From aaf176e66888d0a209fd96591eceb46afc7f8a44 Mon Sep 17 00:00:00 2001 From: matuskalas Date: Tue, 1 Nov 2016 03:45:22 +0100 Subject: [PATCH] History of releases: 1.5 --- releases/EDAM.owl | 4988 ++++++++++++++++++++++++++++------------------------- 1 file changed, 2625 insertions(+), 2363 deletions(-) diff --git a/releases/EDAM.owl b/releases/EDAM.owl index 4c61f3d..27b617d 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -8,6 +8,7 @@ + @@ -15,42 +16,44 @@ + xmlns:doap="http://usefulinc.com/ns/doap#" + xmlns:edam="&oboOther;edam#"> - 3424 - 06:10:2014 23:58 - EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Co-authors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. EDAM: An ontology of bioinformatics operations, types of data and identifiers, data formats, and topics - 1.4 - Jon Ison - Matúš Kalaš + EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. Hervé Ménager + topics "EDAM topics" + 14:11:2014 09:26 + EDAM_format http://edamontology.org/format_ "EDAM data formats" Jon Ison, Matus Kalas, Herve Menager - 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. + Matúš Kalaš + 3429 + 1.5 + Jon Ison + concept_properties "EDAM concept properties" + EDAM_data http://edamontology.org/data_ "EDAM types of data" + application/rdf+xml + EDAM http://edamontology.org/ "EDAM relations and concept properties" operations "EDAM operations" + EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. edam "EDAM" relations "EDAM relations" bioinformatics "Bioinformatics" data "EDAM types of data" identifiers "EDAM types of identifiers" - formats "EDAM data formats" - topics "EDAM topics" - concept_properties "EDAM concept properties" EDAM + formats "EDAM data formats" EDAM_operation http://edamontology.org/operation_ "EDAM operations" EDAM_topic http://edamontology.org/topic_ "EDAM topics" - EDAM_data http://edamontology.org/data_ "EDAM types of data" - EDAM_format http://edamontology.org/format_ "EDAM data formats" - EDAM http://edamontology.org/ "EDAM relations and concept properties" - application/rdf+xml @@ -65,94 +68,248 @@ /////////////////////////////////////////////////////////////////////////////////////// --> - - + + + + + + + Created in + concept_properties + true + Version in which a concept was created. + + + + + + + Documentation + concept_properties + true + '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. + Specification + + + + + + + + Example + concept_properties + true + 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + + + + + + - - + + + + + Obsolete since Version in which a concept was made obsolete. concept_properties true - + + + + + + + Regular expression + true + concept_properties + 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + - - - - Example - concept_properties - true - 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + + + + + + + - + + + + + + - + + + + + - - - - - - Regular expression - true - concept_properties - 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. - + + + + + - + + + + + + - - - - - - Documentation - concept_properties - true - '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. - Specification - - - + + + + + + - - - Created in - concept_properties - true - Version in which a concept was created. - + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -172,7 +329,7 @@ has format false - 'A has_format B' defines for the subject A, that it has the object B as its data format. + 'A has_format B' defines for the subject A, that it has the object B as its data format. edam false false @@ -180,14 +337,14 @@ bioinformatics OBO_REL:is_a false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. - '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. + '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. @@ -201,10 +358,10 @@ has function false relations - 'A has_function B' defines for the subject A, that it has the object B as its function. + 'A has_function B' defines for the subject A, that it has the object B as its function. true - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. false + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. edam OBO_REL:bearer_of bioinformatics @@ -216,22 +373,22 @@ - true - In very unusual cases. + '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. - + + OBO_REL:bearer_of - 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. + 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. - '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. + true + In very unusual cases. - - + @@ -242,8 +399,8 @@ has identifier false false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. - 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. + 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. edam OBO_REL:is_a bioinformatics @@ -264,11 +421,11 @@ true bioinformatics false - 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. + 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. false OBO_REL:is_a relations - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. + Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. false OBO_REL:has_participant @@ -277,16 +434,16 @@ - 'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. + OBO_REL:has_participant - - + - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. - OBO_REL:has_participant + '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). - + + In very unusual cases. @@ -304,34 +461,34 @@ false false false - 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. + 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. true OBO_REL:has_participant relations OBO_REL:is_a bioinformatics edam - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. + Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. - '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). + 'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. OBO_REL:has_participant + '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. - In very unusual cases. true + In very unusual cases. @@ -347,11 +504,11 @@ false OBO_REL:is_a edam - '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). + '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). false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. - relations + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. true + relations @@ -367,27 +524,27 @@ - In very unusual cases. true + In very unusual cases. - 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. + 'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object. - + - 'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource. - + 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. + - 'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object. + '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. + - @@ -398,10 +555,10 @@ is format of OBO_REL:quality_of - Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. + Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. relations edam - 'A is_format_of B' defines for the subject A, that it is a data format of the object B. + 'A is_format_of B' defines for the subject A, that it is a data format of the object B. false false false @@ -414,8 +571,8 @@ - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. OBO_REL:quality_of + 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. @@ -432,22 +589,22 @@ relations edam OBO_REL:function_of - 'A is_function_of B' defines for the subject A, that it is a function of the object B. + 'A is_function_of B' defines for the subject A, that it is a function of the object B. false - true OBO_REL:is_a + true OBO_REL:inheres_in - Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. + Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. - OBO_REL:function_of + OBO_REL:inheres_in + 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. - + In very unusual cases. @@ -456,10 +613,10 @@ - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. - OBO_REL:inheres_in + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. + OBO_REL:function_of - + @@ -469,13 +626,13 @@ is identifier of false - 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. + 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. OBO_REL:is_a - Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. + Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. relations false - edam bioinformatics + edam false false @@ -489,15 +646,15 @@ is input of - 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. + '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. false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. edam OBO_REL:is_a - false OBO_REL:participates_in - bioinformatics + false true + bioinformatics relations false @@ -507,22 +664,22 @@ - '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). + true + In very unusual cases. - - + - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. OBO_REL:participates_in + '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. - In very unusual cases. - true + 'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). - + + @@ -534,10 +691,10 @@ relations true OBO_REL:participates_in - '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. + '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. false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. edam + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. false bioinformatics false @@ -549,23 +706,23 @@ - '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). + In very unusual cases. + true + + + + + 'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. OBO_REL:participates_in + '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. - - true - In very unusual cases. - - - @@ -574,16 +731,16 @@ is topic of edam - false OBO_REL:is_a - Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. + false + Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. false true false bioinformatics OBO_REL:quality_of relations - '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). + '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). @@ -597,14 +754,14 @@ - In very unusual cases. true + In very unusual cases. - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. OBO_REL:quality_of + 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. @@ -647,9 +804,9 @@ Datum beta12orEarlier - Data set Data record - Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. + Data set + 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. @@ -663,39 +820,27 @@ - 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. - - - - - Data record EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). - Datum - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - - - - - IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity. + Data does 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). - + - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - Data set + 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. - + + - Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019). + IAO '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. - + @@ -705,11 +850,23 @@ - GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. + Data set + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + + + + + GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. + + Datum + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + + + @@ -745,7 +902,7 @@ Ontology - + @@ -764,13 +921,14 @@ - Directory metadata - + DEP_Directory metadata + + true beta12orEarlier A directory on disk from which files are read. - - - + 1.5 + + @@ -782,8 +940,8 @@ beta12orEarlier Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. - beta12orEarlier true + beta12orEarlier @@ -833,7 +991,6 @@ - A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). ID beta12orEarlier @@ -961,7 +1118,7 @@ Sequence set - + SO:0001260 beta12orEarlier This concept may be used for arbitrary sequence sets and associated data arising from processing. @@ -976,13 +1133,14 @@ - Sequence mask character - + DEP_Sequence mask character + A character used to replace (mask) other characters in a molecular sequence. + 1.5 beta12orEarlier - - - + true + + @@ -990,15 +1148,15 @@ - Sequence mask type - - + DEP_Sequence mask type + + true + 1.5 beta12orEarlier Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. A label (text token) describing the type of sequence masking to perform. - - - + + @@ -1008,12 +1166,11 @@ DNA sense specification - - beta12orEarlier - DNA strand specification - The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. + The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. The strand of a DNA sequence (forward or reverse). Strand + beta12orEarlier + DNA strand specification @@ -1024,13 +1181,14 @@ - Sequence length specification - + DEP_Sequence length specification + + 1.5 beta12orEarlier A specification of sequence length(s). - - - + true + + @@ -1038,16 +1196,15 @@ - Sequence metadata - - - + DEP_Sequence metadata + + true + 1.5 This is used for such things as a report including the sequence identifier, type and length. Basic or general information concerning molecular sequences. beta12orEarlier - - - + + @@ -1056,11 +1213,10 @@ Sequence feature source - beta12orEarlier How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. - 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). + 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). @@ -1073,8 +1229,10 @@ Database hits (sequence) - A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. + 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. + Sequence search hits + Sequence database hits beta12orEarlier @@ -1090,7 +1248,9 @@ A report of hits from a search of a protein secondary or domain database. beta12orEarlier - Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'. + Secondary database hits + 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'. + Secondary database search hits @@ -1132,14 +1292,15 @@ - Sequence alignment (words) - + DEP_Sequence alignment (words) + Alignment of exact matches between subsequences (words) within two or more molecular sequences. Sequence word alignment + true beta12orEarlier - - - + 1.5 + + @@ -1148,7 +1309,7 @@ Dotplot - + beta12orEarlier A dotplot of sequence similarities identified from word-matching or character comparison. @@ -1184,13 +1345,14 @@ - Sequence alignment parameter - + DEP_Sequence alignment parameter + beta12orEarlier - Some simple value controlling a sequence alignment (or similar 'match') operation. - - - + 1.5 + true + Some simple value controlling a sequence alignment (or similar 'match') operation. + + @@ -1212,14 +1374,14 @@ - Sequence alignment metadata - - + DEP_Sequence alignment metadata + + 1.5 + true beta12orEarlier Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score. - - - + + @@ -1231,7 +1393,7 @@ beta12orEarlier An informative report of molecular sequence alignment-derived data or metadata. - This is a broad data type and is used a placeholder for other, more specific types. + Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score. @@ -1291,8 +1453,8 @@ Phylogenetic character data beta12orEarlier - Basic character data from which a phylogenetic tree may be generated. As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments + Basic character data from which a phylogenetic tree may be generated. @@ -1305,7 +1467,7 @@ Phylogenetic tree - + @@ -1316,7 +1478,7 @@ beta12orEarlier The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length. Moby:phylogenetic_tree - 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'. + A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. Moby:Tree Phylogeny @@ -1335,8 +1497,8 @@ Substitution matrix Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. - beta12orEarlier 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). + beta12orEarlier @@ -1365,17 +1527,17 @@ Protein features (secondary structure) - - beta12orEarlier The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). Protein secondary structure + beta12orEarlier Secondary structure assignment (predicted or real) of a protein. + Secondary structure (protein) @@ -1388,7 +1550,6 @@ Protein features (super-secondary) - Protein structure report (super-secondary) beta12orEarlier Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. @@ -1433,8 +1594,8 @@ - RNA secondary structure record - + RNA secondary structure + @@ -1442,6 +1603,7 @@ beta12orEarlier + Secondary structure (RNA) Moby:RNAStructML This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. An informative report of secondary structure (predicted or real) of an RNA molecule. @@ -1486,7 +1648,7 @@ Structure - + @@ -1527,6 +1689,8 @@ Database hits (structure) This includes alignment and score data. + Structure database hits + Structure search hits beta12orEarlier Results (hits) from searching a database of tertiary structure. @@ -1540,7 +1704,6 @@ Structure alignment - @@ -1590,17 +1753,18 @@ - Structural (3D) profile - + Structural profile + + Structural (3D) profile Some type of structural (3D) profile or template (representing a structure or structure alignment). - beta12orEarlier 3D profile + beta12orEarlier @@ -1626,14 +1790,15 @@ - Sequence-3D profile alignment - + DEP_Sequence-3D profile alignment + + true beta12orEarlier An alignment of a sequence to a 3D profile (representing structures or a structure alignment). + 1.5 Sequence-structural profile alignment - - - + + @@ -1672,8 +1837,8 @@ Amino acid annotation beta12orEarlier - 1.4 true + 1.4 An informative report about a specific amino acid. @@ -1700,16 +1865,10 @@ Protein report - - - - - - - - Gene product annotation - beta12orEarlier + An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. + beta12orEarlier + Gene product annotation @@ -1739,17 +1898,16 @@ Protein features (3D motif) - - beta12orEarlier - Protein structure report (3D motif) An informative report on the 3D structural motifs in a protein. This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. + beta12orEarlier + Protein structure report (3D motif) @@ -1760,19 +1918,14 @@ - Protein domain classification - - - - - - - + DEP_Protein domain classification + beta12orEarlier + 1.5 Data concerning the classification of the sequences and/or structures of protein structural domain(s). - - - + true + + @@ -1821,7 +1974,7 @@ Protein folding report - + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Protein property (folding) A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. @@ -1871,18 +2024,17 @@ - Protein interaction + Protein interaction report - + An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand. Protein report (interaction) beta12orEarlier - An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand. @@ -1893,17 +2045,18 @@ - Protein family - + Protein family report + + Protein classification data Protein family annotation + An informative report on a specific protein family or other classification or group of protein sequences or structures. beta12orEarlier - An informative report on a specific protein family or other group of classified proteins. @@ -1974,8 +2127,8 @@ - Codon usage report - + Codon usage data + @@ -1995,22 +2148,20 @@ - Gene annotation + Gene report - - - - - - - Gene annotation (functional) Moby:GeneInfo + Gene function (report) Moby_namespace:Human_Readable_Description beta12orEarlier - 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). + Gene annotation + This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). Moby:gene - Gene report - An informative report on a particular locus, gene, gene system or groups of genes. + Nucleic acid features (gene and transcript structure) + Gene features report + Gene and transcript structure (report) + A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. + Gene structure (repot) @@ -2036,8 +2187,8 @@ - Nucleic acid features (variation) - + DNA variation (report) + @@ -2045,9 +2196,12 @@ beta12orEarlier + DNA variation report + Nucleic acid features (variation) 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. Sequence variation annotation SO:0001059 + Sequence variation report @@ -2058,8 +2212,8 @@ - Gene annotation (chromosome) - + Chromosome (report) + @@ -2079,9 +2233,10 @@ - Genotype/phenotype annotation - + Genotype/phenotype report + beta12orEarlier + Genotype/phenotype annotation 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. @@ -2093,15 +2248,17 @@ - Nucleic acid features (primers) - + Primer binding sites (report) + + Primers (report) beta12orEarlier + Nucleic acid features (primers) Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence. @@ -2113,7 +2270,7 @@ - Experiment annotation (PCR assay data) + PCR experiment annotation @@ -2123,7 +2280,8 @@ PCR assay data beta12orEarlier - Data on a PCR assay or electronic / virtual PCR. + Experiment annotation (PCR) + Information about a PCR experiment, e.g. quantitative real-time PCR. @@ -2135,7 +2293,7 @@ Sequence trace - + beta12orEarlier This is the raw data produced by a DNA sequencing machine. @@ -2152,8 +2310,8 @@ Sequence assembly - 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. SO:0000353 + 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. SO:0001248 An assembly of fragments of a (typically genomic) DNA sequence. beta12orEarlier @@ -2163,7 +2321,7 @@ - Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. + Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. SO:0001248 @@ -2189,9 +2347,10 @@ - Gene annotation (linkage) - + Genetic linkage (report) + An informative report on the linkage of alleles. + Gene annotation (linkage) beta12orEarlier @@ -2204,10 +2363,10 @@ Gene expression profile - + Gene expression pattern - Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. beta12orEarlier + Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. @@ -2218,7 +2377,7 @@ - Experiment annotation (microarray) + Microarray experiment report @@ -2228,8 +2387,10 @@ beta12orEarlier This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. - Experimental design annotation + Microarray experiment metadata + Experiment metadata (microarray) Information on a microarray experiment such as conditions, protocol, sample:data relationships etc. + Experimental design annotation @@ -2289,8 +2450,8 @@ SBS experimental data - Sequencing by synthesis (SBS) experimental data Sequencing by synthesis (SBS) data. + Sequencing by synthesis (SBS) experimental data true beta12orEarlier beta12orEarlier @@ -2381,7 +2542,7 @@ Electron microscopy model - + @@ -2402,8 +2563,7 @@ 2D PAGE image - - + @@ -2516,13 +2676,14 @@ - Data resource definition - + DEP_Data resource definition + A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. + 1.5 + true beta12orEarlier - - - + + @@ -2544,16 +2705,17 @@ - Biological model - + Mathematical model + + A biological model represented in mathematical terms. beta12orEarlier - A biological model which can be represented in mathematical terms. + Biological model @@ -2566,7 +2728,6 @@ Statistical estimate score - A value representing estimated statistical significance of some observed data; typically sequence database hits. beta12orEarlier @@ -2579,13 +2740,14 @@ - EMBOSS database resource definition - - beta12orEarlier + DEP_EMBOSS database resource definition + + 1.5 + true Resource definition for an EMBOSS database. - - - + beta12orEarlier + + @@ -2593,15 +2755,16 @@ - Version information - - beta12orEarlier + DEP_Version information + + true Information on a version of software or data, for example name, version number and release date. + beta12orEarlier Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. + 1.5 + - - - + @@ -2634,7 +2797,7 @@ Data index - + @@ -2654,7 +2817,7 @@ Data index report - + @@ -2675,7 +2838,7 @@ Database metadata - + beta12orEarlier Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. @@ -2689,7 +2852,7 @@ Tool metadata - + Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. beta12orEarlier @@ -2702,14 +2865,15 @@ - Job metadata - + DEP_Job metadata + Textual metadata on a submitted or completed job. Moby:PDGJOB + 1.5 + true beta12orEarlier - - - + + @@ -2718,7 +2882,7 @@ User metadata - + Textual metadata on a software author or end-user, for example a person or other software. beta12orEarlier @@ -2733,17 +2897,16 @@ Small molecule report - - An informative report on a specific chemical compound. - Small molecule report Chemical compound annotation beta12orEarlier + An informative report on a specific chemical compound. + Small molecule report Small molecule annotation @@ -2801,18 +2964,12 @@ - Ontology concept metadata - - - - - - - + Ontology concept data + Data concerning or derived from a concept from a biological ontology. Ontology term metadata - beta12orEarlier Ontology class metadata + beta12orEarlier @@ -2824,14 +2981,14 @@ Keyword - + Moby:Global_Keyword Moby:Wildcard_Query Moby:BooleanQueryString beta12orEarlier Moby:QueryString - Keyword(s) or phrase(s) used (typically) for text-searching purposes. Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. + Keyword(s) or phrase(s) used (typically) for text-searching purposes. @@ -2843,8 +3000,7 @@ Citation - - + beta12orEarlier Moby:Publication Bibliographic reference @@ -2863,15 +3019,15 @@ Article - + - A body of scientific text, typically a full text article from a scientific journal. beta12orEarlier + A document of scientific text, typically a full text article from a scientific journal. @@ -2883,8 +3039,9 @@ Text mining report - + A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. + Text mining output beta12orEarlier An abstract of the results of text mining. @@ -2930,7 +3087,7 @@ Identifier (typed) An identifier that identifies a particular type of data. - This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. + 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'. beta12orEarlier @@ -3006,8 +3163,8 @@ Phenomenon identifier Name or other identifier of a physical, observable biological occurrence or event. - true beta12orEarlier + true beta12orEarlier @@ -3020,12 +3177,6 @@ Molecule identifier - - - - - - beta12orEarlier Name or other identifier of a molecule. @@ -3071,15 +3222,16 @@ - Molecule type - + DEP_Molecule type + Protein|DNA|RNA - beta12orEarlier A label (text token) describing the type a molecule. - For example, 'Protein', 'DNA', 'RNA' etc. - - - + beta12orEarlier + 1.5 + true + For example, 'Protein', 'DNA', 'RNA' etc. + + @@ -3164,8 +3316,8 @@ beta12orEarlier - Chemical name Unique name of a chemical compound. + Chemical name @@ -3315,7 +3467,7 @@ Chemical name (INN) - International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). + International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). beta12orEarlier INN chemical name @@ -3331,8 +3483,8 @@ Chemical name (brand) - Brand chemical name beta12orEarlier + Brand chemical name Brand name of a chemical compound. @@ -3380,8 +3532,8 @@ Chemical registry number (Beilstein) Beilstein registry number of a chemical compound. - Beilstein chemical registry number beta12orEarlier + Beilstein chemical registry number @@ -3428,8 +3580,8 @@ Amino acid name - String of one or more ASCII characters representing an amino acid. beta12orEarlier + String of one or more ASCII characters representing an amino acid. @@ -3468,8 +3620,8 @@ Polypeptide chain identifier This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA PDB chain identifier - Protein chain identifier PDB strand id + Protein chain identifier PDBML:pdbx_PDB_strand_id Identifier of a polypeptide chain from a protein. Chain identifier @@ -3504,12 +3656,6 @@ Enzyme identifier - - - - - - Name or other identifier of an enzyme or record from a database of enzymes. beta12orEarlier @@ -3530,8 +3676,8 @@ Moby:Annotated_EC_Number EC An Enzyme Commission (EC) number of an enzyme. - EC code Moby:EC_Number + EC code [0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ @@ -3562,12 +3708,6 @@ Restriction enzyme name - - - - - - beta12orEarlier Name of a restriction enzyme. @@ -3581,13 +3721,14 @@ - Sequence position specification - + DEP_Sequence position specification + + true beta12orEarlier A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. - - - + 1.5 + + @@ -3612,13 +3753,13 @@ Sequence position - + + A position of one or more points (base or residue) in a sequence, or part of such a specification. + SO:0000735 PDBML:_atom_site.id beta12orEarlier - WHATIF: number - SO:0000735 - A position of a single point (base or residue) in a sequence, or part of such a specification. WHATIF: PDBx_atom_site + WHATIF: number @@ -3630,7 +3771,7 @@ Sequence range - + Specification of range(s) of sequence positions. beta12orEarlier @@ -3707,8 +3848,8 @@ Sequence feature label - A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. beta12orEarlier + 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. Typically an EMBL or Swiss-Prot feature label. Sequence feature name @@ -3725,8 +3866,8 @@ The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. - beta12orEarlier UFO + beta12orEarlier @@ -3739,8 +3880,8 @@ Codon name - String of one or more ASCII characters representing a codon. true + String of one or more ASCII characters representing a codon. beta12orEarlier beta12orEarlier @@ -3799,8 +3940,8 @@ An NCBI unique identifier of a gene. http://www.geneontology.org/doc/GO.xrf_abbs:LocusID Gene identifier (Entrez) - http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene Entrez gene ID + http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene Gene identifier (NCBI) NCBI geneid @@ -3816,8 +3957,8 @@ Gene identifier (NCBI RefSeq) - beta12orEarlier An NCBI RefSeq unique identifier of a gene. + beta12orEarlier true beta12orEarlier @@ -3848,8 +3989,8 @@ beta12orEarlier [0-9]+ - beta12orEarlier true + beta12orEarlier An Entrez unique identifier of a gene. @@ -3928,11 +4069,11 @@ Gene ID (GeneDB) - [a-zA-Z_0-9\.-]* - Moby_namespace:GeneDB Identifier of a gene from the GeneDB database. + [a-zA-Z_0-9\.-]* beta12orEarlier GeneDB identifier + Moby_namespace:GeneDB @@ -4002,12 +4143,6 @@ SCOP domain identifier - - - - - - beta12orEarlier Identifier of a protein domain (or other node) from the SCOP database. @@ -4228,8 +4363,8 @@ URL - Moby:Link beta12orEarlier + Moby:Link Moby:URL A Uniform Resource Locator (URL). @@ -4244,8 +4379,8 @@ URN - beta12orEarlier A Uniform Resource Name (URN). + beta12orEarlier @@ -4322,7 +4457,7 @@ File name extension beta12orEarlier - A file extension is the characters appearing after the final '.' in the file name. + A file extension is the characters appearing after the final '.' in the file name. The extension of a file name. @@ -4516,8 +4651,8 @@ beta12orEarlier - An identifier of a comparison matrix. Substitution matrix identifier + An identifier of a comparison matrix. @@ -4664,8 +4799,8 @@ - Unique name of a codon usage table. beta12orEarlier + Unique name of a codon usage table. @@ -4811,12 +4946,6 @@ Workflow ID - - - - - - Identifier of a biological or biomedical workflow, typically from a database of workflows. beta12orEarlier @@ -4854,8 +4983,8 @@ - beta12orEarlier Identifier of a mathematical model, typically an entry from a database. + beta12orEarlier Biological model identifier @@ -4876,10 +5005,10 @@ - beta12orEarlier Small molecule identifier Identifier of an entry from a database of chemicals. Chemical compound identifier + beta12orEarlier @@ -4917,9 +5046,9 @@ + Article identifier Unique identifier of a scientific article. beta12orEarlier - Article identifier @@ -4934,8 +5063,8 @@ FlyBase ID - FB[a-zA-Z_0-9]{2}[0-9]{7} beta12orEarlier + FB[a-zA-Z_0-9]{2}[0-9]{7} Identifier of an object from the FlyBase database. @@ -4966,7 +5095,7 @@ WormBase class - A WormBase class describes the type of object such as 'sequence' or 'protein'. + A WormBase class describes the type of object such as 'sequence' or 'protein'. Class of an object from the WormBase database. beta12orEarlier @@ -4997,15 +5126,15 @@ - Sequence type - - + DEP_Sequence type + beta12orEarlier + true A label (text token) describing a type of molecular sequence. Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). - - - + 1.5 + + @@ -5093,8 +5222,8 @@ UniProt accession (extended) - Q7M1G0|P43353-2|P01012.107 1.0 + Q7M1G0|P43353-2|P01012.107 beta12orEarlier [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]+ Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. @@ -5116,10 +5245,10 @@ + PIR accession number PIR ID beta12orEarlier An identifier of PIR sequence database entry. - PIR accession number @@ -5236,7 +5365,7 @@ See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. true beta12orEarlier - + @@ -5245,13 +5374,14 @@ - EMBOSS listfile - + DEP_EMBOSS listfile + beta12orEarlier + true List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). - - - + 1.5 + + @@ -5327,8 +5457,8 @@ A sequence profile typically represents a sequence alignment. - Identifier of a sequence profile. beta12orEarlier + Identifier of a sequence profile. @@ -5357,8 +5487,8 @@ Prosite accession number - PS[0-9]{5} Prosite ID + PS[0-9]{5} Accession number of an entry from the Prosite database. beta12orEarlier @@ -5408,15 +5538,15 @@ - Sequence alignment type - - + DEP_Sequence alignment type + A label (text token) describing the type of a sequence alignment. Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. + true + 1.5 beta12orEarlier - - - + + @@ -5430,7 +5560,7 @@ beta12orEarlier beta12orEarlier true - + @@ -5439,15 +5569,16 @@ - Phylogenetic tree type - + DEP_Phylogenetic tree type + nj|upgmp + 1.5 A label (text token) describing the type of a phylogenetic tree. + true beta12orEarlier - For example 'nj', 'upgmp' etc. - - - + For example 'nj', 'upgmp' etc. + + @@ -5485,17 +5616,17 @@ - Comparison matrix type - - - For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. + DEP_Comparison matrix type + + For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. Substitution matrix type A label (text token) describing the type of a comparison matrix. - beta12orEarlier blosum|pam|gonnet|id - - - + beta12orEarlier + true + 1.5 + + @@ -5529,10 +5660,10 @@ PDB ID - [a-zA-Z_0-9]{4} beta12orEarlier PDB identifier PDBID + [a-zA-Z_0-9]{4} An identifier of an entry from the PDB database. @@ -5884,8 +6015,8 @@ GermOnline ID - beta12orEarlier Identifier of an entry from the GermOnline database. + beta12orEarlier @@ -5998,10 +6129,10 @@ Pathway ID (reactome) - beta12orEarlier REACT_[0-9]+(\.[0-9]+)? - Identifier of an entry from the Reactome database. + beta12orEarlier Reactome ID + Identifier of an entry from the Reactome database. @@ -6117,14 +6248,14 @@ - + MIR:[0-9]{8} MIR:00100005 Unique identifier of a MIRIAM data resource. - This is the identifier used internally by MIRIAM for a data type. beta12orEarlier + This is the identifier used internally by MIRIAM for a data type. @@ -6141,7 +6272,7 @@ - + The name of a data type from the MIRIAM database. @@ -6163,7 +6294,7 @@ - + urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 @@ -6185,8 +6316,8 @@ MIRIAM data type primary name The primary name of a data type from the MIRIAM database. - The primary name of a MIRIAM data type is taken from a controlled vocabulary. UniProt|Enzyme Nomenclature + The primary name of a MIRIAM data type is taken from a controlled vocabulary. beta12orEarlier @@ -6194,8 +6325,8 @@ + A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. UniProt|Enzyme Nomenclature - A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. @@ -6435,8 +6566,8 @@ beta12orEarlier Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. - An identifier of a concept from Foundational Model of Anatomy. FMA:[0-9]+ + An identifier of a concept from Foundational Model of Anatomy. @@ -6597,7 +6728,7 @@ BLAST name beta12orEarlier The name of a BLAST tool. - This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. + This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. @@ -6611,7 +6742,7 @@ Tool name (FASTA) - This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. + This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. The name of a FASTA tool. beta12orEarlier @@ -6717,8 +6848,8 @@ QSAR descriptor (molecular) - QSAR molecular descriptor beta12orEarlier + QSAR molecular descriptor A QSAR molecular descriptor. @@ -6746,7 +6877,6 @@ Sequence set (nucleic acid) - Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. beta12orEarlier @@ -6764,13 +6894,13 @@ - + - + beta12orEarlier @@ -6791,7 +6921,7 @@ A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. true beta12orEarlier - A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. + A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. beta12orEarlier @@ -6929,8 +7059,8 @@ Sequence cluster (protein) - beta12orEarlier A cluster of protein sequences. + beta12orEarlier The sequences are typically related, for example a family of sequences. Protein sequence cluster @@ -6946,8 +7076,8 @@ Sequence cluster (nucleic acid) - beta12orEarlier The sequences are typically related, for example a family of sequences. + beta12orEarlier Nucleotide sequence cluster A cluster of nucleotide sequences. @@ -6961,9 +7091,9 @@ Sequence length - + + The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths. beta12orEarlier - The size (length) of a sequence, subsequence or region in a sequence. @@ -6974,15 +7104,16 @@ - Word size - + DEP_Word size + beta12orEarlier + true Size of a sequence word. + 1.5 Word length Word size is used for example in word-based sequence database search methods. - - - + + @@ -6990,14 +7121,15 @@ - Window size - + DEP_Window size + Size of a sequence window. beta12orEarlier A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. - - - + true + 1.5 + + @@ -7005,13 +7137,14 @@ - Sequence length range - - Specification of range(s) of length of sequences. + DEP_Sequence length range + + 1.5 beta12orEarlier - - - + Specification of range(s) of length of sequences. + true + + @@ -7025,7 +7158,6 @@ beta12orEarlier beta12orEarlier Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. - @@ -7050,9 +7182,9 @@ - Feature record - - Sequence features + Sequence features + + Feature record Features Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. General sequence features @@ -7106,8 +7238,8 @@ beta12orEarlier true - A report of general sequence properties derived from nucleotide sequence data. beta12orEarlier + A report of general sequence properties derived from nucleotide sequence data. @@ -7117,7 +7249,7 @@ - Sequence complexity + Sequence complexity (report) Sequence property (complexity) beta12orEarlier @@ -7132,7 +7264,7 @@ - Sequence ambiguity + Sequence ambiguity (report) beta12orEarlier Sequence property (ambiguity) @@ -7147,7 +7279,7 @@ - Sequence composition + Sequence composition (report) Sequence property (composition) A report (typically a table) on character or word composition / frequency of a molecular sequence(s). @@ -7176,9 +7308,9 @@ - Sequence composition (base position variability) + Base position variability plot - Report on or plot of third base position variability in a nucleotide sequence. + A plot of third base position variability in a nucleotide sequence. beta12orEarlier @@ -7205,7 +7337,8 @@ - Sequence composition (base frequencies) + Base frequencies table + A table of base frequencies of a nucleotide sequence. beta12orEarlier @@ -7219,10 +7352,11 @@ - Sequence composition (base words) + Base word frequencies table + - A table of word composition of a nucleotide sequence. beta12orEarlier + A table of word composition of a nucleotide sequence. @@ -7233,10 +7367,11 @@ - Amino acid frequencies + Amino acid frequencies table + - A table of amino acid frequencies of a protein sequence. beta12orEarlier + A table of amino acid frequencies of a protein sequence. Sequence composition (amino acid frequencies) @@ -7248,7 +7383,8 @@ - Amino acid word frequencies + Amino acid word frequencies table + beta12orEarlier Sequence composition (amino acid words) @@ -7278,11 +7414,11 @@ - Sequence feature table + Feature table - Feature table Annotation of positional sequence features, organized into a standard feature table. beta12orEarlier + Sequence feature table @@ -7294,7 +7430,7 @@ Map - + @@ -7317,11 +7453,11 @@ Nucleic acid features - Feature table (nucleic acid) - Nucleic acid feature table - Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence). This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. + Feature table (nucleic acid) beta12orEarlier + Nucleic acid feature table + An informative report on intrinsic positional features of a nucleotide sequence. @@ -7336,10 +7472,10 @@ Protein feature table - This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. Feature table (protein) - Protein sequence-specific feature annotation (positional features of a protein sequence). + This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. beta12orEarlier + An informative report on intrinsic positional features of a protein sequence. @@ -7580,11 +7716,10 @@ - Sequence features (motifs) - + Sequence motif matches + Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. beta12orEarlier - Use this concept if another, more specific concept is not available. @@ -7595,15 +7730,17 @@ - Sequence features (repeats) - + DEP_Sequence features (repeats) + Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. The report might include derived data map such as classification, annotation, organization, periodicity etc. Repeat sequence map + 1.5 + true beta12orEarlier - - - + + + @@ -7611,15 +7748,14 @@ - Nucleic acid features (gene and transcript structure) - - + DEP_Gene and transcript structure (report) + + true A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. beta12orEarlier - Gene annotation (structure) - - - + 1.5 + + @@ -7627,8 +7763,9 @@ - Nucleic acid features (mobile genetic elements) + Mobile genetic elements (report) + Nucleic acid features (mobile genetic elements) beta12orEarlier A report on a region of a nucleic acid sequence containin mobile genetic elements. Nucleic acid features (transposons) @@ -7643,9 +7780,10 @@ - Nucleic acid features (PolyA signal or site) + PolyA signal or sites (report) beta12orEarlier + Nucleic acid features (PolyA signal or site) A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. 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. PolyA site @@ -7660,13 +7798,14 @@ - Nucleic acid features (quadruplexes) - + DEP_Nucleic acid features (quadruplexes) + beta12orEarlier A report on quadruplex-forming motifs in a nucleotide sequence. - - - + 1.5 + true + + @@ -7674,10 +7813,11 @@ - Nucleic acid features (CpG island and isochore) - + CpG island and isochore (report) + A report or plot of CpG rich regions (isochores) in a nucleotide sequence. beta12orEarlier + Nucleic acid features (CpG island and isochore) @@ -7688,9 +7828,11 @@ - Nucleic acid features (restriction sites) + Restriction sites (report) + Nucleic acid features (restriction sites) Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. + Nucleic acid restriction sites (report) beta12orEarlier @@ -7702,10 +7844,11 @@ - Nucleic acid features (nucleosome exclusion sequences) + Nucleosome exclusion sequences (report) A report on nucleosome formation potential or exclusion sequence(s). beta12orEarlier + Nucleic acid features (nucleosome exclusion sequences) @@ -7716,12 +7859,13 @@ - Nucleic acid features (splice sites) + Splice sites (report) Nucleic acid report (RNA splicing) + Nucleic acid features (splice sites) Nucleic acid report (RNA splice model) - beta12orEarlier A report on splice sites in a nucleotide sequence or alternative RNA splicing events. + beta12orEarlier @@ -7732,8 +7876,9 @@ - Nucleic acid features (matrix/scaffold attachment sites) - + Matrix/scaffold attachment sites (report) + + Nucleic acid features (matrix/scaffold attachment sites) beta12orEarlier A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. @@ -7761,19 +7906,14 @@ - Nucleic acid features (microRNA) - - - - - - - + DEP_Nucleic acid features (microRNA) + + 1.5 A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. beta12orEarlier - - - + true + + @@ -7781,10 +7921,11 @@ - Nucleic acid features (operon) - + Operon (report) + beta12orEarlier A report on operons (operators, promoters and genes) from a bacterial genome. + Nucleic acid features (operon) The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. Gene features (operon) @@ -7797,10 +7938,11 @@ - Gene features (promoter) - + Promoters (report) + beta12orEarlier 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. + Nucleic acid features (promoters) @@ -7811,9 +7953,10 @@ - Nucleic acid features (coding sequence) + Coding region (report) Gene features (coding sequence) + Nucleic acid features (coding sequence) Gene annotation (translation) beta12orEarlier Gene features (coding region) @@ -7831,10 +7974,10 @@ Gene features (SECIS element) true - beta13 A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. + beta13 beta12orEarlier - + @@ -7843,7 +7986,7 @@ - Gene features (TFBS) + Transcription factor binding sites (report) @@ -7853,7 +7996,9 @@ A report on the transcription factor binding sites (TFBS) in a DNA sequence. + TFBS (report) beta12orEarlier + Nucleic acid features (TFBS) @@ -7964,8 +8109,8 @@ true Epitope mapping is commonly done during vaccine design. beta12orEarlier - A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. beta13 + A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. @@ -7991,8 +8136,8 @@ MHC Class I epitopes report - true A report on epitopes that bind to MHC class I molecules. + true beta12orEarlier beta12orEarlier @@ -8021,9 +8166,9 @@ Protein features (PEST sites) - true + 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. beta13 - 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. + true A report or plot of PEST sites in a protein sequence. beta12orEarlier @@ -8097,8 +8242,8 @@ MEME background frequencies file - beta12orEarlier beta12orEarlier + beta12orEarlier true MEME background frequencies file. @@ -8155,13 +8300,14 @@ - Regular expression - + DEP_Regular expression + beta12orEarlier + true + 1.5 Regular expression pattern. - - - + + @@ -8170,7 +8316,7 @@ Sequence motif - + @@ -8190,7 +8336,7 @@ Sequence profile - + @@ -8211,10 +8357,15 @@ Protein signature - - beta12orEarlier + + Protein domain signature InterPro entry + Protein family signature + beta12orEarlier + Protein site signature + Protein region signature An entry (sequence classifier and associated data) from the InterPro database. + Protein repeat signature @@ -8229,8 +8380,8 @@ beta12orEarlier true - A nucleotide regular expression pattern from the Prosite database. beta12orEarlier + A nucleotide regular expression pattern from the Prosite database. @@ -8257,8 +8408,8 @@ Position frequency matrix - PFM A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. + PFM beta12orEarlier @@ -8360,14 +8511,15 @@ - Protein family signature - + DEP_Protein family signature + A protein family signature (sequence classifier) from the InterPro database. + 1.5 + true beta12orEarlier Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. - - - + + @@ -8375,14 +8527,15 @@ - Protein domain signature - + DEP_Protein domain signature + Protein domain signatures identify structural or functional domains or other units with defined boundaries. A protein domain signature (sequence classifier) from the InterPro database. + true + 1.5 beta12orEarlier - - - + + @@ -8390,14 +8543,15 @@ - Protein region signature - + DEP_Protein region signature + A protein region signature defines a region which cannot be described as a protein family or domain signature. + 1.5 beta12orEarlier + true A protein region signature (sequence classifier) from the InterPro database. - - - + + @@ -8405,14 +8559,15 @@ - Protein repeat signature - + DEP_Protein repeat signature + A protein repeat signature (sequence classifier) from the InterPro database. beta12orEarlier A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. - - - + 1.5 + true + + @@ -8420,14 +8575,15 @@ - Protein site signature - + DEP_Protein site signature + + 1.5 + true A protein site signature (sequence classifier) from the InterPro database. beta12orEarlier A protein site signature is a classifier for a specific site in a protein. - - - + + @@ -8442,7 +8598,7 @@ 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. true 1.4 - + @@ -8456,9 +8612,9 @@ beta12orEarlier 1.4 true - A protein active site signature (sequence classifier) from the InterPro database. A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. - + A protein active site signature (sequence classifier) from the InterPro database. + @@ -8474,7 +8630,7 @@ true A protein binding site signature (sequence classifier) from the InterPro database. 1.4 - + @@ -8490,7 +8646,7 @@ 1.4 A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. A protein post-translational modification signature (sequence classifier) from the InterPro database. - + @@ -8531,7 +8687,6 @@ Sequence alignment (nucleic acid) - Alignment of multiple nucleotide sequences. beta12orEarlier @@ -8650,8 +8805,7 @@ Alignment score or penalty - - + A simple floating point number defining the penalty for opening or extending a gap in an alignment. beta12orEarlier @@ -8685,7 +8839,7 @@ true beta12orEarlier beta12orEarlier - + @@ -8740,7 +8894,7 @@ beta12orEarlier true - 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. + 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. beta12orEarlier @@ -8754,7 +8908,7 @@ Match reward score - The score for a 'match' used in various sequence database search applications with simple scoring schemes. + The score for a 'match' used in various sequence database search applications with simple scoring schemes. beta12orEarlier @@ -8768,7 +8922,7 @@ Mismatch penalty score - The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. + The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. beta12orEarlier @@ -8886,7 +9040,7 @@ Terminal gap opening penalty - 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. + 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. beta12orEarlier @@ -8901,7 +9055,7 @@ Terminal gap extension penalty beta12orEarlier - A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + 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. @@ -8958,10 +9112,10 @@ Sequence alignment report (site conservation) - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. true - Data on character conservation in a molecular sequence alignment. + 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. 1.4 + Data on character conservation in a molecular sequence alignment. beta12orEarlier @@ -9002,13 +9156,14 @@ - Sequence-profile alignment (HMM) - + DEP_Sequence-profile alignment (HMM) + Alignment of molecular sequence(s) to a hidden Markov model(s). + true + 1.5 beta12orEarlier - - - + + @@ -9016,13 +9171,14 @@ - Sequence-profile alignment (fingerprint) - + DEP_Sequence-profile alignment (fingerprint) + + true beta12orEarlier + 1.5 Alignment of molecular sequences to a protein fingerprint from the PRINTS database. - - - + + @@ -9099,15 +9255,18 @@ - Phylogenetic tree report - - A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. - beta12orEarlier + DEP_Phylogenetic report + + true This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. Phylogenetic tree-derived report - - - + Phylogenetic report + 1.5 + Phylogenetic tree report + A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. + beta12orEarlier + + @@ -9138,7 +9297,7 @@ 1.4 true beta12orEarlier - + @@ -9153,7 +9312,7 @@ 1.4 true beta12orEarlier - + @@ -9163,7 +9322,7 @@ Phylogenetic tree distances - + Distances, such as Branch Score distance, between two or more phylogenetic trees. Phylogenetic tree report (tree distances) beta12orEarlier @@ -9183,7 +9342,7 @@ true 1.4 beta12orEarlier - + @@ -9210,8 +9369,8 @@ Comparison matrix (integers) true - beta12orEarlier Matrix of integer numbers for sequence comparison. + beta12orEarlier Substitution matrix (integers) beta12orEarlier @@ -9260,6 +9419,7 @@ Amino acid substitution matrix Matrix of integer or floating point numbers for amino acid comparison. beta12orEarlier + Amino acid comparison matrix @@ -9289,8 +9449,8 @@ Nucleotide comparison matrix (floats) Nucleotide substitution matrix (floats) - Matrix of floating point numbers for nucleotide comparison. beta12orEarlier + Matrix of floating point numbers for nucleotide comparison. true beta12orEarlier @@ -9336,12 +9496,12 @@ Protein features (membrane regions) + Transmembrane region report + Protein report (membrane protein) An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. beta12orEarlier Intramembrane region report - Transmembrane region report - Protein report (membrane protein) @@ -9377,13 +9537,13 @@ - + - + beta12orEarlier @@ -9400,7 +9560,7 @@ Protein-ligand complex - This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. + 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. beta12orEarlier The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule. @@ -9418,13 +9578,13 @@ - + - + 3D coordinate and associated data for a carbohydrate (3D) structure. @@ -9474,7 +9634,7 @@ - RNA structure record + RNA structure @@ -9494,7 +9654,7 @@ - tRNA structure record + tRNA structure beta12orEarlier 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. @@ -9542,13 +9702,14 @@ - Protein structure (all atoms) - + DEP_Protein structure (all atoms) + 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). + true + 1.5 beta12orEarlier - - - + + @@ -9556,14 +9717,15 @@ - Protein structure (C-alpha atoms) - + DEP_Protein structure (C-alpha atoms) + + 1.5 beta12orEarlier + true C-beta atoms from amino acid side-chains may be included. 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). - - - + + @@ -9578,7 +9740,6 @@ beta12orEarlier 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). - @@ -9595,7 +9756,6 @@ 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). true - @@ -9611,7 +9771,6 @@ beta12orEarlier 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). - @@ -9628,7 +9787,6 @@ true C-beta atoms from amino acid side-chains may be included. - @@ -9639,6 +9797,7 @@ Structure alignment (pair) + Pair structure alignment beta12orEarlier Alignment (superimposition) of exactly two molecular tertiary (3D) structures. @@ -9671,6 +9830,7 @@ Alignment (superimposition) of protein tertiary (3D) structures. beta12orEarlier + Protein structure alignment @@ -9683,7 +9843,7 @@ Structure alignment (nucleic acid) - + Nucleic acid structure alignment Alignment (superimposition) of nucleic acid tertiary (3D) structures. beta12orEarlier @@ -9701,7 +9861,7 @@ Alignment (superimposition) of exactly two protein tertiary (3D) structures. beta12orEarlier - Pairwise protein structural alignment + Protein pair structural alignment @@ -9727,13 +9887,14 @@ - Structure alignment (protein all atoms) - + DEP_Structure alignment (protein all atoms) + + true beta12orEarlier Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). - - - + 1.5 + + @@ -9741,15 +9902,16 @@ - Structure alignment (protein C-alpha atoms) - + DEP_Structure alignment (protein C-alpha atoms) + beta12orEarlier + true C-alpha trace + 1.5 C-beta atoms from amino acid side-chains may be considered. Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). - - - + + @@ -9763,7 +9925,7 @@ beta12orEarlier true Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). - + @@ -9779,7 +9941,7 @@ beta12orEarlier true C-beta atoms from amino acid side-chains may be included. - + @@ -9794,7 +9956,7 @@ Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). true beta12orEarlier - + @@ -9810,7 +9972,7 @@ true Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). beta12orEarlier - + @@ -9823,6 +9985,7 @@ Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. + Nucleic acid pair structure alignment beta12orEarlier @@ -9853,6 +10016,7 @@ beta12orEarlier Alignment (superimposition) of RNA tertiary (3D) structures. + RNA structure alignment @@ -9971,6 +10135,7 @@ beta12orEarlier Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. + Chemical classes (amino acids) @@ -9985,6 +10150,7 @@ beta12orEarlier Statistical protein contact potentials. + Contact potentials (amino acid pair-wise) @@ -9998,6 +10164,7 @@ Amino acid index (molecular weight) beta12orEarlier + Molecular weight (amino acids) Molecular weights of amino acids. @@ -10011,6 +10178,7 @@ Amino acid index (hydropathy) + Hydropathy (amino acids) beta12orEarlier Hydrophobic, hydrophilic or charge properties of amino acids. @@ -10026,6 +10194,7 @@ Amino acid index (White-Wimley data) Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. + White-Wimley data (amino acids) beta12orEarlier @@ -10041,6 +10210,7 @@ beta12orEarlier Van der Waals radii of atoms for different amino acid residues. + van der Waals radii (amino acids) @@ -10051,21 +10221,16 @@ - Enzyme property - - - - - - - + DEP_Enzyme report + An informative report on a specific enzyme. Enzyme report beta12orEarlier Protein report (enzyme) - - - + 1.5 + true + + @@ -10073,17 +10238,18 @@ - Restriction enzyme property - + DEP_Restriction enzyme report + + true Restriction enzyme report Protein report (restriction enzyme) This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. + 1.5 beta12orEarlier Restriction enzyme pattern data An informative report on a specific restriction enzyme such as enzyme reference data. - - - + + @@ -10297,8 +10463,8 @@ Protein subcellular localization beta13 - beta12orEarlier true + beta12orEarlier An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). Protein report (subcellular localization) @@ -10331,8 +10497,8 @@ beta12orEarlier true - A report on the immunogenicity of MHC class I or class II binding peptides. beta13 + A report on the immunogenicity of MHC class I or class II binding peptides. @@ -10347,8 +10513,8 @@ Protein structure report (domain) Protein report (structure) - Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains. beta12orEarlier + Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains. Protein property (structural) This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure). Protein structure-derived report @@ -10370,8 +10536,8 @@ Protein report (structural quality) Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. Protein property (structural quality) - Protein structure report (quality evaluation) Protein structure validation report + Protein structure report (quality evaluation) Report on the quality of a protein three-dimensional model. @@ -10384,17 +10550,16 @@ Protein residue interactions - - + - 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. Atom interaction data beta12orEarlier + 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. Residue interaction data @@ -10442,8 +10607,8 @@ Protein surface report - beta12orEarlier true + beta12orEarlier Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. 1.4 Protein structure report (surface) @@ -10557,15 +10722,16 @@ - CATH node - + DEP_DEP_CATH node + CATH classification node report + true beta12orEarlier - Information on a node from the CATH database. + 1.5 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. - - - + Information on a node from the CATH database. + + @@ -10573,14 +10739,15 @@ - SCOP node - + DEP_DEP_SCOP node + beta12orEarlier + 1.5 Information on a node from the SCOP database. SCOP classification node - - - + true + + @@ -10594,7 +10761,6 @@ true beta12orEarlier beta12orEarlier - @@ -10603,13 +10769,14 @@ - CATH class - - Information on a protein 'class' node from the CATH database. + DEP_CATH class + + true + Information on a protein 'class' node from the CATH database. + 1.5 beta12orEarlier - - - + + @@ -10617,13 +10784,14 @@ - CATH architecture - - Information on a protein 'architecture' node from the CATH database. + DEP_CATH architecture + + true + Information on a protein 'architecture' node from the CATH database. + 1.5 beta12orEarlier - - - + + @@ -10631,13 +10799,14 @@ - CATH topology - + DEP_CATH topology + beta12orEarlier - Information on a protein 'topology' node from the CATH database. - - - + Information on a protein 'topology' node from the CATH database. + 1.5 + true + + @@ -10645,13 +10814,14 @@ - CATH homologous superfamily - - Information on a protein 'homologous superfamily' node from the CATH database. + DEP_CATH homologous superfamily + + Information on a protein 'homologous superfamily' node from the CATH database. beta12orEarlier - - - + true + 1.5 + + @@ -10659,13 +10829,14 @@ - CATH structurally similar group - - Information on a protein 'structurally similar group' node from the CATH database. + DEP_CATH structurally similar group + + Information on a protein 'structurally similar group' node from the CATH database. beta12orEarlier - - - + true + 1.5 + + @@ -10673,13 +10844,14 @@ - CATH functional category - + DEP_CATH functional category + beta12orEarlier - Information on a protein 'functional category' node from the CATH database. - - - + 1.5 + true + Information on a protein 'functional category' node from the CATH database. + + @@ -10703,7 +10875,7 @@ - Protein-protein interaction + Protein-protein interaction report @@ -10714,7 +10886,7 @@ For example, an informative report about a specific protein complex (of multiple polypeptide chains). Protein structure report (protein complex) beta12orEarlier - Data on protein-protein interaction(s). + An informative report on protein-protein interaction(s). @@ -10725,16 +10897,10 @@ - Protein-ligand interaction + Protein-ligand interaction report - - - - - - + An informative report on protein-ligand (small molecule) interaction(s). beta12orEarlier - Data on protein-ligand (small molecule) interaction(s). @@ -10745,16 +10911,10 @@ - Protein-nucleic acid interaction + Protein-nucleic acid interaction report - - - - - - - Data on protein-DNA/RNA interaction(s). beta12orEarlier + An informative report on protein-DNA/RNA interaction(s). @@ -10884,8 +11044,8 @@ Vienna RNA parameters beta12orEarlier - true beta12orEarlier + true RNA parameters used by the Vienna package. @@ -10915,8 +11075,8 @@ beta12orEarlier true - RNA concentration data used by the Vienna package. beta12orEarlier + RNA concentration data used by the Vienna package. @@ -10959,8 +11119,8 @@ Nucleic acid folding report This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Nucleic acid report (folding model) A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. + Nucleic acid report (folding model) beta12orEarlier Nucleic acid report (folding) @@ -10974,7 +11134,7 @@ Codon usage table - + @@ -10995,7 +11155,7 @@ Genetic code - + A genetic code need not include detailed codon usage information. A genetic code for an organism. beta12orEarlier @@ -11069,7 +11229,7 @@ - Pharmacogenomic annotation + Pharmacogenomic test report Data on the influence of genotype on drug response. The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. @@ -11106,9 +11266,11 @@ - Gene annotation (linkage disequilibrium) + Linkage disequilibrium (report) + Genetic linkage disequilibrium (report) beta12orEarlier + Gene annotation (linkage disequilibrium) A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). @@ -11121,7 +11283,8 @@ Heat map - + + A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. beta12orEarlier A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. @@ -11181,11 +11344,12 @@ - Pathway or network (metabolic) - + Metabolic pathway report + A report typically including a map (diagram) of a metabolic pathway. beta12orEarlier This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. + Pathway or network (metabolic) @@ -11196,8 +11360,9 @@ - Pathway or network (genetic information processing) - + Genetic information processing pathway + + Pathway or network (genetic information processing) A report typically including a map (diagram) of a genetic information processing pathway. beta12orEarlier @@ -11210,10 +11375,11 @@ - Pathway or network (environmental information processing) - + Environmental information processing pathway + beta12orEarlier A report typically including a map (diagram) of an environmental information processing pathway. + Pathway or network (environmental information processing) @@ -11224,10 +11390,11 @@ - Pathway or network (signal transduction) - + Signal transduction pathway report + beta12orEarlier A report typically including a map (diagram) of a signal transduction pathway. + Pathway or network (signal transduction) @@ -11239,7 +11406,8 @@ Pathway or network (cellular process) - + Cellular process pathway + beta12orEarlier A report typically including a map (diagram) of a cellular process pathway. @@ -11252,10 +11420,11 @@ - Pathway or network (disease) - + Disease pathway report + A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease. beta12orEarlier + Pathway or network (disease) @@ -11266,8 +11435,8 @@ - Pathway or network (drug structure relationship) - + Drug structure relationship map + beta12orEarlier A report typically including a map (diagram) of drug structure relationships. @@ -11280,9 +11449,11 @@ - Pathway or network (protein-protein interaction) - + Protein interaction network + + beta12orEarlier + Pathway or network (protein-protein interaction) A report typically including a map (diagram) of a network of protein interactions. @@ -11294,14 +11465,15 @@ - MIRIAM datatype - + DEP_MIRIAM datatype + + 1.5 + true beta12orEarlier An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. 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. - - - + + @@ -11355,15 +11527,15 @@ - Database version information - - + DEP_Database version information + beta12orEarlier Information on a database (or ontology) version, for example name, version number and release date. + 1.5 Ontology version information - - - + true + + @@ -11371,14 +11543,14 @@ - Tool version information - - - beta12orEarlier + DEP_Tool version information + + 1.5 + true Information on an application version, for example name, version number and release date. - - - + beta12orEarlier + + @@ -11392,7 +11564,7 @@ true beta12orEarlier beta12orEarlier - + @@ -11431,14 +11603,15 @@ - Job status - - 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). + DEP_Job status + + 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). + true + 1.5 beta12orEarlier Metadata on the status of a submitted job. - - - + + @@ -11452,7 +11625,6 @@ beta12orEarlier The (typically numeric) unique identifier of a submitted job. 1.0 - @@ -11461,13 +11633,14 @@ - Job type - + DEP_Job type + A label (text token) describing the type of job, for example interactive or non-interactive. beta12orEarlier - - - + true + 1.5 + + @@ -11475,13 +11648,14 @@ - Tool log - + DEP_Tool log + beta12orEarlier + true A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages. - - - + 1.5 + + @@ -11493,9 +11667,9 @@ beta12orEarlier DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. - true beta12orEarlier - + true + @@ -11511,6 +11685,7 @@ true STRIDE log file. + @@ -11526,6 +11701,7 @@ beta12orEarlier beta12orEarlier + @@ -11540,7 +11716,7 @@ beta12orEarlier beta12orEarlier EMBOSS wordfinder log file. - + @@ -11555,7 +11731,7 @@ beta12orEarlier EMBOSS (EMBASSY) domainatrix application log file. beta12orEarlier - + @@ -11570,7 +11746,7 @@ beta12orEarlier beta12orEarlier true - + @@ -11585,7 +11761,7 @@ beta12orEarlier beta12orEarlier EMBOSS (EMBASSY) supermatcher error file. - + @@ -11600,7 +11776,7 @@ EMBOSS megamerger log file. beta12orEarlier beta12orEarlier - + @@ -11615,7 +11791,7 @@ EMBOSS megamerger log file. true beta12orEarlier - + @@ -11630,7 +11806,7 @@ beta12orEarlier beta12orEarlier true - + @@ -11701,13 +11877,14 @@ - Number of iterations - + DEP_Number of iterations + beta12orEarlier + true Number of iterations of an algorithm. - - - + 1.5 + + @@ -11715,13 +11892,14 @@ - Number of output entities - + DEP_Number of output entities + + true beta12orEarlier + 1.5 Number of entities (for example database hits, sequences, alignments etc) to write to an output file. - - - + + @@ -11736,6 +11914,7 @@ beta12orEarlier Controls the order of hits (reported matches) in an output file from a database search. + @@ -11767,11 +11946,10 @@ Phylogenetic tree image - - See also 'Phylogenetic tree' - beta12orEarlier + See also 'Phylogenetic tree' 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. + beta12orEarlier @@ -11783,9 +11961,9 @@ RNA secondary structure image - - beta12orEarlier + Image of RNA secondary structure, knots, pseudoknots etc. + beta12orEarlier @@ -11797,7 +11975,7 @@ Protein secondary structure image - + beta12orEarlier Image of protein secondary structure. @@ -11811,7 +11989,6 @@ Structure image - Image of one or more molecular tertiary (3D) structures. beta12orEarlier @@ -11826,7 +12003,6 @@ Sequence alignment image - Image of two or more aligned molecular sequences possibly annotated with alignment features. beta12orEarlier @@ -11840,14 +12016,12 @@ - Structure image (small molecule) - + Chemical structure image beta12orEarlier Small molecule structure image The molecular identifier and formula are typically included. An image of the structure of a small chemical compound. - Chemical structure image @@ -11859,9 +12033,16 @@ Fate map - - beta12orEarlier + + + + + + + + A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. + beta12orEarlier @@ -11873,8 +12054,8 @@ Microarray spots image - - + + An image of spots from a microarray experiment. beta12orEarlier @@ -11971,8 +12152,8 @@ A term from the Plant Ontology (PO). beta12orEarlier - beta12orEarlier true + beta12orEarlier @@ -12032,8 +12213,8 @@ beta12orEarlier true - beta12orEarlier A term from the ChEBI ontology. + beta12orEarlier @@ -12045,8 +12226,8 @@ MGED - A term from the MGED ontology. beta12orEarlier + A term from the MGED ontology. true beta12orEarlier @@ -12122,13 +12303,14 @@ - Ontology relation type - + DEP_Ontology relation type + A relation type defined in an ontology. + true beta12orEarlier - - - + 1.5 + + @@ -12367,10 +12549,10 @@ PDB model number WHATIF: model_number - beta12orEarlier - Identifier of a model structure from a PDB file. Model number PDBML:pdbx_PDB_model_num + beta12orEarlier + Identifier of a model structure from a PDB file. @@ -12384,12 +12566,12 @@ CATH domain report - The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. Summary of domain classification information for a CATH domain. - true + 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. beta13 + true beta12orEarlier - + @@ -12458,9 +12640,9 @@ - Sequence version information - - + Sequence version + + Sequence version information Information on an molecular sequence version. beta12orEarlier @@ -12473,10 +12655,10 @@ - Score or penalty - - A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty). + Score + beta12orEarlier + A numerical value, that is some type of scored value arising for example from a prediction method. @@ -12492,7 +12674,7 @@ beta12orEarlier Report on general functional properties of specific protein(s). beta13 - For properties that can be mapped to a sequence, use 'Sequence report' instead. + For properties that can be mapped to a sequence, use 'Sequence report' instead. true @@ -12557,8 +12739,8 @@ true 1.3 EcoGene primary gene name - http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G Primary name of a gene from EcoGene Database. + http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G @@ -12758,9 +12940,9 @@ Gene ID (GeneDB Leishmania major) - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor - beta12orEarlier beta13 + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor true Gene identifier from Leishmania major GeneDB database. @@ -12793,8 +12975,8 @@ Gene identifier from Schizosaccharomyces pombe GeneDB database. beta13 true - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe @@ -13018,7 +13200,7 @@ Deletion-based cytogenetic map A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. beta12orEarlier - A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. + 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. @@ -13059,11 +13241,11 @@ - Map set + Map set data Moby:GCP_CorrelatedMapSet - Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. Moby:GCP_CorrelatedLinkageMapSet + Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. beta12orEarlier @@ -13077,7 +13259,7 @@ Map feature - Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. + Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. beta12orEarlier Moby:MapFeature A feature which may mapped (positioned) on a genetic or other type of map. @@ -13094,15 +13276,15 @@ - Map type - - + DEP_Map type + beta12orEarlier - Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. + true + 1.5 + Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. A designation of the type of map (genetic map, physical map, sequence map etc) or map set. - - - + + @@ -13131,8 +13313,8 @@ The name of a group of organisms belonging to the same taxonomic rank. For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. Taxonomic rank - Taxonomy rank beta12orEarlier + Taxonomy rank Moby:PotentialTaxon @@ -13186,7 +13368,7 @@ Moby:TaxonTCS Moby:TaxonScientificName Taxonomic information - 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. + Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. Taxonomic name Moby:iANT_organism-xml The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. @@ -13284,8 +13466,8 @@ Acronym beta12orEarlier - An abbreviation of a phrase or word. beta12orEarlier + An abbreviation of a phrase or word. true @@ -13344,7 +13526,6 @@ Annotated URI - Moby:DescribedLink A URI along with annotation describing the data found at the address. beta12orEarlier @@ -13495,8 +13676,8 @@ GeneFarm gene ID Moby_namespace:GENEFARM_GeneName Name of a gene from the GeneFarm database. - 1.3 true + 1.3 @@ -13555,8 +13736,8 @@ Identifier for loci from ASPGD (Aspergillus Genome Database). http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID - beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD + beta12orEarlier @@ -13570,8 +13751,8 @@ Locus ID (MGG) - http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG Identifier for loci from Magnaporthe grisea Database at the Broad Institute. @@ -13675,8 +13856,8 @@ Locus ID (DictyBase) - Identifier of locus from DictyBase (Dictyostelium discoideum). beta12orEarlier + Identifier of locus from DictyBase (Dictyostelium discoideum). Moby_namespace:DDB_gene @@ -13725,11 +13906,11 @@ Quantitative trait locus Moby:SO_QTL - true - A QTL sometimes but does not necessarily correspond to a gene. 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). beta12orEarlier beta12orEarlier + true + A QTL sometimes but does not necessarily correspond to a gene. QTL @@ -13773,7 +13954,7 @@ Alignment - + beta12orEarlier An alignment of molecular sequences, structures or profiles derived from them. @@ -13840,9 +14021,9 @@ Moby:GCP_MapPoint Moby:GCP_MapPosition Moby:GCP_MapInterval - beta12orEarlier Moby:Locus Moby:MapPosition + beta12orEarlier Moby:HitPosition 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. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position. Moby:GenePosition @@ -13863,8 +14044,8 @@ Amino acid property - Amino acid data beta12orEarlier + Amino acid data Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids. @@ -13879,8 +14060,8 @@ Annotation 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. - beta13 This is a broad data type and is used a placeholder for other, more specific types. + beta13 true beta12orEarlier @@ -13892,16 +14073,17 @@ - Map attribute - + Map data + + An attribute of a molecular map (genetic or physical), or data extracted from or derived from the analysis of such a map. beta12orEarlier - An attribute of a molecular map (genetic or physical). + Map attribute @@ -13927,13 +14109,14 @@ - Sequence mask parameter - + DEP_Sequence mask parameter + Data used to replace (mask) characters in a molecular sequence. + true + 1.5 beta12orEarlier - - - + + @@ -13942,6 +14125,7 @@ Enzyme kinetics data + This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier @@ -13986,8 +14170,8 @@ Experimental data - Experimental measurement data beta13 + Experimental measurement data beta12orEarlier Raw data from or annotation on laboratory experiments. true @@ -14002,14 +14186,14 @@ - Genome version information - - + DEP_Genome version information + + 1.5 Information on a genome version. + true beta12orEarlier - - - + + @@ -14018,7 +14202,7 @@ Evidence - + beta12orEarlier 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. @@ -14046,7 +14230,7 @@ Sequence - + @@ -14054,8 +14238,8 @@ One or more molecular sequences, possibly with associated annotation. - This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. beta12orEarlier + 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. @@ -14068,10 +14252,12 @@ - Sequence record lite (nucleic acid) + Nucleic acid sequence record (lite) + Sequence record lite (nucleic acid) A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. + Nucleotide sequence record (lite) beta12orEarlier @@ -14083,11 +14269,12 @@ - Sequence record lite (protein) + Protein sequence record (lite) A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. beta12orEarlier + Sequence record lite (protein) @@ -14101,11 +14288,9 @@ Report beta12orEarlier - document - 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. + A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself. Document - 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. + You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing. Text @@ -14152,8 +14337,11 @@ Sequence motif (nucleic acid) + RNA sequence motif beta12orEarlier A nucleotide sequence motif. + DNA sequence motif + Nucleic acid sequence motif @@ -14166,6 +14354,7 @@ Sequence motif (protein) + Protein sequence motif An amino acid sequence motif. beta12orEarlier @@ -14178,13 +14367,14 @@ - Search parameter - + DEP_Search parameter + Some simple value controlling a search operation, typically a search of a database. + true + 1.5 beta12orEarlier - - - + + @@ -14206,13 +14396,14 @@ - Secondary structure - + DEP_Secondary structure + The secondary structure assignment (predicted or real) of a nucleic acid or protein. beta12orEarlier - - - + true + 1.5 + + @@ -14221,7 +14412,7 @@ Matrix - + An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences. This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier @@ -14235,10 +14426,11 @@ - Alignment report - + Alignment data + + Alignment report This is a broad data type and is used a placeholder for other, more specific types. - An informative report about a molecular alignment of some type, including alignment-derived data or metadata. + Data concerning, extracted from, or derived from the analysis of molecular alignment of some type. beta12orEarlier @@ -14251,7 +14443,7 @@ Nucleic acid report - + beta12orEarlier An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data. @@ -14265,7 +14457,7 @@ Structure report - + Structure-derived report beta12orEarlier An informative report on general information, properties or features of one or more molecular tertiary (3D) structures. @@ -14279,14 +14471,13 @@ - Nucleic acid structure report + Nucleic acid structure data - 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). beta12orEarlier - Nucleic acid property (structural) Nucleic acid structural property This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. + Nucleic acid property (structural) @@ -14298,7 +14489,7 @@ Molecular property - + Physicochemical property A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. SO:0000400 @@ -14314,7 +14505,6 @@ DNA base structural data - beta12orEarlier Structural data for DNA base pairs or runs of bases, such as energy or angle data. @@ -14328,14 +14518,14 @@ - Database entry version information - - + DEP_Database entry version information + 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. + 1.5 beta12orEarlier - - - + true + + @@ -14360,10 +14550,10 @@ - Nucleic acid features (SNP) + SNP (report) - SNP annotation An SNP is an individual point mutation or substitution of a single nucleotide. + SNP annotation Single nucleotide polymorphism Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence. beta12orEarlier @@ -14378,7 +14568,7 @@ Data reference - + beta12orEarlier Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology. A list of database accessions or identifiers are usually included. @@ -14433,13 +14623,14 @@ - Type - + DEP_Type + + true beta12orEarlier + 1.5 A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values). - - - + + @@ -14466,8 +14657,8 @@ KEGG organism code - A three-letter code used in the KEGG databases to uniquely identify organisms. beta12orEarlier + A three-letter code used in the KEGG databases to uniquely identify organisms. @@ -14481,10 +14672,10 @@ Gene name (KEGG GENES) - Moby_namespace:GeneId - Name of an entry (gene) from the KEGG GENES database. 1.3 true + Moby_namespace:GeneId + Name of an entry (gene) from the KEGG GENES database. [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* KEGG GENES entry name beta12orEarlier @@ -14517,9 +14708,9 @@ beta12orEarlier + BioCyc compound ID Identifier of a compound from the BioCyc chemical compounds database. BioCyc compound identifier - BioCyc compound ID @@ -14594,8 +14785,8 @@ Identifier (hybrid) + 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'. beta12orEarlier - This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. An identifier that is re-used for data objects of fundamentally different types (typically served from a single database). @@ -14643,8 +14834,8 @@ - Codon usage table identifier beta12orEarlier + Codon usage table identifier Identifier of a codon usage table, for example a genetic code. @@ -14707,8 +14898,8 @@ Nucleic acid features (codon) beta12orEarlier - true 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. + true beta12orEarlier @@ -14843,14 +15034,14 @@ - Sequence profile type - - + DEP_Sequence profile type + beta12orEarlier A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. - - - + 1.5 + true + + @@ -14879,7 +15070,7 @@ beta12orEarlier true beta12orEarlier - + @@ -14903,14 +15094,15 @@ - Results sort order - + DEP_Results sort order + A control of the order of data that is output, for example the order of sequences in an alignment. + 1.5 + true beta12orEarlier Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. - - - + + @@ -14991,13 +15183,14 @@ - Window step size - - Size of the incremental 'step' a sequence window is moved over a sequence. + DEP_Window step size + + Size of the incremental 'step' a sequence window is moved over a sequence. + true beta12orEarlier - - - + 1.5 + + @@ -15035,14 +15228,14 @@ - Sequence offset - - + DEP_Sequence offset + An offset for a single-point sequence position. + 1.5 beta12orEarlier - - - + true + + @@ -15050,13 +15243,14 @@ - Threshold - + DEP_Threshold + A value that serves as a threshold for a tool (usually to control scoring or output). + true beta12orEarlier - - - + 1.5 + + @@ -15070,8 +15264,8 @@ Transcription factor binding site data An informative report on a transcription factor protein. This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. - beta13 true + beta13 @@ -15087,7 +15281,7 @@ beta12orEarlier The name of a category of biological or bioinformatics database. true - + @@ -15117,7 +15311,7 @@ true beta12orEarlier Specification of one or more colors. - + @@ -15126,15 +15320,16 @@ - Rendering parameter - - Graphics parameter + DEP_Rendering parameter + Graphical parameter + Graphics parameter A parameter that is used to control rendering (drawing) to a device or image. + 1.5 beta12orEarlier - - - + true + + @@ -15145,8 +15340,8 @@ Sequence name - Any arbitrary name of a molecular sequence. beta12orEarlier + Any arbitrary name of a molecular sequence. @@ -15158,13 +15353,14 @@ - Date - + DEP_Date + + true beta12orEarlier A temporal date. - - - + 1.5 + + @@ -15202,13 +15398,15 @@ - Sequence similarity report + Sequence similarity plot + A plot of sequence similarities identified from word-matching or character comparison. - Sequence similarity plot Sequence conservation report 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. + Sequence similarity plot beta12orEarlier + @@ -15292,7 +15490,7 @@ Nucleic acid density plot - + Density plot (of base composition) for a nucleotide sequence. beta12orEarlier @@ -15319,19 +15517,14 @@ - Nucleic acid features (siRNA) - - - - - - - + DEP_Nucleic acid features (siRNA) + A report on siRNA duplexes in mRNA. beta12orEarlier - - - + 1.5 + true + + @@ -15377,6 +15570,7 @@ true beta12orEarlier The number of a certain thing. + @@ -15442,14 +15636,13 @@ Sequence checksum - - Hash - Hash code - A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing. Hash value + Hash Hash sum + Hash code beta12orEarlier + A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing. @@ -15477,13 +15670,14 @@ - Error - + DEP_Error + + true + 1.5 Data on an error generated by computer system or tool. beta12orEarlier - - - + + @@ -15492,7 +15686,7 @@ Database entry metadata - + Basic information on any arbitrary database entry. beta12orEarlier @@ -15656,13 +15850,14 @@ - Server metadata - + DEP_Server metadata + + true + 1.5 beta12orEarlier Basic information about a server on the web, such as an SRS server. - - - + + @@ -15688,8 +15883,8 @@ Sequence cluster ID (SYSTERS) beta12orEarlier - SYSTERS cluster ID Unique identifier of a sequence cluster from the SYSTERS database. + SYSTERS cluster ID @@ -15728,7 +15923,7 @@ Raw SCOP domain classification data files. beta12orEarlier true - + @@ -15740,11 +15935,11 @@ Raw CATH domain classification beta12orEarlier - true beta13 + true These are the parsable data files provided by CATH. Raw CATH domain classification data files. - + @@ -15755,7 +15950,7 @@ Heterogen annotation - An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. + An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. beta12orEarlier true 1.4 @@ -15783,14 +15978,15 @@ - Sequence set (bootstrapped) - + DEP_Sequence set (bootstrapped) + A collection of sequences output from a bootstrapping (resampling) procedure. + true Bootstrapping is often performed in phylogenetic analysis. beta12orEarlier - - - + 1.5 + + @@ -15813,13 +16009,14 @@ - Schema - + DEP_Schema + + 1.5 A data schema for organising or transforming data of some type. + true beta12orEarlier - - - + + @@ -15827,13 +16024,14 @@ - DTD - + DEP_DTD + + 1.5 beta12orEarlier + true A DTD (document type definition). - - - + + @@ -15841,14 +16039,15 @@ - XML Schema - + DEP_XML Schema + + 1.5 + true An XML Schema. XSD beta12orEarlier - - - + + @@ -15856,13 +16055,14 @@ - Relax-NG schema - + DEP_Relax-NG schema + + true A relax-NG schema. + 1.5 beta12orEarlier - - - + + @@ -15870,13 +16070,13 @@ - XSLT stylesheet - + DEP_XSLT stylesheet + + true An XSLT stylesheet. beta12orEarlier - - - + 1.5 + @@ -15949,8 +16149,8 @@ Sequence identifier (nucleic acid) beta12orEarlier - beta12orEarlier true + beta12orEarlier An identifier of nucleotide sequence(s) or nucleotide sequence database entries. @@ -15963,9 +16163,9 @@ EMBL accession + An accession number of an entry from the EMBL sequence database. EMBL identifier EMBL accession number - An accession number of an entry from the EMBL sequence database. beta12orEarlier EMBL ID @@ -16006,11 +16206,11 @@ GenBank accession - GenBank identifier - GenBank ID GenBank accession number beta12orEarlier Accession number of an entry from the GenBank sequence database. + GenBank identifier + GenBank ID @@ -16059,10 +16259,10 @@ Gene ID - beta12orEarlier - Gene accession Gene code A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. + beta12orEarlier + Gene accession @@ -16093,8 +16293,8 @@ Gene ID (ECK) http://www.geneontology.org/doc/GO.xrf_abbs: ECK - E. coli K-12 gene identifier Identifier of an E. coli K-12 gene from EcoGene Database. + E. coli K-12 gene identifier beta12orEarlier ECK accession @@ -16145,8 +16345,8 @@ true Name of an entry (gene) from the NCBI genes database. - 1.3 NCBI gene name + 1.3 beta12orEarlier @@ -16232,7 +16432,7 @@ - Carbohydrate structure report + Carbohydrate report beta12orEarlier Annotation on or information derived from one or more specific carbohydrate 3D structure(s). @@ -16267,10 +16467,10 @@ NCBI version accession.version - Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. - beta12orEarlier An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number. + 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. NCBI accession.version + beta12orEarlier @@ -16407,11 +16607,11 @@ GI number (protein) - A unique identifier assigned to NCBI protein sequence records. - Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. - beta12orEarlier protein gi + Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. + A unique identifier assigned to NCBI protein sequence records. protein gi number + beta12orEarlier @@ -16440,7 +16640,6 @@ Translation phase specification - Phase Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. beta12orEarlier @@ -16454,12 +16653,12 @@ - Metadata - + Resource metadata + beta12orEarlier Provenance metadata This is a broad data type and is used a placeholder for other, more specific types. - 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. + Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing. @@ -16540,9 +16739,9 @@ Pathway ID (KEGG) + KEGG pathway ID [a-zA-Z_0-9]{2,3}[0-9]{5} beta12orEarlier - KEGG pathway ID Identifier of a pathway from the KEGG pathway database. @@ -16641,8 +16840,8 @@ Sequence cluster ID (UniRef50) Unique identifier of an entry from the UniRef50 database. - UniRef50 cluster id UniRef50 entry accession + UniRef50 cluster id beta12orEarlier @@ -16655,16 +16854,21 @@ - Ontological data - - Data concerning an ontology. - true + Ontology data + + + + + + + This is a broad data type and is used a placeholder for other, more specific types. - beta13 beta12orEarlier - - - + Ontological data + Data concerning or derived from an ontology. + + + @@ -16672,8 +16876,9 @@ - RNA family annotation - + RNA family report + + RNA family annotation An informative report on a specific RNA family or other group of classified RNA sequences. beta12orEarlier @@ -16723,14 +16928,14 @@ - Protein signature type - - + DEP_Protein signature type + + 1.5 A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. + true beta12orEarlier - - - + + @@ -16738,13 +16943,14 @@ - Domain-nucleic acid interaction - + DEP_Domain-nucleic acid interaction report + beta12orEarlier - Data on protein domain-DNA/RNA interaction(s). - - - + An informative report on protein domain-DNA/RNA interaction(s). + true + 1.5 + + @@ -16752,10 +16958,10 @@ - Domain-domain interaction - + Domain-domain interaction report + beta12orEarlier - Data on protein domain-protein domain interaction(s). + An informative report on protein domain-protein domain interaction(s). @@ -16805,9 +17011,9 @@ 2D PAGE data Data concerning two-dimensional polygel electrophoresis. + true beta12orEarlier beta13 - true 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. @@ -16819,8 +17025,8 @@ - Experiment annotation (2D PAGE) - + 2D PAGE experiment report + @@ -16829,6 +17035,7 @@ An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel. beta12orEarlier + Experiment annotation (2D PAGE) @@ -16945,8 +17152,8 @@ - 2D PAGE spot (annotated) - + 2D PAGE spot report + An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. beta12orEarlier 2D PAGE spot annotation @@ -17052,10 +17259,13 @@ - Experiment annotation (genotype) + Genotyping experiment report Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. beta12orEarlier + Experiment report (genotyping) + Genotyping experiment metadata + Experiment annotation (genotype) @@ -17230,8 +17440,8 @@ UniParc accession UPI - Accession number of a UniParc (protein sequence) database entry. UniParc ID + Accession number of a UniParc (protein sequence) database entry. UPI[A-F0-9]{10} beta12orEarlier @@ -17290,7 +17500,7 @@ - Nucleic acid features (exon) + Exons (report) Gene features (exon) beta12orEarlier @@ -17323,12 +17533,21 @@ - Gene annotation (transcript) + Transcriptional features (report) - An informative report on a specific gene transcript, clone or EST. - Gene annotation (clone or EST) - Gene transcript annotation - beta12orEarlier + Enhancers (report) + Terminators (report) + beta12orEarlier + Attenuators (report) + GC signals (report) + TATA signals (report) + CAAT signals (report) + -10 signals (report) + 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. + An informative report on features concerning transcription of DNA into RNA including the regulation of transcription. + Nucleic acid features (transcriptional) + -35 signals (report) + Ribosome binding sites (report) @@ -17369,13 +17588,14 @@ - Protein-drug interaction - + DEP_Protein-drug interaction report + beta12orEarlier - Informative report on protein-drug interaction(s) including binding affinity data. - - - + 1.5 + true + An informative report on protein-drug interaction(s) including binding affinity data. + + @@ -17400,12 +17620,12 @@ - Phylogenetic raw data - + Phylogenetic data + beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. - Data concerning phylogeny, typically of molecular sequences. Phylogenetic data + Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. @@ -17449,14 +17669,15 @@ Article data - - beta13 - true - Data concerning the scientific literature. + + Article report This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. + Data concerning, extracted from, or derived from the analysis of a scientific text such as a full text article from a scientific journal. beta12orEarlier - + + + @@ -17466,7 +17687,6 @@ Parameter - Parameter or primitive Tool parameter Tool-specific parameter @@ -17498,7 +17718,7 @@ Data concerning a specific type of molecule. true Molecule-specific data - + @@ -17507,14 +17727,16 @@ - Molecule report - + DEP_Molecule report + + true + 1.5 Molecular report beta12orEarlier An informative report on a specific molecule. - - - + + + @@ -17523,7 +17745,7 @@ Organism report - + Organism annotation beta12orEarlier An informative report on a specific organism. @@ -17537,10 +17759,12 @@ - Experiment annotation - + Experiment report + Annotation on a wet lab experiment, such as experimental conditions. + Experiment annotation beta12orEarlier + Experiment metadata @@ -17551,10 +17775,11 @@ - Nucleic acid features (mutation) + DNA mutation report Annotation on a mutation. Mutation annotation + Nucleic acid features (mutation) beta12orEarlier @@ -17566,10 +17791,11 @@ - Sequence parameter - + Sequence attribute + beta12orEarlier - A parameter concerning calculations on molecular sequences. + Sequence parameter + An attribute of a molecular sequence, possibly in reference to some other sequence. @@ -17662,11 +17888,10 @@ This is a broad data type and is used a placeholder for other, more specific types. Database index beta13 - Data concerning an index of data. beta12orEarlier + Data concerning an index of data. true - @@ -17756,14 +17981,15 @@ - Expressed gene list - + DEP_Expressed gene list + A simple summary of expressed genes. Gene annotation (expressed gene list) + 1.5 + true beta12orEarlier - - - + + @@ -17773,8 +17999,8 @@ BindingDB Monomer ID - Unique identifier of a monomer from the BindingDB database. beta12orEarlier + Unique identifier of a monomer from the BindingDB database. @@ -17803,7 +18029,7 @@ GO concept ID (biological process) - An identifier of a 'biological process' concept from the the Gene Ontology. + An identifier of a 'biological process' concept from the the Gene Ontology. beta12orEarlier [0-9]{7}|GO:[0-9]{7} @@ -17819,7 +18045,7 @@ GO concept ID (molecular function) - An identifier of a 'molecular function' concept from the the Gene Ontology. + An identifier of a 'molecular function' concept from the the Gene Ontology. [0-9]{7}|GO:[0-9]{7} beta12orEarlier @@ -17849,7 +18075,7 @@ Northern blot image - + An image arising from a Northern Blot experiment. beta12orEarlier @@ -17894,9 +18120,9 @@ Hierarchy - + Hierarchy annotation - A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation. + Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation. beta12orEarlier @@ -17912,8 +18138,8 @@ true beta12orEarlier - Identifier of an entry from a database of biological hierarchies. beta12orEarlier + Identifier of an entry from a database of biological hierarchies. @@ -18034,8 +18260,8 @@ Secondary structure alignment metadata true - beta12orEarlier beta12orEarlier + beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. @@ -18046,14 +18272,13 @@ - Molecular interaction - + Molecule interaction report + Molecular interaction data + Molecular interaction report beta12orEarlier - Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). - - - + An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). + @@ -18062,7 +18287,7 @@ Pathway or network - + @@ -18101,8 +18326,8 @@ Genotype and phenotype data Data concerning a particular genotype, phenotype or a genotype / phenotype relation. - true beta13 + true beta12orEarlier @@ -18114,7 +18339,7 @@ Microarray data - + @@ -18247,8 +18472,8 @@ CluSTr cluster ID beta12orEarlier - [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? CluSTr ID + [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? Unique identifier of a sequence cluster from the CluSTr database. @@ -18508,8 +18733,8 @@ Enzyme ID (MEROPS) S[0-9]{2}\.[0-9]{3} - Unique identifier of a peptidase enzyme from the MEROPS database. beta12orEarlier + Unique identifier of a peptidase enzyme from the MEROPS database. MEROPS ID @@ -18709,8 +18934,8 @@ miRNA name beta12orEarlier - miRNA identifier MI[0-9]{7} + miRNA identifier Identifier for a gene from the miRBase database. miRNA ID @@ -18842,8 +19067,8 @@ Pathway ID (PharmGKB) - Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). beta12orEarlier + Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). PA[0-9]+ @@ -18877,8 +19102,8 @@ PA[0-9]+ - beta12orEarlier Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + beta12orEarlier @@ -18940,8 +19165,8 @@ NeuronDB ID - beta12orEarlier A unique identifier of a neuron from the NeuronDB database. + beta12orEarlier [0-9]+ @@ -19006,8 +19231,8 @@ BioNumbers ID beta12orEarlier - Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. [0-9]+ + Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. @@ -19040,13 +19265,13 @@ - + - + Identifier of a carbohydrate. @@ -19112,8 +19337,8 @@ MMDB ID - An identifier of an entry from the MMDB database. MMDB accession + An identifier of an entry from the MMDB database. beta12orEarlier [0-9]{1,5} @@ -19177,8 +19402,8 @@ Ensembl ID (Homo sapiens) + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). ENS([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). beta12orEarlier true beta12orEarlier @@ -19191,12 +19416,12 @@ - Ensembl ID ('Bos taurus') + Ensembl ID ('Bos taurus') ENSBTA([EGTP])[0-9]{11} beta12orEarlier true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). beta12orEarlier @@ -19207,12 +19432,12 @@ - Ensembl ID ('Canis familiaris') + Ensembl ID ('Canis familiaris') beta12orEarlier ENSCAF([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). beta12orEarlier @@ -19223,11 +19448,11 @@ - Ensembl ID ('Cavia porcellus') + Ensembl ID ('Cavia porcellus') beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). true ENSCPO([EGTP])[0-9]{11} @@ -19239,12 +19464,12 @@ - Ensembl ID ('Ciona intestinalis') + Ensembl ID ('Ciona intestinalis') ENSCIN([EGTP])[0-9]{11} beta12orEarlier beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). true @@ -19255,13 +19480,13 @@ - Ensembl ID ('Ciona savignyi') + Ensembl ID ('Ciona savignyi') true beta12orEarlier beta12orEarlier ENSCSAV([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). @@ -19271,13 +19496,13 @@ - Ensembl ID ('Danio rerio') + Ensembl ID ('Danio rerio') ENSDAR([EGTP])[0-9]{11} beta12orEarlier beta12orEarlier true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). @@ -19287,13 +19512,13 @@ - Ensembl ID ('Dasypus novemcinctus') + Ensembl ID ('Dasypus novemcinctus') true ENSDNO([EGTP])[0-9]{11} beta12orEarlier beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). @@ -19303,11 +19528,11 @@ - Ensembl ID ('Echinops telfairi') + Ensembl ID ('Echinops telfairi') - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). - beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). beta12orEarlier + beta12orEarlier true ENSETE([EGTP])[0-9]{11} @@ -19319,10 +19544,10 @@ - Ensembl ID ('Erinaceus europaeus') + Ensembl ID ('Erinaceus europaeus') beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). beta12orEarlier ENSEEU([EGTP])[0-9]{11} true @@ -19335,10 +19560,10 @@ - Ensembl ID ('Felis catus') + Ensembl ID ('Felis catus') beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). ENSFCA([EGTP])[0-9]{11} true beta12orEarlier @@ -19351,12 +19576,12 @@ - Ensembl ID ('Gallus gallus') + Ensembl ID ('Gallus gallus') beta12orEarlier true beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). ENSGAL([EGTP])[0-9]{11} @@ -19367,12 +19592,12 @@ - Ensembl ID ('Gasterosteus aculeatus') + Ensembl ID ('Gasterosteus aculeatus') beta12orEarlier - true ENSGAC([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). beta12orEarlier @@ -19383,10 +19608,10 @@ - Ensembl ID ('Homo sapiens') + Ensembl ID ('Homo sapiens') true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). beta12orEarlier beta12orEarlier ENSHUM([EGTP])[0-9]{11} @@ -19399,12 +19624,12 @@ - Ensembl ID ('Loxodonta africana') + Ensembl ID ('Loxodonta africana') beta12orEarlier ENSLAF([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). beta12orEarlier @@ -19415,13 +19640,13 @@ - Ensembl ID ('Macaca mulatta') + Ensembl ID ('Macaca mulatta') beta12orEarlier true ENSMMU([EGTP])[0-9]{11} beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). @@ -19431,12 +19656,12 @@ - Ensembl ID ('Monodelphis domestica') + Ensembl ID ('Monodelphis domestica') beta12orEarlier ENSMOD([EGTP])[0-9]{11} true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). beta12orEarlier @@ -19447,11 +19672,11 @@ - Ensembl ID ('Mus musculus') + Ensembl ID ('Mus musculus') beta12orEarlier beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). true ENSMUS([EGTP])[0-9]{11} @@ -19463,9 +19688,9 @@ - Ensembl ID ('Myotis lucifugus') + Ensembl ID ('Myotis lucifugus') - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). beta12orEarlier true ENSMLU([EGTP])[0-9]{11} @@ -19483,7 +19708,7 @@ beta12orEarlier ENSOAN([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). true beta12orEarlier @@ -19495,10 +19720,10 @@ - Ensembl ID ('Oryctolagus cuniculus') + Ensembl ID ('Oryctolagus cuniculus') beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). true ENSOCU([EGTP])[0-9]{11} beta12orEarlier @@ -19511,10 +19736,10 @@ - Ensembl ID ('Oryzias latipes') + Ensembl ID ('Oryzias latipes') beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). beta12orEarlier true ENSORL([EGTP])[0-9]{11} @@ -19527,12 +19752,12 @@ - Ensembl ID ('Otolemur garnettii') + Ensembl ID ('Otolemur garnettii') - beta12orEarlier ENSSAR([EGTP])[0-9]{11} + beta12orEarlier true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). beta12orEarlier @@ -19543,10 +19768,10 @@ - Ensembl ID ('Pan troglodytes') + Ensembl ID ('Pan troglodytes') true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). ENSPTR([EGTP])[0-9]{11} beta12orEarlier beta12orEarlier @@ -19559,12 +19784,12 @@ - Ensembl ID ('Rattus norvegicus') + Ensembl ID ('Rattus norvegicus') beta12orEarlier ENSRNO([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). beta12orEarlier @@ -19575,10 +19800,10 @@ - Ensembl ID ('Spermophilus tridecemlineatus') + Ensembl ID ('Spermophilus tridecemlineatus') - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). ENSSTO([EGTP])[0-9]{11} beta12orEarlier true @@ -19591,11 +19816,11 @@ - Ensembl ID ('Takifugu rubripes') + Ensembl ID ('Takifugu rubripes') true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). ENSFRU([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). beta12orEarlier beta12orEarlier @@ -19607,11 +19832,11 @@ - Ensembl ID ('Tupaia belangeri') + Ensembl ID ('Tupaia belangeri') ENSTBE([EGTP])[0-9]{11} true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). beta12orEarlier beta12orEarlier @@ -19623,13 +19848,13 @@ - Ensembl ID ('Xenopus tropicalis') + Ensembl ID ('Xenopus tropicalis') ENSXET([EGTP])[0-9]{11} true beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). @@ -19641,12 +19866,6 @@ CATH identifier - - - - - - Identifier of a protein domain (or other node) from the CATH database. beta12orEarlier @@ -19662,12 +19881,6 @@ CATH node ID (family) - - - - - - 2.10.10.10 A code number identifying a family from the CATH database. beta12orEarlier @@ -19720,7 +19933,7 @@ GO concept identifier (cellular compartment) beta12orEarlier [0-9]{7}|GO:[0-9]{7} - An identifier of a 'cellular compartment' concept from the Gene Ontology. + An identifier of a 'cellular compartment' concept from the Gene Ontology. @@ -19777,10 +19990,10 @@ - Genome metadata - + Genome report + beta12orEarlier - Provenance metadata or other general information concerning a genome as a whole. + An informative report of general information concerning a genome as a whole. @@ -19935,7 +20148,6 @@ Protein features (disordered structure) - Protein structure report (disordered structure) An informative report about disordered structure in a protein. beta12orEarlier @@ -19965,20 +20177,15 @@ - Embryo report - - - - - - - + DEP_Embryo report + + 1.5 beta12orEarlier Embryo annotation + true Annotation on an embryo or concerning embryological development. - - - + + @@ -20116,8 +20323,8 @@ beta12orEarlier beta13 - true The name of a genus of viruses. + true @@ -20148,7 +20355,7 @@ The name of a SwissRegulon database. beta13 true - + @@ -20224,8 +20431,8 @@ Name of an entry (gene) from the Genolist genes database. 1.3 Genolist gene name - beta12orEarlier true + beta12orEarlier @@ -20332,7 +20539,7 @@ The name of a subdivision of the Collagen Mutation Database (CMD) database. true beta12orEarlier - + @@ -20347,7 +20554,7 @@ beta13 true beta12orEarlier - + @@ -20403,7 +20610,7 @@ Carbohydrate conformational map - + A conformational energy map of the glycosidic linkages in a carbohydrate molecule. beta12orEarlier @@ -20416,11 +20623,12 @@ - Nucleic acid features (intron) + Introns (report) Gene features (intron) beta12orEarlier An informative report on an intron in a nucleotide sequences. + Nucleic acid features (intron) @@ -20525,8 +20733,8 @@ - Sequence motif metadata - + Sequence motif report + @@ -20534,7 +20742,8 @@ beta12orEarlier - Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. + Sequence motif metadata + Data about 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. @@ -20547,8 +20756,8 @@ Locus annotation - An informative report on a particular locus. beta12orEarlier + An informative report on a particular locus. beta12orEarlier true Locus report @@ -20576,14 +20785,15 @@ - Term ID list - + DEP_Term ID list + + 1.5 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. + true beta12orEarlier One or more terms from one or more controlled vocabularies which are annotations on an entity. - - - + + @@ -20857,8 +21067,8 @@ Protein family ID (PANTHER) - Panther family ID Accession number of an entry (family) from the PANTHER database. + Panther family ID beta12orEarlier @@ -20933,8 +21143,8 @@ - Sequence profile metadata - + Sequence profile data + @@ -20942,7 +21152,7 @@ beta12orEarlier - 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. + Data concerning, extracted from, or derived from the analysis of 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. @@ -21211,13 +21421,13 @@ - + - + beta12orEarlier @@ -21325,7 +21535,7 @@ Abstract - + An abstract of a scientific article. beta12orEarlier @@ -21423,20 +21633,14 @@ - Article metadata - - - - - - - - + DEP_Article metadata + + 1.5 Bibliographic data concerning scientific article(s). beta12orEarlier - - - + true + + @@ -21445,13 +21649,7 @@ Ontology concept - - - - - - - + A concept from a biological ontology. This includes any fields from the concept definition such as concept name, definition, comments and so on. beta12orEarlier @@ -21479,9 +21677,11 @@ - Experiment annotation (Northern blot) - + Northern blot experiment report + + Experiment report (Northern blot) beta12orEarlier + Experiment annotation (Northern blot) General annotation on a Northern Blot experiment. @@ -21493,8 +21693,9 @@ - Nucleic acid features (VNTR) + VNTR (report) + Nucleic acid features (VNTR) VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. Variable number of tandem repeat polymorphism VNTR annotation @@ -21510,9 +21711,10 @@ - Nucleic acid features (microsatellite) + Microsatellites (report) beta12orEarlier + Nucleic acid features (microsatellite) A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. Microsatellite annotation Annotation on a microsatellite polymorphism in a DNA sequence. @@ -21526,10 +21728,11 @@ - Nucleic acid features (RFLP) + RFLP (report) Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence. An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. + Nucleic acid features (RFLP) RFLP annotation beta12orEarlier @@ -21544,8 +21747,8 @@ Radiation hybrid map - beta12orEarlier RH map + beta12orEarlier A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. 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. @@ -21601,13 +21804,14 @@ - DRCAT resource - + DEP_DRCAT resource + + true beta12orEarlier An entry (resource) from the DRCAT bioinformatics resource catalogue. - - - + 1.5 + + @@ -21643,7 +21847,7 @@ - Lipid structure report + Lipid report Annotation on or information derived from one or more specific lipid 3D structure(s). beta12orEarlier @@ -21661,9 +21865,9 @@ true Image of one or more molecular secondary structures. - 1.4 beta12orEarlier - + 1.4 + @@ -21672,14 +21876,15 @@ - Secondary structure report - + DEP_Secondary structure report + + 1.5 An informative report on general information, properties or features of one or more molecular secondary structures. + true beta12orEarlier Secondary structure-derived report - - - + + @@ -21702,14 +21907,16 @@ - Nucleic acid features (RNA features) - + DEP_RNA features report + + Nucleic acid features (RNA features) RNA features Features concerning RNA or regions of DNA that encode an RNA molecule. + 1.5 beta12orEarlier - - - + true + + @@ -21732,10 +21939,11 @@ - Nucleic acid features (polymorphism annotation) + DNA polymorphism (report) - beta12orEarlier Annotation on a polymorphism. + beta12orEarlier + Nucleic acid features (polymorphism) Polymorphism annotation @@ -21747,9 +21955,10 @@ - Sequence record (protein) + Protein sequence record + Sequence record (protein) Protein sequence record beta12orEarlier A protein sequence and associated metadata. @@ -21763,11 +21972,11 @@ - Sequence record (nucleic acid) + Nucleic acid sequence record + Sequence record (nucleic acid) beta12orEarlier - Nucleic acid sequence record A nucleic acid sequence and associated metadata. Nucleotide sequence record @@ -21780,12 +21989,13 @@ - Sequence record full (protein) + Protein sequence record (full) beta12orEarlier A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. SO:2000061 + Sequence record full (protein) @@ -21796,12 +22006,14 @@ - Sequence record full (nucleic acid) + Nucleic acid sequence record (full) + Nucleotide sequence record (full) SO:2000061 beta12orEarlier A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. + Sequence record full (nucleic acid) @@ -22128,8 +22340,8 @@ Protein family accession - beta12orEarlier Accession of a protein family (that is deposited in a database). + beta12orEarlier @@ -22196,7 +22408,7 @@ Sequence features metadata - + Metadata on sequence features. beta12orEarlier @@ -22227,10 +22439,10 @@ DDBJ accession An identifier of an entry from the DDBJ sequence database. - DDBJ identifier DDBJ ID - beta12orEarlier + DDBJ identifier DDBJ accession number + beta12orEarlier @@ -22258,15 +22470,13 @@ Sequence data - - Data concerning molecular sequence(s). - true - beta13 + + Data concerning, extracted from, or derived from the analysis of molecular sequence(s). beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. - - - + + + @@ -22274,7 +22484,7 @@ - Codon usage data + Codon usage This is a broad data type and is used a placeholder for other, more specific types. Data concerning codon usage. @@ -22282,7 +22492,6 @@ true beta12orEarlier - @@ -22291,13 +22500,14 @@ - Article report - - Data concerning or derived from the analysis of a scientific article. + DEP_Article report + + true + Data derived from the analysis of a scientific text such as a full text article from a scientific journal. + 1.5 beta12orEarlier - - - + + @@ -22306,10 +22516,10 @@ Sequence report - - 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). + Sequence-derived report beta12orEarlier + An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties. @@ -22321,7 +22531,7 @@ Protein secondary structure report - + beta12orEarlier An informative report about the properties or features of one or more protein secondary structures. @@ -22366,8 +22576,8 @@ Nucleic acid probability profile Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature - A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). beta12orEarlier + A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). @@ -22394,8 +22604,8 @@ - Pathway or network (gene regulation) - + Gene regulatory network report + @@ -22404,6 +22614,8 @@ beta12orEarlier A report typically including a map (diagram) of a gene regulatory network. + Gene regulation network report + Pathway or network (gene regulation) @@ -22414,10 +22626,12 @@ - 2D PAGE image (annotated) - + 2D PAGE gel report + 2D PAGE image annotation beta12orEarlier + 2D PAGE gel annotation + 2D PAGE image report An informative report on a two-dimensional (2D PAGE) gel. @@ -22443,15 +22657,15 @@ - Microarray image - - + DEP_Microarray image + + true An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. Gene expression image beta12orEarlier - - - + 1.5 + + @@ -22460,7 +22674,7 @@ Image - + Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type. beta12orEarlier Image data @@ -22513,7 +22727,6 @@ beta13 beta12orEarlier - @@ -22522,13 +22735,14 @@ - Workflow - + DEP_Workflow + A computational workflow. + 1.5 beta12orEarlier - - - + true + + @@ -22542,8 +22756,7 @@ beta12orEarlier true beta13 - - + @@ -22552,11 +22765,13 @@ - Raw sequence (protein) + Protein sequence (raw) A raw protein sequence (string of characters). + Raw sequence (protein) beta12orEarlier + Raw protein sequence @@ -22567,11 +22782,14 @@ - Raw sequence (nucleic acid) + Nucleic acid sequence (raw) A raw nucleic acid sequence. + Raw sequence (nucleic acid) + Nucleotide sequence (raw) beta12orEarlier + Nucleic acid raw sequence @@ -22600,10 +22818,10 @@ Nucleic acid sequence Nucleic acid sequences - One or more nucleic acid sequences, possibly with associated annotation. Nucleotide sequences Nucleotide sequence beta12orEarlier + One or more nucleic acid sequences, possibly with associated annotation. @@ -22616,7 +22834,7 @@ Reaction data - + Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. Reaction annotation beta12orEarlier @@ -22648,21 +22866,12 @@ Protein classification - - - - - - - - + beta12orEarlier - Data concerning the classification of protein sequences or structures. + An informative report concerning the classification of protein sequences or structures. Protein classification data This is a broad data type and is used a placeholder for other, more specific types. - - - + @@ -22671,14 +22880,13 @@ Sequence motif data - + This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier Data concerning specific or conserved pattern in molecular sequences. - beta13 - true - - + + + @@ -22719,7 +22927,7 @@ Pathway or network report - + @@ -22755,21 +22963,12 @@ Nucleic acid classification - - - - - - - - - This is a broad data type and is used a placeholder for other, more specific types. + Nucleic acid classification data Data concerning the classification of nucleic acid sequences or structures. beta12orEarlier - - - + This is a broad data type and is used a placeholder for other, more specific types. + @@ -22777,15 +22976,16 @@ - Classification - + DEP_Classification report + + 1.5 + A report on a classification of molecular sequences, structures or other entities. Classification data - Data concerning a classification of molecular sequences, structures or other entities. + true beta12orEarlier This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. - - - + + @@ -22852,12 +23052,12 @@ - Sequence annotation track + Annotation track + Sequence annotation track Genome track Genome-browser track Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. - Annotation track Genomic track Genome annotation track beta12orEarlier @@ -22903,10 +23103,10 @@ NCBI genetic code ID - Identifier of a genetic code in the NCBI list of genetic codes. beta12orEarlier 16 [1-9][0-9]? + Identifier of a genetic code in the NCBI list of genetic codes. @@ -22958,8 +23158,8 @@ beta12orEarlier The name of a concept for a molecular function from the GO ontology. - true beta12orEarlier + true @@ -22970,7 +23170,7 @@ Taxonomy - + @@ -23007,14 +23207,15 @@ - Core data - + DEP_Core data + beta13 + true + 1.5 A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation. Core data entities typically have a format and may be identified by an accession number. - - - + + @@ -23100,7 +23301,7 @@ - Nucleic acid sequence composition + Nucleic acid sequence composition (report) beta13 @@ -23116,13 +23317,14 @@ - Protein domain classification node - + DEP_Protein domain classification node + + 1.5 + true A node from a classification of protein structural domain(s). beta13 - - - + + @@ -23177,13 +23379,14 @@ - Geotemporal metadata - + DEP_Geotemporal metadata + Basic information concerning geographical location or time. + true beta13 - - - + 1.5 + + @@ -23222,7 +23425,7 @@ Experimental measurement - + Raw experimental data Measurement data Measurement metadata @@ -23270,8 +23473,8 @@ Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. Gene expression report - Microarray probe set data beta13 + Microarray probe set data Gene annotation (expression) Data generated from processing and analysis of probe set data from a microarray experiment. @@ -23288,8 +23491,8 @@ Gene expression data matrix The final processed (normalised) data for a set of hybridisations in a microarray experiment. - This combines data from all hybridisations. beta13 + This combines data from all hybridisations. Gene expression matrix @@ -23316,8 +23519,8 @@ - Microarray annotation - + Microarray metadata + beta13 Annotation on the array itself used in a microarray experiment. This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. @@ -23381,13 +23584,14 @@ - Sequence features (compositionally-biased regions) - + DEP_Sequence features (compositionally-biased regions) + A report of regions in a molecular sequence that are biased to certain characters. + true beta13 - - - + 1.5 + + @@ -23409,13 +23613,14 @@ - Nucleic acid features (difference and change) - + DEP_Nucleic acid features (difference and change) + + true + 1.5 A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. beta13 - - - + + @@ -23423,8 +23628,9 @@ - Nucleic acid features (expression signal) - + Expression signal (report) + + Nucleic acid features (expression signal) A report on regions within a nucleic acid sequence containing a signal that alters a biological function. beta13 @@ -23437,11 +23643,12 @@ - Nucleic acid features (binding) + DNA binding sites (report) A report on regions of a nucleic acid sequence that bind some other molecule. This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). beta13 + Nucleic acid features (binding) @@ -23454,7 +23661,6 @@ Nucleic acid features (repeats) - beta13 A report on repetitive elements within a nucleic acid sequence. This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. @@ -23468,9 +23674,10 @@ - Nucleic acid features (replication and recombination) - + DNA replication and recombination sites (report) + 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. + Nucleic acid features (replication and recombination) A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination. beta13 @@ -23483,10 +23690,15 @@ - Nucleic acid features (structure) - - beta13 + Nucleic acid structure report + + + Quadruplexes (report) + Nucleic acid features (structure) + d-loop (report) A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. + beta13 + Stem loop (report) @@ -23499,7 +23711,6 @@ Protein features (repeats) - beta13 Location of short repetitive subsequences (repeat sequences) in a protein sequence. @@ -23512,10 +23723,8 @@ - Protein features (motifs) - + Sequence motif matches (protein) - Use this concept if another, more specific concept is not available. beta13 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. @@ -23528,12 +23737,10 @@ - Nucleic acid features (motifs) - + Sequence motif matches (nucleic acid) beta13 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. - Use this concept if another, more specific concept is not available. @@ -23544,14 +23751,15 @@ - Nucleic acid features (d-loop) - + DEP_Nucleic acid features (d-loop) + A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. A report on displacement loops in a mitochondrial DNA sequence. + 1.5 + true beta13 - - - + + @@ -23559,14 +23767,15 @@ - Nucleic acid features (stem loop) - + DEP_Nucleic acid features (stem loop) + A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. + 1.5 A report on stem loops in a DNA sequence. + true beta13 - - - + + @@ -23574,12 +23783,18 @@ - Nucleic acid features (mRNA features) - - beta13 - Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. - This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + Gene transcript report + + An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST. + + mRNA (report) + Clone or EST (report) + Gene transcript annotation mRNA features + Transcript (report) + beta13 + Nucleic acid features (mRNA features) + This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). @@ -23590,9 +23805,10 @@ - Nucleic acid features (signal or transit peptide) + Signal or transit peptide (report) beta13 + Nucleic acid features (signal or transit peptide) A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. A report on a coding sequence for a signal or transit peptide. @@ -23605,12 +23821,19 @@ - Nucleic acid features (non-coding RNA) - + Non-coding RNA (report) + + + + + + + Non-coding RNA features beta13 Features concerning non-coding or functional RNA molecules, including tRNA and rRNA. ncRNA features + Nucleic acid features (non-coding RNA) @@ -23621,14 +23844,15 @@ - Nucleic acid features (transcriptional) - + DEP_Transcriptional features (report) + beta13 Features concerning transcription of DNA into RNA including the regulation of transcription. 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. - - - + true + 1.5 + + @@ -23636,11 +23860,12 @@ - Nucleic acid features (STS) + Sequence tagged sites (report) beta13 A report on sequence tagged sites (STS) in nucleic acid sequences. 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. + Nucleic acid features (STS) @@ -23651,13 +23876,14 @@ - Nucleic acid features (immunoglobulin gene structure) - + DEP_Nucleic acid features (immunoglobulin gene structure) + A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments. + 1.5 beta13 - - - + true + + @@ -23665,13 +23891,14 @@ - SCOP class - - Information on a 'class' node from the SCOP database. + DEP_SCOP class + + Information on a 'class' node from the SCOP database. + true beta13 - - - + 1.5 + + @@ -23679,13 +23906,14 @@ - SCOP fold - - Information on a 'fold' node from the SCOP database. + DEP_SCOP fold + + true + 1.5 + Information on a 'fold' node from the SCOP database. beta13 - - - + + @@ -23693,13 +23921,14 @@ - SCOP superfamily - - Information on a 'superfamily' node from the SCOP database. + DEP_SCOP superfamily + + true + 1.5 + Information on a 'superfamily' node from the SCOP database. beta13 - - - + + @@ -23707,13 +23936,14 @@ - SCOP family - + DEP_SCOP family + beta13 - Information on a 'family' node from the SCOP database. - - - + Information on a 'family' node from the SCOP database. + true + 1.5 + + @@ -23721,13 +23951,14 @@ - SCOP protein - + DEP_SCOP protein + + 1.5 beta13 - Information on a 'protein' node from the SCOP database. - - - + true + Information on a 'protein' node from the SCOP database. + + @@ -23735,13 +23966,14 @@ - SCOP species - - Information on a 'species' node from the SCOP database. + DEP_SCOP species + + Information on a 'species' node from the SCOP database. beta13 - - - + true + 1.5 + + @@ -23749,10 +23981,12 @@ - Experiment annotation (mass spectrometry) - + Mass spectrometry experiment report + General annotation on a mass spectrometry experiment. beta13 + Experiment annotation (mass spectrometry) + Experiment report (mass spectrometry) @@ -23763,10 +23997,16 @@ - Gene family annotation - - - 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. + Gene family report + + Gene homology (report) + Gene family annotation + Nucleic acid classification + Gene annotation (homology) + Homology information + Gene annotation (homology information) + This includes reports on on gene homologues between species. + 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, or any other classification of nucleic acid sequences or structures that reflects gene structure. beta13 @@ -23779,7 +24019,7 @@ Protein image - + An image of a protein. beta13 @@ -23793,7 +24033,6 @@ Protein alignment - beta13 An alignment of protein sequences and/or structures. @@ -23807,7 +24046,7 @@ - Experiment annotation (sequencing) + NGS experiment report @@ -23816,7 +24055,9 @@ Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. + Experiment metadata (NGS) 1.0 + NGS experiment metadata @@ -23829,7 +24070,6 @@ Sequence assembly report - Assembly report This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc. 1.1 @@ -23859,11 +24099,12 @@ - Experiment annotation (GWAS) + GWAS study metadata Experiment annotation (genome-wide association study) - Metadata on a genome-wide association study (GWAS). 1.1 + Genome-wide association study experiment metadata + Experiment metadata (GWAS) @@ -23909,7 +24150,7 @@ Kinetic model - + Mathematical model of a network, that contains biochemical kinetics. 1.2 @@ -23976,13 +24217,14 @@ - Sequence feature type - + DEP_Sequence feature type + + 1.5 1.3 A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory. - - - + true + + @@ -23990,16 +24232,14 @@ - Gene annotation (homology) - - This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. + DEP_Gene homology (report) + + 1.5 An informative report on gene homologues between species. - Homology information + true beta12orEarlier - Gene annotation (homology information) - - - + + @@ -24011,9 +24251,9 @@ 1.3 - ENSGT00390000003602 Unique identifier for a gene tree from the Ensembl database. Ensembl ID (gene tree) + ENSGT00390000003602 @@ -24027,7 +24267,7 @@ Gene tree - A phylogenetic tree that is an estimate of the character's phylogeny. + A phylogenetic tree that is an estimate of the character's phylogeny. 1.3 @@ -24096,9 +24336,9 @@ Phenotype - 1.3 Phenotypes Name of a phenotype. + 1.3 @@ -24113,6 +24353,7 @@ Transition matrix 1.4 + HMM transition matrix Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa. A HMM transition matrix contains the probabilities of switching from one HMM state to another. @@ -24125,6 +24366,7 @@ Emission matrix + HMM emission matrix Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state. 1.4 A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM. @@ -24138,8 +24380,8 @@ Hidden Markov model - A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. 1.4 + A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. @@ -24157,6 +24399,87 @@ + + + + Raw image + + Raw biological or biomedical image generated by some experimental technique. + Image data + beta12orEarlier + Amino acid data + 1.5 + + + + + + + + + + + + Carbohydrate property + + 1.5 + Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates. + Carbohydrate data + + + + + + + + + + + Proteomics experiment report + + Experiment report (proteomics) + Information about a proteomics experiment. + 1.5 + Experiment annotation (proteomics experiment) + + + + + + + + + + + RNAi experiment report + + Experiment report (RNAi) + 1.5 + Experiment annotation (RNAi experiment) + Information about an RNAi experiment. + + + + + + + + + + + Simulation experiment report + + Experiment annotation (simulation experiment) + Experiment report (simulation) + 1.5 + Information about a biological computational model experiment (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. + + + + + + + @@ -24170,8 +24493,8 @@ - + @@ -24672,8 +24995,8 @@ Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. - The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. beta12orEarlier + The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. @@ -24930,7 +25253,7 @@ beta12orEarlier - EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family. + EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family. The format is clustal-like and includes annotation of domain family classification information. @@ -25202,8 +25525,8 @@ Dot-bracket format - Vienna RNA secondary structure format Vienna RNA format + Vienna RNA secondary structure format Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server. beta12orEarlier @@ -25240,8 +25563,8 @@ Format of an entry (or part of an entry) from the PDB database. - beta12orEarlier PDB entry format + beta12orEarlier @@ -25392,8 +25715,8 @@ REBASE proto enzyme report format - beta12orEarlier beta12orEarlier + beta12orEarlier true Format of an entry from the proto section of the REBASE enzyme database. @@ -25485,8 +25808,8 @@ IntAct entry format - Entry format for the IntAct database of protein interaction. true + Entry format for the IntAct database of protein interaction. beta12orEarlier beta12orEarlier @@ -25501,10 +25824,10 @@ InterPro entry format beta12orEarlier - beta12orEarlier 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. - Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. + beta12orEarlier true + Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. @@ -25549,8 +25872,8 @@ beta12orEarlier true - beta12orEarlier Entry format for the PIRSF protein secondary database. + beta12orEarlier @@ -25622,10 +25945,10 @@ Superfamily entry format - beta12orEarlier true - Entry format for the Superfamily protein secondary database. + beta12orEarlier beta12orEarlier + Entry format for the Superfamily protein secondary database. @@ -25669,8 +25992,8 @@ beta12orEarlier true - Entry format for the FSSP database. beta12orEarlier + Entry format for the FSSP database. @@ -25712,8 +26035,8 @@ DictyBase gene report format - Entry format of DictyBase genome database. beta12orEarlier + Entry format of DictyBase genome database. beta12orEarlier true @@ -25862,8 +26185,8 @@ SGD gene report format - beta12orEarlier Entry format of the Saccharomyces Genome Database (SGD). + beta12orEarlier beta12orEarlier true @@ -25877,8 +26200,8 @@ GeneDB gene report format - beta12orEarlier beta12orEarlier + beta12orEarlier true Entry format of the Sanger GeneDB genome database. @@ -25922,8 +26245,8 @@ ZFIN gene report format - true Entry format of the Zebrafish Information Network (ZFIN) genome database. + true beta12orEarlier beta12orEarlier @@ -26371,8 +26694,8 @@ CPDB entry format beta12orEarlier - beta12orEarlier true + beta12orEarlier The format of an entry from the CPDB database. @@ -26493,8 +26816,8 @@ beta12orEarlier true - beta12orEarlier The format of an entry from PubChem. + beta12orEarlier @@ -26614,7 +26937,7 @@ CiteXplore-core - CiteXplore 'core' citation format including title, journal, authors and abstract. + CiteXplore 'core' citation format including title, journal, authors and abstract. beta12orEarlier @@ -26630,7 +26953,7 @@ beta12orEarlier - CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. + CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. @@ -26691,8 +27014,8 @@ Format of an ATOM record (describing data for an individual atom) from a PDB file. beta12orEarlier - true beta13 + true @@ -26721,8 +27044,8 @@ CATH PDB report format 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. - true Format of CATH domain classification information for a protein PDB file. + true beta12orEarlier beta12orEarlier @@ -26753,8 +27076,8 @@ true Moby:GI_Gene - beta12orEarlier beta12orEarlier + beta12orEarlier This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service. @@ -26768,8 +27091,8 @@ BacMap gene card format - beta12orEarlier Moby:BacMapGeneCard + beta12orEarlier beta12orEarlier true Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database. @@ -26784,8 +27107,8 @@ ColiCard report format - Moby:ColiCard beta12orEarlier + Moby:ColiCard beta12orEarlier true Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). @@ -26863,7 +27186,7 @@ - The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. + The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. Data format A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. beta12orEarlier @@ -26889,25 +27212,19 @@ - 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. + 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. - File format - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. - - - - - Closely related concept focusing on the specification of a data format. + Data model + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - - + - 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. + 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. @@ -26919,13 +27236,19 @@ - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - Data model + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + File format - + + + + Closely related concept focusing on the specification of a data format. + + + - Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format. + Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format. @@ -27057,8 +27380,8 @@ dbid - beta12orEarlier Fasta format variant with database name before ID. + beta12orEarlier @@ -27221,8 +27544,8 @@ genpept - Genpept protein entry format. Currently identical to refseqp format + Genpept protein entry format. beta12orEarlier @@ -27311,8 +27634,8 @@ igstrict - beta12orEarlier Intelligenetics sequence format (strict version). + beta12orEarlier @@ -27501,8 +27824,8 @@ beta12orEarlier true - beta12orEarlier Phylip interleaved sequence format. + beta12orEarlier @@ -27576,8 +27899,8 @@ Staden format - beta12orEarlier Staden suite sequence format. + beta12orEarlier @@ -27626,8 +27949,8 @@ UniProtKB format - beta12orEarlier UniProtKB entry sequence format. + beta12orEarlier @@ -27762,8 +28085,8 @@ NCBI format - beta12orEarlier There are several variants of this. + beta12orEarlier NCBI FASTA sequence format with NCBI-style IDs. @@ -27858,8 +28181,8 @@ beta12orEarlier DASGFF feature - DAS GFF (XML) feature format. das feature + DAS GFF (XML) feature format. @@ -27889,8 +28212,8 @@ beta12orEarlier true - beta12orEarlier EMBL feature format. + beta12orEarlier @@ -28077,8 +28400,8 @@ MSF format for (aligned) sequences. beta12orEarlier - true beta12orEarlier + true @@ -28091,8 +28414,8 @@ nexus alignment format true - beta12orEarlier beta12orEarlier + beta12orEarlier Nexus/paup format for (aligned) sequences. @@ -28163,8 +28486,8 @@ scores format - Alignment format for score values for pairs of sequences. beta12orEarlier + Alignment format for score values for pairs of sequences. @@ -28466,12 +28789,6 @@ Workflow format - - - - - - Format of a workflow. beta12orEarlier @@ -28670,8 +28987,8 @@ Polymorphism report format - 1.0 Format for sequence polymorphism data. + 1.0 true beta12orEarlier @@ -28690,8 +29007,8 @@ - beta12orEarlier Format for reports on a protein family. + beta12orEarlier @@ -29194,12 +29511,6 @@ Sequence features (repeats) format - - - - - - Format used for map of repeats in molecular (typically nucleotide) sequences. beta12orEarlier @@ -29555,7 +29866,7 @@ - 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. + 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. beta12orEarlier @@ -29614,8 +29925,8 @@ Strain data format - true 1.0 + true beta12orEarlier Format of a report on organism strain data / cell line. @@ -29766,8 +30077,8 @@ ENZYME enzyme report format true - beta12orEarlier beta12orEarlier + beta12orEarlier Format of an entry from the Enzyme nomenclature database (ENZYME). @@ -29826,15 +30137,15 @@ - fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + Tabular format + Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. - - Tabular format - Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + @@ -29880,8 +30191,8 @@ XML Extensible Markup Language - eXtensible Markup Language (XML) format. beta12orEarlier + eXtensible Markup Language (XML) format. Data in XML format can be serialised into text, or binary format. @@ -29904,7 +30215,7 @@ Binary format. beta12orEarlier - Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. + 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. @@ -29949,7 +30260,7 @@ A broad class of format distinguished by the scientific nature of the data that is identified. beta12orEarlier - This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. + 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. @@ -29969,19 +30280,19 @@ - + - + - + BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). @@ -30497,13 +30808,13 @@ - + - + beta12orEarlier @@ -30629,7 +30940,7 @@ AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). - AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. + AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. beta12orEarlier @@ -30713,8 +31024,8 @@ bigWig - beta12orEarlier bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. + beta12orEarlier @@ -30733,8 +31044,8 @@ beta12orEarlier PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. - + @@ -30767,11 +31078,11 @@ 2bit - 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. + 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. beta12orEarlier - + @@ -30785,7 +31096,7 @@ .nib - .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. + .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. beta12orEarlier @@ -30805,8 +31116,8 @@ beta12orEarlier genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. genePred table format for gene prediction tracks. - + @@ -30837,8 +31148,8 @@ axt - beta12orEarlier axt format of alignments, typically produced from BLASTZ. + beta12orEarlier @@ -30994,7 +31305,7 @@ - + beta13 @@ -31011,8 +31322,8 @@ Raw SCOP domain classification format - These are the parsable data files provided by SCOP. beta13 + These are the parsable data files provided by SCOP. Format of raw SCOP domain classification data files. @@ -31161,13 +31472,13 @@ - 1.0 MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). + 1.0 - + @@ -31179,8 +31490,8 @@ - MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). 1.0 + MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). @@ -31202,8 +31513,8 @@ - GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). 1.0 + GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). @@ -31277,8 +31588,8 @@ 1.2 - Reflects a UCSC Browser DB table. Cytoband format for chromosome cytobands. + Reflects a UCSC Browser DB table. @@ -31362,11 +31673,11 @@ mzML - 1.2 mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. + 1.2 mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. - + @@ -31457,8 +31768,8 @@ - 1.2 GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. + 1.2 @@ -31560,8 +31871,8 @@ N-Triples - 1.2 A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. + 1.2 N-Triples should not be confused with Notation 3 which is a superset of Turtle. @@ -31791,8 +32102,8 @@ BLC - Block file format A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge. + Block file format 1.3 @@ -31913,8 +32224,8 @@ Mathematical function Computational procedure Computational subroutine - Computational operation Process + Computational operation beta12orEarlier sumo:Function Mathematical operation @@ -31945,94 +32256,94 @@ - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - Function + However, operation is not a GFO 'Concept' present only in someone's mind. + - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. + 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). - + - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. + However, one may think that an operation is not a process. + - - However, operation is not a GFO 'Concept' present only in someone's mind. + Function + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'. + 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. - - + + - Method may in addition focus on how to achieve the result, not just on what to achieve as with operation. + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Process - - However, one may think that an operation is not a process and not a physical entity. + Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool. - + - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. - Process + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. + - BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s). + Function, including an operation, can be a quality/property of e.g. a computational tool. - + - Computational tool Computational tool provides one or more operations. + Computational tool - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. + However, one may think that an operation is not a process and not a physical entity. + - - However, one may think that an operation is not a process. + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - + - Function, including an operation, can be a quality/property of e.g. a computational tool. + Method may in addition focus on how to achieve the result, not just on what to achieve as with operation. + - - 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. + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - + - Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool. + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'. - - + + @@ -32086,14 +32397,14 @@ - - + + - - + + This is a broad concept and is used a placeholder for other, more specific concepts. @@ -32134,14 +32445,14 @@ - - + + - - + + beta12orEarlier @@ -32260,14 +32571,14 @@ - - + + - - + + beta12orEarlier @@ -32286,14 +32597,14 @@ - - + + - - + + Calculate character or word composition or frequency of a molecular sequence. @@ -32338,9 +32649,9 @@ - beta12orEarlier Motif discovery Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). + beta12orEarlier Motifs and patterns might be conserved or over-represented (occur with improbable frequency). @@ -32406,9 +32717,9 @@ Transcription regulatory sequence analysis true + For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. beta13 - For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. beta12orEarlier @@ -32490,14 +32801,14 @@ - - + + - - + + Protein structural feature identification @@ -32572,8 +32883,8 @@ WHATIF: SymShellFiveXML Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s). WHATIF:ListContactsNormal - beta12orEarlier WHATIF:ListSideChainContactsNormal + beta12orEarlier WHATIF:ListSideChainContactsRelaxed WHATIF: SymShellTwoXML WHATIF:ListContactsRelaxed @@ -32613,20 +32924,20 @@ - + - - + + - - + + Protein property rendering @@ -32648,14 +32959,14 @@ - - + + - - + + Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. @@ -32702,8 +33013,8 @@ Data retrieval (feature table) - true beta12orEarlier + true Extract a sequence feature table from a sequence database entry. beta13 @@ -32719,14 +33030,14 @@ - - + + - - + + @@ -32753,13 +33064,13 @@ - + - + Feature table comparison @@ -32796,14 +33107,14 @@ - - + + - - + + beta12orEarlier @@ -32821,7 +33132,7 @@ Sequence alignment comparison - See also 'Sequence profile alignment'. + See also 'Sequence profile alignment'. beta12orEarlier Compare (typically by aligning) two molecular sequence alignments. @@ -32947,19 +33258,19 @@ - + - - + + - - + + beta12orEarlier @@ -33156,18 +33467,18 @@ - - + + - - + + - beta12orEarlier Analyse a network of protein interactions. + beta12orEarlier @@ -33214,9 +33525,9 @@ + Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). beta12orEarlier Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc). - Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). @@ -33317,14 +33628,14 @@ - - + + - - + + Analyse genetic linkage. @@ -33379,6 +33690,12 @@ + + + + + + @@ -33397,12 +33714,6 @@ - - - - - - @@ -33425,14 +33736,14 @@ - - + + - - + + beta12orEarlier @@ -33449,12 +33760,6 @@ Sequence word comparison - - - - - - beta12orEarlier Find exact character or word matches between molecular sequences without full sequence alignment. @@ -33550,14 +33855,14 @@ - - + + - - + + Sequence alignment computation @@ -33578,8 +33883,8 @@ Hybrid sequence alignment construction Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). - beta13 beta12orEarlier + beta13 true Hybrid sequence alignment @@ -33623,8 +33928,8 @@ Structure alignment - beta12orEarlier Align (superimpose) molecular tertiary structures. + beta12orEarlier @@ -33702,18 +34007,18 @@ - - + + - - + + Align sequence profiles (representing sequence alignments). - See also 'Sequence alignment comparison'. + See also 'Sequence alignment comparison'. beta12orEarlier Sequence profile alignment @@ -33731,20 +34036,20 @@ - - + + - - + + - - + + Structural (3D) profile alignment @@ -33767,14 +34072,14 @@ - - + + - - + + A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -33804,7 +34109,7 @@ - + Sequence-3D profile alignment @@ -33826,20 +34131,20 @@ - - + + - - + + - - + + Sequence-structure alignment @@ -33862,14 +34167,14 @@ - - + + - - + + Protein fold prediction @@ -33940,14 +34245,14 @@ - - + + - - + + @@ -33957,8 +34262,8 @@ Process and analyse text (typically the biomedical and informatics literature) to extract information from it. - Text data mining beta12orEarlier + Text data mining @@ -33999,14 +34304,14 @@ - - + + - - + + Design or predict oligonucleotide primers for PCR and DNA amplification etc. @@ -34028,20 +34333,20 @@ - - + + - - + + - - + + @@ -34215,8 +34520,8 @@ EST and cDNA sequence analysis - beta12orEarlier true + beta12orEarlier beta12orEarlier For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. Analyse EST or cDNA sequences. @@ -34233,8 +34538,8 @@ true Methods will typically navigate a graph of protein families of known structure. - Identify and select targets for protein structural determination. beta12orEarlier + Identify and select targets for protein structural determination. beta12orEarlier @@ -34276,14 +34581,14 @@ - - + + - - + + Assign a protein tertiary structure (3D coordinates) from raw experimental data. @@ -34303,8 +34608,8 @@ - - + + @@ -34316,19 +34621,19 @@ - + - + - - + + beta12orEarlier @@ -34350,8 +34655,8 @@ 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. beta12orEarlier - Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc. WHATIF: CorrectedPDBasXML + Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc. @@ -34367,14 +34672,14 @@ - - + + - - + + Phylogenetic tree generation @@ -34396,14 +34701,14 @@ - - + + - - + + Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. @@ -34439,13 +34744,13 @@ - + - + @@ -34471,7 +34776,7 @@ Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing). beta12orEarlier - 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. + 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. @@ -34543,13 +34848,13 @@ - + - + beta12orEarlier @@ -34674,14 +34979,14 @@ - - + + - - + + Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. @@ -34702,18 +35007,18 @@ - - + + - - + + - beta12orEarlier This excludes direct retrieval methods (e.g. the dbfetch program). + beta12orEarlier Search a sequence database by sequence comparison and retrieve similar sequences. @@ -34730,14 +35035,14 @@ - - + + - - + + Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data. @@ -34757,14 +35062,14 @@ - - + + - - + + Sequence profile database search @@ -34823,8 +35128,8 @@ beta12orEarlier Search a database of transmembrane proteins, for example for sequence or structural similarities. - true beta12orEarlier + true @@ -34866,8 +35171,8 @@ - beta12orEarlier Search a sequence database and retrieve sequences that are similar to a query sequence. + beta12orEarlier Sequence similarity search @@ -34904,14 +35209,14 @@ - - + + - - + + beta12orEarlier @@ -35006,8 +35311,8 @@ - Sequence similarity search (global alignment-based methods) beta12orEarlier + Sequence similarity search (global alignment-based methods) Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. This includes tools based on the Needleman and Wunsch algorithm. @@ -35046,8 +35351,8 @@ - - + + @@ -35058,14 +35363,14 @@ - - + + beta12orEarlier Peptide mass fingerprinting - Protein fingerprinting 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. + Protein fingerprinting @@ -35301,12 +35606,6 @@ Sequence masking - - - - - - beta12orEarlier For example, SNPs or repeats in a DNA sequence might be masked. Mask characters in a molecular sequence (replacing those characters with a mask character). @@ -35427,12 +35726,6 @@ Repeat sequence detection - - - - - - Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. beta12orEarlier @@ -35576,14 +35869,14 @@ - - + + - - + + beta12orEarlier @@ -36120,19 +36413,19 @@ - - + + - - + + - beta12orEarlier Epitope mapping is commonly done during vaccine design. Predict antigenic determinant sites (epitopes) in protein sequences. + beta12orEarlier @@ -36147,14 +36440,14 @@ - - + + - - + + 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. @@ -36175,19 +36468,19 @@ - - + + - - + + - beta12orEarlier Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. + beta12orEarlier @@ -36259,14 +36552,14 @@ - - + + - - + + Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. @@ -36283,8 +36576,8 @@ Epitope mapping (MHC Class I) - beta12orEarlier Predict epitopes that bind to MHC class I molecules. + beta12orEarlier @@ -36389,13 +36682,13 @@ - + - Quadruplex structure prediction - beta12orEarlier Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. Detect quadruplex-forming motifs in nucleotide sequences. + Quadruplex structure prediction + beta12orEarlier @@ -36439,20 +36732,20 @@ - - + + - - + + - + Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. @@ -36567,7 +36860,7 @@ - + beta12orEarlier @@ -36612,8 +36905,8 @@ - Predict translation initiation sites, possibly by searching a database of sites. beta12orEarlier + Predict translation initiation sites, possibly by searching a database of sites. @@ -36648,7 +36941,7 @@ Transcription regulatory element prediction (DNA-cis) Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences. - 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. + 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. beta12orEarlier @@ -36664,7 +36957,7 @@ beta12orEarlier Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences. - Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. + 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. @@ -36785,8 +37078,8 @@ 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. Residue conservation analysis - beta12orEarlier Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. + beta12orEarlier @@ -36900,8 +37193,8 @@ - A melting profile is used to visualise and analyse partly melted DNA conformations. beta12orEarlier + A melting profile is used to visualise and analyse partly melted DNA conformations. Calculate and plot a DNA or DNA/RNA melting profile. @@ -36942,8 +37235,8 @@ - Calculate and plot a DNA or DNA/RNA melting curve. beta12orEarlier + Calculate and plot a DNA or DNA/RNA melting curve. @@ -36998,14 +37291,14 @@ - - + + - - + + This includes properties such as. @@ -37026,7 +37319,7 @@ - + beta12orEarlier @@ -37069,8 +37362,8 @@ - beta12orEarlier Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. + beta12orEarlier @@ -37236,14 +37529,14 @@ - - + + - - + + Methods might identify thermodynamically stable or evolutionarily conserved structures. @@ -37291,10 +37584,10 @@ Protein structure comparative modelling Homology structure modelling - The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. Homology modelling - Build a three-dimensional protein model based on known (for example homologs) structures. + 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. beta12orEarlier + Build a three-dimensional protein model based on known (for example homologs) structures. Comparative modelling @@ -37311,20 +37604,20 @@ - - + + - - + + - + 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. @@ -37388,20 +37681,20 @@ - - + + - - + + + Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. Virtual ligand screening Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. beta12orEarlier - Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. @@ -37417,14 +37710,14 @@ - - + + - - + + Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. @@ -37489,8 +37782,8 @@ beta12orEarlier Map the genetic architecture of dynamic complex traits. - true This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + true beta12orEarlier @@ -37511,7 +37804,7 @@ Haplotype reconstruction - Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). + Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). beta12orEarlier Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. Haplotype inference @@ -37734,11 +38027,11 @@ - Multiple sequence alignment (phylogenetic tree-based) - Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. Phylogenetic tree-based multiple sequence alignment construction beta12orEarlier This is supposed to give a more biologically meaningful alignment than standard alignments. + Multiple sequence alignment (phylogenetic tree-based) + Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. @@ -37755,14 +38048,14 @@ - - + + - - + + Align molecular secondary structure (represented as a 1D string). @@ -37787,10 +38080,10 @@ - Secondary structure alignment (protein) - Align protein secondary structures. Protein secondary structure alignment + Secondary structure alignment (protein) beta12orEarlier + Align protein secondary structures. @@ -37806,14 +38099,14 @@ - - + + - - + + beta12orEarlier @@ -37847,8 +38140,8 @@ Multiple structure alignment construction - Multiple structure alignment beta12orEarlier + Multiple structure alignment This includes methods that use an existing alignment. Align (superimpose) two or more molecular tertiary structures. @@ -37893,11 +38186,11 @@ Pairwise structure alignment construction (local) - beta12orEarlier Local alignment methods identify regions of local similarity, common substructures etc. Pairwise structure alignment (local) - Locally align (superimpose) exactly two molecular tertiary structures. + beta12orEarlier Local pairwise structure alignment construction + Locally align (superimpose) exactly two molecular tertiary structures. @@ -37912,8 +38205,8 @@ beta12orEarlier Pairwise structure alignment (global) - Globally align (superimpose) exactly two molecular tertiary structures. Global alignment methods identify similarity across the entire structures. + Globally align (superimpose) exactly two molecular tertiary structures. Global pairwise structure alignment construction @@ -37945,8 +38238,8 @@ Multiple structure alignment construction (global) beta12orEarlier - Globally align (superimpose) two or more molecular tertiary structures. Global multiple structure alignment construction + Globally align (superimpose) two or more molecular tertiary structures. Multiple structure alignment (global) Global alignment methods identify similarity across the entire structures. @@ -37961,8 +38254,8 @@ Sequence profile alignment construction (pairwise) - Pairwise sequence profile alignment construction Align exactly two molecular profiles. + Pairwise sequence profile alignment construction beta12orEarlier Sequence profile alignment (pairwise) Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -37997,8 +38290,8 @@ beta12orEarlier Align exactly two molecular Structural (3D) profiles. Structural (3D) profile alignment (pairwise) - Methods might perform one-to-one, one-to-many or many-to-many comparisons. Pairwise structural (3D) profile alignment construction + Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -38125,8 +38418,8 @@ PCR primer design (for conserved primers) - Predict primers that are conserved across multiple genomes or species. beta12orEarlier + Predict primers that are conserved across multiple genomes or species. @@ -38174,8 +38467,8 @@ Sequence assembly (mapping assembly) The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. - beta12orEarlier Sequence assembly by combining fragments using an existing backbone sequence. + beta12orEarlier @@ -38240,9 +38533,9 @@ beta12orEarlier - Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts. Tag to gene assignment + Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. @@ -38290,8 +38583,8 @@ true Process (read and / or write) sequencing by synthesis (SBS) data. beta12orEarlier - beta12orEarlier Sequencing by synthesis data processing + beta12orEarlier @@ -38641,14 +38934,14 @@ - - + + - - + + Identify a plausible model of DNA substitution that explains a DNA sequence alignment. @@ -38697,14 +38990,14 @@ - - + + - - + + beta12orEarlier @@ -38805,8 +39098,8 @@ - - + + @@ -38817,8 +39110,8 @@ - - + + Predict and optimise peptide ligands that elicit an immunological response. @@ -38839,13 +39132,13 @@ - + - + Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. @@ -39085,14 +39378,14 @@ - - + + - - + + beta12orEarlier @@ -39116,12 +39409,6 @@ - - - - - - beta12orEarlier Visualise microarray data. @@ -39316,7 +39603,7 @@ - For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. + For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. Predict general functional properties of a protein. beta12orEarlier @@ -39405,9 +39692,9 @@ - Data submission beta12orEarlier Prepare or load a user-specified data file so that it is available for use. + Data submission Database submission WHATIF:UploadPDB @@ -39430,9 +39717,9 @@ beta12orEarlier - This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. Data retrieval (sequences) + This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. @@ -39487,7 +39774,7 @@ Protein atom surface calculation (accessible) Waters are not considered. - Calculate the solvent accessibility ('accessible surface') for each atom in a structure. + Calculate the solvent accessibility ('accessible surface') for each atom in a structure. WHATIF:AtomAccessibilitySolvent WHATIF:AtomAccessibilitySolventPlus beta12orEarlier @@ -39506,7 +39793,7 @@ WHATIF:AtomAccessibilityMolecularPlus WHATIF:AtomAccessibilityMolecular Waters are not considered. - Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. + Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. beta12orEarlier @@ -39520,9 +39807,9 @@ Protein residue surface calculation (accessible) - Calculate the solvent accessibility ('accessible surface') for each residue in a structure. - beta12orEarlier + Calculate the solvent accessibility ('accessible surface') for each residue in a structure. Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + beta12orEarlier WHATIF:ResidueAccessibilitySolvent @@ -39538,7 +39825,7 @@ beta12orEarlier WHATIF:ResidueAccessibilityVacuum - 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. + Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). @@ -39554,8 +39841,8 @@ beta12orEarlier Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. WHATIF:ResidueAccessibilityMolecular + Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. @@ -39569,7 +39856,7 @@ Protein residue surface calculation (vacuum molecular) WHATIF:ResidueAccessibilityVacuumMolecular - Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. + Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. beta12orEarlier Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). @@ -39584,9 +39871,9 @@ Protein surface calculation (accessible molecular) - Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. - WHATIF:TotAccessibilityMolecular + Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. beta12orEarlier + WHATIF:TotAccessibilityMolecular @@ -39599,8 +39886,8 @@ Protein surface calculation (accessible) - Calculate the solvent accessibility ('accessible surface') for a structure as a whole. beta12orEarlier + Calculate the solvent accessibility ('accessible surface') for a structure as a whole. WHATIF:TotAccessibilitySolvent @@ -39644,8 +39931,8 @@ Cysteine torsion angle calculation - Calculate for each cysteine (bridge) all its torsion angles. WHATIF:CysteineTorsions + Calculate for each cysteine (bridge) all its torsion angles. beta12orEarlier @@ -39692,8 +39979,8 @@ WHATIF:ShowCysteineFree Detect free cysteines in a protein structure. - beta12orEarlier A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. + beta12orEarlier @@ -39723,9 +40010,9 @@ + WHATIF:HasNucleicContacts Calculate protein residue contacts with nucleic acids in a structure. WHATIF:ShowProteiNucleicContacts - WHATIF:HasNucleicContacts beta12orEarlier @@ -39772,7 +40059,7 @@ Residue bump detection - Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance. + 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. beta12orEarlier WHATIF:ShowBumps @@ -39805,10 +40092,10 @@ WHATIF:ShowDrugContacts - WHATIF:ShowDrugContactsShort - beta12orEarlier WHATIF:ShowLigandContacts + WHATIF:ShowDrugContactsShort Calculate contacts between residues and ligands in a protein structure. + beta12orEarlier @@ -39880,8 +40167,8 @@ Residue packing validation - Identify poorly packed residues in protein structures. WHATIF: PackingQuality + Identify poorly packed residues in protein structures. beta12orEarlier @@ -39929,8 +40216,8 @@ A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. beta12orEarlier - Identify HET groups in PDB files. WHATIF: HETGroupNames + Identify HET groups in PDB files. @@ -39943,9 +40230,9 @@ DSSP secondary structure assignment - WHATIF: ResidueDSSP true beta12orEarlier + WHATIF: ResidueDSSP beta12orEarlier Determine for residue the DSSP determined secondary structure in three-state (HSC). @@ -40028,12 +40315,6 @@ - - - - - - @@ -40143,10 +40424,10 @@ Data retrieval (ontology concept) Ontology retrieval - beta13 beta12orEarlier - Query an ontology and retrieve concepts or relations. + beta13 true + Query an ontology and retrieve concepts or relations. @@ -40194,8 +40475,8 @@ Data retrieval (sequence profile) beta12orEarlier - This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. beta13 + This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. true Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. @@ -40226,18 +40507,18 @@ - - + + - - + + - Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. + Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. beta12orEarlier @@ -40254,14 +40535,14 @@ - - + + - - + + beta12orEarlier @@ -40338,12 +40619,6 @@ - - - - - - @@ -40354,6 +40629,12 @@ + + + + + + Sequence analysis (general) beta12orEarlier Analyse one or more known molecular sequences. @@ -40412,19 +40693,19 @@ - - + + - - + + + Analyse protein tertiary structural data. beta12orEarlier Structure analysis (protein) - Analyse protein tertiary structural data. @@ -40492,8 +40773,8 @@ beta12orEarlier true - Analyse gene expression and regulation data. beta12orEarlier + Analyse gene expression and regulation data. @@ -40566,8 +40847,8 @@ - beta12orEarlier Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report. + beta12orEarlier This is a broad concept and is used a placeholder for other, more specific concepts. @@ -40853,8 +41134,8 @@ Design true - Design a biological entity (typically a molecular sequence or structure) with specific properties. beta13 + Design a biological entity (typically a molecular sequence or structure) with specific properties. beta12orEarlier @@ -41173,20 +41454,20 @@ - - + + - - + + - - + + beta12orEarlier @@ -41225,8 +41506,8 @@ - - + + @@ -41237,14 +41518,14 @@ - - + + - + beta12orEarlier @@ -41270,7 +41551,7 @@ - + Gene finding @@ -41382,8 +41663,8 @@ Protein surface calculation - beta12orEarlier Calculate the solvent accessibility of a structure as a whole. + beta12orEarlier @@ -41418,14 +41699,14 @@ - - + + - - + + beta12orEarlier @@ -41548,8 +41829,8 @@ beta13 beta12orEarlier RNA family information retrieval - true Retrieve information on an RNA family. + true @@ -41562,8 +41843,8 @@ Data retrieval (gene annotation) beta13 - Retrieve information on a specific gene. true + Retrieve information on a specific gene. Gene information retrieval beta12orEarlier @@ -41629,14 +41910,14 @@ - - + + - - + + @@ -41662,14 +41943,14 @@ - - + + - - + + Sequence analysis (nucleic acid) @@ -41717,8 +41998,8 @@ - - + + @@ -41729,8 +42010,8 @@ - - + + Analyse known molecular tertiary structures. @@ -41893,8 +42174,8 @@ - Compare protein secondary structures. beta12orEarlier + Compare protein secondary structures. Protein secondary structure Secondary structure comparison (protein) @@ -41916,10 +42197,10 @@ - Predict the subcellular localization of a protein sequence. - The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. beta12orEarlier Protein targeting prediction + Predict the subcellular localization of a protein sequence. + The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. @@ -42041,20 +42322,20 @@ - - + + - - + + beta12orEarlier Network analysis - Analyse a known biological pathway or network. Pathway analysis + Analyse a known biological pathway or network. @@ -42086,18 +42367,18 @@ - - + + - - + + - beta12orEarlier Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences. + beta12orEarlier Splicing modelling @@ -42168,8 +42449,8 @@ true beta13 - beta12orEarlier Process (read and / or write) molecular sequence data. + beta12orEarlier @@ -42213,14 +42494,14 @@ - - + + - - + + beta12orEarlier @@ -42241,14 +42522,14 @@ - - + + - - + + Analyse a protein sequence alignment, typically to detect features or make predictions. @@ -42414,11 +42695,11 @@ Sequence rendering (protein) - Protein sequence visualisation - beta12orEarlier Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. + Protein sequence visualisation Protein sequence rendering Visualise, format or render a protein sequence. + beta12orEarlier @@ -42513,14 +42794,14 @@ - - + + - - + + Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). @@ -42539,14 +42820,14 @@ - - + + - - + + @@ -42578,8 +42859,8 @@ Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). 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. - beta12orEarlier Sequence mapping + beta12orEarlier @@ -42650,18 +42931,6 @@ - - - - - - - - - - - - @@ -42843,14 +43112,14 @@ - - + + - - + + 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. @@ -42870,7 +43139,7 @@ beta12orEarlier true beta12orEarlier - For non-analytical operations, see the 'Processing' branch. + For non-analytical operations, see the 'Processing' branch. Apply analytical methods to existing data of a specific type. @@ -42911,20 +43180,20 @@ - - + + - - + + - - + + beta12orEarlier @@ -42975,8 +43244,8 @@ Residue contact calculation - Calculate contacts between residues and some other group in a protein structure. beta12orEarlier + Calculate contacts between residues and some other group in a protein structure. @@ -43083,12 +43352,6 @@ Classification - - - - - - Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. beta12orEarlier @@ -43210,8 +43473,8 @@ - beta13 Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. + beta13 @@ -43269,7 +43532,7 @@ Predict general (non-positional) functional properties of a protein from analysing its sequence. - For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. + For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. beta13 @@ -43429,20 +43692,20 @@ - - + + - - + + - - + + 1.1 @@ -43511,11 +43774,11 @@ + Phred base-calling Base calling + Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. 1.1 Phred base calling - Phred base-calling - Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. @@ -43566,8 +43829,8 @@ Trim ends For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. - 1.1 Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. + 1.1 @@ -43659,7 +43922,7 @@ Genotyping - Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. + Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. 1.1 @@ -43680,11 +43943,11 @@ - Genetic variation annotation - 1.1 Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. + Genetic variation annotation Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. Sequence variation analysis + 1.1 @@ -43703,8 +43966,8 @@ Short read alignment 1.1 Read alignment - The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. Oligonucleotide alignment + The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. Oligonucleotide alignment construction Short read mapping Oligonucleotide mapping @@ -43838,9 +44101,9 @@ Methylation level analysis (gene-specific) - Many different techniques are available for this. - Measure the level of methyl cytosines in specific genes. 1.1 + Measure the level of methyl cytosines in specific genes. + Many different techniques are available for this. Gene-specific methylation analysis @@ -44067,7 +44330,7 @@ 1.1 Protein binding peak detection Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. - Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). + Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). @@ -44129,7 +44392,7 @@ 1.1 Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. - Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. + Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. @@ -44143,8 +44406,8 @@ Variant mapping Variant calling - Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. Methods often utilise a database of aligned reads. + Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. 1.1 @@ -44210,11 +44473,11 @@ - 1.1 - expression quantitative trait loci profiling expression QTL profiling Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes. eQTL profiling + 1.1 + expression quantitative trait loci profiling @@ -44262,18 +44525,18 @@ - - + + - - + + - Infer a transcriptome sequence by analysis of short sequence reads. 1.2 + Infer a transcriptome sequence by analysis of short sequence reads. @@ -44317,13 +44580,13 @@ - + - + @@ -44369,8 +44632,8 @@ Named entity recognition - Recognise named entities (text tokens) within documents. 1.3 + Recognise named entities (text tokens) within documents. @@ -44442,14 +44705,14 @@ - - + + - - + + 1.4 @@ -44539,18 +44802,18 @@ - - + + - - + + Format inference - 'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology. + 'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology. Format recognition Format identification 1.4 @@ -44605,10 +44868,10 @@ containing one item - 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. + 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. - + Topic can be a quality of an entity. @@ -44617,16 +44880,16 @@ containing one item - 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. + GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated. - + - GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated. + 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. - + @@ -44772,8 +45035,8 @@ containing one item Topic concerning the study of evolutionary relationships amongst organisms. Phylogenetic clocks Phylogenetic dating - beta12orEarlier BioCatalogue:Tree Inference + beta12orEarlier Phylogenetic stratigraphy Phylogeny reconstruction @@ -44853,9 +45116,9 @@ containing one item Bioinformatics - This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. - Topic concerning the archival, curation, processing and analysis of complex biological data. beta12orEarlier + Topic concerning the archival, curation, processing and analysis of complex biological data. + This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. @@ -44902,10 +45165,10 @@ containing one item Nucleic acid structure analysis RNA structure - Nucleic acid structure Nucleic acid thermodynamics - beta12orEarlier + Nucleic acid structure RNA structure alignment + beta12orEarlier Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. RNA alignment Nucleic acid denaturation @@ -44952,11 +45215,11 @@ containing one item Mapping - This includes 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. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. - beta12orEarlier Linkage mapping + This includes 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. It also includes resources for physical (sequence) maps 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. Linkage Genetic linkage + beta12orEarlier Topic concerning the mapping of complete (typically nucleotide) sequences. @@ -45139,14 +45402,14 @@ containing one item BioCatalogue:Protein Interaction Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. - Protein-DNA interaction BioCatalogue:Ligand Interaction - Protein-ligand interactions + Protein-DNA interaction beta12orEarlier + Protein-ligand interactions Protein-protein interactions This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. - Protein-nucleic acid interactions Protein-RNA interaction + Protein-nucleic acid interactions @@ -45212,7 +45475,6 @@ containing one item true Topic concerning protein microarray data. - @@ -45240,9 +45502,9 @@ containing one item beta12orEarlier Protein localization - Protein targeting - Protein sorting Topic concerning the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. + Protein sorting + Protein targeting @@ -45271,8 +45533,8 @@ containing one item Protein structure comparison beta12orEarlier - true Use this concept for methods that are exclusively for protein structure. + true beta12orEarlier Topic concerning the comparison of two or more protein structures. @@ -45289,8 +45551,8 @@ containing one item beta12orEarlier 1.3 - Protein residue interactions true + Protein residue interactions The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. @@ -45423,8 +45685,8 @@ containing one item Sequence editing - beta12orEarlier Edit, convert or otherwise change a molecular sequence, either randomly or specifically. + beta12orEarlier true beta12orEarlier @@ -45475,10 +45737,10 @@ containing one item Sequence comparison - beta12orEarlier BioCatalogue:Protein Sequence Similarity - BioCatalogue:Nucleotide Sequence Similarity + beta12orEarlier The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. + BioCatalogue:Nucleotide Sequence Similarity Topic concerning the comparison of two or more molecular sequences. @@ -45492,8 +45754,8 @@ containing one item Sequence sites, features and motifs - HMMs beta12orEarlier + HMMs Sequence sites Sequence profiles Protein sequence features @@ -45553,8 +45815,8 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. - Protein structural features Structural motifs + Protein structural features @@ -45683,8 +45945,8 @@ positional features such as functional and other key sites, in molecular sequenc Protein secondary structure prediction true - beta12orEarlier 1.3 + beta12orEarlier Topic concerning the prediction of secondary or supersecondary structure of protein sequences. @@ -45730,8 +45992,8 @@ positional features such as functional and other key sites, in molecular sequenc Sequence alignment BioCatalogue:Protein Multiple Alignment - Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). BioCatalogue:Protein Pairwise Alignment + Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). beta12orEarlier This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. BioCatalogue:Nucleotide Multiple Alignment @@ -45800,13 +46062,13 @@ positional features such as functional and other key sites, in molecular sequenc Phylogeny reconstruction BioCatalogue:Tree Inference - Currently too specific for the topic sub-ontology (but might be unobsoleted). - Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. - BioCatalogue:Evolutionary Distance Measurements beta12orEarlier + Currently too specific for the topic sub-ontology (but might be unobsoleted). true 1.3 - http://edamontology.org/topic_0084 + Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. + BioCatalogue:Evolutionary Distance Measurements + @@ -45850,9 +46112,9 @@ positional features such as functional and other key sites, in molecular sequenc Sequence assembly - Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. - beta12orEarlier This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. + beta12orEarlier + Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. Assembly @@ -45866,11 +46128,11 @@ positional features such as functional and other key sites, in molecular sequenc Genetic variation - DNA variation beta12orEarlier Polymorphism Mutation Topic concerning DNA sequence variation (mutation and polymorphism) data. + DNA variation @@ -45885,11 +46147,11 @@ positional features such as functional and other key sites, in molecular sequenc Microarrays beta12orEarlier + DNA microarrays Topic concerning microarrays, for example, to process microarray data or design probes and experiments. 1.3 - BioCatalogue:Microarrays - DNA microarrays true + BioCatalogue:Microarrays @@ -45975,8 +46237,8 @@ positional features such as functional and other key sites, in molecular sequenc Medicinal chemistry - Drug design beta12orEarlier + Drug design Topic concerning the design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. @@ -46115,8 +46377,8 @@ positional features such as functional and other key sites, in molecular sequenc Data file handling Report processing Datatypes - Data types Report handling + Data types This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. Topic concerning basic manipulations of files or reports of generic biological data. File handling @@ -46166,10 +46428,10 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning an analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. + NMR Spectroscopy Nuclear magnetic resonance spectroscopy beta12orEarlier - NMR @@ -46230,8 +46492,8 @@ positional features such as functional and other key sites, in molecular sequenc Protein modifications beta12orEarlier - MOD:00000 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) + MOD:00000 Protein post-translational modification Topic concerning protein chemical modifications, e.g. post-translational modifications. GO:0006464 @@ -46285,8 +46547,8 @@ positional features such as functional and other key sites, in molecular sequenc Literature data resources - 1.3 beta12orEarlier + 1.3 true Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. @@ -46336,8 +46598,8 @@ positional features such as functional and other key sites, in molecular sequenc Environmental science Ecoinformatics - Computational ecology beta12orEarlier + Computational ecology Ecological informatics Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics). @@ -46407,14 +46669,14 @@ positional features such as functional and other key sites, in molecular sequenc true Nucleus Ribosome - Lysosome Centriole + Lysosome beta12orEarlier Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). Smooth endoplasmic reticulum - Cell membrane - Cytoplasm Organelle genes and proteins + Cytoplasm + Cell membrane @@ -46477,8 +46739,8 @@ positional features such as functional and other key sites, in molecular sequenc Model organisms Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology. - This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. beta12orEarlier + This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. @@ -46561,8 +46823,8 @@ positional features such as functional and other key sites, in molecular sequenc Gene expression and microarray beta12orEarlier - true beta12orEarlier + true Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. @@ -46617,8 +46879,8 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier Specific protein true - 1.3 Topic concerning a particular protein, protein family or other group of proteins. + 1.3 @@ -46754,10 +47016,10 @@ positional features such as functional and other key sites, in molecular sequenc Functional, regulatory and non-coding RNA - beta12orEarlier Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). - Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). + beta12orEarlier Regulatory RNA + Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). Functional RNA Non-coding RNA @@ -46787,8 +47049,8 @@ positional features such as functional and other key sites, in molecular sequenc tRNA Topic concerning one or more transfer RNA (tRNA) sequences. - 1.3 true + 1.3 @@ -46803,8 +47065,8 @@ positional features such as functional and other key sites, in molecular sequenc This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. BioCatalogue:Protein Secondary Structure Topic concerning protein secondary structure or secondary structure alignments. - Protein secondary structure analysis beta12orEarlier + Protein secondary structure analysis @@ -46817,8 +47079,8 @@ positional features such as functional and other key sites, in molecular sequenc RNA structure - beta12orEarlier true + beta12orEarlier Topic concerning RNA secondary or tertiary structure and alignments. 1.3 @@ -46882,11 +47144,11 @@ positional features such as functional and other key sites, in molecular sequenc Protein domains and folds - BioCatalogue:Domains Protein domains + BioCatalogue:Domains Protein folds - Topic concerning protein tertiary structural domains and folds. beta12orEarlier + Topic concerning protein tertiary structural domains and folds. @@ -46914,8 +47176,8 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence alignment - A sequence profile typically represents a sequence alignment. Topic concerning protein sequence alignments. + A sequence profile typically represents a sequence alignment. true beta12orEarlier 1.3 @@ -47042,8 +47304,8 @@ positional features such as functional sites in nucleotide sequences.Workflows 1.0 - beta12orEarlier true + beta12orEarlier Topic concerning biological or biomedical analytical workflows or pipelines. @@ -47099,11 +47361,11 @@ positional features such as functional sites in nucleotide sequences.Plants beta12orEarlier - Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. - Plant Botany + Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. Plant biology The resource may be specific to a plant, a group of plants or all plants. + Plant @@ -47163,8 +47425,8 @@ positional features such as functional sites in nucleotide sequences. Arabidopsis - 1.3 true + 1.3 beta12orEarlier Topic concerning Arabidopsis-specific data. @@ -47275,10 +47537,10 @@ positional features such as functional sites in nucleotide sequences.Membrane and lipoproteins Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. - Lipoproteins Transmembrane proteins - beta12orEarlier + Lipoproteins Membrane proteins + beta12orEarlier @@ -47292,8 +47554,8 @@ positional features such as functional sites in nucleotide sequences.Enzymes Enzymology - beta12orEarlier Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. + beta12orEarlier @@ -47308,8 +47570,8 @@ positional features such as functional sites in nucleotide sequences. Structural determination This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen. - This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. 1.3 + This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. Structure determination Structural assignment Topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. @@ -47342,9 +47604,9 @@ positional features such as functional sites in nucleotide sequences. Function analysis - Topic concerning the study of gene and protein function including the prediction of functional properties of a protein. beta12orEarlier Protein function analysis + Topic concerning the study of gene and protein function including the prediction of functional properties of a protein. BioCatalogue:Function Prediction Protein function prediction @@ -47375,8 +47637,8 @@ positional features such as functional sites in nucleotide sequences. Protein databases - Protein data resources Topic concerning protein data resources. + Protein data resources beta12orEarlier 1.3 true @@ -47393,8 +47655,8 @@ positional features such as functional sites in nucleotide sequences. 1.3 true - Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. beta12orEarlier + Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. @@ -47424,7 +47686,7 @@ positional features such as functional sites in nucleotide sequences.Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. beta12orEarlier beta13 - + @@ -47549,8 +47811,8 @@ positional features such as functional sites in nucleotide sequences.Comparative modeling Molecular modeling Homology modelling - beta12orEarlier Comparative modelling + beta12orEarlier Homology modeling @@ -47580,8 +47842,8 @@ positional features such as functional sites in nucleotide sequences. SNPs - A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. + A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. beta12orEarlier @@ -47599,7 +47861,7 @@ positional features such as functional sites in nucleotide sequences.beta12orEarlier beta12orEarlier Predict transmembrane domains and topology in protein sequences. - + @@ -47646,10 +47908,10 @@ positional features such as functional sites in nucleotide sequences.Toxins and targets - Toxins beta12orEarlier Targets Topic concerning structural and associated data for toxic chemical substances. + Toxins @@ -47694,8 +47956,8 @@ positional features such as functional sites in nucleotide sequences.Nomenclature beta12orEarlier - 1.3 Topic concerning biological nomenclature (naming), symbols and terminology. + 1.3 true @@ -47850,8 +48112,8 @@ positional features such as functional sites in nucleotide sequences. 1.3 true - beta12orEarlier Topic concerning protein secondary or tertiary structure alignments. + beta12orEarlier @@ -47918,8 +48180,8 @@ positional features such as functional sites in nucleotide sequences. true beta12orEarlier - beta12orEarlier Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. + beta12orEarlier CHEBI:23367 @@ -47999,8 +48261,8 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier true - Informatics resources dedicated to one or more specific diseases (not diseases in general). beta12orEarlier + Informatics resources dedicated to one or more specific diseases (not diseases in general). @@ -48073,12 +48335,12 @@ positional features such as functional sites in nucleotide sequences. Sequence databases - 1.3 - Sequence data resources - beta13 Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles. + 1.3 Sequence data resource Sequence data + Sequence data resources + beta13 true @@ -48150,9 +48412,9 @@ positional features such as functional sites in nucleotide sequences. Mammals - Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. 1.3 beta13 + Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. true @@ -48183,11 +48445,11 @@ positional features such as functional sites in nucleotide sequences. beta13 Sequence clusters + true 1.3 Sequence families - Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity. - true This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. + Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity. @@ -48280,8 +48542,8 @@ positional features such as functional sites in nucleotide sequences.Genetic organisation true - beta13 Topic concerning the structural and functional organisation of genes and other genetic elements. + beta13 1.3 @@ -48362,10 +48624,10 @@ positional features such as functional sites in nucleotide sequences. Literature and reference - Literature sources - Literature search Topic concerning the scientific literature, reference information and documentation. + Literature sources beta13 + Literature search @@ -48451,7 +48713,7 @@ positional features such as functional sites in nucleotide sequences.1.3 Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites. beta13 - + @@ -48465,10 +48727,10 @@ positional features such as functional sites in nucleotide sequences.Topic for modelling biological systems in mathematical terms. beta13 true - BioCatalogue:Model Execution 1.2 + BioCatalogue:Model Execution BioCatalogue:Model Analysis - + @@ -48480,10 +48742,10 @@ positional features such as functional sites in nucleotide sequences.Data acquisition and deposition Topic concerning the acquisition and deposition of biological data. - Data deposition Data acquisition Database submission beta13 + Data deposition Deposition @@ -48514,10 +48776,10 @@ positional features such as functional sites in nucleotide sequences. Sequencing + Next gen sequencing Next generation sequencing 1.1 Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. - Next gen sequencing @@ -48532,14 +48794,14 @@ positional features such as functional sites in nucleotide sequences. ChIP-seq + Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. Chip-sequencing 1.1 Chip seq - 1.3 - Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. Chip sequencing + 1.3 true - + @@ -48557,8 +48819,8 @@ positional features such as functional sites in nucleotide sequences.A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. 1.3 1.1 - Whole transcriptome shotgun sequencing RNA-seq + Whole transcriptome shotgun sequencing Small RNA-seq @@ -48605,8 +48867,8 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. - Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. 1.1 + Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. @@ -48705,10 +48967,10 @@ positional features such as functional sites in nucleotide sequences. ChIP-chip 1.1 - Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. + Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. 1.3 true - + @@ -48756,8 +49018,8 @@ positional features such as functional sites in nucleotide sequences.Biochemistry - Topic concerning chemical substances and physico-chemical processes and that occur within living organisms. Biological chemistry + Topic concerning chemical substances and physico-chemical processes and that occur within living organisms. 1.3 Chemical biology @@ -49035,8 +49297,8 @@ positional features such as functional sites in nucleotide sequences. Computer science - 1.3 Topic concerning the theory and practical use of computer systems. + 1.3 @@ -49098,8 +49360,8 @@ positional features such as functional sites in nucleotide sequences. Pulmonary disorders 1.3 - Pulmonary medicine Respiratory disease + Pulmonary medicine Topic concerning the study of respiratory system. Pulmonology @@ -49116,9 +49378,9 @@ positional features such as functional sites in nucleotide sequences.Metabolic disease Topic concerning the study of metabolic diseases. + true 1.3 1.4 - true @@ -49131,8 +49393,8 @@ positional features such as functional sites in nucleotide sequences.Infectious disease 1.3 - Communicable disease Topic concerning the branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). + Communicable disease Transmissable disease @@ -49194,11 +49456,11 @@ positional features such as functional sites in nucleotide sequences. Cardiology + Cardiovascular disease Heart disease Topic concerning the diseases and abnormalities of the heart and circulatory system. 1.3 Cardiovascular medicine - Cardiovascular disease @@ -49214,8 +49476,8 @@ positional features such as functional sites in nucleotide sequences. 1.3 - This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. Topic concerning the discovery and design of drugs or potential drug compounds. + This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. @@ -49307,7 +49569,7 @@ positional features such as functional sites in nucleotide sequences.Translational medicine 1.3 - Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. + Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. @@ -49665,8 +49927,8 @@ positional features such as functional sites in nucleotide sequences. Medical imaging - Topic concerning the use of imaging techniques for clinical purposes for medical research. 1.4 + Topic concerning the use of imaging techniques for clinical purposes for medical research. @@ -49750,8 +50012,8 @@ positional features such as functional sites in nucleotide sequences. Omics - Topic concerning the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. 1.4 + Topic concerning the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. @@ -49767,9 +50029,9 @@ positional features such as functional sites in nucleotide sequences.1.4 Good laboratory practice Quality assurance - Good clinical practice Topic concerning the processes that need to be in place to ensure the quality of products for human or animal use. Good manufacturing practice + Good clinical practice @@ -49857,8 +50119,8 @@ positional features such as functional sites in nucleotide sequences.Geriatrics 1.4 Aging - Ageing Topic concerning the branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. + Ageing @@ -49924,8 +50186,8 @@ positional features such as functional sites in nucleotide sequences.Topic concerning the multidisciplinary that cares for patients with acute, life-threatening illness or injury. 1.4 Emergency medicine - Acute medicine Geriatrics + Acute medicine @@ -49967,8 +50229,8 @@ positional features such as functional sites in nucleotide sequences. Ear, nose and throat medicine - Audiovestibular medicine Head and neck disorders + Audiovestibular medicine 1.4 Otolaryngology Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. @@ -50184,12 +50446,12 @@ positional features such as functional sites in nucleotide sequences. Reproductive health - Fertility medicine - Family planning - Topic concerning the health of the reproductive processes, functions and systems at all stages of life. 1.4 + Fertility medicine Audiovestibular medicine + Family planning Reproductive disorders + Topic concerning the health of the reproductive processes, functions and systems at all stages of life. @@ -50218,10 +50480,10 @@ positional features such as functional sites in nucleotide sequences. Nephrology Urological disorders - Topic concerning the branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. Kidney disease Urology 1.4 + Topic concerning the branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. @@ -50266,5 +50528,5 @@ positional features such as functional sites in nucleotide sequences. +