diff --git a/releases/EDAM.owl b/releases/EDAM.owl index b39f42e..680f943 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -1,139 +1,128 @@ - - + + + + + + + + + + + + +]> + + + - EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics, and formats - - - 1.2 - application/rdf+xml - - - 14:12:2012 12:45 - 3263 - EDAM - EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web. EDAM editors: Jon Ison and Matus Kalas. Co-authors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE (FP6, EU), EMBOSS (BBSRC, UK), eSysbio and FUGE Bioinformatics Platform (both Research Council of Norway). See http://edamontology.org for documentation and licence. - Jon Ison - Matúš Kalaš - EDAM http://edamontology.org/ "EDAM relations and concept properties" - EDAM_data http://edamontology.org/data_ "EDAM types of data" + topics "EDAM topics" EDAM_format http://edamontology.org/format_ "EDAM data formats" - EDAM_operation http://edamontology.org/operation_ "EDAM operations" - EDAM_topic http://edamontology.org/topic_ "EDAM topics" + Matúš Kalaš + 3347 + Jon Ison + EDAM: An ontology of bioinformatics operations, types of data and identifiers, data formats, and topics + 1.3 Jon Ison, Matus Kalas - operations "EDAM operations" - data "EDAM types of data" - topics "EDAM topics" - formats "EDAM data formats" - identifiers "EDAM types of identifiers" - relations "EDAM relations" + 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. 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 "EDAM" + relations "EDAM relations" + 20:02:2014 15:33 bioinformatics "Bioinformatics" + data "EDAM types of data" + identifiers "EDAM types of identifiers" + EDAM + formats "EDAM data formats" + EDAM_operation http://edamontology.org/operation_ "EDAM operations" + EDAM_topic http://edamontology.org/topic_ "EDAM topics" + + - - Singular, bioinformatics-specific operations that are functions of tools, workflows, or scripts, or can be performed manually. - operations "EDAM operations" - - - - - Types of data that are relevant in bioinformatics, commonly used as inputs, outputs, or intermediate data of analyses, or provided by databases and portals. - data "EDAM types of data" - - - - - Application domains of bioinformatics tools and resources; topics of research, studies, or analyses; approaches, techniques, and paradigms within - or directly related to - bioinformatics. - topics "EDAM topics" - - - - - Data formats commonly used in - and specific to - bioinformatics. Many format concepts in EDAM include references to their definition and documentation. - formats "EDAM data formats" - - - - - Types of identifiers that identify biological or computational entities; including resource-specific data accessions. Several identifier concepts in EDAM include regular expressions and examples. - identifiers "EDAM types of identifiers" - - - - - Types of relations - defined in EDAM - that apply between concepts, entities subject to semantic annotation, and entities and concepts (or possibly even vice versa). - relations "EDAM relations" - - - - - Types of concept properties and property modifiers, that are defined and used in EDAM in addition to the standard markup from the OBO and OWL formats and the standard Semantic Web vocabularies. - concept_properties "EDAM concept properties" - - - - - - - Created in + + + 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 - Version in which a concept was created. 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 - - + + Obsolete since Version in which a concept was made obsolete. concept_properties true - - - - Regular expression - true - 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. - concept_properties - - - + + + + Example - true - 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. concept_properties - - - - - Documentation - 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. true + 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + + + Created in concept_properties - Specification + true + Version in which a concept was created. + + + + + + + + + + @@ -141,37 +130,38 @@ + + - relations - edam - bioinformatics has format - 'A has_format B' defines for the subject A, that it has the object B as its data format. - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. - false - false false + 'A has_format B' defines for the subject A, that it has the object B as its data format. + edam + false + false + relations + 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'. - - + + + - '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. - + + @@ -179,41 +169,40 @@ - relations - edam - bioinformatics has function - 'A has_function B' defines for the subject A, that it has the object B as its function. - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. - false false - false + relations + '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 + edam + OBO_REL:bearer_of + bioinformatics OBO_REL:is_a + false - - - - OBO_REL:bearer_of + + + - In very unusual cases. - true + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. + OBO_REL:bearer_of - + - '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. - + 'OBI:has_function' only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes, with objects that are a 'function' (snap:Function). It does not define explicitly that the object is a function of the subject. - + + - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. - OBO_REL:bearer_of + In very unusual cases. + true - + @@ -221,20 +210,19 @@ - relations - edam - bioinformatics has identifier - 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. false - false false - false + 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'. + edam + 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. OBO_REL:is_a - + bioinformatics + relations + false + false + @@ -242,41 +230,40 @@ - relations + has input edam + true bioinformatics - has input - 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. - false false + '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 - true - - - - + 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. + false OBO_REL:has_participant + + + + - In very unusual cases. - true + 'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). - + + - '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. + true - + - '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. - + @@ -284,41 +271,40 @@ - relations - edam - bioinformatics has output - 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. + false false false - false - OBO_REL:is_a + '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. + + + + - In very unusual cases. - true + 'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). - + + - '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 + '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' 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 + In very unusual cases. + true - + @@ -326,55 +312,54 @@ - relations - edam - bioinformatics has topic - 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. false - false + bioinformatics 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). + 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 true + + + + + - - - - - - + + + + + + - - - - - - In very unusual cases. - true + 'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource. + - + - '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. - + '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. - + + - '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. - + + - '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. - + true + In very unusual cases. - + @@ -382,29 +367,28 @@ + 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. relations edam - bioinformatics - is format of - 'A is_format_of B' defines for the subject A, that it is a data format of the object B. - Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. + 'A is_format_of B' defines for the subject A, that it is a data format of the object B. + false false false - false - false OBO_REL:is_a - - + bioinformatics + false - - 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. + 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 - + @@ -412,42 +396,41 @@ - relations - edam - bioinformatics is function of - 'A is_function_of B' defines for the subject A, that it is a function of the object B. - Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. + bioinformatics false - false false + 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. + false true OBO_REL:is_a + 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. - - OBO_REL:function_of - - OBO_REL:inheres_in + + - In very unusual cases. - true + 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. - + - 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 + true + In very unusual cases. - + - 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 + OBO_REL:function_of + 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. - + @@ -455,21 +438,20 @@ + is identifier of + false + '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. relations + false edam bioinformatics - is identifier of - 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. - Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. false - false false - OBO_REL:is_a - false - + @@ -477,42 +459,41 @@ - relations - edam - bioinformatics is input of - 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. + '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 - 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 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 true - + relations + false + - - - OBO_REL:participates_in + + - In very unusual cases. - true + 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. - + - '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 + '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). - + + @@ -520,42 +501,41 @@ + is output of 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. + 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 + false bioinformatics - is output of - 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. false - false - false OBO_REL:is_a - true - + - - - OBO_REL:participates_in + + - In very unusual cases. - true + 'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). - + + - '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 + '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' 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 + In very unusual cases. + true - + @@ -563,51 +543,49 @@ - relations - edam - bioinformatics is topic of - 'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B). - Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. + edam false - false - 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 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). + - - - - - - + + + + + + - - OBO_REL:quality_of - In very unusual cases. - true + 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. - + - 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 + In very unusual cases. + true - + - @@ -619,7 +597,7 @@ Resource type - + true data edam @@ -635,74 +613,76 @@ - beta12orEarlier - data - edam - bioinformatics - data - - Data - Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. - Data record + + + + Datum + data + beta12orEarlier Data set - - - - - - - - + Data record + bioinformatics + data + edam + 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. + + + + + + + + - EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). - Data record + Data does however not necessarily contain statements and not necessarily about an entity. - + + - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - Datum + 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 '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. - + + - GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. - + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Data set - + - 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). - + 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). - + - 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. - + GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. - + + - 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. - + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Datum - + - Data does however not necessarily contain statements and not necessarily about an entity. - + 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. - + + @@ -711,9 +691,9 @@ Tool - - true + edam + true beta12orEarlier beta12orEarlier A bioinformatics package or tool, e.g. a standalone application or web service. @@ -728,9 +708,9 @@ Database - - true + beta12orEarlier + true data beta12orEarlier bioinformatics @@ -781,14 +761,14 @@ MeSH vocabulary - - true + data beta12orEarlier - Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. data bioinformatics beta12orEarlier + true + Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. edam @@ -799,13 +779,13 @@ HGNC vocabulary - + true + beta12orEarlier bioinformatics data Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. beta12orEarlier - beta12orEarlier edam data @@ -817,15 +797,15 @@ UMLS vocabulary - - true - edam - bioinformatics + data beta12orEarlier - beta12orEarlier data Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). + true + edam + bioinformatics + beta12orEarlier @@ -834,33 +814,34 @@ - beta12orEarlier - data - identifiers - bioinformatics - edam - identifier Identifier - A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). - - + + + + identifiers + identifier + data + bioinformatics + 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). + edam ID - - - + beta12orEarlier + + + Almost exact but limited to identifying resources. - - + + @@ -869,14 +850,14 @@ Database entry - - true + data + true An entry (retrievable via URL) from a biological database. + data bioinformatics beta12orEarlier beta12orEarlier - data edam @@ -935,11 +916,10 @@ QSAR descriptor - QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. edam beta12orEarlier data + QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. A QSAR quantitative descriptor (name-value pair) of chemical structure. data bioinformatics @@ -986,7 +966,7 @@ data bioinformatics data - SO:0001260 + SO:0001260 beta12orEarlier This concept may be used for arbitrary sequence sets and associated data arising from processing. edam @@ -1039,7 +1019,7 @@ edam DNA strand specification data - The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. + The 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 @@ -1089,7 +1069,7 @@ beta12orEarlier How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. edam - This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). + This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). data bioinformatics @@ -1123,7 +1103,7 @@ data edam beta12orEarlier - Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'. + 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'. @@ -1132,13 +1112,13 @@ Sequence signature model - + + data true + beta12orEarlier data bioinformatics - data edam - beta12orEarlier beta12orEarlier Data files used by motif or profile methods. @@ -1150,14 +1130,14 @@ Sequence signature - - true + data edam beta12orEarlier A classifier of sequences such as a sequence motif, profile or other diagnostic element. beta12orEarlier data + true bioinformatics @@ -1208,14 +1188,14 @@ Alignment of multiple molecular sequences. - beta12orEarlier data - edam + beta12orEarlier bioinformatics + edam data - - - + + + @@ -1230,7 +1210,7 @@ edam data data - Some simple value controlling a sequence alignment (or similar 'match') operation. + Some simple value controlling a sequence alignment (or similar 'match') operation. @@ -1343,7 +1323,7 @@ data Basic character data from which a phylogenetic tree may be generated. As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments - + @@ -1366,12 +1346,12 @@ The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length. Moby:phylogenetic_tree data - A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. + A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. Moby:Tree Phylogeny edam - - + + @@ -1397,14 +1377,14 @@ Protein topology - - true + edam + true beta12orEarlier bioinformatics beta12orEarlier - data The location and size of the secondary structure elements and intervening loop regions is usually indicated. + data data Predicted or actual protein topology represented as a string of protein secondary structure elements. @@ -1474,11 +1454,11 @@ Secondary structure alignment metadata (protein) - + true - beta12orEarlier edam beta12orEarlier + beta12orEarlier data An informative report on protein secondary structure alignment-derived data or metadata. bioinformatics @@ -1496,7 +1476,7 @@ - + beta12orEarlier @@ -1520,8 +1500,8 @@ beta12orEarlier data Alignment of the (1D representations of) secondary structure of two or more RNA molecules. - bioinformatics data + bioinformatics Moby:RNAStructAlignmentML @@ -1531,15 +1511,15 @@ Secondary structure alignment metadata (RNA) - + + edam + beta12orEarlier + bioinformatics true beta12orEarlier data data - edam An informative report of RNA secondary structure alignment-derived data or metadata. - beta12orEarlier - bioinformatics @@ -1564,7 +1544,8 @@ data beta12orEarlier edam - + Coordinate model + @@ -1573,15 +1554,15 @@ Tertiary structure record - - true + An entry from a molecular tertiary (3D) structure database. beta12orEarlier beta12orEarlier bioinformatics + edam data + true data - edam @@ -1665,7 +1646,7 @@ - + bioinformatics @@ -1928,8 +1909,7 @@ Protein features (mutation) - - true + Protein report (mutation) beta13 Protein structure report (mutation) @@ -1938,6 +1918,7 @@ Protein property (mutation) beta12orEarlier bioinformatics + true Data on the effect of (typically point) mutation on protein folding, stability, structure and function. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. edam @@ -2078,7 +2059,7 @@ - + This is a broad data type and is used a placeholder for other, more specific types. @@ -2123,15 +2104,15 @@ Gene classification - - true - beta12orEarlier + edam A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. - bioinformatics - data + true beta12orEarlier data + beta12orEarlier + bioinformatics + data @@ -2155,7 +2136,7 @@ Sequence variation annotation data edam - SO:0001059 + SO:0001059 @@ -2263,21 +2244,21 @@ Sequence assembly data - SO:0000353 - SO:0001248 - beta12orEarlier - An assembly of fragments of a (typically genomic) DNA sequence. - - edam data Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. + edam bioinformatics + SO:0000353 + An assembly of fragments of a (typically genomic) DNA sequence. + SO:0001248 + beta12orEarlier + - Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. - SO:0001248 + Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. + SO:0001248 - + @@ -2337,7 +2318,7 @@ - + beta12orEarlier @@ -2356,14 +2337,14 @@ Oligonucleotide probe data - - true - Data on oligonucleotide probes (typically for use with DNA microarrays). + bioinformatics - data beta13 - edam data + Data on oligonucleotide probes (typically for use with DNA microarrays). + true + data + edam beta12orEarlier @@ -2374,15 +2355,15 @@ SAGE experimental data - - true + edam data + true beta12orEarlier data beta12orEarlier - Serial analysis of gene expression (SAGE) experimental data bioinformatics + Serial analysis of gene expression (SAGE) experimental data Output from a serial analysis of gene expression (SAGE) experiment. @@ -2393,7 +2374,7 @@ MPSS experimental data - + true data edam @@ -2412,14 +2393,14 @@ SBS experimental data - + true data - bioinformatics edam + bioinformatics beta12orEarlier - Sequencing by synthesis (SBS) experimental data Sequencing by synthesis (SBS) data. + Sequencing by synthesis (SBS) experimental data data beta12orEarlier @@ -2495,7 +2476,7 @@ - + edam @@ -2517,7 +2498,7 @@ - + This might include the location in the model of the known features of a particular macromolecule. @@ -2579,12 +2560,12 @@ Peptide mass fingerprint - + - + edam @@ -2607,7 +2588,7 @@ - + beta12orEarlier @@ -2624,13 +2605,13 @@ Pathway or network annotation - - true + beta12orEarlier bioinformatics data - An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. + true data + An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. edam beta12orEarlier @@ -2642,14 +2623,14 @@ Biological pathway map - - true + + edam beta12orEarlier data A map (typically a diagram) of a biological pathway. data bioinformatics - edam + true beta12orEarlier @@ -2680,8 +2661,8 @@ edam data bioinformatics - Basic information, annotation or documentation concerning a workflow (but not the workflow itself). data + Basic information, annotation or documentation concerning a workflow (but not the workflow itself). @@ -2694,7 +2675,7 @@ - + edam @@ -2743,23 +2724,23 @@ Version information - beta12orEarlier + edam + data Information on a version of software or data, for example name, version number and release date. - Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. + beta12orEarlier bioinformatics - - - data - + Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. data - edam - + + + + Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. - - + + @@ -3057,13 +3038,13 @@ Entity identifier - - true + An identifier of a biological entity or phenomenon. identifier beta12orEarlier beta12orEarlier data + true bioinformatics edam identifiers @@ -3076,8 +3057,7 @@ Data resource identifier - - true + beta12orEarlier An identifier of a data resource. edam @@ -3085,6 +3065,7 @@ identifiers beta12orEarlier bioinformatics + true data @@ -3101,7 +3082,7 @@ data bioinformatics An identifier that identifies a particular type of data. - This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. + This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. identifier beta12orEarlier @@ -3128,12 +3109,12 @@ Discrete entity identifier - - true + identifier - identifiers bioinformatics + identifiers data + true beta12orEarlier Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). beta12orEarlier @@ -3147,16 +3128,16 @@ Entity feature identifier - - true + identifiers identifier data edam beta12orEarlier Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing). - beta12orEarlier bioinformatics + true + beta12orEarlier @@ -3166,13 +3147,13 @@ Entity collection identifier - - true + edam Name or other identifier of a collection of discrete biological entities. + true data - identifiers identifier + identifiers bioinformatics beta12orEarlier beta12orEarlier @@ -3185,11 +3166,11 @@ Phenomenon identifier - - true + data identifiers edam + true beta12orEarlier Name or other identifier of a physical, observable biological occurrence or event. beta12orEarlier @@ -3225,12 +3206,13 @@ - Atom identifier + Atom ID beta12orEarlier data Identifier (e.g. character symbol) of a specific atom. identifier + Atom identifier bioinformatics identifiers edam @@ -3245,8 +3227,8 @@ identifiers - edam beta12orEarlier + edam identifier bioinformatics data @@ -3267,7 +3249,7 @@ data edam data - For example, 'Protein', 'DNA', 'RNA' etc. + For example, 'Protein', 'DNA', 'RNA' etc. @@ -3276,8 +3258,7 @@ Chemical identifier - - true + bioinformatics edam beta12orEarlier @@ -3286,6 +3267,7 @@ identifiers identifier data + true @@ -3390,11 +3372,11 @@ Ligand identifier - - true + beta12orEarlier Code word for a ligand, for example from a PDB file. identifier + true edam data identifiers @@ -3525,7 +3507,7 @@ edam identifier data - 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). bioinformatics identifiers beta12orEarlier @@ -3841,8 +3823,8 @@ beta12orEarlier data WHATIF: number + SO:0000735 data - SO:0000735 A position of a single point (base or residue) in a sequence, or part of such a specification. bioinformatics edam @@ -3870,13 +3852,13 @@ Nucleic acid feature identifier - - true + bioinformatics Name or other identifier of an nucleic acid feature. beta12orEarlier beta12orEarlier data + true identifiers identifier edam @@ -3889,16 +3871,16 @@ Protein feature identifier - - true - edam + bioinformatics + edam identifier Name or other identifier of a protein feature. beta12orEarlier data - identifiers beta12orEarlier + identifiers + true @@ -3943,7 +3925,7 @@ 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. + A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. beta12orEarlier bioinformatics Typically an EMBL or Swiss-Prot feature label. @@ -3976,14 +3958,14 @@ Codon name - - true + bioinformatics beta12orEarlier - identifier beta12orEarlier + identifier data String of one or more ASCII characters representing a codon. + true identifiers edam @@ -4060,13 +4042,13 @@ Gene identifier (NCBI RefSeq) - - true - beta12orEarlier + An NCBI RefSeq unique identifier of a gene. + beta12orEarlier edam bioinformatics data + true identifier identifiers beta12orEarlier @@ -4079,14 +4061,14 @@ Gene identifier (NCBI UniGene) - - true + edam identifiers An NCBI UniGene unique identifier of a gene. bioinformatics identifier data + true beta12orEarlier beta12orEarlier @@ -4098,14 +4080,14 @@ Gene identifier (Entrez) - - true + data [0-9]+ edam beta12orEarlier beta12orEarlier identifier + true An Entrez unique identifier of a gene. bioinformatics identifiers @@ -4150,9 +4132,10 @@ - Gene ID (Ensembl) + Ensembl gene ID + Gene ID (Ensembl) bioinformatics data edam @@ -4160,7 +4143,6 @@ beta12orEarlier identifier identifiers - Ensembl Gene ID @@ -4400,8 +4382,8 @@ The name of a strain of an organism variant, typically a plant, virus or bacterium. beta12orEarlier identifier - bioinformatics identifiers + bioinformatics edam data @@ -4412,7 +4394,6 @@ URI - edam bioinformatics @@ -4427,7 +4408,7 @@ - Database identifier + Database ID @@ -4435,13 +4416,14 @@ + An identifier of a biological or bioinformatics database. + bioinformatics + identifiers edam identifier data beta12orEarlier - An identifier of a biological or bioinformatics database. - bioinformatics - identifiers + Database identifier @@ -4450,7 +4432,6 @@ Directory name - identifiers bioinformatics @@ -4512,8 +4493,8 @@ data Moby:URL A Uniform Resource Locator (URL). - edam bioinformatics + edam data @@ -4572,10 +4553,10 @@ Sequence database name - - true + beta13 edam + true bioinformatics The name of a molecular sequence database. identifier @@ -4612,7 +4593,7 @@ data bioinformatics identifier - 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. identifiers edam The extension of a file name. @@ -4664,12 +4645,12 @@ Database entry identifier - - true + beta12orEarlier edam identifier This concept is required for completeness. It should never have child concepts. + true identifiers beta12orEarlier An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. @@ -4684,7 +4665,6 @@ Sequence identifier - @@ -4694,10 +4674,10 @@ beta12orEarlier identifier - An identifier of molecular sequence(s) or entries from a molecular sequence database. - edam identifiers + An identifier of molecular sequence(s) or entries from a molecular sequence database. bioinformatics + edam data @@ -4730,14 +4710,14 @@ Sequence signature identifier - - true + Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. identifiers bioinformatics data edam beta12orEarlier + true beta12orEarlier identifier @@ -4773,11 +4753,11 @@ Phylogenetic distance matrix identifier - - true + identifiers data Identifier of a phylogenetic distance matrix. + true beta12orEarlier beta12orEarlier identifier @@ -4969,13 +4949,13 @@ - + - + identifiers @@ -5152,8 +5132,9 @@ - Data resource definition identifier + Data resource definition ID + Data resource definition identifier identifier Identifier of a data type definition from some provider. identifiers @@ -5168,7 +5149,7 @@ - Biological model identifier + Biological model ID @@ -5177,11 +5158,12 @@ beta12orEarlier + edam Identifier of a mathematical model, typically an entry from a database. bioinformatics identifiers + Biological model identifier data - edam identifier @@ -5195,21 +5177,9 @@ - - - - - - - - - - - - beta12orEarlier identifier Small molecule identifier @@ -5255,10 +5225,11 @@ identifier Unique identifier of a scientific article. - data bioinformatics + data identifiers beta12orEarlier + Article identifier edam @@ -5305,7 +5276,7 @@ WormBase class data - 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'. edam bioinformatics Class of an object from the WormBase database. @@ -5322,7 +5293,6 @@ Sequence accession - Sequence accession number data identifiers @@ -5341,25 +5311,13 @@ Sequence type - - data - edam - Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). - A label (text token) describing a type of molecular sequence. beta12orEarlier bioinformatics + data + edam data + 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). @@ -5450,8 +5408,7 @@ UniProt accession (extended) - - true + bioinformatics 1.0 Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. @@ -5461,6 +5418,7 @@ identifiers Q7M1G0|P43353-2|P01012.107 beta12orEarlier + true identifier @@ -5495,24 +5453,17 @@ TREMBL accession - - true + data identifier bioinformatics identifiers 1.2 edam + true Identifier of a TREMBL sequence database entry. beta12orEarlier - @@ -5609,9 +5560,9 @@ EMBOSS sequence type - - true + edam + true identifiers bioinformatics data @@ -5818,8 +5769,7 @@ BLAST sequence alignment type - - true + The type of a BLAST sequence alignment. identifiers bioinformatics @@ -5828,6 +5778,7 @@ data beta12orEarlier identifier + true @@ -5838,20 +5789,14 @@ Phylogenetic tree type - nj|upgmp data edam - A label (text token) describing the type of a phylogenetic tree. - bioinformatics data + A label (text token) describing the type of a phylogenetic tree. beta12orEarlier - For example 'nj', 'upgmp' etc. + bioinformatics + For example 'nj', 'upgmp' etc. @@ -5894,7 +5839,7 @@ 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. + For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. A label (text token) describing the type of a comparison matrix. Substitution matrix type beta12orEarlier @@ -6114,8 +6059,8 @@ identifiers edam beta12orEarlier - bioinformatics identifier + bioinformatics PIRSF[0-9]{6} data @@ -6383,16 +6328,16 @@ HIVDB identifier - - true + Identifier of an entry from the HIVDB database. beta12orEarlier - identifier bioinformatics + identifier + true beta12orEarlier identifiers - edam data + edam @@ -6454,8 +6399,7 @@ Pathway ID (aMAZE) - - true + identifier Identifier of an entry from the aMAZE database. bioinformatics @@ -6465,6 +6409,7 @@ beta12orEarlier data edam + true @@ -6620,11 +6565,12 @@ identifier urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. + identifiers.org synonym data identifiers The URI (URL or URN) of a data entity from the MIRIAM database. - beta12orEarlier bioinformatics + beta12orEarlier edam @@ -6646,7 +6592,7 @@ identifier - A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. + A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. UniProt|Enzyme Nomenclature @@ -6846,6 +6792,7 @@ NCBI taxonomy ID + beta12orEarlier identifier 9662|3483|182682 @@ -6998,15 +6945,16 @@ - Digital Object Identifier + DOI - data bioinformatics Digital Object Identifier (DOI) of a published article. + Digital Object Identifier + beta12orEarlier + data identifier (doi\:)?[0-9]{2}\.[0-9]{4}/.* identifiers - beta12orEarlier edam @@ -7054,8 +7002,8 @@ Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. edam bioinformatics - identifiers The unique name of a signature (sequence classifier) method. + identifiers identifier data beta12orEarlier @@ -7076,7 +7024,7 @@ data bioinformatics identifier - This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. + This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. @@ -7087,7 +7035,7 @@ Tool name (FASTA) identifiers - This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. + This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. identifier edam data @@ -7249,13 +7197,13 @@ - + - + beta12orEarlier @@ -7273,12 +7221,12 @@ Psiblast checkpoint file - - true + A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. bioinformatics + 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 edam data @@ -7292,11 +7240,11 @@ HMMER synthetic sequences set - - true - beta12orEarlier + data beta12orEarlier + true + beta12orEarlier Sequences generated by HMMER package in FASTA-style format. bioinformatics edam @@ -7314,15 +7262,15 @@ - + edam data A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. beta12orEarlier - bioinformatics data + bioinformatics @@ -7362,14 +7310,14 @@ vectorstrip cloning vector definition file - - true - beta12orEarlier + File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. - data edam - data bioinformatics + beta12orEarlier + data + data + true beta12orEarlier @@ -7380,15 +7328,15 @@ Primer3 internal oligo mishybridizing library - - true + beta12orEarlier bioinformatics edam data A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. - beta12orEarlier data + beta12orEarlier + true @@ -7398,14 +7346,14 @@ Primer3 mispriming library file - + + data + data + A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format. true edam beta12orEarlier - data beta12orEarlier - data - A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format. bioinformatics @@ -7416,15 +7364,15 @@ primersearch primer pairs sequence record - - true + data - edam - File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. beta12orEarlier - bioinformatics beta12orEarlier data + true + edam + File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. + bioinformatics @@ -7533,14 +7481,14 @@ Sequence information report - + true edam bioinformatics Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. beta12orEarlier - data beta12orEarlier + data data @@ -7577,11 +7525,11 @@ data General sequence features This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. - SO:0000110 + SO:0000110 bioinformatics beta12orEarlier Sequence features report - + @@ -7590,8 +7538,7 @@ Sequence features (comparative) - - true + bioinformatics beta12orEarlier data @@ -7600,6 +7547,7 @@ beta13 Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc. data + true @@ -7609,15 +7557,15 @@ Sequence property (protein) - + + edam + A report of general sequence properties derived from protein sequence data. true data beta12orEarlier data bioinformatics beta12orEarlier - edam - A report of general sequence properties derived from protein sequence data. @@ -7627,14 +7575,14 @@ Sequence property (nucleic acid) - - true + + beta12orEarlier + data beta12orEarlier + true edam data A report of general sequence properties derived from nucleotide sequence data. - beta12orEarlier - data bioinformatics @@ -7723,14 +7671,14 @@ Sequence composition table - + + beta12orEarlier true + beta12orEarlier + A table of character or word composition / frequency of a molecular sequence. data - beta12orEarlier data edam - beta12orEarlier - A table of character or word composition / frequency of a molecular sequence. bioinformatics @@ -7803,14 +7751,14 @@ DAS sequence feature annotation - - true + edam data - beta12orEarlier + true bioinformatics Annotation of a molecular sequence in DAS format. beta12orEarlier + beta12orEarlier data @@ -7898,20 +7846,14 @@ Genetic map - - - - - - Moby:GeneticMap Linkage map beta12orEarlier data edam A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. - data bioinformatics + data A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies. @@ -7927,8 +7869,8 @@ data beta12orEarlier bioinformatics - A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. edam + A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. @@ -7953,15 +7895,15 @@ Sequence signature map - - true + bioinformatics - beta12orEarlier edam beta12orEarlier data data Image of a sequence with matches to signatures, motifs or profiles. + true + beta12orEarlier @@ -8067,11 +8009,11 @@ InterPro compact match image - - true + edam data data + true bioinformatics beta12orEarlier The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. @@ -8086,7 +8028,7 @@ InterPro detailed match image - + true The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Image showing detailed information on matches between protein sequence(s) and InterPro Entries. @@ -8105,15 +8047,15 @@ InterPro architecture image - + true bioinformatics beta12orEarlier data Image showing the architecture of InterPro domains in a protein sequence. The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. - data edam + data beta12orEarlier @@ -8124,13 +8066,13 @@ SMART protein schematic - - true - SMART protein schematic in PNG format. + beta12orEarlier beta12orEarlier - edam + true data + SMART protein schematic in PNG format. + edam data bioinformatics @@ -8142,14 +8084,14 @@ GlobPlot domain image - - true - data + bioinformatics + beta12orEarlier + data edam Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. + true beta12orEarlier - beta12orEarlier data @@ -8337,13 +8279,13 @@ Gene features (exonic splicing enhancer) - + true - data - A report on exonic splicing enhancers (ESE) in an exon. edam bioinformatics beta13 + data + A report on exonic splicing enhancers (ESE) in an exon. beta12orEarlier data @@ -8359,14 +8301,14 @@ - + data A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. edam - beta12orEarlier data + beta12orEarlier bioinformatics @@ -8426,13 +8368,13 @@ Gene features (SECIS element) - + + beta12orEarlier true data data beta13 A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. - beta12orEarlier edam bioinformatics @@ -8466,8 +8408,7 @@ Protein features (sites) - - true + A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites. bioinformatics beta12orEarlier @@ -8475,6 +8416,7 @@ data Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. edam + true data @@ -8504,7 +8446,7 @@ - + data @@ -8569,10 +8511,10 @@ Protein features (epitopes) - + true - 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. data Epitope mapping is commonly done during vaccine design. beta12orEarlier @@ -8603,15 +8545,15 @@ MHC Class I epitopes report - - true - data + edam + true A report on epitopes that bind to MHC class I molecules. - beta12orEarlier bioinformatics - data beta12orEarlier + data + beta12orEarlier + data @@ -8621,13 +8563,13 @@ MHC Class II epitopes report - - true - A report on predicted epitopes that bind to MHC class II molecules. - data + data beta12orEarlier beta12orEarlier + A report on predicted epitopes that bind to MHC class II molecules. + data + true edam bioinformatics @@ -8639,12 +8581,12 @@ Protein features (PEST sites) - - true + data bioinformatics + '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 data edam A report or plot of PEST sites in a protein sequence. @@ -8658,15 +8600,15 @@ Sequence database hits scores list - - true + data beta12orEarlier + Scores from a sequence database search (for example a BLAST search). + data bioinformatics + true edam beta12orEarlier - Scores from a sequence database search (for example a BLAST search). - data @@ -8676,13 +8618,13 @@ Sequence database hits alignments list - + true - edam beta12orEarlier data Alignments from a sequence database search (for example a BLAST search). beta12orEarlier + edam bioinformatics data @@ -8694,15 +8636,15 @@ Sequence database hits evaluation data - - true + data data - bioinformatics edam beta12orEarlier - A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). beta12orEarlier + true + bioinformatics + A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). @@ -8712,13 +8654,13 @@ MEME motif alphabet - - true + bioinformatics + beta12orEarlier data + true data beta12orEarlier - beta12orEarlier Alphabet for the motifs (patterns) that MEME will search for. edam @@ -8730,14 +8672,14 @@ MEME background frequencies file - + + data + edam true + data beta12orEarlier - data beta12orEarlier bioinformatics - edam - data MEME background frequencies file. @@ -8748,14 +8690,14 @@ MEME motifs directive file - + + File of directives for ordering and spacing of MEME motifs. true + data + data beta12orEarlier edam - File of directives for ordering and spacing of MEME motifs. - data beta12orEarlier - data bioinformatics @@ -8815,7 +8757,7 @@ - + edam @@ -8836,7 +8778,7 @@ - + edam @@ -8845,7 +8787,7 @@ data beta12orEarlier Some type of statistical model representing a (typically multiple) sequence alignment. - + @@ -8870,13 +8812,13 @@ Prosite nucleotide pattern - - true + + beta12orEarlier + bioinformatics beta12orEarlier + true data A nucleotide regular expression pattern from the Prosite database. - beta12orEarlier - bioinformatics data edam @@ -8888,13 +8830,13 @@ Prosite protein pattern - - true - beta12orEarlier + data edam beta12orEarlier bioinformatics + true + beta12orEarlier data A protein regular expression pattern from the Prosite database. @@ -8986,15 +8928,15 @@ Domainatrix signature - - true + + data beta12orEarlier beta12orEarlier bioinformatics + true data edam A protein signature of the type used in the EMBASSY Signature package. - data @@ -9004,14 +8946,14 @@ HMMER NULL hidden Markov model - - true + bioinformatics + true + data + edam NULL hidden Markov model representation used by the HMMER package. data - data beta12orEarlier - edam beta12orEarlier @@ -9173,7 +9115,7 @@ beta12orEarlier data edam - + @@ -9182,14 +9124,14 @@ Sequence alignment (multiple) - - true + data + true edam - Alignment of more than two molecular sequences. beta12orEarlier - beta12orEarlier bioinformatics + Alignment of more than two molecular sequences. + beta12orEarlier data @@ -9280,15 +9222,15 @@ Hybrid sequence alignment (pair) - - true + Alignment of exactly two molecular sequences of different types. + data + beta12orEarlier edam bioinformatics beta12orEarlier - data data - beta12orEarlier + true @@ -9298,15 +9240,15 @@ Multiple nucleotide sequence alignment - - true - edam + beta12orEarlier + true data - Alignment of more than two nucleotide sequences. bioinformatics data beta12orEarlier + edam + Alignment of more than two nucleotide sequences. @@ -9316,15 +9258,15 @@ Multiple protein sequence alignment - - true + + bioinformatics data edam Alignment of more than two protein sequences. beta12orEarlier data beta12orEarlier - bioinformatics + true @@ -9350,15 +9292,15 @@ Score end gaps control - - true + bioinformatics - edam Whether end gaps are scored or not. - beta12orEarlier beta12orEarlier - data data + true + edam + beta12orEarlier + data @@ -9368,12 +9310,12 @@ Aligned sequence order - - true + Controls the order of sequences in an output sequence alignment. data data bioinformatics + true edam beta12orEarlier beta12orEarlier @@ -9431,12 +9373,12 @@ Terminal gap penalty - - true + beta12orEarlier + true data bioinformatics - A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. data edam beta12orEarlier @@ -9451,8 +9393,8 @@ Match reward score - The score for a 'match' used in various sequence database search applications with simple scoring schemes. data + The score for a 'match' used in various sequence database search applications with simple scoring schemes. edam beta12orEarlier data @@ -9466,7 +9408,7 @@ 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 bioinformatics data @@ -9495,15 +9437,15 @@ Gap opening penalty (integer) - + + beta12orEarlier true + data data - beta12orEarlier A simple floating point number defining the penalty for opening a gap in an alignment. beta12orEarlier bioinformatics edam - data @@ -9513,15 +9455,15 @@ Gap opening penalty (float) - - true + A simple floating point number defining the penalty for opening a gap in an alignment. beta12orEarlier bioinformatics beta12orEarlier + edam + true data data - edam @@ -9531,14 +9473,14 @@ Gap extension penalty (integer) - - true + edam beta12orEarlier - beta12orEarlier A simple floating point number defining the penalty for extending a gap in an alignment. - bioinformatics data + beta12orEarlier + bioinformatics + true data @@ -9549,15 +9491,15 @@ Gap extension penalty (float) - - true + data + beta12orEarlier + bioinformatics beta12orEarlier edam data A simple floating point number defining the penalty for extending a gap in an alignment. - beta12orEarlier - bioinformatics + true @@ -9567,15 +9509,15 @@ Gap separation penalty (integer) - + true + data + bioinformatics + A simple floating point number defining the penalty for gaps that are close together in an alignment. edam beta12orEarlier data - data - bioinformatics beta12orEarlier - A simple floating point number defining the penalty for gaps that are close together in an alignment. @@ -9585,15 +9527,15 @@ Gap separation penalty (float) - - true - A simple floating point number defining the penalty for gaps that are close together in an alignment. + data bioinformatics + true + edam + A simple floating point number defining the penalty for gaps that are close together in an alignment. beta12orEarlier data beta12orEarlier - edam @@ -9605,7 +9547,7 @@ Terminal gap opening penalty data - A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. edam data beta12orEarlier @@ -9624,7 +9566,7 @@ data edam beta12orEarlier - A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + 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. @@ -9664,15 +9606,15 @@ Sequence alignment metadata (quality report) - - true - Data on molecular sequence alignment quality (estimated accuracy). - beta12orEarlier + edam data bioinformatics + true data beta12orEarlier + Data on molecular sequence alignment quality (estimated accuracy). + beta12orEarlier @@ -9700,8 +9642,8 @@ Sequence alignment report (site correlation) Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures. - beta12orEarlier data + beta12orEarlier bioinformatics edam data @@ -9713,14 +9655,14 @@ Sequence-profile alignment (Domainatrix signature) - - true + beta12orEarlier - data Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). - edam beta12orEarlier bioinformatics + true + data + edam data @@ -9813,6 +9755,12 @@ Phylogenetic invariants + + + + + + bioinformatics Phylogenetic report (invariants) data @@ -9940,12 +9888,12 @@ Comparison matrix (integers) - - true + bioinformatics - beta12orEarlier Matrix of integer numbers for sequence comparison. + beta12orEarlier data + true edam data Substitution matrix (integers) @@ -9959,15 +9907,15 @@ Comparison matrix (floats) - - true + data beta12orEarlier bioinformatics - edam Substitution matrix (floats) + edam data Matrix of floating point numbers for sequence comparison. + true beta12orEarlier @@ -10011,7 +9959,7 @@ Nucleotide comparison matrix (integers) - + true Matrix of integer numbers for nucleotide comparison. beta12orEarlier @@ -10030,11 +9978,11 @@ Nucleotide comparison matrix (floats) - - true + edam Nucleotide substitution matrix (floats) beta12orEarlier + true data bioinformatics Matrix of floating point numbers for nucleotide comparison. @@ -10049,11 +9997,11 @@ Amino acid comparison matrix (integers) - - true + data - beta12orEarlier data + beta12orEarlier + true beta12orEarlier bioinformatics Amino acid substitution matrix (integers) @@ -10068,8 +10016,7 @@ Amino acid comparison matrix (floats) - - true + data beta12orEarlier data @@ -10077,6 +10024,7 @@ bioinformatics edam Matrix of floating point numbers for amino acid comparison. + true beta12orEarlier @@ -10131,13 +10079,13 @@ - + - + beta12orEarlier @@ -10155,7 +10103,7 @@ 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. data bioinformatics edam @@ -10174,13 +10122,13 @@ - + - + bioinformatics @@ -10207,7 +10155,7 @@ data beta12orEarlier bioinformatics - CHEBI:23367 + CHEBI:23367 edam data 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound. @@ -10238,7 +10186,7 @@ - + edam @@ -10337,10 +10285,10 @@ Protein chain (all atoms) - + true - data edam + data beta12orEarlier 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). data @@ -10356,8 +10304,7 @@ Protein chain (C-alpha atoms) - - true + data edam beta12orEarlier @@ -10366,6 +10313,7 @@ bioinformatics C-beta atoms from amino acid side-chains may be included. beta12orEarlier + true @@ -10376,9 +10324,9 @@ Protein domain (all atoms) - - true + data + true data beta12orEarlier 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). @@ -10395,16 +10343,16 @@ Protein domain (C-alpha atoms) - - true + beta12orEarlier beta12orEarlier bioinformatics - C-beta atoms from amino acid side-chains may be included. data + C-beta atoms from amino acid side-chains may be included. edam data 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). + true @@ -10430,15 +10378,15 @@ Structure alignment (multiple) - - true + data - edam Alignment (superimposition) of more than two molecular tertiary (3D) structures. - data - beta12orEarlier bioinformatics beta12orEarlier + edam + data + true + beta12orEarlier @@ -10496,14 +10444,14 @@ Multiple protein tertiary structure alignment - - true - bioinformatics + beta12orEarlier + true beta12orEarlier + data + bioinformatics Alignment (superimposition) of more than two protein tertiary (3D) structures. edam - data data @@ -10545,14 +10493,14 @@ Pairwise protein tertiary structure alignment (all atoms) - - true + edam + data + true + Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). beta12orEarlier beta12orEarlier - data data - Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). bioinformatics @@ -10563,10 +10511,10 @@ Pairwise protein tertiary structure alignment (C-alpha atoms) - - true + beta12orEarlier edam + true data data beta12orEarlier @@ -10582,14 +10530,14 @@ Multiple protein tertiary structure alignment (all atoms) - - true + + data + bioinformatics edam beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). data - data - bioinformatics + true beta12orEarlier @@ -10600,12 +10548,12 @@ Multiple protein tertiary structure alignment (C-alpha atoms) - - true + data data beta12orEarlier bioinformatics + true beta12orEarlier C-beta atoms from amino acid side-chains may be included. edam @@ -10635,15 +10583,15 @@ Multiple nucleic acid tertiary structure alignment - - true + beta12orEarlier - data + true Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. - data edam beta12orEarlier bioinformatics + data + data @@ -10683,13 +10631,13 @@ DaliLite hit table - - true + data data beta12orEarlier DaliLite hit table of protein chain tertiary structure alignment data. beta12orEarlier + true bioinformatics The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. edam @@ -10702,13 +10650,13 @@ Molecular similarity score - + true + edam + data beta12orEarlier bioinformatics - edam A score reflecting structural similarities of two molecules. - data data beta12orEarlier @@ -11132,13 +11080,13 @@ Protein subcellular localization - - true + beta13 An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). data - data Protein report (subcellular localization) + data + true beta12orEarlier edam bioinformatics @@ -11169,12 +11117,12 @@ MHC peptide immunogenicity report - - true + edam data bioinformatics beta12orEarlier + true data A report on the immunogenicity of MHC class I or class II binding peptides. beta13 @@ -11233,7 +11181,7 @@ - + bioinformatics @@ -11446,15 +11394,15 @@ EMBASSY domain classification - + true - An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. edam + data + beta12orEarlier + An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. bioinformatics beta12orEarlier - data data - beta12orEarlier @@ -11469,7 +11417,7 @@ edam data data - Information on a protein 'class' node from the CATH database. + Information on a protein 'class' node from the CATH database. beta12orEarlier @@ -11482,7 +11430,7 @@ data bioinformatics - Information on a protein 'architecture' node from the CATH database. + Information on a protein 'architecture' node from the CATH database. edam beta12orEarlier data @@ -11497,7 +11445,7 @@ beta12orEarlier bioinformatics - Information on a protein 'topology' node from the CATH database. + Information on a protein 'topology' node from the CATH database. edam data data @@ -11510,7 +11458,7 @@ CATH homologous superfamily - Information on a protein 'homologous superfamily' node from the CATH database. + Information on a protein 'homologous superfamily' node from the CATH database. data beta12orEarlier data @@ -11526,7 +11474,7 @@ CATH structurally similar group edam - Information on a protein 'structurally similar group' node from the CATH database. + Information on a protein 'structurally similar group' node from the CATH database. bioinformatics beta12orEarlier data @@ -11544,7 +11492,7 @@ beta12orEarlier edam bioinformatics - Information on a protein 'functional category' node from the CATH database. + Information on a protein 'functional category' node from the CATH database. data @@ -11554,10 +11502,10 @@ Protein fold recognition report - - true + beta12orEarlier edam + true data Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. bioinformatics @@ -11577,7 +11525,7 @@ - + data @@ -11600,7 +11548,7 @@ - + data @@ -11621,7 +11569,7 @@ - + Data on protein-DNA/RNA interaction(s). @@ -11685,14 +11633,14 @@ Nucleic acid melting temperature - + true - bioinformatics - beta12orEarlier - beta12orEarlier Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). data edam + bioinformatics + beta12orEarlier + beta12orEarlier data @@ -11764,14 +11712,14 @@ Vienna RNA parameters - - true + bioinformatics - edam - beta12orEarlier data + true beta12orEarlier RNA parameters used by the Vienna package. + edam + beta12orEarlier data @@ -11782,15 +11730,15 @@ Vienna RNA structure constraints - - true - beta12orEarlier + beta12orEarlier data bioinformatics Structure constraints used by the Vienna package. - data edam + true + beta12orEarlier + data @@ -11800,13 +11748,13 @@ Vienna RNA concentration data - - true + beta12orEarlier - bioinformatics + true edam data data + bioinformatics RNA concentration data used by the Vienna package. beta12orEarlier @@ -11818,14 +11766,14 @@ Vienna RNA calculated energy - + + edam true + beta12orEarlier + beta12orEarlier bioinformatics data - edam RNA calculated energy data generated by the Vienna package. - beta12orEarlier - beta12orEarlier data @@ -11874,7 +11822,7 @@ - + beta12orEarlier @@ -11908,16 +11856,16 @@ Codon adaptation index - - true - data + edam - data + data beta12orEarlier + data bioinformatics beta12orEarlier CAI A simple measure of synonymous codon usage bias often used to predict gene expression levels. + true @@ -11928,8 +11876,8 @@ Codon usage bias plot - data bioinformatics + data edam A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. data @@ -11943,8 +11891,7 @@ Nc statistic - - true + data beta12orEarlier The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons. @@ -11952,6 +11899,7 @@ data bioinformatics beta12orEarlier + true @@ -12044,11 +11992,11 @@ Affymetrix probe sets library file - - true + bioinformatics - data edam + data + true beta12orEarlier data beta12orEarlier @@ -12063,15 +12011,15 @@ Affymetrix probe sets information library file - - true + beta12orEarlier GIN file bioinformatics data - beta12orEarlier data + beta12orEarlier Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. + true edam @@ -12316,14 +12264,14 @@ CATH version information - - true - Information on a version of the CATH database. + edam + true beta12orEarlier - data bioinformatics beta12orEarlier + Information on a version of the CATH database. + data data @@ -12334,14 +12282,14 @@ Swiss-Prot to PDB mapping - - true + data - edam beta12orEarlier + beta12orEarlier + edam + true data bioinformatics - beta12orEarlier Cross-mapping of Swiss-Prot codes to PDB identifiers. @@ -12352,15 +12300,15 @@ Sequence database cross-references - - true + + data + beta12orEarlier + Cross-references from a sequence record to other databases. bioinformatics edam beta12orEarlier - data data - beta12orEarlier - Cross-references from a sequence record to other databases. + true @@ -12372,7 +12320,7 @@ Job status data - Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). + Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). bioinformatics data edam @@ -12386,12 +12334,12 @@ Job ID - - true + beta12orEarlier 1.0 edam bioinformatics + true The (typically numeric) unique identifier of a submitted job. identifiers data @@ -12435,12 +12383,12 @@ DaliLite log file - + + bioinformatics + data true beta12orEarlier - bioinformatics data - data edam DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. beta12orEarlier @@ -12453,14 +12401,14 @@ STRIDE log file - + + beta12orEarlier true + data edam - beta12orEarlier beta12orEarlier data STRIDE log file. - data bioinformatics @@ -12471,13 +12419,13 @@ NACCESS log file - - true + data - NACCESS log file. data bioinformatics beta12orEarlier + NACCESS log file. + true beta12orEarlier edam @@ -12489,14 +12437,14 @@ EMBOSS wordfinder log file - + true - data edam beta12orEarlier - beta12orEarlier bioinformatics EMBOSS wordfinder log file. + data + beta12orEarlier data @@ -12507,11 +12455,11 @@ EMBOSS domainatrix log file - - true - bioinformatics + edam data + bioinformatics + true beta12orEarlier data EMBOSS (EMBASSY) domainatrix application log file. @@ -12525,14 +12473,14 @@ EMBOSS sites log file - - true + EMBOSS (EMBASSY) sites application log file. + edam + beta12orEarlier + true data beta12orEarlier - edam data - beta12orEarlier bioinformatics @@ -12543,13 +12491,13 @@ EMBOSS supermatcher error file - - true + bioinformatics - edam - beta12orEarlier beta12orEarlier data + true + edam + beta12orEarlier EMBOSS (EMBASSY) supermatcher error file. data @@ -12561,15 +12509,15 @@ EMBOSS megamerger log file - + true - data data EMBOSS megamerger log file. beta12orEarlier beta12orEarlier edam bioinformatics + data @@ -12579,15 +12527,15 @@ EMBOSS whichdb log file - - true + beta12orEarlier data + true + data + beta12orEarlier EMBOSS megamerger log file. bioinformatics edam - data - beta12orEarlier @@ -12597,14 +12545,14 @@ EMBOSS vectorstrip log file - + + data + beta12orEarlier true EMBOSS vectorstrip log file. - data bioinformatics data edam - beta12orEarlier beta12orEarlier @@ -12711,15 +12659,15 @@ Hit sort order - + + data true + beta12orEarlier + Controls the order of hits (reported matches) in an output file from a database search. bioinformatics data - data edam - beta12orEarlier beta12orEarlier - Controls the order of hits (reported matches) in an output file from a database search. @@ -12752,7 +12700,7 @@ Phylogenetic tree image - See also 'Phylogenetic tree' + See also 'Phylogenetic tree' bioinformatics beta12orEarlier An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information. @@ -12851,8 +12799,8 @@ Fate map beta12orEarlier - A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. edam + A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. data data bioinformatics @@ -12880,15 +12828,15 @@ BioPax - - true + data bioinformatics + beta12orEarlier + edam + true data beta12orEarlier A term from the BioPax ontology. - beta12orEarlier - edam @@ -12898,12 +12846,12 @@ GO - - true + Moby:GO_Term Moby:GOTerm beta12orEarlier A term definition from The Gene Ontology (GO). + true Moby:Annotated_GO_Term_With_Probability data Moby:Annotated_GO_Term @@ -12921,14 +12869,14 @@ MeSH - - true + + A term from the MeSH vocabulary. + edam beta12orEarlier beta12orEarlier bioinformatics - A term from the MeSH vocabulary. data - edam + true data @@ -12939,13 +12887,13 @@ HGNC - - true + + data bioinformatics beta12orEarlier edam A term from the HGNC controlled vocabulary. - data + true beta12orEarlier data @@ -12957,13 +12905,13 @@ NCBI taxonomy vocabulary - - true + + beta12orEarlier + bioinformatics data A term from the NCBI taxonomy vocabulary. edam - beta12orEarlier - bioinformatics + true beta12orEarlier data @@ -12975,15 +12923,15 @@ Plant ontology term - - true + bioinformatics + beta12orEarlier + beta12orEarlier + true data edam A term from the Plant Ontology (PO). data - beta12orEarlier - beta12orEarlier @@ -12993,15 +12941,15 @@ UMLS - - true + data A term from the UMLS vocabulary. - edam beta12orEarlier beta12orEarlier bioinformatics data + true + edam @@ -13011,9 +12959,9 @@ FMA - - true + edam + true data beta12orEarlier bioinformatics @@ -13030,12 +12978,12 @@ EMAP - - true - beta12orEarlier - data + edam beta12orEarlier + beta12orEarlier + data + true bioinformatics A term from the EMAP mouse ontology. data @@ -13048,15 +12996,15 @@ ChEBI - - true + edam + beta12orEarlier + A term from the ChEBI ontology. beta12orEarlier data data bioinformatics - beta12orEarlier - A term from the ChEBI ontology. + true @@ -13066,13 +13014,13 @@ MGED - - true + data A term from the MGED ontology. + beta12orEarlier beta12orEarlier data - beta12orEarlier + true bioinformatics edam @@ -13084,12 +13032,12 @@ myGrid - - true - beta12orEarlier + bioinformatics + beta12orEarlier A term from the myGrid ontology. data + true data edam beta12orEarlier @@ -13103,11 +13051,11 @@ GO (biological process) - - true + Data Type is an enumerated string. beta12orEarlier data + true A term definition for a biological process from the Gene Ontology (GO). edam data @@ -13122,12 +13070,12 @@ GO (molecular function) - - true + beta12orEarlier bioinformatics Data Type is an enumerated string. data + true beta12orEarlier edam data @@ -13141,13 +13089,13 @@ GO (cellular component) - - true + A term definition for a cellular component from the Gene Ontology (GO). beta12orEarlier + true data - Data Type is an enumerated string. data + Data Type is an enumerated string. beta12orEarlier bioinformatics edam @@ -13205,15 +13153,15 @@ Ontology concept reference - - true + data edam beta12orEarlier data + true + beta12orEarlier bioinformatics Reference for a concept from an ontology. - beta12orEarlier @@ -13223,12 +13171,12 @@ doc2loc document information - - true + Information on a published article provided by the doc2loc program. The doc2loc output includes the url, format, type and availability code of a document for every service provider. data edam + true beta12orEarlier data beta12orEarlier @@ -13357,7 +13305,7 @@ data bioinformatics Data on a single atom from a protein structure. - CHEBI:33250 + CHEBI:33250 Atom data edam @@ -13438,16 +13386,16 @@ CATH domain report - - true + edam bioinformatics + true beta12orEarlier data - The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. Summary of domain classification information for a CATH domain. - data + 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 + data @@ -13457,15 +13405,15 @@ CATH representative domain sequences (ATOM) - - true + data + true FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). + data + bioinformatics beta12orEarlier beta12orEarlier edam - data - bioinformatics @@ -13475,14 +13423,14 @@ CATH representative domain sequences (COMBS) - - true + beta12orEarlier + FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). + edam beta12orEarlier bioinformatics - FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). data - edam + true data @@ -13493,15 +13441,15 @@ CATH domain sequences (ATOM) - - true + + edam + FASTA sequence database for all CATH domains (based on PDB ATOM records). + bioinformatics data beta12orEarlier data beta12orEarlier - edam - FASTA sequence database for all CATH domains (based on PDB ATOM records). - bioinformatics + true @@ -13511,15 +13459,15 @@ CATH domain sequences (COMBS) - - true + data beta12orEarlier edam - bioinformatics beta12orEarlier FASTA sequence database for all CATH domains (based on COMBS sequence data). data + true + bioinformatics @@ -13560,16 +13508,16 @@ Protein report (function) - - true + beta12orEarlier - edam bioinformatics + edam 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. data data + true @@ -13579,8 +13527,10 @@ Gene name (ASPGD) - + edam + true + 1.3 http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS identifier identifiers @@ -13588,6 +13538,7 @@ Name of a gene from Aspergillus Genome Database. beta12orEarlier bioinformatics + @@ -13596,15 +13547,18 @@ Gene name (CGD) - + data - identifier - beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS - bioinformatics + beta12orEarlier + identifier + true edam Name of a gene from Candida Genome Database. identifiers + 1.3 + bioinformatics + @@ -13613,15 +13567,18 @@ Gene name (dictyBase) - + Name of a gene from dictyBase database. + 1.3 beta12orEarlier edam identifiers - bioinformatics + true data + bioinformatics http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase identifier + @@ -13630,16 +13587,19 @@ Gene name (EcoGene primary) - + identifier + 1.3 + true EcoGene primary gene name - identifiers data + identifiers Primary name of a gene from EcoGene Database. edam beta12orEarlier bioinformatics http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G + @@ -13648,15 +13608,18 @@ Gene name (MaizeGDB) - - beta12orEarlier + identifier - identifiers bioinformatics + identifiers edam - Name of a gene from MaizeGDB (maize genes) database. + 1.3 data + beta12orEarlier + true + Name of a gene from MaizeGDB (maize genes) database. http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus + @@ -13665,16 +13628,18 @@ Gene name (SGD) - - + data bioinformatics beta12orEarlier + 1.3 identifier edam Name of a gene from Saccharomyces Genome Database. identifiers http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS + true + @@ -13683,15 +13648,18 @@ Gene name (TGD) - + data - http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS + true identifiers - Name of a gene from Tetrahymena Genome Database. edam - bioinformatics identifier beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS + 1.3 + Name of a gene from Tetrahymena Genome Database. + bioinformatics + @@ -13700,15 +13668,18 @@ Gene name (CGSC) - + Symbol of a gene from E.coli Genetic Stock Center. + identifiers + http://www.geneontology.org/doc/GO.xrf_abbs: CGSC + 1.3 + beta12orEarlier bioinformatics data - identifiers identifier - http://www.geneontology.org/doc/GO.xrf_abbs: CGSC + true edam - beta12orEarlier + @@ -13717,7 +13688,7 @@ Gene name (HGNC) - + Symbol of a gene approved by the HUGO Gene Nomenclature Committee. HGNC gene symbol Gene name (HUGO) @@ -13732,9 +13703,12 @@ Official gene name bioinformatics HGNC symbol + true + 1.3 HUGO symbol beta12orEarlier data + @@ -13743,16 +13717,19 @@ Gene name (MGD) - + identifier beta12orEarlier + true + 1.3 http://www.geneontology.org/doc/GO.xrf_abbs: MGD MGI:[0-9]+ - edam bioinformatics + edam identifiers data Symbol of a gene from the Mouse Genome Database. + @@ -13761,15 +13738,18 @@ Gene name (Bacillus subtilis) - + data + 1.3 + true + edam bioinformatics beta12orEarlier identifier Symbol of a gene from Bacillus subtilis Genome Sequence Project. identifiers http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG - edam + @@ -13831,13 +13811,13 @@ Gene ID (GeneDB Glossina morsitans) - - true + beta12orEarlier Gene identifier from Glossina morsitans GeneDB database. beta13 http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans identifier + true bioinformatics identifiers data @@ -13851,10 +13831,10 @@ Gene ID (GeneDB Leishmania major) - - true + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor + true bioinformatics identifiers Gene identifier from Leishmania major GeneDB database. @@ -13871,8 +13851,7 @@ Gene ID (GeneDB Plasmodium falciparum) - - true + beta12orEarlier identifiers edam @@ -13881,6 +13860,7 @@ identifier beta13 data + true bioinformatics @@ -13891,13 +13871,13 @@ Gene ID (GeneDB Schizosaccharomyces pombe) - - true + bioinformatics identifier edam - beta12orEarlier + true http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe + beta12orEarlier Gene identifier from Schizosaccharomyces pombe GeneDB database. beta13 data @@ -13911,11 +13891,11 @@ Gene ID (GeneDB Trypanosoma brucei) - - true + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei beta12orEarlier identifier + true edam data bioinformatics @@ -14004,8 +13984,7 @@ Gene synonym - - true + identifier Any name (other than the recommended one) for a gene. Gene name synonym @@ -14013,8 +13992,9 @@ identifiers bioinformatics beta12orEarlier - edam beta12orEarlier + edam + true @@ -14041,15 +14021,15 @@ Sequence assembly component - - true + data - beta12orEarlier - bioinformatics beta12orEarlier - A component of a larger sequence assembly. edam data + beta12orEarlier + bioinformatics + true + A component of a larger sequence assembly. @@ -14059,13 +14039,13 @@ Chromosome annotation (aberration) - - true - edam + A report on a chromosome aberration such as abnormalities in chromosome structure. beta12orEarlier beta12orEarlier bioinformatics + edam + true data data @@ -14147,10 +14127,10 @@ Deletion-based cytogenetic map bioinformatics edam - data A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. + data 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. data @@ -14209,13 +14189,13 @@ Map feature - - true - Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. + + Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. beta12orEarlier edam Moby:MapFeature A feature which may mapped (positioned) on a genetic or other type of map. + true data beta12orEarlier bioinformatics @@ -14237,7 +14217,7 @@ data data edam - Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. + Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. A designation of the type of map (genetic map, physical map, sequence map etc) or map set. bioinformatics @@ -14330,7 +14310,7 @@ identifier Taxonomic information bioinformatics - Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. + Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. Taxonomic name Moby:iANT_organism-xml data @@ -14353,8 +14333,8 @@ A unique identifier for an organism used in the iHOP database. Moby_namespace:iHOPorganism beta12orEarlier - bioinformatics edam + bioinformatics identifiers @@ -14396,15 +14376,15 @@ Synonym - - true + An alternative for a word. + true data edam data beta12orEarlier - Alternative name bioinformatics + Alternative name beta12orEarlier @@ -14415,14 +14395,14 @@ Misspelling - - true - beta12orEarlier + bioinformatics edam beta12orEarlier data data + beta12orEarlier + true A common misspelling of a word. @@ -14433,15 +14413,15 @@ Acronym - - true + beta12orEarlier - data edam data bioinformatics - An abbreviation of a phrase or word. beta12orEarlier + true + data + An abbreviation of a phrase or word. @@ -14451,13 +14431,13 @@ Misnomer - - true + bioinformatics edam beta12orEarlier beta12orEarlier data + true A term which is likely to be misleading of its meaning. data @@ -14471,8 +14451,8 @@ Author ID beta12orEarlier - identifiers Moby:Author + identifiers edam data identifier @@ -14509,8 +14489,8 @@ data bioinformatics A URI along with annotation describing the data found at the address. - beta12orEarlier edam + beta12orEarlier @@ -14519,15 +14499,15 @@ UniProt keywords - - true - A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. + bioinformatics data beta12orEarlier + data + A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. beta12orEarlier + true edam - data @@ -14571,12 +14551,12 @@ Gene ID (MIPS Maize) - - true + bioinformatics edam identifiers data + true identifier beta13 Moby_namespace:MIPS_GE_Maize @@ -14592,8 +14572,7 @@ Gene ID (MIPS Medicago) - - true + bioinformatics beta13 identifier @@ -14601,8 +14580,9 @@ MIPS genetic element identifier (Medicago) Identifier for genetic elements in MIPS Medicago database. Moby_namespace:MIPS_GE_Medicago - edam + true data + edam identifiers @@ -14613,15 +14593,18 @@ Gene name (DragonDB) - - Moby_namespace:DragonDB_Gene + beta12orEarlier + edam + true + Moby_namespace:DragonDB_Gene + 1.3 bioinformatics identifiers data - edam The name of an Antirrhinum Gene from the DragonDB database. identifier + @@ -14630,15 +14613,18 @@ Gene name (Arabidopsis) - + + 1.3 + edam + true bioinformatics data beta12orEarlier identifier - edam A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. identifiers Moby_namespace:ArabidopsisGeneSymbol + @@ -14666,7 +14652,7 @@ Gene name (GeneFarm) - + identifiers edam GeneFarm gene ID @@ -14675,7 +14661,10 @@ beta12orEarlier identifier data + 1.3 + true Name of a gene from the GeneFarm database. + @@ -14912,10 +14901,10 @@ Quantitative trait locus - - true + Moby:SO_QTL edam + true A QTL sometimes but does not necessarily correspond to a gene. data A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment). @@ -15015,12 +15004,12 @@ Ordered locus name - - true - beta12orEarlier + edam + beta12orEarlier A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. bioinformatics + true identifiers data identifier @@ -15033,27 +15022,29 @@ - Map position + Sequence coordinates + Moby:GCP_MapInterval + beta12orEarlier + Moby:HitPosition + bioinformatics + Moby:Position + Map position PDBML:_atom_site.id Moby:GCP_MapPoint Moby:GCP_MapPosition - Moby:GCP_MapInterval - This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. - beta12orEarlier Moby:Locus Moby:MapPosition - Moby:HitPosition + 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 data A position in a map (for example a genetic map), either a single position (point) or a region / interval. data edam - bioinformatics + Sequence co-ordinates Locus - Moby:Position @@ -15078,16 +15069,16 @@ Annotation - - true + A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. bioinformatics beta12orEarlier - data data - beta13 + data This is a broad data type and is used a placeholder for other, more specific types. + beta13 edam + true @@ -15118,15 +15109,15 @@ Vienna RNA structural data - - true + beta12orEarlier edam beta12orEarlier - data - data bioinformatics Data used by the Vienna RNA analysis package. + true + data + data @@ -15197,8 +15188,7 @@ Experimental data - - true + Experimental measurement data edam data @@ -15206,6 +15196,7 @@ bioinformatics beta12orEarlier Raw data from or annotation on laboratory experiments. + 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. data @@ -15275,11 +15266,11 @@ data One or more molecular sequences, possibly with associated annotation. data - bioinformatics - This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. beta12orEarlier - - + 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. + bioinformatics + + @@ -15325,14 +15316,14 @@ data document data - bioinformatics - This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location + 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. + bioinformatics Document edam A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself. Text - + @@ -15357,11 +15348,11 @@ Structural data - - true + edam beta13 Data concerning molecular structural data. + true data data beta12orEarlier @@ -15541,7 +15532,7 @@ data edam A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. - SO:0000400 + SO:0000400 beta12orEarlier @@ -15584,15 +15575,15 @@ Accession + identifier data bioinformatics - edam A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. beta12orEarlier - - identifier + edam identifiers - + + @@ -15636,14 +15627,14 @@ Job identifier - bioinformatics + identifier identifiers - beta12orEarlier - edam - An identifier of a submitted job. + beta12orEarlier + bioinformatics data - identifier + An identifier of a submitted job. + @@ -15653,23 +15644,23 @@ Name - - - - edam - A name of a thing, which need not necessarily uniquely identify it. Symbolic name - bioinformatics - identifier identifiers - data + A name of a thing, which need not necessarily uniquely identify it. beta12orEarlier + identifier + edam + data + bioinformatics + + + Closely related, but focusing on labeling and human readability but not on identification. - - + + @@ -15681,11 +15672,11 @@ data data - edam beta12orEarlier - + edam A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values). bioinformatics + @@ -15727,18 +15718,20 @@ Gene name (KEGG GENES) - - - edam + identifiers + edam Moby_namespace:GeneId Name of an entry (gene) from the KEGG GENES database. data + 1.3 bioinformatics + true identifier [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* KEGG GENES entry name beta12orEarlier + @@ -15850,7 +15843,7 @@ edam beta12orEarlier - This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. + This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. An identifier that is re-used for data objects of fundamentally different types (typically served from a single database). identifiers data @@ -15885,7 +15878,7 @@ - Codon usage table identifier + Codon usage table ID @@ -15899,6 +15892,7 @@ + Codon usage table identifier data identifier edam @@ -15964,13 +15958,13 @@ Nucleic acid features (codon) - - true + beta12orEarlier data data - bioinformatics An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon. + bioinformatics + true beta12orEarlier edam @@ -16010,8 +16004,8 @@ bioinformatics edam data - identifier An identifier of a software end-user (typically a person). + identifier @@ -16144,15 +16138,15 @@ Mutation type - - true + bioinformatics - A type of point or block mutation, including insertion, deletion, change, duplication and moves. - beta12orEarlier + true data - edam data beta12orEarlier + A type of point or block mutation, including insertion, deletion, change, duplication and moves. + beta12orEarlier + edam @@ -16194,15 +16188,15 @@ Toggle - - true - data + edam beta12orEarlier + data + data + true bioinformatics A simple parameter that is a toggle (boolean value), typically a control for a modal tool. beta12orEarlier - data @@ -16212,14 +16206,14 @@ Sequence width - - true + The width of an output sequence or alignment. beta12orEarlier bioinformatics data - beta12orEarlier edam + true + beta12orEarlier data @@ -16277,7 +16271,7 @@ Window step size - Size of the incremental 'step' a sequence window is moved over a sequence. + Size of the incremental 'step' a sequence window is moved over a sequence. bioinformatics data beta12orEarlier @@ -16291,12 +16285,12 @@ EMBOSS graph - - true + An image of a graph generated by the EMBOSS suite. + true + beta12orEarlier bioinformatics beta12orEarlier - beta12orEarlier data data edam @@ -16309,14 +16303,14 @@ EMBOSS report - - true + edam + An application report generated by the EMBOSS suite. + bioinformatics + true beta12orEarlier data beta12orEarlier - An application report generated by the EMBOSS suite. - bioinformatics data @@ -16358,11 +16352,11 @@ Protein report (transcription factor) - - true + data edam An informative report on a transcription factor protein. + true data beta12orEarlier Transcription factor binding site data @@ -16378,12 +16372,12 @@ Database category name - - true + identifiers beta12orEarlier identifier The name of a category of biological or bioinformatics database. + true edam bioinformatics beta12orEarlier @@ -16397,8 +16391,7 @@ Sequence profile name - - true + data bioinformatics edam @@ -16407,6 +16400,7 @@ beta12orEarlier beta12orEarlier identifiers + true @@ -16416,9 +16410,9 @@ Color - - true + beta12orEarlier + true beta12orEarlier data Specification of one or more colors. @@ -16483,7 +16477,7 @@ Word composition - + true edam beta12orEarlier @@ -16563,14 +16557,14 @@ Protein sequence properties plot - - true + A plot of general physicochemical properties of a protein sequence. - edam - beta12orEarlier data beta12orEarlier data + edam + beta12orEarlier + true bioinformatics @@ -16645,7 +16639,7 @@ - + A report on siRNA duplexes in mRNA. @@ -16662,11 +16656,11 @@ Sequence set (stream) - - true + data - This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. data + true + This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. beta12orEarlier edam bioinformatics @@ -16698,10 +16692,10 @@ Cardinality - - true + beta12orEarlier data + true beta12orEarlier edam data @@ -16715,7 +16709,7 @@ Exactly 1 - + true bioinformatics edam @@ -16732,11 +16726,11 @@ 1 or more - - true + beta12orEarlier edam bioinformatics + true beta12orEarlier One or more things. data @@ -16749,11 +16743,11 @@ Exactly 2 - - true + data beta12orEarlier edam + true beta12orEarlier bioinformatics Exactly two things. @@ -16766,11 +16760,11 @@ 2 or more - - true + data edam data + true beta12orEarlier bioinformatics beta12orEarlier @@ -16804,15 +16798,15 @@ Protein features (chemical modification) - Protein modification annotation - data + GO:0006464 + edam + data + MOD:00000 bioinformatics + Protein modification annotation Data on a chemical modification of a protein. + data beta12orEarlier - MOD:00000 - GO:0006464 - edam - data @@ -16851,15 +16845,15 @@ Gene cluster - - true + A cluster of similar genes. - beta12orEarlier - data edam + true beta13 - data bioinformatics + beta12orEarlier + data + data @@ -16877,7 +16871,7 @@ edam bioinformatics data - + @@ -16919,13 +16913,13 @@ Mutation annotation (basic) - - true + data + beta12orEarlier beta12orEarlier + true edam data - beta12orEarlier bioinformatics Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style. @@ -16937,15 +16931,15 @@ Mutation annotation (prevalence) - - true + edam data beta12orEarlier An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. - bioinformatics data beta12orEarlier + true + bioinformatics @@ -16955,15 +16949,15 @@ Mutation annotation (prognostic) - - true + data + true beta12orEarlier + beta12orEarlier + bioinformatics An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study. edam - beta12orEarlier data - bioinformatics @@ -16973,15 +16967,15 @@ Mutation annotation (functional) - - true + data + edam + true + An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on. beta12orEarlier data beta12orEarlier bioinformatics - edam - An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on. @@ -17090,15 +17084,15 @@ Raw SCOP domain classification - - true + Raw SCOP domain classification data files. beta12orEarlier + true These are the parsable data files provided by SCOP. beta13 data - bioinformatics data + bioinformatics edam @@ -17109,14 +17103,14 @@ Raw CATH domain classification - - true + beta12orEarlier bioinformatics data beta13 Raw CATH domain classification data files. data + true These are the parsable data files provided by CATH. edam @@ -17132,7 +17126,7 @@ bioinformatics edam data - 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 data @@ -17143,15 +17137,15 @@ Phylogenetic property values - - true + beta12orEarlier + true data data + bioinformatics Phylogenetic property values data. edam beta12orEarlier - bioinformatics @@ -17177,13 +17171,13 @@ Phylogenetic consensus tree - - true - data + beta12orEarlier - beta12orEarlier bioinformatics + data + beta12orEarlier A consensus phylogenetic tree derived from comparison of multiple trees. + true edam data @@ -17306,8 +17300,8 @@ Gene ID (MIPS) MIPS genetic element identifier - identifiers beta12orEarlier + identifiers data bioinformatics Identifier for genetic elements in MIPS database. @@ -17321,7 +17315,7 @@ Sequence identifier (protein) - + true identifier data @@ -17340,9 +17334,9 @@ Sequence identifier (nucleic acid) - - true + beta12orEarlier + true identifiers An identifier of nucleotide sequence(s) or nucleotide sequence database entries. edam @@ -17478,15 +17472,18 @@ Gene name (AceView) - + + Name of an entry (gene) from the AceView genes database. + AceView gene name + data beta12orEarlier edam - Name of an entry (gene) from the AceView genes database. identifier + true identifiers - AceView gene name - data + 1.3 bioinformatics + @@ -17534,12 +17531,13 @@ beta12orEarlier - bioinformatics identifiers + Allele name + The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol. + bioinformatics edam data identifier - The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol. @@ -17548,15 +17546,18 @@ Gene name (NCBI) - + edam - identifier - bioinformatics + true Name of an entry (gene) from the NCBI genes database. - NCBI gene name - identifiers + bioinformatics + 1.3 data beta12orEarlier + identifier + NCBI gene name + identifiers + @@ -18092,10 +18093,10 @@ Ontological data - - true + beta13 edam + true Data concerning an ontology. This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier @@ -18212,7 +18213,8 @@ Domain-domain interaction (indirect) - + + beta12orEarlier true data data @@ -18220,7 +18222,6 @@ beta12orEarlier bioinformatics edam - beta12orEarlier @@ -18252,10 +18253,10 @@ 2D PAGE data - - true + beta12orEarlier edam + true bioinformatics This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. data @@ -18325,7 +18326,7 @@ ASTD ID - + Identifier of an object from the ASTD database. identifier @@ -18471,14 +18472,14 @@ Protein-motif interaction - - true + + edam + beta13 data beta12orEarlier Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. - edam + true data - beta13 bioinformatics @@ -18712,8 +18713,8 @@ data UPI UniParc ID - identifier Accession number of a UniParc (protein sequence) database entry. + identifier UPI[A-F0-9]{10} identifiers edam @@ -18788,14 +18789,15 @@ - Protein ID (Ensembl) + Ensembl protein ID bioinformatics Unique identifier for a protein from the Ensembl database. data - Ensembl protein ID + Protein ID (Ensembl) beta12orEarlier + Ensembl ID (protein) identifier edam identifiers @@ -18839,15 +18841,15 @@ Protein report (membrane protein) - - true - beta12orEarlier - data + bioinformatics - An informative report on a membrane protein. + true data edam beta12orEarlier + beta12orEarlier + data + An informative report on a membrane protein. @@ -18872,7 +18874,7 @@ Map data - + true edam bioinformatics @@ -18909,8 +18911,7 @@ Protein data - - true + data data beta13 @@ -18918,6 +18919,7 @@ beta12orEarlier bioinformatics Data concerning one or more protein molecules. + true This is a broad data type and is used a placeholder for other, more specific types. @@ -18928,12 +18930,12 @@ Nucleic acid data - - true + bioinformatics This is a broad data type and is used a placeholder for other, more specific types. data data + true beta12orEarlier beta13 Data concerning one or more nucleic acid molecules. @@ -18947,16 +18949,16 @@ Article data - - true + beta13 edam bioinformatics + true Data concerning the scientific literature. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. data - beta12orEarlier data + beta12orEarlier @@ -18965,27 +18967,26 @@ - - Parameter - - bioinformatics - data - edam + + Parameter or primitive Tool parameter - + bioinformatics Tool-specific parameter + data data - Parameter or primitive - beta12orEarlier Typically a simple numerical or string value that controls the operation of a tool. + beta12orEarlier + edam + + Slightly narrower in the sense of changing the characteristics of a system/function. - - + + @@ -18994,8 +18995,7 @@ Molecular data - - true + This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier beta13 @@ -19004,6 +19004,7 @@ bioinformatics data data + true Molecule-specific data @@ -19018,8 +19019,8 @@ data data edam - beta12orEarlier Molecular report + beta12orEarlier bioinformatics An informative report on a specific molecule. @@ -19108,16 +19109,13 @@ Mass spectrometry data - beta12orEarlier - + Data concerning a mass spectrometry measurement. + beta12orEarlier bioinformatics data edam data - @@ -19158,10 +19156,10 @@ Alignment data - - true + bioinformatics edam + true This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. data data @@ -19178,8 +19176,7 @@ Data index data - - true + This is a broad data type and is used a placeholder for other, more specific types. Database index beta13 @@ -19189,6 +19186,7 @@ edam data beta12orEarlier + true @@ -19317,11 +19315,11 @@ GO concept name - - true + data The name of a concept from the GO ontology. edam + true bioinformatics beta12orEarlier beta12orEarlier @@ -19337,7 +19335,7 @@ 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. bioinformatics identifiers identifier @@ -19354,7 +19352,7 @@ 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. data bioinformatics identifier @@ -19370,11 +19368,11 @@ GO concept name (cellular component) - - true + identifier bioinformatics beta12orEarlier + true identifiers edam beta12orEarlier @@ -19453,11 +19451,11 @@ Hierarchy identifier - - true + bioinformatics identifier data + true Identifier of an entry from a database of biological hierarchies. identifiers edam @@ -19488,15 +19486,15 @@ Cancer type - - true + beta12orEarlier - bioinformatics beta12orEarlier - edam A type (represented as a string) of cancer. data data + bioinformatics + edam + true @@ -19554,8 +19552,9 @@ - Catalogue identifier + Catalogue ID + Catalogue identifier An identifier of a catalogue of biological resources. beta12orEarlier identifier @@ -19588,14 +19587,14 @@ Secondary structure alignment metadata - - true + data - edam + true data bioinformatics - beta12orEarlier beta12orEarlier + edam + beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. @@ -19644,12 +19643,12 @@ Small molecule data - - true + data beta13 edam beta12orEarlier + true Data concerning one or more small molecules. data This is a broad data type and is used a placeholder for other, more specific types. @@ -19663,12 +19662,12 @@ Genotype and phenotype data - - true + Data concerning a particular genotype, phenotype or a genotype / phenotype relation. - bioinformatics data data + true + bioinformatics edam beta13 beta12orEarlier @@ -19682,14 +19681,20 @@ Microarray data - This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 - data + + + + + + edam - beta12orEarlier Image or hybridisation data for a microarray, typically a study of gene expression. + beta12orEarlier data Gene expression data bioinformatics + This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 + data @@ -20264,16 +20269,17 @@ - PubChem identifier + PubChem ID - Identifier of an entry from the PubChem database. bioinformatics - edam beta12orEarlier + PubChem identifier identifier data identifiers + Identifier of an entry from the PubChem database. + edam @@ -20465,8 +20471,8 @@ data edam Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - bioinformatics identifiers + bioinformatics PA[0-9]+ identifier beta12orEarlier @@ -20533,6 +20539,7 @@ edam A unique identifier of a type or group of cells. + Cell type ID identifier data bioinformatics @@ -20588,8 +20595,8 @@ edam identifiers Identifier of a chemical from the ChemIDplus database. - bioinformatics identifier + bioinformatics @@ -20748,8 +20755,8 @@ iRefIndex ID [0-9]+ - beta12orEarlier data + beta12orEarlier bioinformatics Unique identifier of an entry from the iRefIndex database of protein-protein interactions. identifiers @@ -20797,12 +20804,12 @@ 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). ENS([EGTP])[0-9]{11} edam bioinformatics + true identifier beta12orEarlier beta12orEarlier @@ -20816,16 +20823,16 @@ - Ensembl ID ('Bos taurus') - - true + Ensembl ID ('Bos taurus') + ENSBTA([EGTP])[0-9]{11} beta12orEarlier identifiers edam bioinformatics identifier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). data beta12orEarlier @@ -20836,8 +20843,8 @@ - Ensembl ID ('Canis familiaris') - + Ensembl ID ('Canis familiaris') + true bioinformatics edam @@ -20845,7 +20852,7 @@ identifier beta12orEarlier ENSCAF([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). data beta12orEarlier @@ -20856,9 +20863,8 @@ - Ensembl ID ('Cavia porcellus') - - true + Ensembl ID ('Cavia porcellus') + beta12orEarlier data beta12orEarlier @@ -20866,7 +20872,8 @@ identifier ENSCPO([EGTP])[0-9]{11} bioinformatics - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). + true edam @@ -20876,13 +20883,13 @@ - Ensembl ID ('Ciona intestinalis') - - true + Ensembl ID ('Ciona intestinalis') + identifier ENSCIN([EGTP])[0-9]{11} - 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). beta12orEarlier + true data bioinformatics edam @@ -20896,17 +20903,17 @@ - Ensembl ID ('Ciona savignyi') - - true + Ensembl ID ('Ciona savignyi') + identifiers + beta12orEarlier edam identifier - beta12orEarlier beta12orEarlier ENSCSAV([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). data + true bioinformatics @@ -20916,17 +20923,17 @@ - Ensembl ID ('Danio rerio') - - true + Ensembl ID ('Danio rerio') + ENSDAR([EGTP])[0-9]{11} beta12orEarlier beta12orEarlier bioinformatics identifiers data + true edam - 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). identifier @@ -20936,17 +20943,17 @@ - Ensembl ID ('Dasypus novemcinctus') - - true + Ensembl ID ('Dasypus novemcinctus') + identifier bioinformatics data + true beta12orEarlier ENSDNO([EGTP])[0-9]{11} beta12orEarlier identifiers - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). edam @@ -20956,10 +20963,9 @@ - Ensembl ID ('Echinops telfairi') - - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). + Ensembl ID ('Echinops telfairi') + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). data edam beta12orEarlier @@ -20967,6 +20973,7 @@ bioinformatics identifiers beta12orEarlier + true ENSETE([EGTP])[0-9]{11} @@ -20976,16 +20983,16 @@ - Ensembl ID ('Erinaceus europaeus') - - true + Ensembl ID ('Erinaceus europaeus') + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). data - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). identifier beta12orEarlier bioinformatics ENSEEU([EGTP])[0-9]{11} + true edam identifiers @@ -20996,17 +21003,17 @@ - Ensembl ID ('Felis catus') - - true + Ensembl ID ('Felis catus') + data edam 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} identifier beta12orEarlier identifiers + true bioinformatics @@ -21016,18 +21023,18 @@ - Ensembl ID ('Gallus gallus') - - true + Ensembl ID ('Gallus gallus') + bioinformatics beta12orEarlier identifier edam data beta12orEarlier + true identifiers + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). ENSGAL([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). @@ -21036,14 +21043,14 @@ - Ensembl ID ('Gasterosteus aculeatus') - - true + Ensembl ID ('Gasterosteus aculeatus') + edam identifier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). bioinformatics beta12orEarlier + true ENSGAC([EGTP])[0-9]{11} data identifiers @@ -21056,11 +21063,11 @@ - Ensembl ID ('Homo sapiens') - - true + Ensembl ID ('Homo sapiens') + identifier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). beta12orEarlier beta12orEarlier data @@ -21076,14 +21083,14 @@ - Ensembl ID ('Loxodonta africana') - - true + Ensembl ID ('Loxodonta africana') + identifiers ENSLAF([EGTP])[0-9]{11} + true identifier beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). beta12orEarlier bioinformatics data @@ -21096,15 +21103,15 @@ - Ensembl ID ('Macaca mulatta') - - true + Ensembl ID ('Macaca mulatta') + bioinformatics beta12orEarlier + true beta12orEarlier ENSMMU([EGTP])[0-9]{11} identifiers - 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). data identifier edam @@ -21116,16 +21123,16 @@ - Ensembl ID ('Monodelphis domestica') - - true + Ensembl ID ('Monodelphis domestica') + ENSMOD([EGTP])[0-9]{11} bioinformatics edam beta12orEarlier identifier + true identifiers - 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 data @@ -21136,18 +21143,18 @@ - Ensembl ID ('Mus musculus') - - true + Ensembl ID ('Mus musculus') + edam data identifiers identifier beta12orEarlier ENSMUS([EGTP])[0-9]{11} + true beta12orEarlier bioinformatics - 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). @@ -21156,15 +21163,15 @@ - Ensembl ID ('Myotis lucifugus') - - true + Ensembl ID ('Myotis lucifugus') + data identifiers beta12orEarlier edam bioinformatics - 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). + true identifier beta12orEarlier ENSMLU([EGTP])[0-9]{11} @@ -21177,16 +21184,16 @@ Ensembl ID ("Ornithorhynchus anatinus") - - true + identifiers ENSOAN([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). edam - beta12orEarlier bioinformatics + beta12orEarlier identifier data + true beta12orEarlier @@ -21196,17 +21203,17 @@ - Ensembl ID ('Oryctolagus cuniculus') - - true + Ensembl ID ('Oryctolagus cuniculus') + edam - 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). bioinformatics beta12orEarlier data identifiers beta12orEarlier ENSOCU([EGTP])[0-9]{11} + true identifier @@ -21216,17 +21223,17 @@ - Ensembl ID ('Oryzias latipes') - - true + 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). data - ENSORL([EGTP])[0-9]{11} identifiers + ENSORL([EGTP])[0-9]{11} edam identifier beta12orEarlier + true bioinformatics @@ -21236,12 +21243,12 @@ - Ensembl ID ('Otolemur garnettii') - - true + Ensembl ID ('Otolemur garnettii') + bioinformatics ENSSAR([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). beta12orEarlier identifiers edam @@ -21256,14 +21263,14 @@ - Ensembl ID ('Pan troglodytes') - - true + Ensembl ID ('Pan troglodytes') + identifier ENSPTR([EGTP])[0-9]{11} data identifiers - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). edam bioinformatics beta12orEarlier @@ -21276,15 +21283,15 @@ - Ensembl ID ('Rattus norvegicus') - - true + Ensembl ID ('Rattus norvegicus') + identifier - 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). bioinformatics + beta12orEarlier edam identifiers - beta12orEarlier ENSRNO([EGTP])[0-9]{11} beta12orEarlier data @@ -21296,11 +21303,10 @@ - Ensembl ID ('Spermophilus tridecemlineatus') - - true + Ensembl ID ('Spermophilus tridecemlineatus') + beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). ENSSTO([EGTP])[0-9]{11} data identifier @@ -21308,6 +21314,7 @@ beta12orEarlier edam bioinformatics + true @@ -21316,13 +21323,13 @@ - Ensembl ID ('Takifugu rubripes') - - true + Ensembl ID ('Takifugu rubripes') + edam - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). beta12orEarlier beta12orEarlier + true identifier ENSFRU([EGTP])[0-9]{11} bioinformatics @@ -21336,9 +21343,8 @@ - Ensembl ID ('Tupaia belangeri') - - true + Ensembl ID ('Tupaia belangeri') + beta12orEarlier bioinformatics beta12orEarlier @@ -21347,7 +21353,8 @@ identifier identifiers ENSTBE([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). @@ -21356,18 +21363,18 @@ - Ensembl ID ('Xenopus tropicalis') - - true + Ensembl ID ('Xenopus tropicalis') + identifiers ENSXET([EGTP])[0-9]{11} edam data + true bioinformatics beta12orEarlier beta12orEarlier identifier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). @@ -21463,7 +21470,7 @@ [0-9]{7}|GO:[0-9]{7} edam identifier - An identifier of a 'cellular compartment' concept from the Gene Ontology. + An identifier of a 'cellular compartment' concept from the Gene Ontology. identifiers bioinformatics GO concept identifier (cellular compartment) @@ -21743,17 +21750,17 @@ - Transcript ID (Ensembl) + Ensembl transcript ID Unique identifier for a gene transcript from the Ensembl database. beta12orEarlier bioinformatics edam + Transcript ID (Ensembl) identifiers data identifier - Ensembl Transcript ID @@ -21813,8 +21820,8 @@ COGEME EST ID Identifier of an EST sequence from the COGEME database. - bioinformatics beta12orEarlier + bioinformatics identifiers identifier edam @@ -21829,8 +21836,8 @@ COGEME unisequence ID identifiers - A unisequence is a single sequence assembled from ESTs. beta12orEarlier + A unisequence is a single sequence assembled from ESTs. Identifier of a unisequence from the COGEME database. bioinformatics edam @@ -21877,8 +21884,7 @@ Genus name (virus) - - true + beta12orEarlier edam data @@ -21887,6 +21893,7 @@ The name of a genus of viruses. identifiers identifier + true @@ -21896,11 +21903,11 @@ Family name (virus) - - true + bioinformatics data identifiers + true The name of a family of viruses. beta13 beta12orEarlier @@ -21915,16 +21922,16 @@ Database name (SwissRegulon) - - true + data bioinformatics beta12orEarlier edam identifier + true The name of a SwissRegulon database. - beta13 identifiers + beta13 @@ -22000,15 +22007,18 @@ Gene name (Genolist) - - Name of an entry (gene) from the Genolist genes database. - data + identifier - Genolist gene name + true beta12orEarlier bioinformatics identifiers edam + Name of an entry (gene) from the Genolist genes database. + data + 1.3 + Genolist gene name + @@ -22050,10 +22060,10 @@ Gene name (HUGO) - - true + Name of an entry (gene) from the HUGO database. bioinformatics + true edam beta12orEarlier beta12orEarlier @@ -22117,15 +22127,15 @@ Database name (CMD) - - true + edam identifier - identifiers beta13 The name of a subdivision of the Collagen Mutation Database (CMD) database. + identifiers data beta12orEarlier + true bioinformatics @@ -22136,9 +22146,9 @@ Database name (Osteogenesis) - - true + data + true beta12orEarlier identifiers bioinformatics @@ -22339,7 +22349,7 @@ - + data @@ -22356,15 +22366,15 @@ Locus annotation - - true + beta12orEarlier beta12orEarlier Locus report data An informative report on a particular locus. - bioinformatics + true edam + bioinformatics data @@ -22438,15 +22448,15 @@ Gene symbol annotation - - true + beta12orEarlier + data + true bioinformatics - data edam + data Annotation about a gene symbol. beta12orEarlier - data @@ -22675,8 +22685,8 @@ SMART domain name - edam beta12orEarlier + edam identifier Name of a domain from the SMART database. bioinformatics @@ -22777,7 +22787,7 @@ - + bioinformatics @@ -22785,7 +22795,7 @@ data beta12orEarlier data - Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on. + 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. @@ -22810,7 +22820,7 @@ - Gel identifier + Gel ID data identifier @@ -22819,6 +22829,7 @@ Identifier of a two-dimensional (protein) gel. identifiers edam + Gel identifier @@ -23090,13 +23101,13 @@ Databank - - true + beta12orEarlier edam A flat-file (textual) data archive. beta12orEarlier data + true bioinformatics data @@ -23107,11 +23118,11 @@ Web portal - - true + beta12orEarlier data edam + true bioinformatics data beta12orEarlier @@ -23175,13 +23186,13 @@ Experimental data (proteomics) - - true + bioinformatics + beta12orEarlier + true edam data beta12orEarlier - beta12orEarlier Data concerning a proteomics experiment. data @@ -23472,14 +23483,14 @@ Sequence set (polymorphic) - - true - A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. - bioinformatics - beta12orEarlier + data edam beta13 + A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. + true + bioinformatics + beta12orEarlier data @@ -23581,15 +23592,15 @@ DNA features - - true + data beta12orEarlier - bioinformatics - DNA sequence-specific feature annotation (not in a feature table). beta12orEarlier data edam + bioinformatics + true + DNA sequence-specific feature annotation (not in a feature table). @@ -23615,15 +23626,15 @@ Plot - - true + beta12orEarlier - data + true edam + data + data bioinformatics Biological data that is plotted as a graph of some type. beta12orEarlier - data @@ -24016,8 +24027,8 @@ identifier identifiers data - An accession of annotation on a (group of) organisms (catalogued in a database). bioinformatics + An accession of annotation on a (group of) organisms (catalogued in a database). @@ -24196,9 +24207,9 @@ Sequence data - - true + Data concerning molecular sequence(s). + true bioinformatics beta13 edam @@ -24216,9 +24227,9 @@ Codon usage data - - true + Data concerning codon usage. + true beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. bioinformatics @@ -24334,8 +24345,8 @@ Melting map beta12orEarlier edam - bioinformatics data + bioinformatics Plots melting temperature versus base position. A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). @@ -24400,19 +24411,13 @@ Microarray image - - - - - - edam bioinformatics An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. data - data Gene expression image beta12orEarlier + data @@ -24422,14 +24427,15 @@ Image - data - data - + Image data edam + bioinformatics + data Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type. beta12orEarlier - bioinformatics - + data + + @@ -24470,14 +24476,14 @@ Workflow data - - true + data + true bioinformatics beta12orEarlier data - edam Data concerning a computational workflow. + edam beta13 @@ -24504,14 +24510,14 @@ Secondary structure data - - true + Data concerning molecular secondary structure data. bioinformatics beta12orEarlier beta13 data data + true edam @@ -24556,13 +24562,13 @@ Protein sequence - data + bioinformatics data - One or more protein sequences, possibly with associated annotation. edam - - bioinformatics beta12orEarlier + One or more protein sequences, possibly with associated annotation. + data + @@ -24572,13 +24578,16 @@ Nucleic acid sequence - bioinformatics - beta12orEarlier - - edam + Nucleic acid sequences + data One or more nucleic acid sequences, possibly with associated annotation. + Nucleotide sequences + Nucleotide sequence + bioinformatics data - data + edam + beta12orEarlier + @@ -24626,7 +24635,7 @@ - + bioinformatics @@ -24645,11 +24654,11 @@ Sequence motif data - - true + This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier beta13 + true bioinformatics Data concerning specific or conserved pattern in molecular sequences. data @@ -24664,12 +24673,12 @@ Sequence profile data - - true + Data concerning models representing a (typically multiple) sequence alignment. data beta13 This is a broad data type and is used a placeholder for other, more specific types. + true bioinformatics beta12orEarlier data @@ -24683,15 +24692,15 @@ Pathway or network data - - true + beta12orEarlier data beta13 data - bioinformatics Data concerning a specific biological pathway or network. + bioinformatics edam + true @@ -24745,7 +24754,7 @@ - + data @@ -24765,20 +24774,14 @@ Classification - - - - - - bioinformatics - data - This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. - edam Classification data data + data Data concerning a classification of molecular sequences, structures or other entities. beta12orEarlier + This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. + edam @@ -24930,8 +24933,8 @@ identifier Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. bioinformatics - data identifiers + data edam @@ -24941,16 +24944,16 @@ GO concept name (biological process) - - true + beta12orEarlier beta12orEarlier bioinformatics The name of a concept for a biological process from the GO ontology. identifiers - edam data + edam identifier + true @@ -24960,15 +24963,15 @@ GO concept name (molecular function) - - true + edam The name of a concept for a molecular function from the GO ontology. identifier - identifiers beta12orEarlier + identifiers bioinformatics data + true beta12orEarlier @@ -24983,7 +24986,7 @@ - + Taxonomic data @@ -25036,7 +25039,6 @@ Sequence feature identifier - @@ -25044,9 +25046,9 @@ Name or other identifier of molecular sequence feature(s). + identifier data beta13 - identifier edam bioinformatics identifiers @@ -25292,7 +25294,7 @@ - + data @@ -25380,12 +25382,6 @@ Microarray hybridisation data - - - - - - beta13 data Data concerning the hybridisations measured during a microarray experiment. @@ -25635,7 +25631,7 @@ beta13 Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. data - This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). mRNA features @@ -25726,7 +25722,7 @@ SCOP class - Information on a 'class' node from the SCOP database. + Information on a 'class' node from the SCOP database. data beta13 data @@ -25743,7 +25739,7 @@ edam data - Information on a 'fold' node from the SCOP database. + Information on a 'fold' node from the SCOP database. beta13 data bioinformatics @@ -25758,7 +25754,7 @@ bioinformatics data - Information on a 'superfamily' node from the SCOP database. + Information on a 'superfamily' node from the SCOP database. data beta13 edam @@ -25773,7 +25769,7 @@ bioinformatics beta13 - Information on a 'family' node from the SCOP database. + Information on a 'family' node from the SCOP database. data data edam @@ -25789,7 +25785,7 @@ data bioinformatics beta13 - Information on a 'protein' node from the SCOP database. + Information on a 'protein' node from the SCOP database. edam data @@ -25803,7 +25799,7 @@ bioinformatics data - Information on a 'species' node from the SCOP database. + Information on a 'species' node from the SCOP database. beta13 edam data @@ -25885,8 +25881,8 @@ data - data Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. + data bioinformatics 1.0 edam @@ -25898,6 +25894,7 @@ Sequence assembly report + data 1.1 @@ -25970,9 +25967,9 @@ CL_[0-9]{7} edam data + 1.2 Cell type ontology concept ID. CL ID - 1.2 @@ -25992,6 +25989,205 @@ + + + + COSMIC ID + + cosmic identifier + 1.3 + bioinformatics + edam + COSMIC identifier + cosmic id + identifier + data + Identifier of a COSMIC database entry. + cosmic ID + identifiers + + + + + + + + HGMD ID + + hgmd identifier + Identifier of a HGMD database entry. + edam + data + hgmd id + HGMD identifier + 1.3 + hgmd ID + identifier + bioinformatics + identifiers + + + + + + + + Sequence assembly ID + + 1.3 + data + identifier + bioinformatics + Unique identifier of sequence assembly. + edam + identifiers + Sequence assembly version + + + + + + + + Sequence feature type + + bioinformatics + 1.3 + data + edam + 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. + data + + + + + + + + Gene annotation (homology) + + An informative report on gene homologues between species. + Homology information + data + Gene annotation (homology information) + This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. + edam + data + bioinformatics + 1.3 + + + + + + + + Ensembl gene tree ID + + + 1.3 + data + identifier + ENSGT00390000003602 + edam + Unique identifier for a gene tree from the Ensembl database. + bioinformatics + Ensembl ID (gene tree) + identifiers + + + + + + + + Gene tree + + edam + A phylogenetic tree that is an estimate of the character's phylogeny. + data + data + bioinformatics + 1.3 + + + + + + + + Species tree + + data + data + bioinformatics + 1.3 + edam + A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. + + + + + + + + Sample ID + + + + + + + + + identifiers + Name or other identifier of an entry from a biosample database. + data + edam + Sample accession + bioinformatics + identifier + 1.3 + + + + + + + + MGI accession + + + 1.3 + identifiers + data + Identifier of an object from the MGI database. + bioinformatics + edam + identifier + + + + + + + + Phenotype name + + + Phenotype + identifier + 1.3 + data + identifiers + Phenotypes + Name of a phenotype. + bioinformatics + edam + + + + @@ -26022,8 +26218,8 @@ bioinformatics edam beta12orEarlier - Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. formats + Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. @@ -26099,14 +26295,14 @@ nucleotide - Non-sequence characters may be used for example for gaps. - format beta12orEarlier - - formats bioinformatics - Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. edam + format + formats + Non-sequence characters may be used for example for gaps. + Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. + @@ -26117,14 +26313,14 @@ protein - beta12orEarlier - bioinformatics - Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. - format + Non-sequence characters may be used for gaps and translation stop. formats edam - - Non-sequence characters may be used for gaps and translation stop. + format + beta12orEarlier + Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. + bioinformatics + @@ -26182,13 +26378,13 @@ dna - format - beta12orEarlier formats edam - bioinformatics Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. - + bioinformatics + beta12orEarlier + format + @@ -26198,13 +26394,13 @@ rna - + beta12orEarlier + format + formats edam Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. bioinformatics - beta12orEarlier - formats - format + @@ -26309,10 +26505,10 @@ UniGene entry format - - true + formats edam + true beta12orEarlier format bioinformatics @@ -26328,14 +26524,14 @@ COG sequence cluster format - - true + edam + beta12orEarlier formats Format of an entry from the COG database of clusters of (related) protein sequences. bioinformatics - beta12orEarlier format + true beta12orEarlier @@ -26737,8 +26933,8 @@ JASPAR format - formats A profile (sequence classifier) in the format used in the JASPAR database. + formats bioinformatics edam beta12orEarlier @@ -26823,7 +27019,7 @@ bioinformatics format edam - 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. @@ -26946,15 +27142,15 @@ Phylogenetic property values format - - true + format formats - bioinformatics - beta12orEarlier + true beta12orEarlier edam Format of phylogenetic property data. + bioinformatics + beta12orEarlier @@ -27215,13 +27411,13 @@ Domainatrix 3D-1D scoring matrix format - - true + formats bioinformatics Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. format beta12orEarlier + true beta12orEarlier edam @@ -27248,14 +27444,14 @@ IntEnz enzyme report format - - true + bioinformatics IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. edam beta12orEarlier beta12orEarlier formats + true format Format of an entry from IntEnz (The Integrated Relational Enzyme Database). @@ -27267,14 +27463,14 @@ BRENDA enzyme report format - + + beta12orEarlier + Format of an entry from the BRENDA enzyme database. + format true edam - beta12orEarlier beta12orEarlier formats - Format of an entry from the BRENDA enzyme database. - format bioinformatics @@ -27285,14 +27481,14 @@ KEGG REACTION enzyme report format - - true + beta12orEarlier Format of an entry from the KEGG REACTION database of biochemical reactions. + bioinformatics + true format edam formats - bioinformatics beta12orEarlier @@ -27303,12 +27499,12 @@ KEGG ENZYME enzyme report format - - true - beta12orEarlier + edam - Format of an entry from the KEGG ENZYME database. format + beta12orEarlier + Format of an entry from the KEGG ENZYME database. + true beta12orEarlier formats bioinformatics @@ -27321,15 +27517,15 @@ REBASE proto enzyme report format - - true + format - bioinformatics beta12orEarlier - beta12orEarlier formats edam Format of an entry from the proto section of the REBASE enzyme database. + bioinformatics + beta12orEarlier + true @@ -27339,15 +27535,15 @@ REBASE withrefm enzyme report format - - true - formats + format + beta12orEarlier + beta12orEarlier + formats Format of an entry from the withrefm section of the REBASE enzyme database. bioinformatics - beta12orEarlier + true edam - beta12orEarlier @@ -27391,11 +27587,11 @@ SMART domain assignment report format - - true + beta12orEarlier The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. Format of SMART domain assignment data. + true beta12orEarlier format edam @@ -27410,15 +27606,15 @@ BIND entry format - - true + formats edam beta12orEarlier + true beta12orEarlier bioinformatics - format Entry format for the BIND database of protein interaction. + format @@ -27428,15 +27624,15 @@ IntAct entry format - - true + formats Entry format for the IntAct database of protein interaction. - bioinformatics - beta12orEarlier + true format edam beta12orEarlier + bioinformatics + beta12orEarlier @@ -27446,16 +27642,16 @@ InterPro entry format - - true + format This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. + true beta12orEarlier edam formats beta12orEarlier - Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. bioinformatics + Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. @@ -27465,15 +27661,15 @@ InterPro entry abstract format - - true - format + beta12orEarlier Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. - formats + format References are included and a functional inference is made where possible. + formats beta12orEarlier edam + true bioinformatics @@ -27484,15 +27680,15 @@ Gene3D entry format - - true - bioinformatics + beta12orEarlier - beta12orEarlier edam format - formats Entry format for the Gene3D protein secondary database. + bioinformatics + beta12orEarlier + true + formats @@ -27502,14 +27698,14 @@ PIRSF entry format - - true - formats - format + beta12orEarlier bioinformatics beta12orEarlier Entry format for the PIRSF protein secondary database. + format + formats + true edam @@ -27520,14 +27716,14 @@ PRINTS entry format - + true + beta12orEarlier formats edam Entry format for the PRINTS protein secondary database. bioinformatics beta12orEarlier - beta12orEarlier format @@ -27538,15 +27734,15 @@ Panther Families and HMMs entry format - - true - formats + bioinformatics + true Entry format for the Panther library of protein families and subfamilies. - format beta12orEarlier edam beta12orEarlier + formats + format @@ -27556,15 +27752,15 @@ Pfam entry format - - true + edam beta12orEarlier formats format + true + Entry format for the Pfam protein secondary database. beta12orEarlier bioinformatics - Entry format for the Pfam protein secondary database. @@ -27574,15 +27770,15 @@ SMART entry format - - true - beta12orEarlier + formats edam + true + bioinformatics + beta12orEarlier Entry format for the SMART protein secondary database. beta12orEarlier format - bioinformatics @@ -27592,13 +27788,13 @@ Superfamily entry format - - true + format beta12orEarlier + true + formats Entry format for the Superfamily protein secondary database. beta12orEarlier - formats bioinformatics edam @@ -27610,15 +27806,15 @@ TIGRFam entry format - - true + + Entry format for the TIGRFam protein secondary database. + format + beta12orEarlier beta12orEarlier bioinformatics - Entry format for the TIGRFam protein secondary database. edam formats - format - beta12orEarlier + true @@ -27628,15 +27824,15 @@ ProDom entry format - + true beta12orEarlier - bioinformatics - formats - format edam beta12orEarlier Entry format for the ProDom protein domain classification database. + bioinformatics + formats + format @@ -27646,15 +27842,15 @@ FSSP entry format - + true - beta12orEarlier bioinformatics Entry format for the FSSP database. beta12orEarlier - formats format edam + beta12orEarlier + formats @@ -27680,12 +27876,12 @@ Ensembl gene report format - + true formats + Entry format of Ensembl genome database. beta12orEarlier format - Entry format of Ensembl genome database. bioinformatics beta12orEarlier edam @@ -27698,15 +27894,15 @@ DictyBase gene report format - - true + beta12orEarlier - Entry format of DictyBase genome database. edam bioinformatics - beta12orEarlier formats format + true + Entry format of DictyBase genome database. + beta12orEarlier @@ -27716,15 +27912,15 @@ CGD gene report format - - true - Entry format of Candida Genome database. + beta12orEarlier format beta12orEarlier bioinformatics edam formats + Entry format of Candida Genome database. + true @@ -27734,14 +27930,14 @@ DragonDB gene report format - + true format - edam beta12orEarlier - formats Entry format of DragonDB genome database. bioinformatics + edam + formats beta12orEarlier @@ -27752,15 +27948,15 @@ EcoCyc gene report format - + true + beta12orEarlier + beta12orEarlier + Entry format of EcoCyc genome database. bioinformatics edam - beta12orEarlier format - beta12orEarlier formats - Entry format of EcoCyc genome database. @@ -27770,15 +27966,15 @@ FlyBase gene report format - - true + Entry format of FlyBase genome database. bioinformatics beta12orEarlier + format + true beta12orEarlier edam formats - format @@ -27788,12 +27984,12 @@ Gramene gene report format - - true - bioinformatics + edam - Entry format of Gramene genome database. beta12orEarlier + bioinformatics + true + Entry format of Gramene genome database. beta12orEarlier format formats @@ -27806,15 +28002,15 @@ KEGG GENES gene report format - - true + beta12orEarlier formats Entry format of KEGG GENES genome database. beta12orEarlier - bioinformatics edam format + bioinformatics + true @@ -27824,13 +28020,13 @@ MaizeGDB gene report format - - true - format + Entry format of the Maize genetics and genomics database (MaizeGDB). edam bioinformatics beta12orEarlier + format + true beta12orEarlier formats @@ -27842,15 +28038,15 @@ MGD gene report format - - true + edam - formats format - beta12orEarlier beta12orEarlier - bioinformatics Entry format of the Mouse Genome Database (MGD). + true + formats + beta12orEarlier + bioinformatics @@ -27860,15 +28056,15 @@ RGD gene report format - - true - beta12orEarlier - format + Entry format of the Rat Genome Database (RGD). - beta12orEarlier edam bioinformatics formats + true + beta12orEarlier + format + beta12orEarlier @@ -27878,15 +28074,15 @@ SGD gene report format - - true + beta12orEarlier Entry format of the Saccharomyces Genome Database (SGD). bioinformatics + formats + true format edam beta12orEarlier - formats @@ -27896,14 +28092,14 @@ GeneDB gene report format - - true - format + beta12orEarlier - formats beta12orEarlier + true bioinformatics edam + format + formats Entry format of the Sanger GeneDB genome database. @@ -27914,13 +28110,13 @@ TAIR gene report format - + true format Entry format of The Arabidopsis Information Resource (TAIR) genome database. - edam beta12orEarlier bioinformatics + edam formats beta12orEarlier @@ -27932,15 +28128,15 @@ WormBase gene report format - + + formats + format + Entry format of the WormBase genomes database. true edam - formats beta12orEarlier beta12orEarlier bioinformatics - format - Entry format of the WormBase genomes database. @@ -27950,14 +28146,14 @@ ZFIN gene report format - + true - Entry format of the Zebrafish Information Network (ZFIN) genome database. beta12orEarlier formats edam beta12orEarlier format + Entry format of the Zebrafish Information Network (ZFIN) genome database. bioinformatics @@ -27968,15 +28164,15 @@ TIGR gene report format - - true + bioinformatics beta12orEarlier beta12orEarlier - edam formats Entry format of the TIGR genome database. format + edam + true @@ -27986,14 +28182,14 @@ dbSNP polymorphism report format - + + bioinformatics true + formats + beta12orEarlier format - bioinformatics beta12orEarlier Entry format for the dbSNP database. - formats - beta12orEarlier edam @@ -28004,14 +28200,14 @@ OMIM entry format - - true + Format of an entry from the OMIM database of genotypes and phenotypes. edam beta12orEarlier + bioinformatics + true beta12orEarlier formats - bioinformatics format @@ -28022,14 +28218,14 @@ HGVbase entry format - - true - formats - beta12orEarlier + beta12orEarlier - bioinformatics format Format of a record from the HGVbase database of genotypes and phenotypes. + formats + beta12orEarlier + bioinformatics + true edam @@ -28040,15 +28236,15 @@ HIVDB entry format - - true - edam - Format of a record from the HIVDB database of genotypes and phenotypes. + formats + true format - bioinformatics beta12orEarlier beta12orEarlier + edam + Format of a record from the HIVDB database of genotypes and phenotypes. + bioinformatics @@ -28058,14 +28254,14 @@ KEGG DISEASE entry format - + + beta12orEarlier true + format + edam formats bioinformatics - beta12orEarlier Format of an entry from the KEGG DISEASE database. - format - edam beta12orEarlier @@ -28256,15 +28452,15 @@ ArrayExpress entry format - - true - beta12orEarlier + format Entry format for the ArrayExpress microarrays database. edam bioinformatics + true formats beta12orEarlier + beta12orEarlier @@ -28314,14 +28510,14 @@ EMDB entry format - - true + edam beta12orEarlier - Format of an entry from the Electron Microscopy DataBase (EMDB). bioinformatics formats beta12orEarlier + true + Format of an entry from the Electron Microscopy DataBase (EMDB). format @@ -28332,15 +28528,15 @@ KEGG PATHWAY entry format - - true + format + true The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. formats - beta12orEarlier edam - bioinformatics beta12orEarlier + beta12orEarlier + bioinformatics @@ -28350,15 +28546,15 @@ MetaCyc entry format - - true - beta12orEarlier + The format of an entry from the MetaCyc metabolic pathways database. beta12orEarlier - bioinformatics formats + bioinformatics format edam + true + beta12orEarlier @@ -28368,13 +28564,13 @@ HumanCyc entry format - - true - bioinformatics - beta12orEarlier + format beta12orEarlier edam + true + bioinformatics + beta12orEarlier formats The format of a report from the HumanCyc metabolic pathways database. @@ -28386,14 +28582,14 @@ INOH entry format - + + bioinformatics + formats true + edam beta12orEarlier - bioinformatics The format of an entry from the INOH signal transduction pathways database. format - formats - edam beta12orEarlier @@ -28404,15 +28600,15 @@ PATIKA entry format - + true - edam - beta12orEarlier format - formats The format of an entry from the PATIKA biological pathways database. beta12orEarlier bioinformatics + edam + beta12orEarlier + formats @@ -28422,12 +28618,12 @@ Reactome entry format - - true + beta12orEarlier + true The format of an entry from the reactome biological pathways database. - beta12orEarlier format + beta12orEarlier formats edam bioinformatics @@ -28440,13 +28636,13 @@ aMAZE entry format - - true + beta12orEarlier + true + bioinformatics edam The format of an entry from the aMAZE biological pathways and molecular interactions database. format - bioinformatics formats beta12orEarlier @@ -28458,15 +28654,15 @@ CPDB entry format - - true - beta12orEarlier + edam + format + formats + beta12orEarlier beta12orEarlier + true The format of an entry from the CPDB database. bioinformatics - format - formats @@ -28476,15 +28672,15 @@ Panther Pathways entry format - - true - format + bioinformatics The format of an entry from the Panther Pathways database. edam - beta12orEarlier formats + true beta12orEarlier + format + beta12orEarlier @@ -28510,12 +28706,12 @@ BioModel mathematical model format - - true + Format of mathematical models from the BioModel database. format beta12orEarlier Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. + true bioinformatics formats edam @@ -28529,14 +28725,14 @@ KEGG LIGAND entry format - - true - format + bioinformatics + true beta12orEarlier - formats beta12orEarlier The format of an entry from the KEGG LIGAND chemical database. + format + formats edam @@ -28547,15 +28743,15 @@ KEGG COMPOUND entry format - - true + bioinformatics + The format of an entry from the KEGG COMPOUND database. + edam beta12orEarlier format + true formats - The format of an entry from the KEGG COMPOUND database. beta12orEarlier - edam @@ -28565,15 +28761,15 @@ KEGG PLANT entry format - - true + edam + format + formats + true The format of an entry from the KEGG PLANT database. bioinformatics beta12orEarlier - format beta12orEarlier - formats @@ -28583,8 +28779,7 @@ KEGG GLYCAN entry format - - true + beta12orEarlier edam bioinformatics @@ -28592,6 +28787,7 @@ formats beta12orEarlier format + true @@ -28601,15 +28797,15 @@ PubChem entry format - - true - edam + bioinformatics beta12orEarlier - formats - beta12orEarlier format The format of an entry from PubChem. + edam + formats + true + beta12orEarlier @@ -28619,14 +28815,14 @@ ChemSpider entry format - - true + edam bioinformatics + format + true beta12orEarlier The format of an entry from a database of chemical structures and property predictions. formats - format beta12orEarlier @@ -28637,11 +28833,11 @@ ChEBI entry format - - true + ChEBI includes an ontological classification defining relations between entities or classes of entities. - The format of an entry from Chemical Entities of Biological Interest (ChEBI). + true formats + The format of an entry from Chemical Entities of Biological Interest (ChEBI). beta12orEarlier edam bioinformatics @@ -28656,14 +28852,14 @@ MSDchem ligand dictionary entry format - - true + beta12orEarlier - bioinformatics formats beta12orEarlier The format of an entry from the MSDchem ligand dictionary. edam + true + bioinformatics format @@ -28690,14 +28886,14 @@ KEGG DRUG entry format - + + format true + bioinformatics formats beta12orEarlier beta12orEarlier - format edam - bioinformatics The format of an entry from the KEGG DRUG database. @@ -28745,7 +28941,7 @@ edam formats - CiteXplore 'core' citation format including title, journal, authors and abstract. + CiteXplore 'core' citation format including title, journal, authors and abstract. format beta12orEarlier bioinformatics @@ -28764,7 +28960,7 @@ formats bioinformatics format - 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. @@ -28809,8 +29005,8 @@ edam bioinformatics - beta12orEarlier formats + beta12orEarlier Text mining abstract format from the Oscar 3 application. format Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. @@ -28822,14 +29018,14 @@ PDB atom record format - - true + Format of an ATOM record (describing data for an individual atom) from a PDB file. format beta12orEarlier bioinformatics formats edam + true beta13 @@ -28840,11 +29036,11 @@ CATH chain report format - + true beta12orEarlier - Format of CATH domain classification information for a polypeptide chain. beta12orEarlier + Format of CATH domain classification information for a polypeptide chain. edam The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. format @@ -28859,10 +29055,10 @@ CATH PDB report format - - true + The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. Format of CATH domain classification information for a protein PDB file. + true beta12orEarlier formats bioinformatics @@ -28878,14 +29074,14 @@ NCBI gene report format - - true + formats beta12orEarlier beta12orEarlier Entry (gene) format of the NCBI database. - bioinformatics format + true + bioinformatics edam @@ -28896,13 +29092,13 @@ GeneIlluminator gene report format - - true + Moby:GI_Gene beta12orEarlier bioinformatics format edam + true formats beta12orEarlier This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. @@ -28916,15 +29112,15 @@ BacMap gene card format - - true + format edam - beta12orEarlier Moby:BacMapGeneCard + beta12orEarlier beta12orEarlier formats bioinformatics + 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. @@ -28935,15 +29131,15 @@ ColiCard report format - - true + beta12orEarlier beta12orEarlier formats + true bioinformatics Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). - format Moby:ColiCard + format edam @@ -28976,6 +29172,7 @@ format formats beta12orEarlier + nh bioinformatics edam @@ -29017,79 +29214,77 @@ - beta12orEarlier - formats - bioinformatics - edam - format + Format - - - Format + + 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. + format + Data format + formats A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. - The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. + bioinformatics + beta12orEarlier Exchange format - Data format Data model File format - - - - - - - - - - - - - - + edam + + + + + + + + + + + + + + - 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 + 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. - + + - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. - File 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. - + + - Closely related concept focusing on the specification of a data format. - + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + File format - + - GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials. - + 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. - + 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'.) - + - 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. - + Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format. - + + Format can be a quality of a data record. - - + + @@ -29098,14 +29293,14 @@ Atomic data format - - true - format - bioinformatics + edam Data format for an individual atom. formats beta13 + format + bioinformatics + true beta12orEarlier @@ -29194,14 +29389,14 @@ clustal sequence format - - true - beta12orEarlier + formats edam Clustalw output format. beta12orEarlier bioinformatics + beta12orEarlier + true format @@ -29276,7 +29471,7 @@ - FASTA format + FASTA FASTA sequence format @@ -29284,8 +29479,8 @@ format FASTA format including NCBI-style IDs. edam + FASTA format formats - FASTA bioinformatics @@ -29699,15 +29894,15 @@ phylip sequence format - - true + bioinformatics beta12orEarlier + Phylip interleaved sequence format. + format + true formats beta12orEarlier - Phylip interleaved sequence format. edam - format @@ -29717,15 +29912,15 @@ phylipnon sequence format - - true - bioinformatics - formats + edam beta12orEarlier beta12orEarlier - Phylip non-interleaved sequence format. format + bioinformatics + formats + Phylip non-interleaved sequence format. + true @@ -29768,15 +29963,15 @@ selex sequence format - - true + Selex sequence format. - edam - beta12orEarlier beta12orEarlier - format formats bioinformatics + edam + beta12orEarlier + true + format @@ -29871,15 +30066,15 @@ treecon sequence format - - true + Treecon output sequence format. - edam bioinformatics format + formats + true + edam beta12orEarlier beta12orEarlier - formats @@ -29971,14 +30166,14 @@ meganon sequence format - - true + + bioinformatics + beta12orEarlier formats edam - bioinformatics + true Mega non-interleaved output sequence format. format - beta12orEarlier beta12orEarlier @@ -30072,13 +30267,13 @@ swiss feature - + + edam + format true bioinformatics beta12orEarlier - edam beta12orEarlier - format Swiss-Prot feature format. formats @@ -30124,15 +30319,15 @@ EMBL feature - + + formats true + bioinformatics + EMBL feature format. beta12orEarlier edam format - formats - bioinformatics beta12orEarlier - EMBL feature format. @@ -30142,15 +30337,15 @@ GenBank feature - + true - bioinformatics edam beta12orEarlier - format Genbank feature format. beta12orEarlier formats + bioinformatics + format @@ -30329,15 +30524,15 @@ msf alignment format - - true - bioinformatics + formats - MSF format for (aligned) sequences. + bioinformatics beta12orEarlier edam format beta12orEarlier + MSF format for (aligned) sequences. + true @@ -30347,14 +30542,14 @@ nexus alignment format - + true edam format formats beta12orEarlier - beta12orEarlier bioinformatics + beta12orEarlier Nexus/paup format for (aligned) sequences. @@ -30365,15 +30560,15 @@ nexusnon alignment format - - true + format edam beta12orEarlier - Nexus/paup non-interleaved format for (aligned) sequences. + true bioinformatics - formats beta12orEarlier + Nexus/paup non-interleaved format for (aligned) sequences. + formats @@ -30431,8 +30626,8 @@ edam - formats Alignment format for score values for pairs of sequences. + formats beta12orEarlier bioinformatics format @@ -30605,15 +30800,15 @@ Sequence-profile alignment (HMM) format - - true - Data format for a sequence-HMM profile alignment. - formats - bioinformatics + beta12orEarlier edam format beta12orEarlier + Data format for a sequence-HMM profile alignment. + formats + true + bioinformatics @@ -30787,23 +30982,16 @@ Biological model format - - true - formats + edam 1.2 - beta12orEarlier bioinformatics - format Data format for a biological model. + true + formats + beta12orEarlier + format - @@ -30938,12 +31126,12 @@ Electron microscopy model format - - true - bioinformatics + Annotation format for electron microscopy models. format + bioinformatics beta12orEarlier + true beta12orEarlier formats edam @@ -30977,13 +31165,13 @@ Polymorphism report format - - true + formats format 1.0 Format for sequence polymorphism data. bioinformatics + true beta12orEarlier edam @@ -31120,14 +31308,14 @@ Genotype and phenotype annotation format - - true + bioinformatics - beta12orEarlier - format edam Format of a report on genotype / phenotype information. + true beta12orEarlier + beta12orEarlier + format formats @@ -31201,15 +31389,15 @@ Protein report (enzyme) format - - true + bioinformatics - format edam - beta12orEarlier - beta12orEarlier Format of a report of general information about a specific enzyme. formats + format + beta12orEarlier + true + beta12orEarlier @@ -31649,14 +31837,14 @@ Gene cluster format - - true + formats - Format used for clusters of genes. - edam format beta12orEarlier beta13 + Format used for clusters of genes. + edam + true bioinformatics @@ -31860,16 +32048,15 @@ OWL format - formats - A serialisation format conforming to the Web Ontology Language (OWL) model. beta12orEarlier + A serialisation format conforming to the Web Ontology Language (OWL) model. edam bioinformatics format - + @@ -31883,9 +32070,9 @@ This concept may also be used for the many non-standard FASTA-like formats. formats bioinformatics - A text format resembling FASTA format. format - + A text format resembling FASTA format. + @@ -31922,7 +32109,7 @@ - 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. bioinformatics format edam @@ -31940,8 +32127,8 @@ formats edam format - bioinformatics This is a placeholder for other more specific concepts. It should not normally be used for annotation. + bioinformatics An XML format for EMBL entries. beta12orEarlier @@ -31984,9 +32171,9 @@ Strain data format - - true + format + true 1.0 beta12orEarlier formats @@ -32001,14 +32188,14 @@ CIP strain data format - - true - formats + beta12orEarlier - edam beta12orEarlier - bioinformatics format + formats + edam + bioinformatics + true Format for a report of strain data as used for CIP database entries. @@ -32019,15 +32206,15 @@ phylip property values - - true + formats + PHYLIP file format for phylogenetic property data. + format beta12orEarlier beta12orEarlier edam - PHYLIP file format for phylogenetic property data. bioinformatics - format + true @@ -32037,15 +32224,15 @@ STRING entry format (HTML) - - true - formats + Entry format (HTML) for the STRING database of protein interaction. beta12orEarlier format edam beta12orEarlier bioinformatics + formats + true @@ -32137,14 +32324,14 @@ BioCyc enzyme report format - + + Format of an entry from the BioCyc enzyme database. + beta12orEarlier true bioinformatics formats format edam - Format of an entry from the BioCyc enzyme database. - beta12orEarlier beta12orEarlier @@ -32155,13 +32342,13 @@ ENZYME enzyme report format - - true - formats + format - beta12orEarlier - beta12orEarlier Format of an entry from the Enzyme nomenclature database (ENZYME). + formats + true + beta12orEarlier + beta12orEarlier bioinformatics edam @@ -32173,14 +32360,14 @@ PseudoCAP gene report format - - true + Format of a report on a gene from the PseudoCAP database. edam - beta12orEarlier format - beta12orEarlier formats + beta12orEarlier + beta12orEarlier + true bioinformatics @@ -32191,14 +32378,14 @@ GeneCards gene report format - - true + bioinformatics + beta12orEarlier + Format of a report on a gene from the GeneCards database. edam + true beta12orEarlier format - beta12orEarlier - Format of a report on a gene from the GeneCards database. formats @@ -32208,37 +32395,38 @@ + Textual format + beta12orEarlier + Plain text + format formats - edam + Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). bioinformatics - format - Textual format Textual format. - Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). - + edam Tabular format - Plain text - - + + + - Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. Tabular format + 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. - - + + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. - - + + @@ -32246,13 +32434,7 @@ - beta12orEarlier - formats - edam - bioinformatics - format HTML - HTML format. @@ -32260,14 +32442,20 @@ + bioinformatics + beta12orEarlier + format + edam + formats Hypertext Markup Language - + HTML format. + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. - - + + @@ -32275,23 +32463,23 @@ - beta12orEarlier + XML + + format formats - edam bioinformatics - format - XML + Extensible Markup Language + edam eXtensible Markup Language (XML) format. + beta12orEarlier Data in XML format can be serialised into text, or binary format. - - Extensible Markup Language - + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. - - + + @@ -32306,7 +32494,7 @@ bioinformatics Binary format. beta12orEarlier - Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. + Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. format @@ -32316,15 +32504,15 @@ URI format - + true + beta13 bioinformatics format beta12orEarlier Typical textual representation of a URI. formats edam - beta13 @@ -32334,14 +32522,14 @@ NCI-Nature pathway entry format - + + format true + formats beta12orEarlier - format The format of an entry from the NCI-Nature pathways database. bioinformatics beta12orEarlier - formats edam @@ -32357,7 +32545,7 @@ A broad class of format distinguished by the scientific nature of the data that is identified. format beta12orEarlier - This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. + This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. bioinformatics formats @@ -32376,13 +32564,13 @@ - + - + @@ -32408,19 +32596,16 @@ RDF format - A serialisation format conforming to the Resource Description Framework (RDF) model. - beta12orEarlier bioinformatics format edam formats - - + @@ -32443,15 +32628,15 @@ Protein features (domains) format - - true + formats Format of a report on protein features (domain composition). bioinformatics - beta12orEarlier - beta12orEarlier + true format edam + beta12orEarlier + beta12orEarlier @@ -32495,8 +32680,8 @@ FASTA-like format - edam A format resembling FASTA format. + edam formats beta12orEarlier bioinformatics @@ -32686,8 +32871,8 @@ edam - beta12orEarlier formats + beta12orEarlier format This concept may be used for the any non-standard EMBL-like XML formats. bioinformatics @@ -32716,15 +32901,15 @@ STRING entry format - - true + bioinformatics - formats beta12orEarlier Entry format for the STRING database of protein interaction. format edam beta12orEarlier + true + formats @@ -32749,14 +32934,14 @@ Amino acid identifier format - + true - beta12orEarlier bioinformatics Text format (representation) of amino acid residues. format beta13 edam + beta12orEarlier formats @@ -32860,7 +33045,7 @@ edam format bioinformatics - + @@ -32869,9 +33054,9 @@ BAM - + BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. beta12orEarlier format @@ -32946,13 +33131,13 @@ - + - + bioinformatics @@ -33086,7 +33271,7 @@ format AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). - AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. + AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. bioinformatics formats edam @@ -33233,7 +33418,7 @@ format edam - 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'. formats bioinformatics beta12orEarlier @@ -33253,7 +33438,7 @@ formats format beta12orEarlier - .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'. bioinformatics edam @@ -33555,15 +33740,14 @@ BioPAX - edam format formats + bioinformatics 1.0 BioPAX is an exchange format for pathway data, with its data model defined in OWL. - bioinformatics - + @@ -33593,15 +33777,15 @@ PSI MI XML (MIF) + MIF edam XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. formats bioinformatics - MIF 1.0 format - + @@ -33823,15 +34007,15 @@ - 1.2 - formats - edam - bioinformatics - format PSI MI TAB (MITAB) - Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. + format + bioinformatics + Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. + 1.2 + edam + formats @@ -33841,14 +34025,14 @@ + PSI-PAR + 1.2 - formats + format edam bioinformatics - format - PSI-PAR + formats Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema. - @@ -33858,18 +34042,18 @@ + mzML + + 1.2 - formats - edam - bioinformatics format - mzML + edam mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. + bioinformatics + formats mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. - - - + @@ -33877,13 +34061,7 @@ - 1.2 - formats - bioinformatics - edam - format Mass spectrometry data format - Format for mass spectrometry data. @@ -33891,6 +34069,12 @@ + Format for mass spectrometry data. + edam + formats + 1.2 + bioinformatics + format @@ -33898,17 +34082,17 @@ + TraML + + + TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. + format 1.2 formats edam bioinformatics - format - TraML - TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. - - - + @@ -33916,15 +34100,15 @@ - 1.2 - formats - edam - bioinformatics - format mzIdentML - mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines. - + + bioinformatics + mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines. + edam + format + formats + 1.2 @@ -33934,17 +34118,17 @@ - 1.2 + mzQuantML + + formats + mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics. + format edam + 1.2 bioinformatics - format - mzQuantML - mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics. - - - + @@ -33952,21 +34136,21 @@ - 1.2 - formats - edam - bioinformatics - format GelML - GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. - + + formats + 1.2 + format + edam + GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. + bioinformatics @@ -33976,21 +34160,21 @@ - 1.2 - formats - edam - bioinformatics - format spML - spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. - + + format + edam + spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. + 1.2 + formats + bioinformatics @@ -34001,35 +34185,33 @@ OWL Functional Syntax - - - A human-readable encoding for the Web Ontology Language (OWL). + 1.2 bioinformatics - format edam formats + A human-readable encoding for the Web Ontology Language (OWL). + format - + - + Manchester OWL Syntax - - - A syntax for writing OWL class expressions. + + edam + bioinformatics This format was influenced by the OWL Abstract Syntax and the DL style syntax. 1.2 - bioinformatics format - edam formats + A syntax for writing OWL class expressions. - + @@ -34038,359 +34220,652 @@ KRSS2 Syntax - A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". - This format is used in Protege 4. 1.2 - bioinformatics - format - edam + format formats + A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". + bioinformatics + This format is used in Protege 4. - + Turtle - The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs. - The SPARQL Query Language incorporates a very similar syntax. + format 1.2 + formats bioinformatics - format edam - formats + The SPARQL Query Language incorporates a very similar syntax. - + N-Triples - - A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. - N-Triples should not be confused with Notation 3 which is a superset of Turtle. 1.2 - bioinformatics + A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. format - edam formats + N-Triples should not be confused with Notation 3 which is a superset of Turtle. + edam + bioinformatics - + Notation3 - + format + bioinformatics A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. N3 - bioinformatics - format edam formats - + RDF/XML - - - - Resource Description Framework (RDF) XML format. + + RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. 1.2 - bioinformatics - format - RDF edam + RDF formats + bioinformatics + Resource Description Framework (RDF) XML format. + format - - + + OWL/XML - - - + + edam + OWL formats - OWL ontology XML serialisation format. 1.2 - OWL - edam + OWL ontology XML serialisation format. bioinformatics format - + - - beta12orEarlier - operations + + A2M + + + bioinformatics + 1.3 + formats edam + format + The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA. + + + + + + + + + + SFF + + + 1.3 + format bioinformatics - operation - - Operation - A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. - Function - Computational operation - Computational procedure - Computational method - Computational subroutine - Function (programming) - Lambda abstraction - Mathematical operation - Mathematical function - Process - Computational tool - - - - - - - - - sumo:Function - - - - - - - - - - + Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. + Standard flowgram format + edam + formats + + - - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - Function - - - - - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. - Process - - - - - Computational tool provides one or more operations. - Computational tool - - - - - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'. - - - - - - However, operation is not a GFO 'Concept' present only in someone's mind. - - - - - - GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. - - - - - - BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s). - - - - - - Function, including an operation, can be a quality/property of e.g. a computational tool. - - - - - - Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool. - - - - - - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - - - - - - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - - - - - - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - - - - - - However, one may think that an operation is not a process. - - - - - - However, one may think that an operation is not a process and not a physical entity. - - - - - - Method may in addition focus on how to achieve the result, not just on what to achieve as with operation. - - - - - + - - Search and retrieval - - - - - - - - - - - - - + + MAP + bioinformatics - operations - operation - Database retrieval - Search or query a data resource and retrieve entries and / or annotation. - beta12orEarlier edam + Plink MAP + format + formats + 1.3 + The MAP file describes SNPs and is used by the Plink package. + - + - - Data retrieval (database cross-reference) - - true - beta13 - operation - operations - Search database to retrieve all relevant references to a particular entity or entry. - beta12orEarlier + + PED + edam + The PED file describes individuals and genetic data and is used by the Plink package. + 1.3 + format + formats + Plink PED bioinformatics - + - + - - Annotation - - - - - - - - - - - - - + + Individual genetic data format + + format + Data format for a metadata on an individual and their genetic data. + formats bioinformatics - Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. - This is a broad concept and is used a placeholder for other, more specific concepts. + 1.3 edam - beta12orEarlier - operation - operations - + - - Data indexing - - - - - - - - Database indexing - bioinformatics - operations + + PED/MAP + + + format + The PED/MAP file describes data used by the Plink package. + formats + 1.3 + Plink PED/MAP edam - Generate an index of (typically a file of) biological data. - beta12orEarlier - operation + bioinformatics + - + - - Data index analysis - - - + + CT + + + Connect format + Connectivity Table file format + bioinformatics + File format of a CT (Connectivity Table) file from the RNAstructure package. + edam + formats + 1.3 + format + + + + + + + + + + SS + + + XRNA old input style format. + edam + format + bioinformatics + 1.3 + formats + + + + + + + + + RNAML + + + + edam + RNA Markup Language. + 1.3 + formats + format + bioinformatics + + + + + + + + + GDE + + + 1.3 + formats + Format for the Genetic Data Environment (GDE). + format + bioinformatics + edam + + + + + + + + + BLC + + formats + bioinformatics + format + edam + Block file format + A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge. + 1.3 + + + + + + + + + Data index format + + + + + + + + 1.3 + edam + format + bioinformatics + formats + + + + + + + + BAI + + + + + + + + BAM indexing format + formats + 1.3 + format + bioinformatics + edam + + + + + + + + + HMMER2 + + 1.3 + format + formats + edam + HMMER profile HMM file for HMMER versions 2.x + bioinformatics + + + + + + + + + HMMER3 + + HMMER profile HMM file for HMMER versions 3.x + formats + bioinformatics + 1.3 + format + edam + + + + + + + + + PO + + 1.3 + EMBOSS simple sequence pair alignment format. + formats + edam + bioinformatics + format + + + + + + + + + BLAST XML results format + + + format + bioinformatics + formats + 1.3 + XML format as produced by the NCBI Blast package + edam + + + + + + + + Operation + + + Function (programming) + bioinformatics + Lambda abstraction + Mathematical function + Computational procedure + Computational subroutine + Computational operation + Process + beta12orEarlier + sumo:Function + Mathematical operation + Computational method + edam + Function + operations + A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. + Computational tool + operation + + + + + + + + + + + + + + + + + + + + + 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. + + + + + + However, one may think that an operation is not a process. + + + + + + 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'. + + + + + + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. + + + + + + However, operation is not a GFO 'Concept' present only in someone's mind. + + + + + + Method may in addition focus on how to achieve the result, not just on what to achieve as with operation. + + + + + + However, one may think that an operation is not a process and not a physical entity. + + + + + + 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. + + + + + + Function, including an operation, can be a quality/property of e.g. a computational tool. + + + + + + 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. + + + + + + Function + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + + + + + Process + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + + + + + Computational tool provides one or more operations. + Computational tool + + + + + + + + + + Search and retrieval + + + + + + + + + + + + + + bioinformatics + operations + operation + Database retrieval + Search or query a data resource and retrieve entries and / or annotation. + beta12orEarlier + edam + + + + + + + + Data retrieval (database cross-reference) + + operations + true + Search database to retrieve all relevant references to a particular entity or entry. + beta13 + operation + beta12orEarlier + edam + bioinformatics + + + + + + + + + Annotation + + + + + + + + + + + + + bioinformatics + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. + This is a broad concept and is used a placeholder for other, more specific concepts. + edam + beta12orEarlier + operation + operations + + + + + + + + Data indexing + + + + + Database indexing + bioinformatics + operations + edam + Generate an index of (typically a file of) biological data. + beta12orEarlier + operation + + + + + + + + Data index analysis + + + + + + + edam beta12orEarlier Analyse an index of biological data. @@ -34406,15 +34881,15 @@ Annotation retrieval (sequence) - - true + beta12orEarlier Retrieve basic information about a molecular sequence. + beta12orEarlier + operation + true operations bioinformatics edam - beta12orEarlier - operation @@ -34496,7 +34971,7 @@ - + operations @@ -34543,14 +35018,14 @@ - - + + - - + + edam @@ -34571,7 +35046,7 @@ - + Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. @@ -34621,6 +35096,12 @@ + + + + + + bioinformatics Sequence motif detection operation @@ -34660,14 +35141,14 @@ Transcription regulatory sequence analysis - + true beta12orEarlier operation edam - Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. beta13 For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. + Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. bioinformatics operations @@ -34704,12 +35185,6 @@ Protein property calculation (from structure) - @@ -34764,14 +35239,14 @@ - - + + - - + + Protein structural feature identification @@ -34841,14 +35316,14 @@ - - + + - - + + operation @@ -34860,8 +35335,8 @@ beta12orEarlier operations WHATIF:ListSideChainContactsNormal - WHATIF:ListSideChainContactsRelaxed edam + WHATIF:ListSideChainContactsRelaxed WHATIF: SymShellTwoXML WHATIF:ListContactsRelaxed WHATIF: SymShellTenXML @@ -34934,14 +35409,14 @@ - - + + - - + + edam @@ -34964,7 +35439,7 @@ - + @@ -34973,7 +35448,7 @@ - SO:0000110 + SO:0000110 bioinformatics beta12orEarlier Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. @@ -34989,15 +35464,15 @@ Data retrieval (feature table) - - true - operations + operation - beta12orEarlier bioinformatics - edam Extract a sequence feature table from a sequence database entry. beta13 + operations + true + beta12orEarlier + edam @@ -35045,13 +35520,13 @@ - + - + edam @@ -35070,14 +35545,14 @@ Data retrieval (sequence alignment) - - true - Display basic information about a sequence alignment. - beta13 + operations beta12orEarlier edam operation + Display basic information about a sequence alignment. + beta13 + true bioinformatics @@ -35090,12 +35565,6 @@ Sequence alignment analysis - @@ -35127,7 +35596,7 @@ bioinformatics edam operation - See also 'Sequence profile alignment'. + See also 'Sequence profile alignment'. beta12orEarlier Compare (typically by aligning) two molecular sequence alignments. operations @@ -35154,15 +35623,15 @@ Nucleic acid property processing - - true - edam - bioinformatics + beta13 Process (read and / or write) physicochemical property data of nucleic acids. - beta12orEarlier + true operations operation + edam + bioinformatics + beta12orEarlier @@ -35259,7 +35728,13 @@ - + + + + + + + @@ -35331,14 +35806,14 @@ - - + + - - + + bioinformatics @@ -35389,7 +35864,7 @@ - + Methods usually involve multiple sequence alignment analysis. @@ -35417,7 +35892,7 @@ - + beta12orEarlier @@ -35521,14 +35996,14 @@ - - + + - - + + beta12orEarlier @@ -35576,13 +36051,13 @@ Data retrieval (restriction enzyme annotation) - - true + Retrieve information on restriction enzymes or restriction enzyme sites. bioinformatics edam beta12orEarlier operations + true Restriction enzyme information retrieval beta13 operation @@ -35595,11 +36070,11 @@ Genetic marker identification - - true + edam operations beta13 + true bioinformatics A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. Identify genetic markers in DNA sequences. @@ -35621,12 +36096,6 @@ - - - - - - operation Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. bioinformatics @@ -35647,14 +36116,14 @@ - - + + - - + + edam @@ -35712,32 +36181,32 @@ - - + + - - + + - + - + - - + + edam @@ -35759,14 +36228,14 @@ - - + + - - + + bioinformatics @@ -35899,12 +36368,6 @@ - Sequence alignment computation operation operations @@ -35922,15 +36385,15 @@ Hybrid sequence alignment construction - - true + Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). edam + true operation Hybrid sequence alignment operations - beta13 beta12orEarlier + beta13 bioinformatics @@ -35966,12 +36429,6 @@ - @@ -35997,14 +36454,14 @@ - - + + - - + + operation @@ -36032,14 +36489,14 @@ - - + + - - + + operation @@ -36061,19 +36518,19 @@ - - + + - - + + Align sequence profiles (representing sequence alignments). beta12orEarlier - See also 'Sequence alignment comparison'. + See also 'Sequence alignment comparison'. bioinformatics operation Sequence profile alignment @@ -36097,14 +36554,14 @@ - - + + - - + + bioinformatics @@ -36128,14 +36585,14 @@ - - + + - - + + operation @@ -36159,20 +36616,14 @@ - - - - - - - - + + - - + + Sequence-3D profile alignment @@ -36202,7 +36653,7 @@ - + @@ -36211,12 +36662,6 @@ - - - - - - Sequence-structure alignment Align molecular sequence to structure in 3D space (threading). beta12orEarlier @@ -36239,7 +36684,7 @@ - + @@ -36299,7 +36744,7 @@ - + bioinformatics @@ -36319,14 +36764,14 @@ - - + + - - + + @@ -36374,20 +36819,20 @@ - - + + - + - - + + operations @@ -36410,26 +36855,26 @@ - - + + - + - - + + - - + + operation @@ -36506,14 +36951,14 @@ Sequencing-based expression profile data processing - - true + + bioinformatics + edam operations beta12orEarlier beta12orEarlier - bioinformatics + true operation - edam Process (read and / or write) SAGE, MPSS or SBS experimental data. @@ -36590,14 +37035,14 @@ Functional profiling - - true + operation beta12orEarlier + beta12orEarlier + true bioinformatics operations Interpret (in functional terms) and annotate gene expression data. - beta12orEarlier edam @@ -36608,9 +37053,9 @@ EST and cDNA sequence analysis - - true + bioinformatics + true operation For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. beta12orEarlier @@ -36627,11 +37072,11 @@ Structural genomics target selection - + true operations - bioinformatics beta12orEarlier + bioinformatics operation Methods will typically navigate a graph of protein families of known structure. Identify and select targets for protein structural determination. @@ -36657,7 +37102,7 @@ - + bioinformatics @@ -36677,14 +37122,14 @@ - - + + - - + + edam @@ -36706,7 +37151,13 @@ - + + + + + + + @@ -36718,13 +37169,13 @@ - + - + beta12orEarlier @@ -36763,24 +37214,18 @@ Phylogenetic tree construction - + - - - - - - Phylogenetic tree generation edam beta12orEarlier @@ -36883,7 +37328,7 @@ bioinformatics operations edam - A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. + 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. @@ -36955,13 +37400,13 @@ - + - + operations @@ -36980,15 +37425,15 @@ Immunogen design - - true - edam + operation - beta12orEarlier beta12orEarlier - Design molecules that elicit an immune response (immunogens). + beta12orEarlier operations + edam + Design molecules that elicit an immune response (immunogens). bioinformatics + true @@ -37003,7 +37448,7 @@ - + @@ -37029,14 +37474,14 @@ - - + + - - + + operation @@ -37151,14 +37596,14 @@ - - + + - - + + operation @@ -37180,7 +37625,7 @@ - + @@ -37214,12 +37659,6 @@ - - - - - - operations bioinformatics Screen a sequence against a motif or pattern database. @@ -37257,15 +37696,15 @@ Transmembrane protein database search - - true + edam operation bioinformatics beta12orEarlier - operations Search a database of transmembrane proteins, for example for sequence or structural similarities. beta12orEarlier + operations + true @@ -37276,8 +37715,8 @@ Sequence retrieval (by code) - edam beta12orEarlier + edam operations operation bioinformatics @@ -37331,17 +37770,11 @@ - - - - - - - operation - operations bioinformatics edam + operation beta12orEarlier + operations Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. @@ -37481,7 +37914,7 @@ - + edam @@ -37510,13 +37943,13 @@ - + - + beta12orEarlier @@ -37704,7 +38137,7 @@ - + @@ -37731,14 +38164,14 @@ - - + + - - + + edam @@ -37811,7 +38244,7 @@ - + beta12orEarlier @@ -37853,7 +38286,7 @@ - + Transcribe a nucleotide sequence into mRNA sequence(s). @@ -37960,7 +38393,7 @@ - + @@ -38023,14 +38456,14 @@ - - + + - - + + Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc. @@ -38074,7 +38507,7 @@ - + beta12orEarlier @@ -38274,14 +38707,14 @@ - - + + - - + + operations @@ -38322,14 +38755,14 @@ - - + + - - + + beta12orEarlier @@ -38614,14 +39047,14 @@ - - + + - - + + operation @@ -38672,14 +39105,14 @@ - - + + - - + + 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. @@ -38789,14 +39222,14 @@ - - + + - - + + operation @@ -38919,14 +39352,14 @@ - - + + - - + + Quadruplex structure prediction @@ -38948,14 +39381,14 @@ - - + + - - + + CpG island and isochores rendering @@ -38978,22 +39411,28 @@ + + + + + + - + - - + + Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. beta12orEarlier + operation edam operations bioinformatics - operation @@ -39026,14 +39465,14 @@ - - + + - - + + operation @@ -39128,20 +39567,14 @@ - - - - - - - This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. - operation beta12orEarlier operations edam + This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. + operation bioinformatics Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences. @@ -39198,7 +39631,7 @@ Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences. edam - Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. + Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. operation beta12orEarlier operations @@ -39218,7 +39651,7 @@ bioinformatics edam Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences. - Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. + 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. @@ -39231,7 +39664,7 @@ - + operation @@ -39296,14 +39729,14 @@ - - + + - - + + edam @@ -39383,12 +39816,6 @@ Sequence alignment analysis (chimeric sequence detection) - operation Detects chimeric sequences (chimeras) from a sequence alignment. edam @@ -39436,14 +39863,14 @@ Nucleosome formation potential prediction - - true - operation + operations beta12orEarlier - Predict nucleosome formation potential of DNA sequences. edam + operation + Predict nucleosome formation potential of DNA sequences. beta12orEarlier + true bioinformatics @@ -39585,14 +40012,14 @@ - - + + - - + + bioinformatics @@ -39635,7 +40062,7 @@ - + edam @@ -39656,7 +40083,7 @@ - + edam @@ -39768,14 +40195,14 @@ - - + + - - + + operation @@ -39800,7 +40227,7 @@ - + @@ -39809,6 +40236,12 @@ + + + + + + Predict tertiary structure (backbone and side-chain conformation) of protein sequences. operation operations @@ -39907,14 +40340,14 @@ - - + + - - + + @@ -39995,7 +40428,7 @@ - + edam @@ -40025,7 +40458,7 @@ - + operations @@ -40044,8 +40477,8 @@ SNP detection - + @@ -40090,11 +40523,11 @@ Functional mapping - - true + beta12orEarlier operations This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + true beta12orEarlier operation edam @@ -40120,7 +40553,7 @@ bioinformatics Haplotype reconstruction edam - Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). + Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). beta12orEarlier Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. operation @@ -40374,14 +40807,14 @@ - - + + - - + + Align molecular secondary structure (represented as a 1D string). @@ -40486,14 +40919,14 @@ Structure alignment (protein) - - true - operation - Align protein tertiary structures. + edam operations beta12orEarlier + operation + Align protein tertiary structures. bioinformatics + true beta13 @@ -40504,13 +40937,13 @@ Structure alignment (RNA) - - true + beta12orEarlier operation + bioinformatics + true Align RNA tertiary structures. edam - bioinformatics operations beta13 @@ -40614,8 +41047,8 @@ Sequence profile alignment construction (multiple) Sequence profile alignment (multiple) - bioinformatics Multiple sequence profile alignment construction + bioinformatics beta12orEarlier operation edam @@ -40786,7 +41219,7 @@ - + operation @@ -40904,10 +41337,10 @@ SAGE data processing - + true - operation bioinformatics + operation edam Serial analysis of gene expression data processing Process (read and / or write) serial analysis of gene expression (SAGE) data. @@ -40923,8 +41356,7 @@ MPSS data processing - - true + operations beta12orEarlier edam @@ -40932,6 +41364,7 @@ Massively parallel signature sequencing data processing beta12orEarlier operation + true Process (read and / or write) massively parallel signature sequencing (MPSS) data. @@ -40942,16 +41375,16 @@ SBS data processing - - true + bioinformatics operations edam + true operation Process (read and / or write) sequencing by synthesis (SBS) data. beta12orEarlier - beta12orEarlier Sequencing by synthesis data processing + beta12orEarlier @@ -41177,14 +41610,14 @@ - - + + - - + + beta12orEarlier @@ -41390,14 +41823,14 @@ - - + + - - + + beta12orEarlier @@ -41491,7 +41924,7 @@ bioinformatics edam beta12orEarlier - + @@ -41504,20 +41937,20 @@ - - + + - + - - + + Predict and optimise peptide ligands that elicit an immunological response. @@ -41539,13 +41972,13 @@ - + - + edam @@ -41564,9 +41997,21 @@ Sequence reformatting - operations + + + + + + + + + + + + bioinformatics operation + operations edam Reformat (a file or other report of) molecular sequence(s). beta12orEarlier @@ -41580,12 +42025,24 @@ Sequence alignment reformatting + + + + + + + + + + + + operation + edam beta12orEarlier Reformat (a file or other report of) molecular sequence alignment(s). operations bioinformatics - edam @@ -41654,14 +42111,14 @@ - - + + - - + + Visualise, format or print a molecular sequence alignment. @@ -41770,14 +42227,14 @@ - - + + - - + + Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. @@ -41867,15 +42324,15 @@ Sequence motif rendering - - true - beta12orEarlier + edam - beta12orEarlier - bioinformatics Render a sequence with motifs. operations operation + beta12orEarlier + beta12orEarlier + bioinformatics + true @@ -41907,15 +42364,15 @@ DNA linear map rendering - - true - operation + bioinformatics - edam Draw a linear maps of DNA. + beta12orEarlier + operation + edam operations + true beta12orEarlier - beta12orEarlier @@ -41944,7 +42401,7 @@ - + beta12orEarlier @@ -41961,14 +42418,14 @@ Nucleic acid folding family identification - - true + operation bioinformatics - beta12orEarlier - Identify folding families of related RNAs. edam beta12orEarlier + true + beta12orEarlier + Identify folding families of related RNAs. operations @@ -41994,11 +42451,11 @@ Annotation retrieval - + true beta12orEarlier - edam operations + edam Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. operation Retrieve existing annotation (or documentation), typically annotation on a database entity. @@ -42018,11 +42475,11 @@ - + operation - 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. beta12orEarlier edam operations @@ -42061,14 +42518,14 @@ - - + + - - + + operation @@ -42199,7 +42656,7 @@ Protein atom surface calculation (accessible) - 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 operation WHATIF:AtomAccessibilitySolventPlus @@ -42223,7 +42680,7 @@ WHATIF:AtomAccessibilityMolecularPlus WHATIF:AtomAccessibilityMolecular edam - 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. bioinformatics beta12orEarlier @@ -42235,7 +42692,7 @@ Protein residue surface calculation (accessible) - Calculate the solvent accessibility ('accessible surface') for each residue in a structure. + Calculate the solvent accessibility ('accessible surface') for each residue in a structure. beta12orEarlier Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). operations @@ -42258,7 +42715,7 @@ WHATIF:ResidueAccessibilityVacuum operation bioinformatics - Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. + 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). @@ -42274,7 +42731,7 @@ bioinformatics Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). operations - Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. + Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. WHATIF:ResidueAccessibilityMolecular operation @@ -42286,9 +42743,9 @@ Protein residue surface calculation (vacuum molecular) - operations WHATIF:ResidueAccessibilityVacuumMolecular - Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. + operations + Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. beta12orEarlier edam operation @@ -42303,7 +42760,7 @@ Protein surface calculation (accessible molecular) - Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. + Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. WHATIF:TotAccessibilityMolecular beta12orEarlier operations @@ -42322,7 +42779,7 @@ operations bioinformatics operation - Calculate the solvent accessibility ('accessible surface') for a structure as a whole. + Calculate the solvent accessibility ('accessible surface') for a structure as a whole. beta12orEarlier WHATIF:TotAccessibilitySolvent edam @@ -42503,7 +42960,7 @@ 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. operation operations edam @@ -42581,8 +43038,8 @@ WHATIF:ShowLikelyRotamers200 WHATIF:ShowLikelyRotamers300 WHATIF:ShowLikelyRotamers400 - operation WHATIF:ShowLikelyRotamers700 + operation Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. WHATIF:ShowLikelyRotamers900 operations @@ -42649,13 +43106,13 @@ PDB file sequence retrieval - - true + beta12orEarlier edam bioinformatics - WHATIF: PDB_sequence + true operations + WHATIF: PDB_sequence beta12orEarlier operation Extract a molecular sequence from a PDB file. @@ -42685,14 +43142,14 @@ DSSP secondary structure assignment - - true + operations beta12orEarlier edam Determine for residue the DSSP determined secondary structure in three-state (HSC). operation bioinformatics + true WHATIF: ResidueDSSP beta12orEarlier @@ -42725,7 +43182,7 @@ - + beta12orEarlier @@ -42785,7 +43242,7 @@ - + operations @@ -42819,18 +43276,6 @@ Listfile processing - beta12orEarlier Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). bioinformatics @@ -42863,24 +43308,12 @@ Sequence alignment file processing - - Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. - operation - edam operations bioinformatics + Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. + operation beta12orEarlier + edam @@ -42889,15 +43322,15 @@ Small molecule data processing - - true + operation - edam Process (read and / or write) physicochemical property data for small molecules. operations beta12orEarlier - bioinformatics beta13 + edam + bioinformatics + true @@ -42907,11 +43340,11 @@ Data retrieval (ontology annotation) - - true + beta12orEarlier - bioinformatics operation + bioinformatics + true Ontology information retrieval operations edam @@ -42926,16 +43359,16 @@ Data retrieval (ontology concept) - - true + bioinformatics - operation - beta13 beta12orEarlier + beta13 + operation Query an ontology and retrieve concepts or relations. operations Ontology retrieval edam + true @@ -42982,10 +43415,10 @@ Data retrieval (sequence profile) - - true - beta13 + This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. + beta13 + true bioinformatics operation edam @@ -43001,10 +43434,10 @@ Statistical calculation - - true - edam + beta12orEarlier + edam + true beta12orEarlier operations bioinformatics @@ -43023,14 +43456,14 @@ - - + + - - + + Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. @@ -43052,14 +43485,14 @@ - - + + - - + + operations @@ -43076,14 +43509,14 @@ Demonstration - - true + beta13 bioinformatics edam operation operations An operation performing purely illustrative (pedagogical) purposes. + true beta12orEarlier @@ -43093,14 +43526,14 @@ Data retrieval (pathway or network) - + + operation true + beta12orEarlier beta13 Query a biological pathways database and retrieve annotation on one or more pathways. - operation bioinformatics operations - beta12orEarlier edam @@ -43111,9 +43544,9 @@ Data retrieval (identifier) - - true + edam + true beta13 bioinformatics Query a database and retrieve one or more data identifiers. @@ -43147,14 +43580,14 @@ - - + + - - + + @@ -43179,30 +43612,18 @@ Sequence motif processing - - + - - operation - edam beta12orEarlier + operation Process (read and / or write) molecular sequence motifs. operations bioinformatics + edam @@ -43218,24 +43639,12 @@ - operations bioinformatics beta12orEarlier + operation edam Process (read and / or write) protein interaction data. - operation @@ -43248,14 +43657,14 @@ - - + + - - + + operation @@ -43273,15 +43682,15 @@ Annotation processing - - true - operation - operations + bioinformatics - Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. edam beta12orEarlier beta12orEarlier + true + operation + operations + Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. @@ -43291,14 +43700,14 @@ Sequence feature analysis - - true + beta12orEarlier operation - Analyse features in molecular sequences. operations - bioinformatics + true beta12orEarlier + Analyse features in molecular sequences. + bioinformatics edam @@ -43310,24 +43719,12 @@ File processing - - Data file processing operations File handling @@ -43345,12 +43742,12 @@ Gene expression analysis - + true - beta12orEarlier - bioinformatics operations Analyse gene expression and regulation data. + beta12orEarlier + bioinformatics beta12orEarlier edam operation @@ -43364,28 +43761,16 @@ Structural (3D) profile processing - - + operations + bioinformatics operation edam - bioinformatics Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. beta12orEarlier @@ -43397,31 +43782,13 @@ Data index processing - + bioinformatics + beta12orEarlier Process (read and / or write) an index of (typically a file of) biological data. + edam operations operation Database index processing - bioinformatics - beta12orEarlier - edam @@ -43431,30 +43798,18 @@ Sequence profile processing - - + - bioinformatics + operation + operations Process (read and / or write) some type of sequence profile. beta12orEarlier edam - operation - operations @@ -43489,14 +43844,14 @@ - - + + - - + + beta12orEarlier @@ -43518,22 +43873,16 @@ - - - - - - - + operation edam Analyse known protein secondary structure data. @@ -43549,15 +43898,15 @@ Physicochemical property data processing - - true + bioinformatics - operation beta12orEarlier Process (read and / or write) data on the physicochemical property of a molecule. + true operations beta13 edam + operation @@ -43572,7 +43921,7 @@ - + bioinformatics @@ -43591,25 +43940,13 @@ Analysis and processing - operation - Process (read and / or write) data of a specific type, for example applying analytical methods. + operations beta12orEarlier + Process (read and / or write) data of a specific type, for example applying analytical methods. edam bioinformatics Calculation - operations Computation @@ -43730,15 +44067,15 @@ Data handling - - true + beta12orEarlier operation + true + edam operations Perform basic operations on some data or a database. bioinformatics beta12orEarlier - edam @@ -43752,8 +44089,8 @@ edam Validate or standardise some data. Validation and standardisation - bioinformatics operation + bioinformatics operations beta12orEarlier @@ -43792,15 +44129,15 @@ Design - - true + + beta13 + operations + bioinformatics edam + true Design a biological entity (typically a molecular sequence or structure) with specific properties. - beta13 operation - operations beta12orEarlier - bioinformatics @@ -43810,13 +44147,13 @@ Microarray data processing - - true - operation + bioinformatics - operations + true beta12orEarlier edam + operation + operations Process (read and / or write) microarray data. beta12orEarlier @@ -43829,18 +44166,6 @@ Codon usage table processing - beta12orEarlier bioinformatics operations @@ -43855,14 +44180,14 @@ Data retrieval (codon usage table) - - true + beta13 + operations edam + true bioinformatics beta12orEarlier Retrieve a codon usage table and / or associated annotation. - operations operation @@ -43874,28 +44199,10 @@ Gene expression profile processing - + bioinformatics beta12orEarlier operations Process (read and / or write) a gene expression profile. - bioinformatics operation edam @@ -43951,30 +44258,18 @@ Pathway or network processing - - operation - bioinformatics - operations edam beta12orEarlier + operation Generate, analyse or handle a biological pathway or network. + bioinformatics + operations @@ -43988,31 +44283,13 @@ - - - - - - - - operations - bioinformatics - edam Process (read and / or write) RNA secondary structure data. + edam + bioinformatics operation beta12orEarlier @@ -44023,15 +44300,15 @@ Structure processing (RNA) - + true + beta13 + beta12orEarlier + operation bioinformatics operations edam - beta13 - beta12orEarlier Process (read and / or write) RNA tertiary structure data. - operation @@ -44090,24 +44367,12 @@ - edam Process (read and / or write) a phylogenetic tree. - beta12orEarlier - operations bioinformatics + beta12orEarlier operation + operations @@ -44118,28 +44383,16 @@ Protein secondary structure processing - - - beta12orEarlier - operations edam bioinformatics + beta12orEarlier + operations operation Process (read and / or write) protein secondary structure data. @@ -44152,22 +44405,10 @@ Protein interaction network processing - - + edam @@ -44185,30 +44426,12 @@ Sequence processing - - bioinformatics edam beta12orEarlier - operation Process (read and / or write) one or more molecular sequences and associated annotation. + operation operations + bioinformatics Sequence processing (general) @@ -44220,24 +44443,12 @@ Sequence processing (protein) - + operations edam bioinformatics operation beta12orEarlier Process (read and / or write) a protein sequence and associated annotation. - operations @@ -44248,24 +44459,12 @@ Sequence processing (nucleic acid) - operations + edam operation + Process (read and / or write) a nucleotide sequence and associated annotation. bioinformatics beta12orEarlier - edam - Process (read and / or write) a nucleotide sequence and associated annotation. @@ -44278,14 +44477,14 @@ - - + + - - + + @@ -44315,18 +44514,6 @@ - operation bioinformatics beta12orEarlier @@ -44344,14 +44531,14 @@ - - + + - + @@ -44362,8 +44549,8 @@ - - + + operations @@ -44390,7 +44577,7 @@ - + Gene finding @@ -44462,24 +44649,12 @@ - Process (read and / or write) a protein tertiary structure. - beta12orEarlier - operations operation + beta12orEarlier bioinformatics edam + operations @@ -44541,23 +44716,11 @@ - + bioinformatics + Process (read and / or write) a molecular sequence alignment. edam operations beta12orEarlier - bioinformatics - Process (read and / or write) a molecular sequence alignment. operation @@ -44570,14 +44733,14 @@ - - + + - - + + bioinformatics @@ -44595,30 +44758,12 @@ Structure processing - beta12orEarlier + bioinformatics Process (read and / or write) a molecular tertiary structure. + operations operation edam - bioinformatics - operations @@ -44655,13 +44800,13 @@ Data retrieval (protein annotation) - - true + operation Protein information retrieval + true edam - beta12orEarlier bioinformatics + beta12orEarlier operations beta13 Retrieve information on a protein. @@ -44674,13 +44819,13 @@ Data retrieval (phylogenetic tree) - - true + operations - Retrieve a phylogenetic tree from a data resource. bioinformatics operation beta13 + true + Retrieve a phylogenetic tree from a data resource. edam beta12orEarlier @@ -44692,15 +44837,15 @@ Data retrieval (protein interaction annotation) - - true + + operations + beta13 + Retrieve information on a protein interaction. operation edam - operations beta12orEarlier bioinformatics - beta13 - Retrieve information on a protein interaction. + true @@ -44710,13 +44855,13 @@ Data retrieval (protein family annotation) - - true + operation operations Retrieve information on a protein family. edam beta12orEarlier + true bioinformatics beta13 Protein family information retrieval @@ -44729,14 +44874,14 @@ Data retrieval (RNA family annotation) - - true + beta13 beta12orEarlier operations RNA family information retrieval operation Retrieve information on an RNA family. + true edam bioinformatics @@ -44748,14 +44893,14 @@ Data retrieval (gene annotation) - - true + bioinformatics beta13 Retrieve information on a specific gene. Gene information retrieval beta12orEarlier operations + true edam operation @@ -44767,7 +44912,7 @@ Data retrieval (genotype and phenotype annotation) - + true bioinformatics operations @@ -44842,14 +44987,14 @@ - - + + - - + + edam @@ -44927,20 +45072,20 @@ - - + + - - + + - - + + operations @@ -44986,18 +45131,6 @@ Secondary structure processing - @@ -45005,10 +45138,10 @@ beta12orEarlier - operations edam Process (read and / or write) a molecular secondary structure. bioinformatics + operations operation @@ -45087,14 +45220,14 @@ - - + + - - + + Compare protein tertiary structures. @@ -45215,15 +45348,15 @@ Codon usage data processing - - true + edam - operation bioinformatics - operations - Process (read and / or write) codon usage data. beta13 beta12orEarlier + true + operation + operations + Process (read and / or write) codon usage data. @@ -45234,30 +45367,12 @@ Gene expression data processing - - - - - - - - Process (read and / or write) gene expression (typically microarray) data. bioinformatics operations @@ -45275,28 +45390,16 @@ Gene regulatory network processing - - operations + operation bioinformatics Process (read and / or write) a network of gene regulation. - operation beta12orEarlier edam @@ -45336,15 +45439,15 @@ Sequencing-based expression profile data analysis - - true + operations - beta12orEarlier operation beta12orEarlier Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. edam bioinformatics + true + beta12orEarlier @@ -45359,14 +45462,14 @@ - - + + - - + + operations @@ -45384,12 +45487,12 @@ Microarray raw data analysis - - true + bioinformatics operations Analyse raw microarray data. beta12orEarlier + true beta12orEarlier edam operation @@ -45409,24 +45512,12 @@ - beta12orEarlier Process (read and / or write) nucleic acid sequence or structural data. operation + bioinformatics operations edam - bioinformatics @@ -45442,24 +45533,12 @@ - + bioinformatics operation + Process (read and / or write) protein sequence or structural data. operations beta12orEarlier edam - bioinformatics - Process (read and / or write) protein sequence or structural data. @@ -45468,16 +45547,15 @@ Sequence data processing - - true + operation + true edam beta13 beta12orEarlier Process (read and / or write) molecular sequence data. operations bioinformatics - @@ -45486,14 +45564,14 @@ Structural data processing - - true + operations edam - beta12orEarlier - operation bioinformatics beta13 + beta12orEarlier + true + operation Process (read and / or write) molecular structural data. @@ -45505,18 +45583,6 @@ Text processing - edam Process (read and / or write) text. operations @@ -45536,14 +45602,14 @@ - - + + - - + + operation @@ -45565,14 +45631,14 @@ - - + + - - + + Analyse a protein sequence alignment, typically to detect features or make predictions. @@ -45782,29 +45848,17 @@ Structure processing (nucleic acid) - - - bioinformatics - operation Process (read and / or write) nucleic acid tertiary structure data. + operation edam beta12orEarlier + bioinformatics operations @@ -45816,12 +45870,6 @@ DNA mapping - @@ -45846,28 +45894,16 @@ - - - - operations - Process (read and / or write) a DNA map of some type. - bioinformatics beta12orEarlier edam - DNA map data processing + Process (read and / or write) a DNA map of some type. operation + DNA map data processing + bioinformatics @@ -45880,7 +45916,7 @@ - + @@ -45906,14 +45942,14 @@ - - + + - - + + @@ -46022,14 +46058,14 @@ - - + + - - + + @@ -46251,12 +46287,12 @@ Analysis - - true + beta12orEarlier edam beta12orEarlier - For non-analytical operations, see the 'Processing' branch. + For non-analytical operations, see the 'Processing' branch. + true bioinformatics operations operation @@ -46273,14 +46309,14 @@ - - + + - - + + Analyse an existing alignment of two or more molecular sequences, structures or derived data. @@ -46300,20 +46336,20 @@ - - + + - - + + - - + + beta12orEarlier @@ -46330,9 +46366,9 @@ Molecular interaction analysis - - true + bioinformatics + true beta13 edam operation @@ -46354,12 +46390,6 @@ - Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. operations edam @@ -46390,18 +46420,6 @@ Alignment processing - beta12orEarlier edam Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. @@ -46417,30 +46435,18 @@ Structure alignment processing - - - edam bioinformatics beta12orEarlier Process (read and / or write) a molecular tertiary (3D) structure alignment. operations operation + edam @@ -46533,14 +46539,14 @@ Molecular interaction data processing - - true + Process (read and / or write) molecular interaction data. edam bioinformatics operation operations beta12orEarlier + true beta13 @@ -46682,12 +46688,6 @@ Pathway or network rendering - @@ -46696,9 +46696,9 @@ beta13 bioinformatics - operations operation edam + operations Render (visualise) a biological pathway or network. @@ -46714,11 +46714,11 @@ - + 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. edam operation bioinformatics @@ -46787,7 +46787,7 @@ - + @@ -46796,6 +46796,12 @@ + + + + + + operations operation edam @@ -46881,12 +46887,6 @@ - - - - - - @@ -46897,6 +46897,12 @@ + + + + + + bioinformatics edam operations @@ -46974,7 +46980,7 @@ Phred base calling Phred base-calling bioinformatics - Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. + Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. edam @@ -47125,7 +47131,7 @@ Genotyping edam - Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. + Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. operations 1.1 @@ -47171,8 +47177,8 @@ Short read alignment 1.1 Read alignment - Oligonucleotide alignment The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. + Oligonucleotide alignment edam Short read mapping bioinformatics @@ -47425,8 +47431,8 @@ Analyse a spectrum from a mass spectrometry (or other) experiment. edam bioinformatics - 1.1 Spectral analysis + 1.1 operations @@ -47556,7 +47562,7 @@ Protein binding peak detection Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. bioinformatics - Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). + Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). edam operations operation @@ -47601,8 +47607,8 @@ Variant classification - + operations edam Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) @@ -47618,14 +47624,14 @@ Variant prioritization - + edam bioinformatics 1.1 operation operations Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. - Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. + Variant 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. @@ -47750,9 +47756,9 @@ 1.2 edam + - @@ -47772,14 +47778,14 @@ - Infer a transcriptome sequence by analysis of short sequence reads. - bioinformatics edam - operation + Infer a transcriptome sequence by analysis of short sequence reads. operations + operation 1.2 + bioinformatics - + @@ -47787,15 +47793,15 @@ Transcriptome assembly (de novo) + operations Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. + 1.2 + operation + edam de novo transcriptome assembly bioinformatics - edam - operation - operations - 1.2 - + @@ -47803,12 +47809,144 @@ Transcriptome assembly (mapping) + bioinformatics + 1.2 + operation Infer a transcriptome sequence by mapping short reads to a reference genome. + operations + edam + + + + + + + + Sequence coordinate conversion + + + + + + + + + + + + + + operations + edam + Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc. + 1.3 + bioinformatics + operation + + + + + + + + Document similarity calculation + + operation + 1.3 + edam + operations + bioinformatics + Calculate similarity between 2 or more documents. + + + + + + + + Document clustering + + 1.3 + operations + operation + Cluster (group) documents on the basis of their calculated similarity. + edam bioinformatics + + + + + + + + Named entity recognition + edam + operations operation + Recognise named entities (text tokens) within documents. + 1.3 + bioinformatics + + + + + + + + ID mapping + operations - 1.2 + Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. + operation + Accession mapping + edam + bioinformatics + 1.3 + Identifier mapping + + + + + + + + Data anonymisation + + edam + 1.3 + bioinformatics + Data anonymization + operation + Process data in such a way that makes it hard to trace to the person which the data concerns. + operations + + + + + + + + ID retrieval + + + + + + + + 1.3 + Search for and retrieve a data identifier of some kind, e.g. a database entry accession. + edam + Accession retrieval + bioinformatics + operation + Data retrieval (id) + Identifier retrieval + Data retrieval (ID) + Data retrieval (accession) + operations + id retrieval @@ -47816,49 +47954,47 @@ + Topic + + sumo:FieldOfStudy beta12orEarlier - topics - edam + A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. bioinformatics + edam topic - - - - Topic - A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. - - - sumo:FieldOfStudy - - - - - - + topics + + + + + + + + - 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. - + + - 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. - + + - 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. - - + + @@ -47866,19 +48002,21 @@ - Nucleic acid analysis - + Nucleic acids + edam + Nucleic acid analysis beta12orEarlier bioinformatics + Nucleic acid physicochemistry + Processing and analysis of nucleic acid sequence, structural and other data. + Nucleic acid properties topic topics Nucleic acid informatics - Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis. Nucleic acid bioinformatics - Nucleic acids - - + + @@ -47886,18 +48024,21 @@ - Protein analysis - + Proteins + beta12orEarlier - Processing and analysis of protein data, typically molecular sequence and structural data. - bioinformatics + Protein data resources + Protein databases Protein bioinformatics + bioinformatics edam + Protein analysis + Topic concerning archival, processing and analysis of protein data, typically molecular sequence and structural data. Proteins topic Protein informatics topics - + @@ -47907,12 +48048,12 @@ Metabolites - beta12orEarlier - Topic concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. bioinformatics This concept excludes macromolecules such as proteins and nucleic acids. topics + Topic concerning the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. + Metabolite structures topic edam @@ -47923,16 +48064,18 @@ Sequence analysis - - Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles. + + events bioinformatics topic BioCatalogue:Sequence Analysis topics Sequences + Sequence databases + Topic concerning the archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. edam beta12orEarlier - + @@ -47941,17 +48084,21 @@ Structure analysis - + beta12orEarlier topics + Structure data resources This includes related concepts such as structural properties, alignments and structural motifs. + Structure databases edam Structural bioinformatics topic + Structure analysis bioinformatics - Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids. - Computation structural biology - + events + Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. + Computational structural biology + @@ -47975,14 +48122,14 @@ Alignment - - true + edam Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). beta12orEarlier beta12orEarlier topic topics + true bioinformatics @@ -47994,20 +48141,24 @@ - Phylogenetics - - Phylogenetic simulation + Phylogeny + + BioCatalogue:Evolutionary Distance Measurements + Phylogenetic clocks, dating and stratigraphy + This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc. bioinformatics BioCatalogue:Phylogeny edam - This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data. + Phylogenetic simulation BioCatalogue:Statistical Robustness topics - Phylogenetic clocks, dating and stratigraphy - Topic concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc. + events topic + Topic concerning the study of evolutionary relationships amongst organisms. beta12orEarlier - + BioCatalogue:Tree Inference + Phylogeny reconstruction + @@ -48017,11 +48168,15 @@ Functional genomics - Topic concerning the study of gene or protein functions and their interactions. + + BioCatalogue:Functional Genomics + topic + Genome annotation bioinformatics topics edam - topic + events + Topic concerning the study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. beta12orEarlier @@ -48030,19 +48185,20 @@ - Ontology - + Ontology and terminology + topics BioCatalogue:Ontology Lookup bioinformatics - This includes the annotation of entities (typically biological database entries) with concepts from a controlled vocabulary. + Topic concerning the conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. + events Applied ontology beta12orEarlier - Topic concerning ontologies, controlled vocabularies, structured glossary or other related resource. Ontologies topic edam BioCatalogue:Ontology + @@ -48050,9 +48206,10 @@ - Data search and retrieval - + Data search, query and retrieval + Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information. + Data query BioCatalogue:Structure Retrieval BioCatalogue:Image Retrieval bioinformatics @@ -48072,16 +48229,21 @@ - Data handling - - Topic for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation. - beta12orEarlier + Bioinformatics + + topics + bioinformatics + events + This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. + Information science + Data handling + Topic concerning the archival, curation, processing and analysis of complex biological data. + beta12orEarlier edam + Informatics topic - bioinformatics - Data types, processing and visualisation - + @@ -48090,7 +48252,7 @@ Data visualisation - + edam bioinformatics Data rendering and visualisation @@ -48108,18 +48270,12 @@ Nucleic acid thermodynamics - - Nucleic acid properties - DNA melting - edam - topic - This includes the study of thermal and conformational properties including DNA or DNA/RNA denaturation (melting). - Topic concerning the study of the thermodynamic properties of a nucleic acid. + topics - Nucleic acid denaturation - beta12orEarlier - bioinformatics - Nucleic acid physicochemistry + 1.3 + true + Topic concerning the study of the thermodynamic properties of a nucleic acid. + @@ -48128,14 +48284,21 @@ Nucleic acid structure analysis - + RNA structure + Nucleic acid structure + Nucleic acid thermodynamics + beta12orEarlier + RNA structure alignment bioinformatics + Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. edam - The processing and analysis of nucleic acid (secondary or tertiary) structural data. topic + RNA alignment + Nucleic acid denaturation topics - beta12orEarlier + DNA melting + Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc. @@ -48144,7 +48307,7 @@ RNA - + Topic concerning RNA sequences and structures. topic edam @@ -48159,14 +48322,16 @@ Nucleic acid restriction - - - topics + bioinformatics - topic + true edam Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. + 1.3 + topics + topic beta12orEarlier + @@ -48178,10 +48343,13 @@ topic edam + 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 topics - Topic concerning the mapping of complete (typically nucleotide) sequences. bioinformatics + Linkage mapping + Genetic linkage + Topic concerning the mapping of complete (typically nucleotide) sequences. @@ -48189,14 +48357,15 @@ - Codon usage analysis - - bioinformatics - topic - edam + Genetic codes and codon usage + + Codon usage analysis + 1.3 topics Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on. + true beta12orEarlier + @@ -48204,13 +48373,15 @@ - Translation - - Topic concerning the translation of mRNA into protein. + Protein expression + bioinformatics beta12orEarlier topic + events + Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell. edam + Translation topics @@ -48220,17 +48391,20 @@ Gene finding - + BioCatalogue:Gene Prediction bioinformatics edam Gene discovery Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. + 1.3 + true Gene prediction topics beta12orEarlier topic + @@ -48239,14 +48413,16 @@ Transcription - - BioCatalogue:Transcription Factors - bioinformatics + beta12orEarlier topic + topics + true + bioinformatics Topic concerning the transcription of DNA into mRNA. edam - topics + 1.3 + @@ -48255,16 +48431,16 @@ Promoters - - true + topic edam Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). BioCatalogue:Promoter Prediction - beta13 topics + beta13 bioinformatics beta12orEarlier + true @@ -48274,14 +48450,14 @@ Nucleic acid folding - - true + beta12orEarlier - edam Topic concerning the folding (in 3D space) of nucleic acid molecules. + true + beta12orEarlier + edam topic bioinformatics - beta12orEarlier topics @@ -48291,18 +48467,17 @@ - Gene structure and RNA splicing - - + Gene structure + topics - This includes splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. - RNA splicing + Topic concerning resources that aim to identify, predict, model, analyse or curate gene structure in DNA sequences. This includes introns, exons, and gene fusion. topic + RNA splicing Gene structure beta12orEarlier bioinformatics edam - Topic concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons). + This includes the study of promoters, coding regions etc. @@ -48311,17 +48486,20 @@ Proteomics - + BioCatalogue:Proteomics - Protein expression - Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues). + Protein expression + Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms. bioinformatics edam - Topic concerning the study of whole proteomes of organisms. + Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. + Peptide identification + Protein and peptide identification beta12orEarlier + events topic topics - + @@ -48331,14 +48509,15 @@ Structural genomics - + edam - beta12orEarlier + Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. BioCatalogue:Structural Genomics topic - topics + events bioinformatics - Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. + beta12orEarlier + topics @@ -48347,11 +48526,12 @@ Protein properties - + topics beta12orEarlier + Topic for the study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. Protein physicochemistry - Topic for the study of the physical and biochemical properties of peptides and proteins. + Protein hydropathy topic edam bioinformatics @@ -48363,15 +48543,21 @@ Protein interactions - - + + topics BioCatalogue:Protein Interaction Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. - edam + Protein-DNA interaction + BioCatalogue:Ligand Interaction + Protein-ligand interactions beta12orEarlier + edam bioinformatics + Protein-protein interactions This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. + Protein-nucleic acid interactions + Protein-RNA interaction topic @@ -48380,14 +48566,17 @@ - Protein folding and stability + Protein folding, stability and design + Rational protein design bioinformatics edam + Protein design + Protein residue interactions beta12orEarlier topic + Topic concerning protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. topics - Topic concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation. @@ -48396,15 +48585,15 @@ Two-dimensional gel electrophoresis - - true + topics + true beta12orEarlier - bioinformatics beta13 - Topic concerning two-dimensional gel electrophoresis image and related data. topic edam + bioinformatics + Topic concerning two-dimensional gel electrophoresis image and related data. @@ -48414,13 +48603,13 @@ Mass spectrometry - - true - topic + topics beta13 - Topic concerning mass spectrometry and related data. beta12orEarlier + topic + Topic concerning mass spectrometry and related data. + true edam bioinformatics @@ -48432,12 +48621,12 @@ Protein microarrays - - true + beta13 edam beta12orEarlier bioinformatics + true topics topic Topic concerning protein microarray data. @@ -48451,13 +48640,13 @@ Protein hydropathy - - topic - bioinformatics + + 1.3 + true topics beta12orEarlier Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein. - edam + @@ -48466,13 +48655,13 @@ Protein targeting and localization - - + edam beta12orEarlier topic topics bioinformatics + Protein sorting Topic for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. @@ -48482,13 +48671,16 @@ Protein cleavage sites and proteolysis - + bioinformatics topic edam topics beta12orEarlier Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. + true + 1.3 + @@ -48497,11 +48689,11 @@ Protein structure comparison - - true + beta12orEarlier topics Use this concept for methods that are exclusively for protein structure. + true beta12orEarlier bioinformatics topic @@ -48516,15 +48708,18 @@ - Protein residue interaction analysis - - beta12orEarlier + Protein residue interactions + bioinformatics + 1.3 Protein residue interactions + edam + beta12orEarlier + true topic topics The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. - edam + @@ -48533,13 +48728,14 @@ Protein-protein interactions - - Topic concerning protein-protein interactions, protein complexes, protein functional coupling etc. + + Topic concerning protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. + 1.3 beta12orEarlier - bioinformatics - edam + true + Protein interaction networks topics - topic + @@ -48548,14 +48744,13 @@ Protein-ligand interactions - - bioinformatics - topic - edam + + 1.3 + true topics Topic concerning protein-ligand (small molecule) interactions. - BioCatalogue:Ligand Interaction beta12orEarlier + @@ -48564,13 +48759,13 @@ Protein-nucleic acid interactions - + topics - bioinformatics - topic + true + 1.3 Topic concerning protein-DNA/RNA interactions. - edam beta12orEarlier + @@ -48579,13 +48774,14 @@ Protein design - + + true bioinformatics - topic Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. topics beta12orEarlier - edam + 1.3 + @@ -48594,15 +48790,15 @@ G protein-coupled receptors (GPCR) - - true + beta12orEarlier + edam + topics beta12orEarlier Topic concerning G-protein coupled receptors (GPCRs). bioinformatics topic - edam - topics + true @@ -48612,7 +48808,7 @@ Carbohydrates - + edam Topic concerning carbohydrates, typically including structural information. topics @@ -48627,7 +48823,7 @@ Lipids - + edam topics Topic concerning lipids and their structures. @@ -48642,12 +48838,12 @@ Small molecules - - Topic concerning small molecules of biological significance, typically including structural information. + edam topic beta12orEarlier CHEBI:23367 + Topic concerning small molecules of biological significance, typically archival, curation, processing and analysis of structural information. bioinformatics Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. topics @@ -48659,14 +48855,14 @@ Sequence editing - - true + beta12orEarlier Edit, convert or otherwise change a molecular sequence, either randomly or specifically. - edam beta12orEarlier + edam bioinformatics topic + true topics @@ -48677,13 +48873,19 @@ - Sequence composition analysis + Sequence composition, complexity and repeats + BioCatalogue:Repeats + Sequence composition + Topic concerning the archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. + bioinformatics + Sequence repeats + Low complexity sequences + Sequence complexity topic topics - bioinformatics beta12orEarlier - Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats. + Repeat sequences edam @@ -48693,14 +48895,17 @@ Sequence motifs - - Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. + + topics bioinformatics + 1.3 + true + Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. topic - topics Motifs edam beta12orEarlier + @@ -48726,14 +48931,24 @@ - Sequence sites and features - + Sequence sites, features and motifs + + HMMs beta12orEarlier - bioinformatics - topic + Sequence sites + Sequence profiles + Protein sequence features + Topic concerning the archival, detection, prediction and analysis of +positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. edam + Sequence feature detection + Sequence motifs + Functional sites + topic + Protein functional sites + bioinformatics topics - Topic concerning the positional features, such as functional and other key sites, in molecular sequences. + Sequence features @@ -48742,7 +48957,7 @@ Sequence database search - + true beta12orEarlier topic @@ -48762,6 +48977,7 @@ Sequence clustering + Sequence clusters Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities. topics bioinformatics @@ -48797,14 +49013,17 @@ Structural (3D) profiles - - Structural profiles + edam - bioinformatics + 1.3 + Structural profiles beta12orEarlier + bioinformatics topics + true The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment. topic + @@ -48832,16 +49051,17 @@ Nucleic acid structure prediction + Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. + Nucleic acid folding topic BioCatalogue:Nucleotide Structure Prediction BioCatalogue:Nucleotide Tertiary Structure - Nucleic acid folding - Topic concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure. bioinformatics edam BioCatalogue:Nucleotide Secondary Structure beta12orEarlier topics + Nucleic acid design RNA/DNA structure prediction @@ -48916,15 +49136,14 @@ Protein secondary structure prediction - - - topic + + true beta12orEarlier - edam + 1.3 Topic concerning the prediction of secondary or supersecondary structure of protein sequences. topics - bioinformatics - BioCatalogue:Protein Secondary Structure + + @@ -48933,15 +49152,15 @@ Protein tertiary structure prediction - - + Topic concerning the prediction of tertiary structure of protein sequences. beta12orEarlier - bioinformatics - edam - BioCatalogue:Protein Tertiary Structure + true + 1.3 topic topics + + @@ -48957,6 +49176,7 @@ Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). edam topics + For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). @@ -48966,7 +49186,6 @@ Sequence alignment - bioinformatics BioCatalogue:Protein Multiple Alignment Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). @@ -48980,7 +49199,7 @@ topics BioCatalogue:Nucleotide Pairwise Alignment BioCatalogue:Nucleotide Sequence Alignment - + @@ -48990,14 +49209,13 @@ Structure alignment - beta12orEarlier - This includes the generation, storage, analysis, rendering etc. of structure alignments. - edam - topics bioinformatics topic + This includes the generation, storage, analysis, rendering etc. of structure alignments. + edam Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). + topics Structure alignment generation @@ -49007,14 +49225,17 @@ Threading - + + true edam - beta12orEarlier Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). + beta12orEarlier + 1.3 topics bioinformatics topic Sequence-structure alignment + @@ -49023,14 +49244,17 @@ Sequence profiles and HMMs - + Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. beta12orEarlier + 1.3 + topics + topic bioinformatics Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment. - topics edam - topic + true + @@ -49039,16 +49263,19 @@ Phylogeny reconstruction - + topic BioCatalogue:Tree Inference - topics Currently too specific for the topic sub-ontology (but might be unobsoleted). + topics Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. BioCatalogue:Evolutionary Distance Measurements bioinformatics beta12orEarlier edam + true + 1.3 + http://edamontology.org/topic_0084 @@ -49057,10 +49284,11 @@ Phylogenomics - + topics edam + events topic Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. bioinformatics @@ -49073,10 +49301,10 @@ Virtual PCR - - true + Topic concerning simulated polymerase chain reaction (PCR). topic + true edam topics PCR @@ -49093,10 +49321,11 @@ Sequence assembly - + bioinformatics 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. topic edam topics @@ -49109,17 +49338,15 @@ Genetic variation - - - Mutation and polymorphism edam - bioinformatics + Mutation and polymorphism DNA variation + bioinformatics topics beta12orEarlier Topic concerning DNA sequence variation (mutation and polymorphism) data. topic - + @@ -49128,16 +49355,19 @@ Microarrays - + beta12orEarlier topics Topic concerning microarrays, for example, to process microarray data or design probes and experiments. - DNA microarrays - edam + 1.3 topic BioCatalogue:Microarrays bioinformatics - + DNA microarrays + true + edam + + @@ -49145,15 +49375,17 @@ - Pharmacoinformatics - - topic - Computational pharmacology - bioinformatics + Pharmacology + edam - Topic for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on. + events beta12orEarlier + topic + bioinformatics + Topic concerning the study of drugs and their effects or responses in living systems. + Pharmacoinformatics topics + Computational pharmacology @@ -49161,22 +49393,26 @@ - Transcriptomics - - + Gene expression + Gene expression resources Gene expression profiling + Codon usage Expression profiling edam - Topic concerning primarily raw or processed gene (mRNA) expression (typically microarray) data, including the analysis of gene expression levels, by identifying, quantifying or comparing mRNA transcripts and the interpretation (in functional terms) of gene expression data. + DNA microarrays Gene expression analysis + events bioinformatics + Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. http://edamontology.org/topic_0197 - topics topic + topics + Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. beta12orEarlier - This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein. - + BioCatalogue:Microarrays + This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. + @@ -49185,7 +49421,7 @@ Gene regulation - + Gene regulation resources bioinformatics beta12orEarlier @@ -49203,13 +49439,14 @@ Pharmacogenomics - bioinformatics - Pharmacogenetics - topic topics Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. edam beta12orEarlier + Pharmacogenetics + bioinformatics + events + topic @@ -49218,13 +49455,13 @@ Drug design - + edam bioinformatics beta12orEarlier topic - This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. Topic concerning the design of drugs or potential drug compounds. + This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. topics @@ -49234,14 +49471,13 @@ Fish - - edam - The resource may be specific to a fish, a group of fish or all fish. + + 1.3 + true topics Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation. - bioinformatics beta12orEarlier - topic + @@ -49250,15 +49486,13 @@ Flies - - Fly - edam + topics beta12orEarlier - topic - bioinformatics + true + 1.3 Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation. - The resource may be specific to a fly, a group of flies or all flies. + @@ -49267,15 +49501,14 @@ Mice or rats - + Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation. + 1.3 topics - Mouse or rat beta12orEarlier - topic - edam - bioinformatics + true The resource may be specific to a group of mice / rats or all mice / rats. + @@ -49284,15 +49517,13 @@ Worms - + beta12orEarlier topics - Worm - bioinformatics - The resource may be specific to a worm, a group of worms or all worms. - edam + 1.3 + true Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation. - topic + @@ -49301,17 +49532,16 @@ Literature analysis - + + true topic topics - BioCatalogue: Document Discovery - BioCatalogue: Literature retrieval + 1.3 beta12orEarlier The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. bioinformatics - Literature search and analysis - Literature sources edam + @@ -49320,7 +49550,7 @@ Text mining - + BioCatalogue:Document Clustering BioCatalogue:Document Similarity edam @@ -49329,7 +49559,10 @@ BioCatalogue:Text Mining beta12orEarlier Topic concerning the analysis of the biomedical and informatics literature. + Literature mining bioinformatics + events + Literature analysis topics BioCatalogue:Named Entity Recognition @@ -49339,15 +49572,18 @@ - Annotation - + Data curation and annotation + + edam - Ontology annotation - Topic for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary. bioinformatics + events + Ontology annotation + Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) and their annotation, typically with terms from a controlled vocabulary. BioCatalogue:Ontology Annotation topics BioCatalogue:Genome Annotation + Genome annotation beta12orEarlier topic @@ -49358,12 +49594,14 @@ Data processing and validation - + topic beta12orEarlier Data file handling Report processing + Datatypes topics + Data types Report handling bioinformatics This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. @@ -49378,15 +49616,15 @@ Sequence annotation - - true + edam Annotate a molecular sequence. bioinformatics - topics beta12orEarlier - topic beta12orEarlier + topics + true + topic @@ -49396,8 +49634,7 @@ Genome annotation - - true + topic topics Annotate a genome. @@ -49405,6 +49642,7 @@ beta12orEarlier bioinformatics BioCatalogue:Genome Annotation + true edam @@ -49416,15 +49654,15 @@ NMR - - true - Topic concerning raw NMR data. + edam - topic - bioinformatics beta13 topics beta12orEarlier + Topic concerning raw NMR data. + bioinformatics + topic + true @@ -49442,6 +49680,7 @@ topic edam bioinformatics + Sequence classification @@ -49450,15 +49689,16 @@ Protein classification - - - + bioinformatics + true + 1.3 + topics beta12orEarlier topic edam Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. - topics + @@ -49467,12 +49707,12 @@ Sequence motif or profile - - true - beta12orEarlier + Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. + beta12orEarlier edam This includes comparison, discovery, recognition etc. of sequence motifs. + true topics bioinformatics topic @@ -49487,18 +49727,17 @@ Protein modifications - - - edam - MOD:00000 - topic + bioinformatics + beta12orEarlier + MOD:00000 + topic + edam EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) topics - GO:0006464 - beta12orEarlier - Topic concerning protein chemical modifications, e.g. post-translational modifications. Protein post-translational modification + Topic concerning protein chemical modifications, e.g. post-translational modifications. + GO:0006464 @@ -49506,16 +49745,20 @@ - Pathways, networks and models + Molecular interactions, pathways and networks - - Topic concerning biological pathways, networks and other models, including their construction and analysis. BioCatalogue:Pathways - Network or pathway analysis edam http://edamontology.org/topic_3076 + Topic concerning molecular interactions, biological pathways, networks and other models. + Biological pathways + Biological models + Molecular interactions + events beta13 bioinformatics + Network or pathway analysis + Biological networks BioCatalogue:Pathway Retrieval topic topics @@ -49527,15 +49770,15 @@ Informatics - - true + bioinformatics topic + A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area. + true + topics beta12orEarlier beta12orEarlier - A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area. edam - topics @@ -49545,14 +49788,16 @@ Literature data resources - - - beta12orEarlier + topics + true + 1.3 + beta12orEarlier topic edam Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. bioinformatics + @@ -49560,14 +49805,17 @@ - Laboratory resources + Laboratory information management + edam + bioinformatics + events + Laboratory resources topic - Topic concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. beta12orEarlier + Topic concerning laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. topics - edam - bioinformatics + @@ -49575,14 +49823,19 @@ - Cell culture resources - + Cell and tissue culture + beta12orEarlier + Cell culture topics - Topic concerning general cell culture or data on a specific cell lines. edam - topic bioinformatics + Topic concerning general cell culture or data on a specific cell lines. + 1.3 + true + topic + Tissue culture + @@ -49590,17 +49843,20 @@ - Ecoinformatics - - Topic concerning the application of information technology to the ecological and environmental sciences. - Computational ecology + Ecology + + Environmental science + Ecoinformatics edam + Computational ecology beta12orEarlier bioinformatics topic + Ecological informatics + Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics). topics - Ecological informatics - + events + @@ -49609,13 +49865,13 @@ Electron microscopy - - true + edam - Topic concerning electron microscopy data. - bioinformatics + true beta12orEarlier topics + Topic concerning electron microscopy data. + bioinformatics beta13 topic @@ -49627,13 +49883,13 @@ Cell cycle - - true + topic + Topic concerning the cell cycle including key genes and proteins. + true beta12orEarlier topics edam - Topic concerning the cell cycle including key genes and proteins. beta13 bioinformatics @@ -49659,14 +49915,28 @@ - Organelle genes and proteins - - beta12orEarlier + Organelles + + 1.3 bioinformatics + Rough endoplasmic reticulum + Golgi apparatus + Mitochondria + true + Nucleus + Ribosome + Centriole + Lysosome + beta12orEarlier topics edam - Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). topic + Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). + Smooth endoplasmic reticulum + Cell membrane + Organelle genes and proteins + Cytoplasm + @@ -49674,15 +49944,15 @@ - Ribosomal genes and proteins - - Ribosome genes and proteins - topic - bioinformatics + Ribosomes + + true + 1.3 topics Topic concerning ribosomes, typically of ribosome-related genes and proteins. + Ribosome genes and proteins beta12orEarlier - edam + @@ -49691,7 +49961,7 @@ Scents - + true beta13 edam @@ -49710,9 +49980,10 @@ Drugs and targets - + topic edam + Drug and target structures topics beta12orEarlier Topic concerning the structures of drugs, drug target, their interactions and binding affinities. @@ -49724,18 +49995,17 @@ - Genome, proteome and model organisms - - - + Organisms + topic - General information on or more organisms, genomes (including molecular sequences and map, genes and annotation) and proteomes may be included. topics + Model organisms + events + 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 - Genome map edam bioinformatics - Topic concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms. + Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology. @@ -49744,8 +50014,8 @@ Genomics - - BioCatalogue:Functional Genomics + + events beta12orEarlier Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. bioinformatics @@ -49753,7 +50023,7 @@ topics BioCatalogue:Genomics edam - + @@ -49761,14 +50031,19 @@ - Genes, gene family or system - - + Gene families + + bioinformatics + Genes, gene family or system + events + Gene and protein families topics edam + Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins. + Genes and proteins resources + Gene family topic - Topic concerning particular gene(s), gene system or groups of genes. beta12orEarlier @@ -49778,7 +50053,7 @@ Chromosomes - + edam Topic concerning chromosomes. beta12orEarlier @@ -49793,15 +50068,16 @@ Genotype and phenotype - - bioinformatics - beta12orEarlier + topics edam Genotyping Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. Genotype and phenotype resources topic + bioinformatics + beta12orEarlier + events @@ -49810,15 +50086,15 @@ Gene expression and microarray - - true + topic beta12orEarlier bioinformatics edam - topics beta12orEarlier + topics Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. + true @@ -49828,16 +50104,22 @@ - Probes and primers - - + Sequence design + edam beta12orEarlier - bioinformatics + Probe design + Primers topics + in silico cloning Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). topic - + Gene design + bioinformatics + This includes the design of primers for PCR and DNA amplification or the design of molecular probes. + Primer design + Probes + @@ -49845,14 +50127,17 @@ - Disease resources - + Pathology + beta12orEarlier - Topic concerning diseases. - topics + events edam + Topic concerning diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. + Diseases + topics bioinformatics topic + Disease @@ -49861,14 +50146,17 @@ Specific protein resources - + topic - beta12orEarlier - topics Specific protein + true edam - Topic concerning a particular protein, protein family or other group of proteins. + 1.3 bioinformatics + beta12orEarlier + topics + Topic concerning a particular protein, protein family or other group of proteins. + @@ -49877,13 +50165,13 @@ Taxonomy - - bioinformatics - topic + + 1.3 + true Topic concerning organism classification, identification and naming. topics beta12orEarlier - edam + @@ -49892,12 +50180,12 @@ Protein sequence analysis - + Protein sequences topic topics + Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. BioCatalogue:Protein Sequence Analysis - Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. edam beta12orEarlier bioinformatics @@ -49909,13 +50197,12 @@ Nucleic acid sequence analysis - + Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. topic topics edam bioinformatics - Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles. BioCatalogue:Nucleotide Sequence Analysis beta12orEarlier @@ -49926,16 +50213,13 @@ Repeat sequences - - - Repeat sequence - edam + + 1.3 topics - beta12orEarlier - bioinformatics - topic - BioCatalogue:Repeats Topic concerning the repetitive nature of molecular sequences. + beta12orEarlier + true + @@ -49944,14 +50228,13 @@ Low complexity sequences - - - edam + topics beta12orEarlier - bioinformatics + 1.3 Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity. - topic + true + @@ -49960,14 +50243,14 @@ Proteome - + true + Topic concerning a specific proteome including protein sequences and annotation. edam bioinformatics beta13 topics beta12orEarlier - Topic concerning a specific proteome including protein sequences and annotation. topic @@ -49979,13 +50262,12 @@ DNA - + topic The DNA sequences might be coding or non-coding sequences. bioinformatics + Topic concerning DNA sequences and structure, including processes such as methylation and replication. topics edam - topic - Topic concerning DNA sequences and structure, including processes such as methylation and replication. beta12orEarlier DNA analysis @@ -49995,17 +50277,15 @@ - mRNA, EST or cDNA database + Coding RNA beta12orEarlier - edam - mRNA, EST or cDNA - topics - Transcriptome database - Topic concerning data resources for messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences. topic - Transcriptome + edam bioinformatics + mRNA, EST or cDNA + topics + Topic concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences. @@ -50013,17 +50293,18 @@ - Functional and non-coding RNA + Functional, regulatory and non-coding RNA bioinformatics topic beta12orEarlier edam Non-coding RNA - For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). - Topic concerning functional or non-coding RNA sequences. Functional RNA + Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). topics + 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). + Regulatory RNA @@ -50032,13 +50313,12 @@ rRNA - + topics - bioinformatics Topic concerning one or more ribosomal RNA (rRNA) sequences. - beta12orEarlier - edam - topic + true + 1.3 + @@ -50047,13 +50327,12 @@ tRNA - - topic - bioinformatics + Topic concerning one or more transfer RNA (tRNA) sequences. - edam - beta12orEarlier + 1.3 + true topics + @@ -50063,14 +50342,15 @@ Protein secondary structure - topics 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. + beta12orEarlier + topics + Protein secondary structure analysis bioinformatics topic - Topic concerning protein secondary structure or secondary structure alignments. edam - Protein secondary structure analysis - beta12orEarlier @@ -50078,17 +50358,14 @@ - RNA structure and alignment - + RNA structure + beta12orEarlier + true Topic concerning RNA secondary or tertiary structure and alignments. - RNA alignment - edam topics - RNA structure alignment - bioinformatics - topic - RNA structure + 1.3 + @@ -50105,6 +50382,7 @@ edam topic bioinformatics + BioCatalogue:Protein Tertiary Structure @@ -50113,15 +50391,16 @@ Nucleic acid classification - - - - topics + beta12orEarlier - topic bioinformatics - Topic concerning nucleic acid classification (typically sequence classification). + topics + Topic concerning classification of nucleic acid sequences and structures. + topic + true + 1.3 edam + @@ -50130,17 +50409,18 @@ Protein families - - - Topic concerning primarily proteins that have been classified as members of a protein family (or other grouping). + + A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. beta12orEarlier + events topics Protein sequence classification Protein secondary topic edam bioinformatics + Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. @@ -50150,7 +50430,6 @@ Protein domains and folds - topic BioCatalogue:Domains topics @@ -50166,14 +50445,16 @@ Nucleic acid sequence alignment - - + bioinformatics + true + beta12orEarlier topic + 1.3 Topic concerning nucleotide sequence alignments. edam - beta12orEarlier topics + @@ -50182,15 +50463,17 @@ Protein sequence alignment - - + + Topic concerning protein sequence alignments. + edam + 1.3 topics topic A sequence profile typically represents a sequence alignment. - Topic concerning protein sequence alignments. + true bioinformatics - edam beta12orEarlier + @@ -50199,16 +50482,15 @@ Nucleic acid sites and features - - - Nucleic acid functional sites + topics - Topic concerning positional features such as functional sites in nucleotide sequences. - bioinformatics - topic - Nucleic acid features - edam + Topic concerning the archival, detection, prediction and analysis of +positional features such as functional sites in nucleotide sequences. + true + 1.3 beta12orEarlier + + @@ -50217,16 +50499,14 @@ Protein sites and features - - - edam - Protein functional sites - topic + + true + Topic concerning the detection, identification and analysis of positional features in proteins, such as functional sites. + 1.3 topics - Topic concerning positional features such as functional sites in protein sequences. beta12orEarlier - Protein sequence features - bioinformatics + + @@ -50235,20 +50515,17 @@ Transcription factors and regulatory sites - - - - - - - Topic concerning transcription factors; proteins that bind to DNA and control transcription of DNA to mRNA, either promoting (as an activator) or blocking (as a repressor) the binding to DNA of RNA polymerase, and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. - This includes promoters, enhancers, silencers and boundary elements / insulators. This includes sequence and structural information, binding profiles etc, and may also include the transcription factor binding site in DNA. + + beta12orEarlier Transcriptional regulatory sites + Topic concerning proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. bioinformatics Transcription factor and binding site Transcription factors + BioCatalogue:Transcription Factors edam + Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. topic topics @@ -50259,14 +50536,14 @@ Phosphorylation sites - - true + beta12orEarlier Topic concerning protein phosphorylation and phosphorylation sites in protein sequences. edam topic topics bioinformatics + true 1.0 @@ -50279,7 +50556,6 @@ Metabolic pathways - topic Topic concerning metabolic pathways. edam @@ -50297,8 +50573,8 @@ topic beta12orEarlier - Topic concerning signaling pathways. topics + Topic concerning signaling pathways. edam bioinformatics @@ -50309,19 +50585,11 @@ Protein and peptide identification - - - + + true beta12orEarlier - Peptide identification and proteolysis - edam - bioinformatics - Proteomics data resources - Topic concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays. - Proteomics data - This includes the results of any methods that separate, characterize and identify expressed proteins. - topics - topic + 1.3 + @@ -50330,12 +50598,12 @@ Workflows - - true + topics 1.0 bioinformatics beta12orEarlier + true Topic concerning biological or biomedical analytical workflows or pipelines. topic edam @@ -50347,15 +50615,15 @@ Data types and objects - + true + beta12orEarlier + edam topics 1.0 - beta12orEarlier topic bioinformatics Topic concerning structuring data into basic types and (computational) objects. - edam @@ -50364,16 +50632,11 @@ - Biological models - - beta12orEarlier - topics - Topic concerning mathematical or other models of biological processes. - bioinformatics - topic - This includes databases of models and methods to construct or analyse a model. - edam - BioCatalogue:Model Creation + Theoretical biology + + true + 1.3 + @@ -50381,15 +50644,14 @@ - Mitochondrial genes and proteins - - Mitochondria genes and proteins - topic + Mitochondria + + 1.3 topics Topic concerning mitochondria, typically of mitochondrial genes and proteins. - bioinformatics + true beta12orEarlier - edam + @@ -50399,14 +50661,16 @@ Plants - bioinformatics - topics beta12orEarlier Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. + Plant + bioinformatics + topics + Botany + Plant biology topic edam The resource may be specific to a plant, a group of plants or all plants. - Plant @@ -50416,14 +50680,15 @@ Viruses - bioinformatics The resource may be specific to a virus, a group of viruses or all viruses. topics + topic + bioinformatics beta12orEarlier Virus Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. edam - topic + Virology @@ -50434,13 +50699,13 @@ Fungi topics - Fungal The resource may be specific to a fungus, a group of fungi or all fungi. bioinformatics Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. edam topic beta12orEarlier + Mycology @@ -50466,13 +50731,16 @@ Arabidopsis - - topic + beta12orEarlier - bioinformatics Topic concerning Arabidopsis-specific data. topics + topic + 1.3 + true + bioinformatics edam + @@ -50481,13 +50749,13 @@ Rice - + beta12orEarlier Topic concerning rice-specific data. topics - edam - bioinformatics - topic + 1.3 + true + @@ -50496,15 +50764,18 @@ Genetic mapping and linkage - + Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. - Genetic linkage topics + Genetic linkage topic - edam bioinformatics + true + edam + 1.3 beta12orEarlier Linkage mapping + @@ -50519,6 +50790,7 @@ topic edam beta12orEarlier + events topics Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. @@ -50529,7 +50801,7 @@ Mobile genetic elements - + edam bioinformatics Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. @@ -50544,15 +50816,15 @@ Human disease - - true + Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease. - bioinformatics edam beta12orEarlier - topic topics + true beta13 + bioinformatics + topic @@ -50561,17 +50833,19 @@ - Immunoinformatics - - Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. + Immunology + edam - beta12orEarlier + Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. topics bioinformatics - Computational immunology + Computational immunology + beta12orEarlier + events + Immunoinformatics topic - - + + @@ -50579,9 +50853,9 @@ - Membrane proteins - - Topic concerning a protein or region of a protein that spans a membrane. + Membrane and lipoproteins + + Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. topics bioinformatics Transmembrane proteins @@ -50595,14 +50869,37 @@ - Enzymes and reactions - + Enzymes + topics + Enzymes and reactions bioinformatics + Enzymology edam beta12orEarlier + Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. topic - Topic concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. + + + + + + + + Structural biology + + Structural determination + A topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. + events + 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. + topics + 1.3 + Structure determination + Structural assignment + topic + bioinformatics + edam @@ -50613,6 +50910,7 @@ Structure comparison beta12orEarlier + events bioinformatics Topic concerning the comparison of two or more molecular structures. topics @@ -50626,14 +50924,18 @@ - Protein function analysis - - beta12orEarlier + Function analysis + edam - Topic for the study of protein function. - bioinformatics topics topic + events + beta12orEarlier + bioinformatics + Protein function analysis + Topic for the study of gene and protein function including the prediction of functional properties of a protein. + BioCatalogue:Function Prediction + Protein function prediction @@ -50659,15 +50961,17 @@ Protein databases - - + topics - Protein data resources - Topic concerning protein data resources. - beta12orEarlier topic + true + beta12orEarlier + Topic concerning protein data resources. + Protein data resources bioinformatics edam + 1.3 + @@ -50676,17 +50980,13 @@ Structure determination - - Raw structural data analysis - Structure assignment + + 1.3 + true topics - Structural determination - edam - Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, including the assignment or modelling of molecular structure from such data. + 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 - Structural assignment - bioinformatics + @@ -50694,7 +50994,7 @@ - Cell biology resources + Cell biology Topic concerning cells, such as key genes and proteins involved in the cell cycle. bioinformatics @@ -50710,12 +51010,12 @@ Classification - - true + edam + beta12orEarlier topics + true Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. - beta12orEarlier bioinformatics topic beta13 @@ -50728,13 +51028,14 @@ Lipoproteins - - topic + topics beta12orEarlier Topic concerning lipoproteins (protein-lipid assemblies). bioinformatics - edam + 1.3 + true + @@ -50743,16 +51044,16 @@ Phylogeny visualisation - - true + bioinformatics edam topics + true beta12orEarlier - beta12orEarlier topic - BioCatalogue:Tree Display + beta12orEarlier Visualise a phylogeny, for example, render a phylogenetic tree. + BioCatalogue:Tree Display @@ -50761,18 +51062,19 @@ - Chemoinformatics - + Cheminformatics + + edam bioinformatics Chemical informatics BioCatalogue:Chemoinformatics + events topic - Computational chemistry + Chemoinformatics + Topic for the application of information technology to chemistry in biological research environment. topics beta12orEarlier - Cheminformatics - Topic for the application of information technology to chemistry. @@ -50781,16 +51083,24 @@ Systems biology - + + Biological modelling + Biological system modelling + events + beta12orEarlier BioCatalogue:Systems Biology - topic + BioCatalogue:Model Analysis edam bioinformatics + topic + Biological models + Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein. + BioCatalogue:Model Creation topics - Topic concerning the holistic modelling and analysis of biological systems and the interactions therein. - beta12orEarlier - - + BioCatalogue:Model Execution + This includes databases of models and methods to construct or analyse a model. + + @@ -50798,8 +51108,9 @@ - Biostatistics - + Statistics + + events Topic for the application of statistical methods to biological problems. beta12orEarlier BioCatalogue:Biostatistics @@ -50809,8 +51120,9 @@ topic Biometrics edam - - + Biostatistics + + @@ -50819,12 +51131,12 @@ Structure database search - - true - edam + Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). + edam topic beta12orEarlier + true beta12orEarlier bioinformatics topics @@ -50839,9 +51151,8 @@ Molecular modelling - edam - Topic for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. + Topic for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. beta12orEarlier topics bioinformatics @@ -50854,14 +51165,17 @@ Protein function prediction - - Topic concerning the prediction of functional properties of a protein. + bioinformatics - topics + Topic concerning the prediction of functional properties of a protein. topic BioCatalogue:Function Prediction - edam beta12orEarlier + 1.2 + topics + true + edam + @@ -50886,14 +51200,14 @@ Transmembrane protein prediction - - true + topics beta12orEarlier beta12orEarlier Predict transmembrane domains and topology in protein sequences. topic bioinformatics + true edam @@ -50905,14 +51219,14 @@ Nucleic acid structure comparison - - true + beta12orEarlier beta12orEarlier topic Use this concept for methods that are exclusively for nucleic acid structures. topics Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. + true edam bioinformatics @@ -50924,15 +51238,18 @@ - Cancer - + Oncology + Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer. - topics - edam beta12orEarlier - Cancer resources topic bioinformatics + Cancer biology + Cancer + topics + edam + events + Cancer resources @@ -50957,14 +51274,14 @@ Tool topic - - true - beta12orEarlier + edam - topic bioinformatics A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. topics + beta12orEarlier + topic + true beta12orEarlier @@ -50975,15 +51292,15 @@ Study topic - - true - beta12orEarlier + bioinformatics - edam topic topics beta12orEarlier A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. + beta12orEarlier + edam + true @@ -50993,13 +51310,13 @@ Nomenclature - + topics - bioinformatics beta12orEarlier + 1.3 Topic concerning biological nomenclature (naming), symbols and terminology. - edam - topic + true + @@ -51008,14 +51325,16 @@ Disease genes and proteins - - - edam - beta12orEarlier + Topic concerning the genes, gene variations and proteins involved in one or more specific diseases. topic - bioinformatics + true topics + 1.3 + edam + beta12orEarlier + bioinformatics + @@ -51024,16 +51343,14 @@ Protein structure analysis - - - Topic concerning protein secondary or tertiary structural data and/or associated annotation. edam + events beta12orEarlier http://edamontology.org/topic_3040 - Protein structure topics + Protein structure bioinformatics topic @@ -51044,15 +51361,13 @@ Humans - - bioinformatics - edam - topic - The resource may be specific to a human, a group of humans or all humans. + + 1.3 Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. - Human + true topics beta12orEarlier + @@ -51061,16 +51376,18 @@ Gene resources - - + Gene database + true Informatics resource (typically a database) primarily focussed on genes. + 1.3 edam bioinformatics topic beta12orEarlier topics Gene resource + @@ -51079,13 +51396,13 @@ Yeast - - edam + + 1.3 topics - topic + true beta12orEarlier Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. - bioinformatics + @@ -51161,14 +51478,13 @@ Protein structure alignment - - + + 1.3 topics + true beta12orEarlier Topic concerning protein secondary or tertiary structure alignments. - edam - topic - bioinformatics + @@ -51177,15 +51493,15 @@ X-ray crystallography - - true + bioinformatics topics + Topic concerning X-ray crystallography data. + beta13 edam beta12orEarlier topic - Topic concerning X-ray crystallography data. - beta13 + true @@ -51195,14 +51511,17 @@ Ontologies, nomenclature and classification - - topics - beta12orEarlier - Topic concerning conceptualisation, categorisation and naming, or that help to identify, group, or name things in a structured way according to some schema based on observable relationships. + topic + beta12orEarlier + Topic concerning conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. + topics + 1.3 edam bioinformatics - + true + + @@ -51210,9 +51529,9 @@ - Immunity genes, immunoproteins and antigens + Immunoproteins, genes and antigens + - edam topics beta12orEarlier @@ -51229,16 +51548,17 @@ Molecules - - true + edam + true beta12orEarlier - beta12orEarlier Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. + beta12orEarlier topics - topic - CHEBI:23367 bioinformatics + topic + CHEBI:23367 + @@ -51246,15 +51566,18 @@ - Toxicoinformatics - - Computational toxicology - topic - Topic concerning the adverse effects of chemical substances on living organisms. + Toxicology + + Computational toxicology beta12orEarlier + topics + Toxicology + topic + Toxicoinformatics + events edam bioinformatics - topics + Topic concerning toxins and the adverse effects of these chemical substances on living organisms. @@ -51263,14 +51586,14 @@ High-throughput sequencing - - true - topics + beta12orEarlier + topics beta13 edam bioinformatics Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. + true topic Next-generation sequencing @@ -51314,15 +51637,15 @@ Disease (specific) - - true + topic edam bioinformatics beta12orEarlier topics - Informatics resources dedicated to one or more specific diseases (not diseases in general). beta12orEarlier + true + Informatics resources dedicated to one or more specific diseases (not diseases in general). @@ -51332,13 +51655,16 @@ Nucleic acid design - + bioinformatics - topics - topic edam beta12orEarlier + topics + topic + true + 1.3 Topic for the design of nucleic acid sequences with specific conformations. + @@ -51347,13 +51673,16 @@ Primer or probe design - + + true + topics + topic + 1.3 beta13 bioinformatics Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes. edam - topics - topic + @@ -51362,15 +51691,17 @@ Structure databases - - + + edam topic - Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. Structure data resources + Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. bioinformatics - edam + true + 1.2 topics beta13 + @@ -51379,13 +51710,16 @@ Nucleic acid structure - - edam + + 1.2 topics bioinformatics Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. - beta13 topic + edam + beta13 + true + @@ -51394,8 +51728,8 @@ Sequence databases - - + + 1.3 edam bioinformatics Sequence data resources @@ -51405,6 +51739,8 @@ Sequence data resource Sequence data topic + true + @@ -51413,13 +51749,17 @@ Nucleic acid sequences - + topic topics bioinformatics - edam + Nucleotide sequences + true Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + 1.3 + edam beta13 + @@ -51428,15 +51768,16 @@ Protein sequences - - - edam - beta13 + + 1.3 topic topics - BioCatalogue:Protein Sequence Analysis - bioinformatics Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + true + edam + beta13 + bioinformatics + @@ -51445,14 +51786,11 @@ Protein interaction networks - - - Topic concerning protein-protein interaction networks. - edam - topic + + true topics - beta13 - bioinformatics + 1.3 + @@ -51460,16 +51798,15 @@ - Molecular biology reference - + Molecular biology + topic bioinformatics - BioCatalogue: Document Discovery topics - BioCatalogue: Literature retrieval - Topic concerning general molecular biology information extracted from the literature. + Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. edam beta13 + events @@ -51478,13 +51815,13 @@ Mammals - - bioinformatics + topics Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. + 1.3 beta13 - topic - edam + true + @@ -51496,13 +51833,14 @@ topics Biodiversity data resources + events Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet. Biodiversity data resource topic bioinformatics beta13 edam - + @@ -51511,16 +51849,19 @@ Sequence clusters and classification - + beta13 Sequence clusters topic + 1.3 Sequence families Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity. edam topics + true bioinformatics This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. + @@ -51529,15 +51870,18 @@ Genetics - + + Gene resource bioinformatics beta13 edam Genetics data resources topic - topics + Gene database Topic concerning the study of genes, genetic variation and heredity in living organisms. - + events + topics + @@ -51546,9 +51890,9 @@ Quantitative genetics - - Topic concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight). + topics + Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). edam bioinformatics topic @@ -51567,6 +51911,7 @@ beta13 Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. edam + events bioinformatics @@ -51576,14 +51921,12 @@ Regulatory RNA - + beta13 - bioinformatics - Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). - edam - topic + 1.3 + Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). topics - Micro RNAs are short single stranded RNA molecules that regulate gene expression. + @@ -51595,10 +51938,11 @@ bioinformatics beta13 + events topics - Topic concerning documentation and getting help. topic edam + Topic concerning the documentation of resources such as tools, services and databases and how to get help. @@ -51607,13 +51951,16 @@ Genetic organisation - + topics - bioinformatics edam beta13 - Topic concerning the structural and functional organisation of genes and other genetic elements. topic + true + bioinformatics + Topic concerning the structural and functional organisation of genes and other genetic elements. + 1.3 + @@ -51621,19 +51968,24 @@ - Medical informatics resources - + Medical informatics + + + Molecular medicine Health and disease beta13 Topic for the application of information technology to health, disease and biomedicine. Healthcare informatics + Translational medicine Biomedical informatics edam Clinical informatics Health informatics + events bioinformatics - topics topic + topics + Medicine @@ -51641,11 +51993,12 @@ - Developmental biology resources + Developmental biology beta13 bioinformatics topic + events edam Topic concerning how organisms grow and develop. topics @@ -51656,9 +52009,10 @@ - Embryology resources + Embryology topic + events Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. topics beta13 @@ -51671,14 +52025,15 @@ - Anatomy resources - + Anatomy + + Topic concerning the form and function of the structures of living organisms. topics topic - Topic concerning the structures of living organisms. beta13 bioinformatics edam + events @@ -51688,13 +52043,18 @@ Literature and reference + events + Literature sources + Literature search + BioCatalogue: Document Discovery bioinformatics edam - Topic concerning the scientific literature, reference information and documentation. topics + Topic concerning the scientific literature, reference information and documentation. + BioCatalogue: Literature retrieval topic beta13 - + @@ -51702,15 +52062,16 @@ - Biological science resources - + Biology + topics - Phenotype resource bioinformatics topic + events edam Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. beta13 + Biological science @@ -51718,17 +52079,19 @@ - Biological data resources - - Biological data resource - topics + Biological databases and data management + bioinformatics - Biological databases + topics topic + A topic concerning the general handling of bioinformatics data stored in digital archives such as databanks, databases proper, web portals and other data resources. + Biological data management + Biological data handling beta13 + Biological databases edam - A topic concerning primarily a specific type of bioinformatics data, typically the broad category of content of a digital archives of biological data, including databanks, databases proper, web portals and other data resources. - + events + @@ -51737,14 +52100,17 @@ Sequence feature detection - + + true + topics edam beta13 - topics Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences. topic bioinformatics - + 1.3 + + @@ -51753,14 +52119,16 @@ Nucleic acid feature detection - - - edam - beta13 + + 1.3 topic Topic concerning the detection of positional features such as functional sites in nucleotide sequences. bioinformatics topics + edam + beta13 + true + @@ -51769,14 +52137,16 @@ Protein feature detection - - + + true + beta13 topic edam bioinformatics topics + 1.3 Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites. - beta13 + @@ -51785,15 +52155,18 @@ Biological system modelling - - Topic for modelling biological systems in mathematical terms. + beta13 - topics - BioCatalogue:Model Execution + true bioinformatics + BioCatalogue:Model Execution topic - BioCatalogue:Model Analysis edam + Topic for modelling biological systems in mathematical terms. + topics + 1.2 + BioCatalogue:Model Analysis + @@ -51802,7 +52175,7 @@ Data acquisition and deposition - + Topic concerning the acquisition and deposition of biological data. edam Database submission @@ -51817,16 +52190,19 @@ - Gene and protein resources - - + Genes and proteins resources + topic - topics - Genes and proteins resources bioinformatics - Topic concerning specific genes and their encoded proteins or a related group of such genes and proteins. beta13 + Gene family + 1.3 + Topic concerning specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. + true + topics + Gene and protein families edam + @@ -51837,12 +52213,13 @@ Sequencing topics + events bioinformatics 1.1 topic Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. edam - + @@ -51851,17 +52228,19 @@ ChIP-seq - - + 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. bioinformatics topics edam Chip sequencing + true topic + @@ -51870,13 +52249,14 @@ RNA-Seq - - + + true This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. WTSS topics - A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. Small RNA-Seq + 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 edam bioinformatics 1.1 @@ -51884,6 +52264,7 @@ Whole transcriptome shotgun sequencing RNA-seq Small RNA-seq + @@ -51892,14 +52273,17 @@ DNA methylation - - topic - 1.1 + bioinformatics + topic topics edam + 1.3 + true + 1.1 Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. - + + @@ -51908,14 +52292,15 @@ Metabolomics - - Topic concerning the study of metabolites and the chemical processes they are involved in, especially the systematic study of the chemical fingerprints of specific cellular processes. + bioinformatics 1.1 topic edam + events + Topic concerning the systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. topics - + @@ -51925,15 +52310,17 @@ Epigenomics - A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. + bioinformatics - topics - edam - 1.1 + events Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. topic Epigenetics - + A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. + topics + edam + 1.1 + @@ -51944,16 +52331,17 @@ Metagenomics + events 1.1 + Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data. edam - Topic concerning the study of genetic material recovered from environmental samples. bioinformatics topic Environmental genomics Ecogenomics topics Community genomics - + @@ -51963,7 +52351,6 @@ Structural variation - Genomic structural variation edam bioinformatics @@ -51979,7 +52366,6 @@ DNA packaging - topic Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. @@ -51987,7 +52373,7 @@ edam beta12orEarlier bioinformatics - + @@ -51996,14 +52382,17 @@ DNA-Seq - - topics - DNA-seq + edam - bioinformatics A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. + bioinformatics + true + topics + 1.3 + DNA-seq 1.1 topic + @@ -52012,14 +52401,17 @@ RNA-Seq alignment - + topics - beta12orEarlier topic + beta12orEarlier bioinformatics RNA-seq alignment Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. + 1.3 + true edam + @@ -52028,32 +52420,739 @@ ChIP-on-chip - - + ChIP-chip + 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 + topics + bioinformatics + true 1.1 - Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. edam + 1.3 + + + + + + + + + Data security + + topics + Security + bioinformatics + 1.3 + Topic concerning the protection of data, for example, patient health data. + Security + topic + edam + Privacy + + + + + + + + Sample collections + + Specimen collections + edam + biosamples + 1.3 + bioinformatics + Topic concerning biological samples and specimens. + events + biobanking + topics + topic + samples + + + + + + + + Biochemistry + + + events + topic + edam + Biological chemistry + bioinformatics + topics + A topic concerning chemical substances and physico-chemical processes and that occur within living organisms. + 1.3 + Chemical biology + + + + + + + + Phylogenetics + + + bioinformatics + edam + 1.3 + Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). + topics + topic + + + + + + + + + Epigenetics + + 1.3 + A topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. + Histone modification + bioinformatics + DNA methylation + topics + edam + This includes sub-topics such as histone modification and DNA methylation. + events + topic + + + + + + + + + Biotechnology + + topics + 1.3 + edam + topic + events + Topic concerning the exploitation of biological processes for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. + bioinformatics + + + + + + + + Phenomics + + + edam + events + 1.3 + topic + topics + Topic concerning phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. + bioinformatics + + + + + + + + Evolutionary biology + + topics + events + 1.3 + edam + bioinformatics + topic + Topic concerning the evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. + + + + + + + + Physiology + + edam + bioinformatics + Topic concerning the functions of living organisms and their constituent parts. + 1.3 + topics + topic + events + + + + + + + + Microbiology + + topics + events + 1.3 + topic + Topic concerning the biology of microorganisms. + bioinformatics + edam + + + + + + + + Parasitology + + topic + 1.3 + events + bioinformatics + Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. + topics + edam + Topic concerning the biology of parasites. + + + + + + + + Medicine + + Biomedical research + Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease. + Experimental medicine + edam + 1.3 + bioinformatics + topics + events + Molecular medicine + topic + + + + + + + + Neurobiology + + topics + bioinformatics + Topic concerning the study of the nervous system and brain; its anatomy, physiology and function. + 1.3 + events + Neuroscience + topic + edam + + + + + + + + Epidemiology + + events + bioinformatics + 1.3 + edam + topics + Topic concerning the the patterns, cause, and effect of disease within populations. + topic + + + + + + + + Biophysics + + + edam + events + topics + Topic concerning the use of physics to study biological system. + topic + bioinformatics + 1.3 + + + + + + + + Computational biology + + + Biomathematics + topic + events + topics + Theoretical biology + 1.3 + Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. + Mathematical biology + This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). + BioCatalogue:Model Execution + edam + bioinformatics + + + + + + + + Transcriptomics + + + topics + Transcriptome + Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. + bioinformatics + topic + edam + events + 1.3 + + + + + + + + Chemistry + + bioinformatics + events + edam + topic + Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. + 1.3 + topics + + + + + + + + Mathematics + + 1.3 + topic + edam + events + bioinformatics + topics + Maths + Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. + + + + + + + + Computer science + + topics + bioinformatics + edam + events + 1.3 + topic + Topic concerning the theory and practical use of computer systems. + + + + + + + + Physics + + 1.3 + events + topics + Topic concerning the study of matter, space and time, and related concepts such as energy and force. + edam + bioinformatics + topic + + + + + + + + RNA splicing + + + topics + 1.3 + This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. + Topic concerning RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. + edam + bioinformatics + topic + + + + + + + + Molecular genetics + + bioinformatics + 1.3 + edam + topic + Topic concerning the structure and function of genes at a molecular level. + topics + events + + + + + + + + Respiratory medicine + + Topic concerning the study of respiratory system. + events + Pulmonology + topics + 1.3 + bioinformatics + topic + edam + + + + + + + + Metabolic disease + + Topic concerning the study of metabolic diseases. + 1.3 + edam + topic + bioinformatics topics + + + + + + + + Infectious disease + topic + 1.3 + Topic concerning to the study of infectious diseases. bioinformatics + topics + edam + + + + + + + + Rare diseases + + topics + edam + Topic concerning the study of rare diseases. + bioinformatics + topic + 1.3 + + + + + + + + Computational chemistry + + + Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. + edam + bioinformatics + 1.3 + events + topics + topic + + + + + + + + Neurology + + 1.3 + bioinformatics + topic + topics + events + Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. + edam + + + + + + + + Cardiology + + topics + bioinformatics + events + Topic concerning the diseases and abnormalities of the heart and circulatory system. + 1.3 + edam + topic + + + + + + + + Drug discovery + + + edam + topics + Medicinal chemistry + topic + 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. + bioinformatics + 1.3 + events + + + + + + + + Biobank + + Tissue collection + Topic concerning repositories of biological samples, typically human, for basic biological and clinical research. + bioinformatics + biobanking + events + edam + topic + 1.3 + topics + + + + + + + + Mouse clinic + + topic + Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. + topics + edam + bioinformatics + 1.3 + events + + + + + + + + Microbial collection + + topic + Topic concerning collections of microbial cells including bacteria, yeasts and moulds. + 1.3 + topics + edam + events + bioinformatics + + + + + + + + Cell culture collection + + topic + events + edam + 1.3 + bioinformatics + topics + Topic concerning collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. + + + + + + + + Clone library + + events + Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. + edam + topic + 1.3 + bioinformatics + topics + + + + + + + + Translational medicine + + bioinformatics + events + Translational medicine + topic + topics + edam + Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. + 1.3 + + + + + + + + Compound libraries and screening + + events + Chemical screening + Compound library + Topic concerning collections of chemicals, typically for use in high-throughput screening experiments. + 1.3 + Chemical library + Translational medicine + edam + topics + bioinformatics + topic + + + + + + + + Biomedical science + + + bioinformatics + topic + topics + edam + 1.3 + Topic concerning biological science that is (typically) performed in the context of medicine. + events + + + + + + + + Data identity and mapping + + 1.3 + topic + Topic concerning the identity of biological data and the mapping of entities in different databases. + events + edam + topics + bioinformatics + + + + + + + + Sequence search + + + bioinformatics + Topic concerning the search and retrieval from a database on the basis of molecular sequence similarity. + Sequence clusters + topics + edam + topic + 1.3 - + Obsolete concept (EDAM) - - + + true An obsolete concept (redefined in EDAM). Needed for conversion to the OBO format. - 1.2 / http://www.geneontology.org/formats/oboInOwl + 1.2 - - + + + + + + + + +