) namespace: data -def: "Alignment of molecular sequences to a protein fingerprint from the PRINTS database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000869 ! Sequence-profile alignment +def: "Alignment of molecular sequences to a protein fingerprint from the PRINTS database." [http://edamontology.org] +is_a: EDAM_data:0869 ! Sequence-profile alignment [Term] -id: EDAM:0001479 +id: EDAM_data:1479 name: Structure alignment (pair) namespace: data -def: "Alignment (superimposition) of exactly two molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000886 ! Structure alignment +def: "Alignment (superimposition) of exactly two molecular tertiary (3D) structures." [http://edamontology.org] +is_a: EDAM_data:0886 ! Structure alignment [Term] -id: EDAM:0001480 +id: EDAM_data:1480 name: Structure alignment (multiple) namespace: data -def: "Alignment (superimposition) of more than two molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000886 ! Structure alignment +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 [Term] -id: EDAM:0001481 +id: EDAM_data:1481 name: Structure alignment (protein) namespace: data -def: "Alignment (superimposition) of protein tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000886 ! Structure alignment -is_a: EDAM:0003154 ! Protein alignment +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 [Term] -id: EDAM:0001482 +id: EDAM_data:1482 name: Structure alignment (nucleic acid) namespace: data -def: "Alignment (superimposition) of nucleic acid tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000886 ! Structure alignment -is_a: EDAM:0002084 ! Nucleic acid report +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 [Term] -id: EDAM:0001483 +id: EDAM_data:1483 name: Structure alignment (protein pair) namespace: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001481 ! Structure alignment (protein) -is_a: EDAM:0001479 ! Structure alignment (pair) +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) [Term] -id: EDAM:0001484 +id: EDAM_data:1484 name: Multiple protein tertiary structure alignment namespace: data -def: "Alignment (superimposition) of more than two protein tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001481 ! Structure alignment (protein) +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) [Term] -id: EDAM:0001485 +id: EDAM_data:1485 name: Structure alignment (protein all atoms) namespace: data -def: "Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001481 ! Structure alignment (protein) +def: "Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] +is_a: EDAM_data:1481 ! Structure alignment (protein) [Term] -id: EDAM:0001486 +id: EDAM_data:1486 name: Structure alignment (protein C-alpha atoms) namespace: data -def: "Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered)." [EDAM:EBI "EMBRACE definition"] -comment: C-beta atoms from amino acid side-chains may be considered. subset: data -is_a: EDAM:0001481 ! Structure alignment (protein) +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) [Term] -id: EDAM:0001487 +id: EDAM_data:1487 name: Pairwise protein tertiary structure alignment (all atoms) namespace: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001485 ! Structure alignment (protein all atoms) +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) [Term] -id: EDAM:0001488 +id: EDAM_data:1488 name: Pairwise protein tertiary structure alignment (C-alpha atoms) namespace: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [EDAM:EBI "EMBRACE definition"] -comment: C-beta atoms from amino acid side-chains may be included. subset: data -is_obsolete: true -consider: EDAM:0001486 ! Structure alignment (protein C-alpha atoms) +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) [Term] -id: EDAM:0001489 +id: EDAM_data:1489 name: Multiple protein tertiary structure alignment (all atoms) namespace: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001485 ! Structure alignment (protein all atoms) +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) [Term] -id: EDAM:0001490 +id: EDAM_data:1490 name: Multiple protein tertiary structure alignment (C-alpha atoms) namespace: data -def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [EDAM:EBI "EMBRACE definition"] -comment: C-beta atoms from amino acid side-chains may be included. subset: data -is_obsolete: true -consider: EDAM:0001486 ! Structure alignment (protein C-alpha atoms) +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) [Term] -id: EDAM:0001491 +id: EDAM_data:1491 name: Structure alignment (nucleic acid pair) namespace: data -def: "Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001482 ! Structure alignment (nucleic acid) -is_a: EDAM:0001479 ! Structure alignment (pair) +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) [Term] -id: EDAM:0001492 +id: EDAM_data:1492 name: Multiple nucleic acid tertiary structure alignment namespace: data -def: "Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001482 ! Structure alignment (nucleic acid) +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) [Term] -id: EDAM:0001493 +id: EDAM_data:1493 name: Structure alignment (RNA) namespace: data -def: "Alignment (superimposition) of RNA tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001482 ! Structure alignment (nucleic acid) +def: "Alignment (superimposition) of RNA tertiary (3D) structures." [http://edamontology.org] +is_a: EDAM_data:1482 ! Structure alignment (nucleic acid) [Term] -id: EDAM:0000866 +id: EDAM_data:0866 name: Sequence alignment metadata namespace: data -def: "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000867 ! Sequence alignment report -is_a: EDAM:0002337 ! Metadata +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 [Term] -id: EDAM:0001414 +id: EDAM_data:1414 name: Sequence alignment metadata (quality report) namespace: data -def: "Data on molecular sequence alignment quality (estimated accuracy)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000867 ! Sequence alignment report +def: "Data on molecular sequence alignment quality (estimated accuracy)." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0867 ! Sequence alignment report [Term] -id: EDAM:0001415 +id: EDAM_data:1415 name: Sequence alignment report (site conservation) namespace: data -def: "Data on character conservation in a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] -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 term for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. subset: data -is_a: EDAM:0000867 ! Sequence alignment report +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 [Term] -id: EDAM:0001416 +id: EDAM_data:1416 name: Sequence alignment report (site correlation) namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000867 ! Sequence alignment report +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 [Term] -id: EDAM:0002242 +id: EDAM_data:2242 name: Phylogenetic property values namespace: data -def: "Phylogenetic property values data." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000871 ! Phylogenetic character data +def: "Phylogenetic property values data." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0871 ! Phylogenetic character data [Term] -id: EDAM:0001444 +id: EDAM_data:1444 name: Phylogenetic character contrasts namespace: data -def: "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Phylogenetic report (character contrasts)" EXACT [] -is_a: EDAM:0002523 ! Phylogenetic raw 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 [Term] -id: EDAM:0001426 +id: EDAM_data:1426 name: Phylogenetic continuous quantitative data namespace: data -def: "Continuous quantitative data that may be read during phylogenetic tree calculation." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Quantitative traits" EXACT [] -synonym: "Phylogenetic continuous quantitative characters" EXACT [] -is_a: EDAM:0000871 ! Phylogenetic character 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 [Term] -id: EDAM:0002873 +id: EDAM_data:2873 name: Phylogenetic gene frequencies data namespace: data -def: "Gene frequencies data that may be read during phylogenetic tree calculation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001426 ! Phylogenetic continuous quantitative 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 [Term] -id: EDAM:0001427 +id: EDAM_data:1427 name: Phylogenetic discrete data namespace: data -def: "Character data with discrete states that may be read during phylogenetic tree calculation." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Discretely coded characters" EXACT [] -synonym: "Discrete characters" EXACT [] -synonym: "Phylogenetic discrete states" EXACT [] -is_a: EDAM:0000871 ! Phylogenetic character 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 [Term] -id: EDAM:0002994 +id: EDAM_data:2994 name: Phylogenetic character weights namespace: data -def: "Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002523 ! Phylogenetic raw 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 [Term] -id: EDAM:0001428 +id: EDAM_data:1428 name: Phylogenetic character cliques namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Phylogenetic report (cliques)" EXACT [] -is_a: EDAM:0002523 ! Phylogenetic raw 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 [Term] -id: EDAM:0001429 +id: EDAM_data:1429 name: Phylogenetic invariants namespace: data -def: "Phylogenetic invariants data for testing alternative tree topologies." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Phylogenetic report (invariants)" EXACT [] -is_a: EDAM:0002523 ! Phylogenetic raw 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 [Term] -id: EDAM:0002247 +id: EDAM_data:2247 name: Phylogenetic consensus tree namespace: data -def: "A consensus phylogenetic tree derived from comparison of multiple trees." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000872 ! Phylogenetic tree +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 [Term] -id: EDAM:0001439 +id: EDAM_data:1439 name: DNA substitution model namespace: data -def: "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequence alignment report (DNA substitution model)" EXACT [] -synonym: "Phylogenetic tree report (DNA substitution model)" EXACT [] -is_a: EDAM:0001438 ! Phylogenetic tree report -is_a: EDAM:0000950 ! Biological model -is_a: EDAM:0000867 ! Sequence alignment report +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 [Term] -id: EDAM:0001440 +id: EDAM_data:1440 name: Phylogenetic tree report (tree shape) namespace: data -def: "Data about the shape of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic tree report +def: "Data about the shape of a phylogenetic tree." [http://edamontology.org] +is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] -id: EDAM:0001441 +id: EDAM_data:1441 name: Phylogenetic tree report (tree evaluation) namespace: data -def: "Data on the confidence of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic tree report +def: "Data on the confidence of a phylogenetic tree." [http://edamontology.org] +is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] -id: EDAM:0001442 +id: EDAM_data:1442 name: Phylogenetic tree report (tree distances) namespace: data -def: "Distances, such as Branch Score distance, between two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic tree report +def: "Distances, such as Branch Score distance, between two or more phylogenetic trees." [http://edamontology.org] +is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] -id: EDAM:0001443 +id: EDAM_data:1443 name: Phylogenetic tree report (tree stratigraphic) namespace: data -def: "Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic tree report +def: "Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis." [http://edamontology.org] +is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] -id: EDAM:0001446 +id: EDAM_data:1446 name: Comparison matrix (integers) namespace: data -def: "Matrix of integer numbers for sequence comparison." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Substitution matrix (integers)" EXACT [] -is_obsolete: true -consider: EDAM:0000874 ! Comparison matrix +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 [Term] -id: EDAM:0001447 +id: EDAM_data:1447 name: Comparison matrix (floats) namespace: data -def: "Matrix of floating point numbers for sequence comparison." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Substitution matrix (floats)" EXACT [] -is_obsolete: true -consider: EDAM:0000874 ! Comparison matrix +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 [Term] -id: EDAM:0001448 +id: EDAM_data:1448 name: Comparison matrix (nucleotide) namespace: data -def: "Matrix of integer or floating point numbers for nucleotide comparison." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Nucleotide substitution matrix" EXACT [] -is_a: EDAM:0000874 ! Comparison matrix +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 [Term] -id: EDAM:0001449 +id: EDAM_data:1449 name: Comparison matrix (amino acid) namespace: data -def: "Matrix of integer or floating point numbers for amino acid comparison." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Amino acid substitution matrix" EXACT [] -is_a: EDAM:0002016 ! Amino acid property -is_a: EDAM:0000874 ! Comparison matrix +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 [Term] -id: EDAM:0001450 +id: EDAM_data:1450 name: Nucleotide comparison matrix (integers) namespace: data -def: "Matrix of integer numbers for nucleotide comparison." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Nucleotide substitution matrix (integers)" EXACT [] -is_obsolete: true -consider: EDAM:0001448 ! Comparison matrix (nucleotide) +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) [Term] -id: EDAM:0001451 +id: EDAM_data:1451 name: Nucleotide comparison matrix (floats) namespace: data -def: "Matrix of floating point numbers for nucleotide comparison." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Nucleotide substitution matrix (floats)" EXACT [] -is_obsolete: true -consider: EDAM:0001448 ! Comparison matrix (nucleotide) +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) [Term] -id: EDAM:0001452 +id: EDAM_data:1452 name: Amino acid comparison matrix (integers) namespace: data -def: "Matrix of integer numbers for amino acid comparison." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Amino acid substitution matrix (integers)" EXACT [] -is_obsolete: true -consider: EDAM:0001449 ! Comparison matrix (amino acid) +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) [Term] -id: EDAM:0001453 +id: EDAM_data:1453 name: Amino acid comparison matrix (floats) namespace: data -def: "Matrix of floating point numbers for amino acid comparison." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Amino acid substitution matrix (floats)" EXACT [] -is_obsolete: true -consider: EDAM:0001449 ! Comparison matrix (amino acid) +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) [Term] -id: EDAM:0001540 +id: EDAM_data:1540 name: Protein residue interactions namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Residue interaction data" EXACT [] -synonym: "Atom interaction data" EXACT [] -is_a: EDAM:0002599 ! Molecular interaction -is_a: EDAM:0000906 ! Protein interaction -relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis +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 [Term] -id: EDAM:0001543 +id: EDAM_data:1543 name: Protein surface report namespace: data -def: "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Protein structure report (surface)" EXACT [] -is_a: EDAM:0001542 ! Protein solvent accessibility -is_a: EDAM:0001537 ! Protein structure report +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 [Term] -id: EDAM:0000875 +id: EDAM_data:0875 name: Protein topology namespace: data -def: "Predicted or actual protein topology represented as a string of protein secondary structure elements." [EDAM:EBI "EMBRACE definition"] -comment: The location and size of the secondary structure elements and intervening loop regions is usually indicated. subset: data -is_obsolete: true -consider: EDAM:0000876 ! Protein features (secondary structure) +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) [Term] -id: EDAM:0002081 +id: EDAM_data:2081 name: Secondary structure namespace: data -def: "The secondary structure assignment (predicted or real) of a nucleic acid or protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0000877 +id: EDAM_data:0877 name: Protein features (super-secondary) namespace: data -def: "A report of predicted or actual super-secondary structure of protein sequence(s)." [EDAM:EBI "EMBRACE definition"] -comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. subset: data -synonym: "Protein structure report (super-secondary)" EXACT [] -is_a: EDAM:0001277 ! Protein features -is_a: EDAM:0001537 ! Protein structure report +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 [Term] -id: EDAM:0000902 +id: EDAM_data:0902 name: Protein architecture report namespace: data -def: "An informative report on architecture (spatial arrangement of secondary structure) of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein structure report (architecture)" EXACT [] -synonym: "Protein property (architecture)" EXACT [] -is_a: EDAM:0000897 ! Protein property -is_a: EDAM:0001537 ! Protein structure report +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 [Term] -id: EDAM:0000883 -name: Structure +id: EDAM_data:0883 +name: Structure data namespace: data -def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [EDAM:EBI "EMBRACE definition"] -comment: The coordinate data may be predicted or real. subset: data -relationship: has_topic EDAM:0000081 ! Structure analysis -is_a: EDAM:0003031 ! Core data +def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [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 [Term] -id: EDAM:0000884 +id: EDAM_data:0884 name: Tertiary structure record namespace: data -def: "An entry from a molecular tertiary (3D) structure database." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000883 ! Structure +def: "An entry from a molecular tertiary (3D) structure database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0883 ! Structure [Term] -id: EDAM:0001546 +id: EDAM_data:1546 name: Protein distance matrix namespace: data -def: "A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001540 ! Protein residue interactions +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 [Term] -id: EDAM:0001547 +id: EDAM_data:1547 name: Protein contact map namespace: data -def: "An amino acid residue contact map for a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001540 ! Protein residue interactions +def: "An amino acid residue contact map for a protein structure." [http://edamontology.org] +is_a: EDAM_data:1540 ! Protein residue interactions [Term] -id: EDAM:0001548 +id: EDAM_data:1548 name: Protein residue 3D cluster namespace: data -def: "Report on clusters of contacting residues in protein structures such as a key structural residue network." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001540 ! Protein residue interactions +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 [Term] -id: EDAM:0001549 +id: EDAM_data:1549 name: Protein hydrogen bonds namespace: data -def: "Patterns of hydrogen bonding in protein structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001540 ! Protein residue interactions +def: "Patterns of hydrogen bonding in protein structures." [http://edamontology.org] +is_a: EDAM_data:1540 ! Protein residue interactions [Term] -id: EDAM:0001550 +id: EDAM_data:1550 name: Protein non-canonical interactions namespace: data -def: "Non-canonical atomic interactions in protein structures." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein non-canonical interactions report" EXACT [] -is_a: EDAM:0001540 ! Protein residue interactions -is_a: EDAM:0001539 ! Protein structural quality report +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 [Term] -id: EDAM:0001542 +id: EDAM_data:1542 name: Protein solvent accessibility namespace: data -def: "Data on the solvent accessible or buried surface area of a protein structure." [EDAM:EBI "EMBRACE definition"] -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 term covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. subset: data -is_a: EDAM:0001540 ! Protein residue interactions +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 [Term] -id: EDAM:0000876 +id: EDAM_data:0876 name: Protein features (secondary structure) namespace: data -def: "Secondary structure assignment (predicted or real) of a protein." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Protein secondary structure" EXACT [] -is_a: EDAM:0002081 ! Secondary structure -is_a: EDAM:0001277 ! Protein features -relationship: has_topic EDAM:0000694 ! Protein secondary structure +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 [Term] -id: EDAM:0000880 -name: RNA secondary structure +id: EDAM_data:0880 +name: RNA secondary structure record namespace: data -def: "An informative report of secondary structure (predicted or real) of an RNA molecule." [EDAM:EBI "EMBRACE definition"] -comment: This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. 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:0002081 ! Secondary structure -relationship: has_topic EDAM:0000697 ! RNA structure and alignment +is_a: EDAM_data:2081 ! Secondary structure record +relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] -id: EDAM:0001456 +id: EDAM_data:1456 name: Protein features (membrane regions) namespace: data -def: "An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Transmembrane region report" EXACT [] -synonym: "Intramembrane region report" EXACT [] -synonym: "Protein report (membrane protein)" EXACT [] -is_a: EDAM:0001277 ! Protein features +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 [Term] -id: EDAM:0001755 +id: EDAM_data:1755 name: Protein atom namespace: data -def: "Data on a single atom from a protein structure." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Atom data" EXACT [] -is_a: EDAM:0001460 ! Protein structure +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 [Term] -id: EDAM:0001756 +id: EDAM_data:1756 name: Protein residue namespace: data -def: "Data on a single amino acid residue position in a protein structure." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Residue" EXACT [] -is_a: EDAM:0001460 ! Protein structure +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 [Term] -id: EDAM:0001459 +id: EDAM_data:1459 name: Nucleic acid structure namespace: data -def: "3D coordinate and associated data for a nucleic acid tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000883 ! Structure -relationship: has_topic EDAM:0000097 ! Nucleic acid structure analysis +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 [Term] -id: EDAM:0001460 +id: EDAM_data:1460 name: Protein structure namespace: data -def: "3D coordinate and associated data for a protein tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000883 ! Structure -relationship: has_topic EDAM:0002814 ! Protein structure analysis -relationship: has_topic EDAM:0000698 ! Protein tertiary structure +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 [Term] -id: EDAM:0001461 +id: EDAM_data:1461 name: Protein-ligand complex namespace: 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." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001460 ! Protein structure +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 [Term] -id: EDAM:0001462 +id: EDAM_data:1462 name: Carbohydrate structure namespace: data -def: "3D coordinate and associated data for a carbohydrate (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000883 ! Structure -relationship: has_topic EDAM:0000152 ! Carbohydrates -relationship: has_topic EDAM:0000153 ! Lipids +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 [Term] -id: EDAM:0002850 +id: EDAM_data:2850 name: Lipid structure namespace: data -def: "3D coordinate and associated data for a lipid structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000883 ! Structure +def: "3D coordinate and associated data for a lipid structure." [http://edamontology.org] +is_a: EDAM_data:0883 ! Structure [Term] -id: EDAM:0001463 +id: EDAM_data:1463 name: Small molecule structure namespace: data -def: "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000883 ! Structure -relationship: has_topic EDAM:0000154 ! Small molecules +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 [Term] -id: EDAM:0002851 +id: EDAM_data:2851 name: Drug structure namespace: data -def: "3D coordinate and associated data for the (3D) structure of a drug." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001463 ! Small molecule structure +def: "3D coordinate and associated data for the (3D) structure of a drug." [http://edamontology.org] +is_a: EDAM_data:1463 ! Small molecule structure [Term] -id: EDAM:0002852 +id: EDAM_data:2852 name: Toxin structure namespace: data -def: "3D coordinate and associated data for the (3D) structure of a toxin." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001463 ! Small molecule structure +def: "3D coordinate and associated data for the (3D) structure of a toxin." [http://edamontology.org] +is_a: EDAM_data:1463 ! Small molecule structure [Term] -id: EDAM:0001464 +id: EDAM_data:1464 name: DNA structure namespace: data -def: "3D coordinate and associated data for a DNA tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001459 ! Nucleic acid structure +def: "3D coordinate and associated data for a DNA tertiary (3D) structure." [http://edamontology.org] +is_a: EDAM_data:1459 ! Nucleic acid structure [Term] -id: EDAM:0001465 -name: RNA structure +id: EDAM_data:1465 +name: RNA structure record namespace: data -def: "3D coordinate and associated data for an RNA tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001459 ! Nucleic acid structure -relationship: has_topic EDAM:0000697 ! RNA structure and alignment +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 [Term] -id: EDAM:0001466 -name: tRNA structure +id: EDAM_data:1466 +name: tRNA structure record namespace: data -def: "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001465 ! RNA structure +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 [Term] -id: EDAM:0001467 +id: EDAM_data:1467 name: Protein chain namespace: data -def: "3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001460 ! Protein structure +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 [Term] -id: EDAM:0001468 +id: EDAM_data:1468 name: Protein domain namespace: data -def: "3D coordinate and associated data for the tertiary (3D) structure of a protein domain." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001460 ! Protein structure -relationship: has_topic EDAM:0000736 ! Protein domains and folds +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 [Term] -id: EDAM:0002877 +id: EDAM_data:2877 name: Protein complex namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001460 ! Protein structure +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 [Term] -id: EDAM:0002878 +id: EDAM_data:2878 name: Protein structural motif namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001460 ! Protein structure +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 [Term] -id: EDAM:0001469 +id: EDAM_data:1469 name: Protein structure (all atoms) namespace: data -def: "3D coordinate and associated data for a protein tertiary (3D) structure (all atoms)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001460 ! Protein structure +def: "3D coordinate and associated data for a protein tertiary (3D) structure (all atoms)." [http://edamontology.org] +is_a: EDAM_data:1460 ! Protein structure [Term] -id: EDAM:0001470 +id: EDAM_data:1470 name: Protein structure (C-alpha atoms) namespace: data -def: "3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only)." [EDAM:EBI "EMBRACE definition"] -comment: C-beta atoms from amino acid side-chains may be included. subset: data -is_a: EDAM:0001460 ! Protein structure +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 [Term] -id: EDAM:0001471 +id: EDAM_data:1471 name: Protein chain (all atoms) namespace: data -def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001467 ! Protein chain -consider: EDAM:0001469 ! Protein structure (all atoms) +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) [Term] -id: EDAM:0001472 +id: EDAM_data:1472 name: Protein chain (C-alpha atoms) namespace: data -def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only)." [EDAM:EBI "EMBRACE definition"] -comment: C-beta atoms from amino acid side-chains may be included. subset: data -is_obsolete: true -consider: EDAM:0001467 ! Protein chain -consider: EDAM:0001470 ! Protein structure (C-alpha atoms) +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) [Term] -id: EDAM:0001473 +id: EDAM_data:1473 name: Protein domain (all atoms) namespace: data -def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001468 ! Protein domain -consider: EDAM:0001469 ! Protein structure (all atoms) +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) [Term] -id: EDAM:0001474 +id: EDAM_data:1474 name: Protein domain (C-alpha atoms) namespace: data -def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only)." [EDAM:EBI "EMBRACE definition"] -comment: C-beta atoms from amino acid side-chains may be included. subset: data -is_obsolete: true -consider: EDAM:0001468 ! Protein domain -consider: EDAM:0001470 ! Protein structure (C-alpha atoms) +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) [Term] -id: EDAM:0001495 +id: EDAM_data:1495 name: DaliLite hit table namespace: data -def: "DaliLite hit table of protein chain tertiary structure alignment data." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0000887 ! Structure alignment report +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 [Term] -id: EDAM:0001499 +id: EDAM_data:1499 name: 3D-1D scoring matrix namespace: data -def: "A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000892 ! Protein sequence-structure scoring matrix +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 [Term] -id: EDAM:0000894 +id: EDAM_data:0894 name: Amino acid annotation namespace: data -def: "An informative report about a specific amino acid." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002016 ! Amino acid property -is_a: EDAM:0000962 ! Small molecule annotation +def: "An informative report about a specific amino acid." [http://edamontology.org] +is_a: EDAM_data:2016 ! Amino acid property +is_a: EDAM_data:0962 ! Small molecule annotation [Term] -id: EDAM:0001501 +id: EDAM_data:1501 name: Amino acid index namespace: data -def: "A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002016 ! Amino acid property -is_a: EDAM:0002082 ! Matrix +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 [Term] -id: EDAM:0001503 +id: EDAM_data:1503 name: Amino acid pair-wise contact potentials namespace: data -def: "Statistical protein contact potentials." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002016 ! Amino acid property +def: "Statistical protein contact potentials." [http://edamontology.org] +is_a: EDAM_data:2016 ! Amino acid property [Term] -id: EDAM:0001502 +id: EDAM_data:1502 name: Amino acid index (chemical classes) namespace: data -def: "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001501 ! Amino acid index +def: "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." [http://edamontology.org] +is_a: EDAM_data:1501 ! Amino acid index [Term] -id: EDAM:0001505 +id: EDAM_data:1505 name: Amino acid index (molecular weight) namespace: data -def: "Molecular weights of amino acids." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001501 ! Amino acid index +def: "Molecular weights of amino acids." [http://edamontology.org] +is_a: EDAM_data:1501 ! Amino acid index [Term] -id: EDAM:0001506 +id: EDAM_data:1506 name: Amino acid index (hydropathy) namespace: data -def: "Hydrophobic, hydrophilic or charge properties of amino acids." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001501 ! Amino acid index +def: "Hydrophobic, hydrophilic or charge properties of amino acids." [http://edamontology.org] +is_a: EDAM_data:1501 ! Amino acid index [Term] -id: EDAM:0001507 +id: EDAM_data:1507 name: Amino acid index (White-Wimley data) namespace: data -def: "Experimental free energy values for the water-interface and water-octanol transitions for the amino acids." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001501 ! Amino acid index +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 [Term] -id: EDAM:0001508 +id: EDAM_data:1508 name: Amino acid index (van der Waals radii) namespace: data -def: "Van der Waals radii of atoms for different amino acid residues." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001501 ! Amino acid index +def: "Van der Waals radii of atoms for different amino acid residues." [http://edamontology.org] +is_a: EDAM_data:1501 ! Amino acid index [Term] -id: EDAM:0001509 +id: EDAM_data:1509 name: Enzyme property namespace: data -def: "An informative report on a specific enzyme." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Enzyme report" EXACT [] -synonym: "Protein report (enzyme)" EXACT [] -is_a: EDAM:0000897 ! Protein property -relationship: has_topic EDAM:0000821 ! Enzymes and reactions +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 [Term] -id: EDAM:0001776 +id: EDAM_data:1776 name: Protein report (function) namespace: data -def: "Report on general functional properties of specific protein(s)." [EDAM:EBI "EMBRACE definition"] -comment: For properties that can be mapped to a sequence, use 'Sequence report' instead. subset: data -is_obsolete: true -consider: EDAM:0000896 ! Protein report +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 [Term] -id: EDAM:0002722 +id: EDAM_data:2722 name: Protein features (disordered structure) namespace: data -def: "An informative report about disordered structure in a protein." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein structure report (disordered structure)" EXACT [] -is_a: EDAM:0001277 ! Protein features -is_a: EDAM:0001537 ! Protein structure report +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 [Term] -id: EDAM:0002147 +id: EDAM_data:2147 name: Protein report (transcription factor) namespace: data -def: "An informative report on a transcription factor protein." [EDAM:EBI "EMBRACE definition"] -comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. subset: data -synonym: "Transcription factor binding site data" EXACT [] -is_obsolete: true -consider: EDAM:0000896 ! Protein report +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 [Term] -id: EDAM:0002401 +id: EDAM_data:2401 name: Protein report (membrane protein) namespace: data -def: "An informative report on a membrane protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001456 ! Protein features (membrane regions) +def: "An informative report on a membrane protein." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1456 ! Protein features (membrane regions) [Term] -id: EDAM:0001517 +id: EDAM_data:1517 name: Restriction enzyme property namespace: data -alt_id: EDAM:0001510 -alt_id: EDAM:0001518 -def: "An informative report on a specific restriction enzyme such as enzyme reference data." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Restriction enzyme report" EXACT [] -synonym: "Restriction enzyme pattern data" EXACT [] -synonym: "Protein report (restriction enzyme)" EXACT [] -is_a: EDAM:0001509 ! Enzyme property +! 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 [Term] -id: EDAM:0001533 +id: EDAM_data:1533 name: Protein subcellular localization namespace: data -def: "An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein report (subcellular localization)" EXACT [] -is_obsolete: true -consider: EDAM:0000896 ! Protein report +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 [Term] -id: EDAM:0002191 -name: Protein features (checmical modification) +id: EDAM_data:2191 +name: Protein features (chemical modification) namespace: data -def: "Data on a chemical modification of a protein." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein modification annotation" EXACT [] -is_a: EDAM:0001277 ! Protein features +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 [Term] -id: EDAM:0002991 +id: EDAM_data:2991 name: Protein torsion angle data namespace: data -def: "Torsion angle data for a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Torsion angle data" EXACT [] -is_a: EDAM:0000897 ! Protein property +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 [Term] -id: EDAM:0001544 +id: EDAM_data:1544 name: Ramachandran plot namespace: data -def: "Phi/psi angle data or a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002991 ! Protein torsion angle 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 [Term] -id: EDAM:0001545 +id: EDAM_data:1545 name: Protein dipole moment namespace: data -def: "Data on the net charge distribution (dipole moment) of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +def: "Data on the net charge distribution (dipole moment) of a protein structure." [http://edamontology.org] +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM:0001519 +id: EDAM_data:1519 name: Peptide molecular weights namespace: data -alt_id: EDAM:0001535 -def: "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents." [EDAM:EBI "EMBRACE definition"] -comment: The report might include associated data such as frequency of peptide fragment molecular weights. subset: data -is_a: EDAM:0000897 ! Protein property +! 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 [Term] -id: EDAM:0001520 +id: EDAM_data:1520 name: Peptide hydrophobic moment namespace: data -def: "Report on the hydrophobic moment of a polypeptide sequence." [EDAM:EBI "EMBRACE definition"] -comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: data -is_a: EDAM:0002970 ! Protein hydropathy 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 [Term] -id: EDAM:0002970 +id: EDAM_data:2970 name: Protein hydropathy data namespace: data -def: "A report on protein properties concerning hydropathy." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein hydropathy report" EXACT [] -is_a: EDAM:0000897 ! Protein property +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 [Term] -id: EDAM:0001521 +id: EDAM_data:1521 name: Protein aliphatic index namespace: data -def: "The aliphatic index of a protein." [EDAM:EBI "EMBRACE definition"] -comment: The aliphatic index is the relative protein volume occupied by aliphatic side chains. subset: data -is_a: EDAM:0002970 ! Protein hydropathy 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 [Term] -id: EDAM:0002164 +id: EDAM_data:2164 name: Protein sequence properties plot namespace: data -def: "A plot of general physicochemical properties of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000897 ! Protein property +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 [Term] -id: EDAM:0002165 +id: EDAM_data:2165 name: Protein ionization curve namespace: data -def: "A plot of pK versus pH for a protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +def: "A plot of pK versus pH for a protein." [http://edamontology.org] +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM:0001522 +id: EDAM_data:1522 name: Protein sequence hydropathy plot namespace: data -def: "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc." [EDAM:EBI "EMBRACE definition"] -comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: data -is_a: EDAM:0002970 ! Protein hydropathy 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 [Term] -id: EDAM:0001523 +id: EDAM_data:1523 name: Protein charge plot namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +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 [Term] -id: EDAM:0001524 +id: EDAM_data:1524 name: Protein solubility namespace: data -def: "The solubility or atomic solvation energy of a protein sequence or structure." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein solubility data" EXACT [] -is_a: EDAM:0002970 ! Protein hydropathy 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 [Term] -id: EDAM:0001525 +id: EDAM_data:1525 name: Protein crystallizability namespace: data -def: "Data on the crystallizability of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein crystallizability data" EXACT [] -is_a: EDAM:0002970 ! Protein hydropathy 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 [Term] -id: EDAM:0001526 +id: EDAM_data:1526 name: Protein globularity namespace: data -def: "Data on the stability, intrinsic disorder or globularity of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein globularity data" EXACT [] -is_a: EDAM:0002970 ! Protein hydropathy 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 [Term] -id: EDAM:0001527 +id: EDAM_data:1527 name: Protein titration curve namespace: data -def: "The titration curve of a protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +def: "The titration curve of a protein." [http://edamontology.org] +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM:0001528 +id: EDAM_data:1528 name: Protein isoelectric point namespace: data -def: "The isoelectric point of one proteins." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +def: "The isoelectric point of one proteins." [http://edamontology.org] +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM:0001529 +id: EDAM_data:1529 name: Protein pKa value namespace: data -def: "The pKa value of a protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +def: "The pKa value of a protein." [http://edamontology.org] +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM:0001530 +id: EDAM_data:1530 name: Protein hydrogen exchange rate namespace: data -def: "The hydrogen exchange rate of a protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +def: "The hydrogen exchange rate of a protein." [http://edamontology.org] +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM:0001531 +id: EDAM_data:1531 name: Protein extinction coefficient namespace: data -def: "The extinction coefficient of a protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +def: "The extinction coefficient of a protein." [http://edamontology.org] +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM:0001532 +id: EDAM_data:1532 name: Protein optical density namespace: data -def: "The optical density of a protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +def: "The optical density of a protein." [http://edamontology.org] +is_a: EDAM_data:0897 ! Protein property [Term] -id: EDAM:0001534 +id: EDAM_data:1534 name: Peptide immunogenicity data namespace: data -def: "An report on allergenicity / immunogenicity of peptides and proteins." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Peptide immunogenicity report" EXACT [] -synonym: "Peptide immunogenicity" EXACT [] -is_a: EDAM:0000897 ! Protein property +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 [Term] -id: EDAM:0002957 +id: EDAM_data:2957 name: Hopp and Woods plot namespace: data -def: "A Hopp and Woods plot of predicted antigenicity of a peptide or protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001534 ! Peptide immunogenicity 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 [Term] -id: EDAM:0001536 +id: EDAM_data:1536 name: MHC peptide immunogenicity report namespace: data -def: "A report on the immunogenicity of MHC class I or class II binding peptides." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001534 ! Peptide immunogenicity 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 [Term] -id: EDAM:0002753 +id: EDAM_data:2753 name: Carbohydrate conformational map namespace: data -def: "A conformational energy map of the glycosidic linkages in a carbohydrate molecule." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002313 ! Carbohydrate structure report +def: "A conformational energy map of the glycosidic linkages in a carbohydrate molecule." [http://edamontology.org] +is_a: EDAM_data:2313 ! Carbohydrate structure report [Term] -id: EDAM:0000899 +id: EDAM_data:0899 name: Protein features (3D motif) namespace: data -def: "An informative report on the 3D structural motifs in a protein." [EDAM:EBI "EMBRACE definition"] -comment: This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. subset: data -synonym: "Protein structure report (3D motif)" EXACT [] -is_a: EDAM:0001277 ! Protein features -is_a: EDAM:0001537 ! Protein structure report -relationship: has_topic EDAM:0000166 ! Protein structural motifs and surfaces +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 [Term] -id: EDAM:0001539 +id: EDAM_data:1539 name: Protein structural quality report namespace: data -def: "Report on the quality of a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] -comment: Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. subset: data -synonym: "Protein structure report (quality evaluation)" EXACT [] -synonym: "Protein report (structural quality)" EXACT [] -synonym: "Protein property (structural quality)" EXACT [] -is_a: EDAM:0000897 ! Protein property -is_a: EDAM:0001537 ! Protein structure report +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 [Term] -id: EDAM:0001541 +id: EDAM_data:1541 name: Protein flexibility or motion report namespace: data -def: "Informative report on flexibility or motion of a protein structure." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Protein structure report (flexibility or motion)" EXACT [] -synonym: "Protein property (flexibility or motion)" EXACT [] -synonym: "Protein flexibility or motion" EXACT [] -is_a: EDAM:0000897 ! Protein property -is_a: EDAM:0001537 ! Protein structure report +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 [Term] -id: EDAM:0002235 +id: EDAM_data:2235 name: Raw SCOP domain classification namespace: data -def: "Raw SCOP domain classification data files." [EDAM:EBI "EMBRACE definition"] -comment: These are the parsable data files provided by SCOP. subset: data -is_obsolete: true -consider: EDAM:0000900 ! Protein domain classification +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 [Term] -id: EDAM:0002236 +id: EDAM_data:2236 name: Raw CATH domain classification namespace: data -def: "Raw CATH domain classification data files." [EDAM:EBI "EMBRACE definition"] -comment: These are the parsable data files provided by CATH. subset: data -is_obsolete: true -consider: EDAM:0000900 ! Protein domain classification +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 [Term] -id: EDAM:0001762 +id: EDAM_data:1762 name: CATH domain report namespace: data -def: "Summary of domain classification information for a CATH domain." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0000900 ! Protein domain classification +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 [Term] -id: EDAM:0001553 +id: EDAM_data:1553 name: CATH node namespace: data -def: "Information on a node from the CATH database." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "CATH classification node report" EXACT [] -is_a: EDAM:0003101 ! Protein domain classification node +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 [Term] -id: EDAM:0001554 +id: EDAM_data:1554 name: SCOP node namespace: data -def: "Information on a node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "SCOP classification node" EXACT [] -is_a: EDAM:0003101 ! Protein domain classification node +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 [Term] -id: EDAM:0003141 +id: EDAM_data:3141 !{since=beta13} name: SCOP class namespace: data -def: "Information on a 'class' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001554 ! SCOP node +def: "Information on a 'class' node from the SCOP database." [http://edamontology.org] +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM:0003142 +id: EDAM_data:3142 !{since=beta13} name: SCOP fold namespace: data -def: "Information on a 'fold' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001554 ! SCOP node +def: "Information on a 'fold' node from the SCOP database." [http://edamontology.org] +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM:0003143 +id: EDAM_data:3143 !{since=beta13} name: SCOP superfamily namespace: data -def: "Information on a 'superfamily' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001554 ! SCOP node +def: "Information on a 'superfamily' node from the SCOP database." [http://edamontology.org] +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM:0003144 +id: EDAM_data:3144 !{since=beta13} name: SCOP family namespace: data -def: "Information on a 'family' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001554 ! SCOP node +def: "Information on a 'family' node from the SCOP database." [http://edamontology.org] +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM:0003145 +id: EDAM_data:3145 !{since=beta13} name: SCOP protein namespace: data -def: "Information on a 'protein' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001554 ! SCOP node +def: "Information on a 'protein' node from the SCOP database." [http://edamontology.org] +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM:0003146 +id: EDAM_data:3146 !{since=beta13} name: SCOP species namespace: data -def: "Information on a 'species' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001554 ! SCOP node +def: "Information on a 'species' node from the SCOP database." [http://edamontology.org] +is_a: EDAM_data:1554 ! SCOP node [Term] -id: EDAM:0001555 +id: EDAM_data:1555 name: EMBASSY domain classification namespace: data -def: "An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000900 ! Protein domain classification +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 [Term] -id: EDAM:0001556 +id: EDAM_data:1556 name: CATH class namespace: data -def: "Information on a protein 'class' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001553 ! CATH node +def: "Information on a protein 'class' node from the CATH database." [http://edamontology.org] +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM:0001557 +id: EDAM_data:1557 name: CATH architecture namespace: data -def: "Information on a protein 'architecture' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001553 ! CATH node +def: "Information on a protein 'architecture' node from the CATH database." [http://edamontology.org] +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM:0001558 +id: EDAM_data:1558 name: CATH topology namespace: data -def: "Information on a protein 'topology' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001553 ! CATH node +def: "Information on a protein 'topology' node from the CATH database." [http://edamontology.org] +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM:0001559 +id: EDAM_data:1559 name: CATH homologous superfamily namespace: data -def: "Information on a protein 'homologous superfamily' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001553 ! CATH node +def: "Information on a protein 'homologous superfamily' node from the CATH database." [http://edamontology.org] +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM:0001560 +id: EDAM_data:1560 name: CATH structurally similar group namespace: data -def: "Information on a protein 'structurally similar group' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001553 ! CATH node +def: "Information on a protein 'structurally similar group' node from the CATH database." [http://edamontology.org] +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM:0001561 +id: EDAM_data:1561 name: CATH functional category namespace: data -def: "Information on a protein 'functional category' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001553 ! CATH node +def: "Information on a protein 'functional category' node from the CATH database." [http://edamontology.org] +is_a: EDAM_data:1553 ! CATH node [Term] -id: EDAM:0001565 +id: EDAM_data:1565 name: Protein-protein interaction namespace: data -alt_id: EDAM:0002712 -def: "Data on protein-protein interaction(s)." [EDAM:EBI "EMBRACE definition"] -comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains). subset: data -synonym: "Protein structure report (protein complex)" EXACT [] -is_a: EDAM:0000906 ! Protein report (interaction) -relationship: has_topic EDAM:0000147 ! Protein-protein interactions +! 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 report (interaction) +relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] -id: EDAM:0001566 +id: EDAM_data:1566 name: Protein-ligand interaction namespace: data -def: "Data on protein-ligand (small molecule) interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000906 ! Protein report (interaction) -relationship: has_topic EDAM:0000148 ! Protein-ligand interactions +def: "Data on protein-ligand (small molecule) interaction(s)." [http://edamontology.org] +is_a: EDAM_data:0906 ! Protein report (interaction) +relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] -id: EDAM:0001567 +id: EDAM_data:1567 name: Protein-nucleic acid interaction namespace: data -def: "Data on protein-DNA/RNA interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000906 ! Protein report (interaction) -relationship: has_topic EDAM:0000149 ! Protein-nucleic acid interactions +def: "Data on protein-DNA/RNA interaction(s)." [http://edamontology.org] +is_a: EDAM_data:0906 ! Protein report (interaction) +relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions [Term] -id: EDAM:0002359 +id: EDAM_data:2359 name: Domain-domain interaction namespace: data -def: "Data on protein domain-protein domain interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001565 ! Protein-protein interaction +def: "Data on protein domain-protein domain interaction(s)." [http://edamontology.org] +is_a: EDAM_data:1565 ! Protein-protein interaction [Term] -id: EDAM:0002378 +id: EDAM_data:2378 name: Protein-motif interaction namespace: data -def: "Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001565 ! Protein-protein interaction +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 [Term] -id: EDAM:0002360 +id: EDAM_data:2360 name: Domain-domain interaction (indirect) namespace: data -def: "Data on indirect protein domain-protein domain interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002359 ! Domain-domain interaction +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 [Term] -id: EDAM:0002402 +id: EDAM_data:2402 name: Protein-drug interaction namespace: data -def: "Informative report on protein-drug interaction(s) including binding affinity data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001566 ! Protein ligand interaction +def: "Informative report on protein-drug interaction(s) including binding affinity data." [http://edamontology.org] +is_a: EDAM_data:1566 ! Protein ligand interaction [Term] -id: EDAM:0002358 +id: EDAM_data:2358 name: Domain-nucleic acid interaction namespace: data -def: "Data on protein domain-DNA/RNA interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001567 ! Protein-nucleic acid interaction +def: "Data on protein domain-DNA/RNA interaction(s)." [http://edamontology.org] +is_a: EDAM_data:1567 ! Protein-nucleic acid interaction [Term] -id: EDAM:0002025 +id: EDAM_data:2025 name: Michaelis Menten plot namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002024 ! Enzyme kinetics 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 [Term] -id: EDAM:0002026 +id: EDAM_data:2026 name: Hanes Woolf plot namespace: 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)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002024 ! Enzyme kinetics 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 [Term] -id: EDAM:0000909 +id: EDAM_data:0909 name: Vmax namespace: data -def: "The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002024 ! Enzyme kinetics 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 [Term] -id: EDAM:0000910 +id: EDAM_data:0910 name: Km namespace: data -def: "Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002024 ! Enzyme kinetics 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 [Term] -id: EDAM:0002720 +id: EDAM_data:2720 name: Dinucleotide property namespace: data -def: "Physicochemical property data for one or more dinucleotides." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002088 ! DNA base structural data +def: "Physicochemical property data for one or more dinucleotides." [http://edamontology.org] +is_a: EDAM_data:2088 ! DNA base structural data -[Term] -id: EDAM:0003149 -name: Nucleic acid property (sequence) -namespace: data -def: "A non-positional property of a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] -subset: data -synonym: "Nucleic acid sequence property" EXACT [] -is_obsolete: true -consider: EDAM:0000912 ! Nucleic acid property +! [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 [Term] -id: EDAM:0002985 +id: EDAM_data:2985 name: Nucleic acid thermodynamic data namespace: data -def: "A thermodynamic or kinetic property of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Nucleic acid property (thermodynamic or kinetic)" EXACT [] -synonym: "Nucleic acid thermodynamic property" EXACT [] -is_a: EDAM:0000912 ! Nucleic acid property +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 [Term] -id: EDAM:0001583 +id: EDAM_data:1583 name: Nucleic acid melting profile namespace: data -def: "Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Nucleic acid stability profile" EXACT [] -is_a: EDAM:0002985 ! Nucleic acid thermodynamic 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 [Term] -id: EDAM:0001584 +id: EDAM_data:1584 name: Nucleic acid enthalpy namespace: data -def: "Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002985 ! Nucleic acid thermodynamic 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 [Term] -id: EDAM:0001585 +id: EDAM_data:1585 name: Nucleic acid entropy namespace: data -def: "Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002985 ! Nucleic acid thermodynamic 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 [Term] -id: EDAM:0001586 +id: EDAM_data:1586 name: Nucleic acid melting temperature namespace: data -def: "Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002139 ! Nucleic acid melting temperature +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 [Term] -id: EDAM:0002088 +id: EDAM_data:2088 name: DNA base structural data namespace: data -def: "Structural data for DNA base pairs or runs of bases, such as energy or angle data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000912 ! Nucleic acid property -is_a: EDAM:0002086 ! Nucleic acid structure report +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 [Term] -id: EDAM:0002167 +id: EDAM_data:2167 name: Nucleic acid density plot namespace: data -def: "Density plot (of base composition) for a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000912 ! Nucleic acid property +def: "Density plot (of base composition) for a nucleotide sequence." [http://edamontology.org] +is_a: EDAM_data:0912 ! Nucleic acid property [Term] -id: EDAM:0001587 +id: EDAM_data:1587 name: Nucleic acid stitch profile namespace: data -def: "Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001583 ! Nucleic acid melting profile +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 [Term] -id: EDAM:0002958 +id: EDAM_data:2958 name: Nucleic acid melting curve namespace: data -def: "A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [EDAM:EBI "EMBRACE definition"] -comment: Shows the proportion of nucleic acid which are double-stranded versus temperature. subset: data -is_a: EDAM:0001583 ! Nucleic acid melting profile +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 [Term] -id: EDAM:0002959 +id: EDAM_data:2959 name: Nucleic acid probability profile namespace: data -def: "A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [EDAM:EBI "EMBRACE definition"] -comment: Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature subset: data -is_a: EDAM:0001583 ! Nucleic acid melting profile +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 [Term] -id: EDAM:0002960 +id: EDAM_data:2960 name: Nucleic acid temperature profile namespace: data -def: "A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [EDAM:EBI "EMBRACE definition"] -comment: Plots melting temperature versus base position. subset: data -synonym: "Melting map" EXACT [] -is_a: EDAM:0001583 ! Nucleic acid melting profile +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 [Term] -id: EDAM:0001594 +id: EDAM_data:1594 name: Vienna RNA calculated energy namespace: data -def: "RNA calculated energy data generated by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001584 ! Nucleic acid enthalpy +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 [Term] -id: EDAM:0001588 +id: EDAM_data:1588 name: DNA base pair stacking energies data namespace: data -def: "DNA base pair stacking energies data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002088 ! DNA base structural data +def: "DNA base pair stacking energies data." [http://edamontology.org] +is_a: EDAM_data:2088 ! DNA base structural data [Term] -id: EDAM:0001589 +id: EDAM_data:1589 name: DNA base pair twist angle data namespace: data -def: "DNA base pair twist angle data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002088 ! DNA base structural data +def: "DNA base pair twist angle data." [http://edamontology.org] +is_a: EDAM_data:2088 ! DNA base structural data [Term] -id: EDAM:0001590 +id: EDAM_data:1590 name: DNA base trimer roll angles data namespace: data -def: "DNA base trimer roll angles data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002088 ! DNA base structural data +def: "DNA base trimer roll angles data." [http://edamontology.org] +is_a: EDAM_data:2088 ! DNA base structural data [Term] -id: EDAM:0001595 +id: EDAM_data:1595 name: Base pairing probability matrix dotplot namespace: data -def: "Dotplot of RNA base pairing probability matrix." [EDAM:EBI "EMBRACE definition"] -comment: Such as generated by the Vienna package. subset: data -is_a: EDAM:0002088 ! DNA base structural 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 [Term] -id: EDAM:0001598 +id: EDAM_data:1598 name: Genetic code namespace: data -def: "A genetic code for an organism." [EDAM:EBI "EMBRACE definition"] -comment: A genetic code need not include detailed codon usage information. subset: data -is_a: EDAM:0001597 ! Codon usage table +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 [Term] -id: EDAM:0002865 +id: EDAM_data:2865 name: Codon usage bias namespace: data -def: "A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000914 ! Codon usage report +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 [Term] -id: EDAM:0001599 +id: EDAM_data:1599 name: Codon adaptation index namespace: data -def: "A simple measure of synonymous codon usage bias often used to predict gene expression levels." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "CAI" EXACT [] -is_obsolete: true -consider: EDAM:0002865 ! Codon usage bias +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 [Term] -id: EDAM:0001600 +id: EDAM_data:1600 name: Codon usage bias plot namespace: data -def: "A plot of the synonymous codon usage calculated for windows over a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Synonymous codon usage statistic plot" EXACT [] -is_a: EDAM:0002865 ! Codon usage bias +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 [Term] -id: EDAM:0001601 +id: EDAM_data:1601 name: Nc statistic namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002865 ! Codon usage bias +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 [Term] -id: EDAM:0001602 +id: EDAM_data:1602 name: Codon usage fraction difference namespace: data -def: "The differences in codon usage fractions between two codon usage tables." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000914 ! Codon usage report +def: "The differences in codon usage fractions between two codon usage tables." [http://edamontology.org] +is_a: EDAM_data:0914 ! Codon usage report [Term] -id: EDAM:0000917 +id: EDAM_data:0917 name: Gene classification namespace: data -def: "A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000916 ! Gene annotation +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 [Term] -id: EDAM:0000927 +id: EDAM_data:0927 name: Gene annotation (linkage) namespace: data -def: "An informative report on the linkage of alleles." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000916 ! Gene annotation +def: "An informative report on the linkage of alleles." [http://edamontology.org] +is_a: EDAM_data:0916 ! Gene annotation [Term] -id: EDAM:0001634 +id: EDAM_data:1634 name: Gene annotation (linkage disequilibrium) namespace: 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)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000927 ! Gene annotation (linkage) +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) [Term] -id: EDAM:0000928 +id: EDAM_data:0928 name: Gene expression profile namespace: data -def: "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene expression pattern" EXACT [] -is_a: EDAM:0003031 ! Core 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 [Term] -id: EDAM:0002579 +id: EDAM_data:2579 name: Expressed gene list namespace: data -def: "A simple summary of expressed genes." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene annotation (expressed gene list)" EXACT [] -is_a: EDAM:0002872 ! ID list +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 [Term] -id: EDAM:0002586 +id: EDAM_data:2586 name: Northern blot image namespace: data -def: "An image arising from a Northern Blot experiment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003108 ! Experimental measurement +def: "An image arising from a Northern Blot experiment." [http://edamontology.org] +is_a: EDAM_data:3108 ! Experimental measurement [Term] -id: EDAM:0001636 +id: EDAM_data:1636 name: Heat map namespace: data -def: "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0002967 ! Microarray image +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 [Term] -id: EDAM:0002092 +id: EDAM_data:2092 name: Nucleic acid features (SNP) namespace: data -def: "Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] -comment: An SNP is an individual point mutation or substitution of a single nucleotide. subset: data -synonym: "Single nucleotide polymorphism" EXACT [] -synonym: "SNP annotation" EXACT [] -is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) +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) [Term] -id: EDAM:0002867 +id: EDAM_data:2867 name: Nucleic acid features (VNTR) namespace: data -def: "Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence." [EDAM:EBI "EMBRACE definition"] -comment: VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. subset: data -synonym: "Variable number of tandem repeat polymorphism" EXACT [] -synonym: "VNTR annotation" EXACT [] -is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) +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) [Term] -id: EDAM:0002868 +id: EDAM_data:2868 name: Nucleic acid features (microsatellite) namespace: data -def: "Annotation on a microsatellite polymorphism in a DNA sequence." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Microsatellite annotation" EXACT [] -is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) +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) [Term] -id: EDAM:0002869 +id: EDAM_data:2869 name: Nucleic acid features (RFLP) namespace: data -def: "Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] -comment: An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. subset: data -synonym: "RFLP annotation" EXACT [] -is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) +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) [Term] -id: EDAM:0001853 +id: EDAM_data:1853 name: Chromosome annotation (aberration) namespace: data -def: "A report on a chromosome aberration such as abnormalities in chromosome structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000919 ! Nucleic acid features (chromosome) +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 ! Nucleic acid features (chromosome) [Term] -id: EDAM:0001621 +id: EDAM_data:1621 name: Pharmacogenomic annotation namespace: data -def: "Data on the influence of genotype on drug response." [EDAM:EBI "EMBRACE definition"] -comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. subset: data -is_a: EDAM:0000920 ! Genotype and phenotype annotation +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 and phenotype annotation [Term] -id: EDAM:0001622 +id: EDAM_data:1622 name: Disease annotation namespace: data -def: "An informative report on a specific disease." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000920 ! Genotype/phenotype annotation -relationship: has_topic EDAM:0000634 ! Disease resources +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 [Term] -id: EDAM:0002533 +id: EDAM_data:2533 name: Nucleic acid features (mutation) namespace: data -def: "Annotation on a mutation." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Mutation annotation" EXACT [] -is_a: EDAM:0000918 ! Nucleic acid features (variation) +def: "Annotation on a mutation." [http://edamontology.org] +synonym: "Mutation annotation" EXACT [http://edamontology.org] +is_a: EDAM_data:0918 ! Nucleic acid features (variation) [Term] -id: EDAM:0002885 +id: EDAM_data:2885 name: Nucleic acid features (polymorphism annotation) namespace: data -def: "Annotation on a polymorphism." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Polymorphism annotation" EXACT [] -is_a: EDAM:0000918 ! Nucleic acid features (variation) +def: "Annotation on a polymorphism." [http://edamontology.org] +synonym: "Polymorphism annotation" EXACT [http://edamontology.org] +is_a: EDAM_data:0918 ! Nucleic acid features (variation) [Term] -id: EDAM:0002212 +id: EDAM_data:2212 name: Mutation annotation (basic) namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002533 ! Nucleic acid features (mutation) +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) [Term] -id: EDAM:0002213 +id: EDAM_data:2213 name: Mutation annotation (prevalence) namespace: data -def: "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002533 ! Nucleic acid features (mutation) +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) [Term] -id: EDAM:0002214 +id: EDAM_data:2214 name: Mutation annotation (prognostic) namespace: data -def: "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002533 ! Nucleic acid features (mutation) +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) [Term] -id: EDAM:0002215 +id: EDAM_data:2215 name: Mutation annotation (functional) namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002533 ! Nucleic acid features (mutation) +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) [Term] -id: EDAM:0002217 +id: EDAM_data:2217 name: Tumor annotation namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001622 ! Disease annotation +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 [Term] -id: EDAM:0001852 +id: EDAM_data:1852 name: Sequence assembly component namespace: data -def: "A component of a larger sequence assembly." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000925 ! Sequence assembly +def: "A component of a larger sequence assembly." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0925 ! Sequence assembly [Term] -id: EDAM:0000923 +id: EDAM_data:0923 name: Experiment annotation (PCR assay data) namespace: data -def: "Data on a PCR assay or electronic / virtual PCR." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "PCR assay data" EXACT [] -is_a: EDAM:0002531 ! Experiment annotation -relationship: has_topic EDAM:0000077 ! Nucleic acid analysis +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 + +[Term] +id: EDAM_data:3165 !{since=1.0} +name: Experiment annotation (sequencing) +namespace: data +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 [Term] -id: EDAM:0000924 +id: EDAM_data:0924 name: Sequence trace namespace: data -def: "A molecular sequence (reads) with associated sequencing metadata (such as base-call quality scores or raw sequencing data)." [EDAM:EBI "EMBRACE definition"] -comment: This is the raw data produced by a DNA sequencing machine. subset: data -is_a: EDAM:0003108 ! Experimental measurement -is_a: EDAM:0002887 ! Sequence record (nucleic acid) +def: "A molecular sequence (reads) with associated sequencing metadata (such as base-call quality scores or raw sequencing data)." [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) [Term] -id: EDAM:0000926 +id: EDAM_data:0926 name: Radiation Hybrid (RH) scores namespace: data -def: "Radiation hybrid scores (RH) scores for one or more markers." [EDAM:EBI "EMBRACE definition"] -comment: Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. subset: data -is_a: EDAM:0003108 ! Experimental measurement +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 [Term] -id: EDAM:0002363 +id: EDAM_data:2363 name: 2D PAGE data namespace: data -def: "Data concerning two-dimensional polygel electrophoresis." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0000942 ! 2D PAGE image -consider: EDAM:0002364 ! Experiment annotation (2D PAGE) +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) [Term] -id: EDAM:0002838 +id: EDAM_data:2838 name: Experimental data (proteomics) namespace: data -def: "Data concerning a proteomics experiment." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0003147 ! Experiment annotation (mass spectrometry) +def: "Data concerning a proteomics experiment." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:3147 ! Experiment annotation (mass spectrometry) [Term] -id: EDAM:0002536 +id: EDAM_data:2536 name: Mass spectrometry data namespace: data -def: "Data concerning a mass spectrometry experiment." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0000943 ! Mass spectrometry spectra -consider: EDAM:0000944 ! Peptide mass fingerprint -consider: EDAM:0003147 ! Experiment annotation (mass spectrometry) +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) [Term] -id: EDAM:0000943 +id: EDAM_data:0943 name: Mass spectrometry spectra namespace: data -def: "Spectra from mass spectrometry." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003108 ! Experimental measurement -relationship: has_topic EDAM:0000121 ! Proteomics +def: "Spectra from mass spectrometry." [http://edamontology.org] +is_a: EDAM_data:3108 ! Experimental measurement +relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] -id: EDAM:0000944 +id: EDAM_data:0944 name: Peptide mass fingerprint namespace: data -def: "A set of peptide masses (peptide mass fingerprint) from mass spectrometry." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Protein fingerprint" EXACT [] -synonym: "Peak list" EXACT [] -is_a: EDAM:0002979 ! Peptide property -is_a: EDAM:0003108 ! Experimental measurement -relationship: has_topic EDAM:0000767 ! Protein and peptide identification +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 [Term] -id: EDAM:0000945 +id: EDAM_data:0945 name: Peptide identification namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002979 ! Peptide property -relationship: has_topic EDAM:0000767 ! Protein and peptide identification +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 [Term] -id: EDAM:0002537 +id: EDAM_data:2537 name: Protein structure raw data namespace: data -def: "Raw data from experimental methods for determining protein structure." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0003108 ! Experimental measurement +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 [Term] -id: EDAM:0000937 +id: EDAM_data:0937 name: Protein X-ray crystallographic data namespace: data -def: "X-ray crystallography data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002537 ! Protein structure raw data +def: "X-ray crystallography data." [http://edamontology.org] +is_a: EDAM_data:2537 ! Protein structure raw data [Term] -id: EDAM:0000938 +id: EDAM_data:0938 name: Protein NMR data namespace: data -def: "Protein nuclear magnetic resonance (NMR) raw data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002537 ! Protein structure raw data +def: "Protein nuclear magnetic resonance (NMR) raw data." [http://edamontology.org] +is_a: EDAM_data:2537 ! Protein structure raw data [Term] -id: EDAM:0000939 +id: EDAM_data:0939 name: Protein circular dichroism (CD) spectroscopic data namespace: data -def: "Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002537 ! Protein structure raw 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 [Term] -id: EDAM:0000940 +id: EDAM_data:0940 name: Electron microscopy volume map namespace: data -def: "Volume map data from electron microscopy." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "EM volume map" EXACT [] -is_a: EDAM:0003108 ! Experimental measurement -relationship: has_topic EDAM:0002226 ! Structure determination +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 [Term] -id: EDAM:0000905 +id: EDAM_data:0905 name: Protein interaction raw data namespace: data -def: "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0003108 ! Experimental measurement +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 [Term] -id: EDAM:0000931 +id: EDAM_data:0931 name: Experiment annotation (microarray) namespace: data -alt_id: EDAM:0003114 -def: "Information on a microarray experiment such as conditions, protocol, sample:data relationships etc." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Experimental design annotation" EXACT [] -is_a: EDAM:0002531 ! Experiment annotation -relationship: has_topic EDAM:0000197 ! Gene expression resources +! 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:0197 ! Gene expression resources [Term] -id: EDAM:0002866 +id: EDAM_data:2866 name: Experiment annotation (Northern blot) namespace: data -def: "General annotation on a Northern Blot experiment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002531 ! Experiment annotation +def: "General annotation on a Northern Blot experiment." [http://edamontology.org] +is_a: EDAM_data:2531 ! Experiment annotation [Term] -id: EDAM:0003147 +id: EDAM_data:3147 !{since=beta13} name: Experiment annotation (mass spectrometry) namespace: data -def: "General annotation on a mass spectrometry experiment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002531 ! Experiment annotation +def: "General annotation on a mass spectrometry experiment." [http://edamontology.org] +is_a: EDAM_data:2531 ! Experiment annotation [Term] -id: EDAM:0000932 +id: EDAM_data:0932 name: Oligonucleotide probe data namespace: data -def: "Data on oligonucleotide probes (typically for use with DNA microarrays)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002717 ! Oligonucleotide probe annotation +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 [Term] -id: EDAM:0002535 +id: EDAM_data:2535 name: Sequence tag profile namespace: 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." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Sequencing-based expression profile" EXACT [] -is_a: EDAM:0000928 ! Gene expression profile +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 [Term] -id: EDAM:0000933 +id: EDAM_data:0933 name: SAGE experimental data namespace: data -def: "Output from a serial analysis of gene expression (SAGE) experiment." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Serial analysis of gene expression (SAGE) experimental data" EXACT [] -is_obsolete: true -consider: EDAM:0002535 ! Sequence tag profile +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 [Term] -id: EDAM:0000934 +id: EDAM_data:0934 name: MPSS experimental data namespace: data -def: "Massively parallel signature sequencing (MPSS) data." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Massively parallel signature sequencing (MPSS) experimental data" EXACT [] -is_obsolete: true -consider: EDAM:0002535 ! Sequence tag profile +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 [Term] -id: EDAM:0000935 +id: EDAM_data:0935 name: SBS experimental data namespace: data -def: "Sequencing by synthesis (SBS) data." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Sequencing by synthesis (SBS) experimental data" EXACT [] -is_obsolete: true -consider: EDAM:0002535 ! Sequence tag profile +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 [Term] -id: EDAM:0000936 +id: EDAM_data:0936 name: Sequence tag profile (with gene assignment) namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002535 ! Sequence tag profile +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 [Term] -id: EDAM:0000942 +id: EDAM_data:0942 name: 2D PAGE image namespace: data -def: "Two-dimensional gel electrophoresis image." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Two-dimensional gel electrophoresis image" EXACT [] -is_a: EDAM:0002968 ! Image -is_a: EDAM:0003108 ! Experimental measurement -relationship: has_topic EDAM:0000121 ! Proteomics +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 [Term] -id: EDAM:0002364 +id: EDAM_data:2364 name: Experiment annotation (2D PAGE) namespace: data -def: "An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002531 ! Experiment annotation -relationship: has_topic EDAM:0000121 ! Proteomics +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 [Term] -id: EDAM:0002965 +id: EDAM_data:2965 name: 2D PAGE image (annotated) namespace: data -def: "An informative report on a two-dimensional (2D PAGE) gel." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "2D PAGE image annotation" EXACT [] -is_a: EDAM:0000942 ! 2D PAGE image +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 [Term] -id: EDAM:0002372 +id: EDAM_data:2372 name: 2D PAGE spot (annotated) namespace: data -def: "An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "2D PAGE spot annotation" EXACT [] -is_a: EDAM:0002965 ! 2D PAGE image (annotated) +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) [Term] -id: EDAM:0001646 +id: EDAM_data:1646 name: Molecular weights standard fingerprint namespace: data -def: "Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000944 ! Peptide mass fingerprint +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 [Term] -id: EDAM:0002717 +id: EDAM_data:2717 name: Oligonucleotide probe annotation namespace: data -def: "General annotation on an oligonucleotide probe." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003115 ! Microarray annotation -relationship: has_topic EDAM:0000632 ! Probes and primers +def: "General annotation on an oligonucleotide probe." [http://edamontology.org] +is_a: EDAM_data:3115 ! Microarray annotation +relationship: has_topic EDAM_topic:0632 ! Probes and primers [Term] -id: EDAM:0002966 +id: EDAM_data:2966 name: Oligonucleotide probe sets annotation namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002717 ! Oligonucleotide probe annotation +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 [Term] -id: EDAM:0001642 +id: EDAM_data:1642 name: Affymetrix probe sets library file namespace: data -def: "Affymetrix library file of information about which probes belong to which probe set." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002966 ! Oligonucleotide probe sets annotation -! synonym: "CDF file" EXACT [] +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] [Term] -id: EDAM:0001643 +id: EDAM_data:1643 name: Affymetrix probe sets information library file namespace: data -def: "Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002966 ! Oligonucleotide probe sets annotation -! synonym: "GIN file" EXACT [] +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] [Term] -id: EDAM:0000856 +id: EDAM_data:0856 name: Sequence feature source namespace: data -def: "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0002042 ! Evidence -is_a: EDAM:0002914 ! Sequence feature metadata +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 feature metadata [Term] -id: EDAM:0000859 +id: EDAM_data:0859 name: Sequence signature model namespace: data -def: "Data files used by motif or profile methods." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000950 ! Biological model +def: "Data files used by motif or profile methods." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0950 ! Biological model [Term] -id: EDAM:0000946 +id: EDAM_data:0946 name: Pathway or network annotation namespace: data -def: "An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002984 ! Pathway or network report +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 [Term] -id: EDAM:0002589 +id: EDAM_data:2589 name: Hierarchy namespace: data -def: "A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Hierarchy annotation" EXACT [] -is_a: EDAM:0002987 ! Classification +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 [Term] -id: EDAM:0000904 +id: EDAM_data:0904 name: Protein features (mutation) namespace: data -def: "Data on the effect of (typically point) mutation on protein folding, stability, structure and function." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Protein property (mutation)" EXACT [] -synonym: "Protein report (mutation)" EXACT [] -synonym: "Protein structure report (mutation)" EXACT [] -is_obsolete: true -consider: EDAM:0000896 ! Protein report +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 [Term] -id: EDAM:0000903 +id: EDAM_data:0903 name: Protein folding report namespace: 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." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Protein report (folding)" EXACT [] -synonym: "Protein property (folding)" EXACT [] -is_a: EDAM:0000897 ! Protein property +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 [Term] -id: EDAM:0001596 +id: EDAM_data:1596 name: Nucleic acid folding report namespace: 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." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Nucleic acid report (folding model)" EXACT [] -synonym: "Nucleic acid report (folding)" EXACT [] -is_a: EDAM:0000912 ! Nucleic acid property +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 [Term] -id: EDAM:0001344 +id: EDAM_data:1344 name: MEME motif alphabet namespace: data -def: "Alphabet for the motifs (patterns) that MEME will search for." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000950 ! Biological model +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 [Term] -id: EDAM:0001345 +id: EDAM_data:1345 name: MEME background frequencies file namespace: data -def: "MEME background frequencies file." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000950 ! Biological model +def: "MEME background frequencies file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0950 ! Biological model [Term] -id: EDAM:0001346 +id: EDAM_data:1346 name: MEME motifs directive file namespace: data -def: "File of directives for ordering and spacing of MEME motifs." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000950 ! Biological model +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 [Term] -id: EDAM:0001347 +id: EDAM_data:1347 name: Dirichlet distribution namespace: data -def: "Dirichlet distribution used by hidden Markov model analysis programs." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000950 ! Biological model +def: "Dirichlet distribution used by hidden Markov model analysis programs." [http://edamontology.org] +is_a: EDAM_data:0950 ! Biological model [Term] -id: EDAM:0001348 +id: EDAM_data:1348 name: HMM emission and transition counts namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000950 ! Biological model +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 [Term] -id: EDAM:0000947 +id: EDAM_data:0947 name: Biological pathway map namespace: data -def: "A map (typically a diagram) of a biological pathway." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002600 ! Pathway or network +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 [Term] -id: EDAM:0001656 +id: EDAM_data:1656 name: Pathway or network (metabolic) namespace: data -def: "A report typically including a map (diagram) of a metabolic pathway." [EDAM:EBI "EMBRACE definition"] -comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. subset: data -is_a: EDAM:0002600 ! Pathway or network +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 [Term] -id: EDAM:0001657 +id: EDAM_data:1657 name: Pathway or network (genetic information processing) namespace: data -def: "A report typically including a map (diagram) of a genetic information processing pathway." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002600 ! Pathway or network +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 [Term] -id: EDAM:0002961 +id: EDAM_data:2961 name: Pathway or network (gene regulation) namespace: data -def: "A report typically including a map (diagram) of a gene regulatory network." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002600 ! Pathway or network -relationship: has_topic EDAM:0002846 ! Gene regulatory networks +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 [Term] -id: EDAM:0001658 +id: EDAM_data:1658 name: Pathway or network (environmental information processing) namespace: data -def: "A report typically including a map (diagram) of an environmental information processing pathway." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002600 ! Pathway or network +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 [Term] -id: EDAM:0001659 +id: EDAM_data:1659 name: Pathway or network (signal transduction) namespace: data -def: "A report typically including a map (diagram) of a signal transduction pathway." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002600 ! Pathway or network +def: "A report typically including a map (diagram) of a signal transduction pathway." [http://edamontology.org] +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM:0001660 +id: EDAM_data:1660 name: Pathway or network (cellular process) namespace: data -def: "A report typically including a map (diagram) of a cellular process pathway." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002600 ! Pathway or network +def: "A report typically including a map (diagram) of a cellular process pathway." [http://edamontology.org] +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM:0001661 +id: EDAM_data:1661 name: Pathway or network (disease) namespace: data -def: "A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002600 ! Pathway or network +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 [Term] -id: EDAM:0001662 +id: EDAM_data:1662 name: Pathway or network (drug structure relationship) namespace: data -def: "A report typically including a map (diagram) of drug structure relationships." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002600 ! Pathway or network +def: "A report typically including a map (diagram) of drug structure relationships." [http://edamontology.org] +is_a: EDAM_data:2600 ! Pathway or network [Term] -id: EDAM:0001663 +id: EDAM_data:1663 name: Pathway or network (protein-protein interaction) namespace: data -def: "A report typically including a map (diagram) of a network of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002600 ! Pathway or network +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 [Term] -id: EDAM:0000951 +id: EDAM_data:0951 name: Statistical estimate score namespace: data -def: "A value representing estimated statistical significance of some observed data; typically sequence database hits." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001772 ! Score or penalty -is_a: EDAM:0002914 ! Sequence feature metadata +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 feature metadata [Term] -id: EDAM:0000865 +id: EDAM_data:0865 name: Sequence similarity score namespace: data -def: "A value representing molecular sequence similarity." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001772 ! Score or penalty +def: "A value representing molecular sequence similarity." [http://edamontology.org] +is_a: EDAM_data:1772 ! Score or penalty [Term] -id: EDAM:0000888 +id: EDAM_data:0888 name: Structure similarity score namespace: data -def: "A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001772 ! Score or penalty +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 [Term] -id: EDAM:0002146 +id: EDAM_data:2146 name: Threshold namespace: data -def: "A value that serves as a threshold for a tool (usually to control scoring or output)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001772 ! Score or penalty +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 [Term] -id: EDAM:0001667 +id: EDAM_data:1667 name: E-value namespace: data -def: "A simple floating point number defining the lower or upper limit of an expectation value (E-value)." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Expectation value" EXACT [] -is_a: EDAM:0000951 ! Statistical estimate score +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 [Term] -id: EDAM:0001668 +id: EDAM_data:1668 name: Z-value namespace: data -def: "The z-value is the number of standard deviations a data value is above or below a mean value." [EDAM:EBI "EMBRACE definition"] -comment: A z-value might be specified as a threshold for reporting hits from database searches. subset: data -is_a: EDAM:0000951 ! Statistical estimate score +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 [Term] -id: EDAM:0001669 +id: EDAM_data:1669 name: P-value namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: A z-value might be specified as a threshold for reporting hits from database searches. subset: data -is_a: EDAM:0000951 ! Statistical estimate score +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 [Term] -id: EDAM:0001412 +id: EDAM_data:1412 name: Sequence identity namespace: data -def: "Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000865 ! Sequence similarity score +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 [Term] -id: EDAM:0001413 +id: EDAM_data:1413 name: Sequence similarity namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: Data Type is float probably. subset: data -is_a: EDAM:0000865 ! Sequence similarity score +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 [Term] -id: EDAM:0002335 +id: EDAM_data:2335 name: Bit score namespace: data -def: "A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system." [EDAM:EBI "EMBRACE definition"] -comment: Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. subset: data -is_a: EDAM:0001413 ! Sequence similarity +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 [Term] -id: EDAM:0001496 +id: EDAM_data:1496 name: Molecular similarity score namespace: data -def: "A score reflecting structural similarities of two molecules." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000888 ! Structure similarity score +def: "A score reflecting structural similarities of two molecules." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0888 ! Structure similarity score [Term] -id: EDAM:0001497 +id: EDAM_data:1497 name: Root-mean-square deviation namespace: data -def: "Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "RMSD" EXACT [] -is_a: EDAM:0000888 ! Structure similarity score +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 [Term] -id: EDAM:0001498 +id: EDAM_data:1498 name: Tanimoto similarity score namespace: data -def: "A measure of the similarity between two ligand fingerprints." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0000888 ! Structure similarity score +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 [Term] -id: EDAM:0001673 +id: EDAM_data:1673 name: Swiss-Prot to PDB mapping namespace: data -def: "Cross-mapping of Swiss-Prot codes to PDB identifiers." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000954 ! Database cross-mapping +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 [Term] -id: EDAM:0001674 +id: EDAM_data:1674 name: Sequence database cross-references namespace: data -def: "Cross-references from a sequence record to other databases." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002093 ! Data reference +def: "Cross-references from a sequence record to other databases." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2093 ! Data reference [Term] -id: EDAM:0002337 +id: EDAM_data:2337 name: Metadata namespace: data -alt_id: EDAM:0002853 -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." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -synonym: "Provenance metadata" EXACT [] -is_a: EDAM:0002048 ! Report +! 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 [Term] -id: EDAM:0002018 +id: EDAM_data:2018 name: Annotation namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_obsolete: true -consider: EDAM:0002048 ! Report +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 [Term] -id: EDAM:0000948 +id: EDAM_data:0948 name: Data resource definition namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001883 ! Annotated URI +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 [Term] -id: EDAM:0000957 +id: EDAM_data:0957 name: Database metadata namespace: data -def: "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003106 ! System metadata +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 [Term] -id: EDAM:0002223 +id: EDAM_data:2223 name: Ontology metadata namespace: data -def: "Data concerning a biological ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Metadata -relationship: has_topic EDAM:0000089 ! Ontologies +def: "Data concerning a biological ontology." [http://edamontology.org] +is_a: EDAM_data:2337 ! Metadata +relationship: has_topic EDAM_topic:0089 ! Ontologies [Term] -id: EDAM:0002193 +id: EDAM_data:2193 name: Database entry metadata namespace: data -def: "Basic information on any arbitrary database entry." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000957 ! Database metadata +def: "Basic information on any arbitrary database entry." [http://edamontology.org] +is_a: EDAM_data:0957 ! Database metadata [Term] -id: EDAM:0000958 +id: EDAM_data:0958 name: Tool metadata namespace: data -def: "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003106 ! System metadata +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 [Term] -id: EDAM:0002218 +id: EDAM_data:2218 name: Server metadata namespace: data -def: "Basic information about a server on the web, such as an SRS server." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003106 ! System metadata +def: "Basic information about a server on the web, such as an SRS server." [http://edamontology.org] +is_a: EDAM_data:3106 ! System metadata [Term] -id: EDAM:0000959 +id: EDAM_data:0959 name: Job metadata namespace: data -def: "Textual metadata on a submitted or completed job." [EDAM:EBI "EMBRACE definition"] subset: data +def: "Textual metadata on a submitted or completed job." [http://edamontology.org] xref: Moby:PDGJOB -is_a: EDAM:0003106 ! System metadata +is_a: EDAM_data:3106 ! System metadata [Term] -id: EDAM:0000960 +id: EDAM_data:0960 name: User metadata namespace: data -def: "Textual metadata on a software author or end-user, for example a person or other software." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003106 ! System metadata +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 [Term] -id: EDAM:0003106 +id: EDAM_data:3106 !{since=beta13} name: System metadata namespace: data -def: "Metadata concerning the software, hardware or other aspects of a computer system." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Metadata +def: "Metadata concerning the software, hardware or other aspects of a computer system." [http://edamontology.org] +is_a: EDAM_data:2337 ! Metadata [Term] -id: EDAM:0000583 +id: EDAM_data:0583 name: Directory metadata namespace: data -def: "A directory on disk from which files are read." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003106 ! System metadata +def: "A directory on disk from which files are read." [http://edamontology.org] +is_a: EDAM_data:3106 ! System metadata [Term] -id: EDAM:0000953 +id: EDAM_data:0953 name: Version information namespace: data -def: "Information on a version of software or data, for example name, version number and release date." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Metadata +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 [Term] -id: EDAM:0002724 +id: EDAM_data:2724 name: Embryo annotation namespace: data -def: "Annotation on an embryo or concerning embryological development." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002530 ! Organism annotation -relationship: has_topic EDAM:0003065 ! Embryology resources +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 [Term] -id: EDAM:0001664 +id: EDAM_data:1664 name: MIRIAM datatype namespace: data -def: "An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0000948 ! Data resource definition +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 [Term] -id: EDAM:0002875 +id: EDAM_data:2875 name: DRCAT resource namespace: data -def: "An entry (resource) from the DRCAT bioinformatics resource catalogue." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000948 ! Data resource definition +def: "An entry (resource) from the DRCAT bioinformatics resource catalogue." [http://edamontology.org] +is_a: EDAM_data:0948 ! Data resource definition [Term] -id: EDAM:0000952 +id: EDAM_data:0952 name: EMBOSS database resource definition namespace: data -def: "Resource definition for an EMBOSS database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000957 ! Database metadata +def: "Resource definition for an EMBOSS database." [http://edamontology.org] +is_a: EDAM_data:0957 ! Database metadata [Term] -id: EDAM:0001675 +id: EDAM_data:1675 name: Job status namespace: data -def: "Metadata on the status of a submitted job." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0000959 ! Job metadata +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 [Term] -id: EDAM:0001678 +id: EDAM_data:1678 name: Tool log namespace: data -def: "A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000959 ! Job metadata +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 [Term] -id: EDAM:0001677 +id: EDAM_data:1677 name: Job type namespace: data -def: "A label (text token) describing the type of job, for example interactive or non-interactive." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002100 ! Type +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 [Term] -id: EDAM:0001679 +id: EDAM_data:1679 name: DaliLite log file namespace: data -def: "DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +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 [Term] -id: EDAM:0001680 +id: EDAM_data:1680 name: STRIDE log file namespace: data -def: "STRIDE log file." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +def: "STRIDE log file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM:0001681 +id: EDAM_data:1681 name: NACCESS log file namespace: data -def: "NACCESS log file." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +def: "NACCESS log file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM:0001682 +id: EDAM_data:1682 name: EMBOSS wordfinder log file namespace: data -def: "EMBOSS wordfinder log file." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +def: "EMBOSS wordfinder log file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM:0001683 +id: EDAM_data:1683 name: EMBOSS domainatrix log file namespace: data -def: "EMBOSS (EMBASSY) domainatrix application log file." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +def: "EMBOSS (EMBASSY) domainatrix application log file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM:0001684 +id: EDAM_data:1684 name: EMBOSS sites log file namespace: data -def: "EMBOSS (EMBASSY) sites application log file." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +def: "EMBOSS (EMBASSY) sites application log file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM:0001685 +id: EDAM_data:1685 name: EMBOSS supermatcher error file namespace: data -def: "EMBOSS (EMBASSY) supermatcher error file." [EDAM:EBI "EMBRACE definition"] + subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +def: "EMBOSS (EMBASSY) supermatcher error file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM:0001686 +id: EDAM_data:1686 name: EMBOSS megamerger log file namespace: data -def: "EMBOSS megamerger log file." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +def: "EMBOSS megamerger log file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM:0001687 +id: EDAM_data:1687 name: EMBOSS whichdb log file namespace: data -def: "EMBOSS megamerger log file." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +def: "EMBOSS megamerger log file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM:0001688 +id: EDAM_data:1688 name: EMBOSS vectorstrip log file namespace: data -def: "EMBOSS vectorstrip log file." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001678 ! Tool log +def: "EMBOSS vectorstrip log file." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1678 ! Tool log [Term] -id: EDAM:0001670 +id: EDAM_data:1670 name: Database version information namespace: data -def: "Information on a database (or ontology) version, for example name, version number and release date." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Ontology version information" EXACT [] -is_a: EDAM:0000953 ! Version information -is_a: EDAM:0000957 ! Database metadata +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 [Term] -id: EDAM:0002090 +id: EDAM_data:2090 name: Database entry version information namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000953 ! Version information -is_a: EDAM:0002193 ! Database entry metadata +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 [Term] -id: EDAM:0001671 +id: EDAM_data:1671 name: Tool version information namespace: data -def: "Information on an application version, for example name, version number and release date." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000953 ! Version information -is_a: EDAM:0000958 ! Tool metadata +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 [Term] -id: EDAM:0001771 +id: EDAM_data:1771 name: Sequence version information namespace: data -def: "Information on an molecular sequence version." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000953 ! Version information -is_a: EDAM:0000855 ! Sequence metadata +def: "Information on an molecular sequence version." [http://edamontology.org] +is_a: EDAM_data:0953 ! Version information +is_a: EDAM_data:0855 ! Sequence metadata [Term] -id: EDAM:0002041 +id: EDAM_data:2041 name: Genome version information namespace: data -def: "Information on a genome version." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000953 ! Version information -is_a: EDAM:0002711 ! Genome metadata +def: "Information on a genome version." [http://edamontology.org] +is_a: EDAM_data:0953 ! Version information +is_a: EDAM_data:2711 ! Genome metadata [Term] -id: EDAM:0001672 +id: EDAM_data:1672 name: CATH version information namespace: data -def: "Information on a version of the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001670 ! Database version information +def: "Information on a version of the CATH database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1670 ! Database version information [Term] -id: EDAM:0001047 +id: EDAM_data:1047 name: URI namespace: data -def: "A string of characters that name or otherwise identify a resource on the Internet." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter +def: "A string of characters that name or otherwise identify a resource on the Internet." [http://edamontology.org] +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0002079 +id: EDAM_data:2079 name: Search parameter namespace: data -def: "Some simple value controlling a search operation, typically a search of a database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter +def: "Some simple value controlling a search operation, typically a search of a database." [http://edamontology.org] +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0002534 +id: EDAM_data:2534 name: Sequence parameter namespace: data -def: "A parameter concerning calculations on molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter +def: "A parameter concerning calculations on molecular sequences." [http://edamontology.org] +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0002130 +id: EDAM_data:2130 name: Sequence profile type namespace: data -def: "A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002534 ! Sequence parameter -is_a: EDAM:0002100 ! Type +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 [Term] -id: EDAM:0002023 +id: EDAM_data:2023 name: Sequence mask parameter namespace: data -def: "Data used to replace (mask) characters in a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002534 ! Sequence parameter +def: "Data used to replace (mask) characters in a molecular sequence." [http://edamontology.org] +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM:0000853 +id: EDAM_data:0853 name: DNA sense specification namespace: data -def: "The strand of a DNA sequence (forward or reverse)." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "DNA strand specification" EXACT [] -synonym: "Strand" EXACT [] -is_a: EDAM:0002534 ! Sequence parameter -is_a: EDAM:0002914 ! Sequence feature metadata +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 feature metadata [Term] -id: EDAM:0002126 +id: EDAM_data:2126 name: Translation frame specification namespace: data -def: "Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002534 ! Sequence parameter3 +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 parameter3 [Term] -id: EDAM:0002336 +id: EDAM_data:2336 name: Translation phase specification namespace: data -def: "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Phase" EXACT [] -is_a: EDAM:0002534 ! Sequence parameter -is_a: EDAM:0002914 ! Sequence feature metadata +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 feature metadata [Term] -id: EDAM:0001014 +id: EDAM_data:1014 name: Sequence position specification namespace: data -def: "A specification (partial or complete) of one or more positions or regions of a molecular sequence or map." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002534 ! Sequence parameter +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 [Term] -id: EDAM:0000854 +id: EDAM_data:0854 name: Sequence length specification namespace: data -def: "A specification of sequence length(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002534 ! Sequence parameter +def: "A specification of sequence length(s)." [http://edamontology.org] +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM:0002357 +id: EDAM_data:2357 name: Protein signature type namespace: data -def: "A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002534 ! Sequence parameter -is_a: EDAM:0002100 ! Type +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 [Term] -id: EDAM:0000864 +id: EDAM_data:0864 name: Sequence alignment parameter namespace: data -def: "Some simple value controlling a sequence alignment (or similar 'match') operation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002534 ! Sequence parameter +def: "Some simple value controlling a sequence alignment (or similar 'match') operation." [http://edamontology.org] +is_a: EDAM_data:2534 ! Sequence parameter [Term] -id: EDAM:0001120 +id: EDAM_data:1120 name: Sequence alignment type namespace: data -def: "A label (text token) describing the type of a sequence alignment." [EDAM:EBI "EMBRACE definition"] -comment: Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. subset: data -is_a: EDAM:0000864 ! Sequence alignment parameter -is_a: EDAM:0002100 ! Type +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 [Term] -id: EDAM:0001052 +id: EDAM_data:1052 name: URL namespace: data -alt_id: EDAM:0001054 -alt_id: EDAM:0001168 -alt_id: EDAM:0001169 -def: "A Uniform Resource Locator (URL)." [EDAM:EBI "EMBRACE definition"] 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:0001047 ! URI +is_a: EDAM_data:1047 ! URI [Term] -id: EDAM:0001053 +id: EDAM_data:1053 name: URN namespace: data -def: "A Uniform Resource Name (URN)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001047 ! URI +def: "A Uniform Resource Name (URN)." [http://edamontology.org] +is_a: EDAM_data:1047 ! URI [Term] -id: EDAM:0001055 +id: EDAM_data:1055 name: LSID namespace: data -def: "A Life Science Identifier (LSID) - a unique identifier of some data." [EDAM:EBI "EMBRACE definition"] -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:::[:] subset: data -synonym: "Life Science Identifier" EXACT [] -is_a: EDAM:0001053 ! URN +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 [Term] -id: EDAM:0000968 +id: EDAM_data:0968 name: Keyword namespace: data -def: "Keyword(s) or phrase(s) used (typically) for text-searching purposes." [EDAM:EBI "EMBRACE definition"] -comment: Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. 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:0002527 ! Parameter +is_a: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0002022 +id: EDAM_data:2022 name: Vienna RNA structural data namespace: data -def: "Data used by the Vienna RNA analysis package." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002527 ! Parameter +def: "Data used by the Vienna RNA analysis package." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0002134 +id: EDAM_data:2134 name: Results sort order namespace: data -def: "A control of the order of data that is output, for example the order of sequences in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002079 ! Search parameter +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 [Term] -id: EDAM:0002135 +id: EDAM_data:2135 name: Toggle namespace: data -def: "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002527 ! Parameter +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 [Term] -id: EDAM:0002139 +id: EDAM_data:2139 name: Nucleic acid melting temperature namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Melting temperature" EXACT [] -is_a: EDAM:0002985 ! Nucleic acid thermodynamic 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 [Term] -id: EDAM:0002140 +id: EDAM_data:2140 name: Concentration namespace: data -def: "The concentration of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002050 ! Molecular property (general) +def: "The concentration of a chemical compound." [http://edamontology.org] +is_a: EDAM_data:2050 ! Molecular property (general) [Term] -id: EDAM:0002151 +id: EDAM_data:2151 name: Color namespace: data -def: "Specification of one or more colors." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002152 ! Rendering parameter +def: "Specification of one or more colors." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2152 ! Rendering parameter [Term] -id: EDAM:0002152 +id: EDAM_data:2152 name: Rendering parameter namespace: data -def: "A parameter that is used to control rendering (drawing) to a device or image." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Graphics parameter" EXACT [] -synonym: "Graphical parameter" EXACT [] -is_a: EDAM:0002527 ! Parameter +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 [Term] -id: EDAM:0003105 +id: EDAM_data:3105 !{since=beta13} name: Geotemporal metadata namespace: data -def: "Basic information concerning geographical location or time." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Metadata +def: "Basic information concerning geographical location or time." [http://edamontology.org] +is_a: EDAM_data:2337 ! Metadata [Term] -id: EDAM:0002156 +id: EDAM_data:2156 name: Date namespace: data -def: "A temporal date." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003105 ! Geotemporal metadata +def: "A temporal date." [http://edamontology.org] +is_a: EDAM_data:3105 ! Geotemporal metadata [Term] -id: EDAM:0001693 +id: EDAM_data:1693 name: Number of iterations namespace: data -def: "Number of iterations of an algorithm." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002079 ! Search parameter +def: "Number of iterations of an algorithm." [http://edamontology.org] +is_a: EDAM_data:2079 ! Search parameter [Term] -id: EDAM:0001694 +id: EDAM_data:1694 name: Number of output entities namespace: data -def: "Number of entities (for example database hits, sequences, alignments etc) to write to an output file." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002079 ! Search parameter +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 + + [Term] -id: EDAM:0001695 +id: EDAM_data:1695 name: Hit sort order namespace: data -def: "Controls the order of hits (reported matches) in an output file from a database search." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002134 ! Results sort order +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 [Term] -id: EDAM:0000851 +id: EDAM_data:0851 name: Sequence mask character namespace: data -def: "A character used to replace (mask) other characters in a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002023 ! Sequence mask parameter +def: "A character used to replace (mask) other characters in a molecular sequence." [http://edamontology.org] +is_a: EDAM_data:2023 ! Sequence mask parameter [Term] -id: EDAM:0000852 +id: EDAM_data:0852 name: Sequence mask type namespace: data -def: "A label (text token) describing the type of sequence masking to perform." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0002023 ! Sequence mask parameter -is_a: EDAM:0002100 ! Type +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 [Term] -id: EDAM:0001016 +id: EDAM_data:1016 name: Sequence position namespace: data -def: "A position of a single point (base or residue) in a sequence, or part of such a specification." [EDAM:EBI "EMBRACE definition"] 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:0001014 ! Sequence position specification +is_a: EDAM_data:1014 ! Sequence position specification ! _atom_site.id in PDBML [Term] -id: EDAM:0002145 +id: EDAM_data:2145 name: Sequence offset namespace: data -def: "An offset for a single-point sequence position." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001016 ! Sequence position -is_a: EDAM:0002914 ! Sequence feature metadata +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 feature metadata [Term] -id: EDAM:0001017 +id: EDAM_data:1017 name: Sequence range namespace: data -def: "Specification of range(s) of sequence positions." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001014 ! Sequence position specification +def: "Specification of range(s) of sequence positions." [http://edamontology.org] +is_a: EDAM_data:1014 ! Sequence position specification [Term] -id: EDAM:0002012 +id: EDAM_data:2012 name: Map position namespace: data -alt_id: EDAM:0001894 -def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Locus" EXACT [] +! 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 @@ -16705,1385 +16505,1441 @@ xref: Moby:MapPosition xref: Moby:Position xref: Moby:GCP_MapInterval xref: Moby:Locus -is_a: EDAM:0001016 ! Sequence position -is_a: EDAM:0001017 ! Sequence range -is_a: EDAM:0002019 ! Map attribute -! seealso: XXX:0000000 ! All the different types of 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 [Term] -id: EDAM:0002216 +id: EDAM_data:2216 name: Codon number namespace: data -def: "The number of a codon, for instance, at which a mutation is located." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001016 ! Sequence position +def: "The number of a codon, for instance, at which a mutation is located." [http://edamontology.org] +is_a: EDAM_data:1016 ! Sequence position [Term] -id: EDAM:0001742 +id: EDAM_data:1742 name: PDB residue number namespace: data -def: "A residue identifier (a string) from a PDB file." [EDAM:EBI "EMBRACE definition"] subset: data +def: "A residue identifier (a string) from a PDB file." [http://edamontology.org] xref: WHATIF: pdb_number -is_a: EDAM:0001016 ! Sequence position +is_a: EDAM_data:1016 ! Sequence position ! PDB_residue_no in PDBML [Term] -id: EDAM:0001856 +id: EDAM_data:1856 name: PDB insertion code namespace: data -def: "An insertion code (part of the residue number) for an amino acid residue from a PDB file." [EDAM:EBI "EMBRACE definition"] 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:0001016 ! Sequence position +is_a: EDAM_data:1016 ! Sequence position ! pdbx_PDB_ins_code in PDBML [Term] -id: EDAM:0001906 +id: EDAM_data:1906 name: Quantitative trait locus namespace: 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)." [EDAM:EBI "EMBRACE definition"] -comment: A QTL sometimes but does not necessarily correspond to a gene. subset: data -synonym: "QTL" EXACT [] +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 -consider: EDAM:0002012 ! Map position +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2012 ! Map position [Term] -id: EDAM:0001249 +id: EDAM_data:1249 name: Sequence length namespace: data -def: "The size (length) of a sequence, subsequence or region in a sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000854 ! Sequence length specification +def: "The size (length) of a sequence, subsequence or region in a sequence." [http://edamontology.org] +is_a: EDAM_data:0854 ! Sequence length specification [Term] -id: EDAM:0001252 +id: EDAM_data:1252 name: Sequence length range namespace: data -def: "Specification of range(s) of length of sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000854 ! Sequence length specification +def: "Specification of range(s) of length of sequences." [http://edamontology.org] +is_a: EDAM_data:0854 ! Sequence length specification [Term] -id: EDAM:0001250 +id: EDAM_data:1250 name: Word size namespace: data -def: "Size of a sequence word." [EDAM:EBI "EMBRACE definition"] -comment: Word size is used for example in word-based sequence database search methods. subset: data -synonym: "Word length" EXACT [] -is_a: EDAM:0001249 ! Sequence length +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 [Term] -id: EDAM:0001251 +id: EDAM_data:1251 name: Window size namespace: data -def: "Size of a sequence window." [EDAM:EBI "EMBRACE definition"] -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: data -is_a: EDAM:0001249 ! Sequence length +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 [Term] -id: EDAM:0002141 +id: EDAM_data:2141 name: Window step size namespace: data -def: "Size of the incremental 'step' a sequence window is moved over a sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001249 ! Sequence length +def: "Size of the incremental 'step' a sequence window is moved over a sequence." [http://edamontology.org] +is_a: EDAM_data:1249 ! Sequence length [Term] -id: EDAM:0001125 +id: EDAM_data:1125 name: Comparison matrix type namespace: data -def: "A label (text token) describing the type of a comparison matrix." [EDAM:EBI "EMBRACE definition"] -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: data -synonym: "Substitution matrix type" EXACT [] -is_a: EDAM:0000864 ! Sequence alignment parameter -is_a: EDAM:0002100 ! Type +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 [Term] -id: EDAM:0001394 +id: EDAM_data:1394 name: Alignment score or penalty namespace: data -def: "A simple floating point number defining the penalty for opening or extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000864 ! Sequence alignment parameter -is_a: EDAM:0001772 ! Score or penalty +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 [Term] -id: EDAM:0001395 +id: EDAM_data:1395 name: Score end gaps control namespace: data -def: "Whether end gaps are scored or not." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002527 ! Parameter +def: "Whether end gaps are scored or not." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0001396 +id: EDAM_data:1396 name: Aligned sequence order namespace: data -def: "Controls the order of sequences in an output sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002134 ! Results sort order +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 [Term] -id: EDAM:0002136 +id: EDAM_data:2136 name: Sequence width namespace: data -def: "The width of an output sequence or alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001249 ! Sequence length +def: "The width of an output sequence or alignment." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1249 ! Sequence length [Term] -id: EDAM:0002137 +id: EDAM_data:2137 name: Gap penalty namespace: data -def: "A penalty for introducing or extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001394 ! Alignment score or penalty +def: "A penalty for introducing or extending a gap in an alignment." [http://edamontology.org] +is_a: EDAM_data:1394 ! Alignment score or penalty [Term] -id: EDAM:0001401 +id: EDAM_data:1401 name: Match reward score namespace: data -def: "The score for a 'match' used in various sequence database search applications with simple scoring schemes." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001394 ! Alignment score or penalty +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 [Term] -id: EDAM:0001402 +id: EDAM_data:1402 name: Mismatch penalty score namespace: data -def: "The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001394 ! Alignment score or penalty +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 [Term] -id: EDAM:0001403 +id: EDAM_data:1403 name: Drop off score namespace: data -def: "This is the threshold drop in score at which extension of word alignment is halted." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001394 ! Alignment score or penalty +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 [Term] -id: EDAM:0001397 +id: EDAM_data:1397 name: Gap opening penalty namespace: data -def: "A penalty for opening a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002137 ! Gap penalty +def: "A penalty for opening a gap in an alignment." [http://edamontology.org] +is_a: EDAM_data:2137 ! Gap penalty [Term] -id: EDAM:0001398 +id: EDAM_data:1398 name: Gap extension penalty namespace: data -def: "A penalty for extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002137 ! Gap penalty +def: "A penalty for extending a gap in an alignment." [http://edamontology.org] +is_a: EDAM_data:2137 ! Gap penalty [Term] -id: EDAM:0001399 +id: EDAM_data:1399 name: Gap separation penalty namespace: data -def: "A penalty for gaps that are close together in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002137 ! Gap penalty +def: "A penalty for gaps that are close together in an alignment." [http://edamontology.org] +is_a: EDAM_data:2137 ! Gap penalty [Term] -id: EDAM:0001400 +id: EDAM_data:1400 name: Terminal gap penalty namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001410 ! Terminal gap opening penalty -consider: EDAM:0001411 ! Terminal gap extension penalty +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 [Term] -id: EDAM:0001404 +id: EDAM_data:1404 name: Gap opening penalty (integer) namespace: data -def: "A simple floating point number defining the penalty for opening a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001397 ! Gap opening penalty +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 [Term] -id: EDAM:0001405 +id: EDAM_data:1405 name: Gap opening penalty (float) namespace: data -def: "A simple floating point number defining the penalty for opening a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001397 ! Gap opening penalty +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 [Term] -id: EDAM:0001406 +id: EDAM_data:1406 name: Gap extension penalty (integer) namespace: data -def: "A simple floating point number defining the penalty for extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001398 ! Gap extension penalty +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 [Term] -id: EDAM:0001407 +id: EDAM_data:1407 name: Gap extension penalty (float) namespace: data -def: "A simple floating point number defining the penalty for extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001398 ! Gap extension penalty +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 [Term] -id: EDAM:0001408 +id: EDAM_data:1408 name: Gap separation penalty (integer) namespace: data -def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001399 ! Gap separation penalty +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 [Term] -id: EDAM:0001409 +id: EDAM_data:1409 name: Gap separation penalty (float) namespace: data -def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001399 ! Gap separation penalty +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 [Term] -id: EDAM:0001410 +id: EDAM_data:1410 name: Terminal gap opening penalty namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001397 ! Gap opening penalty +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 [Term] -id: EDAM:0001411 +id: EDAM_data:1411 name: Terminal gap extension penalty namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001398 ! Gap extension penalty +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 [Term] -id: EDAM:0002007 +id: EDAM_data:2007 name: UniProt keyword namespace: data -def: "A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database." [EDAM:EBI "EMBRACE definition"] 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:0000968 ! Keyword +is_a: EDAM_data:0968 ! Keyword [Term] -id: EDAM:0001877 +id: EDAM_data:1877 name: Synonym namespace: data -def: "An alternative for a word." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Alternative name" EXACT [] -is_obsolete: true -consider: EDAM:0000968 ! Keyword +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 [Term] -id: EDAM:0001878 +id: EDAM_data:1878 name: Misspelling namespace: data -def: "A common misspelling of a word." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000968 ! Keyword +def: "A common misspelling of a word." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0968 ! Keyword [Term] -id: EDAM:0001879 +id: EDAM_data:1879 name: Acronym namespace: data -def: "An abbreviation of a phrase or word." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000968 ! Keyword +def: "An abbreviation of a phrase or word." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0968 ! Keyword [Term] -id: EDAM:0001880 +id: EDAM_data:1880 name: Misnomer namespace: data -def: "A term which is likely to be misleading of its meaning." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000968 ! Keyword +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 [Term] -id: EDAM:0001591 +id: EDAM_data:1591 name: Vienna RNA parameters namespace: data -def: "RNA parameters used by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002527 ! Parameter +def: "RNA parameters used by the Vienna package." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0001592 +id: EDAM_data:1592 name: Vienna RNA structure constraints namespace: data -def: "Structure constraints used by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002527 ! Parameter +def: "Structure constraints used by the Vienna package." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0001593 +id: EDAM_data:1593 name: Vienna RNA concentration data namespace: data -def: "RNA concentration data used by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002527 ! Parameter +def: "RNA concentration data used by the Vienna package." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2527 ! Parameter [Term] -id: EDAM:0001696 +id: EDAM_data:1696 name: Drug annotation namespace: data -def: "An informative report on a specific drug." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule annotation -relationship: has_topic EDAM:0000620 ! Drugs and targets +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 [Term] -id: EDAM:0002400 +id: EDAM_data:2400 name: Toxin annotation namespace: data -def: "An informative report on a specific toxin." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule annotation +def: "An informative report on a specific toxin." [http://edamontology.org] +is_a: EDAM_data:0962 ! Small molecule annotation [Term] -id: EDAM:0002240 +id: EDAM_data:2240 name: Heterogen annotation namespace: data -def: "An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule annotation +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 [Term] -id: EDAM:0002726 +id: EDAM_data:2726 name: Inhibitor annotation namespace: data -def: "An informative report on one or more small molecules that are enzyme inhibitors." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule annotation +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 [Term] -id: EDAM:0002396 +id: EDAM_data:2396 name: Fungi annotation (anamorph) namespace: data -def: "An informative report on a specific fungus anamorph." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002395 ! Fungi annotation +def: "An informative report on a specific fungus anamorph." [http://edamontology.org] +is_a: EDAM_data:2395 ! Fungi annotation [Term] -id: EDAM:0002142 +id: EDAM_data:2142 name: EMBOSS graph namespace: data -def: "An image of a graph generated by the EMBOSS suite." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002968 ! Image +def: "An image of a graph generated by the EMBOSS suite." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2968 ! Image [Term] -id: EDAM:0001707 +id: EDAM_data:1707 name: Phylogenetic tree image namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: See also 'Phylogenetic tree' subset: data -is_a: EDAM:0002968 ! Image -is_a: EDAM:0001438 ! Phylogenetic tree report +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 [Term] -id: EDAM:0001708 +id: EDAM_data:1708 name: RNA secondary structure image namespace: data -def: "Image of RNA secondary structure, knots, pseudoknots etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002880 ! Secondary structure image +def: "Image of RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] +is_a: EDAM_data:2880 ! Secondary structure image [Term] -id: EDAM:0001709 +id: EDAM_data:1709 name: Protein secondary structure image namespace: data -def: "Image of protein secondary structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002880 ! Secondary structure image -is_a: EDAM:0002956 ! Protein secondary structure report +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 [Term] -id: EDAM:0001710 +id: EDAM_data:1710 name: Structure image namespace: data -alt_id: EDAM:0002604 -def: "Image of one or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002085 ! Structure report -is_a: EDAM:0002968 ! Image +! 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 [Term] -id: EDAM:0002880 +id: EDAM_data:2880 name: Secondary structure image namespace: data -def: "Image of one or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002881 ! Secondary structure report +def: "Image of one or more molecular secondary structures." [http://edamontology.org] +is_a: EDAM_data:2881 ! Secondary structure report [Term] -id: EDAM:0001711 +id: EDAM_data:1711 name: Sequence alignment image namespace: data -def: "Image of two or more aligned molecular sequences possibly annotated with alignment features." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002968 ! Image -is_a: EDAM:0000867 ! Sequence alignment report +def: "Image of two or more aligned molecular sequences possibly annotated with alignment features." [http://edamontology.org] +is_a: EDAM_data:2968 ! Image +is_a: EDAM_data:0867 ! Sequence alignment report [Term] -id: EDAM:0002168 +id: EDAM_data:2168 name: Sequence trace image namespace: data -def: "Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002969 ! Sequence image +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 [Term] -id: EDAM:0002969 +id: EDAM_data:2969 name: Sequence image namespace: data -def: "Image of a molecular sequence, possibly with sequence features or properties shown." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002968 ! Image -is_a: EDAM:0002955 ! Sequence report +def: "Image of a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org] +is_a: EDAM_data:2968 ! Image +is_a: EDAM_data:2955 ! Sequence report [Term] -id: EDAM:0001712 +id: EDAM_data:1712 name: Structure image (small molecule) namespace: data -def: "An image of the structure of a small chemical compound." [EDAM:EBI "EMBRACE definition"] -comment: The molecular identifier and formula are typically included. subset: data -synonym: "Chemical structure image" EXACT [] -synonym: "Small molecule structure image" EXACT [] -is_a: EDAM:0001710 ! Structure image -is_a: EDAM:0000962 ! Small molecule annotation +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 [Term] -id: EDAM:0002992 +id: EDAM_data:2992 name: Protein structure image namespace: data -def: "An image of protein structure." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Structure image (protein)" EXACT [] -is_a: EDAM:0001710 ! Structure image -is_a: EDAM:0003153 ! Protein image +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 [Term] -id: EDAM:0003154 +id: EDAM_data:3154 !{since=beta13} name: Protein alignment namespace: data -def: "An alignment of protein sequences and/or structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000896 ! Protein report -is_a: EDAM:0001916 ! Alignment +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 [Term] -id: EDAM:0003153 +id: EDAM_data:3153 !{since=beta13} name: Protein image namespace: data -def: "An image of a protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000896 ! Protein report +def: "An image of a protein." [http://edamontology.org] +is_a: EDAM_data:0896 ! Protein report [Term] -id: EDAM:0001713 +id: EDAM_data:1713 name: Fate map namespace: 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." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002724 ! Embryo annotation +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 [Term] -id: EDAM:0002967 +id: EDAM_data:2967 name: Microarray image namespace: data -alt_id: EDAM:0001635 -def: "An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene expression image" EXACT [] -is_a: EDAM:0002603 ! Microarray data -is_a: EDAM:0002968 ! Image -relationship: has_topic EDAM:0000197 ! Gene expression resources +! 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:0197 ! Gene expression resources [Term] -id: EDAM:0001714 +id: EDAM_data:1714 name: Microarray spots image namespace: data -def: "An image of spots from a microarray experiment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002967 ! Microarray image -is_a: EDAM:0003108 ! Experimental measurement +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 [Term] -id: EDAM:0002162 +id: EDAM_data:2162 name: Helical wheel namespace: data -def: "An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001709 ! Protein secondary structure image +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 [Term] -id: EDAM:0002163 +id: EDAM_data:2163 name: Helical net namespace: 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." [EDAM:EBI "EMBRACE definition"] -comment: Useful for highlighting amphipathicity and other properties. subset: data -is_a: EDAM:0001709 ! Protein secondary structure image +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 [Term] -id: EDAM:0002308 +id: EDAM_data:2308 name: Virus annotation (taxonomy) namespace: data -def: "An informative report on the taxonomy of a specific virus." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002307 ! Virus annotation +def: "An informative report on the taxonomy of a specific virus." [http://edamontology.org] +is_a: EDAM_data:2307 ! Virus annotation [Term] -id: EDAM:0000582 +id: EDAM_data:0582 name: Ontology namespace: data -alt_id: EDAM:0000829 -alt_id: EDAM:0000830 -alt_id: EDAM:0000834 -alt_id: EDAM:0000836 -alt_id: EDAM:0000837 -alt_id: EDAM:0000838 -alt_id: EDAM:0000839 -alt_id: EDAM:0000840 -alt_id: EDAM:0002221 -def: "An ontology of biological or bioinformatics terms and relations, a controlled vocabulary, structured glossary etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000089 ! Ontologies +! 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] +is_a: EDAM_data:3031 ! Core data +relationship: has_topic EDAM_topic:0089 ! Ontologies [Term] -id: EDAM:0002858 +id: EDAM_data:2858 name: Ontology concept namespace: data -def: "A concept from a biological ontology." [EDAM:EBI "EMBRACE definition"] -comment: This includes any fields from the term definition such as term name, definition, comments and so on. subset: data -is_a: EDAM:0003031 ! Core data -relationship: has_topic EDAM:0000089 ! Ontologies +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 ! Ontologies [Term] -id: EDAM:0000966 +id: EDAM_data:0966 name: Ontology term namespace: data -def: "A term (name) from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000967 ! Ontology concept metadata +def: "A term (name) from an ontology." [http://edamontology.org] +is_a: EDAM_data:0967 ! Ontology concept metadata [Term] -id: EDAM:0000967 +id: EDAM_data:0967 name: Ontology concept metadata namespace: data -def: "Data concerning or derived from a concept from a biological ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Metadata -relationship: has_topic EDAM:0000089 ! Ontologies +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 ! Ontologies [Term] -id: EDAM:0001715 +id: EDAM_data:1715 name: BioPax namespace: data -def: "A term from the BioPax ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +def: "A term from the BioPax ontology." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001716 +id: EDAM_data:1716 name: GO namespace: data -def: "A term definition from The Gene Ontology (GO)." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "Gene Ontology term" EXACT [] +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 -consider: EDAM:0000966 ! Ontology term +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001717 +id: EDAM_data:1717 name: MeSH namespace: data -def: "A term from the MeSH vocabulary." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +def: "A term from the MeSH vocabulary." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001718 +id: EDAM_data:1718 name: HGNC namespace: data -def: "A term from the HGNC controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +def: "A term from the HGNC controlled vocabulary." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001719 +id: EDAM_data:1719 name: NCBI taxonomy vocabulary namespace: data -def: "A term from the NCBI taxonomy vocabulary." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +def: "A term from the NCBI taxonomy vocabulary." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001720 +id: EDAM_data:1720 name: Plant ontology term namespace: data -def: "A term from the Plant Ontology (PO)." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +def: "A term from the Plant Ontology (PO)." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001721 +id: EDAM_data:1721 name: UMLS namespace: data -def: "A term from the UMLS vocabulary." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +def: "A term from the UMLS vocabulary." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001722 +id: EDAM_data:1722 name: FMA namespace: data -def: "A term from Foundational Model of Anatomy." [EDAM:EBI "EMBRACE definition"] -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: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +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 [Term] -id: EDAM:0001723 +id: EDAM_data:1723 name: EMAP namespace: data -def: "A term from the EMAP mouse ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +def: "A term from the EMAP mouse ontology." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001724 +id: EDAM_data:1724 name: ChEBI namespace: data -def: "A term from the ChEBI ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +def: "A term from the ChEBI ontology." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001725 +id: EDAM_data:1725 name: MGED namespace: data -def: "A term from the MGED ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +def: "A term from the MGED ontology." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0966 ! Ontology term [Term] -id: EDAM:0001726 +id: EDAM_data:1726 name: myGrid namespace: data -def: "A term from the myGrid ontology." [EDAM:EBI "EMBRACE definition"] -comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides terms for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. subset: data -is_obsolete: true -consider: EDAM:0000966 ! Ontology term +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 [Term] -id: EDAM:0001727 +id: EDAM_data:1727 name: GO (biological process) namespace: data -def: "A term definition for a biological process from the Gene Ontology (GO)." [EDAM:EBI "EMBRACE definition"] -comment: Data Type is an enumerated string. subset: data -is_obsolete: true -consider: EDAM:0002858 ! Ontology concept +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 [Term] -id: EDAM:0001728 +id: EDAM_data:1728 name: GO (molecular function) namespace: data -def: "A term definition for a molecular function from the Gene Ontology (GO)." [EDAM:EBI "EMBRACE definition"] -comment: Data Type is an enumerated string. subset: data -is_obsolete: true -consider: EDAM:0002858 ! Ontology concept +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 [Term] -id: EDAM:0001729 +id: EDAM_data:1729 name: GO (cellular component) namespace: data -def: "A term definition for a cellular component from the Gene Ontology (GO)." [EDAM:EBI "EMBRACE definition"] -comment: Data Type is an enumerated string. subset: data -is_obsolete: true -consider: EDAM:0002858 ! Ontology concept +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 [Term] -id: EDAM:0001730 -name: Ontology relation +id: EDAM_data:1730 +name: Ontology relation type namespace: data -def: "A relation defined for a term from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000967 ! Ontology concept metadata +def: "A relation type defined in an ontology." [http://edamontology.org] +is_a: EDAM_data:0967 ! Ontology concept metadata [Term] -id: EDAM:0001731 -name: Ontology term definition +id: EDAM_data:1731 +name: Ontology concept definition namespace: data -def: "The definition of a term from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000967 ! Ontology concept metadata +def: "The definition of a concept from an ontology." [http://edamontology.org] +is_a: EDAM_data:0967 ! Ontology concept metadata [Term] -id: EDAM:0001732 -name: Ontology term comment +id: EDAM_data:1732 +name: Ontology concept comment namespace: data -def: "A comment on a term from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000967 ! Ontology concept metadata +def: "A comment on a concept from an ontology." [http://edamontology.org] +is_a: EDAM_data:0967 ! Ontology concept metadata [Term] -id: EDAM:0001733 -name: Ontology term cross-reference +id: EDAM_data:1733 +name: Ontology concept reference namespace: data -def: "Cross-references for a term from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002093 ! Data reference +def: "Reference for a concept from an ontology." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2093 ! Data reference [Term] -id: EDAM:0001738 +id: EDAM_data:1738 name: doc2loc document information namespace: data -def: "Information on a published article provided by the doc2loc program." [EDAM:EBI "EMBRACE definition"] -comment: The doc2loc output includes the url, format, type and availability code of a document for every service provider. subset: data -is_obsolete: true -consider: EDAM:0000970 ! Bibliographic reference +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 [Term] -id: EDAM:0002177 +id: EDAM_data:2177 name: Exactly 1 namespace: data -def: "A single thing." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +def: "A single thing." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} [Term] -id: EDAM:0002178 +id: EDAM_data:2178 name: 1 or more namespace: data -def: "One or more things." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +def: "One or more things." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} [Term] -id: EDAM:0002179 +id: EDAM_data:2179 name: Exactly 2 namespace: data -def: "Exactly two things." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +def: "Exactly two things." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} [Term] -id: EDAM:0002180 +id: EDAM_data:2180 name: 2 or more namespace: data -def: "Two or more things." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true +def: "Two or more things." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} -! Identifier -[Term] -id: EDAM:0000973 -name: Undefined -namespace: identifier -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true +! +! Identifier +! [Term] -id: EDAM:0001121 +id: EDAM_data:1121 name: BLAST sequence alignment type namespace: identifier -def: "The type of a BLAST sequence alignment." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001120 ! Sequence alignment type +subset: identifiers +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 [Term] -id: EDAM:0000974 +id: EDAM_data:0974 name: Entity identifier namespace: identifier -def: "An identifier of a biological entity or phenomenon." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0000842 ! Identifier +subset: identifiers +subset: data +def: "An identifier of a biological entity or phenomenon." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0842 ! Identifier [Term] -id: EDAM:0000975 +id: EDAM_data:0975 name: Data resource identifier namespace: identifier -def: "An identifier of a data resource." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0000842 ! Identifier +subset: identifiers +subset: data +def: "An identifier of a data resource." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:0842 ! Identifier [Term] -id: EDAM:0000978 +id: EDAM_data:0978 name: Discrete entity identifier namespace: identifier -def: "Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0000842 ! Identifier +subset: identifiers +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 [Term] -id: EDAM:0000979 +id: EDAM_data:0979 name: Entity feature identifier namespace: identifier -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)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0000842 ! Identifier +subset: identifiers +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 [Term] -id: EDAM:0000980 +id: EDAM_data:0980 name: Entity collection identifier namespace: identifier -def: "Name or other identifier of a collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0000842 ! Identifier +subset: identifiers +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 [Term] -id: EDAM:0000981 +id: EDAM_data:0981 name: Phenomenon identifier namespace: identifier -def: "Name or other identifier of a physical, observable biological occurrence or event." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0000842 ! Identifier +subset: identifiers +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 [Term] -id: EDAM:0002091 +id: EDAM_data:2091 name: Accession namespace: identifier -alt_id: EDAM:0002862 -def: "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000842 ! Identifier +subset: identifiers +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 [Term] -id: EDAM:0002099 +id: EDAM_data:2099 name: Name namespace: identifier -alt_id: EDAM:0002863 -def: "A name of a thing, which need not necessarily uniquely identify it." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Symbolic name" EXACT [] -is_a: EDAM:0000842 ! Identifier +subset: identifiers +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 [Term] -id: EDAM:0000976 +id: EDAM_data:0976 name: Identifier (typed) namespace: identifier -def: "An identifier that identifies a particular type of data." [EDAM:EBI "EMBRACE definition"] -comment: This term 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 terms nested under 'Accession' and 'Name'. All terms under here are already included under 'Accession' or 'Name'. -subset: identifier -is_a: EDAM:0000842 ! Identifier +subset: identifiers +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 [Term] -id: EDAM:0002109 +id: EDAM_data:2109 name: Identifier (hybrid) namespace: identifier -def: "An identifier that is re-used for data objects of fundamentally different types (typically served from a single database)." [EDAM:EBI "EMBRACE definition"] -comment: This branch provides an alternative organisation of the terms nested under 'Accession' and 'Name'. All terms under here are already included under 'Accession' or 'Name'. -subset: identifier -is_a: EDAM:0000842 ! Identifier +subset: identifiers +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 [Term] -id: EDAM:0000977 +id: EDAM_data:0977 name: Tool identifier namespace: identifier -def: "An identifier of a bioinformatics tool, e.g. an application or web service." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +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) [Term] -id: EDAM:0001190 +id: EDAM_data:1190 name: Tool name namespace: identifier -def: "The name of a computer package, application, method or function." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000977 ! Tool identifier +subset: identifiers +subset: data +def: "The name of a computer package, application, method or function." [http://edamontology.org] +is_a: EDAM_data:0977 ! Tool identifier [Term] -id: EDAM:0001191 +id: EDAM_data:1191 name: Tool name (signature) namespace: identifier -def: "The unique name of a signature (sequence classifier) method." [EDAM:EBI "EMBRACE definition"] +subset: identifiers +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. -subset: identifier -is_a: EDAM:0001190 ! Tool name +is_a: EDAM_data:1190 ! Tool name [Term] -id: EDAM:0001192 +id: EDAM_data:1192 name: Tool name (BLAST) namespace: identifier -def: "The name of a BLAST tool." [EDAM:EBI "EMBRACE definition"] +subset: identifiers +subset: data +def: "The name of a BLAST tool." [http://edamontology.org] comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. -subset: identifier -synonym: "BLAST name" EXACT [] -is_a: EDAM:0001190 ! Tool name +synonym: "BLAST name" EXACT [http://edamontology.org] +is_a: EDAM_data:1190 ! Tool name [Term] -id: EDAM:0001193 +id: EDAM_data:1193 name: Tool name (FASTA) namespace: identifier -def: "The name of a FASTA tool." [EDAM:EBI "EMBRACE definition"] +subset: identifiers +subset: data +def: "The name of a FASTA tool." [http://edamontology.org] comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. -subset: identifier -is_a: EDAM:0001190 ! Tool name +is_a: EDAM_data:1190 ! Tool name [Term] -id: EDAM:0001194 +id: EDAM_data:1194 name: Tool name (EMBOSS) namespace: identifier -def: "The name of an EMBOSS application." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001190 ! Tool name +subset: identifiers +subset: data +def: "The name of an EMBOSS application." [http://edamontology.org] +is_a: EDAM_data:1190 ! Tool name [Term] -id: EDAM:0001195 +id: EDAM_data:1195 name: Tool name (EMBASSY package) namespace: identifier -def: "The name of an EMBASSY package." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001190 ! Tool name +subset: identifiers +subset: data +def: "The name of an EMBASSY package." [http://edamontology.org] +is_a: EDAM_data:1190 ! Tool name [Term] -id: EDAM:0002098 +id: EDAM_data:2098 name: Job identifier namespace: identifier -def: "An identifier of a submitted job." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +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) [Term] -id: EDAM:0001676 +id: EDAM_data:1676 name: Job ID namespace: identifier -def: "The (typically numeric) unique identifier of a submitted job." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002098 ! Job identifier +subset: identifiers +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 [Term] -id: EDAM:0002118 +id: EDAM_data:2118 name: Person identifier namespace: identifier -def: "An identifier of a software end-user (typically a person)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +subset: data +def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM:0002101 +id: EDAM_data:2101 name: User ID namespace: identifier -def: "An identifier of a software end-user (typically a person)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002118 ! Person identifier +subset: identifiers +subset: data +def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] +is_a: EDAM_data:2118 ! Person identifier [Term] -id: EDAM:0001689 +id: EDAM_data:1689 name: Username namespace: identifier -def: "A username on a computer system." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002101 ! User ID +subset: identifiers +subset: data +def: "A username on a computer system." [http://edamontology.org] +is_a: EDAM_data:2101 ! User ID [Term] -id: EDAM:0001690 +id: EDAM_data:1690 name: Password namespace: identifier -def: "A password on a computer system." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002101 ! User ID +subset: identifiers +subset: data +def: "A password on a computer system." [http://edamontology.org] +is_a: EDAM_data:2101 ! User ID [Term] -id: EDAM:0001691 +id: EDAM_data:1691 name: Email address namespace: identifier -def: "A valid email address of an end-user." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "A valid email address of an end-user." [http://edamontology.org] xref: Moby:Email xref: Moby:EmailAddress -is_a: EDAM:0002101 ! User ID +is_a: EDAM_data:2101 ! User ID [Term] -id: EDAM:0001692 +id: EDAM_data:1692 name: Person name namespace: identifier -def: "The name of a person." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002118 ! Person identifier +subset: identifiers +subset: data +def: "The name of a person." [http://edamontology.org] +is_a: EDAM_data:2118 ! Person identifier [Term] -id: EDAM:0001881 +id: EDAM_data:1881 name: Author ID namespace: identifier -def: "Information on the authors of a published work." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Information on the authors of a published work." [http://edamontology.org] xref: Moby:Author -is_a: EDAM:0002118 ! Person identifier +is_a: EDAM_data:2118 ! Person identifier [Term] -id: EDAM:0001882 +id: EDAM_data:1882 name: DragonDB author identifier namespace: identifier -def: "An identifier representing an author in the DragonDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001881 ! Author ID +subset: identifiers +subset: data +def: "An identifier representing an author in the DragonDB database." [http://edamontology.org] +is_a: EDAM_data:1881 ! Author ID [Term] -id: EDAM:0002596 +id: EDAM_data:2596 name: Catalogue identifier namespace: identifier -def: "An identifier of a catalogue of biological resources." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +subset: data +def: "An identifier of a catalogue of biological resources." [http://edamontology.org] +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM:0002779 +id: EDAM_data:2779 name: Stock number namespace: identifier -def: "An identifier of stock from a catalogue of biological resources." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession +subset: identifiers + +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 [Term] -id: EDAM:0003022 +id: EDAM_data:3022 name: NCBI genetic code ID namespace: identifier -def: "Identifier of a genetic code in the NCBI list of genetic codes." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +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:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession +example: "16" +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM:0000982 +id: EDAM_data:0982 name: Molecule identifier namespace: identifier -def: "Name or other identifier of a molecule." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0002529 ! Molecule report +subset: identifiers +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 [Term] -id: EDAM:0001015 +id: EDAM_data:1015 name: Sequence feature ID namespace: identifier -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." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002091 ! Accession -is_a: EDAM:0003034 ! Sequence feature identifier +subset: identifiers +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 [Term] -id: EDAM:0003107 +id: EDAM_data:3107 !{since=beta13} name: Sequence feature name namespace: identifier -def: "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002099 ! Name -is_a: EDAM:0003034 ! Sequence feature identifier +subset: identifiers +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 [Term] -id: EDAM:0003034 +id: EDAM_data:3034 !{since=beta13} name: Sequence feature identifier namespace: identifier -def: "Name or other identifier of molecular sequence feature(s)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002914 ! Sequence feature metadata -relationship: is_identifier_of EDAM:0001255 ! Sequence features +subset: identifiers +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 feature metadata +relationship: is_identifier_of EDAM_data:1255 ! Sequence features [Term] -id: EDAM:0001023 +id: EDAM_data:1023 name: EMBOSS Uniform Feature Object namespace: data -def: "The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"] subset: data -synonym: "UFO" EXACT [] -is_a: EDAM:0003034 ! Sequence feature identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0001893 +id: EDAM_data:1893 name: Locus ID namespace: identifier -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." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Locus name" EXACT [] -synonym: "Locus identifier" EXACT [] -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0002012 ! Map position +subset: identifiers +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 [Term] -id: EDAM:0002340 +id: EDAM_data:2340 name: Genome build identifier namespace: identifier -def: "An identifier of a build of a particular genome." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002749 ! Genome 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 [Term] -id: EDAM:0002749 +id: EDAM_data:2749 name: Genome identifier namespace: identifier -def: "An identifier of a particular genome." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +subset: data +def: "An identifier of a particular genome." [http://edamontology.org] +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM:0002903 +id: EDAM_data:2903 name: Genome accession namespace: identifier -def: "An accession of a particular genome (in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002749 ! Genome identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001025 +id: EDAM_data:1025 name: Gene identifier namespace: identifier -def: "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000916 ! Gene annotation +is_a: EDAM_data:0976 ! Identifier (typed) +relationship: is_identifier_of EDAM_data:0916 ! Gene annotation [Term] -id: EDAM:0002795 +id: EDAM_data:2795 name: ORF identifier namespace: identifier -def: "An identifier of an open reading frame." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +subset: data +def: "An identifier of an open reading frame." [http://edamontology.org] +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM:0002727 +id: EDAM_data:2727 name: Promoter ID namespace: identifier -def: "An identifier of a promoter of a gene that is catalogued in a database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM:0002630 +id: EDAM_data:2630 name: Mobile genetic element ID namespace: identifier -def: "An identifier of a mobile genetic element." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002127 +id: EDAM_data:2127 name: Genetic code identifier namespace: identifier -def: "An identifier of a genetic code." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0001598 ! Genetic code +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 [Term] -id: EDAM:0001038 +id: EDAM_data:1038 name: Protein domain ID namespace: identifier -def: "Identifier of a protein structural domain." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0001468 ! Protein domain +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:0002618 +id: EDAM_data:2618 name: Protein modification ID namespace: identifier -def: "Identifier of a protein modification catalogued in a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001867 +id: EDAM_data:1867 name: Protein fold name namespace: identifier -def: "The name of a protein fold." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002099 ! Name +subset: identifiers +subset: data +def: "The name of a protein fold." [http://edamontology.org] +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM:0002655 +id: EDAM_data:2655 name: Cell type identifier namespace: identifier -def: "A unique identifier of a type or group of cells." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +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) [Term] -id: EDAM:0002893 +id: EDAM_data:2893 name: Cell type accession namespace: identifier -def: "Accession of a type or group of cells (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002655 ! Cell type identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001869 +id: EDAM_data:1869 name: Organism identifier namespace: identifier -def: "A unique identifier of a (group of) organisms." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0002530 ! Organism annotation +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 [Term] -id: EDAM:0002908 +id: EDAM_data:2908 name: Organism accession namespace: identifier -def: "An accession of annotation on a (group of) organisms (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001869 ! Organism identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002909 +id: EDAM_data:2909 name: Organism name namespace: identifier -def: "The name of an organism (or group of organisms)." [EDAM:EBI "EMBRACE definition"] -subset: 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 @@ -18091,5260 +17947,5801 @@ xref: Moby:FirstEpithet xref: Moby:InfraspecificEpithet xref: Moby:OccurrenceRecord xref: Moby:BriefOccurrenceRecord -is_a: EDAM:0001869 ! Organism identifier -is_a: EDAM:0002099 ! Name +is_a: EDAM_data:1869 ! Organism identifier +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM:0001048 +id: EDAM_data:1048 name: Database identifier namespace: identifier -def: "An identifier of a biological or bioinformatics database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000957 ! Database metadata +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 [Term] -id: EDAM:0001049 +id: EDAM_data:1049 name: Directory name namespace: identifier -def: "The name of a directory." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002099 ! Name -is_a: EDAM:0000583 ! Directory metadata +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 [Term] -id: EDAM:0001050 +id: EDAM_data:1050 name: File name namespace: identifier -def: "The name (or part of a name) of a file (of any type)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0001051 +id: EDAM_data:1051 name: Ontology name namespace: identifier -def: "Name of an ontology of biological or bioinformatics terms and relations." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002099 ! Name -is_a: EDAM:0002338 ! Ontology identifier -relationship: is_identifier_of EDAM:0000582 ! Ontology +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 [Term] -id: EDAM:0002110 +id: EDAM_data:2110 name: Molecular property identifier namespace: identifier -def: "Identifier of a molecular property." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0002087 ! Molecular property +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 [Term] -id: EDAM:0001062 +id: EDAM_data:1062 name: Database entry identifier namespace: identifier -def: "An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type." [EDAM:EBI "EMBRACE definition"] -comment: This term is required for completeness. It should never have child terms. -subset: identifier -is_obsolete: true -consider: EDAM:0000842 ! 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 [Term] -id: EDAM:0002117 +id: EDAM_data:2117 name: Map identifier namespace: identifier -def: "An identifier of a map of a molecular sequence." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0001274 ! Map +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 [Term] -id: EDAM:0002904 +id: EDAM_data:2904 name: Map accession namespace: identifier -def: "An accession of a map of a molecular sequence (deposited in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002117 ! Map identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001063 +id: EDAM_data:1063 name: Sequence identifier namespace: identifier -def: "An identifier of molecular sequence(s) or entries from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0000855 ! Sequence metadata -relationship: is_identifier_of EDAM:0002044 ! Sequence +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 [Term] -id: EDAM:0002294 +id: EDAM_data:2294 name: Sequence variation ID namespace: identifier -def: "An identifier of an entry from a database of molecular sequence variation." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001064 +id: EDAM_data:1064 name: Sequence set ID namespace: identifier -def: "An identifier of a set of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000850 ! Sequence set +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 [Term] -id: EDAM:0001065 +id: EDAM_data:1065 name: Sequence signature identifier namespace: identifier -def: "Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001114 ! Sequence motif identifier -consider: EDAM:0001115 ! Sequence profile ID +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 [Term] -id: EDAM:0001066 +id: EDAM_data:1066 name: Sequence alignment ID namespace: identifier -def: "Identifier of a molecular sequence alignment, for example a record from an alignment database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000863 ! Sequence alignment +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 [Term] -id: EDAM:0001067 +id: EDAM_data:1067 name: Phylogenetic distance matrix identifier namespace: identifier -def: "Identifier of a phylogenetic distance matrix." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0000976 ! Identifier (typed) +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) [Term] -id: EDAM:0001068 +id: EDAM_data:1068 name: Phylogenetic tree ID namespace: identifier -def: "Identifier of a phylogenetic tree for example from a phylogenetic tree database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000872 ! Phylogenetic tree +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 [Term] -id: EDAM:0003036 +id: EDAM_data:3036 !{since=beta13} name: Matrix identifier namespace: identifier -def: "An identifier of an array of numerical values, such as a comparison matrix." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0002082 ! Matrix +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 [Term] -id: EDAM:0001069 +id: EDAM_data:1069 name: Comparison matrix identifier namespace: identifier -def: "An identifier of a comparison matrix." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Substitution matrix identifier" EXACT [] -is_a: EDAM:0003036 ! Matrix identifier -relationship: is_identifier_of EDAM:0000874 ! Comparison matrix +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 [Term] -id: EDAM:0003035 +id: EDAM_data:3035 !{since=beta13} name: Structure identifier namespace: identifier -def: "An identifier of a molecular tertiary structure, typically an entry from a structure database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000883 ! Structure +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 [Term] -id: EDAM:0001070 +id: EDAM_data:1070 name: Structure ID namespace: identifier -def: "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0003035 ! Structure identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001759 +id: EDAM_data:1759 name: PDB model number namespace: identifier -def: "Identifier of a model structure from a PDB file." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Model number" EXACT [] +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:0003035 ! Structure identifier +is_a: EDAM_data:3035 ! Structure identifier ! pdbx_PDB_model_num in PDBML [Term] -id: EDAM:0001071 +id: EDAM_data:1071 name: Structural (3D) profile ID namespace: identifier -def: "Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Structural profile identifier" EXACT [] -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000889 ! Structural (3D) profile +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 [Term] -id: EDAM:0001072 +id: EDAM_data:1072 name: Structure alignment ID namespace: identifier -def: "Identifier of an entry from a database of tertiary structure alignments." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000886 ! Structure alignment +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 [Term] -id: EDAM:0001073 +id: EDAM_data:1073 name: Amino acid index ID namespace: identifier -def: "Identifier of an index of amino acid physicochemical and biochemical property data." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0003036 ! Matrix identifier -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0001501 ! Amino acid index +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 [Term] -id: EDAM:0002627 +id: EDAM_data:2627 name: Molecular interaction ID namespace: identifier -def: "Identifier of a report of molecular interactions from a database (typically)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0002599 ! Molecular interaction +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 [Term] -id: EDAM:0001075 +id: EDAM_data:1075 name: Protein family identifier namespace: identifier -def: "Identifier of a protein family." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Protein secondary database record identifier" EXACT [] -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000907 ! Protein family +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 [Term] -id: EDAM:0002910 +id: EDAM_data:2910 name: Protein family accession namespace: identifier -def: "Accession of a protein family (that is deposited in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002091 ! Accession -is_a: EDAM:0001075 ! Protein family 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 [Term] -id: EDAM:0001131 +id: EDAM_data:1131 name: Protein family name namespace: identifier -def: "Name of a protein family." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001075 ! Protein family identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002355 +id: EDAM_data:2355 name: RNA family identifier namespace: identifier -def: "Identifier of an RNA family, typically an entry from a RNA sequence classification database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0002354 ! RNA family annotation +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 [Term] -id: EDAM:0002111 +id: EDAM_data:2111 name: Codon usage table identifier namespace: identifier -def: "Identifier of a codon usage table, for example a genetic code." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0001597 ! Codon usage table -relationship: is_identifier_of EDAM:0001598 ! Genetic code +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 [Term] -id: EDAM:0001077 +id: EDAM_data:1077 name: Transcription factor identifier namespace: identifier -def: "Identifier of a transcription factor (or a TF binding site)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0000989 ! Protein identifier -relationship: is_identifier_of EDAM:0001315 ! Gene features (TFBS) +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) [Term] -id: EDAM:0002911 +id: EDAM_data:2911 name: Transcription factor accession namespace: identifier -def: "Accession of an entry from a database of transcription factors or binding sites." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001077 ! Transcription factor identifier -is_a: EDAM:0002907 ! Protein accession -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001078 +id: EDAM_data:1078 name: Microarray experiment annotation ID namespace: identifier -def: "Identifier of an entry from a database of microarray data." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000931 ! Microarray experiment annotation +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 ! Microarray experiment annotation [Term] -id: EDAM:0001079 +id: EDAM_data:1079 name: Electron microscopy model ID namespace: identifier -def: "Identifier of an entry from a database of electron microscopy data." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000941 ! Electron microscopy model +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 [Term] -id: EDAM:0001080 +id: EDAM_data:1080 name: Gene expression report ID namespace: identifier -alt_id: EDAM:0002708 -def: "Accession of a report of gene expression (e.g. a gene expression profile) from a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Gene expression profile identifier" EXACT [] -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0003111 ! Processed microarray data +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 [Term] -id: EDAM:0001081 +id: EDAM_data:1081 name: Genotype and phenotype annotation ID namespace: identifier -def: "Identifier of an entry from a database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000920 ! Genotype and phenotype annotation +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 and phenotype annotation [Term] -id: EDAM:0002382 +id: EDAM_data:2382 name: Genotype experiment ID namespace: identifier -def: "Identifier of an entry from a database of genotype experiment metadata." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0002381 ! Experiment annotation (genotype) +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) [Term] -id: EDAM:0002638 +id: EDAM_data:2638 name: PubChem bioassay ID namespace: identifier -def: "Identifier of an assay from the PubChem database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of an assay from the PubChem database." [http://edamontology.org] regex: "[0-9]+" -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002639 ! PubChem identifier +is_a: EDAM_data:0976 ! Identifier (typed) +is_a: EDAM_data:2639 ! PubChem identifier [Term] -id: EDAM:0001082 +id: EDAM_data:1082 name: Pathway or network identifier namespace: identifier -def: "Identifier of an entry from a database of biological pathways or networks." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0002600 ! Pathway or network +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 [Term] -id: EDAM:0002590 +id: EDAM_data:2590 name: Hierarchy identifier namespace: identifier -def: "Identifier of an entry from a database of biological hierarchies." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0002891 ! Biological model accession +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 [Term] -id: EDAM:0002108 +id: EDAM_data:2108 name: Reaction ID namespace: identifier -def: "Identifier of a biological reaction from a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002091 ! Accession -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0002978 ! Reaction data +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 [Term] -id: EDAM:0001083 +id: EDAM_data:1083 name: Workflow ID namespace: identifier -def: "Identifier of a biological or biomedical workflow, typically from a database of workflows." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0002972 ! Workflow +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 [Term] -id: EDAM:0001084 +id: EDAM_data:1084 name: Data resource definition identifier namespace: identifier -def: "Identifier of a data type definition from some provider." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +subset: data +def: "Identifier of a data type definition from some provider." [http://edamontology.org] +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM:0002219 +id: EDAM_data:2219 name: Database field name namespace: identifier -def: "The name of a field in a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002099 ! Name +subset: identifiers +subset: data +def: "The name of a field in a database." [http://edamontology.org] +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM:0001085 +id: EDAM_data:1085 name: Biological model identifier namespace: identifier -def: "Identifier of a mathematical model, typically an entry from a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000950 ! Biological model +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 [Term] -id: EDAM:0002891 +id: EDAM_data:2891 name: Biological model accession namespace: identifier -def: "Accession of a mathematical model, typically an entry from a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001085 ! Biological model identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001086 +id: EDAM_data:1086 name: Compound identifier namespace: identifier -def: "Identifier of an entry from a database of chemicals." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Small molecule identifier" EXACT [] -synonym: "Chemical compound identifier" EXACT [] -is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0000962 ! Small molecule annotation -relationship: is_identifier_of EDAM:0001712 ! Structure image (small molecule) -relationship: is_identifier_of EDAM:0000846 ! Chemical formula +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 [Term] -id: EDAM:0002894 +id: EDAM_data:2894 name: Compound accession namespace: identifier -def: "Accession of an entry from a database of chemicals." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Small molecule accession" EXACT [] -synonym: "Chemical compound accession" EXACT [] -is_a: EDAM:0001086 ! Compound identifier -is_a: EDAM:0002901 ! Molecule accession +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 [Term] -id: EDAM:0002338 +id: EDAM_data:2338 name: Ontology identifier namespace: identifier -def: "Any arbitrary identifier of an ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000582 ! Ontology +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 [Term] -id: EDAM:0003025 -name: Ontology term identifier +id: EDAM_data:3025 +name: Ontology concept identifier namespace: identifier -def: "Identifier of a term in an ontology of biological or bioinformatics terms and relations." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0002858 ! Ontology concept +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 [Term] -id: EDAM:0001087 -name: Ontology term ID +id: EDAM_data:1087 +name: Ontology concept ID namespace: identifier -def: "A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics terms and relations." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Ontology concept ID" EXACT [] -is_a: EDAM:0003025 ! Ontology term identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001088 +id: EDAM_data:1088 name: Article ID namespace: identifier -def: "Unique identifier of a scientific article." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002091 ! Accession -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000971 ! Article +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 [Term] -id: EDAM:0002633 +id: EDAM_data:2633 name: Book ID namespace: identifier -def: "Unique identifier of a book." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002091 ! Accession -is_a: EDAM:0000976 ! Identifier (typed) +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) [Term] -id: EDAM:0002790 +id: EDAM_data:2790 name: Gel identifier namespace: identifier -def: "Identifier of a two-dimensional (protein) gel." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +subset: data +def: "Identifier of a two-dimensional (protein) gel." [http://edamontology.org] +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM:0002791 +id: EDAM_data:2791 name: Reference map name (SWISS-2DPAGE) namespace: identifier -def: "Name of a reference map gel from the SWISS-2DPAGE database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002790 ! Gel identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002373 +id: EDAM_data:2373 name: Spot ID namespace: identifier -def: "Unique identifier of a spot from a two-dimensional (protein) gel." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002587 +id: EDAM_data:2587 name: Blot ID namespace: identifier -def: "Unique identifier of a blot from a Northern Blot." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002091 ! Accession -is_a: EDAM:0000976 ! Identifier (typed) +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) [Term] -id: EDAM:0002379 +id: EDAM_data:2379 name: Strain identifier namespace: identifier -def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001869 ! Organism 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 [Term] -id: EDAM:0002912 +id: EDAM_data:2912 name: Strain accession namespace: identifier -def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002379 ! Strain identifier -is_a: EDAM:0002908 ! Organism accession -relationship: is_identifier_of EDAM:0000963 ! Cell line annotation +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 [Term] -id: EDAM:0002917 +id: EDAM_data:2917 name: ConsensusPathDB identifier namespace: identifier -def: "An identifier of an entity from the ConsensusPathDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002109 ! Identifier (hybrid) +subset: identifiers +subset: data +def: "An identifier of an entity from the ConsensusPathDB database." [http://edamontology.org] +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM:0002776 +id: EDAM_data:2776 name: ConsensusPathDB entity ID namespace: identifier -def: "Identifier of a physical entity from the ConsensusPathDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002917 ! ConsensusPathDB identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002777 +id: EDAM_data:2777 name: ConsensusPathDB entity name namespace: identifier -def: "Name of a physical entity from the ConsensusPathDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002917 ! ConsensusPathDB identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002639 +id: EDAM_data:2639 name: PubChem identifier namespace: identifier -def: "Identifier of an entry from the PubChem database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002367 +id: EDAM_data:2367 name: ASTD ID namespace: identifier -def: "Identifier of an object from the ASTD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001089 +id: EDAM_data:1089 name: FlyBase ID namespace: identifier -def: "Identifier of an object from the FlyBase database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM:0002113 +id: EDAM_data:2113 name: WormBase identifier namespace: identifier -def: "Identifier of an object from the WormBase database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002109 ! Identifier (hybrid) +subset: identifiers +subset: data +def: "Identifier of an object from the WormBase database." [http://edamontology.org] +is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] -id: EDAM:0002104 +id: EDAM_data:2104 name: BioCyc ID namespace: identifier -def: "Identifier of an object from one of the BioCyc databases." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001154 +id: EDAM_data:1154 name: KEGG object identifier namespace: identifier -def: "Unique identifier of an object from one of the KEGG databases (excluding the GENES division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002380 +id: EDAM_data:2380 name: CABRI accession namespace: identifier -def: "A unique identifier of an item from the CABRI database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002387 +id: EDAM_data:2387 name: TAIR accession namespace: identifier -def: "Identifier of an entry from the TAIR database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002610 +id: EDAM_data:2610 name: Ensembl ID namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM:0002620 +id: EDAM_data:2620 name: RGD ID namespace: identifier -def: "Identifier of an entry from the RGD database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM:0002632 +id: EDAM_data:2632 name: SGD ID namespace: identifier -def: "Identifier of an entry from the Saccharomyces genome database (SGD)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM:0002649 +id: EDAM_data:2649 name: PharmGKB ID namespace: identifier -def: "Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002109 ! Identifier (hybrid) -is_a: EDAM:0002091 ! Accession +is_a: EDAM_data:2109 ! Identifier (hybrid) +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM:0002368 +id: EDAM_data:2368 name: ASTD ID (exon) namespace: identifier -def: "Identifier of an exon from the ASTD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002367 ! ASTD ID +subset: identifiers +subset: data +def: "Identifier of an exon from the ASTD database." [http://edamontology.org] +is_a: EDAM_data:2367 ! ASTD ID [Term] -id: EDAM:0002369 +id: EDAM_data:2369 name: ASTD ID (intron) namespace: identifier -def: "Identifier of an intron from the ASTD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002367 ! ASTD ID +subset: identifiers +subset: data +def: "Identifier of an intron from the ASTD database." [http://edamontology.org] +is_a: EDAM_data:2367 ! ASTD ID [Term] -id: EDAM:0002370 +id: EDAM_data:2370 name: ASTD ID (polya) namespace: identifier -def: "Identifier of a polyA signal from the ASTD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002367 ! ASTD ID +subset: identifiers +subset: data +def: "Identifier of a polyA signal from the ASTD database." [http://edamontology.org] +is_a: EDAM_data:2367 ! ASTD ID [Term] -id: EDAM:0002371 +id: EDAM_data:2371 name: ASTD ID (tss) namespace: identifier -def: "Identifier of a transcription start site from the ASTD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002367 ! ASTD ID +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 [Term] -id: EDAM:0002671 +id: EDAM_data:2671 name: Ensembl ID (Homo sapiens) namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002672 +id: EDAM_data:2672 name: Ensembl ID ("Bos taurus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Bos taurus" division)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002673 +id: EDAM_data:2673 name: Ensembl ID ("Canis familiaris") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Canis familiaris" division)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002674 +id: EDAM_data:2674 name: Ensembl ID ("Cavia porcellus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Cavia porcellus" division)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002675 +id: EDAM_data:2675 name: Ensembl ID ("Ciona intestinalis") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Ciona intestinalis" division)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002676 +id: EDAM_data:2676 name: Ensembl ID ("Ciona savignyi") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Ciona savignyi" division)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002677 +id: EDAM_data:2677 name: Ensembl ID ("Danio rerio") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Danio rerio" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002678 +id: EDAM_data:2678 name: Ensembl ID ("Dasypus novemcinctus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Dasypus novemcinctus" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002679 +id: EDAM_data:2679 name: Ensembl ID ("Echinops telfairi") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Echinops telfairi" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002680 +id: EDAM_data:2680 name: Ensembl ID ("Erinaceus europaeus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Erinaceus europaeus" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002681 +id: EDAM_data:2681 name: Ensembl ID ("Felis catus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Felis catus" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002682 +id: EDAM_data:2682 name: Ensembl ID ("Gallus gallus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Gallus gallus" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002683 +id: EDAM_data:2683 name: Ensembl ID ("Gasterosteus aculeatus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Gasterosteus aculeatus" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002684 +id: EDAM_data:2684 name: Ensembl ID ("Homo sapiens") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Homo sapiens" division)." [EDAM:EBI "EMBRACE definition"] -subset: 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: "ENSHUM([EGTP])[0-9]{11}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002685 +id: EDAM_data:2685 name: Ensembl ID ("Loxodonta africana") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Loxodonta africana" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002686 +id: EDAM_data:2686 name: Ensembl ID ("Macaca mulatta") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Macaca mulatta" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002687 +id: EDAM_data:2687 name: Ensembl ID ("Monodelphis domestica") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Monodelphis domestica" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002688 +id: EDAM_data:2688 name: Ensembl ID ("Mus musculus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Mus musculus" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002689 +id: EDAM_data:2689 name: Ensembl ID ("Myotis lucifugus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Myotis lucifugus" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002690 +id: EDAM_data:2690 name: Ensembl ID ("Ornithorhynchus anatinus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Ornithorhynchus anatinus" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002691 +id: EDAM_data:2691 name: Ensembl ID ("Oryctolagus cuniculus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Oryctolagus cuniculus" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002692 +id: EDAM_data:2692 name: Ensembl ID ("Oryzias latipes") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Oryzias latipes" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002693 +id: EDAM_data:2693 name: Ensembl ID ("Otolemur garnettii") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Otolemur garnettii" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002694 +id: EDAM_data:2694 name: Ensembl ID ("Pan troglodytes") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Pan troglodytes" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002695 +id: EDAM_data:2695 name: Ensembl ID ("Rattus norvegicus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Rattus norvegicus" division)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002696 +id: EDAM_data:2696 name: Ensembl ID ("Spermophilus tridecemlineatus") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Spermophilus tridecemlineatus" division)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002697 +id: EDAM_data:2697 name: Ensembl ID ("Takifugu rubripes") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Takifugu rubripes" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002698 +id: EDAM_data:2698 name: Ensembl ID ("Tupaia belangeri") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Tupaia belangeri" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002699 +id: EDAM_data:2699 name: Ensembl ID ("Xenopus tropicalis") namespace: identifier -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Xenopus tropicalis" division)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +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}" -is_obsolete: true -consider: EDAM:0002610 ! Ensembl ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:2610 ! Ensembl ID [Term] -id: EDAM:0002725 +id: EDAM_data:2725 name: Transcript ID (Ensembl) namespace: identifier -def: "Unique identifier for a gene transcript from the Ensembl database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Ensembl Transcript ID" EXACT [] -is_a: EDAM:0002610 ! Ensembl ID -is_a: EDAM:0002769 ! Transcript ID +subset: identifiers +subset: data +def: "Unique identifier for a gene transcript from the Ensembl database." [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 [Term] -id: EDAM:0002597 +id: EDAM_data:2597 name: CABRI catalogue name namespace: identifier -def: "The name of a catalogue of biological resources from the CABRI database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002596 ! Catalogue identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002780 +id: EDAM_data:2780 name: Stock number (TAIR) namespace: identifier -def: "A stock number from The Arabidopsis information resource (TAIR)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002779 ! Stock number +subset: identifiers +subset: data +def: "A stock number from The Arabidopsis information resource (TAIR)." [http://edamontology.org] +is_a: EDAM_data:2779 ! Stock number [Term] -id: EDAM:0002129 +id: EDAM_data:2129 name: File format name namespace: identifier -def: "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002099 ! Name +subset: identifiers +subset: data +def: "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." [http://edamontology.org] +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM:0002131 +id: EDAM_data:2131 name: Operating system name namespace: identifier -def: "Name of a computer operating system such as Linux, PC or Mac." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002099 ! Name +subset: identifiers +subset: data +def: "Name of a computer operating system such as Linux, PC or Mac." [http://edamontology.org] +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM:0002538 +id: EDAM_data:2538 name: Mutation identifier namespace: identifier -def: "An identifier of a mutation." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +subset: data +def: "An identifier of a mutation." [http://edamontology.org] +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM:0002209 +id: EDAM_data:2209 name: Mutation ID namespace: identifier -def: "A unique identifier of a specific mutation catalogued in a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002538 ! Mutation identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002133 +id: EDAM_data:2133 name: Logical operator namespace: identifier -def: "A logical operator such as OR, AND, XOR, and NOT." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002099 ! Name +subset: identifiers +subset: data +def: "A logical operator such as OR, AND, XOR, and NOT." [http://edamontology.org] +is_a: EDAM_data:2099 ! Name [Term] -id: EDAM:0001114 +id: EDAM_data:1114 name: Sequence motif identifier namespace: identifier -def: "Identifier of a sequence motif, for example an entry from a motif database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0001353 ! Sequence motif +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 [Term] -id: EDAM:0001115 +id: EDAM_data:1115 name: Sequence profile ID namespace: identifier -def: "Identifier of a sequence profile." [EDAM:EBI "EMBRACE definition"] +subset: identifiers +subset: data +def: "Identifier of a sequence profile." [http://edamontology.org] comment: A sequence profile typically represents a sequence alignment. -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0001354 ! Sequence profile +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:0002660 +id: EDAM_data:2660 name: BioNumbers ID namespace: identifier -def: "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002091 ! Accession +is_a: EDAM_data:2091 ! Accession [Term] -id: EDAM:0000983 +id: EDAM_data:0983 name: Atom identifier namespace: identifier -def: "Identifier (e.g. character symbol) of a specific atom." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +subset: identifiers +subset: data +def: "Identifier (e.g. character symbol) of a specific atom." [http://edamontology.org] +is_a: EDAM_data:0976 ! Identifier (typed) [Term] -id: EDAM:0000984 +id: EDAM_data:0984 name: Molecule name namespace: identifier -def: "Name of a specific molecule." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000982 ! Molecule identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002901 +id: EDAM_data:2901 name: Molecule accession namespace: identifier -def: "Accession of a specific molecule (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000982 ! Molecule identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0000986 +id: EDAM_data:0986 name: Chemical identifier namespace: identifier -def: "Unique identifier of a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001086 ! Compound 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 [Term] -id: EDAM:0002119 +id: EDAM_data:2119 name: Nucleic acid identifier namespace: identifier -def: "Name or other identifier of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0002084 ! Nucleic acid report +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 [Term] -id: EDAM:0000988 +id: EDAM_data:0988 name: Peptide identifier namespace: identifier -def: "Identifier of a peptide chain." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000982 ! Molecule identifier +subset: identifiers +subset: data +def: "Identifier of a peptide chain." [http://edamontology.org] +is_a: EDAM_data:0982 ! Molecule identifier [Term] -id: EDAM:0002906 +id: EDAM_data:2906 name: Peptide ID namespace: identifier -def: "Accession of a peptide deposited in a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000988 ! Peptide identifier -is_a: EDAM:0002901 ! Molecule accession +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 [Term] -id: EDAM:0001008 +id: EDAM_data:1008 name: Polypeptide chain ID namespace: identifier -def: "Identifier of a polypeptide chain from a protein." [EDAM:EBI "EMBRACE definition"] +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 -subset: identifier -synonym: "Polypeptide chain identifier" EXACT [] -synonym: "Protein chain identifier" EXACT [] -synonym: "PDB chain identifier" EXACT [] -synonym: "Chain identifier" EXACT [] -synonym: "PDB strand id" EXACT [] +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:0000988 ! Peptide identifier -relationship: is_identifier_of EDAM:0001467 ! Protein chain +is_a: EDAM_data:0988 ! Peptide identifier +relationship: is_identifier_of EDAM_data:1467 ! Protein chain ! pdbx_PDB_strand_id in PDBML [Term] -id: EDAM:0000989 +id: EDAM_data:0989 name: Protein identifier namespace: identifier -def: "Identifier of a protein." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0000896 ! Protein report +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 [Term] -id: EDAM:0002907 +id: EDAM_data:2907 name: Protein accession namespace: identifier -def: "Accession of a protein deposited in a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000989 ! Protein identifier -is_a: EDAM:0002901 ! Molecule accession +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 [Term] -id: EDAM:0001757 +id: EDAM_data:1757 name: Atom name namespace: identifier -def: "Name of an atom." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000983 ! Atom identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0001748 +id: EDAM_data:1748 name: PDB atom name namespace: identifier -def: "Identifier (a string) of a specific atom from a PDB file for a molecular structure." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001757 ! Atom name +is_a: EDAM_data:1757 ! Atom name ! pdbx_PDB_atom_name in PDBML [Term] -id: EDAM:0000990 +id: EDAM_data:0990 name: Compound name namespace: identifier -def: "Unique name of a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Chemical name" EXACT [] -is_a: EDAM:0001086 ! Compound identifier -is_a: EDAM:0000984 ! Molecule name +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 [Term] -id: EDAM:0000991 +id: EDAM_data:0991 name: Chemical registry number namespace: identifier -def: "Unique registry number of a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002894 ! Compound accession +subset: identifiers +subset: data +def: "Unique registry number of a chemical compound." [http://edamontology.org] +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM:0000992 +id: EDAM_data:0992 name: Ligand identifier namespace: identifier -def: "Code word for a ligand, for example from a PDB file." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001086 ! Compound 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 [Term] -id: EDAM:0000993 +id: EDAM_data:0993 name: Drug identifier namespace: identifier -def: "Identifier of a drug." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0002851 ! Drug structure +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 [Term] -id: EDAM:0002895 +id: EDAM_data:2895 name: Drug accession namespace: identifier -def: "Accession of a drug." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000993 ! Drug identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002899 +id: EDAM_data:2899 name: Drug name namespace: identifier -def: "Common name of a drug." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000993 ! Drug identifier -is_a: EDAM:0000990 ! Compound name +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 [Term] -id: EDAM:0002576 +id: EDAM_data:2576 name: Toxin identifier namespace: identifier -def: "Identifier of a toxin." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0002852 ! Toxin structure +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 [Term] -id: EDAM:0002896 +id: EDAM_data:2896 name: Toxin name namespace: identifier -def: "Name of a toxin." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002576 ! Toxin identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002897 +id: EDAM_data:2897 name: Toxin accession namespace: identifier -def: "Accession of a toxin (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002576 ! Toxin identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0000994 +id: EDAM_data:0994 name: Amino acid identifier namespace: identifier -def: "Identifier of an amino acid." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Residue identifier" EXACT [] -is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0002016 ! Amino acid property +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 [Term] -id: EDAM:0000995 +id: EDAM_data:0995 name: Nucleotide identifier namespace: identifier -def: "Name or other identifier of a nucleotide." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001086 ! Compound identifier +subset: identifiers +subset: data +def: "Name or other identifier of a nucleotide." [http://edamontology.org] +is_a: EDAM_data:1086 ! Compound identifier [Term] -id: EDAM:0000996 +id: EDAM_data:0996 name: Monosaccharide identifier namespace: identifier -def: "Identifier of a monosaccharide." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001086 ! Compound identifier +subset: identifiers +subset: data +def: "Identifier of a monosaccharide." [http://edamontology.org] +is_a: EDAM_data:1086 ! Compound identifier [Term] -id: EDAM:0002898 +id: EDAM_data:2898 name: Monosaccharide accession namespace: identifier -def: "Accession of a monosaccharide (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000996 ! Monosaccharide identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002812 +id: EDAM_data:2812 name: Lipid identifier namespace: identifier -def: "Identifier of a lipid." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0002850 ! Lipid structure -relationship: is_identifier_of EDAM:0002879 ! Lipid structure report +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 [Term] -id: EDAM:0002905 +id: EDAM_data:2905 name: Lipid accession namespace: identifier -def: "Accession of an entry from a database of lipids." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002812 ! Lipid identifier -is_a: EDAM:0002901 ! Molecule accession +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 [Term] -id: EDAM:0002663 +id: EDAM_data:2663 name: Carbohydrate identifier namespace: identifier -def: "Identifier of a carbohydrate." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0002313 ! Carbohydrate structure report -relationship: is_identifier_of EDAM:0001462 ! Carbohydrate structure +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 [Term] -id: EDAM:0002900 +id: EDAM_data:2900 name: Carbohydrate accession namespace: identifier -def: "Accession of an entry from a database of carbohydrates." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002663 ! Carbohydrate identifier -is_a: EDAM:0002901 ! Molecule accession +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 [Term] -id: EDAM:0002605 +id: EDAM_data:2605 name: Compound ID (KEGG) namespace: identifier -def: "Unique identifier of a chemical compound from the KEGG database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "KEGG compound ID" EXACT [] -synonym: "KEGG compound identifier" EXACT [] +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:0002894 ! Compound accession -is_a: EDAM:0001154 ! KEGG object identifier +is_a: EDAM_data:2894 ! Compound accession +is_a: EDAM_data:1154 ! KEGG object identifier [Term] -id: EDAM:0002580 +id: EDAM_data:2580 name: BindingDB Monomer ID namespace: identifier -def: "Unique identifier of a monomer from the BindingDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002894 ! Compound accession +subset: identifiers +subset: data +def: "Unique identifier of a monomer from the BindingDB database." [http://edamontology.org] +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM:0001172 +id: EDAM_data:1172 name: PubChem CID namespace: identifier -def: "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "PubChem compound accession identifier" EXACT [] +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:0002894 ! Compound accession -is_a: EDAM:0002639 ! PubChem identifier +is_a: EDAM_data:2894 ! Compound accession +is_a: EDAM_data:2639 ! PubChem identifier [Term] -id: EDAM:0001173 +id: EDAM_data:1173 name: ChemSpider ID namespace: identifier -def: "Identifier of an entry from the ChemSpider database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of an entry from the ChemSpider database." [http://edamontology.org] regex: "[0-9]+" -is_a: EDAM:0002894 ! Compound accession +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM:0001174 +id: EDAM_data:1174 name: ChEBI ID namespace: identifier -def: "Identifier of an entry from the ChEBI database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "ChEBI identifier" EXACT [] +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:0002894 ! Compound accession +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM:0002105 +id: EDAM_data:2105 name: Compound ID (BioCyc) namespace: identifier -def: "Identifier of a compound from the BioCyc chemical compounds database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "BioCyc compound ID" EXACT [] -synonym: "BioCyc compound identifier" EXACT [] -is_a: EDAM:0002104 ! BioCyc ID -is_a: EDAM:0002894 ! Compound accession +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 [Term] -id: EDAM:0002622 +id: EDAM_data:2622 name: Compound ID (HMDB) namespace: identifier -def: "Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "HMDB ID" EXACT [] +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:0002894 ! Compound accession +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM:0002635 +id: EDAM_data:2635 name: Compound ID (3DMET) namespace: identifier -def: "Identifier of a metabolite from the 3DMET database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "3DMET ID" EXACT [] +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:0002894 ! Compound accession +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM:0002646 +id: EDAM_data:2646 name: Compound ID (ChEMBL) namespace: identifier -def: "Identifier of a small molecular from the ChEMBL database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "ChEMBL ID" EXACT [] +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:0002894 ! Compound accession +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM:0002658 +id: EDAM_data:2658 name: Compound ID (ChemIDplus) namespace: identifier -def: "Identifier of a chemical from the ChemIDplus database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "ChemIDplus ID" EXACT [] +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:0002894 ! Compound accession +is_a: EDAM_data:2894 ! Compound accession [Term] -id: EDAM:0000997 +id: EDAM_data:0997 name: Chemical name (ChEBI) namespace: identifier -def: "Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "ChEBI chemical name" EXACT [] -is_a: EDAM:0000990 ! Compound name +synonym: "ChEBI chemical name" EXACT [http://edamontology.org] +is_a: EDAM_data:0990 ! Compound name [Term] -id: EDAM:0000998 +id: EDAM_data:0998 name: Chemical name (IUPAC) namespace: identifier -def: "IUPAC recommended name of a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "IUPAC chemical name" EXACT [] -is_a: EDAM:0000990 ! Compound name +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 [Term] -id: EDAM:0000999 +id: EDAM_data:0999 name: Chemical name (INN) namespace: identifier -def: "International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "INN chemical name" EXACT [] -is_a: EDAM:0000990 ! Compound name +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 [Term] -id: EDAM:0001000 +id: EDAM_data:1000 name: Chemical name (brand) namespace: identifier -def: "Brand name of a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Brand chemical name" EXACT [] -is_a: EDAM:0000990 ! Compound name +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 [Term] -id: EDAM:0001001 +id: EDAM_data:1001 name: Chemical name (synonymous) namespace: identifier -def: "Synonymous name of a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Synonymous chemical name" EXACT [] -is_a: EDAM:0000990 ! Compound name +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 [Term] -id: EDAM:0001002 +id: EDAM_data:1002 name: Chemical registry number (CAS) namespace: identifier -def: "CAS registry number of a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "CAS chemical registry number" EXACT [] -is_a: EDAM:0000991 ! Chemical registry number +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 [Term] -id: EDAM:0001003 +id: EDAM_data:1003 name: Chemical registry number (Beilstein) namespace: identifier -def: "Beilstein registry number of a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Beilstein chemical registry number" EXACT [] -is_a: EDAM:0000991 ! Chemical registry number +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 [Term] -id: EDAM:0001004 +id: EDAM_data:1004 name: Chemical registry number (Gmelin) namespace: identifier -def: "Gmelin registry number of a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Gmelin chemical registry number" EXACT [] -is_a: EDAM:0000991 ! Chemical registry number +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 [Term] -id: EDAM:0001005 +id: EDAM_data:1005 name: HET group name namespace: identifier -def: "3-letter code word for a ligand (HET group) from a PDB file, for example ATP." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Short ligand name" EXACT [] -synonym: "Component identifier code" EXACT [] -is_a: EDAM:0000990 ! Compound name +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 [Term] -id: EDAM:0002613 +id: EDAM_data:2613 name: KEGG Glycan ID namespace: identifier -def: "Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002900 ! Carbohydrate accession -is_a: EDAM:0001154 ! KEGG object identifier +is_a: EDAM_data:2900 ! Carbohydrate accession +is_a: EDAM_data:1154 ! KEGG object identifier [Term] -id: EDAM:0002326 +id: EDAM_data:2326 name: DrugBank ID namespace: identifier -def: "Unique identifier of a drug from the DrugBank database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002895 ! Drug accession +is_a: EDAM_data:2895 ! Drug accession [Term] -id: EDAM:0002609 +id: EDAM_data:2609 name: Drug ID (KEGG) namespace: identifier -def: "Unique identifier of a drug from the KEGG Drug database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002895 ! Drug accession -is_a: EDAM:0001154 ! KEGG object identifier +is_a: EDAM_data:2895 ! Drug accession +is_a: EDAM_data:1154 ! KEGG object identifier [Term] -id: EDAM:0002652 +id: EDAM_data:2652 name: Drug ID (PharmGKB) namespace: identifier -def: "Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002895 ! Drug accession -is_a: EDAM:0002649 ! PharmGKB ID +is_a: EDAM_data:2895 ! Drug accession +is_a: EDAM_data:2649 ! PharmGKB ID [Term] -id: EDAM:0002653 +id: EDAM_data:2653 name: Drug ID (TTD) namespace: identifier -def: "Identifier of a drug from the Therapeutic Target Database (TTD)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002895 ! Drug accession +is_a: EDAM_data:2895 ! Drug accession [Term] -id: EDAM:0003102 +id: EDAM_data:3102 !{since=beta13} name: CAS number namespace: identifier -def: "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "CAS registry number" EXACT [] -is_a: EDAM:0002895 ! Drug accession +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 [Term] -id: EDAM:0003103 +id: EDAM_data:3103 !{since=beta13} name: ATC code namespace: identifier -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)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002895 ! Drug accession +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 [Term] -id: EDAM:0003104 +id: EDAM_data:3104 !{since=beta13} name: UNII namespace: identifier -def: "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Unique Ingredient Identifier" EXACT [] -is_a: EDAM:0001086 ! Compound 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 [Term] -id: EDAM:0002578 +id: EDAM_data:2578 name: ArachnoServer ID namespace: identifier -def: "Unique identifier of a toxin from the ArachnoServer database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002897 ! Toxin accession +subset: identifiers +subset: data +def: "Unique identifier of a toxin from the ArachnoServer database." [http://edamontology.org] +is_a: EDAM_data:2897 ! Toxin accession [Term] -id: EDAM:0002662 +id: EDAM_data:2662 name: T3DB ID namespace: identifier -def: "Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002897 ! Toxin accession +is_a: EDAM_data:2897 ! Toxin accession [Term] -id: EDAM:0001006 +id: EDAM_data:1006 name: Amino acid name namespace: identifier -def: "String of one or more ASCII characters representing an amino acid." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000994 ! Amino acid 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 [Term] -id: EDAM:0002563 +id: EDAM_data:2563 name: Amino acid name (single letter) namespace: identifier -def: "Single letter amino acid identifier, e.g. G." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001006 ! Amino acid name +subset: identifiers +subset: data +def: "Single letter amino acid identifier, e.g. G." [http://edamontology.org] +is_a: EDAM_data:1006 ! Amino acid name [Term] -id: EDAM:0002564 +id: EDAM_data:2564 name: Amino acid name (three letter) namespace: identifier -def: "Three letter amino acid identifier, e.g. GLY." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001006 ! Amino acid name +subset: identifiers +subset: data +def: "Three letter amino acid identifier, e.g. GLY." [http://edamontology.org] +is_a: EDAM_data:1006 ! Amino acid name [Term] -id: EDAM:0001758 +id: EDAM_data:1758 name: PDB residue name namespace: identifier -def: "Three-letter amino acid residue names as used in PDB files." [EDAM:EBI "EMBRACE definition"] -subset: format +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:0002564 ! Amino acid name (three letter) +is_a: EDAM_data:2564 ! Amino acid name (three letter) [Term] -id: EDAM:0002565 +id: EDAM_data:2565 name: Amino acid name (full name) namespace: identifier -def: "Full name of an amino acid, e.g. Glycine." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001006 ! Amino acid name +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 [Term] -id: EDAM:0001007 +id: EDAM_data:1007 name: Nucleotide code namespace: identifier -def: "String of one or more ASCII characters representing a nucleotide." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000995 ! Nucleotide identifier -is_a: EDAM:0000990 ! Compound name +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 [Term] -id: EDAM:0002746 +id: EDAM_data:2746 name: MonosaccharideDB ID namespace: identifier -def: "Unique identifier of a monosaccharide from the MonosaccharideDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002898 ! Monosaccharide accession +subset: identifiers +subset: data +def: "Unique identifier of a monosaccharide from the MonosaccharideDB database." [http://edamontology.org] +is_a: EDAM_data:2898 ! Monosaccharide accession [Term] -id: EDAM:0002625 +id: EDAM_data:2625 name: LIPID MAPS ID namespace: identifier -def: "Identifier of an entry from the LIPID MAPS database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "LM ID" EXACT [] +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:0002905 ! Lipid accession +is_a: EDAM_data:2905 ! Lipid accession [Term] -id: EDAM:0002665 +id: EDAM_data:2665 name: LipidBank ID namespace: identifier -def: "Identifier of an entry from the LipidBank database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002905 ! Lipid accession +is_a: EDAM_data:2905 ! Lipid accession [Term] -id: EDAM:0002664 +id: EDAM_data:2664 name: GlycomeDB ID namespace: identifier -def: "Identifier of an entry from the GlycomeDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of an entry from the GlycomeDB database." [http://edamontology.org] regex: "[0-9]+" -is_a: EDAM:0002900 ! Carbohydrate accession +is_a: EDAM_data:2900 ! Carbohydrate accession [Term] -id: EDAM:0002752 +id: EDAM_data:2752 name: GlycoMap ID namespace: identifier -def: "Identifier of an entry from the GlycosciencesDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] regex: "[0-9]+" -is_a: EDAM:0002900 ! Carbohydrate accession +is_a: EDAM_data:2900 ! Carbohydrate accession [Term] -id: EDAM:0002796 +id: EDAM_data:2796 name: Linucs ID namespace: identifier -def: "Identifier of an entry from the GlycosciencesDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002900 ! Carbohydrate accession +subset: identifiers +subset: data +def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] +is_a: EDAM_data:2900 ! Carbohydrate accession [Term] -id: EDAM:0000987 +id: EDAM_data:0987 name: Chromosome name namespace: identifier -def: "Name of a chromosome." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002119 ! Nucleic acid identifier -is_a: EDAM:0000984 ! Molecule name -relationship: is_identifier_of EDAM:0000919 ! Nucleic acid features (chromosome) +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 ! Nucleic acid features (chromosome) [Term] -id: EDAM:0002208 +id: EDAM_data:2208 name: Plasmid identifier namespace: identifier -def: "An identifier of a plasmid in a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002119 ! Nucleic acid 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 [Term] -id: EDAM:0002718 +id: EDAM_data:2718 name: Oligonucleotide ID namespace: identifier -def: "Identifier of an oligonucleotide from a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002119 ! Nucleic acid identifier -is_a: EDAM:0002901 ! Molecule accession +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 [Term] -id: EDAM:0002769 +id: EDAM_data:2769 name: Transcript ID namespace: identifier -def: "Identifier of a RNA transcript." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002119 ! Nucleic acid identifier -is_a: EDAM:0002901 ! Molecule accession -relationship: is_identifier_of EDAM:0002399 ! Gene annotation (transcript) +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) [Term] -id: EDAM:0002706 +id: EDAM_data:2706 name: Chromosome name (BioCyc) namespace: identifier -def: "Name of a chromosome as used in the BioCyc database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000987 ! Chromosome name +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 [Term] -id: EDAM:0002719 +id: EDAM_data:2719 name: dbProbe ID namespace: identifier -def: "Identifier of an oligonucleotide probe from the dbProbe database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002718 ! Oligonucleotide ID +subset: identifiers +subset: data +def: "Identifier of an oligonucleotide probe from the dbProbe database." [http://edamontology.org] +is_a: EDAM_data:2718 ! Oligonucleotide ID [Term] -id: EDAM:0002721 +id: EDAM_data:2721 name: DiProDB ID namespace: identifier -def: "Identifier of an dinucleotide property from the DiProDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002718 ! Oligonucleotide ID +subset: identifiers +subset: data +def: "Identifier of an dinucleotide property from the DiProDB database." [http://edamontology.org] +is_a: EDAM_data:2718 ! Oligonucleotide ID [Term] -id: EDAM:0002770 +id: EDAM_data:2770 name: HIT ID namespace: identifier -def: "Identifier of an RNA transcript from the H-InvDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002769 ! Transcript ID +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 [Term] -id: EDAM:0002626 +id: EDAM_data:2626 name: PeptideAtlas ID namespace: identifier -def: "Identifier of a peptide from the PeptideAtlas peptide databases." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002906 ! Peptide ID +is_a: EDAM_data:2906 ! Peptide ID ! pdbx_PDB_strand_id in PDBML [Term] -id: EDAM:0001009 +id: EDAM_data:1009 name: Protein name namespace: identifier -def: "Name of a protein." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000989 ! Protein identifier -is_a: EDAM:0000984 ! Molecule name +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 [Term] -id: EDAM:0001010 +id: EDAM_data:1010 name: Enzyme identifier namespace: identifier -def: "Name or other identifier of an enzyme or record from a database of enzymes." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000989 ! Protein identifier -relationship: is_identifier_of EDAM:0001509 ! Enzyme property +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 [Term] -id: EDAM:0002114 +id: EDAM_data:2114 name: WormBase wormpep ID namespace: identifier -def: "Protein identifier used by WormBase database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Protein identifier used by WormBase database." [http://edamontology.org] regex: "CE[0-9]{5}" -is_a: EDAM:0002907 ! Protein accession -is_a: EDAM:0002113 ! WormBase identifier +is_a: EDAM_data:2907 ! Protein accession +is_a: EDAM_data:2113 ! WormBase identifier [Term] -id: EDAM:0002804 +id: EDAM_data:2804 name: Protein ID (ConoServer) namespace: identifier -def: "Unique identifier for a cone snail toxin protein from the ConoServer database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0002802 +id: EDAM_data:2802 name: Protein ID (EcID) namespace: identifier -def: "Unique identifier for a protein from the EcID database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002907 ! Protein accession +subset: identifiers +subset: data +def: "Unique identifier for a protein from the EcID database." [http://edamontology.org] +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM:0003029 +id: EDAM_data:3029 !{since=beta13} name: Protein ID (EMBL/GenBank/DDBJ) namespace: identifier -def: "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_a: EDAM:0002907 ! Protein accession +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM:0002398 +id: EDAM_data:2398 name: Protein ID (Ensembl) namespace: identifier -def: "Unique identifier for a protein from the Ensembl database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Ensembl protein ID" EXACT [] -is_a: EDAM:0002907 ! Protein accession -is_a: EDAM:0002610 ! Ensembl ID +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 [Term] -id: EDAM:0002713 +id: EDAM_data:2713 name: Protein ID (CORUM) namespace: identifier -def: "Unique identifier for a protein complex from the CORUM database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "CORUM complex ID" EXACT [] -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0002715 +id: EDAM_data:2715 name: Protein ID (CuticleDB) namespace: identifier -def: "Unique identifier for a protein from the CuticleDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "CuticleDB ID" EXACT [] -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0002723 +id: EDAM_data:2723 name: Protein ID (DisProt) namespace: identifier -def: "Unique identifier for a protein from the DisProt database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "DisProt ID" EXACT [] -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0002789 +id: EDAM_data:2789 name: Protein ID (TopDB) namespace: identifier -def: "Unique identifier for a membrane protein from the TopDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "TopDB ID" EXACT [] -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0002792 +id: EDAM_data:2792 name: Protein ID (PeroxiBase) namespace: identifier -def: "Unique identifier for a peroxidase protein from the PeroxiBase database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "PeroxiBase ID" EXACT [] -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0002797 +id: EDAM_data:2797 name: Protein ID (LGICdb) namespace: identifier -def: "Unique identifier for a ligand-gated ion channel protein from the LGICdb database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "LGICdb ID" EXACT [] -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0002617 +id: EDAM_data:2617 name: Signaling Gateway protein ID namespace: identifier -def: "Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002907 ! Protein accession +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM:0002647 +id: EDAM_data:2647 name: LGICdb identifier namespace: identifier -def: "Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002907 ! Protein accession +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM:0002654 +id: EDAM_data:2654 name: Target ID (TTD) namespace: identifier -def: "Identifier of a target protein from the Therapeutic Target Database (TTD)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002907 ! Protein accession +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM:0002756 +id: EDAM_data:2756 name: TCID namespace: identifier -def: "Identifier of a membrane transport proteins from the transport classification database (TCDB)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0002772 +id: EDAM_data:2772 name: HPA antibody id namespace: identifier -def: "Identifier of a antibody from the HPA database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002907 ! Protein accession +subset: identifiers +subset: data +def: "Identifier of a antibody from the HPA database." [http://edamontology.org] +is_a: EDAM_data:2907 ! Protein accession [Term] -id: EDAM:0002773 +id: EDAM_data:2773 name: IMGT/HLA ID namespace: identifier -def: "Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0002764 +id: EDAM_data:2764 name: Protein name (UniProt) namespace: identifier -def: "Official name of a protein as used in the UniProt database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001009 ! Protein name +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 [Term] -id: EDAM:0002775 +id: EDAM_data:2775 name: Kinase name namespace: identifier -def: "The name of a kinase protein." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001009 ! Protein name +subset: identifiers +subset: data +def: "The name of a kinase protein." [http://edamontology.org] +is_a: EDAM_data:1009 ! Protein name [Term] -id: EDAM:0002321 +id: EDAM_data:2321 name: Enzyme ID namespace: identifier -def: "A unique, persistent identifier of an enzyme." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Enzyme accession" EXACT [] -is_a: EDAM:0001010 ! Enzyme identifier -is_a: EDAM:0002907 ! Protein accession +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 [Term] -id: EDAM:0001012 +id: EDAM_data:1012 name: Enzyme name namespace: identifier -def: "Name of an enzyme." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001010 ! Enzyme identifier -is_a: EDAM:0001009 ! Protein name +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 [Term] -id: EDAM:0001011 +id: EDAM_data:1011 name: EC number namespace: identifier -def: "An Enzyme Commission (EC) number of an enzyme." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "EC code" EXACT [] -synonym: "EC" EXACT [] -synonym: "Enzyme Commission number" EXACT [] +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:0002321 ! Enzyme accession +is_a: EDAM_data:2321 ! Enzyme accession [Term] -id: EDAM:0002107 +id: EDAM_data:2107 name: Enzyme ID (BioCyc) namespace: identifier -def: "Identifier of an enzyme from the BioCyc enzymes database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "BioCyc enzyme ID" EXACT [] -is_a: EDAM:0002104 ! BioCyc ID -is_a: EDAM:0002321 ! Enzyme ID +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 [Term] -id: EDAM:0002629 +id: EDAM_data:2629 name: Enzyme ID (MEROPS) namespace: identifier -def: "Unique identifier of a peptidase enzyme from the MEROPS database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "MEROPS ID" EXACT [] +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:0002321 ! Enzyme ID +is_a: EDAM_data:2321 ! Enzyme ID [Term] -id: EDAM:0002702 +id: EDAM_data:2702 name: Enzyme ID (CAZy) namespace: identifier -def: "Identifier of an enzyme from the CAZy enzymes database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "CAZy ID" EXACT [] -is_a: EDAM:0002321 ! Enzyme ID +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 [Term] -id: EDAM:0002325 +id: EDAM_data:2325 name: REBASE enzyme number namespace: identifier -def: "Identifier of an enzyme from the REBASE enzymes database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002091 ! Enzyme accession +subset: identifiers +subset: data +def: "Identifier of an enzyme from the REBASE enzymes database." [http://edamontology.org] +is_a: EDAM_data:2091 ! Enzyme accession [Term] -id: EDAM:0001013 +id: EDAM_data:1013 name: Restriction enzyme name namespace: identifier -def: "Name of a restriction enzyme." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001012 ! Enzyme name -relationship: is_identifier_of EDAM:0001517 ! Restriction enzyme property +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 [Term] -id: EDAM:0001018 +id: EDAM_data:1018 name: Nucleic acid feature identifier namespace: identifier -def: "Name or other identifier of an nucleic acid feature." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001015 ! Sequence feature ID +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 [Term] -id: EDAM:0001019 +id: EDAM_data:1019 name: Protein feature identifier namespace: identifier -def: "Name or other identifier of a protein feature." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001015 ! Sequence feature ID +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 [Term] -id: EDAM:0002736 +id: EDAM_data:2736 name: Sequence feature ID (SwissRegulon) namespace: identifier -def: "A feature identifier as used in the SwissRegulon database." [EDAM:EBI "EMBRACE definition"] +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". -subset: identifier -is_a: EDAM:0001015 ! Sequence feature ID +is_a: EDAM_data:1015 ! Sequence feature ID [Term] -id: EDAM:0001024 +id: EDAM_data:1024 name: Codon name namespace: identifier -def: "String of one or more ASCII characters representing a codon." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001276 ! Nucleic acid features +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 ! Don't know whether the loci identifiers listed here are 'ordered' or not. [Term] -id: EDAM:0002009 +id: EDAM_data:2009 name: Ordered locus name namespace: identifier -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." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001893 ! Locus ID +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 [Term] -id: EDAM:0001895 +id: EDAM_data:1895 name: Locus ID (AGI) namespace: identifier -def: "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "AGI locus code" EXACT [] -synonym: "AGI ID" EXACT [] -synonym: "AGI identifier" EXACT [] -synonym: "Arabidopsis gene loci number" EXACT [] +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:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001896 +id: EDAM_data:1896 name: Locus ID (ASPGD) namespace: identifier -def: "Identifier for loci from ASPGD (Aspergillus Genome Database)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001897 +id: EDAM_data:1897 name: Locus ID (MGG) namespace: identifier -def: "Identifier for loci from Magnaporthe grisea Database at the Broad Institute." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001898 +id: EDAM_data:1898 name: Locus ID (CGD) namespace: identifier -def: "Identifier for loci from CGD (Candida Genome Database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "CGD locus identifier" EXACT [] -synonym: "CGDID" EXACT [] +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:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001899 +id: EDAM_data:1899 name: Locus ID (CMR) namespace: identifier -def: "Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001900 +id: EDAM_data:1900 name: NCBI locus tag namespace: identifier -def: "Identifier for loci from NCBI database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Locus ID (NCBI)" EXACT [] +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:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001901 +id: EDAM_data:1901 name: Locus ID (SGD) namespace: identifier -def: "Identifier for loci from SGD (Saccharomyces Genome Database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "SGDID" EXACT [] +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:0001893 ! Locus ID -is_a: EDAM:0002632 ! SGD ID +is_a: EDAM_data:1893 ! Locus ID +is_a: EDAM_data:2632 ! SGD ID [Term] -id: EDAM:0001902 +id: EDAM_data:1902 name: Locus ID (MMP) namespace: identifier -def: "Identifier of loci from Maize Mapping Project." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of loci from Maize Mapping Project." [http://edamontology.org] xref: Moby_namespace:MMP_Locus -is_a: EDAM:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001903 +id: EDAM_data:1903 name: Locus ID (DictyBase) namespace: identifier -def: "Identifier of locus from DictyBase (Dictyostelium discoideum)." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of locus from DictyBase (Dictyostelium discoideum)." [http://edamontology.org] xref: Moby_namespace:DDB_gene -is_a: EDAM:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001904 +id: EDAM_data:1904 name: Locus ID (EntrezGene) namespace: identifier -def: "Identifier of a locus from EntrezGene database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001905 +id: EDAM_data:1905 name: Locus ID (MaizeGDB) namespace: identifier -def: "Identifier of locus from MaizeGDB (Maize genome database)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0001908 +id: EDAM_data:1908 name: Locus ID (Tropgene) namespace: identifier -def: "Identifier of a locus from the Tropgene database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of a locus from the Tropgene database." [http://edamontology.org] xref: Moby:Tropgene_locus -is_a: EDAM:0001893 ! Locus ID +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0002744 +id: EDAM_data:2744 name: Locus ID (PseudoCAP) namespace: identifier -def: "Identifier of a locus from the PseudoCAP database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001893 ! Locus ID +subset: identifiers +subset: data +def: "Identifier of a locus from the PseudoCAP database." [http://edamontology.org] +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0002745 +id: EDAM_data:2745 name: Locus ID (UTR) namespace: identifier -def: "Identifier of a locus from the UTR database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001893 ! Locus ID +subset: identifiers +subset: data +def: "Identifier of a locus from the UTR database." [http://edamontology.org] +is_a: EDAM_data:1893 ! Locus ID [Term] -id: EDAM:0002794 +id: EDAM_data:2794 name: ORF ID namespace: identifier -def: "Accession of an open reading frame (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002795 ! ORF identifier -is_a: EDAM:0001893 ! Locus ID +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 [Term] -id: EDAM:0001026 +id: EDAM_data:1026 name: Gene symbol namespace: identifier -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." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002299 ! Gene name +is_a: EDAM_data:2299 ! Gene name [Term] -id: EDAM:0002299 +id: EDAM_data:2299 name: Gene name namespace: identifier -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." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001025 ! Gene identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002295 +id: EDAM_data:2295 name: Gene ID namespace: identifier -def: "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Gene code" EXACT [] -synonym: "Gene accession" EXACT [] -is_a: EDAM:0001025 ! Gene identifier -is_a: EDAM:0001893 ! Locus ID +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 [Term] -id: EDAM:0001891 +id: EDAM_data:1891 name: iHOP symbol namespace: identifier -def: "A unique identifier of a protein or gene used in the iHOP database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID -is_a: EDAM:0002907 ! Protein accession -is_a: EDAM:0002109 ! Identifier (hybrid) +is_a: EDAM_data:2295 ! Gene ID +is_a: EDAM_data:2907 ! Protein accession +is_a: EDAM_data:2109 ! Identifier (hybrid) ! Suspect this identifiers more than just genes [Term] -id: EDAM:0001036 +id: EDAM_data:1036 name: TIGR identifier namespace: identifier -def: "Identifier of an entry from the TIGR database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002295 ! Gene ID -is_a: EDAM:0002109 ! Identifier (hybrid) +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) [Term] -id: EDAM:0001037 +id: EDAM_data:1037 name: TAIR accession (gene) namespace: identifier -def: "Identifier of an gene from the TAIR database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID -is_a: EDAM:0002387 ! TAIR accession +is_a: EDAM_data:2295 ! Gene ID +is_a: EDAM_data:2387 ! TAIR accession [Term] -id: EDAM:0002388 +id: EDAM_data:2388 name: TAIR accession (At gene) namespace: identifier -def: "Identifier of an Arabidopsis thaliana gene from the TAIR database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001037 ! TAIR accession (gene) +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) [Term] -id: EDAM:0001806 +id: EDAM_data:1806 name: Gene synonym namespace: identifier -def: "Any name (other than the recommended one) for a gene." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Gene name synonym" EXACT [] -is_obsolete: true -consider: EDAM:0001026 ! Gene name +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 name [Term] -id: EDAM:0001807 +id: EDAM_data:1807 name: ORF name namespace: identifier -def: "The name of an open reading frame attributed by a sequencing project." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002795 ! ORF identifier -is_a: EDAM:0002099 ! Name +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 ! GeneFarm gene ID is also given [Term] -id: EDAM:0001892 +id: EDAM_data:1892 name: Gene name (GeneFarm) namespace: identifier -def: "Name of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001889 +id: EDAM_data:1889 name: Gene name (DragonDB) namespace: identifier -def: "The name of an Antirrhinum Gene from the DragonDB database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001890 +id: EDAM_data:1890 name: Gene name (Arabidopsis) namespace: identifier -def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001783 +id: EDAM_data:1783 name: Gene name (ASPGD) namespace: identifier -def: "Name of a gene from Aspergillus Genome Database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001784 +id: EDAM_data:1784 name: Gene name (CGD) namespace: identifier -def: "Name of a gene from Candida Genome Database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001785 +id: EDAM_data:1785 name: Gene name (dictyBase) namespace: identifier -def: "Name of a gene from dictyBase database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001786 +id: EDAM_data:1786 name: Gene name (EcoGene primary) namespace: identifier -def: "Primary name of a gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "EcoGene primary gene name" EXACT [] +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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001787 +id: EDAM_data:1787 name: Gene name (MaizeGDB) namespace: identifier -def: "Name of a gene from MaizeGDB (maize genes) database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001788 +id: EDAM_data:1788 name: Gene name (SGD) namespace: identifier -def: "Name of a gene from Saccharomyces Genome Database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol -is_a: EDAM:0002632 ! SGD ID +is_a: EDAM_data:1026 ! Gene symbol +is_a: EDAM_data:2632 ! SGD ID [Term] -id: EDAM:0001789 +id: EDAM_data:1789 name: Gene name (TGD) namespace: identifier -def: "Name of a gene from Tetrahymena Genome Database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001790 +id: EDAM_data:1790 name: Gene name (CGSC) namespace: identifier -def: "Symbol of a gene from E.coli Genetic Stock Center." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001791 +id: EDAM_data:1791 name: Gene name (HGNC) namespace: identifier -def: "Symbol of a gene approved by the HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Official gene name" EXACT [] -synonym: "Gene name (HUGO)" EXACT [] -synonym: "HGNC symbol" EXACT [] -synonym: "HUGO symbol" EXACT [] -synonym: "HGNC gene symbol" EXACT [] -synonym: "HUGO gene symbol" EXACT [] -synonym: "HUGO gene name" EXACT [] -synonym: "HGNC gene name" EXACT [] +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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001792 +id: EDAM_data:1792 name: Gene name (MGD) namespace: identifier -def: "Symbol of a gene from the Mouse Genome Database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0001793 +id: EDAM_data:1793 name: Gene name (Bacillus subtilis) namespace: identifier -def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001026 ! Gene symbol +is_a: EDAM_data:1026 ! Gene symbol [Term] -id: EDAM:0002103 +id: EDAM_data:2103 name: Gene name (KEGG GENES) namespace: identifier -def: "Name of an entry (gene) from the KEGG GENES database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "KEGG GENES entry name" EXACT [] +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:0001026 ! Gene symbol -is_a: EDAM:0001154 ! KEGG object identifier +is_a: EDAM_data:1026 ! Gene symbol +is_a: EDAM_data:1154 ! KEGG object identifier [Term] -id: EDAM:0002296 +id: EDAM_data:2296 name: Gene name (AceView) namespace: identifier -def: "Name of an entry (gene) from the AceView genes database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "AceView gene name" EXACT [] -is_a: EDAM:0001026 ! Gene symbol +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 [Term] -id: EDAM:0002300 +id: EDAM_data:2300 name: Gene name (NCBI) namespace: identifier -def: "Name of an entry (gene) from the NCBI genes database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "NCBI gene name" EXACT [] -is_a: EDAM:0001026 ! Gene symbol +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 [Term] -id: EDAM:0002740 +id: EDAM_data:2740 name: Gene name (Genolist) namespace: identifier -def: "Name of an entry (gene) from the Genolist genes database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Genolist gene name" EXACT [] -is_a: EDAM:0001026 ! Gene symbol +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 [Term] -id: EDAM:0002743 +id: EDAM_data:2743 name: Gene name (HUGO) namespace: identifier -def: "Name of an entry (gene) from the HUGO database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001791 ! Gene name (HGNC) +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) [Term] -id: EDAM:0002771 +id: EDAM_data:2771 name: HIX ID namespace: identifier -def: "A unique identifier of gene cluster in the H-InvDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002295 ! Gene ID +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 [Term] -id: EDAM:0002737 +id: EDAM_data:2737 name: FIG ID namespace: identifier -def: "A unique identifier of gene in the NMPDR database." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_a: EDAM:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0002774 +id: EDAM_data:2774 name: Gene ID (JCVI) namespace: identifier -def: "A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002295 ! Gene ID +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 [Term] -id: EDAM:0002738 +id: EDAM_data:2738 name: Gene ID (Xenbase) namespace: identifier -def: "A unique identifier of gene in the Xenbase database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002295 ! Gene ID +subset: identifiers +subset: data +def: "A unique identifier of gene in the Xenbase database." [http://edamontology.org] +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0002799 +id: EDAM_data:2799 name: Gene ID (MfunGD) namespace: identifier -def: "A unique identifier of gene in the MfunGD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002295 ! Gene ID +subset: identifiers +subset: data +def: "A unique identifier of gene in the MfunGD database." [http://edamontology.org] +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0002739 +id: EDAM_data:2739 name: Gene ID (Genolist) namespace: identifier -def: "A unique identifier of gene in the Genolist database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002295 ! Gene ID +subset: identifiers +subset: data +def: "A unique identifier of gene in the Genolist database." [http://edamontology.org] +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001028 +id: EDAM_data:1028 name: Gene identifier (NCBI RefSeq) namespace: identifier -def: "An NCBI RefSeq unique identifier of a gene." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001027 ! NCBI gene ID +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 ! NCBI gene ID [Term] -id: EDAM:0001029 +id: EDAM_data:1029 name: Gene identifier (NCBI UniGene) namespace: identifier -def: "An NCBI UniGene unique identifier of a gene." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001104 ! Sequence cluster ID (UniGene) +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) [Term] -id: EDAM:0001030 +id: EDAM_data:1030 name: Gene identifier (Entrez) namespace: identifier -def: "An Entrez unique identifier of a gene." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "An Entrez unique identifier of a gene." [http://edamontology.org] regex: "[0-9]+" -is_obsolete: true -consider: EDAM:0001027 ! NCBI gene ID +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1027 ! NCBI gene ID [Term] -id: EDAM:0001886 +id: EDAM_data:1886 name: Blattner number namespace: identifier -def: "The blattner identifier for a gene." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "The blattner identifier for a gene." [http://edamontology.org] xref: Moby_namespace:Blattner_number -is_a: EDAM:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001027 +id: EDAM_data:1027 name: Gene ID (NCBI) namespace: identifier -def: "An NCBI unique identifier of a gene." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Gene identifier (NCBI)" EXACT [] -synonym: "NCBI gene ID" EXACT [] -synonym: "NCBI geneid" EXACT [] -synonym: "Gene identifier (Entrez)" EXACT [] -synonym: "Entrez gene ID" EXACT [] +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:0002295 ! Gene ID -is_a: EDAM:0001098 ! RefSeq accession +is_a: EDAM_data:2295 ! Gene ID +is_a: EDAM_data:1098 ! RefSeq accession [Term] -id: EDAM:0001031 +id: EDAM_data:1031 name: Gene ID (CGD) namespace: identifier -def: "Identifier of a gene or feature from the CGD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "CGD ID" EXACT [] -is_a: EDAM:0002295 ! Gene ID +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 [Term] -id: EDAM:0001032 +id: EDAM_data:1032 name: Gene ID (DictyBase) namespace: identifier -def: "Identifier of a gene from DictyBase." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002295 ! Gene ID +subset: identifiers +subset: data +def: "Identifier of a gene from DictyBase." [http://edamontology.org] +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001033 +id: EDAM_data:1033 name: Gene ID (Ensembl) namespace: identifier -def: "Unique identifier for a gene (or other feature) from the Ensembl database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Ensembl Gene ID" EXACT [] -is_a: EDAM:0002295 ! Gene ID -is_a: EDAM:0002610 ! Ensembl ID +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 [Term] -id: EDAM:0001034 +id: EDAM_data:1034 name: Gene ID (SGD) namespace: identifier -def: "Identifier of an entry from the SGD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "SGD identifier" EXACT [] +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:0002295 ! Gene ID -is_a: EDAM:0002632 ! SGD ID +is_a: EDAM_data:2295 ! Gene ID +is_a: EDAM_data:2632 ! SGD ID [Term] -id: EDAM:0001885 +id: EDAM_data:1885 name: Gene ID (GeneFarm) namespace: identifier -def: "Identifier of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001907 +id: EDAM_data:1907 name: Gene ID (KOME) namespace: identifier -def: "Identifier of a gene from the KOME database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of a gene from the KOME database." [http://edamontology.org] xref: Moby_namespace:GeneId -is_a: EDAM:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001794 +id: EDAM_data:1794 name: Gene ID (PlasmoDB) namespace: identifier -def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001795 +id: EDAM_data:1795 name: Gene ID (EcoGene) namespace: identifier -def: "Identifier of a gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "EcoGene Accession" EXACT [] -synonym: "EcoGene ID" EXACT [] -is_a: EDAM:0002295 ! Gene ID +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 [Term] -id: EDAM:0002297 +id: EDAM_data:2297 name: Gene ID (ECK) namespace: identifier -def: "Identifier of an E. coli K-12 gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "E. coli K-12 gene identifier" EXACT [] -synonym: "ECK accession" EXACT [] +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:0001795 ! Gene ID (EcoGene) +is_a: EDAM_data:1795 ! Gene ID (EcoGene) [Term] -id: EDAM:0001796 +id: EDAM_data:1796 name: Gene ID (FlyBase) namespace: identifier -def: "Gene identifier from FlyBase database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001802 +id: EDAM_data:1802 name: Gene ID (Gramene) namespace: identifier -def: "Gene identifier from Gramene database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001803 +id: EDAM_data:1803 name: Gene ID (Virginia microbial) namespace: identifier -def: "Gene identifier from Virginia Bioinformatics Institute microbial database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001804 +id: EDAM_data:1804 name: Gene ID (SGN) namespace: identifier -def: "Gene identifier from Sol Genomics Network." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0001805 +id: EDAM_data:1805 name: Gene ID (WormBase) namespace: identifier -def: "Gene identifier used by WormBase database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID -is_a: EDAM:0002113 ! WormBase identifier +is_a: EDAM_data:2295 ! Gene ID +is_a: EDAM_data:2113 ! WormBase identifier [Term] -id: EDAM:0001035 +id: EDAM_data:1035 name: Gene ID (GeneDB) namespace: identifier -def: "Identifier of a gene from the GeneDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "GeneDB identifier" EXACT [] +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:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0002285 +id: EDAM_data:2285 name: Gene ID (MIPS) namespace: identifier -def: "Identifier for genetic elements in MIPS database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "MIPS genetic element identifier" EXACT [] -is_a: EDAM:0002295 ! Gene ID +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 [Term] -id: EDAM:0002298 +id: EDAM_data:2298 name: Gene ID (HGNC) namespace: identifier -def: "Identifier for a gene approved by the HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "HGNC ID" EXACT [] -is_a: EDAM:0002295 ! Gene ID +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 [Term] -id: EDAM:0002642 +id: EDAM_data:2642 name: Gene ID (miRBase) namespace: identifier -def: "Identifier for a gene from the miRBase database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "miRNA name" EXACT [] -synonym: "miRNA identifier" EXACT [] -synonym: "miRNA ID" EXACT [] +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:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0002643 +id: EDAM_data:2643 name: Gene ID (ZFIN) namespace: identifier -def: "Identifier for a gene from the Zebrafish information network genome (ZFIN) database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002295 ! Gene ID +is_a: EDAM_data:2295 ! Gene ID [Term] -id: EDAM:0002759 +id: EDAM_data:2759 name: Gene ID (VectorBase) namespace: identifier -def: "Identifier for a gene from the VectorBase database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "VectorBase ID" EXACT [] -is_a: EDAM:0002295 ! Gene ID +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 [Term] -id: EDAM:0002835 +id: EDAM_data:2835 name: Gene ID (VBASE2) namespace: identifier -def: "Identifier for a gene from the VBASE2 database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "VBASE2 ID" EXACT [] -is_a: EDAM:0002295 ! Gene ID +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 [Term] -id: EDAM:0001797 +id: EDAM_data:1797 name: Gene ID (GeneDB Glossina morsitans) namespace: identifier -def: "Gene identifier from Glossina morsitans GeneDB database." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true !{since=beta13} +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM:0001798 +id: EDAM_data:1798 name: Gene ID (GeneDB Leishmania major) namespace: identifier -def: "Gene identifier from Leishmania major GeneDB database." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true !{since=beta13} +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM:0001799 +id: EDAM_data:1799 name: Gene ID (GeneDB Plasmodium falciparum) namespace: identifier -def: "Gene identifier from Plasmodium falciparum GeneDB database." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true !{since=beta13} +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM:0001800 +id: EDAM_data:1800 name: Gene ID (GeneDB Schizosaccharomyces pombe) namespace: identifier -def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true !{since=beta13} +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM:0001801 +id: EDAM_data:1801 name: Gene ID (GeneDB Trypanosoma brucei) namespace: identifier -def: "Gene identifier from Trypanosoma brucei GeneDB database." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true !{since=beta13} +consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] -id: EDAM:0001887 +id: EDAM_data:1887 name: Gene ID (MIPS Maize) namespace: identifier -def: "Identifier for genetic elements in MIPS Maize database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "MIPS genetic element identifier (Maize)" EXACT [] +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 -consider: EDAM:0002285 ! Gene ID (MIPS) +is_obsolete: true !{since=beta13} +consider: EDAM_data:2285 ! Gene ID (MIPS) [Term] -id: EDAM:0001888 +id: EDAM_data:1888 name: Gene ID (MIPS Medicago) namespace: identifier -def: "Identifier for genetic elements in MIPS Medicago database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "MIPS genetic element identifier (Medicago)" EXACT [] +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 -consider: EDAM:0002285 ! Gene ID (MIPS) +is_obsolete: true !{since=beta13} +consider: EDAM_data:2285 ! Gene ID (MIPS) [Term] -id: EDAM:0002751 +id: EDAM_data:2751 name: GenomeReviews ID namespace: identifier -def: "An identifier of a particular genome." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002903 ! Genome accession +subset: identifiers +subset: data +def: "An identifier of a particular genome." [http://edamontology.org] +is_a: EDAM_data:2903 ! Genome accession [Term] -id: EDAM:0002786 +id: EDAM_data:2786 name: NCBI Genome Project ID namespace: identifier -def: "An identifier of a genome project assigned by NCBI." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002903 ! Genome accession +subset: identifiers +subset: data +def: "An identifier of a genome project assigned by NCBI." [http://edamontology.org] +is_a: EDAM_data:2903 ! Genome accession [Term] -id: EDAM:0002787 +id: EDAM_data:2787 name: NCBI genome accession namespace: identifier -def: "A unique identifier of a whole genome assigned by the NCBI." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002903 ! Genome accession +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 [Term] -id: EDAM:0002631 +id: EDAM_data:2631 name: ACLAME ID namespace: identifier -def: "An identifier of a mobile genetic element from the Aclame database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002630 ! Mobile genetic element ID +is_a: EDAM_data:2630 ! Mobile genetic element ID [Term] -id: EDAM:0002128 +id: EDAM_data:2128 name: Genetic code name namespace: identifier -def: "Informal name for a genetic code, typically an organism name." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002127 ! Genetic code identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0001039 +id: EDAM_data:1039 name: SCOP domain identifier namespace: identifier -def: "Identifier of a protein domain (or other node) from the SCOP database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001038 ! Protein domain ID -relationship: is_identifier_of EDAM:0001554 ! SCOP node +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 [Term] -id: EDAM:0002700 +id: EDAM_data:2700 name: CATH identifier namespace: identifier -def: "Identifier of a protein domain (or other node) from the CATH database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001038 ! Protein domain ID -relationship: is_identifier_of EDAM:0001553 ! CATH node +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 [Term] -id: EDAM:0002666 +id: EDAM_data:2666 name: CDD ID namespace: identifier -def: "Identifier of a conserved domain from the Conserved Domain Database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001038 ! Protein domain ID +is_a: EDAM_data:1038 ! Protein domain ID [Term] -id: EDAM:0001041 +id: EDAM_data:1041 name: SCOP concise classification string (sccs) namespace: identifier -def: "A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_a: EDAM:0001039 ! SCOP domain identifier +is_a: EDAM_data:1039 ! SCOP domain identifier [Term] -id: EDAM:0001042 +id: EDAM_data:1042 name: SCOP sunid namespace: identifier -def: "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "sunid" EXACT [] -synonym: "SCOP unique identifier" EXACT [] -is_a: EDAM:0001039 ! SCOP domain identifier +example: "33229" +synonym: "sunid" EXACT [http://edamontology.org] +synonym: "SCOP unique identifier" EXACT [http://edamontology.org] +is_a: EDAM_data:1039 ! SCOP domain identifier [Term] -id: EDAM:0001040 +id: EDAM_data:1040 name: CATH domain ID namespace: identifier -def: "Identifier of a protein domain from CATH." [EDAM:EBI "EMBRACE definition"] -comment: For example '1nr3A00'. -subset: identifier -synonym: "CATH domain identifier" EXACT [] -is_a: EDAM:0002700 ! CATH 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 [Term] -id: EDAM:0001043 +id: EDAM_data:1043 name: CATH node ID namespace: identifier -def: "A code number identifying a node from the CATH database." [EDAM:EBI "EMBRACE definition"] -comment: For example '3.30.1190.10.1.1.1.1.1'. -subset: identifier -synonym: "CATH code" EXACT [] -synonym: "CATH node identifier" EXACT [] -is_a: EDAM:0002700 ! CATH 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 [Term] -id: EDAM:0002701 +id: EDAM_data:2701 name: CATH node ID (family) namespace: identifier -def: "A code number identifying a family from the CATH database." [EDAM:EBI "EMBRACE definition"] -comment: For example '2.10.10.10'. -subset: identifier -is_a: EDAM:0001043 ! CATH node ID -relationship: is_identifier_of EDAM:0001553 ! CATH node +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 [Term] -id: EDAM:0002619 +id: EDAM_data:2619 name: RESID ID namespace: identifier -def: "Identifier of a protein modification catalogued in the RESID database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002618 ! Protein modification ID +is_a: EDAM_data:2618 ! Protein modification ID [Term] -id: EDAM:0002892 +id: EDAM_data:2892 name: Cell type name namespace: identifier -def: "The name of a type or group of cells." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002655 ! Cell type identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002656 +id: EDAM_data:2656 name: NeuronDB ID namespace: identifier -def: "A unique identifier of a neuron from the NeuronDB database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002893 ! Cell type accession +is_a: EDAM_data:2893 ! Cell type accession [Term] -id: EDAM:0002657 +id: EDAM_data:2657 name: NeuroMorpho ID namespace: identifier -def: "A unique identifier of a neuron from the NeuroMorpho database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002893 ! Cell type accession +is_a: EDAM_data:2893 ! Cell type accession [Term] -id: EDAM:0001868 +id: EDAM_data:1868 name: Taxon namespace: identifier -def: "The name of a group of organisms belonging to the same taxonomic rank." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "Taxonomy rank" EXACT [] -synonym: "Taxonomic rank" EXACT [] +synonym: "Taxonomy rank" EXACT [http://edamontology.org] +synonym: "Taxonomic rank" EXACT [http://edamontology.org] xref: Moby:BriefTaxonConcept xref: Moby:PotentialTaxon -is_a: EDAM:0002909 ! Organism name +is_a: EDAM_data:2909 ! Organism name [Term] -id: EDAM:0001872 +id: EDAM_data:1872 name: Taxonomic classification namespace: identifier -def: "The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "Taxonomic name" EXACT [] -synonym: "Taxonomic information" EXACT [] +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:0002909 ! Organism name +is_a: EDAM_data:2909 ! Organism name [Term] -id: EDAM:0001874 +id: EDAM_data:1874 name: Genbank common name namespace: identifier -def: "Common name for an organism as used in the GenBank database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002909 ! Organism name +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 [Term] -id: EDAM:0001873 +id: EDAM_data:1873 name: iHOP organism ID namespace: identifier -def: "A unique identifier for an organism used in the iHOP database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002908 ! Organism accession +is_a: EDAM_data:2908 ! Organism accession [Term] -id: EDAM:0002102 +id: EDAM_data:2102 name: KEGG organism code namespace: identifier -def: "A three-letter code used in the KEGG databases to uniquely identify organisms." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002909 ! Organism name -is_a: EDAM:0001154 ! KEGG object 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 [Term] -id: EDAM:0002593 +id: EDAM_data:2593 name: BRENDA organism ID namespace: identifier -def: "A unique identifier for an organism used in the BRENDA database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002908 ! Organism accession +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 [Term] -id: EDAM:0002913 +id: EDAM_data:2913 name: Virus identifier namespace: identifier -def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001869 ! Organism identifier -relationship: is_identifier_of EDAM:0002307 ! Virus annotation +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 [Term] -id: EDAM:0002785 +id: EDAM_data:2785 name: Virus ID namespace: identifier -def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002913 ! Virus identifier -is_a: EDAM:0002908 ! Organism accession +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 [Term] -id: EDAM:0002836 +id: EDAM_data:2836 name: DPVweb ID namespace: identifier -def: "A unique identifier for a virus from the DPVweb database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "DPVweb virus ID" EXACT [] -is_a: EDAM:0002785 ! Virus ID +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 [Term] -id: EDAM:0002784 +id: EDAM_data:2784 name: RNAVirusDB ID namespace: identifier -def: "A unique identifier for a virus from the RNAVirusDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002785 ! Virus ID +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 ! Could list (or cross-reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. [Term] -id: EDAM:0001875 +id: EDAM_data:1875 name: NCBI taxon namespace: identifier -def: "The name of a taxon from the NCBI taxonomy database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001868 ! Taxon +subset: identifiers +subset: data +def: "The name of a taxon from the NCBI taxonomy database." [http://edamontology.org] +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM:0002594 +id: EDAM_data:2594 name: UniGene taxon namespace: identifier -def: "The name of a taxon using the controlled vocabulary of the UniGene database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "UniGene organism abbreviation" EXACT [] -is_a: EDAM:0001868 ! Taxon +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 [Term] -id: EDAM:0002595 +id: EDAM_data:2595 name: UTRdb taxon namespace: identifier -def: "The name of a taxon using the controlled vocabulary of the UTRdb database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001868 ! Taxon +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 [Term] -id: EDAM:0001044 +id: EDAM_data:1044 name: Kingdom name namespace: identifier -def: "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001868 ! Taxon +subset: identifiers +subset: data +def: "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." [http://edamontology.org] +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM:0001870 +id: EDAM_data:1870 name: Genus name namespace: identifier -def: "The name of a genus of organism." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001868 ! Taxon +subset: identifiers +subset: data +def: "The name of a genus of organism." [http://edamontology.org] +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM:0002732 +id: EDAM_data:2732 name: Family name namespace: identifier -def: "The name of a family of organism." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001868 ! Taxon +subset: identifiers +subset: data +def: "The name of a family of organism." [http://edamontology.org] +is_a: EDAM_data:1868 ! Taxon [Term] -id: EDAM:0001045 +id: EDAM_data:1045 name: Species name namespace: identifier -def: "The name of a species (typically a taxonomic group) of organism." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Organism species" EXACT [] -is_a: EDAM:0001868 ! Taxon +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 [Term] -id: EDAM:0002733 +id: EDAM_data:2733 name: Genus name (virus) namespace: identifier -def: "The name of a genus of viruses." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001870 ! Genus name +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 [Term] -id: EDAM:0002734 +id: EDAM_data:2734 name: Family name (virus) namespace: identifier -def: "The name of a family of viruses." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0002732 ! Family name +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 [Term] -id: EDAM:0002317 +id: EDAM_data:2317 name: Cell line name (exact) namespace: identifier -def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002316 ! Cell line name +subset: identifiers +subset: data +def: "The name of a cell line." [http://edamontology.org] +is_a: EDAM_data:2316 ! Cell line name [Term] -id: EDAM:0002318 +id: EDAM_data:2318 name: Cell line name (truncated) namespace: identifier -def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002316 ! Cell line name +subset: identifiers +subset: data +def: "The name of a cell line." [http://edamontology.org] +is_a: EDAM_data:2316 ! Cell line name [Term] -id: EDAM:0002319 +id: EDAM_data:2319 name: Cell line name (no punctuation) namespace: identifier -def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002316 ! Cell line name +subset: identifiers +subset: data +def: "The name of a cell line." [http://edamontology.org] +is_a: EDAM_data:2316 ! Cell line name [Term] -id: EDAM:0002320 +id: EDAM_data:2320 name: Cell line name (assonant) namespace: identifier -def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002316 ! Cell line name +subset: identifiers +subset: data +def: "The name of a cell line." [http://edamontology.org] +is_a: EDAM_data:2316 ! Cell line name [Term] -id: EDAM:0001056 +id: EDAM_data:1056 name: Database name namespace: identifier -def: "The name of a biological or bioinformatics database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001048 ! Database identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002149 +id: EDAM_data:2149 name: Database category name namespace: identifier -def: "The name of a category of biological or bioinformatics database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001056 ! Database name +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 [Term] -id: EDAM:0001057 +id: EDAM_data:1057 name: Sequence database name namespace: identifier -def: "The name of a molecular sequence database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001056 ! Database name +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 [Term] -id: EDAM:0002735 +id: EDAM_data:2735 name: Database name (SwissRegulon) namespace: identifier -def: "The name of a SwissRegulon database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001056 ! Database name +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 [Term] -id: EDAM:0002747 +id: EDAM_data:2747 name: Database name (CMD) namespace: identifier -def: "The name of a subdivision of the Collagen Mutation Database (CMD) database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001056 ! Database name +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 [Term] -id: EDAM:0002748 +id: EDAM_data:2748 name: Database name (Osteogenesis) namespace: identifier -def: "The name of a subdivision of the Osteogenesis database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001056 ! Database name +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 [Term] -id: EDAM:0001058 +id: EDAM_data:1058 name: Enumerated file name namespace: identifier -def: "The name of a file (of any type) with restricted possible values." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001050 ! File name +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 [Term] -id: EDAM:0001059 +id: EDAM_data:1059 name: File name extension namespace: identifier -def: "The extension of a file name." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_a: EDAM:0001050 ! File name +is_a: EDAM_data:1050 ! File name [Term] -id: EDAM:0001060 +id: EDAM_data:1060 name: File base name namespace: identifier -def: "The base name of a file." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_a: EDAM:0001050 ! File name +is_a: EDAM_data:1050 ! File name [Term] -id: EDAM:0001061 +id: EDAM_data:1061 name: QSAR descriptor name namespace: identifier -def: "Name of a QSAR descriptor." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002110 ! Molecular property identifier -is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000847 ! QSAR descriptor +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 [Term] -id: EDAM:0002288 +id: EDAM_data:2288 name: Sequence identifier (protein) namespace: identifier -def: "An identifier of protein sequence(s) or protein sequence database entries." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001096 ! Sequence accession (protein) +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) [Term] -id: EDAM:0002289 +id: EDAM_data:2289 name: Sequence identifier (nucleic acid) namespace: identifier -def: "An identifier of nucleotide sequence(s) or nucleotide sequence database entries." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001097 ! Sequence accession (nucleic acid) +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) [Term] -id: EDAM:0001093 +id: EDAM_data:1093 name: Sequence accession namespace: identifier -def: "A persistent, unique identifier of a molecular sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Sequence accession number" EXACT [] -is_a: EDAM:0001063 ! Sequence identifier -is_a: EDAM:0002091 ! Accession -is_a: EDAM:0002914 ! Sequence feature metadata +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 feature metadata [Term] -id: EDAM:0002154 +id: EDAM_data:2154 name: Sequence name namespace: identifier -def: "Any arbitrary name of a molecular sequence." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001063 ! Sequence identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0001095 +id: EDAM_data:1095 name: EMBOSS Uniform Sequence Address namespace: identifier -def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"] +subset: identifiers subset: data -synonym: "USA" EXACT [] -is_a: EDAM:0001063 ! Sequence identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002291 +id: EDAM_data:2291 name: UniProt ID namespace: identifier -def: "An identifier of a polypeptide in the UniProt database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "UniProt identifier" EXACT [] -is_a: EDAM:0001096 ! Sequence accession (protein) -relationship: is_identifier_of EDAM:0000849 ! Sequence record +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 [Term] -id: EDAM:0001100 +id: EDAM_data:1100 name: PIR identifier namespace: identifier -def: "An identifier of PIR sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "PIR accession number" EXACT [] -synonym: "PIR ID" EXACT [] -is_a: EDAM:0001096 ! Sequence identifier (protein) -relationship: is_identifier_of EDAM:0000849 ! Sequence record +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 identifier (protein) +relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] -id: EDAM:0001101 +id: EDAM_data:1101 name: TREMBL accession namespace: identifier -def: "Identifier of a TREMBL sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0003021 ! UniProt accession -synonym: "TREMBL accession number" EXACT [] -synonym: "TREMBL ID" EXACT [] -relationship: is_identifier_of EDAM:0000849 ! Sequence record +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 [Term] -id: EDAM:0002621 +id: EDAM_data:2621 name: TAIR accession (protein) namespace: identifier -def: "Identifier of a protein sequence from the TAIR database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001096 ! Sequence identifier (protein) -is_a: EDAM:0002387 ! TAIR accession -relationship: is_identifier_of EDAM:0000849 ! Sequence record +is_a: EDAM_data:1096 ! Sequence identifier (protein) +is_a: EDAM_data:2387 ! TAIR accession +relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] -id: EDAM:0002290 +id: EDAM_data:2290 name: EMBL accession namespace: identifier -alt_id: EDAM:0001107 -def: "An accession number of an entry from the EMBL sequence database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "EMBL accession number" EXACT [] -synonym: "EMBL identifier" EXACT [] -synonym: "EMBL ID" EXACT [] -is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ ID +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 [Term] -id: EDAM:0002292 +id: EDAM_data:2292 name: GenBank accession namespace: identifier -alt_id: EDAM:0001108 -def: "Accession number of an entry from the GenBank sequence database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ ID -synonym: "GenBank accession number" EXACT [] -synonym: "GenBank identifier" EXACT [] -synonym: "GenBank ID" EXACT [] +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] [Term] -id: EDAM:0002916 +id: EDAM_data:2916 name: DDBJ accession namespace: identifier -alt_id: EDAM:0001109 -def: "An identifier of an entry from the DDBJ sequence database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ ID -synonym: "DDBJ accession number" EXACT [] -synonym: "DDBJ identifier" EXACT [] -synonym: "DDBJ ID" EXACT [] +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] [Term] -id: EDAM:0001855 +id: EDAM_data:1855 name: Clone ID namespace: identifier -def: "An identifier of a clone (cloned molecular sequence) from a database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002769 ! Transcript ID +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 [Term] -id: EDAM:0002386 +id: EDAM_data:2386 name: EPD ID namespace: identifier -def: "Identifier of an entry (promoter) from the EPD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "EPD identifier" EXACT [] -is_a: EDAM:0002727 ! Promoter ID +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 [Term] -id: EDAM:0002741 +id: EDAM_data:2741 name: ABS ID namespace: identifier -def: "Identifier of an entry (promoter) from the ABS database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "ABS identifier" EXACT [] -is_a: EDAM:0002727 ! Promoter ID +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 [Term] -id: EDAM:0001096 +id: EDAM_data:1096 name: Sequence accession (protein) namespace: identifier -def: "Accession number of a protein sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Protein sequence accession number" EXACT [] -is_a: EDAM:0001093 ! Sequence accession -relationship: is_identifier_of EDAM:0002976 ! Protein sequence +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 [Term] -id: EDAM:0001097 +id: EDAM_data:1097 name: Sequence accession (nucleic acid) namespace: identifier -def: "Accession number of a nucleotide sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Nucleotide sequence accession number" EXACT [] -is_a: EDAM:0001093 ! Sequence accession -relationship: is_identifier_of EDAM:0002977 ! Nucleotide sequence +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 ! Nucleotide sequence [Term] -id: EDAM:0002362 +id: EDAM_data:2362 name: Sequence accession (hybrid) namespace: identifier -def: "Accession number of a nucleotide or protein sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001093 ! Sequence accession -relationship: is_identifier_of EDAM:0000849 ! Sequence record +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 [Term] -id: EDAM:0001098 +id: EDAM_data:1098 name: RefSeq accession namespace: identifier -def: "Accession number of a RefSeq database entry." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002362 ! Sequence accession (hybrid) -synonym: "RefSeq ID" EXACT [] +is_a: EDAM_data:2362 ! Sequence accession (hybrid) +synonym: "RefSeq ID" EXACT [http://edamontology.org] [Term] -id: EDAM:0002314 +id: EDAM_data:2314 name: GI number namespace: identifier -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "NCBI GI number" EXACT [] -synonym: "gi number" EXACT [] -is_a: EDAM:0002362 ! Sequence accession (hybrid) +synonym: "NCBI GI number" EXACT [http://edamontology.org] +synonym: "gi number" EXACT [http://edamontology.org] +is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] -id: EDAM:0002315 +id: EDAM_data:2315 name: NCBI version namespace: identifier -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "accession.version" EXACT [] -synonym: "NCBI accession.version" EXACT [] -is_a: EDAM:0002362 ! Sequence accession (hybrid) +synonym: "accession.version" EXACT [http://edamontology.org] +synonym: "NCBI accession.version" EXACT [http://edamontology.org] +is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] -id: EDAM:0002385 +id: EDAM_data:2385 name: RefSeq accession (protein) namespace: identifier -def: "Accession number of a protein from the RefSeq database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001098 ! RefSeq accession -synonym: "RefSeq protein ID" EXACT [] +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] [Term] -id: EDAM:0002327 +id: EDAM_data:2327 name: GI number (protein) namespace: identifier -def: "A unique identifier assigned to NCBI protein sequence records." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "protein gi number" EXACT [] -synonym: "protein gi" EXACT [] -is_a: EDAM:0002314 ! GI number +synonym: "protein gi number" EXACT [http://edamontology.org] +synonym: "protein gi" EXACT [http://edamontology.org] +is_a: EDAM_data:2314 ! GI number [Term] -id: EDAM:0001099 +id: EDAM_data:1099 name: UniProt accession (extended) namespace: identifier -def: "Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number." [EDAM:EBI "EMBRACE definition"] -subset: identifier -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 -! 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: Q7M1G0 P43353-2 P01012.107 ! Q9C199 A5A6J6 -is_a: EDAM:0003021 ! UniProt accession -relationship: is_identifier_of EDAM:0001208 ! Protein sequence -relationship: is_identifier_of EDAM:0000849 ! Sequence record +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 [Term] -id: EDAM:0003021 +id: EDAM_data:3021 name: UniProt accession namespace: identifier -def: "Accession number of a UniProt (protein sequence) database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -! 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 Q9C199 A5A6J6 -synonym: "UniProtKB accession number" EXACT [] -synonym: "UniProtKB entry accession" EXACT [] -synonym: "UniProt accession number" EXACT [] -synonym: "Swiss-Prot accession" EXACT [] -is_a: EDAM:0002291 ! UniProt ID +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? [Term] -id: EDAM:0002392 +id: EDAM_data:2392 name: UniParc accession namespace: identifier -def: "Accession number of a UniParc (protein sequence) database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "UniParc ID" EXACT [] -synonym: "UPI" EXACT [] +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:0002291 ! UniProt ID +is_a: EDAM_data:2291 ! UniProt ID [Term] -id: EDAM:0002915 +id: EDAM_data:2915 name: Gramene identifier namespace: identifier -def: "Identifier of a Gramene database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001096 ! Sequence accession (protein) +subset: identifiers +subset: data +def: "Identifier of a Gramene database entry." [http://edamontology.org] +is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] -id: EDAM:0001102 +id: EDAM_data:1102 name: Gramene primary identifier namespace: identifier -def: "Primary identifier of a Gramene database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Gramene primary ID" EXACT [] -is_a: EDAM:0002915 ! Gramene 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 [Term] -id: EDAM:0002293 +id: EDAM_data:2293 name: Gramene secondary identifier namespace: identifier -def: "Secondary (internal) identifier of a Gramene database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Gramene secondary ID" EXACT [] -synonym: "Gramene internal ID" EXACT [] -synonym: "Gramene internal identifier" EXACT [] -is_a: EDAM:0002915 ! Gramene 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 [Term] -id: EDAM:0002384 +id: EDAM_data:2384 name: IPI protein ID namespace: identifier -def: "Identifier of a protein entry catalogued in the International Protein Index (IPI) database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001096 ! Sequence accession (protein) +is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] -id: EDAM:0002728 +id: EDAM_data:2728 name: EST accession namespace: identifier -def: "Identifier of an EST sequence." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001855 ! Clone ID +subset: identifiers +subset: data +def: "Identifier of an EST sequence." [http://edamontology.org] +is_a: EDAM_data:1855 ! Clone ID [Term] -id: EDAM:0001103 +id: EDAM_data:1103 name: EMBL/GenBank/DDBJ ID namespace: identifier -def: "Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001097 ! Sequence accession (nucleic acid) +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) [Term] -id: EDAM:0002389 +id: EDAM_data:2389 name: UniSTS accession namespace: identifier -def: "Identifier of an entry from the UniSTS database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001097 ! Sequence accession (nucleic acid) +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) [Term] -id: EDAM:0002390 +id: EDAM_data:2390 name: UNITE accession namespace: identifier -def: "Identifier of an entry from the UNITE database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001097 ! Sequence accession (nucleic acid) +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) [Term] -id: EDAM:0002391 +id: EDAM_data:2391 name: UTR accession namespace: identifier -def: "Identifier of an entry from the UTR database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001097 ! Sequence accession (nucleic acid) +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) [Term] -id: EDAM:0002393 +id: EDAM_data:2393 name: mFLJ/mKIAA number namespace: identifier -def: "Identifier of an entry from the Rouge or HUGE databases." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002295 ! Gene ID +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 [Term] -id: EDAM:0002781 +id: EDAM_data:2781 name: REDIdb ID namespace: identifier -def: "Identifier of an entry from the RNA editing database (REDIdb)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001097 ! Sequence accession (nucleic acid) +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) [Term] -id: EDAM:0002729 +id: EDAM_data:2729 name: COGEME EST ID namespace: identifier -def: "Identifier of an EST sequence from the COGEME database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002728 ! EST accession +subset: identifiers +subset: data +def: "Identifier of an EST sequence from the COGEME database." [http://edamontology.org] +is_a: EDAM_data:2728 ! EST accession [Term] -id: EDAM:0002730 +id: EDAM_data:2730 name: COGEME unisequence ID namespace: identifier -def: "Identifier of a unisequence from the COGEME database." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_a: EDAM:0002728 ! EST accession +is_a: EDAM_data:2728 ! EST accession [Term] -id: EDAM:0002798 +id: EDAM_data:2798 name: MaizeDB ID namespace: identifier -def: "Identifier of an EST sequence from the MaizeDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002728 ! EST accession +subset: identifiers +subset: data +def: "Identifier of an EST sequence from the MaizeDB database." [http://edamontology.org] +is_a: EDAM_data:2728 ! EST accession [Term] -id: EDAM:0001105 +id: EDAM_data:1105 name: dbEST accession namespace: identifier -def: "Identifier of a dbEST database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "dbEST ID" EXACT [] -is_a: EDAM:0002292 ! GenBank accession -is_a: EDAM:0002728 ! EST accession +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 [Term] -id: EDAM:0002704 +id: EDAM_data:2704 name: Clone ID (IMAGE) namespace: identifier -def: "A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "I.M.A.G.E. cloneID" EXACT [] -synonym: "IMAGE cloneID" EXACT [] -is_a: EDAM:0001855 ! Clone ID +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 [Term] -id: EDAM:0002803 +id: EDAM_data:2803 name: Clone ID (RefSeq) namespace: identifier -def: "A unique identifier of a cDNA molecule catalogued in the RefSeq database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001855 ! Clone ID -is_a: EDAM:0001098 ! RefSeq accession +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 [Term] -id: EDAM:0001110 +id: EDAM_data:1110 name: EMBOSS sequence type namespace: identifier -def: "The EMBOSS type of a molecular sequence." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_obsolete: true -consider: EDAM:0001094 ! Sequence type +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_data:1094 ! Sequence type [Term] -id: EDAM:0001106 +id: EDAM_data:1106 name: dbSNP ID namespace: identifier -def: "Identifier of a dbSNP database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "dbSNP identifier" EXACT [] -is_a: EDAM:0002294 ! Sequence variation ID +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 [Term] -id: EDAM:0002805 +id: EDAM_data:2805 name: GeneSNP ID namespace: identifier -def: "Identifier of a GeneSNP database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002294 ! Sequence variation ID +subset: identifiers +subset: data +def: "Identifier of a GeneSNP database entry." [http://edamontology.org] +is_a: EDAM_data:2294 ! Sequence variation ID [Term] -id: EDAM:0001112 +id: EDAM_data:1112 name: Sequence cluster ID namespace: identifier -def: "An identifier of a cluster of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001064 ! Sequence set ID -relationship: is_identifier_of EDAM:0001235 ! Sequence cluster +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 [Term] -id: EDAM:0002346 +id: EDAM_data:2346 name: Sequence cluster ID (UniRef) namespace: identifier -def: "Unique identifier of an entry from the UniRef database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "UniRef entry accession" EXACT [] -synonym: "UniRef cluster id" EXACT [] -is_a: EDAM:0001112 ! Sequence cluster ID +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 [Term] -id: EDAM:0001113 +id: EDAM_data:1113 name: Sequence cluster ID (COG) namespace: identifier -def: "Unique identifier of an entry from the COG database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "COG ID" EXACT [] -is_a: EDAM:0001112 ! Sequence cluster ID +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 [Term] -id: EDAM:0001104 +id: EDAM_data:1104 name: Sequence cluster ID (UniGene) namespace: identifier -def: "A unique identifier of an entry (gene cluster) from the NCBI UniGene database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "UniGene ID" EXACT [] -synonym: "UniGene identifier" EXACT [] -synonym: "UniGene cluster ID" EXACT [] -synonym: "UniGene cluster id" EXACT [] -is_a: EDAM:0001112 ! Sequence cluster ID +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 [Term] -id: EDAM:0002220 +id: EDAM_data:2220 name: Sequence cluster ID (SYSTERS) namespace: identifier -def: "Unique identifier of a sequence cluster from the SYSTERS database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "SYSTERS cluster ID" EXACT [] -is_a: EDAM:0001112 ! Sequence cluster ID +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 [Term] -id: EDAM:0002612 +id: EDAM_data:2612 name: Sequence cluster ID (CluSTr) namespace: identifier -def: "Unique identifier of a sequence cluster from the CluSTr database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "CluSTr cluster ID" EXACT [] -synonym: "CluSTr ID" EXACT [] +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:0001112 ! Sequence cluster ID +is_a: EDAM_data:1112 ! Sequence cluster ID [Term] -id: EDAM:0002347 +id: EDAM_data:2347 name: Sequence cluster ID (UniRef100) namespace: identifier -def: "Unique identifier of an entry from the UniRef100 database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "UniRef100 entry accession" EXACT [] -synonym: "UniRef100 cluster id" EXACT [] -is_a: EDAM:0002346 ! Sequence cluster ID (UniRef) +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) [Term] -id: EDAM:0002348 +id: EDAM_data:2348 name: Sequence cluster ID (UniRef90) namespace: identifier -def: "Unique identifier of an entry from the UniRef90 database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "UniRef90 entry accession" EXACT [] -synonym: "UniRef90 cluster id" EXACT [] -is_a: EDAM:0002346 ! Sequence cluster ID (UniRef) +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) [Term] -id: EDAM:0002349 +id: EDAM_data:2349 name: Sequence cluster ID (UniRef50) namespace: identifier -def: "Unique identifier of an entry from the UniRef50 database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "UniRef50 entry accession" EXACT [] -synonym: "UniRef50 cluster id" EXACT [] -is_a: EDAM:0002346 ! Sequence cluster ID (UniRef) +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) [Term] -id: EDAM:0002761 +id: EDAM_data:2761 name: UTRSite ID namespace: identifier -def: "Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001114 ! Sequence motif 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 [Term] -id: EDAM:0001116 +id: EDAM_data:1116 name: ELM ID namespace: identifier -def: "Identifier of an entry from the ELMdb database of protein functional sites." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001114 ! Sequence motif 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 [Term] -id: EDAM:0001117 +id: EDAM_data:1117 name: Prosite accession number namespace: identifier -def: "Accession number of an entry from the Prosite database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Prosite ID" EXACT [] +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:0001114 ! Sequence motif identifier +is_a: EDAM_data:1114 ! Sequence motif identifier [Term] -id: EDAM:0002714 +id: EDAM_data:2714 name: CDD PSSM-ID namespace: identifier -def: "Unique identifier of a position-specific scoring matrix from the CDD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001115 ! Sequence profile ID +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 [Term] -id: EDAM:0001118 +id: EDAM_data:1118 name: HMMER hidden Markov model ID namespace: identifier -def: "Unique identifier or name of a HMMER hidden Markov model." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001115 ! Sequence profile ID -relationship: is_identifier_of EDAM:0001364 ! Hidden Markov model +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 [Term] -id: EDAM:0001119 +id: EDAM_data:1119 name: JASPAR profile ID namespace: identifier -def: "Unique identifier or name of a profile from the JASPAR database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001115 ! Sequence profile ID +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 [Term] -id: EDAM:0002150 +id: EDAM_data:2150 name: Sequence profile name namespace: identifier -def: "Name of a sequence profile." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001115 ! Sequence profile ID +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 [Term] -id: EDAM:0001123 +id: EDAM_data:1123 name: TreeBASE study accession number namespace: identifier -def: "Accession number of an entry from the TreeBASE database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001068 ! Phylogenetic tree ID +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 [Term] -id: EDAM:0001124 +id: EDAM_data:1124 name: TreeFam accession number namespace: identifier -def: "Accession number of an entry from the TreeFam database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001068 ! Phylogenetic tree ID +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 [Term] -id: EDAM:0001126 +id: EDAM_data:1126 name: Comparison matrix name namespace: identifier -def: "Unique name or identifier of a comparison matrix." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "Substitution matrix name" EXACT [] -is_a: EDAM:0001069 ! Comparison matrix identifier -is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000874 ! Comparison 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 [Term] -id: EDAM:0001127 +id: EDAM_data:1127 name: PDB ID namespace: identifier -def: "An identifier of an entry from the PDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "PDB identifier" EXACT [] -synonym: "PDBID" EXACT [] +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:0001070 ! Structure ID +is_a: EDAM_data:1070 ! Structure ID [Term] -id: EDAM:0002667 +id: EDAM_data:2667 name: MMDB ID namespace: identifier -def: "An identifier of an entry from the MMDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "MMDB accession" EXACT [] +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:0001070 ! Structure ID +is_a: EDAM_data:1070 ! Structure ID [Term] -id: EDAM:0002793 +id: EDAM_data:2793 name: SISYPHUS ID namespace: identifier -def: "Identifier of an entry from the SISYPHUS database of tertiary structure alignments." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001072 ! Structure alignment ID +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 [Term] -id: EDAM:0001128 +id: EDAM_data:1128 name: AAindex ID namespace: identifier -def: "Identifier of an entry from the AAindex database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001073 ! Amino acid index ID +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 [Term] -id: EDAM:0001074 +id: EDAM_data:1074 name: Protein interaction ID namespace: identifier -def: "Identifier of a report of protein interactions from a protein interaction database (typically)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002627 ! Molecular interaction ID +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 [Term] -id: EDAM:0002628 +id: EDAM_data:2628 name: BioGRID interaction ID namespace: identifier -def: "A unique identifier of an interaction from the BioGRID database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002627 ! Molecular interaction ID +is_a: EDAM_data:2627 ! Molecular interaction ID [Term] -id: EDAM:0002636 +id: EDAM_data:2636 name: MatrixDB interaction ID namespace: identifier -def: "A unique identifier of an interaction from the MatrixDB database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002627 ! Molecular interaction ID +is_a: EDAM_data:2627 ! Molecular interaction ID [Term] -id: EDAM:0001129 +id: EDAM_data:1129 name: BIND accession number namespace: identifier -def: "Accession number of an entry from the BIND database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001074 ! Protein interaction ID +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 [Term] -id: EDAM:0001130 +id: EDAM_data:1130 name: IntAct accession number namespace: identifier -def: "Accession number of an entry from the IntAct database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001074 ! Protein interaction ID +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM:0002302 +id: EDAM_data:2302 name: STRING ID namespace: identifier -def: "Unique identifier of an entry from the STRING database of protein-protein interactions." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001074 ! Protein interaction ID +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 [Term] -id: EDAM:0002615 +id: EDAM_data:2615 name: MINT ID namespace: identifier -def: "Unique identifier of an entry from the MINT database of protein-protein interactions." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001074 ! Protein interaction ID +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM:0002616 +id: EDAM_data:2616 name: DIP ID namespace: identifier -def: "Unique identifier of an entry from the DIP database of protein-protein interactions." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001074 ! Protein interaction ID +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM:0002668 +id: EDAM_data:2668 name: iRefIndex ID namespace: identifier -def: "Unique identifier of an entry from the iRefIndex database of protein-protein interactions." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001074 ! Protein interaction ID +is_a: EDAM_data:1074 ! Protein interaction ID [Term] -id: EDAM:0001076 +id: EDAM_data:1076 name: Codon usage table name namespace: identifier -def: "Unique name of a codon usage table." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002111 ! Codon usage table identifier -is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0001597 ! Codon usage table -relationship: is_identifier_of EDAM:0001598 ! Genetic code +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 [Term] -id: EDAM:0002356 +id: EDAM_data:2356 name: RFAM accession namespace: identifier -def: "Stable accession number of an entry (RNA family) from the RFAM database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002355 ! RNA family identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002606 +id: EDAM_data:2606 name: RFAM name namespace: identifier -def: "Name (not necessarily stable) an entry (RNA family) from the RFAM database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002355 ! RNA family identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002766 +id: EDAM_data:2766 name: HAMAP ID namespace: identifier -def: "Name of a protein family from the HAMAP database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002910 ! Protein family accession +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 [Term] -id: EDAM:0001132 +id: EDAM_data:1132 name: InterPro entry name namespace: identifier -def: "Name of an InterPro entry, usually indicating the type of protein matches for that entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001131 ! Protein family name -relationship: is_identifier_of EDAM:0001355 ! Protein signature +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 [Term] -id: EDAM:0001133 +id: EDAM_data:1133 name: InterPro accession namespace: identifier -def: "Primary accession number of an InterPro entry." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "InterPro primary accession number" EXACT [] -synonym: "InterPro primary accession" EXACT [] +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:0002910 ! Protein family accession -relationship: is_identifier_of EDAM:0001355 ! Protein signature +example: "IPR015590" +is_a: EDAM_data:2910 ! Protein family accession +relationship: is_identifier_of EDAM_data:1355 ! Protein signature [Term] -id: EDAM:0001134 +id: EDAM_data:1134 name: InterPro secondary accession namespace: identifier -def: "Secondary accession number of an InterPro entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "InterPro secondary accession number" EXACT [] -is_a: EDAM:0001133 ! InterPro accession -relationship: is_identifier_of EDAM:0001355 ! Protein signature +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 [Term] -id: EDAM:0001135 +id: EDAM_data:1135 name: Gene3D ID namespace: identifier -def: "Unique identifier of an entry from the Gene3D database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002910 ! Protein family accession +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 [Term] -id: EDAM:0001136 +id: EDAM_data:1136 name: PIRSF ID namespace: identifier -def: "Unique identifier of an entry from the PIRSF database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002910 ! Protein family accession +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM:0001137 +id: EDAM_data:1137 name: PRINTS code namespace: identifier -def: "The unique identifier of an entry in the PRINTS database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002910 ! Protein family accession +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM:0001138 +id: EDAM_data:1138 name: Pfam accession number namespace: identifier -def: "Accession number of a Pfam entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Accession number of a Pfam entry." [http://edamontology.org] regex: "PF[0-9]{5}" -is_a: EDAM:0002910 ! Protein family accession +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM:0002758 +id: EDAM_data:2758 name: Pfam clan ID namespace: identifier -def: "Accession number of a Pfam clan." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Accession number of a Pfam clan." [http://edamontology.org] regex: "CL[0-9]{4}" -is_a: EDAM:0002910 ! Protein family accession +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM:0002757 +id: EDAM_data:2757 name: Pfam domain name namespace: identifier -def: "Name of a domain from the Pfam database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001131 ! Protein family name +is_a: EDAM_data:1131 ! Protein family name [Term] -id: EDAM:0002782 +id: EDAM_data:2782 name: SMART domain name namespace: identifier -def: "Name of a domain from the SMART database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001131 ! Protein family name +subset: identifiers +subset: data +def: "Name of a domain from the SMART database." [http://edamontology.org] +is_a: EDAM_data:1131 ! Protein family name [Term] -id: EDAM:0001139 +id: EDAM_data:1139 name: SMART accession number namespace: identifier -def: "Accession number of an entry from the SMART database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002910 ! Protein family accession +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM:0001140 +id: EDAM_data:1140 name: Superfamily hidden Markov model number namespace: identifier -def: "Unique identifier (number) of a hidden Markov model from the Superfamily database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002910 ! Protein family accession +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 [Term] -id: EDAM:0001141 +id: EDAM_data:1141 name: TIGRFam ID namespace: identifier -def: "Accession number of an entry (family) from the TIGRFam database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "TIGRFam accession number" EXACT [] -is_a: EDAM:0002910 ! Protein family accession +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 [Term] -id: EDAM:0001142 +id: EDAM_data:1142 name: ProDom accession number namespace: identifier -def: "A ProDom domain family accession number." [EDAM:EBI "EMBRACE definition"] +subset: identifiers +subset: data +def: "A ProDom domain family accession number." [http://edamontology.org] comment: ProDom is a protein domain family database. -subset: identifier regex: "PD[0-9]+" -is_a: EDAM:0002910 ! Protein family accession +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM:0002614 +id: EDAM_data:2614 name: TCDB ID namespace: identifier -def: "A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "TC number" EXACT [] +synonym: "TC number" EXACT [http://edamontology.org] regex: "[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+" -is_a: EDAM:0002910 ! Protein family accession +is_a: EDAM_data:2910 ! Protein family accession [Term] -id: EDAM:0002731 +id: EDAM_data:2731 name: Protein family ID (GeneFarm) namespace: identifier -def: "Accession number of an entry (family) from the TIGRFam database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "GeneFarm family ID" EXACT [] -is_a: EDAM:0002910 ! Protein family accession +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 [Term] -id: EDAM:0002783 +id: EDAM_data:2783 name: Protein family ID (PANTHER) namespace: identifier -def: "Accession number of an entry (family) from the PANTHER database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Panther family ID" EXACT [] -is_a: EDAM:0002910 ! Protein family accession +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 [Term] -id: EDAM:0001143 +id: EDAM_data:1143 name: TRANSFAC accession number namespace: identifier -def: "Identifier of an entry from the TRANSFAC database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002911 ! Transcription factor accession +subset: identifiers +subset: data +def: "Identifier of an entry from the TRANSFAC database." [http://edamontology.org] +is_a: EDAM_data:2911 ! Transcription factor accession [Term] -id: EDAM:0002716 +id: EDAM_data:2716 name: DBD ID namespace: identifier -def: "Identifier of a predicted transcription factor from the DBD database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002911 ! Transcription factor accession +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 [Term] -id: EDAM:0002742 +id: EDAM_data:2742 name: AraC-XylS ID namespace: identifier -def: "Identifier of a transcription factor from the AraC-XylS database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002911 ! Transcription factor accession +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 [Term] -id: EDAM:0002755 +id: EDAM_data:2755 name: Transcription factor name namespace: identifier -def: "The name of a transcription factor." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001077 ! Transcription factor identifier -is_a: EDAM:0001009 ! Protein name +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 [Term] -id: EDAM:0001144 +id: EDAM_data:1144 name: ArrayExpress accession number namespace: identifier -def: "Accession number of an entry from the ArrayExpress database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "ArrayExpress experiment ID" EXACT [] +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:0001078 ! Microarray experiment annotation ID +is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] -id: EDAM:0001145 +id: EDAM_data:1145 name: PRIDE experiment accession number namespace: identifier -def: "PRIDE experiment accession number." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "PRIDE experiment accession number." [http://edamontology.org] regex: "[0-9]+" -is_a: EDAM:0001078 ! Microarray experiment annotation ID +is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] -id: EDAM:0002710 +id: EDAM_data:2710 name: CleanEx dataset code namespace: identifier -def: "An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001078 ! Microarray experiment annotation ID +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 [Term] -id: EDAM:0001146 +id: EDAM_data:1146 name: EMDB ID namespace: identifier -def: "Identifier of an entry from the EMDB electron microscopy database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001079 ! Electron microscopy model ID +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 [Term] -id: EDAM:0001147 +id: EDAM_data:1147 name: GEO accession number namespace: identifier -def: "Accession number of an entry from the GEO database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001080 ! Gene expression report ID +is_a: EDAM_data:1080 ! Gene expression report ID [Term] -id: EDAM:0001148 +id: EDAM_data:1148 name: GermOnline ID namespace: identifier -def: "Identifier of an entry from the GermOnline database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001080 ! Gene expression report ID +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 [Term] -id: EDAM:0001149 +id: EDAM_data:1149 name: EMAGE ID namespace: identifier -def: "Identifier of an entry from the EMAGE database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001080 ! Gene expression report ID +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 [Term] -id: EDAM:0002709 +id: EDAM_data:2709 name: CleanEx entry name namespace: identifier -def: "An identifier of a gene expression profile from the CleanEx database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001080 ! Gene expression report ID +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 [Term] -id: EDAM:0001150 +id: EDAM_data:1150 name: Disease ID namespace: identifier -def: "Identifier of an entry from a database of disease." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0001622 ! Disease annotation +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 [Term] -id: EDAM:0001151 +id: EDAM_data:1151 name: HGVbase ID namespace: identifier -def: "Identifier of an entry from the HGVbase database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001081 ! Genotype and phenotype annotation ID +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 [Term] -id: EDAM:0001152 +id: EDAM_data:1152 name: HIVDB identifier namespace: identifier -def: "Identifier of an entry from the HIVDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0000842 ! 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 [Term] -id: EDAM:0001153 +id: EDAM_data:1153 name: OMIM ID namespace: identifier -def: "Identifier of an entry from the OMIM database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of an entry from the OMIM database." [http://edamontology.org] regex: "[*#+%^]?[0-9]{6}" -is_a: EDAM:0001081 ! Genotype and phenotype annotation ID +is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID [Term] -id: EDAM:0002611 +id: EDAM_data:2611 name: ICD identifier namespace: identifier -def: "An identifier of a disease from the International Classification of Diseases (ICD) database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001150 ! Disease ID -relationship: is_identifier_of EDAM:0001622 ! Disease annotation +is_a: EDAM_data:1150 ! Disease ID +relationship: is_identifier_of EDAM_data:1622 ! Disease annotation [Term] -id: EDAM:0002800 +id: EDAM_data:2800 name: Orpha number namespace: identifier -def: "An identifier of a disease from the Orpha database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001150 ! Disease ID -relationship: is_identifier_of EDAM:0001622 ! Disease annotation +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 [Term] -id: EDAM:0002651 +id: EDAM_data:2651 name: Disease ID (PharmGKB) namespace: identifier -def: "Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001150 ! Disease ID -is_a: EDAM:0002649 ! PharmGKB ID +is_a: EDAM_data:1150 ! Disease ID +is_a: EDAM_data:2649 ! PharmGKB ID [Term] -id: EDAM:0002383 +id: EDAM_data:2383 name: EGA accession namespace: identifier -def: "Identifier of an entry from the EGA database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002382 ! Genotype experiment ID +subset: identifiers +subset: data +def: "Identifier of an entry from the EGA database." [http://edamontology.org] +is_a: EDAM_data:2382 ! Genotype experiment ID [Term] -id: EDAM:0002342 +id: EDAM_data:2342 name: Pathway or network name namespace: identifier -def: "The name of a biological pathway or network." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001082 ! Pathway or network 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 [Term] -id: EDAM:0002365 +id: EDAM_data:2365 name: Pathway or network accession namespace: identifier -def: "A persistent, unique identifier of a biological pathway or network (typically a database entry)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001082 ! Pathway or network identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0002637 +id: EDAM_data:2637 name: cPath ID namespace: identifier -def: "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier regex: "[0-9]+" -is_a: EDAM:0002109 ! Identifier (hybrid) -is_a: EDAM:0002365 ! Pathway or network accession +is_a: EDAM_data:2109 ! Identifier (hybrid) +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM:0002659 +id: EDAM_data:2659 name: Pathway ID (SMPDB) namespace: identifier -def: "Identifier of a pathway from the Small Molecule Pathway Database (SMPDB)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002365 ! Pathway or network accession +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM:0002837 +id: EDAM_data:2837 name: Pathway ID (BioSystems) namespace: identifier -def: "Identifier of a pathway from the BioSystems pathway database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Identifier of a pathway from the BioSystems pathway database." [http://edamontology.org] regex: "[0-9]+" -is_a: EDAM:0002365 ! Pathway or network accession +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM:0002650 +id: EDAM_data:2650 name: Pathway ID (PharmGKB) namespace: identifier -def: "Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002365 ! Pathway or network accession -is_a: EDAM:0002649 ! PharmGKB ID +is_a: EDAM_data:2365 ! Pathway or network accession +is_a: EDAM_data:2649 ! PharmGKB ID [Term] -id: EDAM:0002345 +id: EDAM_data:2345 name: Pathway ID (ConsensusPathDB) namespace: identifier -def: "Identifier of a pathway from the ConsensusPathDB pathway database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002917 ! ConsensusPathDB identifier -is_a: EDAM:0002365 ! Pathway or network accession +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 [Term] -id: EDAM:0002343 +id: EDAM_data:2343 name: Pathway ID (KEGG) namespace: identifier -def: "Identifier of a pathway from the KEGG pathway database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "KEGG pathway ID" EXACT [] +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:0002365 ! Pathway or network accession -is_a: EDAM:0001154 ! KEGG object identifier +is_a: EDAM_data:2365 ! Pathway or network accession +is_a: EDAM_data:1154 ! KEGG object identifier [Term] -id: EDAM:0002344 +id: EDAM_data:2344 name: Pathway ID (NCI-Nature) namespace: identifier -def: "Identifier of a pathway from the NCI-Nature pathway database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002365 ! Pathway or network accession +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM:0001155 +id: EDAM_data:1155 name: Pathway ID (reactome) namespace: identifier -def: "Identifier of an entry from the Reactome database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Reactome ID" EXACT [] +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:0002365 ! Pathway or network accession +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM:0001156 +id: EDAM_data:1156 name: Pathway ID (aMAZE) namespace: identifier -def: "Identifier of an entry from the aMAZE database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "aMAZE ID" EXACT [] -is_obsolete: true -consider: EDAM:0001082 ! Pathway or network 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 [Term] -id: EDAM:0001157 +id: EDAM_data:1157 name: Pathway ID (BioCyc) namespace: identifier -def: "Identifier of an pathway from the BioCyc biological pathways database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "BioCyc pathway ID" EXACT [] -is_a: EDAM:0002365 ! Pathway or network accession -is_a: EDAM:0002104 ! BioCyc ID +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 [Term] -id: EDAM:0001158 +id: EDAM_data:1158 name: Pathway ID (INOH) namespace: identifier -def: "Identifier of an entry from the INOH database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "INOH identifier" EXACT [] -is_a: EDAM:0002365 ! Pathway or network accession +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 [Term] -id: EDAM:0001159 +id: EDAM_data:1159 name: Pathway ID (PATIKA) namespace: identifier -def: "Identifier of an entry from the PATIKA database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "PATIKA ID" EXACT [] -is_a: EDAM:0002365 ! Pathway or network accession +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 [Term] -id: EDAM:0001160 +id: EDAM_data:1160 name: Pathway ID (CPDB) namespace: identifier -def: "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB." [EDAM:EBI "EMBRACE definition"] -comment: This term refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. -subset: identifier -synonym: "CPDB ID" EXACT [] -is_a: EDAM:0002365 ! Pathway or network accession +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 [Term] -id: EDAM:0001161 +id: EDAM_data:1161 name: Pathway ID (Panther) namespace: identifier -def: "Identifier of a biological pathway from the Panther Pathways database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Panther Pathways ID" EXACT [] +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:0002365 ! Pathway or network accession +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM:0002645 +id: EDAM_data:2645 name: Pathway ID (Unipathway) namespace: identifier -def: "Identifier of a biological pathway from the Unipathway database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "upaid" EXACT [] +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:0002365 ! Pathway or network accession +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM:0002670 +id: EDAM_data:2670 name: Pathway ID (DQCS) namespace: identifier -def: "Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS)." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002365 ! Pathway or network accession +is_a: EDAM_data:2365 ! Pathway or network accession [Term] -id: EDAM:0002591 +id: EDAM_data:2591 name: Brite hierarchy ID namespace: identifier -def: "Identifier of an entry from the Brite database of biological hierarchies." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002891 ! Biological model accession +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 [Term] -id: EDAM:0001162 +id: EDAM_data:1162 name: MIRIAM identifier namespace: identifier -def: "Unique identifier of a MIRIAM data resource." [EDAM:EBI "EMBRACE definition"] -comment: This is the identifier used internally by MIRIAM for a data type. For example 'MIR:00100005'. -subset: 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}" -is_a: EDAM:0002902 ! Data resource definition accession -relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype +example: "MIR:00100005" +is_a: EDAM_data:2902 ! Data resource definition accession +relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype [Term] -id: EDAM:0001163 +id: EDAM_data:1163 name: MIRIAM data type name namespace: identifier -def: "The name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002253 ! Data resource definition name -relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype +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 [Term] -id: EDAM:0002253 +id: EDAM_data:2253 name: Data resource definition name namespace: identifier -def: "The name of a data type." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001084 ! Data resource definition identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0002902 +id: EDAM_data:2902 name: Data resource definition accession namespace: identifier -def: "Accession of a data definition (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001084 ! Data resource definition identifier -is_a: EDAM:0002091 ! Accession +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 [Term] -id: EDAM:0001164 +id: EDAM_data:1164 name: MIRIAM URI namespace: identifier -def: "The URI (URL or URN) of a data entity from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] -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. For example: urn:miriam:pubmed:16333295 is the MIRIAM URI of the publication about MIRIAM, whereas 'urn:miriam:obo.go:GO%3A0045202' refers to GO. -subset: identifier -is_a: EDAM:0002902 ! Data resource definition accession -is_a: EDAM:0001047 ! URI -relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype +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 [Term] -id: EDAM:0001165 +id: EDAM_data:1165 name: MIRIAM data type primary name namespace: identifier -def: "The primary name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] -comment: The primary name of a MIRIAM data type is taken from a controlled vocabulary. For example, a protein entity has the data type 'UniProt', an enzyme has the type 'Enzyme Nomenclature' etc. -subset: identifier -is_a: EDAM:0001163 ! MIRIAM data type name +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 [Term] -id: EDAM:0001166 +id: EDAM_data:1166 name: MIRIAM data type synonymous name namespace: identifier -def: "A synonymous name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_a: EDAM:0001163 ! MIRIAM data type name +is_a: EDAM_data:1163 ! MIRIAM data type name [Term] -id: EDAM:0002106 +id: EDAM_data:2106 name: Reaction ID (BioCyc) namespace: identifier -def: "Identifier of a biological reaction from the BioCyc reactions database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002108 ! Reaction ID -is_a: EDAM:0002104 ! BioCyc ID -relationship: has_topic EDAM:0000613 ! Peptides and amino acids +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 [Term] -id: EDAM:0002309 +id: EDAM_data:2309 name: Reaction ID (SABIO-RK) namespace: identifier -def: "Identifier of a biological reaction from the SABIO-RK reactions database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002108 ! Reaction ID +is_a: EDAM_data:2108 ! Reaction ID [Term] -id: EDAM:0002648 +id: EDAM_data:2648 name: Reaction kinetics ID (SABIO-RK) namespace: identifier -def: "Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002309 ! Reaction ID (SABIO-RK) +is_a: EDAM_data:2309 ! Reaction ID (SABIO-RK) [Term] -id: EDAM:0002608 +id: EDAM_data:2608 name: Reaction ID (KEGG) namespace: identifier -def: "Identifier of a biological reaction from the KEGG reactions database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002108 ! Reaction ID -is_a: EDAM:0001154 ! KEGG object identifier +is_a: EDAM_data:2108 ! Reaction ID +is_a: EDAM_data:1154 ! KEGG object identifier [Term] -id: EDAM:0002641 +id: EDAM_data:2641 name: Reaction ID (MACie) namespace: identifier -def: "Identifier of an enzyme reaction mechanism from the MACie database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "MACie entry number" EXACT [] +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:0002108 ! Reaction ID +is_a: EDAM_data:2108 ! Reaction ID [Term] -id: EDAM:0002644 +id: EDAM_data:2644 name: Reaction ID (Rhea) namespace: identifier -def: "Identifier of an enzyme-catalysed reaction from the Rhea database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002108 ! Reaction ID +is_a: EDAM_data:2108 ! Reaction ID [Term] -id: EDAM:0001167 +id: EDAM_data:1167 name: Taverna workflow ID namespace: identifier -def: "Unique identifier of a Taverna workflow." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001083 ! Workflow ID +subset: identifiers +subset: data +def: "Unique identifier of a Taverna workflow." [http://edamontology.org] +is_a: EDAM_data:1083 ! Workflow ID [Term] -id: EDAM:0001170 +id: EDAM_data:1170 name: Biological model name namespace: identifier -def: "Name of a biological (mathematical) model." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001085 ! Biological model identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0001171 +id: EDAM_data:1171 name: BioModel ID namespace: identifier -def: "Unique identifier of an entry from the BioModel database." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002891 ! Biological model accession +is_a: EDAM_data:2891 ! Biological model accession [Term] -id: EDAM:0002669 +id: EDAM_data:2669 name: ModelDB ID namespace: identifier -def: "Unique identifier of an entry from the ModelDB database." [EDAM:EBI "EMBRACE definition"] -subset: identifier +subset: identifiers +subset: data +def: "Unique identifier of an entry from the ModelDB database." [http://edamontology.org] regex: "[0-9]+" -is_a: EDAM:0002891 ! Biological model accession +is_a: EDAM_data:2891 ! Biological model accession [Term] -id: EDAM:0002339 -name: Ontology term name +id: EDAM_data:2339 +name: Ontology concept name namespace: identifier -def: "The name of a term in an ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0003025 ! Ontology term identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0001175 -name: BioPax term ID +id: EDAM_data:1175 +name: BioPax concept ID namespace: identifier -def: "An identifier of a term from the BioPax ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001176 -name: GO term ID +id: EDAM_data:1176 +name: GO concept ID namespace: identifier -def: "An identifier of a term from The Gene Ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "GO term identifier" EXACT [] -regex: "[0-9]{7}" "GO:[0-9]{7}" ! Isn't the string with "GO:" not an ID but an ontology reference + ID, in GO-style format? Check that with GO. Check the same with other ids having "regex.+:" (doi & ISBN should probably work both with & without(?)) -! regex: "GO:[0-9]{7}" -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001177 -name: MeSH term ID +id: EDAM_data:1177 +name: MeSH concept ID namespace: identifier -def: "An identifier of a term from the MeSH vocabulary." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001178 -name: HGNC term ID +id: EDAM_data:1178 +name: HGNC concept ID namespace: identifier -def: "An identifier of a term from the HGNC controlled vocabulary." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001179 +id: EDAM_data:1179 name: NCBI taxonomy ID namespace: identifier -def: "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." [EDAM:EBI "EMBRACE definition"] -subset: 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}" -! regex: "[0-9]+" - -synonym: "NCBI taxonomy term identifier" EXACT [] -synonym: "NCBI tax ID" EXACT [] -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001180 -name: Plant Ontology term ID +id: EDAM_data:1180 +name: Plant Ontology concept ID namespace: identifier -def: "An identifier of a term from the Plant Ontology (PO)." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001181 -name: UMLS term ID +id: EDAM_data:1181 +name: UMLS concept ID namespace: identifier -def: "An identifier of a term from the UMLS vocabulary." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001182 -name: FMA term ID +id: EDAM_data:1182 +name: FMA concept ID namespace: identifier -def: "An identifier of a term from Foundational Model of Anatomy." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier regex: "FMA:[0-9]+" -is_a: EDAM:0001087 ! Ontology term ID +is_a: EDAM_data:1087 ! Ontology concept ID [Term] -id: EDAM:0001183 -name: EMAP term ID +id: EDAM_data:1183 +name: EMAP concept ID namespace: identifier -def: "An identifier of a term from the EMAP mouse ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001184 -name: ChEBI term ID +id: EDAM_data:1184 +name: ChEBI concept ID namespace: identifier -def: "An identifier of a term from the ChEBI ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001185 -name: MGED term ID +id: EDAM_data:1185 +name: MGED concept ID namespace: identifier -def: "An identifier of a term from the MGED ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0001186 -name: myGrid term ID +id: EDAM_data:1186 +name: myGrid concept ID namespace: identifier -def: "An identifier of a term from the myGrid ontology." [EDAM:EBI "EMBRACE definition"] -comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides terms for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. -subset: identifier -is_a: EDAM:0001087 ! Ontology term ID +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 [Term] -id: EDAM:0002705 -name: GO term ID (cellular compartment) +id: EDAM_data:2705 +name: GO concept ID (cellular compartment) namespace: identifier -def: "An identifier of a 'cellular compartment' term from the Gene Ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "GO term identifier (cellular compartment)" EXACT [] +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:0001176 ! GO term ID +is_a: EDAM_data:1176 ! GO concept ID [Term] -id: EDAM:0002582 -name: GO term ID (biological process) +id: EDAM_data:2582 +name: GO concept ID (biological process) namespace: identifier -def: "An identifier of a 'biological process' term from the the Gene Ontology." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001176 ! GO term ID +is_a: EDAM_data:1176 ! GO concept ID [Term] -id: EDAM:0002583 -name: GO term ID (molecular function) +id: EDAM_data:2583 +name: GO concept ID (molecular function) namespace: identifier -def: "An identifier of a 'molecular function' term from the the Gene Ontology." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001176 ! GO term ID +is_a: EDAM_data:1176 ! GO concept ID [Term] -id: EDAM:0002581 -name: GO term name +id: EDAM_data:2581 +name: GO concept name namespace: identifier -def: "The name of a term from the GO ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0002339 ! Ontology term name +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 [Term] -id: EDAM:0003026 -name: GO term name (biological process) +id: EDAM_data:3026 +name: GO concept name (biological process) namespace: identifier -def: "The name of a term for a biological process from the GO ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0002339 ! Ontology term name +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 [Term] -id: EDAM:0003027 -name: GO term name (molecular function) +id: EDAM_data:3027 +name: GO concept name (molecular function) namespace: identifier -def: "The name of a term for a molecular function from the GO ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0002339 ! Ontology term name +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 [Term] -id: EDAM:0002584 -name: GO term name (cellular component) +id: EDAM_data:2584 +name: GO concept name (cellular component) namespace: identifier -def: "The name of a term for a cellular component from the GO ontology." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0002339 ! Ontology term name +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 @@ -23352,4167 +23749,4340 @@ consider: EDAM:0002339 ! Ontology term name ! Different biological types of signature are listed below. Bioinformatics types (motif, profile, HMM etc) are given elsewhere [Term] -id: EDAM:0001187 +id: EDAM_data:1187 name: PubMed ID namespace: identifier -def: "PubMed unique identifier of an article." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "PMID" EXACT [] +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}" -! regex: "^[0-9]+" -is_a: EDAM:0001088 ! Article ID +example: "4963447" +is_a: EDAM_data:1088 ! Article ID [Term] -id: EDAM:0001188 +id: EDAM_data:1188 name: Digital Object Identifier namespace: identifier -def: "Digital Object Identifier (DOI) of a published article." [EDAM:EBI "EMBRACE definition"] -subset: 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:0001088 ! Article ID +is_a: EDAM_data:1088 ! Article ID [Term] -id: EDAM:0001189 +id: EDAM_data:1189 name: Medline UI namespace: identifier -def: "Medline UI (unique identifier) of an article." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -synonym: "Medline unique identifier" EXACT [] -is_a: EDAM:0001088 ! Article ID +synonym: "Medline unique identifier" EXACT [http://edamontology.org] +is_a: EDAM_data:1088 ! Article ID [Term] -id: EDAM:0002634 +id: EDAM_data:2634 name: ISBN namespace: identifier -def: "The International Standard Book Number (ISBN) is for identifying printed books." [EDAM:EBI "EMBRACE definition"] -subset: 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:0002633 ! Book ID +is_a: EDAM_data:2633 ! Book ID [Term] -id: EDAM:0002374 +id: EDAM_data:2374 name: Spot serial number namespace: identifier -def: "Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002373 ! Spot ID +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 [Term] -id: EDAM:0002375 +id: EDAM_data:2375 name: Spot ID (HSC-2DPAGE) namespace: identifier -def: "Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002373 ! Spot ID +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 [Term] -id: EDAM:0002588 +id: EDAM_data:2588 name: BlotBase blot ID namespace: identifier -def: "Unique identifier of a blot from a Northern Blot from the BlotBase database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002587 ! Blot ID +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 [Term] -id: EDAM:0001046 +id: EDAM_data:1046 name: Strain name namespace: identifier -def: "The name of a strain of an organism variant, typically a plant, virus or bacterium." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002909 ! Organism name -is_a: EDAM:0002379 ! Strain 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 [Term] -id: EDAM:0002778 +id: EDAM_data:2778 name: CCAP strain number namespace: identifier -def: "The number of a strain of algae and protozoa from the CCAP database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002912 ! Strain accession +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 [Term] -id: EDAM:0002316 +id: EDAM_data:2316 name: Cell line name namespace: identifier -def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001046 ! Strain name +subset: identifiers +subset: data +def: "The name of a cell line." [http://edamontology.org] +is_a: EDAM_data:1046 ! Strain name [Term] -id: EDAM:0002112 +id: EDAM_data:2112 name: FlyBase primary identifier namespace: identifier -def: "Primary identifier of an object from the FlyBase database." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0001089 ! FlyBase ID +subset: identifiers +subset: data +def: "Primary identifier of an object from the FlyBase database." [http://edamontology.org] +is_a: EDAM_data:1089 ! FlyBase ID [Term] -id: EDAM:0002174 +id: EDAM_data:2174 name: FlyBase secondary identifier namespace: identifier -def: "Secondary identifier of an object from the FlyBase database." [EDAM:EBI "EMBRACE definition"] +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. -subset: identifier -is_a: EDAM:0001089 ! FlyBase ID +is_a: EDAM_data:1089 ! FlyBase ID [Term] -id: EDAM:0001091 +id: EDAM_data:1091 name: WormBase name namespace: identifier -def: "Name of an object from the WormBase database, usually a human-readable name." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002113 ! WormBase identifier -is_a: EDAM:0002099 ! Name +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 [Term] -id: EDAM:0001092 +id: EDAM_data:1092 name: WormBase class namespace: identifier -def: "Class of an object from the WormBase database." [EDAM:EBI "EMBRACE definition"] +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'. -subset: identifier -is_a: EDAM:0002113 ! WormBase identifier +is_a: EDAM_data:2113 ! WormBase identifier [Term] -id: EDAM:0002254 +id: EDAM_data:2254 name: OBO file format name namespace: identifier -def: "Name of an OBO file format such as OBO-XML, plain and so on." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002129 ! File format name - +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 -! Format -[Term] -id: EDAM:0002351 -name: Undefined -namespace: format -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true +! +! Format +! [Term] -id: EDAM:0002350 +id: EDAM_format:2350 name: Format (typed) namespace: format -def: "A broad class of format distinguished by the scientific nature of the data that is identified." [EDAM:EBI "EMBRACE definition"] -comment: This term exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The term branch under 'Format (typed)' provides an alternative organisation of the terms nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All terms under here are already included under those branches. -subset: format -is_a: EDAM:0001915 ! 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 [Term] -id: EDAM:0002330 -name: Text -! synonym: "Tabular format" SPECIALISATION WITHOUT WELL-DEFINED BORDERS(to find this for users who search for 'tabular format') [] +id: EDAM_format:2330 +name: Textual format namespace: format -def: "Text format." [EDAM:EBI "EMBRACE definition"] -comment: Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. -subset: format -is_a: EDAM:0001915 ! 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] +synonym: "Symbol sequence" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence] +is_a: EDAM_format:1915 ! Format [Term] -id: EDAM:0002331 +id: EDAM_format:2331 name: HTML namespace: format -def: "HTML format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001915 ! 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 [Term] -id: EDAM:0002332 +id: EDAM_format:2332 name: XML namespace: format -def: "Extensible Markup Language (XML) format." [EDAM:EBI "EMBRACE definition"] +subset: formats +def: "eXtensible Markup Language (XML) format." [http://edamontology.org] comment: Data in XML format can be serialised into text, or binary format. -subset: format -is_a: EDAM:0001915 ! Format - -[Term] -id: EDAM:0002333 -name: Binary -namespace: format -def: "Binary format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001915 ! 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 [Term] -id: EDAM:0002352 -name: BioXSD -synonym: "BioXSD XML format" EXACT [] +id: EDAM_format:2333 +name: Binary format namespace: format -def: "BioXSD XML format of some of basic bioinformatics data types (sequences, sequence records, annotated sequences, sequence alignments, references to resources, and more)." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://bioxsd.org -is_a: EDAM:0002332 ! XML +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 [Term] -id: EDAM:0002376 +id: EDAM_format:2376 name: RDF namespace: format -def: "Resource Description Framework (RDF) format." [EDAM:EBI "EMBRACE definition"] -comment: Data in RDF format can be serialised into XML, text, or binary format. -subset: format -is_a: EDAM:0001915 ! 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 [Term] -id: EDAM:0002921 +id: EDAM_format:2921 name: Sequence variation annotation format namespace: format -def: "Format of sequence variation annotation." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000918 ! Nucleic acid features (variation) +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) [Term] -id: EDAM:0002919 +id: EDAM_format:2919 name: Sequence annotation track format namespace: format -def: "Format of a sequence annotation track." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0003002 ! Sequence annotation track +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 [Term] -id: EDAM:0002848 +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 + +[Term] +id: EDAM_format:2848 name: Bibliographic reference format namespace: format -def: "Format of a bibliographic reference." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000970 ! Bibliographic reference -relationship: is_format_of EDAM:0002849 ! Abstract +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 [Term] -id: EDAM:0002334 +id: EDAM_format:2334 name: URI format namespace: format -def: "Typical textual representation of a URI." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001047 ! URI +subset: formats +def: "Typical textual representation of a URI." [http://edamontology.org] +is_obsolete: true !{since=beta13} +consider: EDAM_data:1047 ! URI [Term] -id: EDAM:0001918 +id: EDAM_format:1918 name: Atomic data format namespace: format -def: "Data format for an individual atom." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001475 ! PDB database entry 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 [Term] -id: EDAM:0001919 +id: EDAM_format:1919 name: Sequence record format namespace: format -def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000849 ! Sequence record +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 [Term] -id: EDAM:0001920 +id: EDAM_format:1920 name: Sequence feature annotation format namespace: format -def: "Data format for molecular sequence feature information." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001255 ! Sequence features +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 ! Sequence features [Term] -id: EDAM:0001921 +id: EDAM_format:1921 name: Alignment format namespace: format -def: "Data format for molecular sequence alignment information." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000863 ! Sequence alignment +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 [Term] -id: EDAM:0002920 +id: EDAM_format:2920 name: Alignment format (pair only) namespace: format -def: "Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001921 ! Alignment format -relationship: is_format_of EDAM:0001381 ! Sequence alignment (pair) +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) [Term] -id: EDAM:0002006 +id: EDAM_format:2006 name: Phylogenetic tree format namespace: format -def: "Data format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000872 ! Phylogenetic tree +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 [Term] -id: EDAM:0002033 +id: EDAM_format:2033 name: Tertiary structure format namespace: format -def: "Data format for a molecular tertiary structure." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) +subset: formats +def: "Data format for a molecular tertiary structure." [http://edamontology.org] +is_a: EDAM_format:2350 ! Format (typed) + +[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) + [Term] -id: EDAM:0002034 +id: EDAM_format:2034 name: Biological model format namespace: format -def: "Data format for a biological model." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000950 ! Biological model +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 [Term] -id: EDAM:0002014 +id: EDAM_format:2014 name: Sequence-profile alignment format namespace: format -def: "Data format for a sequence-profile alignment." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000869 ! Sequence-profile alignment +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 [Term] -id: EDAM:0002562 +id: EDAM_format:2562 name: Amino acid identifier format namespace: format -def: "Text format (representation) of amino acid residues." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0000994 ! Amino acid identifier +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 [Term] -id: EDAM:0002017 +id: EDAM_format:2017 name: Amino acid index format namespace: format -def: "Data format for an amino acid index." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0003033 ! Matrix format -relationship: is_format_of EDAM:0001501 ! Amino acid index +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 [Term] -id: EDAM:0002020 +id: EDAM_format:2020 name: Article format namespace: format -def: "Data format for a full-text scientific article." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "Literature format" EXACT [] -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000971 ! Article +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 [Term] -id: EDAM:0002021 +id: EDAM_format:2021 name: Text mining report format namespace: format -def: "Data format for an abstract (report) from text mining." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000972 ! Text mining report +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 [Term] -id: EDAM:0002027 +id: EDAM_format:2027 name: Enzyme kinetics report format namespace: format -def: "Data format for reports on enzyme kinetics." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0002024 ! Enzyme kinetics data +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 [Term] -id: EDAM:0002030 +id: EDAM_format:2030 name: Small molecule report format namespace: format -def: "Format of a report on a chemical compound." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "Chemical compound annotation format" EXACT [] -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000962 ! Small molecule annotation +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 [Term] -id: EDAM:0002031 +id: EDAM_format:2031 name: Gene annotation format namespace: format -def: "Format of a report on a particular locus, gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000916 ! Gene annotation +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 [Term] -id: EDAM:0002032 +id: EDAM_format:2032 name: Workflow format namespace: format -def: "Format of a workflow." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0002972 ! Workflow +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 [Term] -id: EDAM:0002035 +id: EDAM_format:2035 name: Chemical formula format namespace: format -def: "Text format of a chemical formula." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000846 ! Chemical formula +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 [Term] -id: EDAM:0002036 +id: EDAM_format:2036 name: Phylogenetic character data format namespace: format -def: "Format of raw (unplotted) phylogenetic data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000871 ! Phylogenetic character data +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 [Term] -id: EDAM:0003097 +id: EDAM_format:3097 !{since=beta13} name: Protein domain classification format namespace: format -def: "Format of data concerning the classification of the sequences and/or structures of protein structural domain(s)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000900 ! Protein domain classification +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 [Term] -id: EDAM:0003098 +id: EDAM_format:3098 !{since=beta13} name: Raw SCOP domain classification format -namespace: data -def: "Format of raw SCOP domain classification data files." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0003097 ! Protein domain classification format +is_a: EDAM_format:3097 ! Protein domain classification format [Term] -id: EDAM:0003099 +id: EDAM_format:3099 !{since=beta13} name: Raw CATH domain classification format -namespace: data -def: "Format of raw CATH domain classification data files." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0003097 ! Protein domain classification format +is_a: EDAM_format:3097 ! Protein domain classification format [Term] -id: EDAM:0003100 +id: EDAM_format:3100 !{since=beta13} name: CATH domain report format -namespace: data -def: "Format of summary of domain classification information for a CATH domain." [EDAM:EBI "EMBRACE definition"] +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. -subset: data -is_a: EDAM:0003097 ! Protein domain classification format +is_a: EDAM_format:3097 ! Protein domain classification format [Term] -id: EDAM:0002045 +id: EDAM_format:2045 name: Electron microscopy model format namespace: format -def: "Annotation format for electron microscopy models." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002350 ! Format (typed) +subset: formats +def: "Annotation format for electron microscopy models." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2350 ! Format (typed) [Term] -id: EDAM:0002049 +id: EDAM_format:2049 name: Phylogenetic tree report (tree distances) format namespace: format -def: "Format for phylogenetic tree distance data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001442 ! Phylogenetic tree report (tree distances) +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) [Term] -id: EDAM:0002051 +id: EDAM_format:2051 name: Polymorphism report format namespace: format -def: "Format for sequence polymorphism data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0002885 ! Nucleic acid features (polymorphism annotation) +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) [Term] -id: EDAM:0002052 +id: EDAM_format:2052 name: Protein family report format namespace: format -def: "Format for reports on a protein family." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000907 ! Protein family +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 [Term] -id: EDAM:0002054 +id: EDAM_format:2054 name: Protein interaction format namespace: format -def: "Format for protein interaction data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000906 ! Protein report (interaction) +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 report (interaction) [Term] -id: EDAM:0002055 +id: EDAM_format:2055 name: Sequence assembly format namespace: format -def: "Format for sequence assembly data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000925 ! Sequence assembly +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 [Term] -id: EDAM:0002056 +id: EDAM_format:2056 name: Microarray experiment data format namespace: format -def: "Format for microarray experimental data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000931 ! Experiment annotation (microarray) +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) [Term] -id: EDAM:0002058 +id: EDAM_format:2058 name: Gene expression report format namespace: format -def: "Format for a report on gene expression." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002031 ! Gene annotation format -relationship: is_format_of EDAM:0003111 ! Processed microarray data +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 [Term] -id: EDAM:0002059 +id: EDAM_format:2059 name: Genotype and phenotype annotation format namespace: format -def: "Format of a report on genotype / phenotype information." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000920 ! Genotype and phenotype annotation +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 and phenotype annotation [Term] -id: EDAM:0002060 +id: EDAM_format:2060 name: Map format namespace: format -def: "Format of a map of (typically one) molecular sequence annotated with features." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001274 ! Map +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 [Term] -id: EDAM:0002061 +id: EDAM_format:2061 name: Nucleic acid features (primers) format namespace: format -def: "Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000922 ! Nucleic acid features (primers) +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) [Term] -id: EDAM:0002062 +id: EDAM_format:2062 name: Protein report format namespace: format -def: "Format of a report of general information about a specific protein." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000896 ! Protein report +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 [Term] -id: EDAM:0003033 +id: EDAM_format:3033 !{since=beta13} name: Matrix format namespace: format -def: "Format of a matrix (array) of numerical values." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0002082 ! Matrix +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 [Term] -id: EDAM:0002064 +id: EDAM_format:2064 name: 3D-1D scoring matrix format namespace: format -def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0003033 ! Matrix format -relationship: is_format_of EDAM:0001499 ! 3D-1D scoring matrix +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 [Term] -id: EDAM:0002065 +id: EDAM_format:2065 name: Protein structure report (quality evaluation) format namespace: format -def: "Format of a report on the quality of a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001539 ! Protein structural quality report +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 [Term] -id: EDAM:0002066 +id: EDAM_format:2066 name: Database hits (sequence) format namespace: format -def: "Format of a report on sequence hits and associated data from searching a sequence database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000857 ! Database hits (sequence) +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) [Term] -id: EDAM:0002067 +id: EDAM_format:2067 name: Sequence distance matrix format namespace: format -def: "Format of a matrix of genetic distances between molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000870 ! Sequence distance matrix +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 [Term] -id: EDAM:0002068 +id: EDAM_format:2068 name: Sequence motif format namespace: format -def: "Format of a sequence motif." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001353 ! Sequence motif +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 [Term] -id: EDAM:0002069 +id: EDAM_format:2069 name: Sequence profile format namespace: format -def: "Format of a sequence profile." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001354 ! Sequence profile +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 [Term] -id: EDAM:0002074 +id: EDAM_format:2074 name: Dirichlet distribution format namespace: format -def: "Data format of a dirichlet distribution." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001347 ! Dirichlet distribution +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 [Term] -id: EDAM:0002075 +id: EDAM_format:2075 name: HMM emission and transition counts format namespace: format -def: "Data format for the emission and transition counts of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001348 ! HMM emission and transition counts +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 [Term] -id: EDAM:0002077 +id: EDAM_format:2077 name: Protein secondary structure format namespace: format -def: "Format for secondary structure (predicted or real) of a protein molecule." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000876 ! Protein features (secondary structure) +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) [Term] -id: EDAM:0002076 +id: EDAM_format:2076 name: RNA secondary structure format namespace: format -def: "Format for secondary structure (predicted or real) of an RNA molecule." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000880 ! RNA secondary structure +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 [Term] -id: EDAM:0002078 +id: EDAM_format:2078 name: Sequence range format namespace: format -def: "Format used to specify range(s) of sequence positions." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001017 ! Sequence range +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 [Term] -id: EDAM:0002155 +id: EDAM_format:2155 name: Sequence features (repeats) format namespace: format -def: "Format used for map of repeats in molecular (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001299 ! Sequence features (repeats) +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) [Term] -id: EDAM:0002158 +id: EDAM_format:2158 name: Nucleic acid features (restriction sites) format namespace: format -def: "Format used for report on restriction enzyme recognition sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001305 ! Nucleic acid features (restriction sites) +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) [Term] -id: EDAM:0002159 +id: EDAM_format:2159 name: Gene features (coding region) format namespace: format -def: "Format used for report on coding regions in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002031 ! Gene annotation format -relationship: is_format_of EDAM:0001313 ! Nucleic acid features (coding sequence) +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) [Term] -id: EDAM:0002170 +id: EDAM_format:2170 name: Sequence cluster format namespace: format -def: "Format used for clusters of molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001235 ! Sequence cluster +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 [Term] -id: EDAM:0002195 +id: EDAM_format:2195 name: Ontology format namespace: format -def: "Format used for ontologies." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000582 ! Ontology +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 [Term] -id: EDAM:0002210 +id: EDAM_format:2210 name: Strain data format namespace: format -def: "Format of a report on organism strain data / cell line." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000963 ! Cell line annotation +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 [Term] -id: EDAM:0002542 +id: EDAM_format:2542 name: Protein features (domains) format namespace: format -def: "Format of a report on protein features (domain composition)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002350 ! Format (typed) +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) [Term] -id: EDAM:0002571 +id: EDAM_format:2571 name: Raw sequence format namespace: format -def: "Format of a raw molecular sequence (i.e. the alphabet used)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000848 ! Raw sequence +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 [Term] -id: EDAM:0001734 +id: EDAM_format:1734 name: PubMed citation namespace: format -def: "Format of bibliographic reference as used by the PubMed database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002848 ! Bibliographic reference format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001735 +id: EDAM_format:1735 name: Medline Display Format namespace: format -def: "Format for abstracts of scientific articles from the Medline database." [EDAM:EBI "EMBRACE definition"] +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 -subset: format xref: Moby:PubMed-MEDLINE -is_a: EDAM:0002848 ! Bibliographic reference format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2848 ! Bibliographic reference format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001736 +id: EDAM_format:1736 name: CiteXplore-core namespace: format -def: "CiteXplore 'core' citation format including title, journal, authors and abstract." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002848 ! Bibliographic reference format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001737 +id: EDAM_format:1737 name: CiteXplore-all namespace: format -def: "CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002848 ! Bibliographic reference format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001747 +id: EDAM_format:1747 name: PDB atom record format namespace: format -def: "Format of an ATOM record (describing data for an individual atom) from a PDB file." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001476 ! PDB 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 [Term] -id: EDAM:0002551 +id: EDAM_format:2551 name: Sequence record format (text) namespace: format -def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001919 ! Sequence record format +subset: formats +def: "Data format for a molecular sequence record." [http://edamontology.org] +is_a: EDAM_format:1919 ! Sequence record format [Term] -id: EDAM:0002552 +id: EDAM_format:2552 name: Sequence record format (XML) namespace: format -def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001919 ! Sequence record format +subset: formats +def: "Data format for a molecular sequence record." [http://edamontology.org] +is_a: EDAM_format:1919 ! Sequence record format [Term] -id: EDAM:0002203 +id: EDAM_format:2203 name: Sequence record lite format namespace: format -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." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001919 ! Sequence record format -relationship: is_format_of EDAM:0002043 ! Sequence record lite +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 [Term] -id: EDAM:0002202 +id: EDAM_format:2202 name: Sequence record full format namespace: format -def: "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001919 ! Sequence record format -relationship: is_format_of EDAM:0002201 ! Sequence record full +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 [Term] -id: EDAM:0002057 +id: EDAM_format:2057 name: Sequence trace format namespace: format -def: "Format for sequence trace data (i.e. including base call information)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001919 ! Sequence record format -relationship: is_format_of EDAM:0000924 ! Sequence trace +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 [Term] -id: EDAM:0001923 +id: EDAM_format:1923 name: acedb namespace: format -def: "ACEDB sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) +subset: formats +def: "ACEDB sequence format." [http://edamontology.org] +is_a: EDAM_format:2551 ! Sequence record format (text) [Term] -id: EDAM:0001924 +id: EDAM_format:1924 name: clustal sequence format namespace: format -def: "Clustalw output format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001982 ! clustal alignment format +subset: formats +def: "Clustalw output format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1982 ! clustal alignment format [Term] -id: EDAM:0001925 +id: EDAM_format:1925 name: codata namespace: format -def: "Codata entry format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001928 +id: EDAM_format:1928 name: experiment namespace: format -def: "Staden experiment file format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001934 +id: EDAM_format:1934 name: fitch namespace: format -def: "Fitch program format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001935 +id: EDAM_format:1935 name: gcg namespace: format -def: "GCG sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001938 +id: EDAM_format:1938 name: GFF2-seq namespace: format -def: "GFF feature file format with sequence in the header." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0001974 ! GFF2 +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 [Term] -id: EDAM:0001939 +id: EDAM_format:1939 name: GFF3-seq namespace: format -def: "GFF3 feature file format with sequence." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0001975 ! GFF2 +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 ! GFF2 [Term] -id: EDAM:0001941 +id: EDAM_format:1941 name: hennig86 namespace: format -def: "Hennig86 output sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001942 +id: EDAM_format:1942 name: ig namespace: format -def: "Intelligenetics sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001943 +id: EDAM_format:1943 name: igstrict namespace: format -def: "Intelligenetics sequence format (strict version)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001944 +id: EDAM_format:1944 name: jackknifer namespace: format -def: "Jackknifer interleaved and non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001945 +id: EDAM_format:1945 name: mase namespace: format -def: "Mase program sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001946 +id: EDAM_format:1946 name: mega-seq namespace: format -def: "Mega interleaved and non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001947 +id: EDAM_format:1947 name: msf namespace: format -def: "GCG MSF (multiple sequence file) file format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001949 +id: EDAM_format:1949 name: nexus-seq namespace: format -def: "Nexus/paup interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001950 +id: EDAM_format:1950 name: pdbatom namespace: format -def: "PDB sequence format (ATOM lines)." [EDAM:EBI "EMBRACE definition"] +subset: formats +def: "PDB sequence format (ATOM lines)." [http://edamontology.org] comment: pdb format in EMBOSS. -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0001475 ! PDB database entry format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001951 +id: EDAM_format:1951 name: pdbatomnuc namespace: format -def: "PDB nucleotide sequence format (ATOM lines)." [EDAM:EBI "EMBRACE definition"] +subset: formats +def: "PDB nucleotide sequence format (ATOM lines)." [http://edamontology.org] comment: pdbnuc format in EMBOSS. -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0001475 ! PDB database entry format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001952 +id: EDAM_format:1952 name: pdbseqresnuc namespace: format -def: "PDB nucleotide sequence format (SEQRES lines)." [EDAM:EBI "EMBRACE definition"] +subset: formats +def: "PDB nucleotide sequence format (SEQRES lines)." [http://edamontology.org] comment: pdbnucseq format in EMBOSS. -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0001475 ! PDB database entry format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001953 +id: EDAM_format:1953 name: pdbseqres namespace: format -def: "PDB sequence format (SEQRES lines)." [EDAM:EBI "EMBRACE definition"] +subset: formats +def: "PDB sequence format (SEQRES lines)." [http://edamontology.org] comment: pdbseq format in EMBOSS. -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0001475 ! PDB database entry format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001955 +id: EDAM_format:1955 name: phylip sequence format namespace: format -def: "Phylip interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001997 ! phylip +subset: formats +def: "Phylip interleaved sequence format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1997 ! phylip [Term] -id: EDAM:0001956 +id: EDAM_format:1956 name: phylipnon sequence format namespace: format -def: "Phylip non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001998 ! phylipnon +subset: formats +def: "Phylip non-interleaved sequence format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1998 ! phylipnon [Term] -id: EDAM:0001957 +id: EDAM_format:1957 name: raw namespace: format -def: "Raw sequence format with no non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002330 ! Text +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 +! For now, identical to genpept [Term] -id: EDAM:0001958 +id: EDAM_format:1958 name: refseqp namespace: format -def: "Refseq protein entry sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001959 +id: EDAM_format:1959 name: selex sequence format namespace: format -def: "Selex sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002000 ! selex alignment format +subset: formats +def: "Selex sequence format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2000 ! selex alignment format [Term] -id: EDAM:0001960 +id: EDAM_format:1960 name: Staden format namespace: format -def: "Staden suite sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001961 +id: EDAM_format:1961 name: stockholm namespace: format -def: "Stockholm multiple sequence alignment format (used by Pfam and Rfam)." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://en.wikipedia.org/wiki/Stockholm_format -is_a: EDAM:0002330 ! Text -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001962 +id: EDAM_format:1962 name: strider namespace: format -def: "DNA strider output sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001964 +id: EDAM_format:1964 name: text namespace: format -def: "Plain text sequence format (essentially unformatted)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001965 +id: EDAM_format:1965 name: treecon sequence format namespace: format -def: "Treecon output sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002005 ! treecon-seq +subset: formats +def: "Treecon output sequence format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2005 ! treecon-seq [Term] -id: EDAM:0001966 +id: EDAM_format:1966 name: asn1 sequence format namespace: format -def: "NCBI ASN.1 sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001969 +id: EDAM_format:1969 name: debug-seq namespace: format -def: "EMBOSS debugging trace sequence format of full internal data content." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001970 +id: EDAM_format:1970 name: jackknifernon namespace: format -def: "Jackknifer output sequence non-interleaved format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001971 +id: EDAM_format:1971 name: meganon sequence format namespace: format -def: "Mega non-interleaved output sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001992 ! meganon +subset: formats +def: "Mega non-interleaved output sequence format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1992 ! meganon [Term] -id: EDAM:0001973 +id: EDAM_format:1973 name: nexusnon namespace: format -def: "Nexus/paup non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001967 +id: EDAM_format:1967 name: das namespace: format -def: "DAS sequence (XML) format (any type)." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "das sequence format" EXACT [] -is_a: EDAM:0002552 ! Sequence record format (XML) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001968 +id: EDAM_format:1968 name: dasdna namespace: format -def: "DAS sequence (XML) format (nucleotide-only)." [EDAM:EBI "EMBRACE definition"] +subset: formats +def: "DAS sequence (XML) format (nucleotide-only)." [http://edamontology.org] comment: The use of this format is deprecated. -subset: format -is_a: EDAM:0002552 ! Sequence record format (XML) -is_a: EDAM:0002332 ! XML +is_a: EDAM_format:2552 ! Sequence record format (XML) +is_a: EDAM_format:2332 ! XML [Term] -id: EDAM:0002546 +id: EDAM_format:2546 name: FASTA-like namespace: format -def: "A format resembling FASTA format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the many non-standard FASTA-like formats. -subset: format -is_a: EDAM:0002203 ! Sequence record lite 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 [Term] -id: EDAM:0002200 +id: EDAM_format:2200 ! This is the one used for annotation in eSysbio name: FASTA-like (text) namespace: format -def: "A text format resembling FASTA format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the many non-standard FASTA-like formats. -subset: format -is_a: EDAM:0002546 ! FASTA-like -is_a: EDAM:0002330 ! Text +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: "FASTA" EXACT [http://filext.com/file-extension/FASTA] !{note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data 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 [Term] -id: EDAM:0002310 +id: EDAM_format:2310 name: FASTA-HTML namespace: format -def: "FASTA format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002546 ! FASTA-like -is_a: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001929 +id: EDAM_format:1929 name: FASTA format namespace: format -def: "FASTA format including NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "FASTA" EXACT [] -synonym: "FASTA sequence format" EXACT [] -is_a: EDAM:0002200 ! FASTA-like (text) -is_a: EDAM:0002554 ! Alignment format (text) +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) [Term] -id: EDAM:0001926 +id: EDAM_format:1926 name: dbid namespace: format -def: "Fasta format variant with database name before ID." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002200 ! FASTA-like (text) +subset: formats +def: "Fasta format variant with database name before ID." [http://edamontology.org] +is_a: EDAM_format:2200 ! FASTA-like (text) [Term] -id: EDAM:0001940 +id: EDAM_format:1940 name: giFASTA format namespace: format -def: "FASTA sequence format including NCBI-style GIs." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002200 ! FASTA-like (text) +subset: formats +def: "FASTA sequence format including NCBI-style GIs." [http://edamontology.org] +is_a: EDAM_format:2200 ! FASTA-like (text) [Term] -id: EDAM:0001954 +id: EDAM_format:1954 name: Pearson format namespace: format -def: "Plain old FASTA sequence format (unspecified format for IDs)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002200 ! FASTA-like (text) +subset: formats +def: "Plain old FASTA sequence format (unspecified format for IDs)." [http://edamontology.org] +is_a: EDAM_format:2200 ! FASTA-like (text) [Term] -id: EDAM:0001972 +id: EDAM_format:1972 name: NCBI format namespace: format -def: "NCBI FASTA sequence format with NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] +subset: formats +def: "NCBI FASTA sequence format with NCBI-style IDs." [http://edamontology.org] comment: There are several variants of this. -subset: format -is_a: EDAM:0002200 ! FASTA-like (text) +is_a: EDAM_format:2200 ! FASTA-like (text) [Term] -id: EDAM:0002543 +id: EDAM_format:2543 name: EMBL-like format namespace: format -def: "A format resembling EMBL entry (plain text) format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the many non-standard EMBL-like formats. -subset: format -is_a: EDAM:0002202 ! Sequence record full 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 [Term] -id: EDAM:0002559 +id: EDAM_format:2559 name: GenBank-like format namespace: format -def: "A format resembling GenBank entry (plain text) format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the non-standard GenBank-like formats. -subset: format -is_a: EDAM:0002202 ! Sequence record full 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 [Term] -id: EDAM:0002547 +id: EDAM_format:2547 name: uniprotkb-like format namespace: format -def: "A sequence format resembling uniprotkb entry format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002202 ! Sequence record full format -is_a: EDAM:0002206 ! Sequence feature table format (text) +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) [Term] -id: EDAM:0001948 +id: EDAM_format:1948 name: nbrf namespace: format -def: "NBRF/PIR entry sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002202 ! Sequence record full format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002181 +id: EDAM_format:2181 name: EMBL-like (text) namespace: format -def: "A text format resembling EMBL entry format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the many non-standard EMBL-like text formats. -subset: format -is_a: EDAM:0002543 ! EMBL-like -is_a: EDAM:0002330 ! Text +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 +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0002558 +id: EDAM_format:2558 name: EMBL-like (XML) namespace: format -def: "An XML format resembling EMBL entry format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the any non-standard EMBL-like XML formats. -subset: format -is_a: EDAM:0002543 ! EMBL-like -is_a: EDAM:0002332 ! XML +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 +is_a: EDAM_format:2332 ! XML [Term] -id: EDAM:0002311 +id: EDAM_format:2311 name: EMBL-HTML namespace: format -def: "EMBL entry format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002543 ! EMBL-like -is_a: EDAM:0002331 ! HTML +subset: formats +def: "EMBL entry format wrapped in HTML elements." [http://edamontology.org] +is_a: EDAM_format:2543 ! EMBL-like +is_a: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001927 +id: EDAM_format:1927 name: EMBL format namespace: format -def: "EMBL entry format." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "EMBL sequence format" EXACT [] -synonym: "EMBL" EXACT [] -is_a: EDAM:0002181 ! EMBL-like (text) -is_a: EDAM:0002206 ! Sequence feature table format (text) +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) [Term] -id: EDAM:0002186 +id: EDAM_format:2186 name: geneseq namespace: format -def: "Geneseq sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002181 ! EMBL-like (text) +subset: formats +def: "Geneseq sequence format." [http://edamontology.org] +is_a: EDAM_format:2181 ! EMBL-like (text) [Term] -id: EDAM:0002204 +id: EDAM_format:2204 name: EMBL format (XML) namespace: format -def: "An XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] -comment: This is a placeholder for other more specific terms. It should not normally be used for annotation. -subset: format -is_a: EDAM:0002558 ! EMBL-like (XML) +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) [Term] -id: EDAM:0002183 +id: EDAM_format:2183 name: EMBLXML namespace: format -def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002204 ! EMBL (XML) +subset: formats +def: "XML format for EMBL entries." [http://edamontology.org] +is_a: EDAM_format:2204 ! EMBL (XML) [Term] -id: EDAM:0002184 +id: EDAM_format:2184 name: cdsxml namespace: format -def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002204 ! EMBL (XML) +subset: formats +def: "XML format for EMBL entries." [http://edamontology.org] +is_a: EDAM_format:2204 ! EMBL (XML) [Term] -id: EDAM:0002185 +id: EDAM_format:2185 name: insdxml namespace: format -def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002204 ! EMBL (XML) +subset: formats +def: "XML format for EMBL entries." [http://edamontology.org] +is_a: EDAM_format:2204 ! EMBL (XML) [Term] -id: EDAM:0002205 +id: EDAM_format:2205 name: GenBank-like format (text) namespace: format -def: "A text format resembling GenBank entry (plain text) format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the non-standard GenBank-like text formats. -subset: format -is_a: EDAM:0002559 ! GenBank-like -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002532 +id: EDAM_format:2532 name: GenBank-HTML namespace: format -def: "Genbank entry format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002559 ! GenBank-like -is_a: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001936 +id: EDAM_format:1936 name: GenBank format namespace: format -def: "Genbank entry format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002205 ! GenBank-like (text) -is_a: EDAM:0002206 ! Sequence feature table format (text) +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) +! For now, identical to refseqp [Term] -id: EDAM:0001937 +id: EDAM_format:1937 name: genpept namespace: format -def: "Genpept protein entry format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002205 ! GenBank-like (text) +subset: formats +def: "Genpept protein entry format." [http://edamontology.org] +is_a: EDAM_format:2205 ! GenBank-like format (text) [Term] -id: EDAM:0002187 +id: EDAM_format:2187 name: uniprotkb-like (text) namespace: format -def: "A text sequence format resembling uniprotkb entry format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002547 ! uniprotkb-like -is_a: EDAM:0002330 ! Text +subset: formats +def: "A text sequence format resembling uniprotkb entry format." [http://edamontology.org] +is_a: EDAM_format:2547 ! uniprotkb-like +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001963 +id: EDAM_format:1963 name: Swiss-Prot format namespace: format -def: "Swiss-Prot entry sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002187 ! uniprotkb-like (text) +subset: formats +def: "Swiss-Prot entry sequence format." [http://edamontology.org] +is_a: EDAM_format:2187 ! uniprotkb-like (text) [Term] -id: EDAM:0002188 +id: EDAM_format:2188 name: uniprot namespace: format -def: "UniProt entry sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002187 ! uniprotkb-like (text) +subset: formats +def: "UniProt entry sequence format." [http://edamontology.org] +is_a: EDAM_format:2187 ! uniprotkb-like (text) [Term] -id: EDAM:0002189 +id: EDAM_format:2189 name: ipi namespace: format -def: "ipi sequence format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002187 ! uniprotkb-like (text) +subset: formats +def: "ipi sequence format." [http://edamontology.org] +is_a: EDAM_format:2187 ! uniprotkb-like (text) [Term] -id: EDAM:0001628 +id: EDAM_format:1628 name: ABI namespace: format -def: "A format of raw sequence read data from an Applied Biosystems sequencing machine." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002057 ! Sequence trace format -is_a: EDAM:0002333 ! Binary +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 [Term] -id: EDAM:0001629 +id: EDAM_format:1629 name: mira namespace: format -def: "Format of MIRA sequence trace information file." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002057 ! Sequence trace format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002545 +id: EDAM_format:2545 name: FASTQ-like format namespace: format -def: "A format resembling FASTQ short read format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for non-standard FASTQ short read-like formats. -subset: format -is_a: EDAM:0002057 ! Sequence trace 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 [Term] -id: EDAM:0002572 +id: EDAM_format:2572 name: BAM namespace: format -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." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://samtools.sourceforge.net/SAM-1.3.pdf -is_a: EDAM:0002057 ! Sequence trace format -is_a: EDAM:0001921 ! Alignment format -is_a: EDAM:0002333 ! Binary +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 [Term] -id: EDAM:0002573 +id: EDAM_format:2573 name: SAM namespace: format -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -spec: http://samtools.sourceforge.net/SAM-1.3.pdf -is_a: EDAM:0002057 ! Sequence trace format -is_a: EDAM:0002920 ! Alignment format (pair only) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002182 +id: EDAM_format:2182 name: FASTQ-like format (text) namespace: format -def: "A text format resembling FASTQ short read format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for non-standard FASTQ short read-like formats. -subset: format -is_a: EDAM:0002545 ! FASTQ-like -is_a: EDAM:0002330 ! Text +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 +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001930 +id: EDAM_format:1930 name: FASTQ namespace: format -def: "FASTQ short read format ignoring quality scores." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002182 ! FASTQ-like (text) +subset: formats +def: "FASTQ short read format ignoring quality scores." [http://edamontology.org] +is_a: EDAM_format:2182 ! FASTQ-like (text) [Term] -id: EDAM:0001931 +id: EDAM_format:1931 name: FASTQ-illumina namespace: format -def: "FASTQ Illumina 1.3 short read format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002182 ! FASTQ-like (text) +subset: formats +def: "FASTQ Illumina 1.3 short read format." [http://edamontology.org] +is_a: EDAM_format:2182 ! FASTQ-like (text) [Term] -id: EDAM:0001932 +id: EDAM_format:1932 name: FASTQ-sanger namespace: format -def: "FASTQ short read format with phred quality." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002182 ! FASTQ-like (text) +subset: formats +def: "FASTQ short read format with phred quality." [http://edamontology.org] +is_a: EDAM_format:2182 ! FASTQ-like (text) [Term] -id: EDAM:0001933 +id: EDAM_format:1933 name: FASTQ-solexa namespace: format -def: "FASTQ Solexa/Illumina 1.0 short read format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002182 ! FASTQ-like (text) +subset: formats +def: "FASTQ Solexa/Illumina 1.0 short read format." [http://edamontology.org] +is_a: EDAM_format:2182 ! FASTQ-like (text) [Term] -id: EDAM:0002548 +id: EDAM_format:2548 name: Sequence feature table format namespace: format -def: "Format for a sequence feature table." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001920 ! Sequence feature annotation format -relationship: is_format_of EDAM:0001255 ! Sequence features +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 ! Sequence features [Term] -id: EDAM:0001979 +id: EDAM_format:1979 name: debug-feat namespace: format -def: "EMBOSS debugging trace feature format of full internal data content." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001920 ! Sequence feature annotation format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002206 +id: EDAM_format:2206 name: Sequence feature table format (text) namespace: format -def: "Text format for a sequence feature table." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002548 ! Sequence feature table format +subset: formats +def: "Text format for a sequence feature table." [http://edamontology.org] +is_a: EDAM_format:2548 ! Sequence feature table format [Term] -id: EDAM:0002553 +id: EDAM_format:2553 name: Sequence feature table format (XML) namespace: format -def: "XML format for a sequence feature table." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002548 ! Sequence feature table format +subset: formats +def: "XML format for a sequence feature table." [http://edamontology.org] +is_a: EDAM_format:2548 ! Sequence feature table format [Term] -id: EDAM:0002305 +id: EDAM_format:2305 name: GFF namespace: format -def: "GFF feature format (of indeterminate version)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002206 ! Sequence feature table format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001976 +id: EDAM_format:1976 name: pir namespace: format -def: "PIR feature format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002206 ! Sequence feature table format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001977 +id: EDAM_format:1977 name: swiss feature namespace: format -def: "Swiss-Prot feature format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001963 ! swiss +subset: formats +def: "Swiss-Prot feature format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1963 ! swiss [Term] -id: EDAM:0001980 +id: EDAM_format:1980 name: EMBL feature namespace: format -def: "EMBL feature format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001927 ! EMBL +subset: formats +def: "EMBL feature format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1927 ! EMBL [Term] -id: EDAM:0001981 +id: EDAM_format:1981 name: GenBank feature namespace: format -def: "Genbank feature format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001936 ! GenBank +subset: formats +def: "Genbank feature format." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1936 ! GenBank [Term] -id: EDAM:0001974 +id: EDAM_format:1974 name: GFF2 namespace: format -def: "General Feature Format (GFF) of sequence features." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://www.sanger.ac.uk/resources/software/gff/spec.html -is_a: EDAM:0002305 ! GFF +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 [Term] -id: EDAM:0001975 +id: EDAM_format:1975 name: GFF3 namespace: format -def: "Generic Feature Format version 3 (GFF3) of sequence features." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://sequenceontology.org/resources/gff3.html -is_a: EDAM:0002305 ! GFF +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 [Term] -id: EDAM:0002306 +id: EDAM_format:2306 name: GTF namespace: format -def: "Gene Transfer Format (GTF), a restricted version of GFF." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://mblab.wustl.edu/GTF22.html http://genome.ucsc.edu/FAQ/FAQformat#format4 -is_a: EDAM:0002305 ! GFF +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 [Term] -id: EDAM:0001978 +id: EDAM_format:1978 name: DASGFF namespace: format -def: "DAS GFF (XML) feature format." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "DASGFF feature" EXACT [] -synonym: "das feature" EXACT [] -is_a: EDAM:0002553 ! Sequence feature table format (XML) -is_a: EDAM:0002332 ! XML +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 [Term] -id: EDAM:0002554 +id: EDAM_format:2554 name: Alignment format (text) namespace: format -def: "Text format for molecular sequence alignment information." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001921 ! Alignment format +subset: formats +def: "Text format for molecular sequence alignment information." [http://edamontology.org] +is_a: EDAM_format:1921 ! Alignment format [Term] -id: EDAM:0002555 +id: EDAM_format:2555 name: Alignment format (XML) namespace: format -def: "XML format for molecular sequence alignment information." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001921 ! Alignment format +subset: formats +def: "XML format for molecular sequence alignment information." [http://edamontology.org] +is_a: EDAM_format:1921 ! Alignment format [Term] -id: EDAM:0001982 +id: EDAM_format:1982 name: clustal namespace: format -def: "Clustalw format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001983 +id: EDAM_format:1983 name: debug namespace: format -def: "EMBOSS alignment format for debugging trace of full internal data content." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001984 +id: EDAM_format:1984 name: FASTA-aln namespace: format -def: "Fasta format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002200 ! FASTA-like (text) +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) [Term] -id: EDAM:0002922 +id: EDAM_format:2922 name: markx0 variant namespace: format -def: "Some variant of Pearson MARKX alignment format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001985 +id: EDAM_format:1985 name: markx0 namespace: format -def: "Pearson MARKX0 alignment format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002922 ! markx0 variant +subset: formats +def: "Pearson MARKX0 alignment format." [http://edamontology.org] +is_a: EDAM_format:2922 ! markx0 variant [Term] -id: EDAM:0001986 +id: EDAM_format:1986 name: markx1 namespace: format -def: "Pearson MARKX1 alignment format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002922 ! markx0 variant +subset: formats +def: "Pearson MARKX1 alignment format." [http://edamontology.org] +is_a: EDAM_format:2922 ! markx0 variant [Term] -id: EDAM:0001987 +id: EDAM_format:1987 name: markx10 namespace: format -def: "Pearson MARKX10 alignment format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002922 ! markx0 variant +subset: formats +def: "Pearson MARKX10 alignment format." [http://edamontology.org] +is_a: EDAM_format:2922 ! markx0 variant [Term] -id: EDAM:0001988 +id: EDAM_format:1988 name: markx2 namespace: format -def: "Pearson MARKX2 alignment format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002922 ! markx0 variant +subset: formats +def: "Pearson MARKX2 alignment format." [http://edamontology.org] +is_a: EDAM_format:2922 ! markx0 variant [Term] -id: EDAM:0001989 +id: EDAM_format:1989 name: markx3 namespace: format -def: "Pearson MARKX3 alignment format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002922 ! markx0 variant +subset: formats +def: "Pearson MARKX3 alignment format." [http://edamontology.org] +is_a: EDAM_format:2922 ! markx0 variant [Term] -id: EDAM:0001990 +id: EDAM_format:1990 name: match namespace: format -def: "Alignment format for start and end of matches between sequence pairs." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002923 +id: EDAM_format:2923 name: mega variant namespace: format -def: "Some variant of Mega format for (typically aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001991 +id: EDAM_format:1991 name: mega namespace: format -def: "Mega format for (typically aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002923 ! mega variant +subset: formats +def: "Mega format for (typically aligned) sequences." [http://edamontology.org] +is_a: EDAM_format:2923 ! mega variant [Term] -id: EDAM:0001992 +id: EDAM_format:1992 name: meganon namespace: format -def: "Mega non-interleaved format for (typically aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002923 ! mega variant +subset: formats +def: "Mega non-interleaved format for (typically aligned) sequences." [http://edamontology.org] +is_a: EDAM_format:2923 ! mega variant [Term] -id: EDAM:0001993 +id: EDAM_format:1993 name: msf alignment format namespace: format -def: "MSF format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001947 ! msf +subset: formats +def: "MSF format for (aligned) sequences." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1947 ! msf [Term] -id: EDAM:0001994 +id: EDAM_format:1994 name: nexus alignment format namespace: format -def: "Nexus/paup format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001949 ! nexus +subset: formats +def: "Nexus/paup format for (aligned) sequences." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1949 ! nexus [Term] -id: EDAM:0001995 +id: EDAM_format:1995 name: nexusnon alignment format namespace: format -def: "Nexus/paup non-interleaved format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0001973 ! nexusnon +subset: formats +def: "Nexus/paup non-interleaved format for (aligned) sequences." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:1973 ! nexusnon [Term] -id: EDAM:0001996 +id: EDAM_format:1996 name: pair namespace: format -def: "EMBOSS simple sequence pair alignment format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) +subset: formats +def: "EMBOSS simple sequence pair alignment format." [http://edamontology.org] +is_a: EDAM_format:2554 ! Alignment format (text) [Term] -id: EDAM:0002924 +id: EDAM_format:2924 name: phylip variant namespace: format -def: "Some variant of Phylip format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001997 +id: EDAM_format:1997 name: phylip namespace: format -def: "Phylip format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002924 ! phylip variant +subset: formats +def: "Phylip format for (aligned) sequences." [http://edamontology.org] +is_a: EDAM_format:2924 ! phylip variant [Term] -id: EDAM:0001998 +id: EDAM_format:1998 name: phylipnon namespace: format -def: "Phylip non-interleaved format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002924 ! phylip variant +subset: formats +def: "Phylip non-interleaved format for (aligned) sequences." [http://edamontology.org] +is_a: EDAM_format:2924 ! phylip variant [Term] -id: EDAM:0001999 +id: EDAM_format:1999 name: score namespace: format -def: "Alignment format for score values for pairs of sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002000 +id: EDAM_format:2000 name: selex namespace: format -def: "SELEX format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002001 +id: EDAM_format:2001 name: simple namespace: format -def: "EMBOSS simple multiple alignment format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002002 +id: EDAM_format:2002 name: srs namespace: format -def: "Simple multiple sequence (alignment) format for SRS." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002003 +id: EDAM_format:2003 name: srspair namespace: format -def: "Simple sequence pair (alignment) format for SRS." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002920 ! Alignment format (pair only) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002004 +id: EDAM_format:2004 name: tcoffee namespace: format -def: "TCOFFEE program alignment format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002005 +id: EDAM_format:2005 name: treecon-seq namespace: format -def: "Treecon format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001391 +id: EDAM_format:1391 name: hmmer-aln namespace: format -def: "FASTA-style format for multiple sequences aligned by HMMER package to an HMM." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001392 +id: EDAM_format:1392 name: dialign namespace: format -def: "Multiple sequences aligned by DIALIGN package." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text + +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:0001393 +id: EDAM_format:1393 name: daf namespace: format -def: "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2554 ! Alignment format (text) +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0002556 +id: EDAM_format:2556 name: Phylogenetic tree format (text) namespace: format -def: "Text format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002006 ! Phylogenetic tree format +subset: formats +def: "Text format for a phylogenetic tree." [http://edamontology.org] +is_a: EDAM_format:2006 ! Phylogenetic tree format [Term] -id: EDAM:0002557 +id: EDAM_format:2557 name: Phylogenetic tree format (XML) namespace: format -def: "XML format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002006 ! Phylogenetic tree format +subset: formats +def: "XML format for a phylogenetic tree." [http://edamontology.org] +is_a: EDAM_format:2006 ! Phylogenetic tree format [Term] -id: EDAM:0001435 +id: EDAM_format:1435 name: phylip tree namespace: format -def: "Phylogenetic tree data format used by the PHYLIP program." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002556 ! Phylogenetic tree format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001425 +id: EDAM_format:1425 name: Phylip tree raw namespace: format -def: "Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002556 ! Phylogenetic tree format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001424 +id: EDAM_format:1424 name: Clustalw dendrogram namespace: format -def: "Dendrogram (tree file) format generated by Clustalw." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002556 ! Phylogenetic tree format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001436 +id: EDAM_format:1436 name: treebase namespace: format -def: "The format of an entry from the TreeBASE database of phylogenetic data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002556 ! Phylogenetic tree format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001437 +id: EDAM_format:1437 name: treefam namespace: format -def: "The format of an entry from the TreeFam database of phylogenetic data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002556 ! Phylogenetic tree format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001910 +id: EDAM_format:1910 name: newick namespace: format -def: "Phylogenetic tree Newick (text) format." [EDAM:EBI "EMBRACE definition"] -subset: format +subset: formats +def: "Phylogenetic tree Newick (text) format." [http://edamontology.org] xref: Moby:Newick_Text -is_a: EDAM:0002556 ! Phylogenetic tree format (text) -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001911 +id: EDAM_format:1911 name: treecon namespace: format -def: "Phylogenetic tree TreeCon (text) format." [EDAM:EBI "EMBRACE definition"] -subset: format +subset: formats +def: "Phylogenetic tree TreeCon (text) format." [http://edamontology.org] xref: Moby:TreeCon -is_a: EDAM:0002556 ! Phylogenetic tree format (text) -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001912 +id: EDAM_format:1912 name: nexus namespace: format -def: "Phylogenetic tree Nexus (text) format." [EDAM:EBI "EMBRACE definition"] -subset: format +subset: formats +def: "Phylogenetic tree Nexus (text) format." [http://edamontology.org] xref: Moby:Nexus_Text -is_a: EDAM:0002556 ! Phylogenetic tree format (text) -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2556 ! Phylogenetic tree format (text) +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001475 +id: EDAM_format:1475 name: PDB database entry format namespace: format -def: "Format of an entry (or part of an entry) from the PDB database." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "PDB entry" EXACT [] -is_a: EDAM:0002033 ! Tertiary structure 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 [Term] -id: EDAM:0001476 +id: EDAM_format:1476 name: PDB format namespace: format -def: "Entry format of PDB database in PDB format." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "PDB" EXACT [] +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:0001475 ! PDB database entry format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:1475 ! PDB database entry format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001477 +id: EDAM_format:1477 name: mmCIF namespace: format -def: "Entry format of PDB database in mmCIF format." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "mmcif" EXACT [] +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:0001475 ! PDB database entry format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:1475 ! PDB database entry format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001478 +id: EDAM_format:1478 name: PDBML namespace: format -def: "Entry format of PDB database in PDBML (XML) format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001475 ! PDB database entry format -is_a: EDAM:0002332 ! XML +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 [Term] -id: EDAM:0002013 +id: EDAM_format:2013 name: Biological pathway or network format namespace: format -def: "Data format for a biological pathway or network." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002034 ! Biological model format -relationship: is_format_of EDAM:0002600 ! Pathway or network +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 + + +[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 + [Term] -id: EDAM:0002585 +id: EDAM_format:2585 name: SBML namespace: format -def: "XML format for models of biological processes such as metabolism, cell signaling and so on." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002034 ! Biological model format -is_a: EDAM:0002332 ! XML +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 + +[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 + + +[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 + +[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 + +[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 + +[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 + +[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 + +[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 + +[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 + +[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) + +[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 [Term] -id: EDAM:0001666 +id: EDAM_format:1666 name: BioModel mathematical model format namespace: format -def: "Format of mathematical models from the BioModel database." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001647 +id: EDAM_format:1647 name: KEGG PATHWAY entry format namespace: format -def: "The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001648 +id: EDAM_format:1648 name: MetaCyc entry format namespace: format -def: "The format of an entry from the MetaCyc metabolic pathways database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001649 +id: EDAM_format:1649 name: HumanCyc entry format namespace: format -def: "The format of a report from the HumanCyc metabolic pathways database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001650 +id: EDAM_format:1650 name: INOH entry format namespace: format -def: "The format of an entry from the INOH signal transduction pathways database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001651 +id: EDAM_format:1651 name: PATIKA entry format namespace: format -def: "The format of an entry from the PATIKA biological pathways database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001652 +id: EDAM_format:1652 name: Reactome entry format namespace: format -def: "The format of an entry from the reactome biological pathways database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001653 +id: EDAM_format:1653 name: aMAZE entry format namespace: format -def: "The format of an entry from the aMAZE biological pathways and molecular interactions database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001654 +id: EDAM_format:1654 name: CPDB entry format namespace: format -def: "The format of an entry from the CPDB database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001655 +id: EDAM_format:1655 name: Panther Pathways entry format namespace: format -def: "The format of an entry from the Panther Pathways database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0002341 +id: EDAM_format:2341 name: NCI-Nature pathway entry format namespace: format -def: "The format of an entry from the NCI-Nature pathways database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0002015 +id: EDAM_format:2015 name: Sequence-profile alignment (HMM) format namespace: format -def: "Data format for a sequence-HMM profile alignment." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002014 ! Sequence-profile alignment 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 [Term] -id: EDAM:0001419 +id: EDAM_format:1419 name: Sequence-MEME profile alignment namespace: format -def: "Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002014 ! Sequence-profile alignment format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001421 +id: EDAM_format:1421 name: HMMER profile alignment (sequences versus HMMs) namespace: format -def: "Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002014 ! Sequence-profile alignment format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001422 +id: EDAM_format:1422 name: HMMER profile alignment (HMM versus sequences) namespace: format -def: "Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002014 ! Sequence-profile alignment format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001504 +id: EDAM_format:1504 name: aaindex namespace: format -def: "Amino acid index format used by the AAindex database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002017 ! Amino acid index format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001739 +id: EDAM_format:1739 name: pmc namespace: format -def: "Article format of the PubMed Central database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002020 ! Article format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002194 +id: EDAM_format:2194 name: medline namespace: format -def: "Abstract format used by MedLine database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002020 ! Article format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001740 +id: EDAM_format:1740 name: iHOP text mining abstract format namespace: format -def: "iHOP abstract format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002021 ! Text mining report format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001741 +id: EDAM_format:1741 name: Oscar3 namespace: format -def: "Text mining abstract format from the Oscar 3 application." [EDAM:EBI "EMBRACE definition"] -comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology terms and chemical data from a document. -subset: format -is_a: EDAM:0002021 ! Text mining report format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001582 +id: EDAM_format:1582 name: findkm namespace: format -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)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002027 ! Enzyme kinetics report format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001697 +id: EDAM_format:1697 name: KEGG LIGAND entry format namespace: format -def: "The format of an entry from the KEGG LIGAND chemical database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001698 +id: EDAM_format:1698 name: KEGG COMPOUND entry format namespace: format -def: "The format of an entry from the KEGG COMPOUND database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001699 +id: EDAM_format:1699 name: KEGG PLANT entry format namespace: format -def: "The format of an entry from the KEGG PLANT database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001700 +id: EDAM_format:1700 name: KEGG GLYCAN entry format namespace: format -def: "The format of an entry from the KEGG GLYCAN database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001706 +id: EDAM_format:1706 name: KEGG DRUG entry format namespace: format -def: "The format of an entry from the KEGG DRUG database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001701 +id: EDAM_format:1701 name: PubChem entry format namespace: format -def: "The format of an entry from PubChem." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "The format of an entry from PubChem." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001702 +id: EDAM_format:1702 name: ChemSpider entry format namespace: format -def: "The format of an entry from a database of chemical structures and property predictions." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001703 +id: EDAM_format:1703 name: ChEBI entry format namespace: format -def: "The format of an entry from Chemical Entities of Biological Interest (ChEBI)." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001704 +id: EDAM_format:1704 name: MSDchem ligand dictionary entry format namespace: format -def: "The format of an entry from the MSDchem ligand dictionary." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001705 +id: EDAM_format:1705 name: HET group dictionary entry format namespace: format -def: "The format of an entry from the HET group dictionary (HET groups from PDB files)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002030 ! Small molecule report format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001808 +id: EDAM_format:1808 name: GeneIlluminator gene report format namespace: format -def: "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service." [EDAM:EBI "EMBRACE definition"] -comment: This includes a gene name and abbreviation of the name which may be in a namespace indicating the gene status and relevant organisation. -subset: 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 -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001809 +id: EDAM_format:1809 name: BacMap gene card format namespace: format -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." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001810 +id: EDAM_format:1810 name: ColiCard report format namespace: format -def: "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [EDAM:EBI "EMBRACE definition"] -subset: 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 -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0002328 +id: EDAM_format:2328 name: PseudoCAP gene report format namespace: format -def: "Format of a report on a gene from the PseudoCAP database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0002329 +id: EDAM_format:2329 name: GeneCards gene report format namespace: format -def: "Format of a report on a gene from the GeneCards database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001603 +id: EDAM_format:1603 name: Ensembl gene report format namespace: format -def: "Entry format of Ensembl genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of Ensembl genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001604 +id: EDAM_format:1604 name: DictyBase gene report format namespace: format -def: "Entry format of DictyBase genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of DictyBase genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001605 +id: EDAM_format:1605 name: CGD gene report format namespace: format -def: "Entry format of Candida Genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of Candida Genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001606 +id: EDAM_format:1606 name: DragonDB gene report format namespace: format -def: "Entry format of DragonDB genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of DragonDB genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001607 +id: EDAM_format:1607 name: EcoCyc gene report format namespace: format -def: "Entry format of EcoCyc genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of EcoCyc genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001608 +id: EDAM_format:1608 name: FlyBase gene report format namespace: format -def: "Entry format of FlyBase genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of FlyBase genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001609 +id: EDAM_format:1609 name: Gramene gene report format namespace: format -def: "Entry format of Gramene genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of Gramene genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001610 +id: EDAM_format:1610 name: KEGG GENES gene report format namespace: format -def: "Entry format of KEGG GENES genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of KEGG GENES genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001611 +id: EDAM_format:1611 name: MaizeGDB gene report format namespace: format -def: "Entry format of the Maize genetics and genomics database (MaizeGDB)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001612 +id: EDAM_format:1612 name: MGD gene report format namespace: format -def: "Entry format of the Mouse Genome Database (MGD)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of the Mouse Genome Database (MGD)." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001613 +id: EDAM_format:1613 name: RGD gene report format namespace: format -def: "Entry format of the Rat Genome Database (RGD)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of the Rat Genome Database (RGD)." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001614 +id: EDAM_format:1614 name: SGD gene report format namespace: format -def: "Entry format of the Saccharomyces Genome Database (SGD)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of the Saccharomyces Genome Database (SGD)." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001615 +id: EDAM_format:1615 name: GeneDB gene report format namespace: format -def: "Entry format of the Sanger GeneDB genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of the Sanger GeneDB genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001616 +id: EDAM_format:1616 name: TAIR gene report format namespace: format -def: "Entry format of The Arabidopsis Information Resource (TAIR) genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001617 +id: EDAM_format:1617 name: WormBase gene report format namespace: format -def: "Entry format of the WormBase genomes database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of the WormBase genomes database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001618 +id: EDAM_format:1618 name: ZFIN gene report format namespace: format -def: "Entry format of the Zebrafish Information Network (ZFIN) genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001619 +id: EDAM_format:1619 name: TIGR gene report format namespace: format -def: "Entry format of the TIGR genome database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format of the TIGR genome database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001782 +id: EDAM_format:1782 name: NCBI gene report format namespace: format -def: "Entry (gene) format of the NCBI database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry (gene) format of the NCBI database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001665 +id: EDAM_format:1665 name: Taverna workflow format namespace: format -def: "Format of Taverna workflows." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002032 ! Workflow format -is_a: EDAM:0002332 ! XML +subset: formats +def: "Format of Taverna workflows." [http://edamontology.org] +is_a: EDAM_format:2032 ! Workflow format +is_a: EDAM_format:2332 ! XML [Term] -id: EDAM:0001196 +id: EDAM_format:1196 name: smiles namespace: format -def: "Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002035 ! Chemical formula format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001197 +id: EDAM_format:1197 name: inchi namespace: format -def: "Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002035 ! Chemical formula format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001198 +id: EDAM_format:1198 name: mf namespace: format -def: "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002035 ! Chemical formula format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2035 ! Chemical formula format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001199 +id: EDAM_format:1199 name: inchikey namespace: format -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." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002035 ! Chemical formula format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2035 ! Chemical formula format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001200 +id: EDAM_format:1200 name: smarts namespace: format -def: "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001196 ! smiles +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 [Term] -id: EDAM:0002037 +id: EDAM_format:2037 name: Phylogenetic continuous quantitative character format namespace: format -def: "Format of phylogenetic continuous quantitative character data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002036 ! Phylogenetic character data format -relationship: is_format_of EDAM:0001426 ! Phylogenetic continuous quantitative data +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 [Term] -id: EDAM:0001431 +id: EDAM_format:1431 name: Phylogenetic property values format namespace: format -def: "Format of phylogenetic property data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002036 ! Phylogenetic character data 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 [Term] -id: EDAM:0002038 +id: EDAM_format:2038 name: Phylogenetic discrete states format namespace: format -def: "Format of phylogenetic discrete states data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002036 ! Phylogenetic character data format -relationship: is_format_of EDAM:0001427 ! Phylogenetic discrete data +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 [Term] -id: EDAM:0002039 +id: EDAM_format:2039 name: Phylogenetic tree report (cliques) format namespace: format -def: "Format of phylogenetic cliques data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002036 ! Phylogenetic character data format -relationship: is_format_of EDAM:0001428 ! Phylogenetic tree report (cliques) +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 tree report (cliques) [Term] -id: EDAM:0002040 +id: EDAM_format:2040 name: Phylogenetic tree report (invariants) format namespace: format -def: "Format of phylogenetic invariants data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002036 ! Phylogenetic character data format -relationship: is_format_of EDAM:0001429 ! Phylogenetic tree report (invariants) +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 tree report (invariants) [Term] -id: EDAM:0001430 +id: EDAM_format:1430 name: phylip continuous quantitative characters namespace: format -def: "PHYLIP file format for continuous quantitative character data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001432 +id: EDAM_format:1432 name: phylip character frequencies namespace: format -def: "PHYLIP file format for phylogenetics character frequency data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002243 +id: EDAM_format:2243 name: phylip property values namespace: format -def: "PHYLIP file format for phylogenetic property data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002036 ! Phylogenetic character data 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 [Term] -id: EDAM:0001433 +id: EDAM_format:1433 name: phylip discrete states namespace: format -def: "Format of PHYLIP discrete states data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002038 ! Phylogenetic discrete states format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001434 +id: EDAM_format:1434 name: phylip cliques namespace: format -def: "Format of PHYLIP cliques data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002039 ! Phylogenetic tree report (cliques) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001645 +id: EDAM_format:1645 name: EMDB entry format namespace: format -def: "Format of an entry from the Electron Microscopy DataBase (EMDB)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001445 +id: EDAM_format:1445 name: phylip tree distance namespace: format -def: "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002049 ! Phylogenetic tree report (tree distances) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001620 +id: EDAM_format:1620 name: dbSNP polymorphism report format namespace: format -def: "Entry format for the dbSNP database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the dbSNP database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001570 +id: EDAM_format:1570 name: InterPro entry format namespace: format -def: "Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001571 +id: EDAM_format:1571 name: InterPro entry abstract format namespace: format -def: "Entry format for the textual abstract of signatures in an InterPro entry and its protein matches." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001572 +id: EDAM_format:1572 name: Gene3D entry format namespace: format -def: "Entry format for the Gene3D protein secondary database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the Gene3D protein secondary database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001573 +id: EDAM_format:1573 name: PIRSF entry format namespace: format -def: "Entry format for the PIRSF protein secondary database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the PIRSF protein secondary database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001574 +id: EDAM_format:1574 name: PRINTS entry format namespace: format -def: "Entry format for the PRINTS protein secondary database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the PRINTS protein secondary database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001575 +id: EDAM_format:1575 name: Panther Families and HMMs entry format namespace: format -def: "Entry format for the Panther library of protein families and subfamilies." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001576 +id: EDAM_format:1576 name: Pfam entry format namespace: format -def: "Entry format for the Pfam protein secondary database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the Pfam protein secondary database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001577 +id: EDAM_format:1577 name: SMART entry format namespace: format -def: "Entry format for the SMART protein secondary database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the SMART protein secondary database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001578 +id: EDAM_format:1578 name: Superfamily entry format namespace: format -def: "Entry format for the Superfamily protein secondary database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the Superfamily protein secondary database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001579 +id: EDAM_format:1579 name: TIGRFam entry format namespace: format -def: "Entry format for the TIGRFam protein secondary database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the TIGRFam protein secondary database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001580 +id: EDAM_format:1580 name: ProDom entry format namespace: format -def: "Entry format for the ProDom protein domain classification database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001581 +id: EDAM_format:1581 name: FSSP entry format namespace: format -def: "Entry format for the FSSP database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the FSSP database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001568 +id: EDAM_format:1568 name: BIND entry format namespace: format -def: "Entry format for the BIND database of protein interaction." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001569 +id: EDAM_format:1569 name: IntAct entry format namespace: format -def: "Entry format for the IntAct database of protein interaction." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0002560 +id: EDAM_format:2560 name: STRING entry format namespace: format -def: "Entry format for the STRING database of protein interaction." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0002303 +id: EDAM_format:2303 name: STRING entry format (HTML) namespace: format -def: "Entry format (HTML) for the STRING database of protein interaction." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0002304 +id: EDAM_format:2304 name: STRING entry format (XML) namespace: format -def: "Entry format (XML) for the STRING database of protein interaction." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002054 ! Protein interaction format -is_a: EDAM:0002332 ! XML +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 [Term] -id: EDAM:0002561 +id: EDAM_format:2561 name: Sequence assembly format (text) namespace: format -def: "Text format for sequence assembly data." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002055 ! Sequence assembly format +subset: formats +def: "Text format for sequence assembly data." [http://edamontology.org] +is_a: EDAM_format:2055 ! Sequence assembly format [Term] -id: EDAM:0001630 +id: EDAM_format:1630 name: CAF namespace: format -def: "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://www.sanger.ac.uk/resources/software/caf/ -is_a: EDAM:0002561 ! Sequence assembly format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001631 +id: EDAM_format:1631 name: exp namespace: format -def: "Sequence assembly project file EXP format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002561 ! Sequence assembly format (text) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001632 +id: EDAM_format:1632 name: SCF namespace: format -def: "Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://staden.sourceforge.net/manual/formats_unix_2.html -is_a: EDAM:0002057 ! Sequence trace format -is_a: EDAM:0002333 ! Binary +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 [Term] -id: EDAM:0001633 +id: EDAM_format:1633 name: PHD namespace: format -def: "PHD sequence trace format to store serialised chromatogram data (reads)." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://www.bioperl.org/wiki/PHD_sequence_format -is_a: EDAM:0002057 ! Sequence trace format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001640 +id: EDAM_format:1640 name: ArrayExpress entry format namespace: format -def: "Entry format for the ArrayExpress microarrays database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +subset: formats +def: "Entry format for the ArrayExpress microarrays database." [http://edamontology.org] +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001641 +id: EDAM_format:1641 name: affymetrix-exp namespace: format -def: "Affymetrix data file format for information about experimental conditions and protocols." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "Affymetrix experimental conditions data file format" EXACT [] -is_a: EDAM:0002056 ! Microarray experiment data format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001638 +id: EDAM_format:1638 name: cel namespace: format -def: "Format of Affymetrix data file of information about (raw) expression levels of the individual probes." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "Affymetrix probe raw data format" EXACT [] -is_a: EDAM:0002058 ! Gene expression report format -is_a: EDAM:0002330 ! Text -relationship: is_format_of EDAM:0003110 ! Raw microarray data +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 [Term] -id: EDAM:0001644 -name: chp +id: EDAM_format:1644 +name: CHP namespace: format -def: "Format of Affymetrix data file of information about (normalised) expression levels of the individual probes." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "Affymetrix probe normalised data format" EXACT [] -is_a: EDAM:0002058 ! Gene expression report format -is_a: EDAM:0002330 ! Text -relationship: is_format_of EDAM:0003111 ! Processed microarray data +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 [Term] -id: EDAM:0001637 +id: EDAM_format:1637 name: dat namespace: format -def: "Format of Affymetrix data file of raw image data." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "Affymetrix image data file format" EXACT [] -is_a: EDAM:0002058 ! Gene expression report format -is_a: EDAM:0002330 ! Text -relationship: is_format_of EDAM:0001714 ! Microarray spots image +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 [Term] -id: EDAM:0001623 +id: EDAM_format:1623 name: OMIM entry format namespace: format -def: "Format of an entry from the OMIM database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001624 +id: EDAM_format:1624 name: HGVbase entry format namespace: format -def: "Format of a record from the HGVbase database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001625 +id: EDAM_format:1625 name: HIVDB entry format namespace: format -def: "Format of a record from the HIVDB database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001626 +id: EDAM_format:1626 name: KEGG DISEASE entry format namespace: format -def: "Format of an entry from the KEGG DISEASE database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001861 +id: EDAM_format:1861 name: PlasMapper TextMap namespace: format -def: "Map of a plasmid (circular DNA) in PlasMapper TextMap format." [EDAM:EBI "EMBRACE definition"] -subset: format +subset: formats +def: "Map of a plasmid (circular DNA) in PlasMapper TextMap format." [http://edamontology.org] xref: Moby:PlasMapperTextMap -is_a: EDAM:0002060 ! Map format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2060 ! Map format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001627 +id: EDAM_format:1627 name: Primer3 primer namespace: format -def: "Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002061 ! Nucleic acid features (primers) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002063 +id: EDAM_format:2063 name: Protein report (enzyme) format namespace: format -def: "Format of a report of general information about a specific enzyme." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002350 ! Format (typed) +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) [Term] -id: EDAM:0001511 +id: EDAM_format:1511 name: IntEnz enzyme report format namespace: format -def: "Format of an entry from IntEnz (The Integrated Relational Enzyme Database)." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001512 +id: EDAM_format:1512 name: BRENDA enzyme report format namespace: format -def: "Format of an entry from the BRENDA enzyme database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0002322 +id: EDAM_format:2322 name: BioCyc enzyme report format namespace: format -def: "Format of an entry from the BioCyc enzyme database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0002323 +id: EDAM_format:2323 name: ENZYME enzyme report format namespace: format -def: "Format of an entry from the Enzyme nomenclature database (ENZYME)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001513 +id: EDAM_format:1513 name: KEGG REACTION enzyme report format namespace: format -def: "Format of an entry from the KEGG REACTION database of biochemical reactions." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001514 +id: EDAM_format:1514 name: KEGG ENZYME enzyme report format namespace: format -def: "Format of an entry from the KEGG ENZYME database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001515 +id: EDAM_format:1515 name: REBASE proto enzyme report format namespace: format -def: "Format of an entry from the proto section of the REBASE enzyme database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001516 +id: EDAM_format:1516 name: REBASE withrefm enzyme report format namespace: format -def: "Format of an entry from the withrefm section of the REBASE enzyme database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001500 +id: EDAM_format:1500 name: Domainatrix 3D-1D scoring matrix format namespace: format -def: "Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true +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} [Term] -id: EDAM:0001551 +id: EDAM_format:1551 name: Pcons report format namespace: format -def: "Format of output of the Pcons Model Quality Assessment Program (MQAP)." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002065 ! Protein structure report (quality evaluation) format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001552 +id: EDAM_format:1552 name: ProQ report format namespace: format -def: "Format of output of the ProQ protein model quality predictor." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002065 ! Protein structure report (quality evaluation) format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001341 +id: EDAM_format:1341 name: InterPro hits format namespace: format -def: "Results format for searches of the InterPro database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002066 ! Database hits (sequence) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001342 +id: EDAM_format:1342 name: InterPro protein view report format namespace: format -def: "Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0001341 ! InterPro hits format +is_a: EDAM_format:1341 ! InterPro hits format [Term] -id: EDAM:0001343 +id: EDAM_format:1343 name: InterPro match table format namespace: format -def: "Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0001341 ! InterPro hits format +is_a: EDAM_format:1341 ! InterPro hits format [Term] -id: EDAM:0001332 +id: EDAM_format:1332 name: FASTA search results format namespace: format -def: "Format of results of a sequence database search using FASTA." [EDAM:EBI "EMBRACE definition"] +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.) -subset: format -is_a: EDAM:0002066 ! Database hits (sequence) format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001333 +id: EDAM_format:1333 name: BLAST results namespace: format -def: "Format of results of a sequence database search using some variant of BLAST." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002066 ! Database hits (sequence) format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001334 +id: EDAM_format:1334 name: mspcrunch namespace: format -def: "Format of results of a sequence database search using some variant of MSPCrunch." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002066 ! Database hits (sequence) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001335 +id: EDAM_format:1335 name: smith-waterman namespace: format -def: "Format of results of a sequence database search using some variant of Smith Waterman." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002066 ! Database hits (sequence) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001336 +id: EDAM_format:1336 name: dhf namespace: format -def: "Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002066 ! Database hits (sequence) format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001337 +id: EDAM_format:1337 name: lhf namespace: format -def: "Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002066 ! Database hits (sequence) format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2066 ! Database hits (sequence) format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001423 +id: EDAM_format:1423 name: phylip distance matrix namespace: format -def: "Format of PHYLIP phylogenetic distance matrix data." [EDAM:EBI "EMBRACE definition"] +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). -subset: format -is_a: EDAM:0002067 ! Sequence distance matrix format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2067 ! Sequence distance matrix format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001360 +id: EDAM_format:1360 name: meme-motif namespace: format -def: "A motif in the format generated by the MEME program." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002068 ! Sequence motif format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001356 +id: EDAM_format:1356 name: prosite-pattern namespace: format -def: "Format of a regular expression pattern from the Prosite database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002068 ! Sequence motif format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001357 +id: EDAM_format:1357 name: EMBOSS sequence pattern namespace: format -def: "Format of an EMBOSS sequence pattern." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002068 ! Sequence motif format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002072 +id: EDAM_format:2072 name: Hidden Markov model format namespace: format -def: "Format of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002069 ! Sequence profile format -relationship: is_format_of EDAM:0001364 ! Hidden Markov model +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 [Term] -id: EDAM:0001367 +id: EDAM_format:1367 name: jaspar namespace: format -def: "A profile (sequence classifier) in the format used in the JASPAR database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002069 ! Sequence profile format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001366 +id: EDAM_format:1366 name: prosite-profile namespace: format -def: "Sequence profile (sequence classifier) format used in the PROSITE database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002069 ! Sequence profile format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001369 +id: EDAM_format:1369 name: MEME background Markov model namespace: format -def: "Format of the model of random sequences used by MEME." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002072 ! Hidden Markov model format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001370 +id: EDAM_format:1370 name: hmmer namespace: format -def: "Format of a hidden Markov model representation used by the HMMER package." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002072 ! Hidden Markov model format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001349 +id: EDAM_format:1349 name: HMMER Dirichlet prior namespace: format -def: "Dirichlet distribution HMMER format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002074 ! Dirichlet distribution format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001350 +id: EDAM_format:1350 name: MEME Dirichlet prior namespace: format -def: "Dirichlet distribution MEME format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002074 ! Dirichlet distribution format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001351 +id: EDAM_format:1351 name: HMMER emission and transition namespace: format -def: "Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002075 ! HMM emission and transition counts format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001454 +id: EDAM_format:1454 name: dssp namespace: format -def: "Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins)." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002077 ! Protein secondary structure format -is_a: EDAM:0002330 ! Text +is_a: EDAM_format:2077 ! Protein secondary structure format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0001455 +id: EDAM_format:1455 name: hssp namespace: format -def: "Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002077 ! Protein secondary structure format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001457 +id: EDAM_format:1457 name: Vienna RNA secondary structure namespace: format -def: "Format of RNA secondary structure (in bracket notation) with free energy values, generated by the Vienna program." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002076 ! RNA secondary structure format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001458 +id: EDAM_format:1458 name: Vienna local RNA secondary structure namespace: format -def: "Format of local RNA secondary structure components with free energy values, generated by the Vienna program." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002076 ! RNA secondary structure format -is_a: EDAM:0002330 ! Text +subset: formats +def: "Format of local RNA secondary structure components 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 [Term] -id: EDAM:0001248 +id: EDAM_format:1248 name: EMBL feature location namespace: format -def: "Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database." [EDAM:EBI "EMBRACE definition"] -subset: format -synonym: "Feature location" EXACT [] -is_a: EDAM:0002078 ! Sequence range format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001295 +id: EDAM_format:1295 name: quicktandem namespace: format -def: "Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002155 ! Sequence features (repeats) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001296 +id: EDAM_format:1296 name: Sanger inverted repeats namespace: format -def: "Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002155 ! Sequence features (repeats) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001297 +id: EDAM_format:1297 name: EMBOSS repeat namespace: format -def: "Report format for tandem repeats in a sequence (an EMBOSS report format)." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002155 ! Sequence features (repeats) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001318 +id: EDAM_format:1318 name: restrict namespace: format -def: "Report format for restriction enzyme recognition sites used by EMBOSS restrict program." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002158 ! Nucleic acid features (restriction sites) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001319 +id: EDAM_format:1319 name: restover namespace: format -def: "Report format for restriction enzyme recognition sites used by EMBOSS restover program." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002158 ! Nucleic acid features (restriction sites) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001320 +id: EDAM_format:1320 name: REBASE restriction sites namespace: format -def: "Report format for restriction enzyme recognition sites used by REBASE database." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002158 ! Nucleic acid features (restriction sites) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001316 +id: EDAM_format:1316 name: est2genome namespace: format -def: "Format of a report on exon-intron structure generated by EMBOSS est2genome." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002159 ! Gene features (coding region) format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002171 +id: EDAM_format:2171 name: Sequence cluster format (protein) namespace: format -def: "Format used for clusters of protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002170 ! Sequence cluster format +subset: formats +def: "Format used for clusters of protein sequences." [http://edamontology.org] +is_a: EDAM_format:2170 ! Sequence cluster format [Term] -id: EDAM:0002172 +id: EDAM_format:2172 name: Sequence cluster format (nucleic acid) namespace: format -def: "Format used for clusters of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002170 ! Sequence cluster format +subset: formats +def: "Format used for clusters of nucleotide sequences." [http://edamontology.org] +is_a: EDAM_format:2170 ! Sequence cluster format [Term] -id: EDAM:0001247 +id: EDAM_format:1247 name: COG sequence cluster format namespace: format -def: "Format of an entry from the COG database of clusters of (related) protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0002175 +id: EDAM_format:2175 name: Gene cluster format namespace: format -alt_id: EDAM:0002918 -def: "Format used for clusters of genes." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002172 ! Sequence cluster format (nucleic acid) +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) [Term] -id: EDAM:0001228 +id: EDAM_format:1228 name: UniGene entry format namespace: format -def: "Format of an entry from UniGene." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001639 +id: EDAM_format:1639 name: affymetrix namespace: format -def: "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002330 ! Text -is_a: EDAM:0002172 ! Sequence cluster format (nucleic acid) +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) [Term] -id: EDAM:0002196 +id: EDAM_format:2196 name: OBO format namespace: format -def: "OBO ontology format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002195 ! Ontology format +subset: formats +def: "OBO ontology format." [http://edamontology.org] +is_a: EDAM_format:2195 ! Ontology format [Term] -id: EDAM:0002549 +id: EDAM_format:2549 name: OBO namespace: format -def: "OBO ontology text format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002196 ! OBO format -is_a: EDAM:0002330 ! Text +subset: formats +def: "OBO ontology text format." [http://edamontology.org] +is_a: EDAM_format:2196 ! OBO format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0002197 +id: EDAM_format:2197 name: OWL namespace: format -def: "OWL ontology format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002195 ! Ontology format -is_a: EDAM:0002330 ! Text +subset: formats +def: "OWL ontology format." [http://edamontology.org] +is_a: EDAM_format:2195 ! Ontology format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0002550 +id: EDAM_format:2550 name: OBO-XML namespace: format -def: "OBO ontology XML format." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002196 ! OBO format -is_a: EDAM:0002332 ! XML +subset: formats +def: "OBO ontology XML format." [http://edamontology.org] +is_a: EDAM_format:2196 ! OBO format +is_a: EDAM_format:2332 ! XML [Term] -id: EDAM:0002211 +id: EDAM_format:2211 name: CIP strain data format namespace: format -def: "Format for a report of strain data as used for CIP database entries." [EDAM:EBI "EMBRACE definition"] -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +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 [Term] -id: EDAM:0001760 +id: EDAM_format:1760 name: CATH chain report format namespace: format -def: "Format of CATH domain classification information for a polypeptide chain." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001761 +id: EDAM_format:1761 name: CATH PDB report format namespace: format -def: "Format of CATH domain classification information for a protein PDB file." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0001563 +id: EDAM_format:1563 name: SMART domain assignment report format namespace: format -def: "Format of SMART domain assignment data." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_obsolete: true -consider: EDAM:0002331 ! HTML +is_obsolete: true !{since=beta12orEarlier} +consider: EDAM_format:2331 ! HTML [Term] -id: EDAM:0003000 +id: EDAM_format:3000 name: AB1 namespace: format -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 EDAM:EBI "EMBRACE definition"] +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). -subset: format -is_a: EDAM:0002333 ! Binary -is_a: EDAM:0002057 ! Sequence trace format +is_a: EDAM_format:2333 ! Binary format +is_a: EDAM_format:2057 ! Sequence trace format [Term] -id: EDAM:0003001 +id: EDAM_format:3001 name: ACE namespace: format -def: "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt -is_a: EDAM:0002330 ! Text -is_a: EDAM:0002055 ! Sequence assembly 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 [Term] -id: EDAM:0003003 +id: EDAM_format:3003 name: BED namespace: format -def: "BED format of sequence annotation track, typically to be displayed in a genome browser." [EDAM:EBI "EMBRACE definition"] +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). -subset: format -spec: http://genome.ucsc.edu/FAQ/FAQformat#format1 -is_a: EDAM:0002919 ! Sequence annotation track format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0003004 +id: EDAM_format:3004 name: bigBed namespace: format -def: "bigBed format for large sequence annotation tracks, similar to textual BED format." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://genome.ucsc.edu/FAQ/FAQformat#format1.5 -is_a: EDAM:0002919 ! Sequence annotation track format -is_a: EDAM:0002333 ! Binary +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 [Term] -id: EDAM:0003005 +id: EDAM_format:3005 name: WIG namespace: format -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." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://genome.ucsc.edu/goldenPath/help/wiggle.html -is_a: EDAM:0002919 ! Sequence annotation track format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0003006 +id: EDAM_format:3006 name: bigWig namespace: format -def: "bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://genome.ucsc.edu/FAQ/FAQformat#format6.1 -is_a: EDAM:0002919 ! Sequence annotation track format -is_a: EDAM:0002333 ! Binary +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 [Term] -id: EDAM:0003007 +id: EDAM_format:3007 name: PSL namespace: format -def: "PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://genome.ucsc.edu/FAQ/FAQformat#format2 -is_a: EDAM:0002919 ! Sequence annotation track format -is_a: EDAM:0002920 ! Alignment format (pair only) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0003008 +id: EDAM_format:3008 name: MAF namespace: format -def: "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -spec: http://genome.ucsc.edu/FAQ/FAQformat#format5 -is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002919 ! Sequence annotation track 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 [Term] -id: EDAM:0003009 +id: EDAM_format:3009 name: 2bit namespace: format -def: "2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://jcomeau.freeshell.org/www/genome/2bitformat.html http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002333 ! Binary +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 [Term] -id: EDAM:0003010 +id: EDAM_format:3010 name: .nib namespace: format -def: ".nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://genome.ucsc.edu/FAQ/FAQformat#format8 -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002333 ! Binary +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 [Term] -id: EDAM:0002094 +id: EDAM_format:2094 name: pure namespace: format -def: "EMBOSS alphabet for molecular sequence with possible unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002095 +id: EDAM_format:2095 name: unpure namespace: format -def: "EMBOSS alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002096 +id: EDAM_format:2096 name: unambiguous sequence namespace: format -def: "EMBOSS alphabet for a molecular sequence with possible unknown positions but without ambiguity characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002330 ! Text +subset: formats +def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters." [http://edamontology.org] + +is_a: EDAM_format:2571 ! Raw sequence format +is_a: EDAM_format:2330 ! Textual format [Term] -id: EDAM:0002566 +id: EDAM_format:2566 name: completely unambiguous namespace: format -def: "EMBOSS alphabet for a molecular sequence without any unknown positions or ambiguity characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0002097 +id: EDAM_format:2097 name: ambiguous namespace: format -def: "EMBOSS alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001207 +id: EDAM_format:1207 name: nucleotide namespace: format -def: "EMBOSS alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001208 +id: EDAM_format:1208 name: protein namespace: format -def: "EMBOSS alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -synonym: "Amino acid sequence" EXACT [] -is_a: EDAM:0002571 ! Raw sequence format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0001206 +id: EDAM_format:1206 name: unambiguous pure namespace: format -def: "EMBOSS alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002094 ! pure -is_a: EDAM:0002096 ! unambiguous +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 [Term] -id: EDAM:0002567 +id: EDAM_format:2567 name: completely unambiguous pure namespace: format -def: "EMBOSS alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002094 ! pure -is_a: EDAM:0002566 ! completely unambiguous +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 [Term] -id: EDAM:0001209 +id: EDAM_format:1209 name: consensus namespace: format -def: "EMBOSS alphabet for the consensus of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002097 ! ambiguous -is_a: EDAM:0002095 ! unpure +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 [Term] -id: EDAM:0001210 +id: EDAM_format:1210 name: pure nucleotide namespace: format -def: "EMBOSS alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002094 ! pure -is_a: EDAM:0001207 ! nucleotide +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 [Term] -id: EDAM:0001211 +id: EDAM_format:1211 name: unambiguous pure nucleotide namespace: format -def: "EMBOSS alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters ." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001207 ! nucleotide -is_a: EDAM:0001206 ! unambiguous pure +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 [Term] -id: EDAM:0002568 +id: EDAM_format:2568 name: completely unambiguous pure nucleotide namespace: format -def: "EMBOSS alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters ." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001207 ! nucleotide -is_a: EDAM:0002567 ! completely unambiguous pure +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 [Term] -id: EDAM:0001212 +id: EDAM_format:1212 name: dna namespace: format -def: "EMBOSS alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001207 ! nucleotide +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 [Term] -id: EDAM:0001213 +id: EDAM_format:1213 name: rna namespace: format -def: "EMBOSS alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001207 ! nucleotide +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 [Term] -id: EDAM:0001214 +id: EDAM_format:1214 name: unambiguous pure dna namespace: format -def: "EMBOSS alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001206 ! unambiguous pure -is_a: EDAM:0001212 ! dna +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 [Term] -id: EDAM:0002569 +id: EDAM_format:2569 name: completely unambiguous pure dna namespace: format -def: "EMBOSS alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002567 ! completely unambiguous pure -is_a: EDAM:0001212 ! dna +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 [Term] -id: EDAM:0001215 +id: EDAM_format:1215 name: pure dna namespace: format -def: "EMBOSS alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001210 ! pure nucleotide -is_a: EDAM:0001212 ! dna +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 [Term] -id: EDAM:0001216 +id: EDAM_format:1216 name: unambiguous pure rna sequence namespace: format -def: "EMBOSS alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001206 ! unambiguous pure -is_a: EDAM:0001213 ! rna +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 [Term] -id: EDAM:0002570 +id: EDAM_format:2570 name: completely unambiguous pure rna sequence namespace: format -def: "EMBOSS alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002567 ! completely unambiguous pure -is_a: EDAM:0001213 ! rna +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 [Term] -id: EDAM:0001217 +id: EDAM_format:1217 name: pure rna namespace: format -def: "EMBOSS alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001210 ! pure nucleotide -is_a: EDAM:0001213 ! rna +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 [Term] -id: EDAM:0001218 +id: EDAM_format:1218 name: unambiguous pure protein namespace: format -def: "EMBOSS alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0001206 ! unambiguous pure -is_a: EDAM:0001208 ! protein +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 [Term] -id: EDAM:0002607 +id: EDAM_format:2607 name: completely unambiguous pure protein namespace: format -def: "EMBOSS alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002567 ! completely unambiguous pure -is_a: EDAM:0001208 ! protein +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 [Term] -id: EDAM:0001219 +id: EDAM_format:1219 name: pure protein namespace: format -def: "EMBOSS alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] -subset: format -is_a: EDAM:0002094 ! pure -is_a: EDAM:0001208 ! protein +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 [Term] -id: EDAM:0003011 +id: EDAM_format:3011 name: genePred namespace: format -def: "genePred table format for gene prediction tracks." [EDAM:EBI "EMBRACE definition"] +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. -subset: format -spec: http://genome.ucsc.edu/FAQ/FAQformat#format9 -is_a: EDAM:0002919 ! Sequence annotation track format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0003012 +id: EDAM_format:3012 name: pgSnp namespace: format -def: "Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser." [EDAM:EBI "EMBRACE definition"] ! UCSC-specific,but also for custom tracks & useful -subset: format -spec: http://genome.ucsc.edu/FAQ/FAQformat#format10 -is_a: EDAM:0002919 ! Sequence annotation track format -is_a: EDAM:0002330 ! Text +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 ! [Term] -! id: EDAM:000todo if desired (but then we could include 100 ucsc db tables) At least, this one is used also in IGV (for importing genome cytobands) +! 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 -! def: "Cytoband format for chromosome cytobands." [EDAM:EBI "EMBRACE definition"] +! subset: formats +! def: "Cytoband format for chromosome cytobands." [http://edamontology.org] ! comment: Reflects a UCSC Browser DB table. -! subset: format -! spec: http://www.broadinstitute.org/software/igv/Cytoband +! xref: http://www.broadinstitute.org/software/igv/Cytoband !{documentation=true} [Term] -id: EDAM:0003013 +id: EDAM_format:3013 name: axt namespace: format -def: "axt format of alignments, typically produced from BLASTZ." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://genome.ucsc.edu/goldenPath/help/axt.html -is_a: EDAM:0002920 ! Alignment format (pair only) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0003014 +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 -subset: format -spec: http://www.bx.psu.edu/miller_lab/dist/lav_format.html -is_a: EDAM:0002920 ! Alignment format (pair only) -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0003015 +id: EDAM_format:3015 name: Pileup namespace: format -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)." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://samtools.sourceforge.net/pileup.shtml -is_a: EDAM:0002920 ! Alignment format (pair only) -is_a: EDAM:0002330 ! Text +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) [Term] -id: EDAM:0003016 +id: EDAM_format:3016 name: VCF namespace: format -def: "Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://vcftools.sourceforge.net/specs.html -is_a: EDAM:0002921 ! Sequence variation annotation format -is_a: EDAM:0002330 ! Text +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 [Term] -id: EDAM:0003017 +id: EDAM_format:3017 name: SRF namespace: format -def: "Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive." [EDAM:EBI "EMBRACE definition" http://srf.sourceforge.net/ShortSequenceFormatDec18th_v_1_3.htm] -subset: format -spec: http://srf.sourceforge.net/ -is_a: EDAM:0002057 ! Sequence trace format -is_a: EDAM:0002333 ! Binary +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 [Term] -id: EDAM:0003018 +id: EDAM_format:3018 name: ZTR namespace: format -def: "ZTR format for storing chromatogram data from DNA sequencing instruments." [http://staden.sourceforge.net/manual/formats_unix_12.html EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://staden.sourceforge.net/manual/formats_unix_12.html -is_a: EDAM:0002057 ! Sequence trace format -is_a: EDAM:0002333 ! Binary +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 [Term] -id: EDAM:0003019 +id: EDAM_format:3019 name: GVF namespace: format -def: "Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://sequenceontology.org/gvf.html -is_a: EDAM:0001975 ! GFF3 +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)) - [Term] -id: EDAM:0003020 +id: EDAM_format:3020 name: BCF namespace: format -def: "BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [EDAM:EBI "EMBRACE definition"] -subset: format -spec: http://samtools.sourceforge.net/mpileup.shtml ! BCF described on this site -is_a: EDAM:0002921 ! Sequence variation annotation format -is_a: EDAM:0002333 ! Binary +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 +