format-version: 1.2 data-version: 1.1 date: 05:07:2012 18:00 ! Always GMT (UTC) or British Summer Time saved-by: Jon Ison subsetdef: operations "EDAM operations" !{note="Singular, bioinformatics-specific operations that are functions of tools, workflows, or scripts, or can be performed manually."} subsetdef: data "EDAM types of data" !{note="Types of data that are relevant in bioinformatics, commonly used as inputs, outputs, or intermediate data of analyses, or provided by databases and portals."} subsetdef: topics "EDAM topics" !{note="Application domains of bioinformatics tools and resources; topics of research, studies, or analyses; approaches, techniques, and paradigms within - or directly related to - bioinformatics."} subsetdef: formats "EDAM data formats" !{note="Data formats commonly used in - and specific to - bioinformatics. Many format concepts in EDAM include references to their definition and documentation."} subsetdef: identifiers "EDAM types of identifiers" !{note="Types of identifiers that identify biological or computational entities; including resource-specific data accessions. Several identifier concepts in EDAM include regular expressions and examples."} subsetdef: relations "EDAM relations" !{note="Types of relations - defined in EDAM - that apply between concepts, entities subject to semantic annotation, and entities and concepts (or possibly even vice versa)."} subsetdef: concept_attributes "EDAM concept attributes" !{note="Types of concept attributes and attribute modifiers or qualifiers, that are defined and used in EDAM in addition to the standard attributes of the OBO format."} idspace: EDAM_operation http://edamontology.org/operation_ "EDAM Operations" idspace: EDAM_data http://edamontology.org/data_ "EDAM Types of Data" idspace: EDAM_topic http://edamontology.org/topic_ "EDAM Topics" idspace: EDAM_format http://edamontology.org/format_ "EDAM Data Formats" idspace: EDAM http://edamontology.org/ "EDAM Relations and Concept Attributes" default-relationship-id-prefix: EDAM remark: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web. remark: EDAM editors: Jon Ison and Matus Kalas. Co-authors: Inge Jonassen, Hamish McWilliam, James Malone, Rodrigo Lopez, Helen Parkinson, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE (FP6, EU), EMBOSS (BBSRC, UK), eSysbio and FUGE Bioinformatics Platform (both Research Council of Norway). See http://edamontology.org for documentation and licence. next_id:3234 !{since=1.2} remark: NB. This is a version for the NCBO BioPortal with all attribute modifiers commented out (due to a problem at BioPortal). Download the full, canonical version from http://edamontology.org/ontology?format=obo (always the latest stable version), or http://edamontology.org/EDAM.obo for latest stable and http://edamontology.org/EDAM_1.1.obo for version 1.1. ! ! Relations ! [Typedef] id: has_input name: has input subset: relations def: "'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument." [http://edamontology.org] comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. !{note="In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined."} synonym: "has input" EXACT [http://wsio.org/has_input] synonym: "has_specified_input" NARROW [http://purl.obolibrary.org/obo/OBI_0000293] !{note="'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant)."} synonym: "has_participant" RELATED [OBO_REL:has_participant] !{note="'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject."} inverse_of: is_input_of transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: true !{note="In very unusual cases"} is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_operation:0004 ! Operation range: EDAM_data:0006 ! Data [Typedef] id: is_input_of name: is input of subset: relations def: "'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B." [http://edamontology.org] comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. !{note="In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'."} synonym: "is input of" EXACT [http://wsio.org/is_input_of] synonym: "is_specified_input_of" NARROW [http://purl.obolibrary.org/obo/OBI_0000295] !{note="'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011)."} synonym: "participates_in" RELATED [OBO_REL:participates_in] !{note="'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments."} inverse_of: has_input transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: true !{note="In very unusual cases"} is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_data:0006 ! Data range: EDAM_operation:0004 ! Operation [Typedef] id: has_output name: has output subset: relations def: "'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument." [http://edamontology.org] comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. !{note="In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined."} synonym: "has output" EXACT [http://wsio.org/has_output] synonym: "has_specified_output" NARROW [http://purl.obolibrary.org/obo/OBI_0000299] !{note="'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant)."} synonym: "has_participant" RELATED [OBO_REL:has_participant] !{note="'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it."} inverse_of: is_output_of transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: true !{note="In very unusual cases"} is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_operation:0004 ! Operation range: EDAM_data:0006 ! Data ! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statement, "An operation has_output An error" implies "An error is Data". ! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. [Typedef] id: is_output_of name: is output of subset: relations def: "'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B." [http://edamontology.org] comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. !{note="In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'."} synonym: "is output of" EXACT [http://wsio.org/is_output_of] synonym: "is_specified_output_of" NARROW [http://purl.obolibrary.org/obo/OBI_0000312] !{note="'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011)."} synonym: "participates_in" RELATED [OBO_REL:participates_in] !{note="'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it."} inverse_of: has_output transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: true !{note="In very unusual cases"} is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_data:0006 ! Data range: EDAM_operation:0004 ! Operation ! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'domain' statement, An error is_output_of An operation" implies "An error is Data". ! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. [Typedef] id: has_topic name: has topic subset: relations def: "'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B)." [http://edamontology.org] comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. !{note="In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined."} synonym: "hasTopic" RELATED [http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic] !{note="'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource."} synonym: "has-quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality] synonym: "has_quality" RELATED [http://purl.obolibrary.org/obo/OBI_0000298] !{note="'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject."} synonym: "is about" RELATED [http://purl.obolibrary.org/obo/IAO_0000136] !{note="'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object."} inverse_of: is_topic_of transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: true !{note="In very unusual cases"} is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_operation:0004 ! Operation domain: EDAM_data:0006 ! Data range: EDAM_topic:0003 ! Topic ! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'domain' statements, "My experiment has_topic Molecular mimicry" implies "My experiment is an Operation" and "My experiment is Data". ! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. ! NB: Second 'domain' line is not visible in OBO-Edit2 [Typedef] id: is_topic_of name: is topic of subset: relations def: "'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B)." [http://edamontology.org] comment: Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. !{note="In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'."} synonym: "inherent-in" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in] synonym: "quality_of" RELATED [OBO_REL:quality_of] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object."} inverse_of: has_topic transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: true !{note="In very unusual cases"} is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_topic:0003 ! Topic range: EDAM_operation:0004 ! Operation range: EDAM_data:0006 ! Data ! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statements, "Molecular mimicry is_topic_of My experiment" implies "My experiment is an Operation" and (even) "My experiment is Data". ! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. ! NB: Second 'range' line is not visible in OBO-Edit2 [Typedef] id: has_format name: has format subset: relations def: "'A has_format B' defines for the subject A, that it has the object B as its data format." [http://edamontology.org] comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. !{note="In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'."} synonym: "has-quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality] synonym: "has_quality" RELATED [http://purl.obolibrary.org/obo/OBI_0000298] !{note="'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject."} inverse_of: is_format_of transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: false is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_data:0006 ! Data range: EDAM_format:1915 ! Format [Typedef] id: is_format_of name: is format of subset: relations def: "'A is_format_of B' defines for the subject A, that it is a data format of the object B." [http://edamontology.org] comment: Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. !{note="In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined."} synonym: "inherent-in" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in] synonym: "quality_of" RELATED [OBO_REL:quality_of] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object."} inverse_of: has_format transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: false is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_format:1915 ! Format range: EDAM_data:0006 ! Data [Typedef] id: has_identifier name: has identifier subset: relations def: "'A has_identifier B' defines for the subject A, that it has the object B as its identifier." [http://edamontology.org] comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. !{note="In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'."} inverse_of: is_identifier_of transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: false is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_data:0006 ! Data range: EDAM_data:0842 ! Identifier ! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statement, "My car has_identifier Licence plate number" implies "My car is Data". ! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. [Typedef] id: is_identifier_of name: is identifier of subset: relations def: "'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B." [http://edamontology.org] comment: Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. !{note="In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined."} inverse_of: has_identifier transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: false is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_data:0842 ! Identifier range: EDAM_data:0006 ! Data ! NB. 'domain' and 'range' are defined in the following way in OBO format: According to that definition and the given 'range' statement, "Licence plate number is_identifier_of My car" implies "My car is Data". ! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. [Typedef] id: has_function name: has function subset: relations def: "'A has_function B' defines for the subject A, that it has the object B as its function." [http://edamontology.org] comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. !{note="In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts."} synonym: "has function" EXACT [http://wsio.org/has_function] synonym: "has_function" NARROW [http://purl.obolibrary.org/obo/OBI_0000306] !{note="'OBI:has_function' only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes, with objects that are a 'function' (snap:Function). It does not define explicitly that the object is a function of the subject."} synonym: "has-quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality] synonym: "bearer_of" RELATED [OBO_REL:bearer_of] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject."} inverse_of: is_function_of transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: true !{note="In very unusual cases"} is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false range: EDAM_operation:0004 ! Operation ! NB. 'range' is defined in the following way in OBO format: According to that definition and the given 'range' statement, "My boss has_function Institute leadership" implies "Institute leadership is an Operation". ! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. [Typedef] id: is_function_of name: is function of subset: relations def: "'A is_function_of B' defines for the subject A, that it is a function of the object B." [http://edamontology.org] comment: Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. !{note="Within EDAM itself, 'is_function_of' is not used."} synonym: "is function of" EXACT [http://wsio.org/is_function_of] synonym: "function_of" NARROW [OBO_REL:function_of] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object."} synonym: "inherent-in" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in] synonym: "inheres_in" RELATED [OBO_REL:inheres_in] !{note="Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions."} inverse_of: has_function transitive_over: OBO_REL:is_a ! Every relation type (not a metadata tag) should be transitive over 'is', shouldn't it? is_cyclic: true !{note="In very unusual cases"} is_reflexive: false is_symmetric: false is_anti_symmetric: false is_transitive: false domain: EDAM_operation:0004 ! Operation ! NB. 'domain' is defined in the following way in OBO format: According to that definition and the given 'domain' statement, "Institute leadership is_function_of My boss" implies "Institute leadership is an Operation". ! NB. Notably, 'domain' and 'range' in EDAM are INFORMATIVE and NOT RESTRICTIVE. They state what 'domain' and 'range' a type of relation relates among EDAM concepts, but they are valid also outside of the 'domain' and 'range', and the OBO-format definition should not apply. ! ! Concept metadata tags, modifiers, and qualifiers ! [Typedef] id: regex name: Regular expression subset: concept_attributes def: "'Regular expression' concept attribute ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too." [http://edamontology.org] is_metadata_tag: true [Typedef] id: example name: Example subset: concept_attributes def: "'Example' concept attribute ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too." [http://edamontology.org] is_metadata_tag: true [Typedef] id: documentation name: Documentation subset: concept_attributes def: "'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format." [http://edamontology.org] synonym: "Specification" NARROW [http.//edamontology.org] is_metadata_tag: true [Typedef] id: min_cardinality name: Minimum cardinality subset: concept_attributes def: "'Minimum cardinality' trailing modifier ('min_cardinality') of 'has input' and 'has output' relations. Specificies the minimum number of data records consumed or produced by an operation." [http://edamontology.org] is_metadata_tag: true [Typedef] id: max_cardinality name: Maximum cardinality subset: concept_attributes def: "'Maximum cardinality' trailing modifier ('max_cardinality') of 'has input' and 'has output' relations. Specificies the maximum number of data records consumed or produced by an operation." [http://edamontology.org] comment: 'max_cardinality' is not (yet) defined among concepts in EDAM. is_metadata_tag: true [Typedef] id: cardinality name: Cardinality subset: concept_attributes def: "'Cardinality' trailing modifier ('cardinality') of 'has input' and 'has output' relations. Specificies the number of data records consumed or produced by an operation." [http://edamontology.org] comment: 'cardinality' is not (yet) defined among concepts in EDAM. is_metadata_tag: true is_a: min_cardinality is_a: max_cardinality [Typedef] id: note name: Note subset: concept_attributes def: "'Note' trailing modifier ('note') of any concept or ontology attributes. Contains a note for a human reader related to the given attribute." [http://edamontology.org] is_metadata_tag: true [Typedef] id: since name: Since subset: concept_attributes def: "'Since' trailing modifier ('since') of 'id' and 'is_obsolete: true' attributes (may be applicable to other attributes, too). Specificies the released version of the ontology in which the attribute received its current value/started to be valid. In case of 'id' this is the version in which the concept has been introduced, and in case of 'is_obsolete: true' the version in which the concept became obsolete." [http://edamontology.org] is_metadata_tag: true ! ! Top-level concepts (sub-ontologies) ! [Term] id: EDAM_operation:0004 name: Operation namespace: operation subset: operations def: "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs)." [http://edamontology.org] comment: A singular case is a constant operation (constant function) that consumes no input (has no input arguments). xref: WSIO_operation:operation, http://wsio.org/operation synonym: "Function" BROAD [http://edamontology.org] !{note="Operation is a function that has input(s) and output(s) that are data."} synonym: "Computational operation" NARROW [http://edamontology.org] synonym: "Computational procedure" NARROW [http://edamontology.org] synonym: "Computational method" NARROW [http://edamontology.org] synonym: "Computational subroutine" NARROW [http://edamontology.org] synonym: "Function (programming)" NARROW [http://edamontology.org] synonym: "Lambda abstraction" NARROW [http://edamontology.org] synonym: "Mathematical operation" NARROW [http://edamontology.org] synonym: "Mathematical function" NARROW [http://edamontology.org] synonym: "Process" RELATED [http://edamontology.org] !{note="Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs."} synonym: "Computational tool" RELATED [http://edamontology.org] !{note="Computational tool provides an operation with inputs and outputs."} synonym: "Operation" EXACT [http://wsio.org/operation_001] synonym: "function" BROAD [http://purl.org/biotop/biotop.owl#Function] !{note="Operation is a function that has input(s) and output(s) that are data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'."} synonym: "function" BROAD [http://semanticscience.org/resource/SIO_000017] synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] synonym: "Function" BROAD [http://www.onto-med.de/ontologies/gfo.owl#Function] !{note="However, operation is not a GFO 'Concept' present only in someone's mind."} synonym: "Subroutine" NARROW [http://en.wikipedia.org/wiki/Subroutine, http://en.wikipedia.org/wiki/Function_(computer_science)] synonym: "Function (mathematics)" NARROW [http://en.wikipedia.org/wiki/Function_(mathematics)] synonym: "function" RELATED [sumo:Function] ! Related external synonyms in EDAM without a note is usually almost exact. synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials."} synonym: "function" RELATED [http://purl.obolibrary.org/obo/BFO_0000034, http://www.ifomis.org/bfo/1.1/snap#Function] !{note="BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s)."} synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] !{note="Function, including an operation, can be a quality/attribute of e.g. a computational tool."} synonym: "quality" RELATED [http://purl.obolibrary.org/obo/BFO_0000019, http://www.ifomis.org/bfo/1.1/snap#Quality] !{note="Function, including an operation, can have a role of a quality/attribute in semantic annotation of e.g. a computational tool."} synonym: "process" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} synonym: "process" RELATED [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/span#Process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} synonym: "Process" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} synonym: "information processing" RELATED [http://www.ebi.ac.uk/swo/SWO_0000003] !{note="However, one may think that an operation is not a process."} synonym: "information processing" RELATED [http://semanticscience.org/resource/SIO_000649] !{note="However, one may think that an operation is not a process and not a physical entity."} synonym: "Method" RELATED [http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method] !{note="Method may in addition focus on how to achieve the result, not just on what to achieve as with operation."} relationship: has_input EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. relationship: has_output EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. relationship: has_topic EDAM_topic:0003 ! Topic ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. [Term] id: EDAM_data:0006 name: Data namespace: data subset: data ! alt_id: EDAM_data:3030 !{since=beta13} ! Not released def: "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output." [http://edamontology.org] synonym: "Datum" EXACT [http://edamontology.org] !{note="The multiplicity is not taken into account."} synonym: "Data record" EXACT [http://edamontology.org] !{note="Currently we are for practical purposes not distinguishing a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable information)."} synonym: "Data set" EXACT [http://edamontology.org] !{note="The multiplicity is not taken into account."} synonym: "Data" EXACT [http://wsio.org/data_002] synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] synonym: "digital entity" RELATED [http://purl.org/biotop/biotop.owl#DigitalEntity] synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual."} synonym: "data item" RELATED [http://semanticscience.org/resource/SIO_000069] !{note="Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019)."} synonym: "data item" RELATED [http://purl.obolibrary.org/obo/IAO_0000027] !{note="IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something."} synonym: "information content entity" RELATED [http://purl.obolibrary.org/obo/IAO_0000030] !{note="IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity."} synonym: "record" RELATED [http://semanticscience.org/resource/SIO_000088] !{note="Data does however not necessarily contain statements and not necessarily about an entity."} relationship: has_topic EDAM_topic:0003 ! Topic ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. [Term] id: EDAM_topic:0003 name: Topic namespace: topic subset: topics def: "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other." [http://edamontology.org] synonym: "quality" BROAD [http://purl.org/biotop/biotop.owl#Quality] synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] synonym: "field of study" RELATED [sumo:FiledOfStudy] ! Related external synonym in EDAM without a note is usually almost exact. synonym: "Area of Research" RELATED [http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research] synonym: "Category" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Category] !{note="GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated."} synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials."} synonym: "Method" RELATED [http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method] synonym: "quality" RELATED [http://purl.obolibrary.org/obo/BFO_0000019, http://www.ifomis.org/bfo/1.1/snap#Quality] !{note="BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the topic."} synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] !{note="Topic can be a quality of an entity."} [Term] id: EDAM_format:1915 name: Format namespace: format subset: formats def: "A specified way or layout of representing, structuring (and in some cases also encoding) data in a computer file, blob, string, message and so on." [http://edamontology.org] synonym: "Data format" EXACT [http://edamontology.org] synonym: "File format" NARROW [http://edamontology.org] !{note="File format denotes only formats of a computer file, but the same formats apply also to data blobs or messages. Thus the synonym is in practical terms exact."} synonym: "Format" BROAD [http://purl.org/dc/elements/1.1/format] synonym: "quality" BROAD [http://purl.org/biotop/biotop.owl#Quality] synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] synonym: "data format specification" RELATED [http://purl.obolibrary.org/obo/IAO_0000098] !{note="Closely related concept focusing on the specification of a data format."} synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials."} synonym: "Symbol structure" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure] synonym: "File format" RELATED [http://en.wikipedia.org/wiki/File_format, http://en.wikipedia.org/wiki/List_of_file_formats] synonym: "machine language" RELATED [http://purl.org/biotop/biotop.owl#MachineLanguage] synonym: "Compression and encoding" RELATED [http://wsio.org/compression_004] !{note="'Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format."} synonym: "standard" RELATED [http://semanticscience.org/resource/SIO_000618] synonym: "representation" RELATED [http://semanticscience.org/resource/SIO_000612] synonym: "quality" RELATED [http://purl.obolibrary.org/obo/BFO_0000019, http://www.ifomis.org/bfo/1.1/snap#Quality] !{note="BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format."} synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] !{note="Format can be a quality of a data record."} relationship: is_format_of EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. [Term] id: EDAM_data:0842 name: Identifier namespace: identifier subset: identifiers subset: data ! alt_id: EDAM_data:2860 ! alt_id: EDAM_data:2861 ! alt_id: EDAM_data:2926 def: "Identifier is a datum identifying an entity and serving only the sole purpose of identification." [http://edamontology.org] comment: An identifier is typically a rather short textual or numerical datum (string or integer). It is usually desired that an identifier identifies the entity uniquely and often also that it is persistent over time. synonym: "ID" EXACT [http://edamontology.org] synonym: "Identifier" EXACT [http://wsio.org/data_005] synonym: "identifier" EXACT [http://semanticscience.org/resource/SIO_000115] synonym: "Identifier" NARROW [http://purl.org/dc/elements/1.1/identifier] !{note="Almost exact but limited to identifying resources."} is_a: EDAM_data:0006 ! Data relationship: is_identifier_of EDAM_data:0006 !{note="However, NB. that an identifier may identify also other entities than data records."} ! Data [Term] id: EDAM_data:3031 !{since=beta13} name: Core data namespace: data subset: data def: "A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation." [http://edamontology.org] comment: Core data entities typically have a format and may be identified by an accession number. is_a: EDAM_data:0006 ! Data ! ! Topic ! [Term] id: EDAM_topic:2807 name: Tool topic namespace: topic subset: topics def: "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2809 name: Study topic namespace: topic subset: topics def: "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:3071 !{since=beta13} name: Biological data resources namespace: topic subset: topics ! alt_id: EDAM_topic:2808 def: "A topic concerning primarily a specific type of bioinformatics data, typically the broad category of content of a digital archives of biological data, including databanks, databases proper, web portals and other data resources." [http://edamontology.org] synonym: "Biological databases" EXACT [http://edamontology.org] synonym: "Biological data resource" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0077 name: Nucleic acid analysis namespace: topic subset: topics ! alt_id: EDAM_topic:3046 !{since=beta13} ! Not released def: "Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis." [http://edamontology.org] synonym: "Nucleic acids" EXACT [http://edamontology.org] synonym: "Nucleic acid informatics" EXACT [http://edamontology.org] synonym: "Nucleic acid bioinformatics" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2839 name: Molecules namespace: topic subset: topics def: "Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [http://edamontology.org] synonym: "molecular entity" RELATED [CHEBI:23367] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_topic:0078 name: Protein analysis namespace: topic subset: topics ! alt_id: EDAM_topic:0586 def: "Processing and analysis of protein data, typically molecular sequence and structural data." [http://edamontology.org] synonym: "Protein informatics" EXACT [http://edamontology.org] synonym: "Protein bioinformatics" EXACT [http://edamontology.org] synonym: "Proteins" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2225 name: Protein databases namespace: topic subset: topics def: "Topic concerning protein data resources." [http://edamontology.org] synonym: "Protein data resources" EXACT [http://edamontology.org] is_a: EDAM_topic:3071 ! Biological data resources is_a: EDAM_topic:0078 ! Protein analysis [Term] id: EDAM_topic:3174 !{since=1.1} name: Metagenomics namespace: topic subset: topics def: "Topic concerning the study of genetic material recovered from environmental samples." [http://edamontology.org] synonym: "Environmental genomics" EXACT [http://edamontology.org] synonym: "Ecogenomics" EXACT [http://edamontology.org] synonym: "Community genomics" EXACT [http://edamontology.org] is_a: EDAM_topic:0610 ! Ecoinformatics is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:3172 !{since=1.1} name: Metabolomics namespace: topic subset: topics def: "Topic concerning the study of metabolites and the chemical processes they are involved in, especially the systematic study of the chemical fingerprints of specific cellular processes." [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0079 name: Metabolites namespace: topic subset: topics def: "Topic concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." [http://edamontology.org] comment: This concept excludes macromolecules such as proteins and nucleic acids. is_a: EDAM_topic:0154 ! Small molecules is_a: EDAM_topic:3172 ! Metabolomics [Term] id: EDAM_topic:0080 name: Sequence analysis namespace: topic subset: topics ! alt_id: EDAM_topic:2228 ! alt_id: EDAM_topic:0584 def: "Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] synonym: "Sequences" EXACT [http://edamontology.org] xref: BioCatalogue:Sequence Analysis is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:3041 !{since=beta13} name: Sequence databases namespace: topic subset: topics def: "Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles." [http://edamontology.org] synonym: "Sequence data" EXACT [http://edamontology.org] synonym: "Sequence data resource" EXACT [http://edamontology.org] synonym: "Sequence data resources" EXACT [http://edamontology.org] is_a: EDAM_topic:3071 ! Biological data resources is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0081 name: Structure analysis namespace: topic subset: topics ! alt_id: EDAM_topic:0693 ! alt_id: EDAM_topic:2827 ! alt_id: EDAM_topic:0585 def: "Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids." [http://edamontology.org] comment: This includes related concepts such as structural properties, alignments and structural motifs. synonym: "Structural bioinformatics" EXACT [http://edamontology.org] synonym: "Computation structural biology" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:3038 !{since=beta13} name: Structure databases namespace: topic subset: topics ! alt_id: EDAM_topic:3059 def: "Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids." [http://edamontology.org] synonym: "Structure data resources" EXACT [http://edamontology.org] is_a: EDAM_topic:3071 ! Biological data resources is_a: EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_topic:0082 name: Structure prediction namespace: topic subset: topics ! alt_id: EDAM_topic:0171 def: "Topic concerning the prediction of molecular (secondary or tertiary) structure." [http://edamontology.org] is_a: EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_topic:0083 name: Alignment namespace: topic subset: topics def: "Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0182 ! Sequence alignment consider: EDAM_topic:0183 ! Structure alignment consider: EDAM_topic:0184 ! Threading [Term] id: EDAM_topic:0084 ! alt_id: EDAM_topic:0192 ! alt_id: EDAM_topic:0193 name: Phylogenetics namespace: topic subset: topics ! alt_id: EDAM_topic:0636 def: "Topic concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc." [http://edamontology.org] comment: This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data. xref: BioCatalogue:Phylogeny xref: BioCatalogue:Statistical Robustness synonym: "Phylogenetic simulation" EXACT [http://edamontology.org] synonym: "Phylogenetic clocks, dating and stratigraphy" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0200 name: Microarrays namespace: topic subset: topics ! alt_id: EDAM_topic:0206 def: "Topic concerning microarrays, for example, to process microarray data or design probes and experiments." [http://edamontology.org] xref: BioCatalogue:Microarrays synonym: "DNA microarrays" EXACT [http://edamontology.org] is_a: EDAM_topic:0607 ! Laboratory resources [Term] id: EDAM_topic:0121 name: Proteomics namespace: topic subset: topics ! alt_id: EDAM_topic:0764 def: "Topic concerning the study of whole proteomes of organisms." [http://edamontology.org] comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues). synonym: "Protein expression" EXACT [http://edamontology.org] xref: BioCatalogue:Proteomics is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0085 name: Functional genomics namespace: topic subset: topics def: "Topic concerning the study of gene or protein functions and their interactions." [http://edamontology.org] is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:0122 name: Structural genomics namespace: topic subset: topics def: "Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism." [http://edamontology.org] xref: BioCatalogue:Structural Genomics is_a: EDAM_topic:2226 ! Structure determination is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:3173 !{since=1.1} name: Epigenomics namespace: topic subset: topics def: "A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc." [http://edamontology.org] comment: Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. synonym: "Epigenetics" EXACT [http://edamontology.org] is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:3061 !{since=beta13} name: Documentation and help namespace: topic subset: topics def: "Topic concerning documentation and getting help." [http://edamontology.org] is_a: EDAM_topic:3068 ! Literature and reference [Term] id: EDAM_topic:3047 !{since=beta13} name: Molecular biology reference namespace: topic subset: topics def: "Topic concerning general molecular biology information extracted from the literature." [http://edamontology.org] xref: BioCatalogue: Document Discovery xref: BioCatalogue: Literature retrieval is_a: EDAM_topic:0606 ! Literature data resources [Term] id: EDAM_topic:0089 name: Ontology namespace: topic subset: topics ! alt_id: EDAM_topic:2255 def: "Topic concerning ontologies, controlled vocabularies, structured glossary or other related resource." [http://edamontology.org] comment: This includes the annotation of entities (typically biological database entries) with concepts from a controlled vocabulary. synonym: "Ontologies" EXACT [http://edamontology.org] synonym: "Applied ontology" NARROW [http://edamontology.org] xref: BioCatalogue:Ontology xref: BioCatalogue:Ontology Lookup is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:0090 name: Data search and retrieval namespace: topic subset: topics ! alt_id: EDAM_topic:0155 ! alt_id: EDAM_topic:2274 ! alt_id: EDAM_topic:0165 def: "Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [http://edamontology.org] comment: This includes, for example, search, query and retrieval of molecular sequences and associated data. synonym: "Data retrieval" EXACT [http://edamontology.org] xref: BioCatalogue:Sequence Retrieval xref: BioCatalogue:Data Retrieval xref: BioCatalogue:Identifier Retrieval xref: BioCatalogue:Image Retrieval xref: BioCatalogue:Structure Retrieval is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0091 name: Data handling namespace: topic subset: topics ! alt_id: EDAM_topic:2282 def: "Topic for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation." [http://edamontology.org] synonym: "Data types, processing and visualisation" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0092 name: Data visualisation namespace: topic subset: topics def: "Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [http://edamontology.org] synonym: "Data rendering and visualisation" EXACT [http://edamontology.org] synonym: "Data rendering" EXACT [http://edamontology.org] synonym: "Data plotting" EXACT [http://edamontology.org] is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:2258 name: Chemoinformatics namespace: topic subset: topics def: "Topic for the application of information technology to chemistry." [http://edamontology.org] synonym: "Cheminformatics" EXACT [http://edamontology.org] synonym: "Chemical informatics" EXACT [http://edamontology.org] synonym: "Computational chemistry" EXACT [http://edamontology.org] xref: BioCatalogue:Chemoinformatics is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2269 name: Biostatistics namespace: topic subset: topics def: "Topic for the application of statistical methods to biological problems." [http://edamontology.org] synonym: "Biometry" EXACT [http://edamontology.org] synonym: "Biometrics" EXACT [http://edamontology.org] synonym: "Biostatistics" EXACT [http://en.wikipedia.org/wiki/Biostatistics] xref: BioCatalogue:Biostatistics is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:3077 !{since=beta13} ! alt_id: EDAM_topic:1779 name: Data acquisition and deposition namespace: topic subset: topics def: "Topic concerning the acquisition and deposition of biological data." [http://edamontology.org] synonym: "Database submission" EXACT [http://edamontology.org] is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0094 name: Nucleic acid thermodynamics namespace: topic subset: topics ! alt_id: EDAM_topic:0614 ! alt_id: EDAM_topic:0104 def: "Topic concerning the study of the thermodynamic properties of a nucleic acid." [http://edamontology.org] comment: This includes the study of thermal and conformational properties including DNA or DNA/RNA denaturation (melting). synonym: "Nucleic acid physicochemistry" EXACT [http://edamontology.org] synonym: "Nucleic acid properties" EXACT [http://edamontology.org] synonym: "Nucleic acid denaturation" EXACT [http://edamontology.org] synonym: "DNA melting" EXACT [http://edamontology.org] is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0097 name: Nucleic acid structure analysis namespace: topic subset: topics ! alt_id: EDAM_topic:0699 ! alt_id: EDAM_topic:0106 def: "The processing and analysis of nucleic acid (secondary or tertiary) structural data." [http://edamontology.org] is_a: EDAM_topic:0081 ! Structure analysis is_a: EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_topic:3039 !{since=beta13} name: Nucleic acid structure namespace: topic subset: topics ! alt_id: EDAM_topic:2833 def: "Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." [http://edamontology.org] is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:0099 name: RNA namespace: topic subset: topics ! alt_id: EDAM_topic:0653 def: "Topic concerning RNA sequences and structures." [http://edamontology.org] is_a: EDAM_topic:3042 ! Nucleic acid sequences [Term] id: EDAM_topic:0100 name: Nucleic acid restriction namespace: topic subset: topics def: "Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." [http://edamontology.org] is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis is_a: EDAM_topic:0821 ! Enzymes and reactions [Term] id: EDAM_topic:0107 name: Codon usage analysis namespace: topic subset: topics def: "Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on." [http://edamontology.org] is_a: EDAM_topic:0110 ! Transcription [Term] id: EDAM_topic:0109 name: Gene finding namespace: topic subset: topics def: "Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences." [http://edamontology.org] comment: This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. synonym: "Gene prediction" EXACT [http://edamontology.org] synonym: "Gene discovery" EXACT [http://edamontology.org] xref: BioCatalogue:Gene Prediction is_a: EDAM_topic:3073 ! Nucleic acid feature detection [Term] id: EDAM_topic:0110 name: Transcription namespace: topic subset: topics def: "Topic concerning the transcription of DNA into mRNA." [http://edamontology.org] xref: BioCatalogue:Transcription Factors is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0108 name: Translation namespace: topic subset: topics def: "Topic concerning the translation of mRNA into protein." [http://edamontology.org] is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0111 name: Promoters namespace: topic subset: topics def: "Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins)." [http://edamontology.org] xref: BioCatalogue:Promoter Prediction is_obsolete: true !{since=beta13} consider: EDAM_topic:0749 ! Transcription factors and regulatory sites [Term] id: EDAM_topic:0112 name: Nucleic acid folding namespace: topic subset: topics def: "Topic concerning the folding (in 3D space) of nucleic acid molecules." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_topic:0114 name: Gene structure and RNA splicing namespace: topic subset: topics ! alt_id: EDAM_topic:0750 def: "Topic concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [http://edamontology.org] comment: This includes splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. synonym: "RNA splicing" EXACT [http://edamontology.org] synonym: "Gene structure" EXACT [http://edamontology.org] is_a: EDAM_topic:3062 ! Genetic organisation is_a: EDAM_topic:0747 ! Nucleic acid sites and features [Term] id: EDAM_topic:0123 name: Protein properties namespace: topic subset: topics ! alt_id: EDAM_topic:0615 def: "Topic for the study of the physical and biochemical properties of peptides and proteins." [http://edamontology.org] synonym: "Protein physicochemistry" EXACT [http://edamontology.org] is_a: EDAM_topic:0639 ! Protein sequence analysis [Term] id: EDAM_topic:1775 name: Protein function analysis namespace: topic subset: topics ! alt_id: EDAM_topic:3057 def: "Topic for the study of protein function." [http://edamontology.org] is_a: EDAM_topic:0078 ! Protein analysis [Term] id: EDAM_topic:0128 name: Protein interactions namespace: topic subset: topics ! alt_id: EDAM_topic:0587 def: "Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." [http://edamontology.org] comment: This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. xref: BioCatalogue:Protein Interaction is_a: EDAM_topic:1775 ! Protein function analysis is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0130 name: Protein folding and stability namespace: topic subset: topics def: "Topic concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation." [http://edamontology.org] is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:2232 name: Lipoproteins namespace: topic subset: topics def: "Topic concerning lipoproteins (protein-lipid assemblies)." [http://edamontology.org] is_a: EDAM_topic:0635 ! Specific protein resources [Term] id: EDAM_topic:0137 name: Protein hydropathy namespace: topic subset: topics def: "Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein." [http://edamontology.org] is_a: EDAM_topic:0123 ! Protein properties [Term] id: EDAM_topic:0140 name: Protein targeting and localization namespace: topic subset: topics ! alt_id: EDAM_topic:0588 def: "Topic for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [http://edamontology.org] is_a: EDAM_topic:2276 ! Protein function prediction is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0143 name: Protein structure comparison namespace: topic subset: topics def: "Topic concerning the comparison of two or more protein structures." [http://edamontology.org] comment: Use this concept for methods that are exclusively for protein structure. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0698 ! Protein tertiary structure consider: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:2280 name: Nucleic acid structure comparison namespace: topic subset: topics def: "Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [http://edamontology.org] comment: Use this concept for methods that are exclusively for nucleic acid structures. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0097 ! Nucleic acid structure analysis consider: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:0144 name: Protein residue interaction analysis namespace: topic subset: topics def: "The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures." [http://edamontology.org] synonym: "Protein residue interactions" EXACT [http://edamontology.org] is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:2276 name: Protein function prediction namespace: topic subset: topics def: "Topic concerning the prediction of functional properties of a protein." [http://edamontology.org] xref: BioCatalogue:Function Prediction is_a: EDAM_topic:1775 ! Protein function analysis [Term] id: EDAM_topic:0147 name: Protein-protein interactions namespace: topic subset: topics ! alt_id: EDAM_topic:0719 def: "Topic concerning protein-protein interactions, protein complexes, protein functional coupling etc." [http://edamontology.org] is_a: EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_topic:0148 name: Protein-ligand interactions namespace: topic subset: topics ! alt_id: EDAM_topic:0717 def: "Topic concerning protein-ligand (small molecule) interactions." [http://edamontology.org] xref: BioCatalogue:Ligand Interaction is_a: EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_topic:0149 name: Protein-nucleic acid interactions namespace: topic subset: topics ! alt_id: EDAM_topic:0718 def: "Topic concerning protein-DNA/RNA interactions." [http://edamontology.org] is_a: EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_topic:0150 name: Protein design namespace: topic subset: topics def: "Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [http://edamontology.org] is_a: EDAM_topic:0172 ! Protein structure prediction [Term] id: EDAM_topic:0151 name: G protein-coupled receptors (GPCR) namespace: topic subset: topics def: "Topic concerning G-protein coupled receptors (GPCRs)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0820 ! Membrane proteins [Term] id: EDAM_topic:2278 name: Transmembrane protein prediction namespace: topic subset: topics def: "Predict transmembrane domains and topology in protein sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0820 ! Membrane proteins consider: EDAM_topic:0178 ! Protein secondary structure prediction [Term] id: EDAM_topic:0152 name: Carbohydrates namespace: topic subset: topics ! alt_id: EDAM_topic:0695 def: "Topic concerning carbohydrates, typically including structural information." [http://edamontology.org] is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:0153 name: Lipids namespace: topic subset: topics ! alt_id: EDAM_topic:2624 def: "Topic concerning lipids and their structures." [http://edamontology.org] is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:0154 name: Small molecules namespace: topic subset: topics ! alt_id: EDAM_topic:0696 def: "Topic concerning small molecules of biological significance, typically including structural information." [http://edamontology.org] comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. synonym: "molecular entity" RELATED [CHEBI:23367] is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:0156 name: Sequence editing namespace: topic subset: topics def: "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0080 ! Sequence analysis consider: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0157 name: Sequence composition analysis namespace: topic subset: topics def: "Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [http://edamontology.org] is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0158 name: Sequence motifs namespace: topic subset: topics ! alt_id: EDAM_topic:0161 ! alt_id: EDAM_topic:0162 def: "Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." [http://edamontology.org] synonym: "Motifs" EXACT [http://edamontology.org] is_a: EDAM_topic:0594 ! Sequence classification [Term] id: EDAM_topic:0188 name: Sequence profiles and HMMs namespace: topic subset: topics ! alt_id: EDAM_topic:0744 ! alt_id: EDAM_topic:0746 ! alt_id: EDAM_topic:1763 def: "Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [http://edamontology.org] comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. is_a: EDAM_topic:0594 ! Sequence classification [Term] id: EDAM_topic:0159 ! alt_id: EDAM_topic:2260 ! alt_id: EDAM_topic:2261 name: Sequence comparison namespace: topic subset: topics def: "Topic concerning the comparison of two or more molecular sequences." [http://edamontology.org] comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. xref: BioCatalogue:Protein Sequence Similarity xref: BioCatalogue:Nucleotide Sequence Similarity is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0160 name: Sequence sites and features namespace: topic subset: topics ! alt_id: EDAM_topic:0600 def: "Topic concerning the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org] is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:3072 !{since=beta13} name: Sequence feature detection namespace: topic subset: topics def: "Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org] is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0163 name: Sequence database search namespace: topic subset: topics def: "Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence)." [http://edamontology.org] comment: The query is a sequence-based entity such as another sequence, a motif or profile. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0159 ! Sequence comparison [Term] id: EDAM_topic:3052 !{since=beta13} name: Sequence clusters and classification namespace: topic subset: topics def: "Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity." [http://edamontology.org] comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. synonym: "Sequence clusters" EXACT [http://edamontology.org] synonym: "Sequence families" EXACT [http://edamontology.org] is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0164 name: Sequence clustering namespace: topic subset: topics def: "Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities." [http://edamontology.org] comment: This includes systems that generate, process and analyse sequence clusters. is_a: EDAM_topic:0159 ! Sequence comparison [Term] id: EDAM_topic:0594 name: Sequence classification namespace: topic subset: topics def: "Topic concerning the classification of molecular sequences based on some measure of their similarity." [http://edamontology.org] comment: Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0166 name: Protein structural motifs and surfaces namespace: topic subset: topics ! alt_id: EDAM_topic:0139 ! alt_id: EDAM_topic:0170 ! alt_id: EDAM_topic:0146 ! alt_id: EDAM_topic:0589 def: "Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules." [http://edamontology.org] comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. synonym: "Protein structural features" EXACT [http://edamontology.org] synonym: "Protein surfaces" EXACT [http://edamontology.org] synonym: "Protein structural motifs" EXACT [http://edamontology.org] synonym: "Structural motifs" EXACT [http://edamontology.org] is_a: EDAM_topic:0698 ! Protein tertiary structure [Term] id: EDAM_topic:0167 name: Structural (3D) profiles namespace: topic subset: topics ! alt_id: EDAM_topic:0599 def: "The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment." [http://edamontology.org] synonym: "Structural profiles" EXACT [http://edamontology.org] is_a: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:1770 ! alt_id: EDAM_topic:0168 ! alt_id: EDAM_topic:0169 name: Structure comparison namespace: topic subset: topics def: "Topic concerning the comparison of two or more molecular structures." [http://edamontology.org] comment: This might involve comparison of secondary or tertiary (3D) structural information. is_a: EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_topic:2844 name: Structural clustering namespace: topic subset: topics def: "Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." [http://edamontology.org] synonym: "Structure classification" EXACT [http://edamontology.org] is_a: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:2271 name: Structure database search namespace: topic subset: topics def: "Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure)." [http://edamontology.org] comment: The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:0172 name: Protein structure prediction namespace: topic subset: topics def: "Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." [http://edamontology.org] xref: BioCatalogue:Protein Structure Prediction is_a: EDAM_topic:0082 ! Structure prediction is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0173 name: Nucleic acid structure prediction namespace: topic subset: topics ! alt_id: EDAM_topic:0181 def: "Topic concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure." [http://edamontology.org] synonym: "Nucleic acid folding" EXACT [http://edamontology.org] synonym: "RNA/DNA structure prediction" EXACT [http://edamontology.org] xref: BioCatalogue:Nucleotide Structure Prediction xref: BioCatalogue:Nucleotide Secondary Structure xref: BioCatalogue:Nucleotide Tertiary Structure is_a: EDAM_topic:0082 ! Structure prediction is_a: EDAM_topic:0097 ! Nucleic acid structure analysis [Term] id: EDAM_topic:2953 name: Nucleic acid design namespace: topic subset: topics def: "Topic for the design of nucleic acid sequences with specific conformations." [http://edamontology.org] is_a: EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_topic:0174 name: Ab initio structure prediction namespace: topic subset: topics def: "Topic for the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [http://edamontology.org] synonym: "de novo protein structure prediction" EXACT [http://edamontology.org] is_a: EDAM_topic:0082 ! Structure prediction [Term] id: EDAM_topic:2275 name: Molecular modelling namespace: topic subset: topics def: "Topic for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. " [http://edamontology.org] is_a: EDAM_topic:0082 ! Structure prediction is_a: EDAM_topic:0172 ! Protein structure prediction [Term] id: EDAM_topic:0175 name: Homology modelling namespace: topic subset: topics def: "Topic for the modelling of the three-dimensional structure of a protein using known sequence and structural data." [http://edamontology.org] synonym: "Comparative modelling" EXACT [http://edamontology.org] is_a: EDAM_topic:2275 ! Molecular modelling [Term] id: EDAM_topic:0176 ! alt_id: EDAM_topic:0145 name: Molecular dynamics namespace: topic subset: topics def: "Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org] comment: This includes resources concerning flexibility and motion in protein and other molecular structures. synonym: "Molecular motions" EXACT [http://edamontology.org] synonym: "Molecular flexibility" EXACT [http://edamontology.org] is_a: EDAM_topic:2275 ! Molecular modelling [Term] id: EDAM_topic:0177 name: Molecular docking namespace: topic subset: topics def: "Topic for modelling the structure of proteins in complex with small molecules or other macromolecules." [http://edamontology.org] is_a: EDAM_topic:2275 ! Molecular modelling [Term] id: EDAM_topic:0178 name: Protein secondary structure prediction namespace: topic subset: topics def: "Topic concerning the prediction of secondary or supersecondary structure of protein sequences." [http://edamontology.org] xref: BioCatalogue:Protein Secondary Structure is_a: EDAM_topic:0172 ! Protein structure prediction is_a: EDAM_topic:0694 ! Protein secondary structure [Term] id: EDAM_topic:0179 name: Protein tertiary structure prediction namespace: topic subset: topics def: "Topic concerning the prediction of tertiary structure of protein sequences." [http://edamontology.org] xref: BioCatalogue:Protein Tertiary Structure is_a: EDAM_topic:0172 ! Protein structure prediction is_a: EDAM_topic:0698 ! Protein tertiary structure [Term] id: EDAM_topic:0180 name: Protein fold recognition namespace: topic subset: topics def: "Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [http://edamontology.org] is_a: EDAM_topic:0172 ! Protein structure prediction [Term] id: EDAM_topic:0182 name: Sequence alignment namespace: topic subset: topics ! alt_id: EDAM_topic:2283 ! alt_id: EDAM_topic:0185 ! alt_id: EDAM_topic:0186 ! alt_id: EDAM_topic:0187 ! alt_id: EDAM_topic:0596 ! alt_id: EDAM_topic:0189 def: "Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments)." [http://edamontology.org] comment: This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. xref: BioCatalogue:Protein Sequence Alignment xref: BioCatalogue:Nucleotide Sequence Alignment xref: BioCatalogue:Protein Pairwise Alignment xref: BioCatalogue:Nucleotide Pairwise Alignment xref: BioCatalogue:Protein Multiple Alignment xref: BioCatalogue:Nucleotide Multiple Alignment is_a: EDAM_topic:0159 ! Sequence comparison is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:3178 name: RNA-Seq alignment namespace: topic subset: topics def: "Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing." [http://edamontology.org] synonym: "RNA-seq alignment" EXACT [http://edamontology.org] is_a: EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_topic:0183 ! alt_id: EDAM_topic:2272 ! alt_id: EDAM_topic:2273 name: Structure alignment namespace: topic subset: topics ! alt_id: EDAM_topic:0597 ! alt_id: EDAM_topic:0190 def: "Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [http://edamontology.org] comment: This includes the generation, storage, analysis, rendering etc. of structure alignments. synonym: "Structure alignment generation" EXACT [http://edamontology.org] is_a: EDAM_topic:1770 ! Structure comparison is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:0184 name: Threading namespace: topic subset: topics def: "Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [http://edamontology.org] synonym: "Sequence-structure alignment" EXACT [http://edamontology.org] is_a: EDAM_topic:0180 ! Protein fold recognition [Term] id: EDAM_topic:0191 name: Phylogeny reconstruction namespace: topic subset: topics def: "Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." [http://edamontology.org] comment: Currently too specific for the topic sub-ontology (but might be unobsoleted). xref: BioCatalogue:Tree Inference xref: BioCatalogue:Evolutionary Distance Measurements is_a: EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_topic:2257 name: Phylogeny visualisation namespace: topic subset: topics def: "Visualise a phylogeny, for example, render a phylogenetic tree." [http://edamontology.org] xref: BioCatalogue:Tree Display is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_topic:0194 name: Phylogenomics namespace: topic subset: topics def: "Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction." [http://edamontology.org] is_a: EDAM_topic:0084 ! Phylogenetics is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:2842 name: High-throughput sequencing namespace: topic subset: topics def: "Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [http://edamontology.org] synonym: "Next-generation sequencing" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:3168 ! Sequencing [Term] id: EDAM_topic:0195 name: Virtual PCR namespace: topic subset: topics def: "Topic concerning simulated polymerase chain reaction (PCR)." [http://edamontology.org] synonym: "PCR" EXACT [http://edamontology.org] synonym: "Polymerase chain reaction" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_topic:0196 name: Sequence assembly namespace: topic subset: topics def: "Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] is_a: EDAM_topic:3168 ! Sequencing [Term] id: EDAM_topic:0133 name: Two-dimensional gel electrophoresis namespace: topic subset: topics ! alt_id: EDAM_topic:0765 def: "Topic concerning two-dimensional gel electrophoresis image and related data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:0121 ! Proteomics [Term] id: EDAM_topic:0134 name: Mass spectrometry namespace: topic subset: topics ! alt_id: EDAM_topic:0766 def: "Topic concerning mass spectrometry and related data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:0121 ! Proteomics [Term] id: EDAM_topic:0135 name: Protein microarrays namespace: topic subset: topics def: "Topic concerning protein microarray data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:0121 ! Proteomics consider: EDAM_topic:0200 ! Microarrays [Term] id: EDAM_topic:0102 name: Mapping namespace: topic subset: topics def: "Topic concerning the mapping of complete (typically nucleotide) sequences." [http://edamontology.org] is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:3168 !{since=1.1} name: Sequencing namespace: topic subset: topics def: "Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes." [http://edamontology.org] is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:3169 !{since=1.1} name: ChIP-seq namespace: topic subset: topics def: "Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins." [http://edamontology.org] synonym: "Chip-sequencing" EXACT [http://edamontology.org] synonym: "Chip sequencing" EXACT [http://edamontology.org] synonym: "Chip seq" EXACT [http://edamontology.org] is_a: EDAM_topic:3168 ! Sequencing is_a: EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_topic:3179 !{since=1.1} name: ChIP-on-chip namespace: topic subset: topics def: "Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions." [http://edamontology.org] synonym: "ChIP-chip" EXACT [http://edamontology.org] is_a: EDAM_topic:3168 ! Sequencing is_a: EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_topic:3170 !{since=1.1} name: RNA-Seq namespace: topic subset: topics def: "A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. " [http://edamontology.org] comment: This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. synonym: "RNA-seq" EXACT [http://edamontology.org] synonym: "Small RNA-Seq" EXACT [http://edamontology.org] synonym: "Small RNA-seq" EXACT [http://edamontology.org] synonym: "Whole transcriptome shotgun sequencing" EXACT [http://edamontology.org] synonym: "WTSS" EXACT [http://edamontology.org] is_a: EDAM_topic:3168 ! Sequencing is_a: EDAM_topic:0203 ! Transcriptomics [Term] id: EDAM_topic:3177 !{since=1.1} name: DNA-Seq namespace: topic subset: topics def: "A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements." [http://edamontology.org] synonym: "DNA-seq" EXACT [http://edamontology.org] is_a: EDAM_topic:3168 ! Sequencing [Term] id: EDAM_topic:3062 !{since=beta13} name: Genetic organisation namespace: topic subset: topics def: "Topic concerning the structural and functional organisation of genes and other genetic elements." [http://edamontology.org] is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:0204 name: Gene regulation namespace: topic subset: topics ! alt_id: EDAM_topic:3049 ! alt_id: EDAM_topic:0631 def: "Topic concerning primarily the regulation of gene expression." [http://edamontology.org] synonym: "Gene regulation resources" EXACT [http://edamontology.org] is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:0199 name: Genetic variation namespace: topic subset: topics ! alt_id: EDAM_topic:0626 def: "Topic concerning DNA sequence variation (mutation and polymorphism) data." [http://edamontology.org] synonym: "Mutation and polymorphism" EXACT [http://edamontology.org] synonym: "DNA variation" EXACT [http://edamontology.org] is_a: EDAM_topic:0625 ! Genotype and phenotype is_a: EDAM_topic:3041 ! Sequence databases is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0202 name: Pharmacoinformatics namespace: topic subset: topics def: "Topic for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on." [http://edamontology.org] synonym: "Computational pharmacology" EXACT [http://edamontology.org] is_a: EDAM_topic:2258 ! Chemoinformatics [Term] id: EDAM_topic:0203 name: Transcriptomics namespace: topic subset: topics alt_id: EDAM_topic:0197 def: "Topic concerning primarily raw or processed gene (mRNA) expression (typically microarray) data, including the analysis of gene expression levels, by identifying, quantifying or comparing mRNA transcripts and the interpretation (in functional terms) of gene expression data." [http://edamontology.org] comment: This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein. synonym: "Gene expression profiling" EXACT [http://edamontology.org] synonym: "Expression profiling" EXACT [http://edamontology.org] synonym: "Gene expression resources" EXACT [http://edamontology.org] synonym: "Gene expression analysis" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:2277 name: SNPs namespace: topic subset: topics def: "Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs." [http://edamontology.org] comment: A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. is_a: EDAM_topic:0199 ! Genetic variation [Term] id: EDAM_topic:0208 name: Pharmacogenomics namespace: topic subset: topics def: "Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [http://edamontology.org] synonym: "Pharmacogenetics" EXACT [http://edamontology.org] is_a: EDAM_topic:0202 ! Pharmacoinformatics is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:0209 name: Drug design namespace: topic subset: topics def: "Topic concerning the design of drugs or potential drug compounds." [http://edamontology.org] comment: This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. is_a: EDAM_topic:0202 ! Pharmacoinformatics [Term] id: EDAM_topic:0210 name: Fish namespace: topic subset: topics def: "Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a fish, a group of fish or all fish. is_a: EDAM_topic:2820 ! Vertebrates [Term] id: EDAM_topic:0211 name: Flies namespace: topic subset: topics def: "Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a fly, a group of flies or all flies. synonym: "Fly" EXACT [http://edamontology.org] is_a: EDAM_topic:2819 ! Invertebrates [Term] id: EDAM_topic:3048 !{since=beta13} name: Mammals namespace: topic subset: topics def: "Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." [http://edamontology.org] is_a: EDAM_topic:2820 ! Vertebrates [Term] id: EDAM_topic:0213 name: Mice or rats namespace: topic subset: topics def: "Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a group of mice / rats or all mice / rats. synonym: "Mouse or rat" EXACT [http://edamontology.org] is_a: EDAM_topic:3048 ! Mammals [Term] id: EDAM_topic:0215 name: Worms namespace: topic subset: topics def: "Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a worm, a group of worms or all worms. synonym: "Worm" EXACT [http://edamontology.org] is_a: EDAM_topic:2819 ! Invertebrates [Term] id: EDAM_topic:0217 name: Literature analysis namespace: topic subset: topics ! alt_id: EDAM_topic:0088 ! alt_id: EDAM_topic:3058 def: "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." [http://edamontology.org] xref: BioCatalogue: Document Discovery xref: BioCatalogue: Literature retrieval synonym: "Literature search and analysis" EXACT [http://edamontology.org] synonym: "Literature sources" EXACT [http://edamontology.org] is_a: EDAM_topic:3068 ! Literature and reference [Term] id: EDAM_topic:0606 name: Literature data resources namespace: topic subset: topics def: "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." [http://edamontology.org] is_a: EDAM_topic:3068 ! Literature and reference is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:3068 !{since=beta13} name: Literature and reference namespace: topic subset: topics def: "Topic concerning the scientific literature, reference information and documentation." [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0218 name: Text mining namespace: topic subset: topics def: "Topic concerning the analysis of the biomedical and informatics literature." [http://edamontology.org] synonym: "Text data mining" EXACT [http://edamontology.org] xref: BioCatalogue:Text Mining xref: BioCatalogue:Document Similarity xref: BioCatalogue:Document Clustering xref: BioCatalogue:Named Entity Recognition is_a: EDAM_topic:0217 ! Literature analysis [Term] id: EDAM_topic:0219 name: Annotation namespace: topic subset: topics ! alt_id: EDAM_topic:2256 def: "Topic for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [http://edamontology.org] synonym: "Ontology annotation" EXACT [http://edamontology.org] xref: BioCatalogue:Genome Annotation xref: BioCatalogue:Ontology Annotation is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:0221 name: Sequence annotation namespace: topic subset: topics def: "Annotate a molecular sequence." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0219 ! Annotation [Term] id: EDAM_topic:0222 name: Genome annotation namespace: topic subset: topics def: "Annotate a genome." [http://edamontology.org] xref: BioCatalogue:Genome Annotation is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0219 ! Annotation consider: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:2230 name: Classification namespace: topic subset: topics def: "Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:2829 name: Ontologies, nomenclature and classification namespace: topic subset: topics def: "Topic concerning conceptualisation, categorisation and naming, or that help to identify, group, or name things in a structured way according to some schema based on observable relationships." [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2811 name: Nomenclature namespace: topic subset: topics ! alt_id: EDAM_topic:0619 def: "Topic concerning biological nomenclature (naming), symbols and terminology." [http://edamontology.org] is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:2229 name: Cell biology resources namespace: topic subset: topics def: "Topic concerning cells, such as key genes and proteins involved in the cell cycle." [http://edamontology.org] is_a: EDAM_topic:3070 ! Biological science resources [Term] id: EDAM_topic:3064 !{since=beta13} name: Developmental biology resources namespace: topic subset: topics def: "Topic concerning how organisms grow and develop." [http://edamontology.org] is_a: EDAM_topic:3070 ! Biological science resources [Term] id: EDAM_topic:3067 !{since=beta13} name: Anatomy resources namespace: topic subset: topics def: "Topic concerning the structures of living organisms." [http://edamontology.org] is_a: EDAM_topic:3070 ! Biological science resources [Term] id: EDAM_topic:3065 !{since=beta13} name: Embryology resources namespace: topic subset: topics def: "Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage." [http://edamontology.org] is_a: EDAM_topic:3064 ! Developmental biology resources [Term] id: EDAM_topic:3053 !{since=beta13} name: Genetics namespace: topic subset: topics ! alt_id: EDAM_topic:2227 def: "Topic concerning the study of genes, genetic variation and heredity in living organisms." [http://edamontology.org] synonym: "Genetics data resources" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2226 name: Structure determination namespace: topic subset: topics ! alt_id: EDAM_topic:0136 def: "Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, including the assignment or modelling of molecular structure from such data." [http://edamontology.org] synonym: "Structural determination" EXACT [http://edamontology.org] synonym: "Structural assignment" EXACT [http://edamontology.org] synonym: "Structure assignment" EXACT [http://edamontology.org] synonym: "Raw structural data analysis" EXACT [http://edamontology.org] is_a: EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_topic:0595 name: Protein classification namespace: topic subset: topics ! alt_id: EDAM_topic:0129 def: "Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." [http://edamontology.org] is_a: EDAM_topic:0078 ! Protein analysis is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification is_a: EDAM_topic:0594 ! Sequence classification [Term] id: EDAM_topic:0598 name: Sequence motif or profile namespace: topic subset: topics def: "Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [http://edamontology.org] comment: This includes comparison, discovery, recognition etc. of sequence motifs. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0158 ! Sequence motifs consider: EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_topic:0601 name: Protein modifications namespace: topic subset: topics ! alt_id: EDAM_topic:0142 def: "Topic concerning protein chemical modifications, e.g. post-translational modifications." [http://edamontology.org] comment: EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) synonym: "Protein post-translation modification" EXACT [http:edamontology.souceforge.net] synonym: "protein modification" RELATED [MOD:00000] synonym: "protein modification process" RELATED [GO:0006464] is_a: EDAM_topic:0123 ! Protein properties is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0602 name: Pathways, networks and models namespace: topic subset: topics alt_id: EDAM_topic:3076 !{since=beta13} ! alt_id: EDAM_topic:0198 ! alt_id: EDAM_topic:0755 def: "Topic concerning biological pathways, networks and other models, including their construction and analysis." [http://edamontology.org] synonym: "Network or pathway analysis" EXACT [http://edamontology.org] xref: BioCatalogue:Pathways xref: BioCatalogue:Pathway Retrieval is_a: EDAM_topic:2259 ! Systems biology is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:3075 !{since=beta13} name: Biological system modelling namespace: topic subset: topics def: "Topic for modelling biological systems in mathematical terms." [http://edamontology.org] xref: BioCatalogue:Model Analysis xref: BioCatalogue:Model Execution is_a: EDAM_topic:2259 ! Systems biology [Term] id: EDAM_topic:2259 name: Systems biology namespace: topic subset: topics def: "Topic concerning the holistic modelling and analysis of biological systems and the interactions therein." [http://edamontology.org] synonym: "Systems biology" EXACT [http://en.wikipedia.org/wiki/Systems_biology] xref: BioCatalogue:Systems Biology is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0605 name: Informatics namespace: topic subset: topics ! alt_id: EDAM_topic:2841 def: "A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0607 name: Laboratory resources namespace: topic subset: topics def: "Topic concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." [http://edamontology.org] is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:0608 name: Cell culture resources namespace: topic subset: topics def: "Topic concerning general cell culture or data on a specific cell lines." [http://edamontology.org] is_a: EDAM_topic:0607 ! Laboratory resources [Term] id: EDAM_topic:0610 name: Ecoinformatics namespace: topic subset: topics def: "Topic concerning the application of information technology to the ecological and environmental sciences." [http://edamontology.org] synonym: "Computational ecology" EXACT [http://edamontology.org] synonym: "Ecological informatics" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:3063 !{since=beta13} name: Medical informatics resources namespace: topic subset: topics ! alt_id: EDAM_topic:0087 def: "Topic for the application of information technology to health, disease and biomedicine." [http://edamontology.org] synonym: "Health and disease" EXACT [http://edamontology.org] synonym: "Healthcare informatics" EXACT [http://edamontology.org] synonym: "Health informatics" EXACT [http://edamontology.org] synonym: "Clinical informatics" EXACT [http://edamontology.org] synonym: "Biomedical informatics" EXACT [http://edamontology.org] is_a: EDAM_topic:0607 ! Laboratory resources [Term] id: EDAM_topic:3050 !{since=beta13} name: Biodiversity namespace: topic subset: topics def: "Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet." [http://edamontology.org] synonym: "Biodiversity data resource" EXACT [http://edamontology.org] synonym: "Biodiversity data resources" EXACT [http://edamontology.org] is_a: EDAM_topic:0610 ! Ecoinformatics [Term] id: EDAM_topic:2840 name: Toxicoinformatics namespace: topic subset: topics def: "Topic concerning the adverse effects of chemical substances on living organisms." [http://edamontology.org] synonym: "Computational toxicology" EXACT [http://edamontology.org] is_a: EDAM_topic:2258 ! Chemoinformatics [Term] id: EDAM_topic:2661 name: Toxins and targets namespace: topic subset: topics def: "Topic concerning structural and associated data for toxic chemical substances." [http://edamontology.org] is_a: EDAM_topic:2840 ! Toxicoinformatics is_a: EDAM_topic:0154 ! Small molecules [Term] id: EDAM_topic:0611 name: Electron microscopy namespace: topic subset: topics def: "Topic concerning electron microscopy data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:2226 ! Structure determination [Term] id: EDAM_topic:2828 name: X-ray crystallography namespace: topic subset: topics def: "Topic concerning X-ray crystallography data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:2226 ! Structure determination [Term] id: EDAM_topic:0593 name: NMR namespace: topic subset: topics def: "Topic concerning raw NMR data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:2226 ! Structure determination [Term] id: EDAM_topic:0612 name: Cell cycle namespace: topic subset: topics ! alt_id: EDAM_topic:0609 def: "Topic concerning the cell cycle including key genes and proteins." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:2229 ! Cell biology resources [Term] id: EDAM_topic:0613 name: Peptides and amino acids namespace: topic subset: topics ! alt_id: EDAM_topic:0604 def: "Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides." [http://edamontology.org] is_a: EDAM_topic:0154 ! Small molecules [Term] id: EDAM_topic:0616 name: Organelle genes and proteins namespace: topic subset: topics def: "Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." [http://edamontology.org] is_a: EDAM_topic:3078 ! Gene and protein resources [Term] id: EDAM_topic:0617 name: Ribosomal genes and proteins namespace: topic subset: topics def: "Topic concerning ribosomes, typically of ribosome-related genes and proteins." [http://edamontology.org] synonym: "Ribosome genes and proteins" EXACT [http://edamontology.org] is_a: EDAM_topic:0616 ! Organelle genes and proteins [Term] id: EDAM_topic:0621 name: Genome, proteome and model organisms namespace: topic subset: topics ! alt_id: EDAM_topic:0086 ! alt_id: EDAM_topic:0591 ! alt_id: EDAM_topic:0643 ! alt_id: EDAM_topic:0800 ! alt_id: EDAM_topic:0795 def: "Topic concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms." [http://edamontology.org] comment: General information on or more organisms, genomes (including molecular sequences and map, genes and annotation) and proteomes may be included. synonym: "Genome map" EXACT [http://edamontology.org] is_a: EDAM_topic:0622 ! Genomics is_a: EDAM_topic:0121 ! Proteomics is_a: EDAM_topic:0625 ! Genotype and phenotype [Term] id: EDAM_topic:0622 name: Genomics namespace: topic subset: topics ! alt_id: EDAM_topic:0093 ! alt_id: EDAM_topic:0794 def: "Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." [http://edamontology.org] xref: BioCatalogue:Genomics xref: BioCatalogue:Functional Genomics is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2816 name: Gene resources namespace: topic subset: topics ! alt_id: EDAM_topic:0630 def: "Informatics resource (typically a database) primarily focussed on genes." [http://edamontology.org] synonym: "Gene database" EXACT [http://edamontology.org] synonym: "Gene resource" EXACT [http://edamontology.org] is_a: EDAM_topic:3071 ! Biological data resources is_a: EDAM_topic:3053 ! Genetics ! [Term] born obsolete ! id: EDAM_topic:3054 !{since=beta13} ! name: Molecular genetics ! namespace: topic ! subset: topics ! def: "Topic concerning the structure and function of genes at a molecular level." [http://edamontology.org] ! is_obsolete: true !{since=beta13} ! consider: EDAM_topic:3053 ! Genetics [Term] id: EDAM_topic:3055 !{since=beta13} name: Quantitative genetics namespace: topic subset: topics def: "Topic concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight)." [http://edamontology.org] is_a: EDAM_topic:3053 ! Genetics [Term] id: EDAM_topic:3056 !{since=beta13} name: Population genetics namespace: topic subset: topics def: "Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow." [http://edamontology.org] is_a: EDAM_topic:3053 ! Genetics [Term] id: EDAM_topic:0623 name: Genes, gene family or system namespace: topic subset: topics def: "Topic concerning particular gene(s), gene system or groups of genes." [http://edamontology.org] is_a: EDAM_topic:3052 ! Sequence clusters and classification is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:0624 name: Chromosomes namespace: topic subset: topics def: "Topic concerning chromosomes." [http://edamontology.org] is_a: EDAM_topic:3062 ! Genetic organisation [Term] id: EDAM_topic:3175 !{since=1.1} name: Structural variation namespace: topic subset: topics def: "Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations." [http://edamontology.org] synonym: "Genomic structural variation" EXACT [http://edamontology.org] is_a: EDAM_topic:0624 ! Chromosomes is_a: EDAM_topic:0199 ! Genetic variation [Term] id: EDAM_topic:0625 name: Genotype and phenotype namespace: topic subset: topics ! alt_id: EDAM_topic:2231 def: "Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on." [http://edamontology.org] synonym: "Genotyping" EXACT [http://edamontology.org] synonym: "Genotype and phenotype resources" EXACT [http://edamontology.org] is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:3078 !{since=beta13} name: Gene and protein resources namespace: topic subset: topics def: "Topic concerning specific genes and their encoded proteins or a related group of such genes and proteins." [http://edamontology.org] synonym: "Genes and proteins resources" EXACT [http://edamontology.org] is_a: EDAM_topic:0635 ! Specific protein resources is_a: EDAM_topic:0623 ! Genes, gene family or system [Term] id: EDAM_topic:3070 !{since=beta13} name: Biological science resources namespace: topic subset: topics ! alt_id: EDAM_topic:3066 def: "Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." [http://edamontology.org] synonym: "Phenotype resource" EXACT [http://edamontology.org] is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:0629 name: Gene expression and microarray namespace: topic subset: topics def: "Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0203 ! Transcriptomics consider: EDAM_topic:0200 ! Microarrays [Term] id: EDAM_topic:0634 name: Disease resources namespace: topic subset: topics def: "Topic concerning diseases." [http://edamontology.org] is_a: EDAM_topic:0625 ! Genotype and phenotype [Term] id: EDAM_topic:2813 name: Disease genes and proteins namespace: topic subset: topics ! alt_id: EDAM_topic:0819 def: "Topic concerning the genes, gene variations and proteins involved in one or more specific diseases." [http://edamontology.org] is_a: EDAM_topic:0634 ! Disease resources is_a: EDAM_topic:3078 ! Gene and protein resources [Term] id: EDAM_topic:0635 name: Specific protein resources namespace: topic subset: topics def: "Topic concerning a particular protein, protein family or other group of proteins." [http://edamontology.org] synonym: "Specific protein" EXACT [http://edamontology.org] is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0637 name: Taxonomy namespace: topic subset: topics def: "Topic concerning organism classification, identification and naming." [http://edamontology.org] is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:0639 name: Protein sequence analysis namespace: topic subset: topics ! alt_id: EDAM_topic:0125 def: "Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org] xref: BioCatalogue:Protein Sequence Analysis is_a: EDAM_topic:0080 ! Sequence analysis is_a: EDAM_topic:0078 ! Protein analysis [Term] id: EDAM_topic:3043 !{since=beta13} name: Protein sequences namespace: topic subset: topics def: "Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] xref: BioCatalogue:Protein Sequence Analysis is_a: EDAM_topic:3041 ! Sequence databases is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0640 name: Nucleic acid sequence analysis namespace: topic subset: topics ! alt_id: EDAM_topic:0096 def: "Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org] xref: BioCatalogue:Nucleotide Sequence Analysis is_a: EDAM_topic:0080 ! Sequence analysis is_a: EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_topic:3042 !{since=beta13} name: Nucleic acid sequences namespace: topic subset: topics def: "Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0641 name: Repeat sequences namespace: topic subset: topics ! alt_id: EDAM_topic:2262 def: "Topic concerning the repetitive nature of molecular sequences." [http://edamontology.org] synonym: "Repeat sequence" EXACT [http://edamontology.org] xref: BioCatalogue:Repeats is_a: EDAM_topic:0157 ! Sequence composition analysis is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0642 name: Low complexity sequences namespace: topic subset: topics ! alt_id: EDAM_topic:2263 def: "Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity." [http://edamontology.org] is_a: EDAM_topic:0157 ! Sequence composition analysis is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0644 name: Proteome namespace: topic subset: topics def: "Topic concerning a specific proteome including protein sequences and annotation." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:0080 ! Sequence analysis ! [Term] ! id: EDAM:0000646 ! name: BLAST ! namespace: resources ! def: "A BLAST-format database of sequences." [http://edamontology.org] ! is_obsolete: true !{since=beta12orEarlier} ! consider: EDAM_topic:3041 ! Sequence database [Term] id: EDAM_topic:0654 name: DNA namespace: topic subset: topics ! alt_id: EDAM_topic:0098 ! alt_id: EDAM_topic:0666 ! alt_id: EDAM_topic:0627 ! alt_id: EDAM_topic:0628 def: "Topic concerning DNA sequences and structure, including processes such as methylation and replication." [http://edamontology.org] comment: The DNA sequences might be coding or non-coding sequences. synonym: "DNA analysis" EXACT [http://edamontology.org] is_a: EDAM_topic:3042 ! Nucleic acid sequences is_a: EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_topic:3176 name: DNA packaging namespace: topic subset: topics def: "Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures." [http://edamontology.org] is_a: EDAM_topic:0654 ! DNA is_a: EDAM_topic:0624 ! Chromosomes [Term] id: EDAM_topic:3171 !{since=1.1} name: DNA methylation namespace: topic subset: topics def: "Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc." [http://edamontology.org] is_a: EDAM_topic:0654 ! DNA [Term] id: EDAM_topic:0655 name: mRNA, EST or cDNA database namespace: topic subset: topics ! alt_id: EDAM_topic:0205 def: "Topic concerning data resources for messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [http://edamontology.org] synonym: "Transcriptome" EXACT [http://edamontology.org] synonym: "Transcriptome database" EXACT [http://edamontology.org] synonym: "mRNA, EST or cDNA" EXACT [http://edamontology.org] is_a: EDAM_topic:0099 ! RNA [Term] id: EDAM_topic:0659 name: Functional and non-coding RNA namespace: topic subset: topics ! alt_id: EDAM_topic:0113 ! alt_id: EDAM_topic:0119 ! alt_id: EDAM_topic:0664 ! alt_id: EDAM_topic:0665 ! alt_id: EDAM_topic:0120 def: "Topic concerning functional or non-coding RNA sequences." [http://edamontology.org] comment: For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). synonym: "Non-coding RNA" EXACT [http://edamontology.org] synonym: "Functional RNA" EXACT [http://edamontology.org] is_a: EDAM_topic:0099 ! RNA [Term] id: EDAM_topic:3060 !{since=beta13} name: Regulatory RNA namespace: topic subset: topics ! alt_id: EDAM_topic:0661 ! alt_id: EDAM_topic:0662 ! alt_id: EDAM_topic:0117 ! alt_id: EDAM_topic:0118 def: "Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA)." [http://edamontology.org] comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] id: EDAM_topic:0660 name: rRNA namespace: topic subset: topics ! alt_id: EDAM_topic:0116 def: "Topic concerning one or more ribosomal RNA (rRNA) sequences." [http://edamontology.org] is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] id: EDAM_topic:0663 name: tRNA namespace: topic subset: topics ! alt_id: EDAM_topic:0115 def: "Topic concerning one or more transfer RNA (tRNA) sequences." [http://edamontology.org] is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] id: EDAM_topic:2814 name: Protein structure analysis namespace: topic subset: topics ! alt_id: EDAM_topic:0126 ! alt_id: EDAM_topic:0590 alt_id: EDAM_topic:3040 !{since=beta13} def: "Topic concerning protein secondary or tertiary structural data and/or associated annotation." [http://edamontology.org] synonym: "Protein structure" EXACT [http://edamontology.org] is_a: EDAM_topic:0078 ! Protein analysis is_a: EDAM_topic:0081 ! Structure analysis is_a: EDAM_topic:3038 ! Structure databases is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0694 name: Protein secondary structure namespace: topic subset: topics ! alt_id: EDAM_topic:2124 def: "Topic concerning protein secondary structure or secondary structure alignments." [http://edamontology.org] comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. synonym: "Protein secondary structure analysis" EXACT [http://edamontology.org] is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0698 name: Protein tertiary structure namespace: topic subset: topics ! alt_id: EDAM_topic:2125 def: "Topic concerning protein tertiary structures." [http://edamontology.org] synonym: "Protein tertiary structure analysis" EXACT [http://edamontology.org] is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0697 name: RNA structure and alignment namespace: topic subset: topics def: "Topic concerning RNA secondary or tertiary structure and alignments." [http://edamontology.org] synonym: "RNA structure" EXACT [http://edamontology.org] synonym: "RNA structure alignment" EXACT [http://edamontology.org] synonym: "RNA alignment" EXACT [http://edamontology.org] is_a: EDAM_topic:0183 ! Structure alignment [Term] id: EDAM_topic:2826 name: Protein structure alignment namespace: topic subset: topics def: "Topic concerning protein secondary or tertiary structure alignments." [http://edamontology.org] is_a: EDAM_topic:0183 ! Structure alignment is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0620 name: Drugs and targets namespace: topic subset: topics def: "Topic concerning the structures of drugs, drug target, their interactions and binding affinities." [http://edamontology.org] is_a: EDAM_topic:0154 ! Small molecules is_a: EDAM_topic:0202 ! Pharmacoinformatics [Term] id: EDAM_topic:0618 name: Scents namespace: topic subset: topics def: "A database about scents." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:0154 ! Small molecules [Term] id: EDAM_topic:0722 name: Nucleic acid classification namespace: topic subset: topics def: "Topic concerning nucleic acid classification (typically sequence classification)." [http://edamontology.org] is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification is_a: EDAM_topic:0077 ! Nucleic acid analysis is_a: EDAM_topic:0594 ! Sequence classification ! [Term] ! id: EDAM:0000723 ! name: Protein structure classification ! namespace: resources ! def: "Topic concerning protein structural classifications." [http://edamontology.org] ! is_obsolete: true !{since=beta12orEarlier} ! consider: EDAM_topic:1770 ! Structure comparison ! consider: EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_topic:0724 name: Protein families namespace: topic subset: topics def: "Topic concerning primarily proteins that have been classified as members of a protein family (or other grouping)." [http://edamontology.org] comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. synonym: "Protein sequence classification" EXACT [http://edamontology.org] synonym: "Protein secondary" EXACT [http://edamontology.org] is_a: EDAM_topic:3052 ! Sequence clusters and classification is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0736 name: Protein domains and folds namespace: topic subset: topics ! alt_id: EDAM_topic:0703 ! alt_id: EDAM_topic:0700 ! alt_id: EDAM_topic:0127 def: "Topic concerning protein tertiary structural domains and folds." [http://edamontology.org] xref: BioCatalogue:Domains is_a: EDAM_topic:0698 ! Protein tertiary structure is_a: EDAM_topic:0724 ! Protein families [Term] id: EDAM_topic:0740 name: Nucleic acid sequence alignment namespace: topic subset: topics def: "Topic concerning nucleotide sequence alignments." [http://edamontology.org] is_a: EDAM_topic:0182 ! Sequence alignment is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0741 name: Protein sequence alignment namespace: topic subset: topics def: "Topic concerning protein sequence alignments." [http://edamontology.org] comment: A sequence profile typically represents a sequence alignment. is_a: EDAM_topic:0182 ! Sequence alignment is_a: EDAM_topic:0639 ! Protein sequence analysis ! [Term] ! id: EDAM:0000742 ! name: Sequence motif or profile (nucleotide) ! namespace: resources ! def: "Topic concerning nucleotide sequence motifs, or sequence profiles derived from an nucleic acid sequence alignment." [http://edamontology.org] ! is_obsolete: true !{since=beta12orEarlier} ! consider: EDAM_topic:0158 ! Sequence motifs ! [Term] ! id: EDAM:0000743 ! name: Sequence motif or profile (protein) ! namespace: resources ! def: "Topic concerning protein sequence motifs, or sequence profiles derived from an protein sequence alignment." [http://edamontology.org] ! is_obsolete: true !{since=beta12orEarlier} ! consider: EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_topic:0747 name: Nucleic acid sites and features namespace: topic subset: topics ! alt_id: EDAM_topic:0105 ! alt_id: EDAM_topic:0095 def: "Topic concerning positional features such as functional sites in nucleotide sequences." [http://edamontology.org] synonym: "Nucleic acid functional sites" EXACT [http://edamontology.org] synonym: "Nucleic acid features" EXACT [http://edamontology.org] is_a: EDAM_topic:0160 ! Sequence sites and features is_a: EDAM_topic:3042 ! Nucleic acid sequences [Term] id: EDAM_topic:3073 !{since=beta13} name: Nucleic acid feature detection namespace: topic subset: topics def: "Topic concerning the detection of positional features such as functional sites in nucleotide sequences." [http://edamontology.org] is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis is_a: EDAM_topic:3072 ! Sequence feature detection [Term] id: EDAM_topic:0748 name: Protein sites and features namespace: topic subset: topics ! alt_id: EDAM_topic:0124 ! alt_id: EDAM_topic:0138 def: "Topic concerning positional features such as functional sites in protein sequences." [http://edamontology.org] synonym: "Protein functional sites" EXACT [http://edamontology.org] synonym: "Protein sequence features" EXACT [http://edamontology.org] is_a: EDAM_topic:0160 ! Sequence sites and features is_a: EDAM_topic:3043 ! Protein sequences [Term] id: EDAM_topic:3074 !{since=beta13} name: Protein feature detection namespace: topic subset: topics def: "Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites." [http://edamontology.org] is_a: EDAM_topic:0639 ! Protein sequence analysis is_a: EDAM_topic:3072 ! Sequence feature detection [Term] id: EDAM_topic:0749 name: Transcription factors and regulatory sites namespace: topic subset: topics ! alt_id: EDAM_topic:0811 def: "Topic concerning transcription factors; proteins that bind to DNA and control transcription of DNA to mRNA, either promoting (as an activator) or blocking (as a repressor) the binding to DNA of RNA polymerase, and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences." [http://edamontology.org] comment: This includes promoters, enhancers, silencers and boundary elements / insulators. This includes sequence and structural information, binding profiles etc, and may also include the transcription factor binding site in DNA. synonym: "Transcriptional regulatory sites" EXACT [http://edamontology.org] synonym: "Transcription factors" EXACT [http://edamontology.org] synonym: "Transcription factor and binding site" EXACT [http://edamontology.org] is_a: EDAM_topic:0204 ! Gene regulation is_a: EDAM_topic:0110 ! Transcription is_a: EDAM_topic:0635 ! Specific protein resources is_a: EDAM_topic:0747 ! Nucleic acid sites and features is_a: EDAM_topic:3062 ! Genetic organisation is_a: EDAM_topic:3073 ! Nucleic acid feature detection [Term] id: EDAM_topic:0751 name: Phosphorylation sites namespace: topic subset: topics def: "Topic concerning protein phosphorylation and phosphorylation sites in protein sequences." [http://edamontology.org] ! is_a: EDAM_topic:0601 ! Protein modifications ! is_a: EDAM_topic:0748 ! Protein sites and features is_obsolete: true !{since=1.0} consider: EDAM_topic:0601 ! Protein modifications consider: EDAM_topic:0748 ! Protein sites and features [Term] id: EDAM_topic:0753 name: Metabolic pathways namespace: topic subset: topics def: "Topic concerning metabolic pathways." [http://edamontology.org] is_a: EDAM_topic:0602 ! Pathways, networks and models is_a: EDAM_topic:3172 ! Metabolomics [Term] id: EDAM_topic:0754 name: Signaling pathways namespace: topic subset: topics def: "Topic concerning signaling pathways." [http://edamontology.org] is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_topic:3044 !{since=beta13} name: Protein interaction networks namespace: topic subset: topics def: "Topic concerning protein-protein interaction networks." [http://edamontology.org] is_a: EDAM_topic:0602 ! Pathways, networks and models is_a: EDAM_topic:0147 ! Protein-protein interactions [Term] id: EDAM_topic:0771 name: Biological models namespace: topic subset: topics ! alt_id: EDAM_topic:2267 ! alt_id: EDAM_topic:2268 def: "Topic concerning mathematical or other models of biological processes." [http://edamontology.org] comment: This includes databases of models and methods to construct or analyse a model. xref: BioCatalogue:Model Creation is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_topic:2846 name: Gene regulatory networks namespace: topic subset: topics def: "Topic concerning gene regulatory networks." [http://edamontology.org] is_a: EDAM_topic:0602 ! Pathways, networks and models is_a: EDAM_topic:0204 ! Gene regulation [Term] id: EDAM_topic:0767 name: Protein and peptide identification namespace: topic subset: topics ! alt_id: EDAM_topic:0603 def: "Topic concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays." [http://edamontology.org] comment: This includes the results of any methods that separate, characterize and identify expressed proteins. synonym: "Peptide identification and proteolysis" EXACT [http://edamontology.org] synonym: "Proteomics data" EXACT [http://edamontology.org] synonym: "Proteomics data resources" EXACT [http://edamontology.org] is_a: EDAM_topic:0121 ! Proteomics is_a: EDAM_topic:0639 ! Protein sequence analysis is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0141 name: Protein cleavage sites and proteolysis namespace: topic subset: topics def: "Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence." [http://edamontology.org] is_a: EDAM_topic:0639 ! Protein sequence analysis [Term] id: EDAM_topic:0769 name: Workflows namespace: topic subset: topics def: "Topic concerning biological or biomedical analytical workflows or pipelines." [http://edamontology.org] ! is_a: EDAM_topic:0091 ! Data handling is_obsolete: true !{since=1.0} ! consider: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0220 name: Data processing and validation namespace: topic subset: topics ! alt_id: EDAM_topic:2286 ! alt_id: EDAM_topic:2270 ! alt_id: EDAM_topic:2834 def: "Topic concerning basic manipulations of files or reports of generic biological data." [http://edamontology.org] comment: This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. synonym: "Report handling" EXACT [http://edamontology.org] synonym: "File handling" EXACT [http://edamontology.org] synonym: "Data file handling" EXACT [http://edamontology.org] synonym: "Report processing" EXACT [http://edamontology.org] is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0770 name: Data types and objects namespace: topic subset: topics def: "Topic concerning structuring data into basic types and (computational) objects." [http://edamontology.org] ! is_a: EDAM_topic:0091 ! Data handling is_obsolete: true !{since=1.0} consider: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0632 name: Probes and primers namespace: topic subset: topics ! alt_id: EDAM_topic:0207 def: "Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR)." [http://edamontology.org] is_a: EDAM_topic:0607 ! Laboratory resources is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:3032 !{since=beta13} name: Primer or probe design namespace: topic subset: topics def: "Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes." [http://edamontology.org] is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0779 name: Mitochondrial genes and proteins namespace: topic subset: topics def: "Topic concerning mitochondria, typically of mitochondrial genes and proteins." [http://edamontology.org] synonym: "Mitochondria genes and proteins" EXACT [http://edamontology.org] is_a: EDAM_topic:0616 ! Organelle genes and proteins [Term] id: EDAM_topic:2818 name: Eukaryotes namespace: topic subset: topics ! alt_id: EDAM_topic:0669 def: "Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. synonym: "Eukaryote" EXACT [http://edamontology.org] is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:2821 name: Unicellular eukaryotes namespace: topic subset: topics ! alt_id: EDAM_topic:0675 def: "Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. synonym: "Unicellular eukaryote" EXACT [http://edamontology.org] is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:2819 name: Invertebrates namespace: topic subset: topics ! alt_id: EDAM_topic:0678 def: "Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:2820 name: Vertebrates namespace: topic subset: topics ! alt_id: EDAM_topic:0679 def: "Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. synonym: "Vertebrate" EXACT [http://edamontology.org] is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:2815 name: Humans namespace: topic subset: topics ! alt_id: EDAM_topic:0692 ! alt_id: EDAM_topic:0687 def: "Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general." [http://edamontology.org] comment: The resource may be specific to a human, a group of humans or all humans. synonym: "Human" EXACT [http://edamontology.org] is_a: EDAM_topic:3048 ! Mammals [Term] id: EDAM_topic:0780 name: Plants namespace: topic subset: topics ! alt_id: EDAM_topic:0677 ! alt_id: EDAM_topic:0785 ! alt_id: EDAM_topic:0784 ! alt_id: EDAM_topic:0214 def: "Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a plant, a group of plants or all plants. synonym: "Plant" EXACT [http://edamontology.org] is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:0781 name: Viruses namespace: topic subset: topics ! alt_id: EDAM_topic:0790 ! alt_id: EDAM_topic:0671 ! alt_id: EDAM_topic:0791 def: "Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a virus, a group of viruses or all viruses. synonym: "Virus" EXACT [http://edamontology.org] is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:0782 name: Fungi namespace: topic subset: topics ! alt_id: EDAM_topic:0792 ! alt_id: EDAM_topic:0793 ! alt_id: EDAM_topic:0676 def: "Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a fungus, a group of fungi or all fungi. synonym: "Fungal" EXACT [http://edamontology.org] is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:0783 name: Pathogens namespace: topic subset: topics def: "Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a pathogen, a group of pathogens or all pathogens. synonym: "Pathogen" EXACT [http://edamontology.org] is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:1811 name: Prokaryotes and archae namespace: topic subset: topics ! alt_id: EDAM_topic:0691 ! alt_id: EDAM_topic:0670 ! alt_id: EDAM_topic:0212 def: "Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] comment: The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. synonym: "Prokaryote and archae" EXACT [http://edamontology.org] is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:0786 name: Arabidopsis namespace: topic subset: topics def: "Topic concerning Arabidopsis-specific data." [http://edamontology.org] is_a: EDAM_topic:0780 ! Plants [Term] id: EDAM_topic:0787 name: Rice namespace: topic subset: topics def: "Topic concerning rice-specific data." [http://edamontology.org] is_a: EDAM_topic:0780 ! Plants [Term] id: EDAM_topic:2817 name: Yeast namespace: topic subset: topics ! alt_id: EDAM_topic:0682 ! alt_id: EDAM_topic:0216 def: "Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." [http://edamontology.org] is_a: EDAM_topic:0782 ! Fungi [Term] id: EDAM_topic:0796 name: Genetic mapping and linkage namespace: topic subset: topics ! alt_id: EDAM_topic:0103 def: "Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny." [http://edamontology.org] synonym: "Genetic linkage" EXACT [http://edamontology.org] synonym: "Linkage mapping" EXACT [http://edamontology.org] is_a: EDAM_topic:0102 ! Mapping relationship: has_topic EDAM_topic:3053 ! Genetics [Term] id: EDAM_topic:0797 name: Comparative genomics namespace: topic subset: topics ! alt_id: EDAM_topic:0101 def: "Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes." [http://edamontology.org] xref: BioCatalogue:Comparative Genomics is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:0798 name: Mobile genetic elements namespace: topic subset: topics def: "Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [http://edamontology.org] is_a: EDAM_topic:3062 ! Genetic organisation ! [Term] ! id: EDAM_topic:0801 ! name: Human genes ! namespace: resources ! def: "Topic concerning human genes." [http://edamontology.org] ! is_obsolete: true !{since=beta12orEarlier} ! consider: EDAM_topic:0623 ! Genes, gene family or system [Term] id: EDAM_topic:0803 name: Human disease namespace: topic subset: topics def: "Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_topic:0634 ! Disease resources [Term] id: EDAM_topic:0804 name: Immunoinformatics namespace: topic subset: topics ! alt_id: EDAM_topic:0201 ! alt_id: EDAM_topic:0633 def: "Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." [http://edamontology.org] synonym: "Computational immunology" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2830 name: Immunity genes, immunoproteins and antigens namespace: topic subset: topics def: "Topic concerning immunity-related genes, proteins and their ligands." [http://edamontology.org] comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." synonym: "Immunoproteins and immunopeptides" EXACT [http://edamontology.org] is_a: EDAM_topic:0804 ! Immunoinformatics is_a: EDAM_topic:3078 ! Gene and protein resources [Term] id: EDAM_topic:2847 name: Disease (specific) namespace: topic subset: topics def: "Informatics resources dedicated to one or more specific diseases (not diseases in general)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_topic:0634 ! Disease resources [Term] id: EDAM_topic:2640 name: Cancer namespace: topic subset: topics ! alt_id: EDAM_topic:0805 def: "Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer." [http://edamontology.org] synonym: "Cancer resources" EXACT [http://edamontology.org] is_a: EDAM_topic:0634 ! Disease resources [Term] id: EDAM_topic:0820 name: Membrane proteins namespace: topic subset: topics ! alt_id: EDAM_topic:0131 def: "Topic concerning a protein or region of a protein that spans a membrane." [http://edamontology.org] synonym: "Transmembrane proteins" EXACT [http://edamontology.org] is_a: EDAM_topic:0635 ! Specific protein resources [Term] id: EDAM_topic:0821 name: Enzymes and reactions namespace: topic subset: topics ! alt_id: EDAM_topic:0132 def: "Topic concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." [http://edamontology.org] is_a: EDAM_topic:0635 ! Specific protein resources !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! ! Operation ! [Term] id: EDAM_operation:2945 name: Analysis namespace: operation subset: operations def: "Apply analytical methods to existing data of a specific type." [http://edamontology.org] comment: For non-analytical operations, see the 'Processing' branch. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2420 name: Analysis and processing namespace: operation subset: operations def: "Process (read and / or write) data of a specific type, for example applying analytical methods." [http://edamontology.org] synonym: "Calculation" EXACT [http://edamontology.org] synonym: "Computation" EXACT [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation relationship: has_input EDAM_data:0006 !{min_cardinality=0} ! Data relationship: has_output EDAM_data:0006 !{min_cardinality=0} ! Data [Term] id: EDAM_operation:2423 name: Prediction, detection and recognition namespace: operation subset: operations def: "Predict, recognise, detect or identify some properties of a biomolecule." [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:3023 name: Prediction, detection and recognition (protein) namespace: operation subset: operations def: "Predict, recognise, detect or identify some properties of proteins." [http://edamontology.org] is_a: EDAM_operation:2423 ! Prediction, detection and recognition [Term] id: EDAM_operation:3024 name: Prediction, detection and recognition (nucleic acid) namespace: operation subset: operations def: "Predict, recognise, detect or identify some properties of nucleic acids." [http://edamontology.org] is_a: EDAM_operation:2423 ! Prediction, detection and recognition [Term] id: EDAM_operation:2946 name: Alignment analysis namespace: operation subset: operations def: "Analyse an existing alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] is_a: EDAM_operation:2951 ! Alignment processing relationship: has_input EDAM_data:1916 !{min_cardinality=1} ! Alignment ! Extends cardinality constraint on parent. relationship: has_output EDAM_data:2083 !{min_cardinality=1} ! Alignment report [Term] id: EDAM_operation:2947 name: Article analysis namespace: operation subset: operations def: "Analyse a body of scientific text (typically a full text article from a scientific journal.)" [http://edamontology.org] is_a: EDAM_operation:2505 ! Text processing relationship: has_input EDAM_data:0971 !{min_cardinality=1} ! Article relationship: has_output EDAM_data:2954 ! Article report relationship: has_topic EDAM_topic:0217 ! Literature analysis [Term] id: EDAM_operation:2993 name: Molecular interaction data processing namespace: operation subset: operations def: "Process (read and / or write) molecular interaction data." [http://edamontology.org] is_obsolete: true !{since=beta13} [Term] id: EDAM_operation:2948 name: Molecular interaction analysis namespace: operation subset: operations def: "Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact." [http://edamontology.org] is_obsolete: true !{since=beta13} [Term] id: EDAM_operation:2949 name: Protein interaction analysis namespace: operation subset: operations def: "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." [http://edamontology.org] is_a: EDAM_operation:2405 ! Protein interaction data processing relationship: has_output EDAM_data:0906 !{min_cardinality=1} ! Protein interaction relationship: has_topic EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_operation:3096 !{since=beta13} name: Editing namespace: operation subset: operations def: "Edit, convert or otherwise change a data entity, either randomly or specifically." [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2928 name: Alignment construction namespace: operation subset: operations def: "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." [http://edamontology.org] synonym: "Alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:2951 ! Alignment processing relationship: has_output EDAM_data:1916 !{min_cardinality=1} ! Alignment [Term] id: EDAM_operation:2424 name: Comparison namespace: operation subset: operations def: "Compare two or more things to identify similarities." [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2997 name: Protein comparison namespace: operation subset: operations def: "Compare two or more proteins (or some aspect) to identify similarities." [http://edamontology.org] is_a: EDAM_operation:2424 ! Comparison [Term] id: EDAM_operation:2998 name: Nucleic acid comparison namespace: operation subset: operations def: "Compare two or more nucleic acids to identify similarities." [http://edamontology.org] is_a: EDAM_operation:2424 ! Comparison [Term] id: EDAM_operation:2990 name: Classification namespace: operation subset: operations def: "Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category." [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation relationship: has_output EDAM_data:2987 !{min_cardinality=1} ! Classification [Term] id: EDAM_operation:2995 name: Sequence classification namespace: operation subset: operations def: "Assign molecular sequence(s) to a group or category." [http://edamontology.org] is_a: EDAM_operation:2990 ! Classification is_a: EDAM_operation:2403 ! Sequence analysis [Term] id: EDAM_operation:3093 !{since=beta13} name: Sequence screening namespace: operation subset: operations def: "Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries." [http://edamontology.org] is_a: EDAM_operation:2995 ! Sequence classification [Term] id: EDAM_operation:2996 name: Structure classification namespace: operation subset: operations def: "Assign molecular structure(s) to a group or category." [http://edamontology.org] is_a: EDAM_operation:2990 ! Classification is_a: EDAM_operation:2480 ! Structure analysis [Term] id: EDAM_operation:2425 name: Optimisation and refinement namespace: operation subset: operations def: "Refine or optimise some data model." [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2426 name: Modelling and simulation namespace: operation subset: operations def: "Model or simulate some biological entity or system." [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation relationship: has_topic EDAM_topic:2275 ! Molecular modelling [Term] id: EDAM_operation:2427 name: Data handling namespace: operation subset: operations def: "Perform basic operations on some data or a database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2428 name: Evaluation and validation namespace: operation subset: operations def: "Validate or standardise some data." [http://edamontology.org] synonym: "Validation and standardisation" EXACT [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2429 name: Mapping and assembly namespace: operation subset: operations def: "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." [http://edamontology.org] comment: This is a broad concept and is used a placeholder for other, more specific concepts. is_a: EDAM_operation:0004 ! Operation relationship: has_topic EDAM_topic:0102 ! Mapping relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] id: EDAM_operation:2430 name: Design namespace: operation subset: operations def: "Design a biological entity (typically a molecular sequence or structure) with specific properties." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) [Term] id: EDAM_operation:2238 name: Statistical calculation namespace: operation subset: operations def: "Perform a statistical data operation of some type, e.g. calibration or validation." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:0224 name: Search and retrieval namespace: operation subset: operations def: "Search or query a data resource and retrieve entries and / or annotation." [http://edamontology.org] synonym: "Database retrieval" EXACT [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation relationship: has_output EDAM_data:0006 !{min_cardinality=0} ! Data relationship: has_topic EDAM_topic:0090 ! Data search and retrieval [Term] id: EDAM_operation:2501 name: Nucleic acid data processing namespace: operation subset: operations def: "Process (read and / or write) nucleic acid sequence or structural data." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:2084 !{min_cardinality=0} ! Nucleic acid report relationship: has_output EDAM_data:2084 !{min_cardinality=0} ! Nucleic acid report relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_operation:2502 name: Protein data processing namespace: operation subset: operations def: "Process (read and / or write) protein sequence or structural data." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:0896 !{min_cardinality=0} ! Protein report relationship: has_output EDAM_data:0896 !{min_cardinality=0} ! Protein report relationship: has_topic EDAM_topic:0078 ! Protein analysis [Term] id: EDAM_operation:2407 name: Annotation processing namespace: operation subset: operations def: "Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2951 name: Alignment processing namespace: operation subset: operations def: "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:1916 !{min_cardinality=0} ! Alignment relationship: has_output EDAM_data:1916 !{min_cardinality=0} ! Alignment [Term] id: EDAM_operation:2412 name: Data index processing namespace: operation subset: operations def: "Process (read and / or write) an index of (typically a file of) biological data." [http://edamontology.org] synonym: "Database index processing" EXACT [http://edamontology.org] is_a: EDAM_operation:2409 ! File processing relationship: has_input EDAM_data:0955 !{min_cardinality=0} ! Data index relationship: has_output EDAM_data:0955 !{min_cardinality=0} ! Data index relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] id: EDAM_operation:2504 name: Structural data processing namespace: operation subset: operations def: "Process (read and / or write) molecular structural data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2465 ! Structure processing [Term] id: EDAM_operation:2403 name: Sequence analysis namespace: operation subset: operations ! alt_id: EDAM_operation:2477 def: "Analyse one or more known molecular sequences." [http://edamontology.org] synonym: "Sequence analysis (general)" EXACT [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 !{min_cardinality=1} ! Sequence relationship: has_output EDAM_data:2955 !{min_cardinality=1} ! Sequence report relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_operation:2408 name: Sequence feature analysis namespace: operation subset: operations def: "Analyse features in molecular sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0253 ! Feature prediction [Term] id: EDAM_operation:2404 name: Sequence motif processing namespace: operation subset: operations def: "Process (read and / or write) molecular sequence motifs." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:1353 !{min_cardinality=0} ! Sequence motif relationship: has_output EDAM_data:1353 !{min_cardinality=0} ! Sequence motif relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_operation:2417 name: Physicochemical property data processing namespace: operation subset: operations def: "Process (read and / or write) data on the physicochemical property of a molecule." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2414 name: Protein function analysis namespace: operation subset: operations def: "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." [http://edamontology.org] comment: This is a broad concept and is used a placeholder for other, more specific concepts. is_a: EDAM_operation:2502 ! Protein data processing relationship: has_output EDAM_data:0896 ! Protein report [Term] id: EDAM_operation:0258 name: Sequence alignment analysis namespace: operation subset: operations def: "Analyse a molecular sequence alignment." [http://edamontology.org] is_a: EDAM_operation:2463 ! Sequence alignment processing is_a: EDAM_operation:2946 ! Alignment analysis relationship: has_input EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment ! Extends cardinality constraint on parent. relationship: has_output EDAM_data:0867 !{min_cardinality=1} ! Sequence alignment report relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:2506 name: Sequence alignment analysis (protein) namespace: operation subset: operations def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org] is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2502 ! Protein data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_input EDAM_data:1384 !{min_cardinality=1} ! Sequence alignment (protein) relationship: has_topic EDAM_topic:0741 ! Protein sequence alignment [Term] id: EDAM_operation:2507 name: Sequence alignment analysis (nucleic acid) namespace: operation subset: operations def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org] is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2501 ! Nucleic acid data processing is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_input EDAM_data:1383 !{min_cardinality=1} ! Sequence alignment (nucleic acid) relationship: has_topic EDAM_topic:0740 ! Nucleic acid sequence alignment [Term] id: EDAM_operation:2416 name: Protein secondary structure analysis namespace: operation subset: operations def: "Analyse known protein secondary structure data." [http://edamontology.org] is_a: EDAM_operation:2444 ! Protein secondary structure processing synonym: "Secondary structure analysis (protein)" EXACT [http://edamontology.org] relationship: has_input EDAM_data:0876 !{min_cardinality=1} ! Protein features (secondary structure) relationship: has_output EDAM_data:2956 ! Protein secondary structure report relationship: has_topic EDAM_topic:0694 ! Protein secondary structure [Term] id: EDAM_operation:0270 name: Transmembrane protein analysis namespace: operation subset: operations def: "Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions." [http://edamontology.org] comment: Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). is_a: EDAM_operation:2502 ! Protein data processing relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) relationship: has_topic EDAM_topic:0820 ! Membrane proteins [Term] id: EDAM_operation:2476 name: Molecular dynamics simulation namespace: operation subset: operations def: "Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org] is_a: EDAM_operation:2423 ! Prediction, detection and recognition is_a: EDAM_operation:2480 ! Structure analysis is_a: EDAM_operation:2426 ! Modelling and simulation relationship: has_output EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0082 ! Structure prediction relationship: has_topic EDAM_topic:0176 ! Molecular dynamics [Term] id: EDAM_operation:0271 name: Structure prediction namespace: operation subset: operations def: "Predict tertiary structure of a molecular (biopolymer) sequence." [http://edamontology.org] is_a: EDAM_operation:2423 ! Prediction, detection and recognition is_a: EDAM_operation:2465 ! Structure processing relationship: has_output EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0082 ! Structure prediction [Term] id: EDAM_operation:2405 name: Protein interaction data processing namespace: operation subset: operations def: "Process (read and / or write) protein interaction data." [http://edamontology.org] is_a: EDAM_operation:2502 ! Protein data processing relationship: has_input EDAM_data:0906 !{min_cardinality=0} ! Protein interaction relationship: has_output EDAM_data:0906 !{min_cardinality=0} ! Protein interaction relationship: has_topic EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_operation:2521 name: Map data processing namespace: operation subset: operations def: "Process (read and / or write) a DNA map of some type." [http://edamontology.org] synonym: "DNA map data processing" EXACT [http://edamontology.org] is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_input EDAM_data:1274 !{min_cardinality=0} ! Map relationship: has_output EDAM_data:1274 !{min_cardinality=0} ! Map relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] id: EDAM_operation:3229 !{since=1.1} name: Exome analysis namespace: operation subset: operations def: "Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome." [http://edamontology.org] comment: Exome sequencing is considered a cheap alternative to whole genome sequencing. synonym: "Exome sequence analysis" EXACT [http://edamontology.org] synonym: "Targeted exome capture" EXACT [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3230 !{since=1.1} name: Read depth analysis namespace: operation subset: operations def: "Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications." [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3225 !{since=1.1} name: Variant classification namespace: operation subset: operations def: "Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins." [http://edamontology.org] comment: Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:2995 ! Sequence classification [Term] id: EDAM_operation:3226 !{since=1.1} name: Variant prioritization namespace: operation subset: operations def: "Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes." [http://edamontology.org] comment: Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3221 !{since=1.1} name: Species frequency estimation namespace: operation subset: operations def: "Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples." [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_topic EDAM_topic:3174 ! Metagenomics [Term] id: EDAM_operation:3216 !{since=1.1} name: Scaffolding namespace: operation subset: operations def: "Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps." [http://edamontology.org] comment: Scaffold may be positioned along a chromosome physical map to create a "golden path". synonym: "Scaffold construction" EXACT [http://edamontology.org] is_a: EDAM_operation:2429 ! Mapping and assembly is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3217 !{since=1.1} name: Scaffold gap completion namespace: operation subset: operations def: "Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences." [http://edamontology.org] comment: Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. is_a: EDAM_operation:2429 ! Mapping and assembly is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3218 !{since=1.1} name: Sequencing quality control namespace: operation subset: operations def: "Raw sequence data quality control." [http://edamontology.org] synonym: "Sequencing QC" EXACT [http://edamontology.org] synonym: "Analyse raw sequence data from a sequencing pipeline and identify problems." EXACT [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:2428 ! Evaluation and validation [Term] id: EDAM_operation:2520 name: DNA mapping namespace: operation subset: operations def: "Generate a map of a DNA sequence annotated with positional or non-positional features of some type." [http://edamontology.org] is_a: EDAM_operation:2521 ! Map data processing is_a: EDAM_operation:2429 ! Mapping and assembly relationship: has_output EDAM_data:1274 !{min_cardinality=1} ! Map relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] id: EDAM_operation:0282 name: Genetic mapping namespace: operation subset: operations def: "Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances." [http://edamontology.org] comment: Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. synonym: "Genetic map generation" EXACT [http://edamontology.org] synonym: "Linkage mapping" EXACT [http://edamontology.org] is_a: EDAM_operation:2520 ! DNA mapping relationship: has_output EDAM_data:1278 !{min_cardinality=1} ! Genetic map relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] id: EDAM_operation:2944 name: Physical mapping namespace: operation subset: operations def: "Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers." [http://edamontology.org] is_a: EDAM_operation:2520 ! DNA mapping relationship: has_output EDAM_data:1280 !{min_cardinality=1} ! Physical map relationship: has_topic EDAM_topic:0102 ! Mapping [Term] id: EDAM_operation:2871 name: Sequence tagged site (STS) mapping namespace: operation subset: operations def: "Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS)." [http://edamontology.org] comment: An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. synonym: "Sequence mapping" EXACT [http://edamontology.org] is_a: EDAM_operation:2944 ! Physical mapping relationship: has_output EDAM_data:1279 !{min_cardinality=1} ! Sequence map [Term] id: EDAM_operation:3233 !{since=1.1} name: Copy number estimation namespace: operation subset: operations def: "Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors." [http://edamontology.org] comment: Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). synonym: "Transcript copy number estimation" EXACT [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3219 !{since=1.1} name: Read pre-processing namespace: operation subset: operations def: "Pre-process sequence reads to ensure (or improve) quality and reliability." [http://edamontology.org] comment: This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. synonym: "Sequence read pre-processing" EXACT [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:0283 name: Linkage analysis namespace: operation subset: operations def: "Analyse genetic linkage." [http://edamontology.org] comment: For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_output EDAM_data:0927 ! Gene annotation (linkage) relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] id: EDAM_operation:2493 name: Codon usage data processing namespace: operation subset: operations def: "Process (read and / or write) codon usage data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:0286 ! Codon usage analysis [Term] id: EDAM_operation:2503 name: Sequence data processing namespace: operation subset: operations def: "Process (read and / or write) molecular sequence data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2446 ! Sequence processing [Term] id: EDAM_operation:2463 name: Sequence alignment processing namespace: operation subset: operations def: "Process (read and / or write) a molecular sequence alignment." [http://edamontology.org] is_a: EDAM_operation:2951 ! Alignment processing relationship: has_input EDAM_data:0863 !{min_cardinality=0} ! Sequence alignment relationship: has_output EDAM_data:0863 !{min_cardinality=0} ! Sequence alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:2952 name: Structure alignment processing namespace: operation subset: operations def: "Process (read and / or write) a molecular tertiary (3D) structure alignment." [http://edamontology.org] is_a: EDAM_operation:2951 ! Alignment processing relationship: has_input EDAM_data:0886 !{min_cardinality=0} ! Structure alignment relationship: has_output EDAM_data:0886 !{min_cardinality=0} ! Structure alignment relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] id: EDAM_operation:0292 name: Sequence alignment construction namespace: operation subset: operations def: "Align (identify equivalent sites within) molecular sequences." [http://edamontology.org] synonym: "Sequence alignment" EXACT [http://edamontology.org] synonym: "Sequence alignment computation" EXACT [http://edamontology.org] synonym: "Sequence alignment generation" EXACT [http://edamontology.org] is_a: EDAM_operation:2463 ! Sequence alignment processing !(?) is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:2044 !{minCardinality=2, note="Applies to both pure/raw sequences and sequence records. Indirectly also to sequence sets or IDs (?)"} ! Sequence relationship: has_output EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:0293 name: Hybrid sequence alignment construction namespace: operation subset: operations def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [http://edamontology.org] synonym: "Hybrid sequence alignment" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:0292 ! Sequence alignment construction [Term] id: EDAM_operation:0294 name: Structure-based sequence alignment construction namespace: operation subset: operations def: "Align molecular sequences using sequence and structural information." [http://edamontology.org] synonym: "Structure-based sequence alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:0292 ! Sequence alignment construction relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:2480 name: Structure analysis namespace: operation subset: operations ! alt_id: EDAM_operation:2431 def: "Analyse known molecular tertiary structures." [http://edamontology.org] is_a: EDAM_operation:2465 ! Structure processing relationship: has_input EDAM_data:0883 !{min_cardinality=1} ! Structure relationship: has_output EDAM_data:2085 !{min_cardinality=1} ! Structure report relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_operation:2931 name: Secondary structure comparison namespace: operation subset: operations def: "Compare two or more molecular secondary structures." [http://edamontology.org] is_a: EDAM_operation:2424 ! Comparison relationship: has_input EDAM_data:2081 !{min_cardinality=2} ! Secondary structure relationship: has_output EDAM_data:2881 !{min_cardinality=1} ! Secondary structure report relationship: has_topic EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_operation:2483 name: Structure comparison namespace: operation subset: operations def: "Compare two or more molecular tertiary structures." [http://edamontology.org] is_a: EDAM_operation:2424 ! Comparison is_a: EDAM_operation:2480 ! Structure analysis relationship: has_topic EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_operation:0295 name: Structure alignment construction namespace: operation subset: operations def: "Align (superimpose) molecular tertiary structures." [http://edamontology.org] synonym: "Structure alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:2928 ! Alignment construction is_a: EDAM_operation:2483 ! Structure comparison is_a: EDAM_operation:2952 ! Structure alignment processing relationship: has_output EDAM_data:0886 !{min_cardinality=1} ! Structure alignment relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] id: EDAM_operation:2413 name: Sequence profile processing namespace: operation subset: operations def: "Process (read and / or write) some type of sequence profile." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:1354 !{min_cardinality=0} ! Sequence profile relationship: has_output EDAM_data:1354 !{min_cardinality=0} ! Sequence profile relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_operation:2411 name: Structural (3D) profile processing namespace: operation subset: operations def: "Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:0889 !{min_cardinality=0} ! Structural (3D) profile relationship: has_output EDAM_data:0889 !{min_cardinality=0} ! Structural (3D) profile relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] id: EDAM_operation:0303 name: Protein fold recognition namespace: operation subset: operations def: "Recognize (predict and identify) known protein structural domains or folds in protein sequence(s)." [http://edamontology.org] comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. synonym: "Protein domain prediction" EXACT [http://edamontology.org] synonym: "Protein fold prediction" EXACT [http://edamontology.org] is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) is_a: EDAM_operation:0474 ! Protein structure prediction is_a: EDAM_operation:2997 ! Protein comparison relationship: has_output EDAM_data:0901 !{min_cardinality=1} ! Protein features (domains) relationship: has_topic EDAM_topic:0184 ! Threading [Term] id: EDAM_operation:2246 name: Demonstration namespace: operation subset: operations def: "An operation performing purely illustrative (pedagogical) purposes." [http://edamontology.org] is_obsolete: true !{since=beta13} [Term] id: EDAM_operation:2505 name: Text processing namespace: operation subset: operations def: "Process (read and / or write) text." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:2048 !{min_cardinality=0} ! Report relationship: has_output EDAM_data:2048 !{min_cardinality=0} ! Report [Term] id: EDAM_operation:0306 name: Text mining namespace: operation subset: operations def: "Process and analyse text (typically the biomedical and informatics literature) to extract information from it." [http://edamontology.org] synonym: "Text data mining" EXACT [http://edamontology.org] is_a: EDAM_operation:2947 ! Article analysis relationship: has_input EDAM_data:2048 !{min_cardinality=0} ! Report relationship: has_output EDAM_data:0972 ! Text mining report relationship: has_topic EDAM_topic:0218 ! Text mining [Term] id: EDAM_operation:2419 name: Primer and probe design namespace: operation subset: operations def: "Predict oligonucleotide primers or probes." [http://edamontology.org] is_a: EDAM_operation:3095 ! Nucleic acid design is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) synonym: "Primer and probe prediction" EXACT [http://edamontology.org] relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] id: EDAM_operation:0310 name: Sequence assembly namespace: operation subset: operations def: "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. is_a: EDAM_operation:2429 ! Mapping and assembly is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_output EDAM_data:0925 ! Sequence assembly relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] id: EDAM_operation:3180 !{since=1.1} name: Sequence assembly evaluation namespace: operation subset: operations def: "Evaluate a DNA sequence assembly, typically for purposes of quality control." [http://edamontology.org] is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_input EDAM_data:0925 ! Sequence assembly relationship: has_output EDAM_data:3181 ! Sequence assembly report relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] id: EDAM_operation:2432 name: Microarray data processing namespace: operation subset: operations def: "Process (read and / or write) microarray data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:2495 name: Gene expression data processing namespace: operation subset: operations def: "Process (read and / or write) gene expression (typically microarray) data." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing synonym: "Gene expression (microarray) data processing" EXACT [http://edamontology.org] synonym: "Microarray data processing" EXACT [http://edamontology.org] relationship: has_input EDAM_data:3117 !{min_cardinality=0} ! Microarray hybridisation data relationship: has_output EDAM_data:3117 !{min_cardinality=0} ! Microarray hybridisation data relationship: has_topic EDAM_topic:0203 ! Transcriptomics relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_operation:2500 name: Microarray raw data analysis namespace: operation subset: operations def: "Analyse raw microarray data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:0311 name: Microarray data standardization and normalization namespace: operation subset: operations def: "Standardize or normalize microarray data." [http://edamontology.org] comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. is_a: EDAM_operation:2495 ! Gene expression data processing is_a: EDAM_operation:2428 ! Evaluation and validation relationship: has_input EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data relationship: has_output EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data [Term] id: EDAM_operation:0318 name: Structural genomics target selection namespace: operation subset: operations def: "Identify and select targets for protein structural determination." [http://edamontology.org] comment: Methods will typically navigate a graph of protein families of known structure. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2406 ! Protein structure analysis [Term] id: EDAM_operation:2406 name: Protein structure analysis namespace: operation subset: operations ! alt_id: EDAM_operation:2458 def: "Analyse protein tertiary structural data." [http://edamontology.org] is_a: EDAM_operation:2480 ! Structure analysis is_a: EDAM_operation:2459 ! Structure processing (protein) synonym: "Structure analysis (protein)" EXACT [http://edamontology.org] relationship: has_input EDAM_data:1460 !{min_cardinality=1} ! Protein structure relationship: has_output EDAM_data:0897 ! Protein property [Term] id: EDAM_operation:2481 name: Nucleic acid structure analysis namespace: operation subset: operations ! alt_id: EDAM_operation:2418 def: "Analyse nucleic acid tertiary structural data." [http://edamontology.org] is_a: EDAM_operation:2480 ! Structure analysis is_a: EDAM_operation:2519 ! Structure processing (nucleic acid) relationship: has_input EDAM_data:1459 !{min_cardinality=1} ! Nucleic acid structure relationship: has_output EDAM_data:0912 !{min_cardinality=1} ! Nucleic acid property [Term] id: EDAM_operation:0324 name: Phylogenetic tree analysis namespace: operation subset: operations def: "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." [http://edamontology.org] is_a: EDAM_operation:2443 ! Phylogenetic tree processing relationship: has_input EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree relationship: has_output EDAM_data:1438 !{min_cardinality=1} ! Phylogenetic tree report [Term] id: EDAM_operation:2438 name: Pathway or network processing namespace: operation subset: operations def: "Generate, analyse or handle a biological pathway or network." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:2600 !{min_cardinality=0} ! Pathway or network relationship: has_output EDAM_data:2600 !{min_cardinality=0} ! Pathway or network relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_operation:3083 !{since=beta13} name: Pathway or network rendering namespace: operation subset: operations def: "Render (visualise) a biological pathway or network." [http://edamontology.org] is_a: EDAM_operation:2438 ! Pathway or network processing is_a: EDAM_operation:0337 ! Plotting and rendering relationship: has_input EDAM_data:2600 !{min_cardinality=1} ! Pathway or network relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_operation:3203 !{since=1.1} name: Chromatogram visualisation namespace: operation subset: operations def: "Visualise, format or render an image of a Chromatogram." [http://edamontology.org] synonym: "Chromatogram viewing" EXACT [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering [Term] id: EDAM_operation:2497 name: Pathway or network analysis namespace: operation subset: operations def: "Analyse a known biological pathway or network." [http://edamontology.org] synonym: "Network analysis" EXACT [http://edamontology.org] synonym: "Pathway analysis" EXACT [http://edamontology.org] is_a: EDAM_operation:2438 ! Pathway or network processing relationship: has_input EDAM_data:2600 !{min_cardinality=1} ! Pathway or network relationship: has_output EDAM_data:2984 !{min_cardinality=1} ! Pathway or network report [Term] id: EDAM_operation:2415 name: Protein folding analysis namespace: operation subset: operations def: "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." [http://edamontology.org] comment: This is a broad concept and is used a placeholder for other, more specific concepts. synonym: "Protein folding modelling" EXACT [http://edamontology.org] is_a: EDAM_operation:2502 ! Protein data processing is_a: EDAM_operation:2426 ! Modelling and simulation relationship: has_output EDAM_data:0903 !{min_cardinality=1} ! Protein folding report relationship: has_topic EDAM_topic:0130 ! Protein folding and stability [Term] id: EDAM_operation:0331 name: Protein modelling (mutation) namespace: operation subset: operations def: "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function." [http://edamontology.org] comment: Methods might predict silent or pathological mutations. is_a: EDAM_operation:0477 ! Protein modelling is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) synonym: "Protein mutation modelling" EXACT [http://edamontology.org] relationship: has_topic EDAM_topic:0130 ! Protein folding and stability relationship: has_topic EDAM_topic:0199 ! Genetic variation [Term] id: EDAM_operation:0332 name: Immunogen design namespace: operation subset: operations def: "Design molecules that elicit an immune response (immunogens)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0559 ! Peptide immunogen prediction and optimisation [Term] id: EDAM_operation:2409 name: File processing namespace: operation subset: operations def: "Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations." [http://edamontology.org] synonym: "Report handling" EXACT [http://edamontology.org] synonym: "File handling" EXACT [http://edamontology.org] synonym: "Data file processing" EXACT [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:0006 !{min_cardinality=0} ! Data relationship: has_output EDAM_data:0006 !{min_cardinality=0} ! Data relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] id: EDAM_operation:0337 name: Plotting and rendering namespace: operation subset: operations def: "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." [http://edamontology.org] synonym: "Visualisation" EXACT [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation relationship: has_input EDAM_data:0006 !{min_cardinality=1} ! Data relationship: has_output EDAM_data:2968 !{min_cardinality=0} ! Image relationship: has_topic EDAM_topic:0092 ! Data visualisation [Term] id: EDAM_operation:2121 name: Sequence file processing namespace: operation subset: operations def: "Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences." [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing is_a: EDAM_operation:2409 ! File processing [Term] id: EDAM_operation:3081 !{since=beta13} name: Sequence alignment editing namespace: operation subset: operations def: "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." [http://edamontology.org] is_a: EDAM_operation:2122 ! Sequence alignment file processing is_a: EDAM_operation:3096 ! Editing [Term] id: EDAM_operation:2122 name: Sequence alignment file processing namespace: operation subset: operations def: "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." [http://edamontology.org] is_a: EDAM_operation:2409 ! File processing is_a: EDAM_operation:2463 ! Sequence alignment processing relationship: has_input EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment relationship: has_output EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment [Term] id: EDAM_operation:3080 !{since=beta13} name: Structure editing namespace: operation subset: operations def: "Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically." [http://edamontology.org] is_a: EDAM_operation:2234 ! Structure file processing is_a: EDAM_operation:3096 ! Editing relationship: has_input EDAM_data:0883 !{min_cardinality=1} ! Structure [Term] id: EDAM_operation:2234 name: Structure file processing namespace: operation subset: operations def: "Perform basic (non-analytical) operations on a file of molecular tertiary structural data." [http://edamontology.org] is_a: EDAM_operation:2409 ! File processing is_a: EDAM_operation:2465 ! Structure processing [Term] id: EDAM_operation:2120 name: Listfile processing namespace: operation subset: operations def: "Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses)." [http://edamontology.org] is_a: EDAM_operation:2409 ! File processing relationship: has_input EDAM_data:1111 ! EMBOSS listfile relationship: has_output EDAM_data:1111 ! EMBOSS listfile [Term] id: EDAM_operation:1812 name: Data loading namespace: operation subset: operations def: "Prepare or load a user-specified data file so that it is available for use." [http://edamontology.org] synonym: "Database submission" EXACT [http://edamontology.org] synonym: "Data submission" EXACT [http://edamontology.org] xref: WHATIF:UploadPDB is_a: EDAM_operation:2409 ! File processing relationship: has_input EDAM_data:0842 !{min_cardinality=1} ! Identifier [Term] id: EDAM_operation:0335 name: File reformatting namespace: operation subset: operations def: "Reformat a file of data (or equivalent entity in memory)." [http://edamontology.org] is_a: EDAM_operation:2409 ! File processing [Term] id: EDAM_operation:0336 name: File validation namespace: operation subset: operations def: "Test and validate the format and content of a data file." [http://edamontology.org] is_a: EDAM_operation:2409 ! File processing is_a: EDAM_operation:2428 ! Evaluation and validation [Term] id: EDAM_operation:2421 name: Database search namespace: operation subset: operations def: "Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query." [http://edamontology.org] comment: Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. is_a: EDAM_operation:0224 ! Search and retrieval is_a: EDAM_operation:2424 ! Comparison relationship: has_output EDAM_data:2080 !{min_cardinality=0} ! Database hits [Term] id: EDAM_operation:2422 name: Data retrieval namespace: operation subset: operations def: "Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords." [http://edamontology.org] synonym: "Information retrieval" BROAD [http://edamontology.org] is_a: EDAM_operation:0224 ! Search and retrieval relationship: has_input EDAM_data:0842 !{min_cardinality=1} ! Identifier [Term] id: EDAM_operation:0343 name: Transmembrane protein database search namespace: operation subset: operations def: "Search a database of transmembrane proteins, for example for sequence or structural similarities." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2421 ! Database search [Term] id: EDAM_operation:0304 name: Data retrieval (metadata and documentation) namespace: operation subset: operations def: "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described." [http://edamontology.org] comment: This includes documentation, general information and other metadata on entities such as databases, database entries and tools. synonym: "Data retrieval (documentation)" EXACT [http://edamontology.org] synonym: "Data retrieval (metadata)" EXACT [http://edamontology.org] relationship: has_output EDAM_data:2337 !{min_cardinality=1} ! Metadata is_a: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0225 name: Data retrieval (database cross-reference) namespace: operation subset: operations def: "Search database to retrieve all relevant references to a particular entity or entry." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:1813 name: Sequence retrieval namespace: operation subset: operations def: "Query a sequence data resource (typically a database) and retrieve sequences and / or annotation." [http://edamontology.org] comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. synonym: "Data retrieval (sequences)" EXACT [http://edamontology.org] is_a: EDAM_operation:2422 ! Data retrieval is_a: EDAM_operation:2446 ! Sequence processing relationship: has_output EDAM_data:2044 !{min_cardinality=0} ! Sequence [Term] id: EDAM_operation:1814 name: Structure retrieval namespace: operation subset: operations def: "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation." [http://edamontology.org] comment: This includes direct retrieval methods but not those that perform calculations on the sequence or structure. xref: WHATIF:DownloadPDB xref: WHATIF:EchoPDB is_a: EDAM_operation:2422 ! Data retrieval is_a: EDAM_operation:2465 ! Structure processing relationship: has_output EDAM_data:0883 !{min_cardinality=0} ! Structure [Term] id: EDAM_operation:2237 name: Data retrieval (sequence profile) namespace: operation subset: operations def: "Query a profile data resource and retrieve one or more profile(s) and / or associated annotation." [http://edamontology.org] comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2434 name: Data retrieval (codon usage table) namespace: operation subset: operations def: "Retrieve a codon usage table and / or associated annotation." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2264 name: Data retrieval (pathway or network) namespace: operation subset: operations def: "Query a biological pathways database and retrieve annotation on one or more pathways." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2265 name: Data retrieval (identifier) namespace: operation subset: operations def: "Query a database and retrieve one or more data identifiers." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2224 name: Data retrieval (ontology concept) namespace: operation subset: operations def: "Query an ontology and retrieve concepts or relations." [http://edamontology.org] synonym: "Ontology retrieval" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2222 name: Data retrieval (ontology annotation) namespace: operation subset: operations def: "Search and retrieve documentation on a bioinformatics ontology." [http://edamontology.org] synonym: "Ontology information retrieval" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2468 name: Data retrieval (phylogenetic tree) namespace: operation subset: operations def: "Retrieve a phylogenetic tree from a data resource." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0257 name: Data retrieval (sequence alignment) namespace: operation subset: operations def: "Display basic information about a sequence alignment." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2473 name: Data retrieval (genotype and phenotype annotation) namespace: operation subset: operations def: "Retrieve information on a specific genotype or phenotype." [http://edamontology.org] synonym: "Genotype and phenotype information retrieval" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2472 name: Data retrieval (gene annotation) namespace: operation subset: operations def: "Retrieve information on a specific gene." [http://edamontology.org] synonym: "Gene information retrieval" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2471 name: Data retrieval (RNA family annotation) namespace: operation subset: operations def: "Retrieve information on an RNA family." [http://edamontology.org] synonym: "RNA family information retrieval" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2470 name: Data retrieval (protein family annotation) namespace: operation subset: operations def: "Retrieve information on a protein family." [http://edamontology.org] synonym: "Protein family information retrieval" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2469 name: Data retrieval (protein interaction annotation) namespace: operation subset: operations def: "Retrieve information on a protein interaction." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2467 name: Data retrieval (protein annotation) namespace: operation subset: operations def: "Retrieve information on a protein." [http://edamontology.org] synonym: "Protein information retrieval" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0280 name: Data retrieval (restriction enzyme annotation) namespace: operation subset: operations def: "Retrieve information on restriction enzymes or restriction enzyme sites." [http://edamontology.org] synonym: "Restriction enzyme information retrieval" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0515 name: Data retrieval (tool metadata) namespace: operation subset: operations def: "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." [http://edamontology.org] synonym: "Tool information retrieval" EXACT [http://edamontology.org] synonym: "Data retrieval (tool annotation)" EXACT [http://edamontology.org] is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) relationship: has_output EDAM_data:0958 !{min_cardinality=0} ! Tool metadata [Term] id: EDAM_operation:0516 name: Data retrieval (database metadata) namespace: operation subset: operations def: "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." [http://edamontology.org] synonym: "Database information retrieval" EXACT [http://edamontology.org] synonym: "Data retrieval (database annotation)" EXACT [http://edamontology.org] is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) relationship: has_output EDAM_data:0957 !{min_cardinality=0} ! Database metadata [Term] id: EDAM_operation:0344 name: Sequence retrieval (by code) namespace: operation subset: operations def: "Query a database and retrieve sequences with a given entry code or accession number." [http://edamontology.org] is_a: EDAM_operation:1813 ! Sequence retrieval [Term] id: EDAM_operation:0345 name: Sequence retrieval (by keyword) namespace: operation subset: operations def: "Query a database and retrieve sequences containing a given keyword." [http://edamontology.org] is_a: EDAM_operation:1813 ! Sequence retrieval [Term] id: EDAM_operation:1845 name: PDB file sequence retrieval namespace: operation subset: operations def: "Extract a molecular sequence from a PDB file." [http://edamontology.org, WHATIF] xref: WHATIF: PDB_sequence is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0344 ! Sequence retrieval (by code) [Term] id: EDAM_operation:0305 name: Literature search namespace: operation subset: operations def: "Query the biomedical and informatics literature." [http://edamontology.org] is_a: EDAM_operation:2421 ! Database search relationship: has_output EDAM_data:0970 !{min_cardinality=0} ! Bibliographic reference relationship: has_topic EDAM_topic:0217 ! Literature analysis [Term] id: EDAM_operation:0338 name: Sequence database search namespace: operation subset: operations def: "Search a sequence database by sequence comparison and retrieve similar sequences." [http://edamontology.org] comment: This excludes direct retrieval methods (e.g. the dbfetch program). is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:2403 ! Sequence analysis relationship: has_output EDAM_data:0857 !{min_cardinality=0} ! Database hits (sequence) relationship: has_topic EDAM_topic:0159 ! Sequence comparison [Term] id: EDAM_operation:0339 name: Structure database search namespace: operation subset: operations def: "Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data." [http://edamontology.org] is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:2996 ! Structure classification relationship: has_output EDAM_data:0885 !{min_cardinality=0} ! Database hits (structure) relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_operation:0340 name: Protein secondary database search namespace: operation subset: operations def: "Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group." [http://edamontology.org] comment: Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). synonym: "Protein sequence classification" EXACT [http://edamontology.org] is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:3093 ! Sequence screening relationship: has_output EDAM_data:0858 !{min_cardinality=0} ! Database hits (secondary) relationship: has_topic EDAM_topic:0595 ! Protein classification [Term] id: EDAM_operation:0341 name: Motif database search namespace: operation subset: operations def: "Screen a sequence against a motif or pattern database." [http://edamontology.org] is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:0239 ! Sequence motif recognition is_a: EDAM_operation:3093 ! Sequence screening relationship: has_output EDAM_data:1298 !{min_cardinality=0} ! Sequence features (motifs) relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_operation:0342 name: Sequence profile database search namespace: operation subset: operations def: "Search a database of sequence profiles with a query sequence." [http://edamontology.org] is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:0300 ! Sequence-profile alignment construction is_a: EDAM_operation:3093 ! Sequence screening relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_operation:0346 name: Sequence database search (by sequence) namespace: operation subset: operations def: "Search a sequence database and retrieve sequences that are similar to a query sequence." [http://edamontology.org] synonym: "Sequence similarity search" EXACT [http://edamontology.org] is_a: EDAM_operation:0338 ! Sequence database search is_a: EDAM_operation:3093 ! Sequence screening is_a: EDAM_operation:2451 ! Sequence comparison [Term] id: EDAM_operation:0347 name: Sequence database search (by motif or pattern) namespace: operation subset: operations def: "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." [http://edamontology.org] is_a: EDAM_operation:0338 ! Sequence database search is_a: EDAM_operation:0239 ! Sequence motif recognition relationship: has_input EDAM_data:1353 !{min_cardinality=1} ! Sequence motif relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_operation:0348 name: Sequence database search (by amino acid composition) namespace: operation subset: operations def: "Search a sequence database and retrieve sequences of a given amino acid composition." [http://edamontology.org] is_a: EDAM_operation:0338 ! Sequence database search relationship: has_input EDAM_data:1267 ! Amino acid frequencies relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] id: EDAM_operation:0349 name: Sequence database search (by physicochemical property) namespace: operation subset: operations def: "Search a sequence database and retrieve sequences with a specified physicochemical property." [http://edamontology.org] is_a: EDAM_operation:0338 ! Sequence database search [Term] id: EDAM_operation:0350 name: Sequence database search (by sequence using word-based methods) namespace: operation subset: operations def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method." [http://edamontology.org] comment: Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. synonym: "Sequence similarity search (word-based methods)" EXACT [http://edamontology.org] is_a: EDAM_operation:0346 ! Sequence database search (by sequence) is_a: EDAM_operation:0288 ! Sequence word comparison [Term] id: EDAM_operation:0351 name: Sequence database search (by sequence using profile-based methods) namespace: operation subset: operations def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query." [http://edamontology.org] comment: This includes tools based on PSI-BLAST. synonym: "Sequence similarity search (profile-based methods)" EXACT [http://edamontology.org] is_a: EDAM_operation:0346 ! Sequence database search (by sequence) is_a: EDAM_operation:0300 ! Sequence-profile alignment construction [Term] id: EDAM_operation:0352 name: Sequence database search (by sequence using local alignment-based methods) namespace: operation subset: operations def: "Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method." [http://edamontology.org] comment: This includes tools based on the Smith-Waterman algorithm or FASTA. synonym: "Sequence similarity search (local alignment-based methods) " EXACT [http://edamontology.org] is_a: EDAM_operation:0346 ! Sequence database search (by sequence) is_a: EDAM_operation:0493 ! Pairwise sequence alignment construction (local) relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:0353 name: Sequence database search (by sequence using global alignment-based methods) namespace: operation subset: operations def: "Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method." [http://edamontology.org] comment: This includes tools based on the Needleman and Wunsch algorithm. synonym: "Sequence similarity search (global alignment-based methods)" EXACT [http://edamontology.org] is_a: EDAM_operation:0346 ! Sequence database search (by sequence) is_a: EDAM_operation:0494 ! Pairwise sequence alignment construction (global) relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:0354 name: Sequence database search (by sequence for primer sequences) namespace: operation subset: operations def: "Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences." [http://edamontology.org] comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. synonym: "Sequence similarity search (primer sequences)" EXACT [http://edamontology.org] is_a: EDAM_operation:0346 ! Sequence database search (by sequence) relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] id: EDAM_operation:0355 name: Sequence database search (by molecular weight) namespace: operation subset: operations def: "Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry." [http://edamontology.org] synonym: "Protein fingerprinting" EXACT [http://edamontology.org] synonym: "Peptide mass fingerprinting" EXACT [http://edamontology.org] is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property) relationship: has_input EDAM_data:0944 ! Peptide mass fingerprint relationship: has_topic EDAM_topic:0123 ! Protein properties relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_operation:0356 name: Sequence database search (by isoelectric point) namespace: operation subset: operations def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [http://edamontology.org] is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property) relationship: has_topic EDAM_topic:0123 ! Protein properties [Term] id: EDAM_operation:0357 name: Structure retrieval (by code) namespace: operation subset: operations def: "Query a tertiary structure database and retrieve entries with a given entry code or accession number." [http://edamontology.org] is_a: EDAM_operation:1814 ! Structure retrieval [Term] id: EDAM_operation:0358 name: Structure retrieval (by keyword) namespace: operation subset: operations def: "Query a tertiary structure database and retrieve entries containing a given keyword." [http://edamontology.org] is_a: EDAM_operation:1814 ! Structure retrieval [Term] id: EDAM_operation:1914 name: Structure retrieval (water) namespace: operation subset: operations def: "Query a tertiary structure database and retrieve water molecules." [http://edamontology.org] xref: WHATIF:MovedWaterPDB is_a: EDAM_operation:1814 ! Structure retrieval [Term] id: EDAM_operation:0359 name: Structure database search (by sequence) namespace: operation subset: operations def: "Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence." [http://edamontology.org] synonym: "Structure retrieval by sequence" EXACT [http://edamontology.org] is_a: EDAM_operation:0339 ! Structure database search is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:3093 ! Sequence screening [Term] id: EDAM_operation:0360 name: Structure database search (by structure) namespace: operation subset: operations def: "Search a tertiary structure database and retrieve structures that are similar to a query structure." [http://edamontology.org] synonym: "Structure retrieval by structure" EXACT [http://edamontology.org] synonym: "Structural similarity search" EXACT [http://edamontology.org] is_a: EDAM_operation:0339 ! Structure database search relationship: has_topic EDAM_topic:1770 ! Structure comparison relationship: has_topic EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_operation:0226 name: Annotation namespace: operation subset: operations def: "Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary." [http://edamontology.org] comment: This is a broad concept and is used a placeholder for other, more specific concepts. is_a: EDAM_operation:0004 ! Operation relationship: has_input EDAM_data:0582 ! Ontology relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_operation:1774 name: Annotation retrieval namespace: operation subset: operations def: "Retrieve existing annotation (or documentation), typically annotation on a database entity." [http://edamontology.org] comment: Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0361 name: Sequence annotation namespace: operation subset: operations def: "Annotate a molecular sequence record with terms from a controlled vocabulary." [http://edamontology.org] is_a: EDAM_operation:0226 ! Annotation relationship: has_input EDAM_data:0849 !{min_cardinality=1} ! Sequence record relationship: has_output EDAM_data:0849 !{min_cardinality=1} ! Sequence record [Term] id: EDAM_operation:0362 name: Genome annotation namespace: operation subset: operations def: "Annotate a genome sequence with terms from a controlled vocabulary." [http://edamontology.org] is_a: EDAM_operation:0361 ! Sequence annotation [Term] id: EDAM_operation:2466 name: Map annotation namespace: operation subset: operations def: "Annotate a DNA map of some type with terms from a controlled vocabulary." [http://edamontology.org] is_a: EDAM_operation:0226 ! Annotation is_a: EDAM_operation:2521 ! Map data processing relationship: has_input EDAM_data:1274 !{min_cardinality=1} ! Map relationship: has_output EDAM_data:1274 !{min_cardinality=1} ! Map [Term] id: EDAM_operation:0227 name: Data indexing namespace: operation subset: operations def: "Generate an index of (typically a file of) biological data." [http://edamontology.org] synonym: "Database indexing" EXACT [http://edamontology.org] is_a: EDAM_operation:2412 ! Data index processing relationship: has_output EDAM_data:0955 ! Data index [Term] id: EDAM_operation:3211 !{since=1.1} name: Genome indexing namespace: operation subset: operations def: "Generate an index of a genome sequence." [http://edamontology.org] comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. is_a: EDAM_operation:0227 ! Data indexing relationship: has_output EDAM_data:3210 ! Genome index [Term] id: EDAM_operation:3212 !{since=1.1} name: Genome indexing (Burrows-Wheeler) namespace: operation subset: operations def: "Generate an index of a genome sequence using the Burrows-Wheeler algorithm." [http://edamontology.org] comment: The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. synonym: "Burrows-Wheeler" EXACT [http://edamontology.org] synonym: "Burrows Wheeler" EXACT [http://edamontology.org] synonym: "Genome indexing (Burrows Wheeler)" EXACT [http://edamontology.org] is_a: EDAM_operation:3211 ! Genome indexing [Term] id: EDAM_operation:3213 !{since=1.1} name: Genome indexing (suffix arrays) namespace: operation subset: operations def: "Generate an index of a genome sequence using a suffix arrays algorithm." [http://edamontology.org] comment: A suffix array consists of the lexicographically sorted list of suffixes of a genome. synonym: "suffix arrays" EXACT [http://edamontology.org] is_a: EDAM_operation:3211 ! Genome indexing [Term] id: EDAM_operation:0228 name: Data index analysis namespace: operation subset: operations def: "Analyse an index of biological data." [http://edamontology.org] is_a: EDAM_operation:2412 ! Data index processing is_a: EDAM_operation:2412 ! Data index processing synonym: "Database index analysis" EXACT [http://edamontology.org] relationship: has_input EDAM_data:0955 !{min_cardinality=1} ! Data index relationship: has_output EDAM_data:0956 !{min_cardinality=1} ! Data index report [Term] id: EDAM_operation:2478 name: Nucleic acid sequence analysis namespace: operation subset: operations def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [http://edamontology.org] synonym: "Sequence analysis (nucleic acid)" EXACT [http://edamontology.org] is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) relationship: has_input EDAM_data:2977 !{min_cardinality=1} ! Nucleic acid sequence relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3095 !{since=beta13} name: Nucleic acid design namespace: operation subset: operations def: "Design (or predict) nucleic acid sequences with specific chemical or physical properties." [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:2479 name: Protein sequence analysis namespace: operation subset: operations def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [http://edamontology.org] synonym: "Sequence analysis (protein)" EXACT [http://edamontology.org] is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2447 ! Sequence processing (protein) synonym: "Sequence analysis (protein)" EXACT [http://edamontology.org] relationship: has_input EDAM_data:2976 !{min_cardinality=1} ! Protein sequence relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis [Term] id: EDAM_operation:3214 !{since=1.1} name: Spectrum analysis namespace: operation subset: operations def: "Analyse a spectrum from a mass spectrometry (or other) experiment." [http://edamontology.org] synonym: "Spectral analysis" EXACT [http://edamontology.org] synonym: "Mass spectrum analysis" EXACT [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:3215 !{since=1.1} name: Peak detection namespace: operation subset: operations def: "Identify peaks in a spectrum from a mass spectrometry experiment." [http://edamontology.org] synonym: "Peak finding" EXACT [http://edamontology.org] is_a: EDAM_operation:3214 ! Spectrum analysis relationship: has_input EDAM_data:0943 !{min_cardinality=1} ! Mass spectrometry spectra [Term] id: EDAM_operation:2446 name: Sequence processing namespace: operation subset: operations ! alt_id: EDAM_operation:2449 def: "Process (read and / or write) one or more molecular sequences and associated annotation." [http://edamontology.org] synonym: "Sequence processing (general)" EXACT [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:2044 !{min_cardinality=0} ! Sequence relationship: has_output EDAM_data:2044 !{min_cardinality=0} ! Sequence relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_operation:2447 name: Sequence processing (protein) namespace: operation subset: operations def: "Process (read and / or write) a protein sequence and associated annotation." [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing is_a: EDAM_operation:2502 ! Protein data processing relationship: has_input EDAM_data:2976 !{min_cardinality=0} ! Protein sequence relationship: has_output EDAM_data:2976 !{min_cardinality=0} ! Protein sequence [Term] id: EDAM_operation:2448 name: Sequence processing (nucleic acid) namespace: operation subset: operations def: "Process (read and / or write) a nucleotide sequence and associated annotation." [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_input EDAM_data:2977 !{min_cardinality=0} ! Nucleic acid sequence relationship: has_output EDAM_data:2977 !{min_cardinality=0} ! Nucleic acid sequence [Term] id: EDAM_operation:0229 name: Annotation retrieval (sequence) namespace: operation subset: operations def: "Retrieve basic information about a molecular sequence." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:1813 ! Sequence retrieval [Term] id: EDAM_operation:0230 name: Sequence generation namespace: operation subset: operations def: "Generate a molecular sequence by some means." [http://edamontology.org] is_a: EDAM_operation:2121 ! Sequence file processing [Term] id: EDAM_operation:2513 name: Sequence generation (nucleic acid) namespace: operation subset: operations def: "Generate a nucleic acid sequence by some means." [http://edamontology.org] is_a: EDAM_operation:0230 ! Sequence generation is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:2514 name: Sequence generation (protein) namespace: operation subset: operations def: "Generate a protein sequence by some means." [http://edamontology.org] is_a: EDAM_operation:0230 ! Sequence generation is_a: EDAM_operation:2447 ! Sequence processing (protein) relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis [Term] id: EDAM_operation:0231 name: Sequence editing namespace: operation subset: operations def: "Edit or change a molecular sequence, either randomly or specifically." [http://edamontology.org] is_a: EDAM_operation:2121 ! Sequence file processing is_a: EDAM_operation:3096 ! Editing [Term] id: EDAM_operation:2511 name: Sequence editing (nucleic acid) namespace: operation subset: operations def: "Edit or change a nucleic acid sequence, either randomly or specifically." [http://edamontology.org] is_a: EDAM_operation:0231 ! Sequence editing is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) [Term] id: EDAM_operation:2512 name: Sequence editing (protein) namespace: operation subset: operations def: "Edit or change a protein sequence, either randomly or specifically." [http://edamontology.org] is_a: EDAM_operation:0231 ! Sequence editing is_a: EDAM_operation:2447 ! Sequence processing (protein) [Term] id: EDAM_operation:0232 name: Sequence merging namespace: operation subset: operations def: "Merge two or more (typically overlapping) molecular sequences." [http://edamontology.org] synonym: "Sequence splicing" EXACT [http://edamontology.org] is_a: EDAM_operation:0231 ! Sequence editing [Term] id: EDAM_operation:0233 name: Sequence conversion namespace: operation subset: operations def: "Convert a molecular sequence from one type to another." [http://edamontology.org] is_a: EDAM_operation:0231 ! Sequence editing [Term] id: EDAM_operation:1780 name: Sequence submission namespace: operation subset: operations def: "Submit a molecular sequence to a database." [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 !{min_cardinality=1} ! Sequence relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition [Term] id: EDAM_operation:0234 name: Sequence complexity calculation namespace: operation subset: operations ! alt_id: EDAM_operation:0373 ! alt_id: EDAM_operation:0374 def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [http://edamontology.org] is_a: EDAM_operation:0236 ! Sequence composition calculation relationship: has_output EDAM_data:1259 !{min_cardinality=1} ! Sequence complexity relationship: has_topic EDAM_topic:0642 ! Low complexity sequences [Term] id: EDAM_operation:0235 name: Sequence ambiguity calculation namespace: operation subset: operations ! alt_id: EDAM_operation:0375 ! alt_id: EDAM_operation:0376 def: "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." [http://edamontology.org] is_a: EDAM_operation:0236 ! Sequence composition calculation relationship: has_output EDAM_data:1260 !{min_cardinality=1} ! Sequence ambiguity relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] id: EDAM_operation:0291 name: Sequence clustering namespace: operation subset: operations def: "Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org] comment: The clusters may be output or used internally for some other purpose. synonym: "Sequence cluster generation" EXACT [http://edamontology.org] is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2452 ! Sequence cluster processing is_a: EDAM_operation:2995 ! Sequence classification relationship: has_output EDAM_data:1235 !{min_cardinality=0} ! Sequence cluster [Term] id: EDAM_operation:0236 name: Sequence composition calculation namespace: operation subset: operations def: "Calculate character or word composition or frequency of a molecular sequence." [http://edamontology.org] is_a: EDAM_operation:2403 ! Sequence analysis relationship: has_output EDAM_data:1261 ! Sequence composition relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] id: EDAM_operation:0237 name: Repeat sequence analysis namespace: operation subset: operations def: "Find and/or analyse repeat sequences in (typically nucleotide) sequences." [http://edamontology.org] comment: Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. is_a: EDAM_operation:2403 ! Sequence analysis relationship: has_topic EDAM_topic:0641 ! Repeat sequences [Term] id: EDAM_operation:0290 name: Sequence redundancy removal namespace: operation subset: operations def: "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." [http://edamontology.org] is_a: EDAM_operation:0291 ! Sequence clustering relationship: has_output EDAM_data:2044 !{min_cardinality=0} ! Sequence relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] id: EDAM_operation:2451 name: Sequence comparison namespace: operation subset: operations def: "Compare two or more molecular sequences." [http://edamontology.org] is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2424 ! Comparison relationship: has_input EDAM_data:2044 !{min_cardinality=2} ! Sequence relationship: has_output EDAM_data:2955 ! Sequence report relationship: has_topic EDAM_topic:0159 ! Sequence comparison [Term] id: EDAM_operation:2508 name: Nucleic acid sequence comparison namespace: operation subset: operations def: "Compare two or more nucleic acid sequences." [http://edamontology.org] synonym: "Sequence comparison (nucleic acid)" EXACT [http://edamontology.org] is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:2998 ! Nucleic acid comparison [Term] id: EDAM_operation:2509 name: Protein sequence comparison namespace: operation subset: operations def: "Compare two or more protein sequences." [http://edamontology.org] synonym: "Sequence comparison (protein)" EXACT [http://edamontology.org] is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2479 ! Protein sequence analysis is_a: EDAM_operation:2997 ! Protein comparison [Term] id: EDAM_operation:0288 name: Sequence word comparison namespace: operation subset: operations def: "Find exact character or word matches between molecular sequences without full sequence alignment." [http://edamontology.org] is_a: EDAM_operation:2451 ! Sequence comparison relationship: has_output EDAM_data:0861 !{min_cardinality=1} ! Sequence alignment (words) [Term] id: EDAM_operation:0289 name: Sequence distance matrix generation namespace: operation subset: operations def: "Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences." [http://edamontology.org] synonym: "Phylogenetic distance matrix generation" EXACT [http://edamontology.org] is_a: EDAM_operation:2451 ! Sequence comparison relationship: has_output EDAM_data:0870 ! Sequence distance matrix relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:3200 !{since=1.1} name: DNA barcoding namespace: operation subset: operations def: "Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms." [http://edamontology.org] synonym: "Sample barcoding" EXACT [http://edamontology.org] is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:3204 !{since=1.1} name: Methylation analysis namespace: operation subset: operations def: "Determine cytosine methylation states in nucleic acid sequences." [http://edamontology.org] is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:3205 !{since=1.1} name: Methylation calling namespace: operation subset: operations def: "Determine cytosine methylation status of specific positions in a nucleic acid sequences." [http://edamontology.org] is_a: EDAM_operation:3204 ! Methylation analysis [Term] id: EDAM_operation:3206 !{since=1.1} name: Methylation level analysis (global) namespace: operation subset: operations def: "Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay." [http://edamontology.org] synonym: "Global methylation analysis" EXACT [http://edamontology.org] is_a: EDAM_operation:3205 ! Methylation calling [Term] id: EDAM_operation:3207 !{since=1.1} name: Methylation level analysis (gene-specific) namespace: operation subset: operations def: "Measure the level of methyl cytosines in specific genes." [http://edamontology.org] comment: Many different techniques are available for this. synonym: "Gene-specific methylation analysis" EXACT [http://edamontology.org] is_a: EDAM_operation:3205 ! Methylation calling [Term] id: EDAM_operation:3209 !{since=1.1} name: Genome comparison namespace: operation subset: operations def: "Compare the sequence or features of two or more genomes, for example, to find matching regions." [http://edamontology.org] synonym: "Genomic region matching" EXACT [http://edamontology.org] is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison [Term] id: EDAM_operation:0266 name: Vector sequence detection namespace: operation subset: operations def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [http://edamontology.org] is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:2233 name: Representative sequence identification namespace: operation subset: operations def: "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org] is_a: EDAM_operation:0291 ! Sequence clustering relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] id: EDAM_operation:0317 name: EST and cDNA sequence analysis namespace: operation subset: operations def: "Analyse EST or cDNA sequences." [http://edamontology.org] comment: For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2403 ! Sequence analysis [Term] id: EDAM_operation:3185 !{since=1.1} name: Base-calling namespace: operation subset: operations def: "Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer." [http://edamontology.org] synonym: "Base calling" EXACT [http://edamontology.org] synonym: "Phred base calling" EXACT [http://edamontology.org] synonym: "Phred base-calling" EXACT [http://edamontology.org] is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:3195 name: Sequencing error detection namespace: operation subset: operations def: "Detect errors in DNA sequences generated from sequencing projects)." [http://edamontology.org] synonym: "Short-read error correction" EXACT [http://edamontology.org] synonym: "Short read error correction" EXACT [http://edamontology.org] is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:0265 name: Frameshift error detection namespace: operation subset: operations def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [http://edamontology.org] comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. is_a: EDAM_operation:3195 ! Sequencing error detection is_a: EDAM_operation:3197 ! Genetic variation analysis relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:0241 name: Transcription regulatory sequence analysis namespace: operation subset: operations def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [http://edamontology.org] comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. is_obsolete: true !{since=beta13} consider: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] id: EDAM_operation:0281 name: Genetic marker identification namespace: operation subset: operations def: "Identify genetic markers in DNA sequences." [http://edamontology.org] comment: A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. is_obsolete: true !{since=beta13} consider: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:0363 name: Nucleic acid sequence reverse and complement namespace: operation subset: operations def: "Generate the reverse and / or complement of a nucleotide sequence." [http://edamontology.org] is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid) [Term] id: EDAM_operation:0364 name: Random sequence generation namespace: operation subset: operations def: "Generate a random sequence, for example, with a specific character composition." [http://edamontology.org] is_a: EDAM_operation:0230 ! Sequence generation [Term] id: EDAM_operation:0365 name: Nucleic acid restriction digest namespace: operation subset: operations def: "Generate digest fragments for a nucleotide sequence containing restriction sites." [http://edamontology.org] is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid) is_a: EDAM_operation:0262 ! Nucleic acid property calculation relationship: has_output EDAM_data:1239 ! Restriction digest relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] id: EDAM_operation:0366 name: Protein sequence cleavage namespace: operation subset: operations def: "Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses." [http://edamontology.org] is_a: EDAM_operation:2514 ! Sequence generation (protein) is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1238 ! Proteolytic digest relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_operation:0367 name: Sequence mutation and randomization namespace: operation subset: operations def: "Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition." [http://edamontology.org] is_a: EDAM_operation:0231 ! Sequence editing [Term] id: EDAM_operation:0368 name: Sequence masking namespace: operation subset: operations def: "Mask characters in a molecular sequence (replacing those characters with a mask character)." [http://edamontology.org] comment: For example, SNPs or repeats in a DNA sequence might be masked. is_a: EDAM_operation:0231 ! Sequence editing relationship: has_input EDAM_data:0851 !{min_cardinality=1} ! Sequence mask character [Term] id: EDAM_operation:0369 name: Sequence cutting namespace: operation subset: operations def: "Cut (remove) characters or a region from a molecular sequence." [http://edamontology.org] is_a: EDAM_operation:0231 ! Sequence editing [Term] id: EDAM_operation:3192 !{since=1.1} name: Sequence trimming namespace: operation subset: operations def: "Cut (remove) the end from a molecular sequence." [http://edamontology.org] is_a: EDAM_operation:0369 ! Sequence cutting [Term] id: EDAM_operation:3212 !{since=1.1} name: Primer removal namespace: operation subset: operations def: "Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products)." [http://edamontology.org] is_a: EDAM_operation:0369 ! Sequence cutting is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid) [Term] id: EDAM_operation:3189 !{since=1.1} name: Trim ends namespace: operation subset: operations def: "Trim sequences (typically from an automated DNA sequencer) to remove misleading ends." [http://edamontology.org] comment: For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. is_a: EDAM_operation:3192 ! Sequence trimming [Term] id: EDAM_operation:3190 !{since=1.1} name: Trim vector namespace: operation subset: operations def: "Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences." [http://edamontology.org] is_a: EDAM_operation:3192 ! Sequence trimming [Term] id: EDAM_operation:3191 !{since=1.1} name: Trim to reference namespace: operation subset: operations def: "Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence." [http://edamontology.org] is_a: EDAM_operation:3192 ! Sequence trimming [Term] id: EDAM_operation:0370 name: Restriction site creation namespace: operation subset: operations def: "Create (or remove) restriction sites in sequences, for example using silent mutations." [http://edamontology.org] is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid) relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] id: EDAM_operation:0371 name: DNA translation namespace: operation subset: operations def: "Translate a DNA sequence into protein." [http://edamontology.org] is_a: EDAM_operation:0233 ! Sequence conversion relationship: has_topic EDAM_topic:0108 ! Translation [Term] id: EDAM_operation:0372 name: DNA transcription namespace: operation subset: operations def: "Transcribe a nucleotide sequence into mRNA sequence(s)." [http://edamontology.org] is_a: EDAM_operation:0233 ! Sequence conversion relationship: has_topic EDAM_topic:0110 ! Transcription [Term] id: EDAM_operation:2510 name: DNA back-translation namespace: operation subset: operations def: "Back-translate a protein sequence into DNA." [http://edamontology.org] is_a: EDAM_operation:0233 ! Sequence conversion relationship: has_topic EDAM_topic:0108 ! Translation [Term] id: EDAM_operation:0377 name: Sequence composition calculation (nucleic acid) namespace: operation subset: operations def: "Calculate base frequency or word composition of a nucleotide sequence." [http://edamontology.org] is_a: EDAM_operation:0236 ! Sequence composition calculation is_a: EDAM_operation:0262 ! Nucleic acid property calculation [Term] id: EDAM_operation:0378 name: Sequence composition calculation (protein) namespace: operation subset: operations def: "Calculate amino acid frequency or word composition of a protein sequence." [http://edamontology.org] is_a: EDAM_operation:0236 ! Sequence composition calculation is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) [Term] id: EDAM_operation:2284 name: Nucleic acid density plotting namespace: operation subset: operations def: "Calculate a density plot (of base composition) for a nucleotide sequence." [http://edamontology.org] is_a: EDAM_operation:0377 ! Sequence composition calculation (nucleic acid) [Term] id: EDAM_operation:0379 name: Repeat sequence detection namespace: operation subset: operations ! alt_id: EDAM_operation:2450 def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] is_a: EDAM_operation:0237 ! Repeat sequence analysis is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1299 ! Sequence features (repeats) [Term] id: EDAM_operation:0380 name: Repeat sequence organisation analysis namespace: operation subset: operations def: "Analyse repeat sequence organization such as periodicity." [http://edamontology.org] is_a: EDAM_operation:0237 ! Repeat sequence analysis is_a: EDAM_operation:0236 ! Sequence composition calculation [Term] id: EDAM_operation:0490 name: Dotplot plotting namespace: operation subset: operations def: "Draw a dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] is_a: EDAM_operation:0288 ! Sequence word comparison is_a: EDAM_operation:0565 ! Sequence alignment rendering relationship: has_output EDAM_data:0862 !{min_cardinality=1} ! Dotplot [Term] id: EDAM_operation:0242 name: Conserved transcription regulatory sequence identification namespace: operation subset: operations def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." [http://edamontology.org] comment: For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. is_a: EDAM_operation:0438 ! Transcription regulatory element prediction is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1315 ! Gene features (TFBS) [Term] id: EDAM_operation:0238 name: Sequence motif discovery namespace: operation subset: operations def: "Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery)." [http://edamontology.org] comment: Motifs and patterns might be conserved or over-represented (occur with improbable frequency). synonym: "Motif discovery" EXACT [http://edamontology.org] is_a: EDAM_operation:0253 ! Feature prediction is_a: EDAM_operation:2404 ! Sequence motif processing relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_operation:0239 name: Sequence motif recognition namespace: operation subset: operations def: "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." [http://edamontology.org] synonym: "Sequence motif detection" EXACT [http://edamontology.org] synonym: "Motif detection" EXACT [http://edamontology.org] synonym: "Motif recognition" EXACT [http://edamontology.org] is_a: EDAM_operation:2404 ! Sequence motif processing is_a: EDAM_operation:0253 ! Feature prediction relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_operation:0240 name: Sequence motif comparison namespace: operation subset: operations def: "Find motifs shared by molecular sequences." [http://edamontology.org] is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2404 ! Sequence motif processing relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_operation:2123 name: Small molecule data processing namespace: operation subset: operations def: "Process (read and / or write) physicochemical property data for small molecules." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:0250 name: Protein property calculation namespace: operation subset: operations ! alt_id: EDAM_operation:2933 def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [http://edamontology.org] comment: This includes methods to render and visualise the properties of a protein sequence. synonym: "Protein property rendering" EXACT [http://edamontology.org] is_a: EDAM_operation:2502 ! Protein data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_input EDAM_data:0897 !{min_cardinality=0} ! Protein property relationship: has_output EDAM_data:0897 !{min_cardinality=0} ! Protein property relationship: has_topic EDAM_topic:0123 ! Protein properties [Term] id: EDAM_operation:3088 !{since=beta13} name: Protein property calculation (from sequence) namespace: operation subset: operations def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [http://edamontology.org] is_a: EDAM_operation:0250 ! Protein property calculation is_a: EDAM_operation:2479 ! Protein sequence analysis [Term] id: EDAM_operation:0261 name: Nucleic acid property processing namespace: operation subset: operations def: "Process (read and / or write) physicochemical property data of nucleic acids." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:0262 ! Nucleic acid property calculation [Term] id: EDAM_operation:0334 name: Enzyme kinetics calculation namespace: operation subset: operations def: "Calculate Km, Vmax and derived data for an enzyme reaction." [http://edamontology.org] is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:2024 !{min_cardinality=1} ! Enzyme kinetics data relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions [Term] id: EDAM_operation:0398 name: Protein molecular weight calculation namespace: operation subset: operations def: "Calculate the molecular weight of a protein sequence or fragments." [http://edamontology.org] is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1519 !{min_cardinality=1} ! Peptide molecular weights relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_operation:2930 name: Protein property comparison namespace: operation subset: operations def: "Compare the physicochemical properties of two or more proteins (or reference data)." [http://edamontology.org] is_a: EDAM_operation:2997 ! Protein comparison relationship: has_output EDAM_data:0897 !{min_cardinality=1} ! Protein property [Term] id: EDAM_operation:2929 name: Protein fragment weight comparison namespace: operation subset: operations def: "Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data." [http://edamontology.org] is_a: EDAM_operation:0398 ! Protein molecular weight calculation is_a: EDAM_operation:2930 ! Protein property comparison [Term] id: EDAM_operation:0399 name: Protein extinction coefficient calculation namespace: operation subset: operations def: "Predict extinction coefficients or optical density of a protein sequence." [http://edamontology.org] is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1531 !{min_cardinality=1} ! Protein extinction coefficient [Term] id: EDAM_operation:0400 name: Protein pH-dependent property calculation namespace: operation subset: operations def: "Calculate pH-dependent properties from pKa calculations of a protein sequence." [http://edamontology.org] is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:0897 ! Protein property relationship: has_topic EDAM_topic:0137 ! Protein hydropathy [Term] id: EDAM_operation:0401 name: Protein hydropathy calculation (from sequence) namespace: operation subset: operations def: "Hydropathy calculation on a protein sequence." [http://edamontology.org] is_a: EDAM_operation:2574 ! Protein hydropathy calculation [Term] id: EDAM_operation:0252 name: Peptide immunogenicity prediction namespace: operation subset: operations def: "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins." [http://edamontology.org] comment: This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. is_a: EDAM_operation:2492 ! Protein interaction prediction is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1534 !{min_cardinality=1} ! Peptide immunogenicity data relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] id: EDAM_operation:2932 name: Hopp and Woods plotting namespace: operation subset: operations def: "Generate a Hopp and Woods plot of antigenicity of a protein." [http://edamontology.org] is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction [Term] id: EDAM_operation:0402 name: Protein titration curve plotting namespace: operation subset: operations def: "Plot a protein titration curve." [http://edamontology.org] is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation relationship: has_output EDAM_data:1527 !{min_cardinality=1} ! Protein titration curve [Term] id: EDAM_operation:0403 name: Protein isoelectric point calculation namespace: operation subset: operations def: "Calculate isoelectric point of a protein sequence." [http://edamontology.org] is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation relationship: has_output EDAM_data:1528 !{min_cardinality=1} ! Protein isoelectric point [Term] id: EDAM_operation:0404 name: Protein hydrogen exchange rate calculation namespace: operation subset: operations def: "Estimate hydrogen exchange rate of a protein sequence." [http://edamontology.org] is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation relationship: has_output EDAM_data:1530 !{min_cardinality=1} ! Protein hydrogen exchange rate [Term] id: EDAM_operation:0405 name: Protein hydrophobic region calculation namespace: operation subset: operations def: "Calculate hydrophobic or hydrophilic / charged regions of a protein sequence." [http://edamontology.org] is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) [Term] id: EDAM_operation:0406 name: Protein aliphatic index calculation namespace: operation subset: operations def: "Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein." [http://edamontology.org] is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1521 !{min_cardinality=1} ! Protein aliphatic index [Term] id: EDAM_operation:0407 name: Protein hydrophobic moment plotting namespace: operation subset: operations def: "Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity." [http://edamontology.org] comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1520 !{min_cardinality=1} ! Peptide hydrophobic moment [Term] id: EDAM_operation:0408 name: Protein globularity prediction namespace: operation subset: operations def: "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." [http://edamontology.org] is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1526 !{min_cardinality=1} ! Protein globularity [Term] id: EDAM_operation:0409 name: Protein solubility prediction namespace: operation subset: operations def: "Predict the solubility or atomic solvation energy of a protein sequence." [http://edamontology.org] is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1524 !{min_cardinality=1} ! Protein solubility [Term] id: EDAM_operation:0410 name: Protein crystallizability prediction namespace: operation subset: operations def: "Predict crystallizability of a protein sequence." [http://edamontology.org] is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1525 !{min_cardinality=1} ! Protein crystallizability [Term] id: EDAM_operation:0455 name: Nucleic acid thermodynamic property calculation namespace: operation subset: operations def: "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." [http://edamontology.org] is_a: EDAM_operation:0262 ! Nucleic acid property calculation relationship: has_output EDAM_data:2985 !{min_cardinality=1} ! Nucleic acid thermodynamic data [Term] id: EDAM_operation:0456 name: Nucleic acid melting profile plotting namespace: operation subset: operations def: "Calculate and plot a DNA or DNA/RNA melting profile." [http://edamontology.org] comment: A melting profile is used to visualise and analyse partly melted DNA conformations. is_a: EDAM_operation:0262 ! Nucleic acid property calculation relationship: has_output EDAM_data:1583 !{min_cardinality=1} ! Nucleic acid melting profile [Term] id: EDAM_operation:0262 name: Nucleic acid property calculation namespace: operation subset: operations def: "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_output EDAM_data:0912 !{min_cardinality=1} ! Nucleic acid property [Term] id: EDAM_operation:2439 name: RNA secondary structure processing namespace: operation subset: operations def: "Process (read and / or write) RNA secondary structure data." [http://edamontology.org] is_a: EDAM_operation:2482 ! Secondary structure processing is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_input EDAM_data:0880 !{min_cardinality=0} ! RNA secondary structure record relationship: has_output EDAM_data:0880 !{min_cardinality=0} ! RNA secondary structure record relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] id: EDAM_operation:2519 name: Structure processing (nucleic acid) namespace: operation subset: operations def: "Process (read and / or write) nucleic acid tertiary structure data." [http://edamontology.org] is_a: EDAM_operation:2465 ! Structure processing is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_input EDAM_data:1459 !{min_cardinality=0} ! Nucleic acid structure relationship: has_output EDAM_data:1459 !{min_cardinality=0} ! Nucleic acid structure relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis [Term] id: EDAM_operation:2440 name: Structure processing (RNA) namespace: operation subset: operations def: "Process (read and / or write) RNA tertiary structure data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2519 ! Structure processing (nucleic acid) [Term] id: EDAM_operation:0278 name: RNA secondary structure prediction namespace: operation subset: operations def: "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." [http://edamontology.org] comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). is_a: EDAM_operation:2439 ! RNA secondary structure processing is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:0880 !{min_cardinality=1} ! RNA secondary structure record relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_operation:2441 name: RNA structure prediction namespace: operation subset: operations def: "Predict RNA tertiary structure." [http://edamontology.org] is_a: EDAM_operation:0475 ! Nucleic acid structure prediction relationship: has_output EDAM_data:1465 !{min_cardinality=1} ! RNA structure record [Term] id: EDAM_operation:2442 name: DNA structure prediction namespace: operation subset: operations def: "Predict DNA tertiary structure." [http://edamontology.org] is_a: EDAM_operation:0475 ! Nucleic acid structure prediction relationship: has_output EDAM_data:1464 !{min_cardinality=1} ! DNA structure [Term] id: EDAM_operation:0279 name: Nucleic acid folding analysis namespace: operation subset: operations def: "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." [http://edamontology.org] is_a: EDAM_operation:2426 ! Modelling and simulation is_a: EDAM_operation:2501 ! Nucleic acid data processing synonym: "Nucleic acid folding" EXACT [http://edamontology.org] synonym: "Nucleic acid folding modelling" EXACT [http://edamontology.org] relationship: has_output EDAM_data:1596 ! Nucleic acid folding report relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_operation:0461 name: Nucleic acid curvature calculation namespace: operation subset: operations def: "Calculate curvature and flexibility / stiffness of a nucleotide sequence." [http://edamontology.org] comment: This includes properties such as. is_a: EDAM_operation:0262 ! Nucleic acid property calculation relationship: has_output EDAM_data:0912 !{min_cardinality=1} ! Nucleic acid property relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:1768 name: Nucleic acid folding family identification namespace: operation subset: operations def: "Identify folding families of related RNAs." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0483 ! Structured RNA prediction and optimisation [Term] id: EDAM_operation:1769 name: Nucleic acid folding energy calculation namespace: operation subset: operations def: "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." [http://edamontology.org] is_a: EDAM_operation:0279 ! Nucleic acid folding analysis [Term] id: EDAM_operation:1777 name: Protein function prediction namespace: operation subset: operations def: "Predict general functional properties of a protein." [http://edamontology.org] comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. is_a: EDAM_operation:2414 ! Protein function analysis is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_topic EDAM_topic:2276 ! Protein function prediction [Term] id: EDAM_operation:3084 !{since=beta13} name: Protein function prediction (from sequence) namespace: operation subset: operations def: "Predict general (non-positional) functional properties of a protein from analysing its sequence." [http://edamontology.org] comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. is_a: EDAM_operation:1777 ! Protein function prediction is_a: EDAM_operation:2479 ! Protein sequence analysis is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_topic EDAM_topic:2276 ! Protein function prediction [Term] id: EDAM_operation:1778 name: Protein function comparison namespace: operation subset: operations def: "Compare the functional properties of two or more proteins." [http://edamontology.org] is_a: EDAM_operation:2414 ! Protein function analysis is_a: EDAM_operation:2997 ! Protein comparison relationship: has_topic EDAM_topic:1775 ! Protein function analysis [Term] id: EDAM_operation:0413 name: MHC peptide immunogenicity prediction namespace: operation subset: operations def: "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." [http://edamontology.org] is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction [Term] id: EDAM_operation:0253 name: Feature prediction namespace: operation subset: operations def: "Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions." [http://edamontology.org] synonym: "Sequence feature detection" EXACT [http://edamontology.org] synonym: "sequence_feature" RELATED [SO:0000110] is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2423 ! Prediction, detection and recognition relationship: has_output EDAM_data:1255 !{min_cardinality=1} ! Feature record relationship: has_topic EDAM_topic:3072 ! Sequence feature detection [Term] id: EDAM_operation:2453 name: Feature table processing namespace: operation subset: operations def: "Process (read and / or write) a sequence feature table." [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:1270 !{min_cardinality=0} ! Sequence feature table relationship: has_input EDAM_data:2201 !{min_cardinality=0} ! Sequence record full relationship: has_output EDAM_data:1255 !{min_cardinality=0} ! Feature record relationship: has_topic EDAM_topic:0160 ! Sequence sites and features [Term] id: EDAM_operation:0254 name: Data retrieval (feature table) namespace: operation subset: operations def: "Extract a sequence feature table from a sequence database entry." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0255 name: Feature table query namespace: operation subset: operations def: "Query the features (in a feature table) of molecular sequence(s)." [http://edamontology.org] is_a: EDAM_operation:2453 ! Feature table processing relationship: has_input EDAM_data:1270 !{min_cardinality=0} ! Sequence feature table relationship: has_input EDAM_data:2201 !{min_cardinality=0} ! Sequence record full relationship: has_output EDAM_data:1255 ! Feature record [Term] id: EDAM_operation:0256 name: Feature comparison namespace: operation subset: operations def: "Compare the feature tables of two or more molecular sequences." [http://edamontology.org] synonym: "Feature table comparison" EXACT [http://edamontology.org] synonym: "Sequence feature comparison" EXACT [http://edamontology.org] is_a: EDAM_operation:2453 ! Feature table processing is_a: EDAM_operation:2424 ! Comparison relationship: has_input EDAM_data:1270 !{min_cardinality=0} ! Sequence feature table relationship: has_input EDAM_data:2201 !{min_cardinality=0} ! Sequence record full [Term] id: EDAM_operation:3092 !{since=beta13} name: Protein feature prediction namespace: operation subset: operations def: "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures." [http://edamontology.org] is_a: EDAM_operation:2502 ! Protein data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) is_a: EDAM_operation:0253 ! Feature prediction relationship: has_output EDAM_data:1277 !{min_cardinality=1} ! Protein features relationship: has_topic EDAM_topic:3074 ! Protein feature detection [Term] id: EDAM_operation:0414 name: Protein feature prediction (from sequence) namespace: operation subset: operations def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." [http://edamontology.org] comment: Methods typically involve scanning for known motifs, patterns and regular expressions. synonym: "Sequence feature detection (protein)" EXACT [http://edamontology.org] is_a: EDAM_operation:3092 ! Protein feature prediction ! is_a: EDAM_operation:0253 ! Feature prediction is_a: EDAM_operation:2479 ! Protein sequence analysis [Term] id: EDAM_operation:3090 !{since=beta13} name: Protein feature prediction (from structure) namespace: operation subset: operations def: "Predict, recognise and identify positional features in proteins from analysing protein structure." [http://edamontology.org] is_a: EDAM_operation:3092 ! Protein feature prediction is_a: EDAM_operation:2406 ! Protein structure analysis [Term] id: EDAM_operation:3087 !{since=beta13} name: Protein site detection namespace: operation subset: operations ! alt_id: EDAM_operation:0382 def: "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org] synonym: "name: Sequence motif recognition (protein)" EXACT [http://edamontology.org] is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) is_a: EDAM_operation:0239 ! Sequence motif recognition [Term] id: EDAM_operation:0415 name: Nucleic acid feature prediction namespace: operation subset: operations ! alt_id: EDAM_operation:0381 def: "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org] comment: Methods typically involve scanning for known motifs, patterns and regular expressions. synonym: "Sequence feature detection (nucleic acid)" EXACT [http://edamontology.org] is_a: EDAM_operation:0239 ! Sequence motif recognition is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) is_a: EDAM_operation:0253 ! Feature prediction relationship: has_output EDAM_data:1276 !{min_cardinality=1} ! Nucleic acid features relationship: has_topic EDAM_topic:3073 ! Nucleic acid feature detection [Term] id: EDAM_operation:0416 name: Epitope mapping namespace: operation subset: operations def: "Predict antigenic determinant sites (epitopes) in protein sequences." [http://edamontology.org] comment: Epitope mapping is commonly done during vaccine design. is_a: EDAM_operation:3087 ! Protein site detection is_a: EDAM_operation:2429 ! Mapping and assembly relationship: has_output EDAM_data:1326 ! Protein features (binding sites) relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] id: EDAM_operation:0417 name: Protein post-translation modification site prediction namespace: operation subset: operations def: "Predict post-translation modification sites in protein sequences." [http://edamontology.org] comment: Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. is_a: EDAM_operation:3087 ! Protein site detection relationship: has_output EDAM_data:1324 ! Protein features (post-translation modifications) relationship: has_topic EDAM_topic:0601 ! Protein modifications [Term] id: EDAM_operation:2489 name: Protein subcellular localization prediction namespace: operation subset: operations def: "Predict the subcellular localization of a protein sequence." [http://edamontology.org] comment: The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. synonym: "Protein targeting prediction" EXACT [http://edamontology.org] is_a: EDAM_operation:3084 ! Protein function prediction (from sequence) is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization [Term] id: EDAM_operation:0418 name: Protein signal peptide detection namespace: operation subset: operations def: "Detect or predict signal peptides and signal peptide cleavage sites in protein sequences." [http://edamontology.org] comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. is_a: EDAM_operation:3087 ! Protein site detection is_a: EDAM_operation:2489 ! Protein subcellular localization prediction relationship: has_output EDAM_data:1322 ! Protein features (signal peptides) relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization [Term] id: EDAM_operation:0419 name: Binding site prediction (from sequence) namespace: operation subset: operations def: "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." [http://edamontology.org] synonym: "Ligand-binding and active site prediction (from sequence)" EXACT [http://edamontology.org] is_a: EDAM_operation:3087 ! Protein site detection is_a: EDAM_operation:2575 ! Binding site prediction [Term] id: EDAM_operation:0420 name: Protein-nucleic acid binding prediction namespace: operation subset: operations def: "Predict RNA and DNA-binding binding sites in protein sequences." [http://edamontology.org] is_a: EDAM_operation:0419 ! Binding site prediction (from sequence) relationship: has_output EDAM_data:1326 !{min_cardinality=0} ! Protein features (binding sites) [Term] id: EDAM_operation:0421 name: Protein folding site prediction namespace: operation subset: operations def: "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization." [http://edamontology.org] is_a: EDAM_operation:3087 ! Protein site detection is_a: EDAM_operation:2415 ! Protein folding analysis relationship: has_output EDAM_data:2989 !{min_cardinality=1} ! Protein features (key folding sites) [Term] id: EDAM_operation:0422 name: Protein cleavage site prediction namespace: operation subset: operations def: "Detect or predict cleavage sites (enzymatic or chemical) in protein sequences." [http://edamontology.org] is_a: EDAM_operation:3087 ! Protein site detection relationship: has_output EDAM_data:1323 ! Protein features (cleavage sites) relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_operation:0423 name: Epitope mapping (MHC Class I) namespace: operation subset: operations def: "Predict epitopes that bind to MHC class I molecules." [http://edamontology.org] is_a: EDAM_operation:0416 ! Epitope mapping [Term] id: EDAM_operation:0424 name: Epitope mapping (MHC Class II) namespace: operation subset: operations def: "Predict epitopes that bind to MHC class II molecules." [http://edamontology.org] is_a: EDAM_operation:0416 ! Epitope mapping [Term] id: EDAM_operation:0411 name: Protein signal peptide detection (eukaryotes) namespace: operation subset: operations def: "Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins." [http://edamontology.org] is_a: EDAM_operation:0418 ! Protein signal peptide detection [Term] id: EDAM_operation:0412 name: Protein signal peptide detection (bacteria) namespace: operation subset: operations def: "Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins." [http://edamontology.org] is_a: EDAM_operation:0418 ! Protein signal peptide detection [Term] id: EDAM_operation:3222 !{since=1.1} name: Peak calling namespace: operation subset: operations def: "Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data." [http://edamontology.org] comment: Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). synonym: "Protein binding peak detection" EXACT [http://edamontology.org] is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:2454 name: Gene and gene component prediction namespace: operation subset: operations def: "Detect, predict and identify genes or components of genes in DNA sequences." [http://edamontology.org] synonym: "Gene finding" EXACT [http://edamontology.org] is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] id: EDAM_operation:0425 name: Whole gene prediction namespace: operation subset: operations def: "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." [http://edamontology.org] is_a: EDAM_operation:2454 ! Gene and gene component prediction [Term] id: EDAM_operation:0426 name: Gene component prediction namespace: operation subset: operations def: "Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences." [http://edamontology.org] comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. is_a: EDAM_operation:2454 ! Gene and gene component prediction [Term] id: EDAM_operation:0427 name: Transposon prediction namespace: operation subset: operations def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [http://edamontology.org] is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1301 ! Nucleic acid features (mobile genetic elements) [Term] id: EDAM_operation:0428 name: PolyA signal detection namespace: operation subset: operations def: "Detect polyA signals in nucleotide sequences." [http://edamontology.org] is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1302 ! Nucleic acid features (PolyA signal or site) [Term] id: EDAM_operation:0429 name: Quadruplex formation site detection namespace: operation subset: operations ! alt_id: EDAM_operation:2455 def: "Detect quadruplex-forming motifs in nucleotide sequences." [http://edamontology.org] comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. is_a: EDAM_operation:0415 ! Nucleic acid feature prediction synonym: "Quadruplex structure prediction" EXACT [http://edamontology.org] relationship: has_output EDAM_data:1303 ! Nucleic acid features (quadruplexes) relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_operation:0430 name: CpG island and isochore detection namespace: operation subset: operations ! alt_id: EDAM_operation:0576 def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences." [http://edamontology.org] comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. synonym: "CpG island and isochores detection" EXACT [http://edamontology.org] synonym: "CpG island and isochores rendering" EXACT [http://edamontology.org] is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1304 ! Nucleic acid features (CpG island and isochore) relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] id: EDAM_operation:0431 name: Restriction site recognition namespace: operation subset: operations def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [http://edamontology.org] is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1305 ! Nucleic acid features (restriction sites) relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] id: EDAM_operation:0433 name: Splice site prediction namespace: operation subset: operations def: "Identify, predict or analyse splice sites in nucleotide sequences." [http://edamontology.org] comment: Methods might require a pre-mRNA or genomic DNA sequence. is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1307 ! Nucleic acid features (splice sites) relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] id: EDAM_operation:0453 name: Nucleosome formation potential prediction namespace: operation subset: operations def: "Predict nucleosome formation potential of DNA sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0432 ! Nucleosome formation or exclusion sequence prediction [Term] id: EDAM_operation:0432 name: Nucleosome formation or exclusion sequence prediction namespace: operation subset: operations def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [http://edamontology.org] is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1306 ! Nucleic acid features (nucleosome exclusion sequences) [Term] id: EDAM_operation:0434 name: Integrated gene prediction namespace: operation subset: operations def: "Predict whole gene structure using a combination of multiple methods to achieve better predictions." [http://edamontology.org] is_a: EDAM_operation:0425 ! Whole gene prediction [Term] id: EDAM_operation:0435 name: Operon prediction namespace: operation subset: operations def: "Find operons (operators, promoters and genes) in bacteria genes." [http://edamontology.org] is_a: EDAM_operation:0425 ! Whole gene prediction [Term] id: EDAM_operation:0464 name: tRNA gene prediction namespace: operation subset: operations def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [http://edamontology.org] is_a: EDAM_operation:0425 ! Whole gene prediction relationship: has_topic EDAM_topic:0663 ! tRNA [Term] id: EDAM_operation:0436 name: Coding region prediction namespace: operation subset: operations def: "Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences." [http://edamontology.org] is_a: EDAM_operation:0426 ! Gene component prediction relationship: has_output EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] id: EDAM_operation:0437 name: Selenocysteine insertion sequence (SECIS) prediction namespace: operation subset: operations def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [http://edamontology.org] comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. is_a: EDAM_operation:0426 ! Gene component prediction relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_operation:0438 name: Transcription regulatory element prediction namespace: operation subset: operations def: "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences." [http://edamontology.org] comment: This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. is_a: EDAM_operation:0426 ! Gene component prediction relationship: has_topic EDAM_topic:0110 ! Transcription relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites [Term] id: EDAM_operation:0439 name: Translation initiation site prediction namespace: operation subset: operations def: "Predict translation initiation sites, possibly by searching a database of sites." [http://edamontology.org] is_a: EDAM_operation:0436 ! Coding region prediction relationship: has_topic EDAM_topic:0108 ! Translation [Term] id: EDAM_operation:0440 name: Promoter prediction namespace: operation subset: operations def: "Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences." [http://edamontology.org] comment: Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. is_a: EDAM_operation:0438 ! Transcription regulatory element prediction relationship: has_output EDAM_data:1312 ! Gene features (promoter) [Term] id: EDAM_operation:0441 name: Transcription regulatory element prediction (DNA-cis) namespace: operation subset: operations def: "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." [http://edamontology.org] comment: Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. is_a: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] id: EDAM_operation:0442 name: Transcription regulatory element prediction (RNA-cis) namespace: operation subset: operations def: "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." [http://edamontology.org] comment: Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. is_a: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] id: EDAM_operation:0443 name: Transcription regulatory element prediction (trans) namespace: operation subset: operations def: "Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets." [http://edamontology.org] comment: Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. synonym: "Functional RNA identification" EXACT [http://edamontology.org] is_a: EDAM_operation:0438 ! Transcription regulatory element prediction relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_operation:0444 name: Matrix/scaffold attachment site prediction namespace: operation subset: operations def: "Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences." [http://edamontology.org] comment: MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. is_a: EDAM_operation:0438 ! Transcription regulatory element prediction relationship: has_output EDAM_data:1308 ! Nucleic acid features (matrix/scaffold attachment sites) [Term] id: EDAM_operation:0445 name: Transcription factor binding site prediction namespace: operation subset: operations def: "Identify or predict transcription factor binding sites in DNA sequences." [http://edamontology.org] is_a: EDAM_operation:0440 ! Promoter prediction relationship: has_output EDAM_data:1315 ! Gene features (TFBS) [Term] id: EDAM_operation:0446 name: Exonic splicing enhancer prediction namespace: operation subset: operations def: "Identify or predict exonic splicing enhancers (ESE) in exons." [http://edamontology.org] comment: An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. is_a: EDAM_operation:0440 ! Promoter prediction relationship: has_output EDAM_data:2397 ! Nucleic acid features (exon) relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] id: EDAM_operation:2008 name: siRNA duplex prediction namespace: operation subset: operations def: "Identify or predict siRNA duplexes in RNA." [http://edamontology.org] is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) relationship: has_output EDAM_data:2169 ! Nucleic acid features (siRNA) relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_operation:0465 name: siRNA binding specificity prediction namespace: operation subset: operations def: "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." [http://edamontology.org] is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_operation:0463 name: microRNA detection namespace: operation subset: operations def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence." [http://edamontology.org] is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) relationship: has_output EDAM_data:1310 ! Nucleic acid features (microRNA) [Term] id: EDAM_operation:0259 name: Sequence alignment comparison namespace: operation subset: operations def: "Compare (typically by aligning) two molecular sequence alignments." [http://edamontology.org] comment: See also 'Sequence profile alignment'. is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2424 ! Comparison [Term] id: EDAM_operation:0260 name: Sequence alignment conversion namespace: operation subset: operations def: "Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence)." [http://edamontology.org] is_a: EDAM_operation:3081 ! Sequence alignment editing [Term] id: EDAM_operation:0447 name: Sequence alignment quality evaluation namespace: operation subset: operations def: "Evaluate molecular sequence alignment accuracy." [http://edamontology.org] comment: Evaluation might be purely sequence-based or use structural information. is_a: EDAM_operation:2428 ! Evaluation and validation is_a: EDAM_operation:0258 ! Sequence alignment analysis [Term] id: EDAM_operation:0448 name: Sequence alignment analysis (conservation) namespace: operation subset: operations def: "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." [http://edamontology.org] comment: Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. is_a: EDAM_operation:0258 ! Sequence alignment analysis relationship: has_output EDAM_data:1415 ! Sequence alignment report (site conservation) [Term] id: EDAM_operation:0449 name: Sequence alignment analysis (site correlation) namespace: operation subset: operations def: "Analyse correlations between sites in a molecular sequence alignment." [http://edamontology.org] comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. is_a: EDAM_operation:0258 ! Sequence alignment analysis relationship: has_output EDAM_data:1416 ! Sequence alignment report (site correlation) [Term] id: EDAM_operation:0450 name: Sequence alignment analysis (chimeric sequence detection) namespace: operation subset: operations def: "Detects chimeric sequences (chimeras) from a sequence alignment." [http://edamontology.org] comment: A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_operation:0451 name: Sequence alignment analysis (recombination detection) namespace: operation subset: operations def: "Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment." [http://edamontology.org] comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] id: EDAM_operation:0452 name: Sequence alignment analysis (indel detection) namespace: operation subset: operations def: "Identify insertion, deletion and duplication events from a sequence alignment." [http://edamontology.org] comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] id: EDAM_operation:0457 name: Nucleic acid stitch profile plotting namespace: operation subset: operations def: "Calculate and plot a DNA or DNA/RNA stitch profile." [http://edamontology.org] comment: A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting relationship: has_output EDAM_data:1587 ! Nucleic acid stitch profile [Term] id: EDAM_operation:0458 name: Nucleic acid melting curve plotting namespace: operation subset: operations def: "Calculate and plot a DNA or DNA/RNA melting curve." [http://edamontology.org] is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting relationship: has_output EDAM_data:2958 ! Nucleic acid melting curve [Term] id: EDAM_operation:0459 name: Nucleic acid probability profile plotting namespace: operation subset: operations def: "Calculate and plot a DNA or DNA/RNA probability profile." [http://edamontology.org] is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting relationship: has_output EDAM_data:2959 ! Nucleic acid probability profile [Term] id: EDAM_operation:0460 name: Nucleic acid temperature profile plotting namespace: operation subset: operations def: "Calculate and plot a DNA or DNA/RNA temperature profile." [http://edamontology.org] is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting relationship: has_output EDAM_data:2960 ! Nucleic acid temperature profile [Term] id: EDAM_operation:2444 name: Protein secondary structure processing namespace: operation subset: operations def: "Process (read and / or write) protein secondary structure data." [http://edamontology.org] is_a: EDAM_operation:2482 ! Secondary structure processing is_a: EDAM_operation:2502 ! Protein data processing relationship: has_input EDAM_data:0876 !{min_cardinality=0} ! Protein features (secondary structure) relationship: has_output EDAM_data:0876 !{min_cardinality=0} ! Protein features (secondary structure) relationship: has_topic EDAM_topic:0694 ! Protein secondary structure [Term] id: EDAM_operation:0319 name: Protein secondary structure assignment namespace: operation subset: operations def: "Assign secondary structure from protein coordinate or experimental data." [http://edamontology.org] is_a: EDAM_operation:2444 ! Protein secondary structure processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:0876 !{min_cardinality=1} ! Protein features (secondary structure) relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] id: EDAM_operation:0267 name: Protein secondary structure prediction namespace: operation subset: operations def: "Predict secondary structure of protein sequences." [http://edamontology.org] comment: Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. synonym: "Secondary structure prediction (protein)" EXACT [http://edamontology.org] is_a: EDAM_operation:2444 ! Protein secondary structure processing is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:0876 !{min_cardinality=1} ! Protein features (secondary structure) relationship: has_topic EDAM_topic:0178 ! Protein secondary structure prediction [Term] id: EDAM_operation:0268 name: Protein super-secondary structure prediction namespace: operation subset: operations def: "Predict super-secondary structure of protein sequence(s)." [http://edamontology.org] comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. is_a: EDAM_operation:0267 ! Protein secondary structure prediction relationship: has_output EDAM_data:0877 ! Protein features (super-secondary) [Term] id: EDAM_operation:0534 name: Protein secondary structure assignment (from coordinate data) namespace: operation subset: operations def: "Assign secondary structure from protein coordinate data." [http://edamontology.org] is_a: EDAM_operation:0319 ! Protein secondary structure assignment is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) [Term] id: EDAM_operation:0535 name: Protein secondary structure assignment (from CD data) namespace: operation subset: operations def: "Assign secondary structure from circular dichroism (CD) spectroscopic data." [http://edamontology.org] is_a: EDAM_operation:0319 ! Protein secondary structure assignment relationship: has_input EDAM_data:0939 ! Protein circular dichroism (CD) spectroscopic data [Term] id: EDAM_operation:1847 name: DSSP secondary structure assignment namespace: operation subset: operations def: "Determine for residue the DSSP determined secondary structure in three-state (HSC)." [http://edamontology.org, WHATIF] xref: WHATIF: ResidueDSSP is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data) [Term] id: EDAM_operation:0467 name: Protein secondary structure prediction (integrated) namespace: operation subset: operations def: "Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions." [http://edamontology.org] is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0468 name: Protein secondary structure prediction (helices) namespace: operation subset: operations def: "Predict helical secondary structure of protein sequences." [http://edamontology.org] is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0469 name: Protein secondary structure prediction (turns) namespace: operation subset: operations def: "Predict turn structure (for example beta hairpin turns) of protein sequences." [http://edamontology.org] is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0470 name: Protein secondary structure prediction (coils) namespace: operation subset: operations def: "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." [http://edamontology.org] is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0471 name: Protein secondary structure prediction (disulfide bonds) namespace: operation subset: operations def: "Predict cysteine bonding state and disulfide bond partners in protein sequences." [http://edamontology.org] is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0269 name: Transmembrane protein prediction namespace: operation subset: operations def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [http://edamontology.org] is_a: EDAM_operation:0270 ! Transmembrane protein analysis is_a: EDAM_operation:0267 ! Protein secondary structure prediction relationship: has_output EDAM_data:1456 !{min_cardinality=1} ! Protein features (membrane regions) [Term] id: EDAM_operation:2456 name: GPCR classification namespace: operation subset: operations def: "Classify G-protein coupled receptors (GPCRs) into families and subfamilies." [http://edamontology.org] synonym: "G protein-coupled receptor (GPCR) classification" EXACT [http://edamontology.org] is_a: EDAM_operation:0473 ! GPCR analysis is_a: EDAM_operation:2995 ! Sequence classification relationship: has_output EDAM_data:0907 !{min_cardinality=1} ! Protein family [Term] id: EDAM_operation:2457 name: GPCR coupling selectivity prediction namespace: operation subset: operations def: "Predict G-protein coupled receptor (GPCR) coupling selectivity." [http://edamontology.org] is_a: EDAM_operation:0473 ! GPCR analysis is_a: EDAM_operation:2492 ! Protein interaction prediction is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:0896 !{min_cardinality=1} ! Protein report [Term] id: EDAM_operation:0473 name: GPCR analysis namespace: operation subset: operations def: "Analyse G-protein coupled receptor proteins (GPCRs)." [http://edamontology.org] synonym: "G protein-coupled receptor (GPCR) analysis" EXACT [http://edamontology.org] is_a: EDAM_operation:0270 ! Transmembrane protein analysis relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) relationship: has_topic EDAM_topic:0820 ! Membrane proteins [Term] id: EDAM_operation:0472 name: GPCR prediction namespace: operation subset: operations def: "Predict G protein-coupled receptors (GPCR)." [http://edamontology.org] synonym: "G protein-coupled receptor (GPCR) prediction" EXACT [http://edamontology.org] is_a: EDAM_operation:0269 ! Transmembrane protein prediction is_a: EDAM_operation:0473 ! GPCR analysis [Term] id: EDAM_operation:0474 name: Protein structure prediction namespace: operation subset: operations def: "Predict tertiary structure (backbone and side-chain conformation) of protein sequences." [http://edamontology.org] is_a: EDAM_operation:0271 ! Structure prediction is_a: EDAM_operation:2459 ! Structure processing (protein) is_a: EDAM_operation:2479 ! Protein sequence analysis is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:1460 !{min_cardinality=1} ! Protein structure relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction [Term] id: EDAM_operation:0475 name: Nucleic acid structure prediction namespace: operation subset: operations def: "Predict tertiary structure of DNA or RNA." [http://edamontology.org] comment: Methods might identify thermodynamically stable or evolutionarily conserved structures. is_a: EDAM_operation:0271 ! Structure prediction is_a: EDAM_operation:2519 ! Structure processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:1459 !{min_cardinality=1} ! Nucleic acid structure relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_operation:0476 name: Ab initio structure prediction namespace: operation subset: operations def: "Predict tertiary structure of protein sequence(s) without homologs of known structure." [http://edamontology.org] is_a: EDAM_operation:0474 ! Protein structure prediction relationship: has_topic EDAM_topic:0174 ! Ab initio structure prediction [Term] id: EDAM_operation:0477 name: Protein modelling namespace: operation subset: operations def: "Build a three-dimensional protein model based on known (for example homologs) structures." [http://edamontology.org] comment: The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. synonym: "Comparative modelling" EXACT [http://edamontology.org] synonym: "Homology modelling" EXACT [http://edamontology.org] synonym: "Homology structure modelling" EXACT [http://edamontology.org] synonym: "Protein structure comparative modelling" EXACT [http://edamontology.org] is_a: EDAM_operation:2406 ! Protein structure analysis is_a: EDAM_operation:0474 ! Protein structure prediction is_a: EDAM_operation:2426 ! Modelling and simulation relationship: has_topic EDAM_topic:0175 ! Homology modelling [Term] id: EDAM_operation:0478 name: Protein docking namespace: operation subset: operations def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [http://edamontology.org] comment: This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. is_a: EDAM_operation:0477 ! Protein modelling is_a: EDAM_operation:2492 ! Protein interaction prediction relationship: has_output EDAM_data:1461 !{min_cardinality=0} ! Protein-ligand complex relationship: has_output EDAM_data:2877 !{min_cardinality=0} ! Protein complex relationship: has_topic EDAM_topic:0177 ! Molecular docking [Term] id: EDAM_operation:0302 name: Protein threading namespace: operation subset: operations def: "Align molecular sequence to structure in 3D space (threading)." [http://edamontology.org] comment: Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. synonym: "Sequence-structure alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:0303 ! Protein fold recognition is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:1460 !{min_cardinality=1} ! Protein structure relationship: has_output EDAM_data:0893 !{min_cardinality=1} ! Sequence-structure alignment relationship: has_topic EDAM_topic:0175 ! Homology modelling relationship: has_topic EDAM_topic:0184 ! Threading [Term] id: EDAM_operation:0479 name: Protein modelling (backbone) namespace: operation subset: operations def: "Model protein backbone conformation." [http://edamontology.org] comment: Methods might require a preliminary C(alpha) trace. is_a: EDAM_operation:0477 ! Protein modelling [Term] id: EDAM_operation:0480 name: Protein modelling (side chains) namespace: operation subset: operations def: "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc." [http://edamontology.org] comment: Methods might use a residue rotamer library. is_a: EDAM_operation:0477 ! Protein modelling [Term] id: EDAM_operation:0481 name: Protein modelling (loops) namespace: operation subset: operations def: "Model loop conformation in protein structures." [http://edamontology.org] is_a: EDAM_operation:0477 ! Protein modelling [Term] id: EDAM_operation:1841 name: Rotamer likelihood prediction namespace: operation subset: operations def: "Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure." [http://edamontology.org, WHATIF] comment: Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. xref: WHATIF:ShowLikelyRotamers xref: WHATIF:ShowLikelyRotamers100 xref: WHATIF:ShowLikelyRotamers200 xref: WHATIF:ShowLikelyRotamers300 xref: WHATIF:ShowLikelyRotamers400 xref: WHATIF:ShowLikelyRotamers500 xref: WHATIF:ShowLikelyRotamers600 xref: WHATIF:ShowLikelyRotamers700 xref: WHATIF:ShowLikelyRotamers800 xref: WHATIF:ShowLikelyRotamers900 is_a: EDAM_operation:0480 ! Protein modelling (side chains) [Term] id: EDAM_operation:0482 name: Protein-ligand docking namespace: operation subset: operations def: "Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques." [http://edamontology.org] comment: Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. synonym: "Virtual ligand screening" EXACT [http://edamontology.org] is_a: EDAM_operation:0478 ! Protein docking relationship: has_output EDAM_data:1461 !{min_cardinality=1} ! Protein-ligand complex relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] id: EDAM_operation:0483 name: Structured RNA prediction and optimisation namespace: operation subset: operations def: "Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection." [http://edamontology.org] synonym: "RNA inverse folding" EXACT [http://edamontology.org] synonym: "Nucleic acid folding family identification" EXACT [http://edamontology.org] is_a: EDAM_operation:3095 ! Nucleic acid design is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_output EDAM_data:1234 ! Sequence set (nucleic acid) relationship: has_topic EDAM_topic:2953 ! Nucleic acid design [Term] id: EDAM_operation:0273 name: Protein interaction raw data analysis namespace: operation subset: operations def: "Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [http://edamontology.org] is_a: EDAM_operation:2949 ! Protein interaction analysis relationship: has_input EDAM_data:0905 ! Protein interaction raw data relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] id: EDAM_operation:2492 name: Protein interaction prediction namespace: operation subset: operations def: "Predict the interactions of proteins with other molecules." [http://edamontology.org] is_a: EDAM_operation:2405 ! Protein interaction data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:0906 !{min_cardinality=1} ! Protein interaction [Term] id: EDAM_operation:2464 name: Protein-protein interaction prediction namespace: operation subset: operations def: "Identify or predict protein-protein interactions, interfaces, binding sites etc." [http://edamontology.org] is_a: EDAM_operation:2492 ! Protein interaction prediction relationship: has_output EDAM_data:1565 !{min_cardinality=1} ! Protein-protein interaction relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] id: EDAM_operation:0274 name: Protein-protein interaction prediction (from protein sequence) namespace: operation subset: operations def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." [http://edamontology.org] is_a: EDAM_operation:2464 ! Protein-protein interaction prediction is_a: EDAM_operation:3084 ! Protein function prediction (from sequence) [Term] id: EDAM_operation:0275 name: Protein-protein interaction prediction (from protein structure) namespace: operation subset: operations def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [http://edamontology.org] is_a: EDAM_operation:2464 ! Protein-protein interaction prediction is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) [Term] id: EDAM_operation:2445 name: Protein interaction network processing namespace: operation subset: operations def: "Process (read and / or write) a network of protein interactions." [http://edamontology.org] is_a: EDAM_operation:2405 ! Protein interaction data processing is_a: EDAM_operation:2438 ! Pathway or network processing relationship: has_input EDAM_data:1663 !{min_cardinality=0} ! Pathway or network (protein-protein interaction) relationship: has_output EDAM_data:1663 !{min_cardinality=0} ! Pathway or network (protein-protein interaction) relationship: has_topic EDAM_topic:3044 ! Protein interaction networks [Term] id: EDAM_operation:0333 name: Zinc finger protein domain prediction and optimisation namespace: operation subset: operations def: "Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases)." [http://edamontology.org] is_a: EDAM_operation:0420 ! Protein-nucleic acid binding prediction is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_output EDAM_data:1567 ! Protein-nucleic acid interaction relationship: has_topic EDAM_topic:0150 ! Protein design [Term] id: EDAM_operation:0276 name: Protein interaction network analysis namespace: operation subset: operations def: "Analyse a network of protein interactions." [http://edamontology.org] is_a: EDAM_operation:2445 ! Protein interaction network processing is_a: EDAM_operation:2949 ! Protein interaction analysis is_a: EDAM_operation:2497 ! Pathway or network analysis relationship: has_input EDAM_data:1663 !{min_cardinality=1} ! Pathway or network (protein-protein interaction) relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_operation:0277 name: Protein interaction network comparison namespace: operation subset: operations def: "Compare two or more networks of protein interactions." [http://edamontology.org] is_a: EDAM_operation:0276 ! Protein interaction network analysis is_a: EDAM_operation:1778 ! Protein function comparison relationship: has_input EDAM_data:1663 !{min_cardinality=2} ! Pathway or network (protein-protein interaction) [Term] id: EDAM_operation:3197 !{since=1.1} name: Genetic variation analysis namespace: operation subset: operations def: "Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model." [http://edamontology.org] comment: Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. synonym: "Sequence variation analysis" EXACT [http://edamontology.org] synonym: "Genetic variation annotation" EXACT [http://edamontology.org] is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison relationship: has_output EDAM_data:0918 ! Nucleic acid features (variation) [Term] id: EDAM_operation:3227 !{since=1.1} name: Variant mapping namespace: operation subset: operations def: "Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence." [http://edamontology.org] comment: Methods often utilise a database of aligned reads. synonym: "Variant calling" EXACT [http://edamontology.org] is_a: EDAM_operation:3197 ! Genetic variation analysis [Term] id: EDAM_operation:3228 !{since=1.1} name: Structural variation discovery namespace: operation subset: operations def: "Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s)." [http://edamontology.org] comment: Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. is_a: EDAM_operation:3197 ! Genetic variation analysis [Term] id: EDAM_operation:3196 !{since=1.1} name: Genotyping namespace: operation subset: operations def: "Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence." [http://edamontology.org] comment: Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. is_a: EDAM_operation:3197 ! Genetic variation analysis ! Link frameshift error detection and SNP detection to this one [Term] id: EDAM_operation:3202 !{since=1.1} name: Mutation detection namespace: operation subset: operations def: "Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware." [http://edamontology.org] synonym: "Polymorphism detection" EXACT [http://edamontology.org] is_a: EDAM_operation:3197 ! Genetic variation analysis [Term] id: EDAM_operation:0484 name: SNP detection namespace: operation subset: operations def: "Find single nucleotide polymorphisms (SNPs) between sequences." [http://edamontology.org] comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. synonym: "Single nucleotide polymorphism detection" EXACT [http://edamontology.org] is_a: EDAM_operation:3202 ! Mutation detection is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_operation:3201 !{since=1.1} name: SNP calling namespace: operation subset: operations def: "Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism." [http://edamontology.org] comment: Operations usually score confidence in the prediction or some other statistical measure of evidence. is_a: EDAM_operation:0484 ! SNP detection [Term] id: EDAM_operation:0485 name: Radiation Hybrid Mapping namespace: operation subset: operations def: "Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers." [http://edamontology.org] is_a: EDAM_operation:2944 ! Physical mapping relationship: has_output EDAM_data:2870 !{min_cardinality=1} ! Radiation hybrid map [Term] id: EDAM_operation:3186 !{since=1.1} name: Bisulfite mapping namespace: operation subset: operations def: "The mapping of methylation sites in a DNA (genome) sequence." [http://edamontology.org] comment: Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. synonym: "Bisulfite sequence mapping" EXACT [http://edamontology.org] synonym: "Bisulfite sequence alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:2944 ! Physical mapping [Term] id: EDAM_operation:0486 name: Functional mapping namespace: operation subset: operations def: "Map the genetic architecture of dynamic complex traits." [http://edamontology.org] comment: This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0282 ! Genetic mapping [Term] id: EDAM_operation:0487 name: Haplotype inference namespace: operation subset: operations def: "Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated." [http://edamontology.org] comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). synonym: "Haplotype mapping" EXACT [http://edamontology.org] synonym: "Haplotype reconstruction" EXACT [http://edamontology.org] is_a: EDAM_operation:0283 ! Linkage analysis relationship: has_output EDAM_data:1863 !{min_cardinality=1} ! Haplotype map [Term] id: EDAM_operation:0488 name: Linkage disequilibrium calculation namespace: operation subset: operations def: "Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [http://edamontology.org] comment: Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. is_a: EDAM_operation:0283 ! Linkage analysis relationship: has_output EDAM_data:1634 !{min_cardinality=1} ! Gene annotation (linkage disequilibrium) [Term] id: EDAM_operation:0286 name: Codon usage analysis namespace: operation subset: operations ! alt_id: EDAM_operation:2494 def: "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." [http://edamontology.org] synonym: "synon: Codon usage table analysis" EXACT [http://edamontology.org] synonym: "synon: Codon usage data analysis" EXACT [http://edamontology.org] is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_input EDAM_data:2977 !{min_cardinality=0} ! Nucleic acid sequence relationship: has_input EDAM_data:1597 !{min_cardinality=0} ! Codon usage table relationship: has_output EDAM_data:1597 !{min_cardinality=0} ! Codon usage table relationship: has_output EDAM_data:0914 !{min_cardinality=0} ! Codon usage report relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] id: EDAM_operation:2433 name: Codon usage table processing namespace: operation subset: operations def: "Process (read and / or write) a codon usage table." [http://edamontology.org] is_a: EDAM_operation:0286 ! Codon usage analysis relationship: has_input EDAM_data:1597 !{min_cardinality=0} ! Codon usage table relationship: has_output EDAM_data:1597 !{min_cardinality=0} ! Codon usage table [Term] id: EDAM_operation:0287 name: Base position variability plotting namespace: operation subset: operations def: "Identify and plot third base position variability in a nucleotide sequence." [http://edamontology.org] is_a: EDAM_operation:0286 ! Codon usage analysis relationship: has_output EDAM_data:1263 !{min_cardinality=1} ! Sequence composition (base position variability) relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] id: EDAM_operation:0489 name: Genetic code prediction namespace: operation subset: operations def: "Predict genetic code from analysis of codon usage data." [http://edamontology.org] is_a: EDAM_operation:0286 ! Codon usage analysis is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:1598 !{min_cardinality=1} ! Genetic code [Term] id: EDAM_operation:2962 name: Codon usage bias calculation namespace: operation subset: operations def: "Calculate codon usage bias." [http://edamontology.org] is_a: EDAM_operation:0286 ! Codon usage analysis relationship: has_output EDAM_data:2865 !{min_cardinality=1} ! Codon usage bias [Term] id: EDAM_operation:2963 name: Codon usage bias plotting namespace: operation subset: operations def: "Generate a codon usage bias plot." [http://edamontology.org] is_a: EDAM_operation:2962 ! Codon usage bias calculation relationship: has_output EDAM_data:1600 !{min_cardinality=1} ! Codon usage bias plot [Term] id: EDAM_operation:2964 name: Codon usage fraction calculation namespace: operation subset: operations def: "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." [http://edamontology.org] is_a: EDAM_operation:0286 ! Codon usage analysis relationship: has_output EDAM_data:1602 !{min_cardinality=1} ! Codon usage fraction difference [Term] id: EDAM_operation:0284 name: Codon usage table generation namespace: operation subset: operations def: "Calculate codon usage statistics and create a codon usage table." [http://edamontology.org] is_a: EDAM_operation:2433 ! Codon usage table processing relationship: has_output EDAM_data:1597 !{min_cardinality=1} ! Codon usage table [Term] id: EDAM_operation:0285 name: Codon usage table comparison namespace: operation subset: operations def: "Compare two or more codon usage tables." [http://edamontology.org] is_a: EDAM_operation:2433 ! Codon usage table processing is_a: EDAM_operation:2998 ! Nucleic acid comparison [Term] id: EDAM_operation:3193 !{since=1.1} name: Genome comparison namespace: operation subset: operations def: "Compare two (tpyically huge) molecular sequences that represent genomes." [http://edamontology.org] is_a: EDAM_operation:2451 ! Sequence comparison [Term] id: EDAM_operation:3194 !{since=1.1} name: Genome feature comparison namespace: operation subset: operations def: "Compare the features of two genome sequences." [http://edamontology.org] comment: Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. is_a: EDAM_operation:0256 ! Feature comparison [Term] id: EDAM_operation:3182 !{since=1.1} name: Genome alignment construction namespace: operation subset: operations def: "Align two or more (tpyically huge) molecular sequences that represent genomes." [http://edamontology.org] synonym: "Genome alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:0292 ! Sequence alignment construction [Term] id: EDAM_operation:3198 !{since=1.1} name: Oligonucleotide alignment construction namespace: operation subset: operations def: "Align short oligonucleotide sequences (reads) to a larger (genomic) sequence." [http://edamontology.org] comment: The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. synonym: "Short sequence read mapping" EXACT [http://edamontology.org] synonym: "Short read mapping" EXACT [http://edamontology.org] synonym: "Read mapping" EXACT [http://edamontology.org] synonym: "Short oligonucleotide alignment" EXACT [http://edamontology.org] synonym: "Oligonucleotide mapping" EXACT [http://edamontology.org] synonym: "Oligonucleotide alignment" EXACT [http://edamontology.org] synonym: "Short read alignment" EXACT [http://edamontology.org] synonym: "Read alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:0292 ! Sequence alignment construction [Term] id: EDAM_operation:3199 !{since=1.1} name: Split read mapping namespace: operation subset: operations def: "A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation." [http://edamontology.org] is_a: EDAM_operation:3198 ! Oligonucleotide alignment construction [Term] id: EDAM_operation:0491 name: Pairwise sequence alignment construction namespace: operation subset: operations def: "Align exactly two molecular sequences." [http://edamontology.org] synonym: "Pairwise sequence alignment" EXACT [http://edamontology.org] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. is_a: EDAM_operation:0292 ! Sequence alignment construction relationship: has_output EDAM_data:1381 !{min_cardinality=1} ! Sequence alignment (pair) [Term] id: EDAM_operation:0492 name: Multiple sequence alignment construction namespace: operation subset: operations def: "Align two or more molecular sequences." [http://edamontology.org] synonym: "Multiple sequence alignment" EXACT [http://edamontology.org] comment: This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. is_a: EDAM_operation:0292 ! Sequence alignment construction [Term] id: EDAM_operation:2089 name: Sequence alignment refinement namespace: operation subset: operations def: "Refine an existing sequence alignment." [http://edamontology.org] is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2425 ! Optimisation and refinement [Term] id: EDAM_operation:0493 name: Pairwise sequence alignment construction (local) namespace: operation subset: operations def: "Locally align exactly two molecular sequences." [http://edamontology.org] synonym: "Pairwise sequence alignment (local)" EXACT [http://edamontology.org] comment: Local alignment methods identify regions of local similarity. synonym: "Local pairwise sequence alignment construction" EXACT [http.//edamontology.org] is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction [Term] id: EDAM_operation:0494 name: Pairwise sequence alignment construction (global) namespace: operation subset: operations def: "Globally align exactly two molecular sequences." [http://edamontology.org] synonym: "Pairwise sequence alignment (global)" EXACT [http://edamontology.org] comment: Global alignment methods identify similarity across the entire length of the sequences. synonym: "Global pairwise sequence alignment construction" EXACT [http://edamontology.org] is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction [Term] id: EDAM_operation:0495 name: Multiple sequence alignment construction (local) namespace: operation subset: operations def: "Locally align two or more molecular sequences." [http://edamontology.org] synonym: "Multiple sequence alignment (local)" EXACT [http://edamontology.org] comment: Local alignment methods identify regions of local similarity. synonym: "Local multiple sequence alignment construction" EXACT [http.//edamontology.org] is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] id: EDAM_operation:0496 name: Multiple sequence alignment construction (global) namespace: operation subset: operations def: "Globally align two or more molecular sequences." [http://edamontology.org] synonym: "Multiple sequence alignment (global)" EXACT [http://edamontology.org] comment: Global alignment methods identify similarity across the entire length of the sequences. synonym: "Global multiple sequence alignment construction" EXACT [http.//edamontology.org] is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] id: EDAM_operation:0497 name: Multiple sequence alignment construction (constrained) namespace: operation subset: operations def: "Align two or more molecular sequences with user-defined constraints." [http://edamontology.org] synonym: "Multiple sequence alignment (constrained)" EXACT [http://edamontology.org] synonym: "Constrained multiple sequence alignment construction" EXACT [http.//edamontology.org] is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] id: EDAM_operation:0498 name: Multiple sequence alignment construction (consensus) namespace: operation subset: operations def: "Align two or more molecular sequences using multiple methods to achieve higher quality." [http://edamontology.org] synonym: "Multiple sequence alignment (consensus)" EXACT [http://edamontology.org] synonym: "Consensus multiple sequence alignment construction" EXACT [http.//edamontology.org] is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] id: EDAM_operation:0499 name: Multiple sequence alignment construction (phylogenetic tree-based) namespace: operation subset: operations def: "Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree." [http://edamontology.org] synonym: "Multiple sequence alignment (phylogenetic tree-based)" EXACT [http://edamontology.org] comment: This is supposed to give a more biologically meaningful alignment than standard alignments. synonym: "Phylogenetic tree-based multiple sequence alignment construction" EXACT [http.//edamontology.org] is_a: EDAM_operation:0492 ! Multiple sequence alignment construction relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:0500 name: Secondary structure alignment construction namespace: operation subset: operations def: "Align molecular secondary structure (represented as a 1D string)." [http://edamontology.org] synonym: "Secondary structure alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:2482 ! Secondary structure processing is_a: EDAM_operation:2931 ! Secondary structure comparison is_a: EDAM_operation:0294 ! Structure-based sequence alignment construction relationship: has_output EDAM_data:2366 !{min_cardinality=1} ! Secondary structure alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:0501 name: Protein secondary structure alignment construction namespace: operation subset: operations def: "Align protein secondary structures." [http://edamontology.org] synonym: "Protein secondary structure alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:0500 ! Secondary structure alignment construction is_a: EDAM_operation:2488 ! Protein secondary structure comparison synonym: "Secondary structure alignment (protein)" EXACT [http://edamontology.org] relationship: has_output EDAM_data:0878 !{min_cardinality=1} ! Secondary structure alignment (protein) [Term] id: EDAM_operation:0502 name: RNA secondary structure alignment construction namespace: operation subset: operations def: "Align RNA secondary structures." [http://edamontology.org] synonym: "RNA secondary structure alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:2439 ! RNA secondary structure processing is_a: EDAM_operation:0500 ! Secondary structure alignment construction synonym: "Secondary structure alignment (RNA)" EXACT [http://edamontology.org] relationship: has_input EDAM_data:0880 !{min_cardinality=2} ! RNA secondary structure record relationship: has_output EDAM_data:0881 !{min_cardinality=1} ! Secondary structure alignment (RNA) [Term] id: EDAM_operation:0503 name: Pairwise structure alignment construction namespace: operation subset: operations def: "Align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] synonym: "Pairwise structure alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:0504 name: Multiple structure alignment construction namespace: operation subset: operations def: "Align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] synonym: "Multiple structure alignment" EXACT [http://edamontology.org] comment: This includes methods that use an existing alignment. is_a: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:2488 name: Protein secondary structure comparison namespace: operation subset: operations def: "Compare protein secondary structures." [http://edamontology.org] synonym: "Protein secondary structure" EXACT [http://edamontology.org] is_a: EDAM_operation:2416 ! Protein secondary structure analysis is_a: EDAM_operation:2931 ! Secondary structure comparison is_a: EDAM_operation:2997 ! Protein comparison synonym: "Secondary structure comparison (protein)" EXACT [http://edamontology.org] relationship: has_input EDAM_data:0876 !{min_cardinality=2} ! Protein features (secondary structure) [Term] id: EDAM_operation:2487 name: Protein structure comparison namespace: operation subset: operations def: "Compare protein tertiary structures." [http://edamontology.org] comment: Methods might identify structural neighbors, find structural similarities or define a structural core. is_a: EDAM_operation:2459 ! Structure processing (protein) is_a: EDAM_operation:2483 ! Structure comparison is_a: EDAM_operation:2997 ! Protein comparison synonym: "Structure comparison (protein)" EXACT [http://edamontology.org] relationship: has_input EDAM_data:1460 !{min_cardinality=2} ! Protein structure relationship: has_output EDAM_data:0897 ! Protein property [Term] id: EDAM_operation:2518 name: Nucleic acid structure comparison namespace: operation subset: operations def: "Compare nucleic acid tertiary structures." [http://edamontology.org] synonym: "Structure comparison (nucleic acid)" EXACT [http://edamontology.org] is_a: EDAM_operation:2483 ! Structure comparison is_a: EDAM_operation:2481 ! Nucleic acid structure analysis is_a: EDAM_operation:2998 ! Nucleic acid comparison [Term] id: EDAM_operation:0505 name: Structure alignment (protein) namespace: operation subset: operations def: "Align protein tertiary structures." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:0506 name: Structure alignment (RNA) namespace: operation subset: operations def: "Align RNA tertiary structures." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:0507 name: Pairwise structure alignment construction (local) namespace: operation subset: operations def: "Locally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] synonym: "Pairwise structure alignment (local)" EXACT [http://edamontology.org] comment: Local alignment methods identify regions of local similarity, common substructures etc. synonym: "Local pairwise structure alignment construction" EXACT [http://edamontology.org] is_a: EDAM_operation:0503 ! Pairwise structure alignment construction [Term] id: EDAM_operation:0508 name: Pairwise structure alignment construction (global) namespace: operation subset: operations def: "Globally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] synonym: "Pairwise structure alignment (global)" EXACT [http://edamontology.org] comment: Global alignment methods identify similarity across the entire structures. synonym: "Global pairwise structure alignment construction" EXACT [http://edamontology.org] is_a: EDAM_operation:0503 ! Pairwise structure alignment construction [Term] id: EDAM_operation:0509 name: Multiple structure alignment construction (local) namespace: operation subset: operations def: "Locally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] synonym: "Multiple structure alignment (local)" EXACT [http://edamontology.org] comment: Local alignment methods identify regions of local similarity, common substructures etc. synonym: "Local multiple structure alignment construction" EXACT [http://edamontology.org] is_a: EDAM_operation:0504 ! Multiple structure alignment construction [Term] id: EDAM_operation:0510 name: Multiple structure alignment construction (global) namespace: operation subset: operations def: "Globally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] synonym: "Multiple structure alignment (global)" EXACT [http://edamontology.org] comment: Global alignment methods identify similarity across the entire structures. synonym: "Global multiple structure alignment construction" EXACT [http://edamontology.org] is_a: EDAM_operation:0504 ! Multiple structure alignment construction [Term] id: EDAM_operation:0296 name: Sequence profile generation namespace: operation subset: operations def: "Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment." [http://edamontology.org] is_a: EDAM_operation:2413 ! Sequence profile processing is_a: EDAM_operation:2463 ! Sequence alignment processing relationship: has_input EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment relationship: has_output EDAM_data:1354 !{min_cardinality=1} ! Sequence profile [Term] id: EDAM_operation:0298 name: Sequence profile alignment construction namespace: operation subset: operations def: "Align sequence profiles (representing sequence alignments)." [http://edamontology.org] synonym: "Sequence profile alignment" EXACT [http://edamontology.org] comment: See also 'Sequence alignment comparison'. is_a: EDAM_operation:2413 ! Sequence profile processing is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:1354 !{min_cardinality=2} ! Sequence profile relationship: has_output EDAM_data:0868 !{min_cardinality=1} ! Sequence profile alignment [Term] id: EDAM_operation:0300 name: Sequence-profile alignment construction namespace: operation subset: operations def: "Align molecular sequence(s) to sequence profile(s)." [http://edamontology.org] synonym: "Sequence-profile alignment" EXACT [http://edamontology.org] comment: A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. is_a: EDAM_operation:2413 ! Sequence profile processing is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:1354 !{min_cardinality=1} ! Sequence profile relationship: has_output EDAM_data:0869 !{min_cardinality=1} ! Sequence-profile alignment [Term] id: EDAM_operation:0511 name: Sequence profile alignment construction (pairwise) namespace: operation subset: operations def: "Align exactly two molecular profiles." [http://edamontology.org] synonym: "Sequence profile alignment (pairwise)" EXACT [http://edamontology.org] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. synonym: "Pairwise sequence profile alignment construction" EXACT [http://edamontology.org] is_a: EDAM_operation:0298 ! Sequence profile alignment construction [Term] id: EDAM_operation:0512 name: Sequence profile alignment construction (multiple) namespace: operation subset: operations def: "Align two or more molecular profiles." [http://edamontology.org] synonym: "Sequence profile alignment (multiple)" EXACT [http://edamontology.org] synonym: "Multiple sequence profile alignment construction" EXACT [http://edamontology.org] is_a: EDAM_operation:0298 ! Sequence profile alignment construction [Term] id: EDAM_operation:0297 name: Structural (3D) profile generation namespace: operation subset: operations def: "Generate some type of structural (3D) profile or template from a structure or structure alignment." [http://edamontology.org] synonym: "Structural profile generation" EXACT [http://edamontology.org] is_a: EDAM_operation:2411 ! Structural (3D) profile processing is_a: EDAM_operation:2952 ! Structure alignment processing is_a: EDAM_operation:2465 ! Structure processing relationship: has_input EDAM_data:0886 !{min_cardinality=1} ! Structure alignment relationship: has_input EDAM_data:0883 !{min_cardinality=1} ! Structure relationship: has_output EDAM_data:0889 !{min_cardinality=1} ! Structural (3D) profile [Term] id: EDAM_operation:0299 name: Structural (3D) profile alignment construction namespace: operation subset: operations def: "Align structural (3D) profiles or templates (representing structures or structure alignments)." [http://edamontology.org] synonym: "Structural (3D) profile alignment" EXACT [http://edamontology.org] synonym: "Structural profile alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:2411 ! Structural (3D) profile processing is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:0889 !{min_cardinality=2} ! Structural (3D) profile relationship: has_output EDAM_data:0890 !{min_cardinality=1} ! Structural (3D) profile alignment relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] id: EDAM_operation:0513 name: Structural (3D) profile alignment construction (pairwise) namespace: operation subset: operations def: "Align exactly two molecular Structural (3D) profiles." [http://edamontology.org] synonym: "Structural (3D) profile alignment (pairwise)" EXACT [http://edamontology.org] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. synonym: "Pairwise structural (3D) profile alignment construction" EXACT [http://edamontology.org] is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction [Term] id: EDAM_operation:0514 name: Structural (3D) profile alignment construction (multiple) namespace: operation subset: operations def: "Align two or more molecular 3D profiles." [http://edamontology.org] synonym: "Structural (3D) profile alignment (multiple)" EXACT [http://edamontology.org] synonym: "Multiple structural (3D) profile alignment construction" EXACT [http://edamontology.org] is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction [Term] id: EDAM_operation:0301 name: Sequence-3D profile alignment construction namespace: operation subset: operations def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment)." [http://edamontology.org] synonym: "Sequence-3D profile alignment" EXACT [http://edamontology.org] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. is_a: EDAM_operation:0303 ! Protein fold recognition is_a: EDAM_operation:2928 ! Alignment construction is_a: EDAM_operation:2403 ! Sequence analysis relationship: has_input EDAM_data:0889 !{min_cardinality=2} ! Structural (3D) profile relationship: has_output EDAM_data:0891 !{min_cardinality=1} ! Sequence-3D profile alignment relationship: has_topic EDAM_topic:0184 ! Threading [Term] id: EDAM_operation:0308 name: PCR primer design namespace: operation subset: operations def: "Design or predict oligonucleotide primers for PCR and DNA amplification etc." [http://edamontology.org] comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. synonym: "PCR primer prediction" EXACT [http://edamontology.org] is_a: EDAM_operation:2419 ! Primer and probe design relationship: has_input EDAM_data:2977 ! Nucleic acid sequence relationship: has_output EDAM_data:1240 !{min_cardinality=0} ! PCR primers relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] id: EDAM_operation:0309 name: Microarray probe design namespace: operation subset: operations def: "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [http://edamontology.org] synonym: "Microarray probe prediction" EXACT [http://edamontology.org] is_a: EDAM_operation:2419 ! Primer and probe design is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_input EDAM_data:2977 ! Nucleic acid sequence relationship: has_output EDAM_data:2717 !{min_cardinality=1} ! Oligonucleotide probe annotation relationship: has_topic EDAM_topic:0200 ! Microarrays relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] id: EDAM_operation:0307 name: Virtual PCR namespace: operation subset: operations def: "Perform in-silico (virtual) PCR." [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_operation:3187 name: Sequence contamination filtering namespace: operation subset: operations def: "Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced." [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_operation:0517 name: PCR primer design (for large scale sequencing) namespace: operation subset: operations def: "Predict primers for large scale sequencing." [http://edamontology.org] is_a: EDAM_operation:0308 ! PCR primer design relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:0518 name: PCR primer design (for genotyping polymorphisms) namespace: operation subset: operations def: "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [http://edamontology.org] is_a: EDAM_operation:0308 ! PCR primer design [Term] id: EDAM_operation:0519 name: PCR primer design (for gene transcription profiling) namespace: operation subset: operations def: "Predict primers for gene transcription profiling." [http://edamontology.org] is_a: EDAM_operation:0308 ! PCR primer design relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] id: EDAM_operation:0520 name: PCR primer design (for conserved primers) namespace: operation subset: operations def: "Predict primers that are conserved across multiple genomes or species." [http://edamontology.org] is_a: EDAM_operation:0308 ! PCR primer design [Term] id: EDAM_operation:0521 name: PCR primer design (based on gene structure) namespace: operation subset: operations def: "Predict primers based on gene structure, promoters, exon-exon junctions etc." [http://edamontology.org] is_a: EDAM_operation:0308 ! PCR primer design relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] id: EDAM_operation:0522 name: PCR primer design (for methylation PCRs) namespace: operation subset: operations def: "Predict primers for methylation PCRs." [http://edamontology.org] is_a: EDAM_operation:0308 ! PCR primer design [Term] id: EDAM_operation:3183 !{since=1.1} name: Localized reassembly namespace: operation subset: operations def: "Reconstruction of a sequence assembly in a localised area." [http://edamontology.org] is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:0523 name: Sequence assembly (mapping assembly) namespace: operation subset: operations def: "Sequence assembly by combining fragments using an existing backbone sequence." [http://edamontology.org] comment: The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:0524 name: Sequence assembly (de-novo assembly) namespace: operation subset: operations def: "Sequence assembly by combining fragments into a new, previously unknown sequence." [http://edamontology.org] comment: De-novo assemblers are much slower and more memory intensive than mapping assemblers. is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:0525 name: Sequence assembly (genome assembly) namespace: operation subset: operations def: "Sequence assembly capable on a very large scale such as assembly of whole genomes." [http://edamontology.org] is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:0526 name: Sequence assembly (EST assembly) namespace: operation subset: operations def: "Sequence assembly for EST sequences (transcribed mRNA)." [http://edamontology.org] comment: Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:2410 name: Gene expression analysis namespace: operation subset: operations def: "Analyse gene expression and regulation data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:2435 name: Gene expression profile processing namespace: operation subset: operations def: "Process (read and / or write) a gene expression profile." [http://edamontology.org] is_a: EDAM_operation:2495 ! Gene expression data processing relationship: has_input EDAM_data:0928 !{min_cardinality=0} ! Gene expression profile relationship: has_output EDAM_data:0928 !{min_cardinality=0} ! Gene expression profile relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] id: EDAM_operation:0312 name: Sequencing-based expression profile data processing namespace: operation subset: operations def: "Process (read and / or write) SAGE, MPSS or SBS experimental data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:2498 name: Sequencing-based expression profile data analysis namespace: operation subset: operations def: "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:2496 name: Gene regulatory network processing namespace: operation subset: operations def: "Process (read and / or write) a network of gene regulation." [http://edamontology.org] is_a: EDAM_operation:2438 ! Pathway or network processing relationship: has_input EDAM_data:2961 !{min_cardinality=0} ! Pathway or network (gene regulation) relationship: has_output EDAM_data:2961 !{min_cardinality=0} ! Pathway or network (gene regulation) relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks [Term] id: EDAM_operation:1781 name: Gene regulatory network analysis namespace: operation subset: operations def: "Analyse a known network of gene regulation." [http://edamontology.org] is_a: EDAM_operation:2496 ! Gene regulatory network processing is_a: EDAM_operation:2497 ! Pathway or network analysis relationship: has_input EDAM_data:2961 !{min_cardinality=1} ! Pathway or network (gene regulation) [Term] id: EDAM_operation:2437 name: Gene regulatory network prediction namespace: operation subset: operations def: "Predict a network of gene regulation." [http://edamontology.org] is_a: EDAM_operation:2496 ! Gene regulatory network processing is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:2961 !{min_cardinality=1} ! Pathway or network (gene regulation) [Term] id: EDAM_operation:3094 !{since=beta13} name: Protein interaction network prediction namespace: operation subset: operations def: "Predict a network of protein interactions." [http://edamontology.org] is_a: EDAM_operation:2445 ! Protein interaction network processing relationship: has_output EDAM_data:1663 !{min_cardinality=1} ! Pathway or network (protein-protein interaction) [Term] id: EDAM_operation:0316 name: Functional profiling namespace: operation subset: operations def: "Interpret (in functional terms) and annotate gene expression data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0532 ! Gene expression profile analysis [Term] id: EDAM_operation:0264 name: Splice transcript prediction namespace: operation subset: operations def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [http://edamontology.org] is_a: EDAM_operation:2499 ! Splicing analysis relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] id: EDAM_operation:2499 name: Splicing analysis namespace: operation subset: operations def: "Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences." [http://edamontology.org] synonym: "Splicing modelling" EXACT [http://edamontology.org] is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison is_a: EDAM_operation:2426 ! Modelling and simulation is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:1307 !{min_cardinality=1} ! Nucleic acid features (splice sites) relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] id: EDAM_operation:0313 name: Gene expression profile clustering namespace: operation subset: operations def: "Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles." [http://edamontology.org] is_a: EDAM_operation:0315 ! Gene expression profile comparison relationship: has_output EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_operation:3223 !{since=1.1} name: Differential expression analysis namespace: operation subset: operations def: "Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups." [http://edamontology.org] comment: Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. synonym: "Differentially expressed gene identification" EXACT [http://edamontology.org] is_a: EDAM_operation:0315 ! Gene expression profile comparison [Term] id: EDAM_operation:3224 !{since=1.1} name: Gene set testing namespace: operation subset: operations def: "Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc." [http://edamontology.org] comment: Gene sets can be defined beforehand by biological function, chromosome locations and so on. is_a: EDAM_operation:2435 ! Gene expression profile processing [Term] id: EDAM_operation:0314 name: Gene expression profile generation namespace: operation subset: operations def: "Generate a gene expression profile or pattern, for example from microarray data." [http://edamontology.org] synonym: "Expression profiling" EXACT [http://edamontology.org] synonym: "Gene expression profiling" EXACT [http://edamontology.org] is_a: EDAM_operation:2435 ! Gene expression profile processing relationship: has_output EDAM_data:0928 !{min_cardinality=1} ! Gene expression profile [Term] id: EDAM_operation:0315 name: Gene expression profile comparison namespace: operation subset: operations def: "Compare gene expression profiles or patterns." [http://edamontology.org] is_a: EDAM_operation:0532 ! Gene expression profile analysis is_a: EDAM_operation:2998 ! Nucleic acid comparison relationship: has_output EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_operation:2436 name: Gene expression profile annotation namespace: operation subset: operations def: "Annotate a gene expression profile with concepts from an ontology of gene functions." [http://edamontology.org] is_a: EDAM_operation:0532 ! Gene expression profile analysis is_a: EDAM_operation:0226 ! Annotation relationship: has_output EDAM_data:0928 !{min_cardinality=1} ! Gene expression profile [Term] id: EDAM_operation:0532 name: Gene expression profile analysis namespace: operation subset: operations def: "Analyse one or more gene expression profiles, typically to interpret them in functional terms." [http://edamontology.org] synonym: "Functional profiling" EXACT [http://edamontology.org] is_a: EDAM_operation:2435 ! Gene expression profile processing relationship: has_input EDAM_data:0928 !{min_cardinality=1} ! Gene expression profile [Term] id: EDAM_operation:0533 name: Gene expression profile pathway mapping namespace: operation subset: operations def: "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." [http://edamontology.org] is_a: EDAM_operation:0532 ! Gene expression profile analysis is_a: EDAM_operation:2497 ! Pathway or network analysis relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_operation:3232 !{since=1.1} name: Gene expression QTL analysis namespace: operation subset: operations def: "Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes." [http://edamontology.org] synonym: "eQTL profiling" EXACT [http://edamontology.org] synonym: "expression QTL profiling" EXACT [http://edamontology.org] synonym: "expression quantitative trait loci profiling" EXACT [http://edamontology.org] is_a: EDAM_operation:0532 ! Gene expression profile analysis relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_operation:0527 name: Tag mapping namespace: operation subset: operations def: "Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts." [http://edamontology.org] comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. synonym: "Tag to gene assignment" EXACT [http://edamontology.org] is_a: EDAM_operation:2436 ! Gene expression profile annotation relationship: has_output EDAM_data:0936 !{min_cardinality=0} ! Sequence tag profile (with gene assignment) [Term] id: EDAM_operation:0528 name: SAGE data processing namespace: operation subset: operations def: "Process (read and / or write) serial analysis of gene expression (SAGE) data." [http://edamontology.org] synonym: "Serial analysis of gene expression data processing" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:0529 name: MPSS data processing namespace: operation subset: operations def: "Process (read and / or write) massively parallel signature sequencing (MPSS) data." [http://edamontology.org] synonym: "Massively parallel signature sequencing data processing" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:0530 name: SBS data processing namespace: operation subset: operations def: "Process (read and / or write) sequencing by synthesis (SBS) data." [http://edamontology.org] synonym: "Sequencing by synthesis data processing" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:0531 name: Heat map generation namespace: operation subset: operations def: "Generate a heat map of gene expression from microarray data." [http://edamontology.org] comment: The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. is_a: EDAM_operation:0571 ! Microarray data rendering relationship: has_output EDAM_data:1636 !{min_cardinality=1} ! Heat map [Term] id: EDAM_operation:2934 name: Microarray cluster textual view rendering namespace: operation subset: operations def: "Visualise gene clusters with gene names." [http://edamontology.org] is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2935 name: Microarray wave graph rendering namespace: operation subset: operations synonym: "Microarray cluster temporal graph rendering" EXACT [http://edamontology.org] def: "Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis." [http://edamontology.org] comment: This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2936 name: Microarray dendrograph rendering namespace: operation subset: operations synonym: "Microarray checks view rendering" EXACT [http://edamontology.org] synonym: "Microarray view rendering" EXACT [http://edamontology.org] def: "Generate a dendrograph of raw, preprocessed or clustered microarray data." [http://edamontology.org] is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2937 name: Microarray proximity map rendering namespace: operation subset: operations synonym: "Microarray distance map rendering" EXACT [http://edamontology.org] def: "Generate a plot of distances (distance matrix) between genes." [http://edamontology.org] is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2938 name: Microarray tree or dendrogram view rendering namespace: operation subset: operations synonym: "Microarray matrix tree plot rendering" EXACT [http://edamontology.org] synonym: "Microarray 2-way dendrogram rendering" EXACT [http://edamontology.org] def: "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." [http://edamontology.org] is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2939 name: Microarray principal component rendering namespace: operation subset: operations def: "Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values." [http://edamontology.org] is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2940 name: Microarray scatter plot rendering namespace: operation subset: operations def: "Generate a scatter plot of microarray data, typically after principal component analysis." [http://edamontology.org] is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2941 name: Whole microarray graph view rendering namespace: operation subset: operations def: "Visualise gene expression data where each band (or line graph) corresponds to a sample." [http://edamontology.org] is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2942 name: Microarray tree-map rendering namespace: operation subset: operations def: "Visualise gene expression data after hierarchical clustering for representing hierarchical relationships." [http://edamontology.org] is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2943 name: Microarray Box-Whisker plot rendering namespace: operation subset: operations def: "Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles." [http://edamontology.org] is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2459 name: Structure processing (protein) namespace: operation subset: operations def: "Process (read and / or write) a protein tertiary structure." [http://edamontology.org] is_a: EDAM_operation:2465 ! Structure processing is_a: EDAM_operation:2502 ! Protein data processing relationship: has_input EDAM_data:1460 !{min_cardinality=0} ! Protein structure relationship: has_output EDAM_data:1460 !{min_cardinality=0} ! Protein structure relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure [Term] id: EDAM_operation:0243 name: Protein property calculation (from structure) namespace: operation subset: operations ! alt_id: EDAM_operation:3089 !{since=beta13} ! Not released def: "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." [http://edamontology.org] comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. is_a: EDAM_operation:2406 ! Protein structure analysis is_a: EDAM_operation:0250 ! Protein property calculation synonym: "Protein structural property calculation" EXACT [http://edamontology.org] relationship: has_output EDAM_data:0897 !{min_cardinality=0} ! Protein property relationship: has_topic EDAM_topic:0123 ! Protein properties relationship: has_topic EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_operation:0244 name: Protein flexibility and motion analysis namespace: operation subset: operations def: "Analyse flexibility and motion in protein structure." [http://edamontology.org] comment: Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. is_a: EDAM_operation:0243 ! Protein property calculation (from structure) is_a: EDAM_operation:2476 ! Molecular dynamics simulation relationship: has_output EDAM_data:1541 !{min_cardinality=1} ! Protein flexibility or motion report [Term] id: EDAM_operation:0245 name: Protein structural motif recognition namespace: operation subset: operations def: "Identify or screen for 3D structural motifs in protein structure(s)." [http://edamontology.org] comment: This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. synonym: "Protein structural feature identification" EXACT [http://edamontology.org] is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) relationship: has_output EDAM_data:0899 !{min_cardinality=1} ! Protein features (3D motif) relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces [Term] id: EDAM_operation:0246 name: Protein domain recognition namespace: operation subset: operations def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [http://edamontology.org] is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) relationship: has_output EDAM_data:0901 !{min_cardinality=1} ! Protein features (domains) relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_operation:0247 name: Protein architecture analysis namespace: operation subset: operations def: "Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s)." [http://edamontology.org] is_a: EDAM_operation:2406 ! Protein structure analysis relationship: has_output EDAM_data:0902 !{min_cardinality=1} ! Protein architecture report [Term] id: EDAM_operation:2474 name: Protein architecture comparison namespace: operation subset: operations def: "Compare the architecture of two or more protein structures." [http://edamontology.org] is_a: EDAM_operation:0247 ! Protein architecture analysis is_a: EDAM_operation:2488 ! Protein secondary structure comparison relationship: has_output EDAM_data:0902 !{min_cardinality=1} ! Protein architecture report [Term] id: EDAM_operation:2475 name: Protein architecture recognition namespace: operation subset: operations def: "Identify the architecture of a protein structure." [http://edamontology.org] is_a: EDAM_operation:0247 ! Protein architecture analysis is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) is_a: EDAM_operation:2996 ! Structure classification relationship: has_output EDAM_data:0902 !{min_cardinality=1} ! Protein architecture report [Term] id: EDAM_operation:0248 name: Residue interaction calculation namespace: operation subset: operations def: "Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s)." [http://edamontology.org] xref: WHATIF:ListContactsNormal xref: WHATIF:ListContactsRelaxed xref: WHATIF:ListSideChainContactsNormal xref: WHATIF:ListSideChainContactsRelaxed xref: WHATIF: SymShellOneXML xref: WHATIF: SymShellTwoXML xref: WHATIF: SymShellFiveXML xref: WHATIF: SymShellTenXML is_a: EDAM_operation:0243 ! Protein property calculation (from structure) relationship: has_output EDAM_data:1540 !{min_cardinality=1} ! Protein residue interactions relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] id: EDAM_operation:0272 name: Residue interaction prediction namespace: operation subset: operations def: "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences." [http://edamontology.org] comment: Methods usually involve multiple sequence alignment analysis. is_a: EDAM_operation:0243 ! Protein property calculation (from structure) is_a: EDAM_operation:2506 ! Sequence alignment analysis (protein) relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] id: EDAM_operation:0249 name: Torsion angle calculation namespace: operation subset: operations def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [http://edamontology.org] is_a: EDAM_operation:0243 ! Protein property calculation (from structure) relationship: has_output EDAM_data:2991 ! Protein torsion angle data [Term] id: EDAM_operation:0320 name: Protein structure assignment namespace: operation subset: operations def: "Assign a protein tertiary structure (3D coordinates) from raw experimental data." [http://edamontology.org] is_a: EDAM_operation:2459 ! Structure processing (protein) relationship: has_output EDAM_data:1460 !{min_cardinality=1} ! Protein structure relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] id: EDAM_operation:0321 name: Protein model evaluation namespace: operation subset: operations def: "Evaluate the quality or correctness a protein three-dimensional model." [http://edamontology.org] comment: Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. xref: WHATIF: UseFileDB is_a: EDAM_operation:0477 ! Protein modelling is_a: EDAM_operation:2428 ! Evaluation and validation relationship: has_output EDAM_data:1539 !{min_cardinality=1} ! Protein structural quality report relationship: has_topic EDAM_topic:2275 ! Molecular modelling relationship: has_topic EDAM_topic:0175 ! Homology modelling relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction [Term] id: EDAM_operation:0322 name: Protein model refinement namespace: operation subset: operations def: "Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc." [http://edamontology.org] comment: The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. xref: WHATIF: CorrectedPDBasXML is_a: EDAM_operation:0321 ! Protein model evaluation is_a: EDAM_operation:2425 ! Optimisation and refinement [Term] id: EDAM_operation:2239 name: 3D-1D scoring matrix generation namespace: operation subset: operations def: "Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data." [http://edamontology.org] comment: A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. is_a: EDAM_operation:0243 ! Protein property calculation (from structure) is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1499 !{min_cardinality=1} ! 3D-1D scoring matrix relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] id: EDAM_operation:2574 name: Protein hydropathy calculation namespace: operation subset: operations def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." [http://edamontology.org] is_a: EDAM_operation:0250 ! Protein property calculation relationship: has_output EDAM_data:2970 !{min_cardinality=1} ! Protein hydropathy data relationship: has_topic EDAM_topic:0137 ! Protein hydropathy [Term] id: EDAM_operation:0383 name: Protein hydropathy calculation (from structure) namespace: operation subset: operations def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." [http://edamontology.org] is_a: EDAM_operation:2574 ! Protein hydropathy calculation is_a: EDAM_operation:0243 ! Protein property calculation (from structure) [Term] id: EDAM_operation:0384 name: Protein solvent accessibility calculation namespace: operation subset: operations def: "Calculate solvent accessible or buried surface areas in protein structures." [http://edamontology.org] is_a: EDAM_operation:0243 ! Protein property calculation (from structure) relationship: has_output EDAM_data:1542 ! Protein solvent accessibility relationship: has_topic EDAM_topic:0137 ! Protein hydropathy [Term] id: EDAM_operation:1850 name: Protein cysteine and disulfide bond assignment namespace: operation subset: operations def: "Assign cysteine bonding state and disulfide bond partners in protein structures." [http://edamontology.org] is_a: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data) relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] id: EDAM_operation:0385 name: Protein hydropathy cluster calculation namespace: operation subset: operations def: "Identify clusters of hydrophobic or charged residues in a protein structure." [http://edamontology.org] is_a: EDAM_operation:0383 ! Protein hydropathy calculation (from structure) is_a: EDAM_operation:0393 ! Protein residue cluster calculation [Term] id: EDAM_operation:0386 name: Protein dipole moment calculation namespace: operation subset: operations def: "Calculate whether a protein structure has an unusually large net charge (dipole moment)." [http://edamontology.org] is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1545 !{min_cardinality=1} ! Protein dipole moment [Term] id: EDAM_operation:0387 name: Protein surface and interior calculation namespace: operation subset: operations def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [http://edamontology.org] is_a: EDAM_operation:0384 ! Protein solvent accessibility calculation relationship: has_output EDAM_data:1543 !{min_cardinality=1} ! Protein surface report relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces [Term] id: EDAM_operation:1816 name: Surface rendering namespace: operation subset: operations def: "Calculate the positions of dots that are homogeneously distributed over the surface of a molecule." [http://edamontology.org, WHATIF] comment: A dot has three coordinates (x,y,z) and (typically) a color. xref: WHATIF:GetSurfaceDots is_a: EDAM_operation:2462 ! Protein surface calculation is_a: EDAM_operation:0570 ! Structure rendering [Term] id: EDAM_operation:2460 name: Protein atom surface calculation namespace: operation subset: operations def: "Calculate the solvent accessibility for each atom in a structure." [http://edamontology.org, WHATIF] comment: Waters are not considered. is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] id: EDAM_operation:1817 name: Protein atom surface calculation (accessible) namespace: operation subset: operations def: "Calculate the solvent accessibility ('accessible surface') for each atom in a structure." [http://edamontology.org, WHATIF] comment: Waters are not considered. xref: WHATIF:AtomAccessibilitySolvent xref: WHATIF:AtomAccessibilitySolventPlus is_a: EDAM_operation:2460 ! Protein atom surface calculation [Term] id: EDAM_operation:1818 name: Protein atom surface calculation (accessible molecular) namespace: operation subset: operations def: "Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure." [http://edamontology.org, WHATIF] comment: Waters are not considered. xref: WHATIF:AtomAccessibilityMolecular xref: WHATIF:AtomAccessibilityMolecularPlus is_a: EDAM_operation:2460 ! Protein atom surface calculation [Term] id: EDAM_operation:2461 name: Protein residue surface calculation namespace: operation subset: operations def: "Calculate the solvent accessibility for each residue in a structure." [http://edamontology.org, WHATIF] is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] id: EDAM_operation:1819 name: Protein residue surface calculation (accessible) namespace: operation subset: operations def: "Calculate the solvent accessibility ('accessible surface') for each residue in a structure." [http://edamontology.org, WHATIF] comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). xref: WHATIF:ResidueAccessibilitySolvent is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] id: EDAM_operation:1820 name: Protein residue surface calculation (vacuum accessible) namespace: operation subset: operations def: "Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [http://edamontology.org, WHATIF] comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). xref: WHATIF:ResidueAccessibilityVacuum is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] id: EDAM_operation:1821 name: Protein residue surface calculation (accessible molecular) namespace: operation subset: operations def: "Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure." [http://edamontology.org, WHATIF] comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). xref: WHATIF:ResidueAccessibilityMolecular is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] id: EDAM_operation:1822 name: Protein residue surface calculation (vacuum molecular) namespace: operation subset: operations def: "Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [http://edamontology.org, WHATIF] comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). xref: WHATIF:ResidueAccessibilityVacuumMolecular is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] id: EDAM_operation:2462 name: Protein surface calculation namespace: operation subset: operations def: "Calculate the solvent accessibility of a structure as a whole." [http://edamontology.org, WHATIF] is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] id: EDAM_operation:1823 name: Protein surface calculation (accessible molecular) namespace: operation subset: operations def: "Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole." [http://edamontology.org, WHATIF] xref: WHATIF:TotAccessibilityMolecular is_a: EDAM_operation:2462 ! Protein surface calculation [Term] id: EDAM_operation:1824 name: Protein surface calculation (accessible) namespace: operation subset: operations def: "Calculate the solvent accessibility ('accessible surface') for a structure as a whole." [http://edamontology.org, WHATIF] xref: WHATIF:TotAccessibilitySolvent is_a: EDAM_operation:2462 ! Protein surface calculation [Term] id: EDAM_operation:1829 name: Cysteine bridge detection namespace: operation subset: operations def: "Detect cysteine bridges (from coordinate data) in a protein structure." [http://edamontology.org, WHATIF] xref: WHATIF:ShowCysteineBridge is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM_operation:1830 name: Free cysteine detection namespace: operation subset: operations def: "Detect free cysteines in a protein structure." [http://edamontology.org, WHATIF] comment: A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. xref: WHATIF:ShowCysteineFree is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM_operation:1831 name: Metal-bound cysteine detection namespace: operation subset: operations def: "Detect cysteines that are bound to metal in a protein structure." [http://edamontology.org, WHATIF] xref: WHATIF:ShowCysteineMetal is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM_operation:2575 name: Binding site prediction namespace: operation subset: operations def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [http://edamontology.org] synonym: "Ligand-binding and active site prediction" EXACT [http://edamontology.org] is_a: EDAM_operation:2492 ! Protein interaction prediction relationship: has_output EDAM_data:1325 !{min_cardinality=0} ! Protein features (active sites) relationship: has_output EDAM_data:1326 !{min_cardinality=0} ! Protein features (binding sites) relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] id: EDAM_operation:0388 name: Binding site prediction (from structure) namespace: operation subset: operations def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." [http://edamontology.org] synonym: "Ligand-binding and active site prediction (from structure)" EXACT [http://edamontology.org] is_a: EDAM_operation:0245 ! Protein structural motif recognition is_a: EDAM_operation:2575 ! Binding site prediction [Term] id: EDAM_operation:0389 name: Protein-nucleic acid binding site analysis namespace: operation subset: operations def: "Analyse RNA or DNA-binding sites in protein structure." [http://edamontology.org] is_a: EDAM_operation:2949 ! Protein interaction analysis relationship: has_input EDAM_data:1567 ! Protein-nucleic acid interaction relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions [Term] id: EDAM_operation:0390 name: Protein peeling namespace: operation subset: operations def: "Decompose a structure into compact or globular fragments (protein peeling)." [http://edamontology.org] is_a: EDAM_operation:0246 ! Protein domain recognition relationship: has_output EDAM_data:0901 !{min_cardinality=1} ! Protein features (domains) [Term] id: EDAM_operation:0391 name: Protein distance matrix calculation namespace: operation subset: operations def: "Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org] is_a: EDAM_operation:0248 ! Residue interaction calculation relationship: has_output EDAM_data:1546 !{min_cardinality=1} ! Protein distance matrix [Term] id: EDAM_operation:0394 name: Hydrogen bond calculation namespace: operation subset: operations def: "Identify potential hydrogen bonds between amino acids and other groups." [http://edamontology.org, WHATIF] comment: The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. xref: WHATIF:ShowHydrogenBondsM xref: WHATIF:ShowHydrogenBonds xref: WHATIF:ShowHydrogenBonds xref: WHATIF:HasHydrogenBonds is_a: EDAM_operation:0248 ! Residue interaction calculation relationship: has_output EDAM_data:1549 !{min_cardinality=1} ! Protein hydrogen bonds [Term] id: EDAM_operation:2491 name: Hydrogen bond calculation (inter-residue) namespace: operation subset: operations def: "Identify potential hydrogen bonds between amino acid residues." [http://edamontology.org, WHATIF] is_a: EDAM_operation:0394 ! Hydrogen bond calculation is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] id: EDAM_operation:1839 name: Salt bridge calculation namespace: operation subset: operations def: "Calculate (and possibly score) salt bridges in a protein structure." [http://edamontology.org, WHATIF] comment: Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. xref: WHATIF:HasSaltBridge xref: WHATIF:HasSaltBridgePlus xref: WHATIF:ShowSaltBridges xref: WHATIF:ShowSaltBridgesH is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] id: EDAM_operation:1846 name: HET group detection namespace: operation subset: operations def: "Identify HET groups in PDB files." [http://edamontology.org, WHATIF] comment: A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. xref: WHATIF: HETGroupNames is_a: EDAM_operation:1838 ! Residue contact calculation (residue-ligand) [Term] id: EDAM_operation:2950 ! alt_id: EDAM_operation:1833 name: Residue contact calculation namespace: operation subset: operations def: "Calculate contacts between residues and some other group in a protein structure." [http://edamontology.org, WHATIF] is_a: EDAM_operation:0248 ! Residue interaction calculation [Term] id: EDAM_operation:1838 name: Residue contact calculation (residue-ligand) namespace: operation subset: operations def: "Calculate contacts between residues and ligands in a protein structure." [http://edamontology.org, WHATIF] xref: WHATIF:ShowLigandContacts xref: WHATIF:ShowDrugContacts xref: WHATIF:ShowDrugContactsShort is_a: EDAM_operation:2950 ! Residue contact calculation is_a: EDAM_operation:0388 ! Binding site prediction (from structure) [Term] id: EDAM_operation:2490 name: Residue contact calculation (residue-residue) namespace: operation subset: operations def: "Calculate contacts between residues in a protein structure." [http://edamontology.org, WHATIF] is_a: EDAM_operation:2950 ! Residue contact calculation [Term] id: EDAM_operation:0392 name: Protein contact map calculation namespace: operation subset: operations def: "Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure." [http://edamontology.org] is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) relationship: has_output EDAM_data:1547 !{min_cardinality=1} ! Protein contact map [Term] id: EDAM_operation:0393 name: Protein residue cluster calculation namespace: operation subset: operations def: "Calculate clusters of contacting residues in protein structures." [http://edamontology.org] comment: Cluster of contacting residues might be key structural residues. is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) relationship: has_output EDAM_data:1548 !{min_cardinality=1} ! Protein residue 3D cluster [Term] id: EDAM_operation:1832 name: Residue contact calculation (residue-nucleic acid) namespace: operation subset: operations def: "Calculate protein residue contacts with nucleic acids in a structure." [http://edamontology.org, WHATIF] xref: WHATIF:HasNucleicContacts xref: WHATIF:ShowProteiNucleicContacts is_a: EDAM_operation:2950 ! Residue contact calculation is_a: EDAM_operation:0389 ! Protein-nucleic acid binding site analysis is_a: EDAM_operation:0245 ! Protein structural motif recognition [Term] id: EDAM_operation:1834 name: Residue contact calculation (residue-metal) namespace: operation subset: operations def: "Calculate protein residue contacts with metal in a structure." [http://edamontology.org, WHATIF] xref: WHATIF:HasMetalContacts xref: WHATIF:HasMetalContactsPlus is_a: EDAM_operation:2950 ! Residue contact calculation is_a: EDAM_operation:0388 ! Binding site prediction (from structure) [Term] id: EDAM_operation:1835 name: Residue contact calculation (residue-negative ion) namespace: operation subset: operations def: "Calculate ion contacts in a structure (all ions for all side chain atoms)." [http://edamontology.org, WHATIF] xref: WHATIF:HasNegativeIonContacts xref: WHATIF:HasNegativeIonContactsPlus is_a: EDAM_operation:2950 ! Residue contact calculation [Term] id: EDAM_operation:1837 name: Residue symmetry contact calculation namespace: operation subset: operations def: "Calculate the number of symmetry contacts made by residues in a protein structure." [http://edamontology.org, WHATIF] comment: A symmetry contact is a contact between two atoms in different asymmetric unit. xref: WHATIF:SymmetryContact is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] id: EDAM_operation:0396 name: Ramachandran plot calculation namespace: operation subset: operations def: "Calculate a Ramachandran plot of a protein structure." [http://edamontology.org] is_a: EDAM_operation:0249 ! Torsion angle calculation relationship: has_output EDAM_data:1544 !{min_cardinality=1} ! Ramachandran plot [Term] id: EDAM_operation:0397 name: Ramachandran plot evaluation namespace: operation subset: operations def: "Analyse (typically to validate) a Ramachandran plot of a protein structure." [http://edamontology.org] is_a: EDAM_operation:1844 ! Dihedral angle validation relationship: has_input EDAM_data:1544 !{min_cardinality=1} ! Ramachandran plot relationship: has_output EDAM_data:1539 ! Protein structural quality report [Term] id: EDAM_operation:1825 name: Backbone torsion angle calculation namespace: operation subset: operations def: "Calculate for each residue in a protein structure all its backbone torsion angles." [http://edamontology.org, WHATIF] xref: WHATIF:ResidueTorsionsBB is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] id: EDAM_operation:1826 name: Full torsion angle calculation namespace: operation subset: operations def: "Calculate for each residue in a protein structure all its torsion angles." [http://edamontology.org, WHATIF] xref: WHATIF:ResidueTorsions is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] id: EDAM_operation:1827 name: Cysteine torsion angle calculation namespace: operation subset: operations def: "Calculate for each cysteine (bridge) all its torsion angles." [http://edamontology.org, WHATIF] xref: WHATIF:CysteineTorsions is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] id: EDAM_operation:1828 name: Tau angle calculation namespace: operation subset: operations def: "For each amino acid in a protein structure calculate the backbone angle tau." [http://edamontology.org, WHATIF] comment: Tau is the backbone angle N-Calpha-C (angle over the C-alpha). xref: WHATIF:ShowTauAngle is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] id: EDAM_operation:0536 name: Protein structure assignment (from X-ray crystallographic data) namespace: operation subset: operations def: "Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data." [http://edamontology.org] is_a: EDAM_operation:0320 ! Protein structure assignment relationship: has_input EDAM_data:0937 !{min_cardinality=1} ! Protein X-ray crystallographic data [Term] id: EDAM_operation:0537 name: Protein structure assignment (from NMR data) namespace: operation subset: operations def: "Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data." [http://edamontology.org] is_a: EDAM_operation:0320 ! Protein structure assignment relationship: has_input EDAM_data:0938 !{min_cardinality=1} ! Protein NMR data [Term] id: EDAM_operation:0395 name: Residue non-canonical interaction detection namespace: operation subset: operations def: "Calculate non-canonical atomic interactions in protein structures." [http://edamontology.org] is_a: EDAM_operation:0248 ! Residue interaction calculation is_a: EDAM_operation:0321 ! Protein model evaluation relationship: has_output EDAM_data:1550 !{min_cardinality=1} ! Protein non-canonical interactions [Term] id: EDAM_operation:1913 name: Residue validation namespace: operation subset: operations def: "Identify poor quality amino acid positions in protein structures." [http://edamontology.org, WHATIF] comment: The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). xref: WHATIF: UseResidueDB is_a: EDAM_operation:0321 ! Protein model evaluation [Term] id: EDAM_operation:1843 name: Residue packing validation namespace: operation subset: operations def: "Identify poorly packed residues in protein structures." [http://edamontology.org, WHATIF] xref: WHATIF: PackingQuality is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection [Term] id: EDAM_operation:1844 name: Dihedral angle validation namespace: operation subset: operations def: "Identify for each residue in a protein structure any improper dihedral (phi/psi) angles." [http://edamontology.org, WHATIF] xref: WHATIF: ImproperQualitySum xref: WHATIF: ImproperQualityMax is_a: EDAM_operation:0321 ! Protein model evaluation [Term] id: EDAM_operation:1836 name: Residue bump detection namespace: operation subset: operations def: "Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance." [http://edamontology.org, WHATIF] xref: WHATIF:ShowBumps is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection [Term] id: EDAM_operation:2443 name: Phylogenetic tree processing namespace: operation subset: operations def: "Process (read and / or write) a phylogenetic tree." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:0872 !{min_cardinality=0} ! Phylogenetic tree relationship: has_output EDAM_data:0872 !{min_cardinality=0} ! Phylogenetic tree relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:0550 name: Sequence alignment analysis (phylogenetic modelling) namespace: operation subset: operations def: "Identify a plausible model of DNA substitution that explains a DNA sequence alignment." [http://edamontology.org] is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) is_a: EDAM_operation:2426 ! Modelling and simulation relationship: has_output EDAM_data:1439 ! DNA substitution model relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:0554 name: Phylogenetic tree analysis (natural selection) namespace: operation subset: operations def: "Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive)." [http://edamontology.org] comment: Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. is_a: EDAM_operation:0324 ! Phylogenetic tree analysis [Term] id: EDAM_operation:0323 name: Phylogenetic tree construction namespace: operation subset: operations def: "Construct a phylogenetic tree." [http://edamontology.org] synonym: "Phylogenetic tree construction" EXACT [http://edamontology.org] comment: Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. synonym: "Phylogenetic tree generation" EXACT [http://edamontology.org] is_a: EDAM_operation:2443 ! Phylogenetic tree processing is_a: EDAM_operation:2995 ! Sequence classification relationship: has_output EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree relationship: has_topic EDAM_topic:0080 ! Sequence analysis relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:0325 name: Phylogenetic tree comparison namespace: operation subset: operations def: "Compare two or more phylogenetic trees." [http://edamontology.org] comment: For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. is_a: EDAM_operation:0324 ! Phylogenetic tree analysis is_a: EDAM_operation:2424 ! Comparison [Term] id: EDAM_operation:0326 name: Phylogenetic tree editing namespace: operation subset: operations def: "Edit a phylogenetic tree." [http://edamontology.org] is_a: EDAM_operation:2443 ! Phylogenetic tree processing is_a: EDAM_operation:3096 ! Editing relationship: has_input EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree relationship: has_output EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree [Term] id: EDAM_operation:0551 name: Phylogenetic tree analysis (shape) namespace: operation subset: operations def: "Analyse the shape (topology) of a phylogenetic tree." [http://edamontology.org] synonym: "Phylogenetic tree topology analysis" EXACT [http://edamontology.org] is_a: EDAM_operation:0324 ! Phylogenetic tree analysis relationship: has_output EDAM_data:1440 !{min_cardinality=1} ! Phylogenetic tree report (tree shape) [Term] id: EDAM_operation:0552 name: Phylogenetic tree bootstrapping namespace: operation subset: operations def: "Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree." [http://edamontology.org] is_a: EDAM_operation:0324 ! Phylogenetic tree analysis is_a: EDAM_operation:2428 ! Evaluation and validation relationship: has_output EDAM_data:1441 !{min_cardinality=1} ! Phylogenetic tree report (tree evaluation) [Term] id: EDAM_operation:0553 name: Phylogenetic tree analysis (gene family prediction) namespace: operation subset: operations def: "Predict families of genes and gene function based on their position in a phylogenetic tree." [http://edamontology.org] is_a: EDAM_operation:0324 ! Phylogenetic tree analysis relationship: has_output EDAM_data:0916 ! Gene annotation relationship: has_topic EDAM_topic:0194 ! Phylogenomics [Term] id: EDAM_operation:0538 name: Phylogenetic tree construction (data centric) namespace: operation subset: operations def: "Construct a phylogenetic tree from a specific type of data." [http://edamontology.org] is_a: EDAM_operation:0323 ! Phylogenetic tree construction [Term] id: EDAM_operation:0539 name: Phylogenetic tree construction (method centric) namespace: operation subset: operations def: "Construct a phylogenetic tree using a specific method." [http://edamontology.org] is_a: EDAM_operation:0323 ! Phylogenetic tree construction [Term] id: EDAM_operation:0540 name: Phylogenetic tree construction (from molecular sequences) namespace: operation subset: operations def: "Phylogenetic tree construction from molecular sequences." [http://edamontology.org] comment: Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) is_a: EDAM_operation:2403 ! Sequence analysis [Term] id: EDAM_operation:0541 name: Phylogenetic tree construction (from continuous quantitative characters) namespace: operation subset: operations def: "Phylogenetic tree construction from continuous quantitative character data." [http://edamontology.org] is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) relationship: has_input EDAM_data:1426 !{min_cardinality=1} ! Phylogenetic continuous quantitative data [Term] id: EDAM_operation:0542 name: Phylogenetic tree construction (from gene frequencies) namespace: operation subset: operations def: "Phylogenetic tree construction from gene frequency data." [http://edamontology.org] is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) relationship: has_input EDAM_data:2873 !{min_cardinality=1} ! Phylogenetic gene frequencies data relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] id: EDAM_operation:0543 name: Phylogenetic tree construction (from polymorphism data) namespace: operation subset: operations def: "Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data." [http://edamontology.org] is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) relationship: has_topic EDAM_topic:0199 ! Genetic variation [Term] id: EDAM_operation:0544 name: Phylogenetic species tree construction namespace: operation subset: operations def: "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." [http://edamontology.org] is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences) [Term] id: EDAM_operation:0327 name: Phylogenetic footprinting / shadowing namespace: operation subset: operations def: "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing)." [http://edamontology.org] comment: A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences) relationship: has_topic EDAM_topic:0194 ! Phylogenomics [Term] id: EDAM_operation:0545 name: Phylogenetic tree construction (parsimony methods) namespace: operation subset: operations def: "Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment." [http://edamontology.org] comment: This includes evolutionary parsimony (invariants) methods. is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0546 name: Phylogenetic tree construction (minimum distance methods) namespace: operation subset: operations def: "Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances." [http://edamontology.org] comment: This includes neighbor joining (NJ) clustering method. is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0547 name: Phylogenetic tree construction (maximum likelihood and Bayesian methods) namespace: operation subset: operations def: "Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution." [http://edamontology.org] comment: Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0548 name: Phylogenetic tree construction (quartet methods) namespace: operation subset: operations def: "Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely." [http://edamontology.org] is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0549 name: Phylogenetic tree construction (AI methods) namespace: operation subset: operations def: "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." [http://edamontology.org] is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0555 name: Phylogenetic tree construction (consensus) namespace: operation subset: operations def: "Compare two or more phylogenetic trees to produce a consensus tree." [http://edamontology.org] comment: Methods typically test for topological similarity between trees using for example a congruence index. is_a: EDAM_operation:0325 ! Phylogenetic tree comparison is_a: EDAM_operation:0323 ! Phylogenetic tree construction [Term] id: EDAM_operation:0556 name: Phylogenetic sub/super tree detection namespace: operation subset: operations def: "Compare two or more phylogenetic trees to detect subtrees or supertrees." [http://edamontology.org] is_a: EDAM_operation:0325 ! Phylogenetic tree comparison [Term] id: EDAM_operation:0557 name: Phylogenetic tree distances calculation namespace: operation subset: operations def: "Compare two or more phylogenetic trees to calculate distances between trees." [http://edamontology.org] is_a: EDAM_operation:0325 ! Phylogenetic tree comparison relationship: has_output EDAM_data:1442 !{min_cardinality=1} ! Phylogenetic tree report (tree distances) [Term] id: EDAM_operation:0558 name: Phylogenetic tree annotation namespace: operation subset: operations def: "Annotate a phylogenetic tree with terms from a controlled vocabulary." [http://edamontology.org] synonym: "CDAOAnnotattion" RELATED [http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation] is_a: EDAM_operation:0326 ! Phylogenetic tree editing is_a: EDAM_operation:0226 ! Annotation [Term] id: EDAM_operation:0328 name: Protein folding simulation namespace: operation subset: operations def: "Simulate the folding of a protein." [http://edamontology.org] is_a: EDAM_operation:2415 ! Protein folding analysis [Term] id: EDAM_operation:0329 name: Protein folding pathway prediction namespace: operation subset: operations def: "Predict the folding pathway(s) or non-native structural intermediates of a protein." [http://edamontology.org] is_a: EDAM_operation:2415 ! Protein folding analysis is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) [Term] id: EDAM_operation:1842 name: Proline mutation value calculation namespace: operation subset: operations def: "Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein." [http://edamontology.org, WHATIF] xref: WHATIF:ProlineMutationValue is_a: EDAM_operation:0331 ! Protein modelling (mutation) [Term] id: EDAM_operation:0330 name: Protein SNP mapping namespace: operation subset: operations def: "Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s)." [http://edamontology.org] is_a: EDAM_operation:0331 ! Protein modelling (mutation) relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) relationship: has_topic EDAM_topic:2277 ! SNPs [Term] id: EDAM_operation:0559 name: Peptide immunogen prediction and optimisation namespace: operation subset: operations def: "Predict and optimise peptide ligands that elicit an immunological response." [http://edamontology.org] is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_output EDAM_data:1460 ! Protein structure relationship: has_topic EDAM_topic:0150 ! Protein design relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] id: EDAM_operation:0560 name: DNA vaccine prediction and optimisation namespace: operation subset: operations def: "Predict or optimise DNA to elicit (via DNA vaccination) an immunological response." [http://edamontology.org] is_a: EDAM_operation:3095 ! Nucleic acid design is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_topic EDAM_topic:0804 ! Immunoinformatics relationship: has_topic EDAM_topic:2953 ! Nucleic acid design [Term] id: EDAM_operation:0561 name: Sequence reformatting namespace: operation subset: operations def: "Reformat (a file or other report of) molecular sequence(s)." [http://edamontology.org] is_a: EDAM_operation:0335 ! File reformatting is_a: EDAM_operation:2121 ! Sequence file processing [Term] id: EDAM_operation:0562 name: Sequence alignment reformatting namespace: operation subset: operations def: "Reformat (a file or other report of) molecular sequence alignment(s)." [http://edamontology.org] is_a: EDAM_operation:0335 ! File reformatting is_a: EDAM_operation:2122 ! Sequence alignment file processing [Term] id: EDAM_operation:0563 name: Codon usage table reformatting namespace: operation subset: operations def: "Reformat a codon usage table." [http://edamontology.org] is_a: EDAM_operation:0335 ! File reformatting is_a: EDAM_operation:2433 ! Codon usage table processing relationship: has_input EDAM_data:1597 !{min_cardinality=1} ! Codon usage table relationship: has_output EDAM_data:1597 !{min_cardinality=1} ! Codon usage table [Term] id: EDAM_operation:1848 name: Structure reformatting namespace: operation subset: operations def: "Reformat (a file or other report of) tertiary structure data." [http://edamontology.org, WHATIF] xref: WHATIF: PDBasXML is_a: EDAM_operation:2234 ! Structure file processing is_a: EDAM_operation:0335 ! File reformatting [Term] id: EDAM_operation:0564 name: Sequence rendering namespace: operation subset: operations def: "Visualise, format or render a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 !{min_cardinality=1} ! Sequence relationship: has_output EDAM_data:2969 !{min_cardinality=1} ! Sequence image [Term] id: EDAM_operation:2515 name: Sequence rendering (nucleic acid) namespace: operation subset: operations def: "Visualise, format or render a nucleic acid sequence." [http://edamontology.org] comment: Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. is_a: EDAM_operation:0564 ! Sequence rendering is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3208 !{since=1.1} name: Genome rendering namespace: operation subset: operations def: "Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence." [http://edamontology.org] synonym: "Genome browsing" EXACT [http://edamontology.org] synonym: "Genome viewing" EXACT [http://edamontology.org] synonym: "Genome visualisation" EXACT [http://edamontology.org] synonym: "Genome visualization" EXACT [http://edamontology.org] is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) [Term] id: EDAM_operation:2516 name: Sequence rendering (protein) namespace: operation subset: operations def: "Visualise, format or render a protein sequence." [http://edamontology.org] comment: Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. is_a: EDAM_operation:0564 ! Sequence rendering is_a: EDAM_operation:2447 ! Sequence processing (protein) [Term] id: EDAM_operation:0565 name: Sequence alignment rendering namespace: operation subset: operations def: "Visualise, format or print a molecular sequence alignment." [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2463 ! Sequence alignment processing relationship: has_input EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment relationship: has_output EDAM_data:1711 !{min_cardinality=1} ! Sequence alignment image [Term] id: EDAM_operation:2452 name: Sequence cluster processing namespace: operation subset: operations def: "Process (read and / or write) a sequence cluster." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:1235 !{min_cardinality=0} ! Sequence cluster relationship: has_output EDAM_data:1235 !{min_cardinality=0} ! Sequence cluster relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] id: EDAM_operation:0566 name: Sequence cluster rendering namespace: operation subset: operations def: "Visualise, format or render sequence clusters." [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2452 ! Sequence cluster processing relationship: has_input EDAM_data:1235 !{min_cardinality=1} ! Sequence cluster [Term] id: EDAM_operation:0567 name: Phylogenetic tree rendering namespace: operation subset: operations def: "Visualise or plot a phylogenetic tree." [http://edamontology.org] is_a: EDAM_operation:2443 ! Phylogenetic tree processing is_a: EDAM_operation:0337 ! Plotting and rendering relationship: has_output EDAM_data:0872 !{min_cardinality=1} ! Phylogenetic tree [Term] id: EDAM_operation:0568 name: RNA secondary structure rendering namespace: operation subset: operations def: "Visualise RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2439 ! RNA secondary structure processing relationship: has_input EDAM_data:0880 !{min_cardinality=1} ! RNA secondary structure record [Term] id: EDAM_operation:0569 name: Protein secondary structure rendering namespace: operation subset: operations def: "Render and visualise protein secondary structure." [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2444 ! Protein secondary structure processing relationship: has_input EDAM_data:0876 !{min_cardinality=1} ! Protein features (secondary structure) [Term] id: EDAM_operation:2485 name: Helical wheel rendering namespace: operation subset: operations def: "Render a helical wheel representation of protein secondary structure." [http://edamontology.org] is_a: EDAM_operation:0569 ! Protein secondary structure rendering relationship: has_output EDAM_data:2162 !{min_cardinality=1} ! Helical wheel [Term] id: EDAM_operation:2486 name: Topology diagram rendering namespace: operation subset: operations def: "Render a topology diagram of protein secondary structure." [http://edamontology.org] is_a: EDAM_operation:0569 ! Protein secondary structure rendering relationship: has_output EDAM_data:2992 ! Protein structure image [Term] id: EDAM_operation:2241 name: Transmembrane protein rendering namespace: operation subset: operations def: "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." [http://edamontology.org] is_a: EDAM_operation:0569 ! Protein secondary structure rendering is_a: EDAM_operation:0270 ! Transmembrane protein analysis relationship: has_input EDAM_data:1456 !{min_cardinality=1} ! Protein features (membrane regions) relationship: has_output EDAM_data:2992 ! Protein structure image [Term] id: EDAM_operation:2482 name: Secondary structure processing namespace: operation subset: operations def: "Process (read and / or write) a molecular secondary structure." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:2081 !{min_cardinality=0} ! Secondary structure relationship: has_output EDAM_data:2081 !{min_cardinality=0} ! Secondary structure relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_operation:2465 name: Structure processing namespace: operation subset: operations ! alt_id: EDAM_operation:2484 def: "Process (read and / or write) a molecular tertiary structure." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:0883 !{min_cardinality=0} ! Structure relationship: has_output EDAM_data:0883 !{min_cardinality=0} ! Structure relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_operation:0570 name: Structure rendering namespace: operation subset: operations def: "Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation." [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2465 ! Structure processing relationship: has_input EDAM_data:0883 !{min_cardinality=1} ! Structure relationship: has_output EDAM_data:1710 ! Structure image [Term] id: EDAM_operation:0571 name: Microarray data rendering namespace: operation subset: operations def: "Visualise microarray data." [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2435 ! Gene expression profile processing relationship: has_input EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data relationship: has_output EDAM_data:2967 !{min_cardinality=1} ! Microarray image [Term] id: EDAM_operation:0572 name: Protein interaction network rendering namespace: operation subset: operations def: "Identify and analyse networks of protein interactions." [http://edamontology.org] is_a: EDAM_operation:3083 ! Pathway or network rendering is_a: EDAM_operation:2445 ! Protein interaction network processing relationship: has_input EDAM_data:1663 !{min_cardinality=1} ! Pathway or network (protein-protein interaction) [Term] id: EDAM_operation:0573 name: Map rendering namespace: operation subset: operations def: "Render and visualise a DNA map." [http://edamontology.org] synonym: "DNA map rendering" EXACT [http://edamontology.org] is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) is_a: EDAM_operation:2521 ! Map data processing relationship: has_input EDAM_data:1274 !{min_cardinality=1} ! Map [Term] id: EDAM_operation:3184 !{since=1.1} name: Sequence assembly rendering namespace: operation subset: operations def: "Render and visualise a DNA sequence assembly." [http://edamontology.org] synonym: "Assembly rendering" EXACT [http://edamontology.org] synonym: "Assembly visualisation" EXACT [http://edamontology.org] synonym: "Sequence assembly visualisation" EXACT [http://edamontology.org] is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) [Term] id: EDAM_operation:0574 name: Sequence motif rendering namespace: operation subset: operations def: "Render a sequence with motifs." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0564 ! Sequence rendering [Term] id: EDAM_operation:0577 name: DNA linear map rendering namespace: operation subset: operations def: "Draw a linear maps of DNA." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:0573 ! Map rendering [Term] id: EDAM_operation:0578 name: DNA circular map rendering namespace: operation subset: operations def: "Draw a circular maps of DNA, for example a plasmid map." [http://edamontology.org] is_a: EDAM_operation:0573 ! Map rendering [Term] id: EDAM_operation:0579 name: Operon rendering namespace: operation subset: operations def: "Visualise operon structure etc." [http://edamontology.org] is_a: EDAM_operation:0573 ! Map rendering relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] id: EDAM_operation:0575 name: Restriction map rendering namespace: operation subset: operations def: "Visualise restriction maps in DNA sequences." [http://edamontology.org] is_a: EDAM_operation:0573 ! Map rendering is_a: EDAM_operation:0431 ! Restriction site recognition relationship: has_output EDAM_data:1289 ! Restriction map !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! ! Data ! [Term] id: EDAM_data:0005 name: Resource type namespace: data subset: data def: "A type of computational resource used in bioinformatics." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_data:2831 name: Databank namespace: data subset: data def: "A flat-file (textual) data archive." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_data:2832 name: Web portal namespace: data subset: data def: "A web site providing data (web pages) on a common theme to a HTTP client." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_data:0581 name: Database namespace: data subset: data def: "A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_data:0007 name: Tool namespace: data subset: data def: "A bioinformatics package or tool, e.g. a standalone application or web service." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_data:1884 name: UniProt keywords namespace: data subset: data def: "A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0582 ! Ontology [Term] id: EDAM_data:0831 name: MeSH vocabulary namespace: data subset: data def: "Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0582 ! Ontology [Term] id: EDAM_data:0832 name: HGNC vocabulary namespace: data subset: data def: "Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0582 ! Ontology [Term] id: EDAM_data:0835 name: UMLS vocabulary namespace: data subset: data def: "Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0582 ! Ontology [Term] id: EDAM_data:2100 name: Type namespace: data subset: data ! alt_id: EDAM_data:2864 def: "A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values)." [http://edamontology.org] synonym: "Type" EXACT [http://purl.org/dc/elements/1.1/type] is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1866 name: Map type namespace: data subset: data def: "A designation of the type of map (genetic map, physical map, sequence map etc) or map set." [http://edamontology.org] comment: Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. is_a: EDAM_data:2100 ! Type is_a: EDAM_data:2019 ! Map attribute [Term] id: EDAM_data:1094 name: Sequence type namespace: data subset: data def: "A label (text token) describing a type of molecular sequence." [http://edamontology.org] comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). is_a: EDAM_data:2100 ! Type is_a: EDAM_data:2534 ! Sequence parameter relationship: is_identifier_of EDAM_data:2044 ! Sequence relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2132 name: Mutation type namespace: data subset: data def: "A type of point or block mutation, including insertion, deletion, change, duplication and moves." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2100 ! Type [Term] id: EDAM_data:0985 name: Molecule type namespace: data subset: data def: "A label (text token) describing the type a molecule." [http://edamontology.org] comment: For example, 'Protein', 'DNA', 'RNA' etc. example: "Protein" "DNA" "RNA" is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1122 name: Phylogenetic tree type namespace: data subset: data def: "A label (text token) describing the type of a phylogenetic tree." [http://edamontology.org] comment: For example 'nj', 'upgmp' etc. example: "nj" "upgmp" is_a: EDAM_data:2100 ! Type relationship: is_identifier_of EDAM_data:0872 ! Phylogenetic tree [Term] id: EDAM_data:2592 name: Cancer type namespace: data subset: data def: "A type (represented as a string) of cancer." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2100 ! Type [Term] id: EDAM_data:2524 name: Protein data namespace: data subset: data def: "Data concerning one or more protein molecules." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:2525 name: Nucleic acid data namespace: data subset: data def: "Data concerning one or more nucleic acid molecules." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:2248 name: Schema namespace: data subset: data def: "A data schema for organising or transforming data of some type." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:0843 name: Database entry namespace: data subset: data def: "An entry (retrievable via URL) from a biological database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0006 ! Data [Term] id: EDAM_data:2767 name: Identifier with metadata namespace: data subset: data def: "Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance." [http://edamontology.org] is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:2768 name: Gene symbol annotation namespace: data subset: data def: "Annotation about a gene symbol." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2767 ! Identifier with metadata [Term] id: EDAM_data:2087 name: Molecular property namespace: data subset: data def: "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." [http://edamontology.org] synonym: "Physicochemical property" EXACT [http://edamontology.org] synonym: "sequence_attribute" RELATED [SO:0000400] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:1917 name: Atomic property namespace: data subset: data def: "Data for an atom (in a molecular structure)." [http://edamontology.org] synonym: "General atomic property" EXACT [http://edamontology.org] is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:2050 name: Molecular property (general) namespace: data subset: data def: "General data for a molecule." [http://edamontology.org] synonym: "General molecular property" EXACT [http://edamontology.org] is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:2925 name: Sequence data namespace: data subset: data def: "Data concerning molecular sequence(s)." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:2044 ! Sequence consider: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:2044 name: Sequence namespace: data subset: data def: "One or more molecular sequences, possibly with associated annotation." [http://edamontology.org] comment: This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. synonym: "bio molecular sequence information" RELATED [http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation] relationship: has_topic EDAM_topic:0080 ! Sequence analysis is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2976 name: Protein sequence namespace: data subset: data def: "One or more protein sequences, possibly with associated annotation." [http://edamontology.org] synonym: "amino acid sequence information" RELATED [http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation] is_a: EDAM_data:2044 ! Sequence [Term] id: EDAM_data:2977 name: Nucleic acid sequence namespace: data subset: data def: "One or more nucleic acid sequences, possibly with associated annotation." [http://edamontology.org] synonym: "nucleotide sequence information" RELATED [http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation] is_a: EDAM_data:2044 ! Sequence [Term] id: EDAM_data:2955 name: Sequence report namespace: data subset: data def: "An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata)." [http://edamontology.org] synonym: "Sequence-derived report" EXACT [http://edamontology.org] is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:0855 name: Sequence metadata namespace: data subset: data def: "Basic or general information concerning molecular sequences." [http://edamontology.org] comment: This is used for such things as a report including the sequence identifier, type and length. is_a: EDAM_data:1254 ! Sequence property is_a: EDAM_data:2955 ! Sequence report is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:2522 name: Map data namespace: data subset: data def: "Data concerning a map of molecular sequence(s)." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:1274 ! Map consider: EDAM_data:2019 ! Map attribute [Term] id: EDAM_data:1274 name: Map namespace: data subset: data def: "A map of (typically one) DNA sequence annotated with positional or non-positional features." [http://edamontology.org] synonym: "DNA map" EXACT [http://edamontology.org] relationship: has_topic EDAM_topic:0102 ! Mapping is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:1864 name: Map set namespace: data subset: data def: "Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped." [http://edamontology.org] xref: Moby:GCP_CorrelatedMapSet xref: Moby:GCP_CorrelatedLinkageMapSet is_a: EDAM_data:2019 ! Map attribute [Term] id: EDAM_data:2019 name: Map attribute namespace: data subset: data def: "An attribute of a molecular map (genetic or physical)." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0102 ! Mapping [Term] id: EDAM_data:2080 name: Database hits namespace: data subset: data def: "A report of hits from searching a database of some type." [http://edamontology.org] is_a: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:0860 name: Sequence signature namespace: data subset: data def: "A classifier of sequences such as a sequence motif, profile or other diagnostic element." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1353 ! Sequence motif consider: EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:2981 name: Sequence motif data namespace: data subset: data def: "Data concerning specific or conserved pattern in molecular sequences." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:1353 name: Sequence motif namespace: data subset: data def: "Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_data:2762 name: Sequence motif metadata namespace: data subset: data def: "Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_data:2982 name: Sequence profile data namespace: data subset: data def: "Data concerning models representing a (typically multiple) sequence alignment." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:1354 name: Sequence profile namespace: data subset: data def: "Some type of statistical model representing a (typically multiple) sequence alignment." [http://edamontology.org] synonym: "sequence profile" EXACT [http://semanticscience.org/resource/SIO_010531] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_data:2788 name: Sequence profile metadata namespace: data subset: data def: "Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_data:1355 name: Protein signature namespace: data subset: data def: "An entry (sequence classifier and associated data) from the InterPro database." [http://edamontology.org] synonym: "InterPro entry" EXACT [http://edamontology.org] is_a: EDAM_data:0907 ! Protein family [Term] id: EDAM_data:2161 name: Sequence similarity plot namespace: data subset: data def: "A plot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] is_a: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:0862 name: Dotplot namespace: data subset: data def: "A dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] is_a: EDAM_data:2161 ! Sequence similarity plot [Term] id: EDAM_data:2539 name: Alignment data namespace: data subset: data def: "Data concerning an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. is_obsolete: true !{since=beta13} consider: EDAM_data:1916 ! Alignment consider: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:1916 name: Alignment namespace: data subset: data def: "An alignment of molecular sequences, structures or profiles derived from them." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2083 name: Alignment report namespace: data subset: data def: "An informative report about a molecular alignment of some type, including alignment-derived data or metadata." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2711 name: Genome metadata namespace: data subset: data def: "Provenance metadata or other general information concerning a genome as a whole." [http://edamontology.org] is_a: EDAM_data:0855 ! Sequence metadata [Term] id: EDAM_data:0867 name: Sequence alignment report namespace: data subset: data def: "An informative report of molecular sequence alignment-derived data or metadata." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_a: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:3181 !{since=1.1} name: Sequence assembly report namespace: data subset: data def: "An informative report about a DNA sequence assembly." [http://edamontology.org] is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:2598 name: Secondary structure alignment metadata namespace: data subset: data def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:0879 name: Secondary structure alignment metadata (protein) namespace: data subset: data def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:0882 name: Secondary structure alignment metadata (RNA) namespace: data subset: data def: "An informative report of RNA secondary structure alignment-derived data or metadata." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:2082 name: Matrix namespace: data subset: data def: "An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2855 name: Distance matrix namespace: data subset: data def: "A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity." [http://edamontology.org] is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:0870 name: Sequence distance matrix namespace: data subset: data def: "A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation." [http://edamontology.org] comment: Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. synonym: "Phylogenetic distance matrix" EXACT [http://edamontology.org] xref: Moby:phylogenetic_distance_matrix is_a: EDAM_data:2855 ! Distance matrix [Term] id: EDAM_data:2856 name: Structural distance matrix namespace: data subset: data def: "Distances (values representing similarity) between a group of molecular structures." [http://edamontology.org] is_a: EDAM_data:2855 ! Distance matrix [Term] id: EDAM_data:2523 name: Phylogenetic raw data namespace: data subset: data def: "Data concerning phylogeny, typically of molecular sequences." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Phylogenetic data" EXACT [http://edamontology.org] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:0871 name: Phylogenetic character data namespace: data subset: data def: "Data from which a phylogenetic tree may be generated." [http://edamontology.org] is_a: EDAM_data:2523 ! Phylogenetic raw data synonym: "Character" RELATED [http://www.evolutionaryontology.org/cdao.owl#Character] ! Phylogenetic character data! Also molecular sequences, microsatellites), polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments [Term] id: EDAM_data:0872 name: Phylogenetic tree namespace: data subset: data def: "The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length." [http://edamontology.org] comment: A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. synonym: "Tree" RELATED [http://www.evolutionaryontology.org/cdao.owl#Tree] xref: Moby:Tree xref: Moby:phylogenetic_tree xref: Moby:myTree relationship: has_topic EDAM_topic:0084 ! Phylogenetics is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:1438 name: Phylogenetic tree report namespace: data subset: data ! alt_id: EDAM_data:0873 def: "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Phylogenetic tree-derived report" EXACT [http://edamontology.org] is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:0874 name: Comparison matrix namespace: data subset: data def: "Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison." [http://edamontology.org] comment: The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). synonym: "Substitution matrix" EXACT [http://edamontology.org] is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:2053 name: Structural data namespace: data subset: data def: "Data concerning molecular structural data." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:0883 ! Structure consider: EDAM_data:2085 ! Structure report [Term] id: EDAM_data:2085 name: Structure report namespace: data subset: data def: "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." [http://edamontology.org] synonym: "Structure-derived report" EXACT [http://edamontology.org] is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2973 name: Secondary structure data namespace: data subset: data def: "Data concerning molecular secondary structure data." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:2081 ! Secondary structure consider: EDAM_data:2881 ! Secondary structure report [Term] id: EDAM_data:2881 name: Secondary structure report namespace: data subset: data def: "An informative report on general information, properties or features of one or more molecular secondary structures." [http://edamontology.org] synonym: "Secondary structure-derived report" EXACT [http://edamontology.org] is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2956 name: Protein secondary structure report namespace: data subset: data def: "An informative report about the properties or features of one or more protein secondary structures." [http://edamontology.org] is_a: EDAM_data:2881 ! Secondary structure report [Term] id: EDAM_data:1494 name: Structural transformation matrix namespace: data subset: data def: "Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures." [http://edamontology.org] is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:0887 name: Structure alignment report namespace: data subset: data def: "An informative report on molecular tertiary structure alignment-derived data." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_a: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:0889 name: Structural (3D) profile namespace: data subset: data def: "Some type of structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org] synonym: "3D profile" EXACT [http://edamontology.org] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] id: EDAM_data:0892 name: Protein sequence-structure scoring matrix namespace: data subset: data def: "Matrix of values used for scoring sequence-structure compatibility." [http://edamontology.org] is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:2528 name: Molecular data namespace: data subset: data def: "Data concerning a specific type of molecule." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Molecule-specific data" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:2529 ! Molecule report [Term] id: EDAM_data:2599 name: Molecular interaction namespace: data subset: data def: "Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." [http://edamontology.org] synonym: "Molecular interaction data" EXACT [http://edamontology.org] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2601 name: Small molecule data namespace: data subset: data def: "Data concerning one or more small molecules." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2016 name: Amino acid property namespace: data subset: data def: "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." [http://edamontology.org] synonym: "Amino acid data" EXACT [http://edamontology.org] is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:2979 name: Peptide property namespace: data subset: data def: "Data concerning small peptides." [http://edamontology.org] synonym: "Peptide data" EXACT [http://edamontology.org] is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:0895 name: Peptide annotation namespace: data subset: data def: "An informative report about a specific peptide." [http://edamontology.org] is_a: EDAM_data:0962 ! Small molecule annotation is_a: EDAM_data:2979 ! Peptide property relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids [Term] id: EDAM_data:2399 name: Gene annotation (transcript) namespace: data subset: data ! alt_id: EDAM_data:2703 def: "An informative report on a specific gene transcript, clone or EST." [http://edamontology.org] synonym: "Gene transcript annotation" EXACT [http://edamontology.org] synonym: "Gene annotation (clone or EST)" EXACT [http://edamontology.org] is_a: EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:0896 name: Protein report namespace: data subset: data def: "An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data." [http://edamontology.org] synonym: "Gene product annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2529 ! Molecule report relationship: has_topic EDAM_topic:0078 ! Protein analysis [Term] id: EDAM_data:0897 name: Protein property namespace: data subset: data def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model." [http://edamontology.org] comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. synonym: "Protein physicochemical property" EXACT [http://edamontology.org] is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:1537 name: Protein structure report namespace: data subset: data def: "Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains." [http://edamontology.org] ! alt_id: EDAM_data:0898 ! alt_id: EDAM_data:1538 ! alt_id: EDAM_data:2377 synonym: "Protein structure report (domain)" EXACT [http://edamontology.org] synonym: "Protein structure-derived report" EXACT [http://edamontology.org] synonym: "Protein structural property" EXACT [http://edamontology.org] synonym: "Protein report (structure)" EXACT [http://edamontology.org] synonym: "Protein property (structural)" EXACT [http://edamontology.org] is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:2085 ! Structure report ! [Term] born obsolete ! id: EDAM_data:3151 !{since=beta13} ! name: Protein property (physicochemical) ! namespace: data ! subset: data ! def: "A report of primarily non-positional data describing intrinsic physicochemical properties of a protein molecule." [http://edamontology.org] ! synonym: "Protein physicochemical property" EXACT [http://edamontology.org] ! is_obsolete: true !{since=beta13} ! consider: EDAM_data:0897 ! Protein property ! [Term] born obsolete ! id: EDAM_data:3152 !{since=beta13} ! name: Protein property (sequence) ! namespace: data ! subset: data ! def: "A non-positional property of a protein sequence." [http://edamontology.org] ! synonym: "Protein sequence property" EXACT [http://edamontology.org] ! is_obsolete: true !{since=beta13} ! consider: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:2313 name: Carbohydrate structure report namespace: data subset: data def: "Annotation on or information derived from one or more specific carbohydrate 3D structure(s)." [http://edamontology.org] is_a: EDAM_data:2085 ! Structure report [Term] id: EDAM_data:2879 name: Lipid structure report namespace: data subset: data def: "Annotation on or information derived from one or more specific lipid 3D structure(s)." [http://edamontology.org] is_a: EDAM_data:2085 ! Structure report [Term] id: EDAM_data:2987 name: Classification namespace: data subset: data def: "Data concerning a classification of molecular sequences, structures or other entities." [http://edamontology.org] comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. synonym: "Classification data" EXACT [http://edamontology.org] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_data:3028 name: Taxonomy namespace: data subset: data def: "Data concerning the classification, identification and naming of organisms." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Taxonomic data" EXACT [http://edamontology.org] is_a: EDAM_data:2987 ! Classification relationship: has_topic EDAM_topic:0637 ! Taxonomy [Term] id: EDAM_data:2986 name: Nucleic acid classification namespace: data subset: data def: "Data concerning the classification of nucleic acid sequences or structures." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Nucleic acid classification data" EXACT [http://edamontology.org] is_a: EDAM_data:2084 ! Nucleic acid report is_a: EDAM_data:2987 ! Classification relationship: has_topic EDAM_topic:0722 ! Nucleic acid classification [Term] id: EDAM_data:2980 name: Protein classification namespace: data subset: data def: "Data concerning the classification of protein sequences or structures." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Protein classification data" EXACT [http://edamontology.org] is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:2987 ! Classification relationship: has_topic EDAM_topic:0595 ! Protein classification [Term] id: EDAM_data:0900 name: Protein domain classification namespace: data subset: data def: "Data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org] is_a: EDAM_data:2980 ! Protein classification relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_data:3101 !{since=beta13} name: Protein domain classification node namespace: data subset: data def: "A node from a classification of protein structural domain(s)." [http://edamontology.org] is_a: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:0906 name: Protein interaction namespace: data subset: data def: "An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand." [http://edamontology.org] synonym: "Protein report (interaction)" EXACT [http://edamontology.org] is_a: EDAM_data:2599 ! Molecular interaction is_a: EDAM_data:0896 ! Protein report relationship: has_topic EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_data:0907 name: Protein family namespace: data subset: data def: "An informative report on a specific protein family or other group of classified proteins." [http://edamontology.org] synonym: "Protein family annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2980 ! Protein classification relationship: has_topic EDAM_topic:0724 ! Protein families [Term] id: EDAM_data:2354 name: RNA family annotation namespace: data subset: data def: "An informative report on a specific RNA family or other group of classified RNA sequences." [http://edamontology.org] is_a: EDAM_data:2986 ! Nucleic acid classification [Term] id: EDAM_data:2978 name: Reaction data namespace: data subset: data ! alt_id: EDAM_data:0908 def: "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Reaction annotation" EXACT [http://edamontology.org] synonym: "Enzyme kinetics annotation" EXACT [http://edamontology.org] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2024 name: Enzyme kinetics data namespace: data subset: data def: "Data concerning chemical reaction(s) catalysed by enzyme(s)." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_a: EDAM_data:2978 ! Reaction data [Term] id: EDAM_data:0911 name: Nucleotide base annotation namespace: data subset: data def: "An informative report about a specific nucleotide base." [http://edamontology.org] is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2116 name: Nucleic acid features (codon) namespace: data subset: data def: "An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:2084 name: Nucleic acid report namespace: data subset: data def: "An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." [http://edamontology.org] is_a: EDAM_data:2529 ! Molecule report [Term] id: EDAM_data:0912 name: Nucleic acid property namespace: data subset: data def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule." [http://edamontology.org] comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. synonym: "Nucleic acid physicochemical property" EXACT [http://edamontology.org] is_a: EDAM_data:2084 ! Nucleic acid report is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:2086 name: Nucleic acid structure report namespace: data subset: data ! alt_id: EDAM_data:0913 def: "A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s)." [http://edamontology.org] comment: This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. synonym: "Nucleic acid structural property" EXACT [http://edamontology.org] synonym: "Nucleic acid property (structural)" EXACT [http://edamontology.org] is_a: EDAM_data:0912 ! Nucleic acid property is_a: EDAM_data:2085 ! Structure report [Term] id: EDAM_data:2927 name: Codon usage data namespace: data subset: data def: "Data concerning codon usage." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:1597 ! Codon usage table consider: EDAM_data:0914 ! Codon usage report [Term] id: EDAM_data:1597 name: Codon usage table namespace: data subset: data def: "Table of codon usage data calculated from one or more nucleic acid sequences." [http://edamontology.org] comment: A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] id: EDAM_data:0914 name: Codon usage report namespace: data subset: data def: "Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_a: EDAM_data:2048 ! Report relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] id: EDAM_data:2603 name: Microarray data namespace: data subset: data ! alt_id: EDAM_data:2541 def: "Image or hybridisation data for a microarray, typically a study of gene expression." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. See also EDAM_data:0931 ! Experiment annotation (microarray) synonym: "Gene expression data" EXACT [http://edamontology.org] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:3110 !{since=beta13} name: Raw microarray data namespace: data subset: data def: "Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment." [http://edamontology.org] comment: Such data as found in Affymetrix CEL or GPR files. is_a: EDAM_data:3117 ! Microarray hybridisation data is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:3111 !{since=beta13} name: Processed microarray data namespace: data subset: data ! alt_id: EDAM_data:0929 def: "Data generated from processing and analysis of probe set data from a microarray experiment." [http://edamontology.org] comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. synonym: "Microarray probe set data" EXACT [http://edamontology.org] synonym: "Gene expression report" EXACT [http://edamontology.org] synonym: "Gene annotation (expression)" EXACT [http://edamontology.org] is_a: EDAM_data:3117 ! Microarray hybridisation data is_a: EDAM_data:0928 ! Gene expression profile relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:3117 !{since=beta13} name: Microarray hybridisation data namespace: data subset: data def: "Data concerning the hybridisations measured during a microarray experiment." [http://edamontology.org] is_a: EDAM_data:2603 ! Microarray data relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:3112 !{since=beta13} name: Normalised microarray data namespace: data subset: data def: "The final processed (normalised) data for a set of hybridisations in a microarray experiment." [http://edamontology.org] comment: This combines data from all hybridisations. synonym: "Gene expression matrix" EXACT [http://edamontology.org] synonym: "Gene expression data matrix" EXACT [http://edamontology.org] is_a: EDAM_data:3117 ! Microarray hybridisation data [Term] id: EDAM_data:3113 !{since=beta13} name: Sample annotation namespace: data subset: data def: "Annotation on a biological sample, for example experimental factors and their values." [http://edamontology.org] comment: This might include compound and dose in a dose response experiment. is_a: EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_data:3115 !{since=beta13} name: Microarray annotation namespace: data subset: data def: "Annotation on the array itself used in a microarray experiment." [http://edamontology.org] comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. is_a: EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_data:3116 !{since=beta13} name: Microarray protocol annotation namespace: data subset: data def: "Annotation on laboratory and/or data processing protocols used in an microarray experiment." [http://edamontology.org] comment: This might describe e.g. the normalisation methods used to process the raw data. is_a: EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_data:2763 name: Locus annotation namespace: data subset: data def: "An informative report on a particular locus." [http://edamontology.org] synonym: "Locus report" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:0916 name: Gene annotation namespace: data subset: data ! alt_id: EDAM_data:2394 ! alt_id: EDAM_data:2361 def: "An informative report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org] comment: This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). synonym: "Gene report" EXACT [http://edamontology.org] synonym: "Gene annotation (functional)" EXACT [http://edamontology.org] xref: Moby:gene xref: Moby:GeneInfo xref: Moby_namespace:Human_Readable_Description is_a: EDAM_data:1276 ! Nucleic acid features relationship: has_topic EDAM_topic:0623 ! Genes, gene family or system [Term] id: EDAM_data:3148 !{since=beta13} name: Gene family annotation namespace: data subset: data def: "An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene." [http://edamontology.org] is_a: EDAM_data:2986 ! Nucleic acid classification is_a: EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:0918 name: Nucleic acid features (variation) namespace: data subset: data def: "A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms." [http://edamontology.org] synonym: "Sequence variation annotation" EXACT [http://edamontology.org] synonym: "sequence_alteration" RELATED [SO:0001059] is_a: EDAM_data:3122 ! Nucleic acid features (difference and change) relationship: has_topic EDAM_topic:0199 ! Genetic variation [Term] id: EDAM_data:0919 name: Gene annotation (chromosome) namespace: data subset: data def: "An informative report on a specific chromosome." [http://edamontology.org] comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. is_a: EDAM_data:0916 ! Gene annotation relationship: has_topic EDAM_topic:0624 ! Chromosomes [Term] id: EDAM_data:2602 name: Genotype and phenotype data namespace: data subset: data def: "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:0920 ! Genotype/phenotype annotation [Term] id: EDAM_data:0920 name: Genotype/phenotype annotation namespace: data subset: data ! alt_id: EDAM_data:2890 def: "An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes." [http://edamontology.org] is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2531 name: Experiment annotation namespace: data subset: data def: "Annotation on a wet lab experiment, such as experimental conditions." [http://edamontology.org] is_a: EDAM_data:2048 ! Report ! [Term] born obsolete ! id: EDAM_data:3109 !{since=beta13} ! name: Experimental measurement annotation ! namespace: data ! subset: data ! def: "Annotation on the result of a wet lab experiment." [http://edamontology.org] ! is_obsolete: true !{since=beta13} ! consider: EDAM_data:3108 ! Experimental measurement ! consider: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:2381 name: Experiment annotation (genotype) namespace: data subset: data def: "Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." [http://edamontology.org] is_a: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:3231 !{since=1.1} name: Experiment annotation (GWAS) namespace: data subset: data def: "Metadata on a genome-wide association study (GWAS)." [http://edamontology.org] synonym: "Experiment annotation (genome-wide association study)" EXACT [http://edamontology.org] is_a: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:0925 name: Sequence assembly namespace: data subset: data def: "An assembly of fragments of a (typically genomic) DNA sequence." [http://edamontology.org] comment: Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. synonym: "Sequence assembly" EXACT [http://en.wikipedia.org/wiki/Sequence_assembly] synonym: "sequence_assembly" EXACT [SO:0000353] synonym: "assembly" NARROW [SO:0001248] !{note="Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'."} is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:2028 name: Experimental data namespace: data subset: data def: "Raw data from or annotation on laboratory experiments." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. synonym: "Experimental measurement data" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:3108 ! Experimental measurement consider: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:3108 !{since=beta13} name: Experimental measurement namespace: data subset: data def: "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. synonym: "Raw experimental data" EXACT [http://edamontology.org] synonym: "Experimental measurement data" EXACT [http://edamontology.org] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2042 name: Evidence namespace: data subset: data def: "Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc." [http://edamontology.org] is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:0941 name: Electron microscopy model namespace: data subset: data def: "Annotation on a structural 3D model (volume map) from electron microscopy." [http://edamontology.org] comment: This might include the location in the model of the known features of a particular macromolecule. is_a: EDAM_data:0940 ! Electron microscopy volume map relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] id: EDAM_data:2971 name: Workflow data namespace: data subset: data def: "Data concerning a computational workflow." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:0949 ! Workflow metadata consider: EDAM_data:2972 ! Workflow [Term] id: EDAM_data:0949 name: Workflow metadata namespace: data subset: data def: "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata ! relationship: has_topic EDAM_topic:0769 ! Workflows [Term] id: EDAM_data:2972 name: Workflow namespace: data subset: data def: "A computational workflow." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data ! relationship: has_topic EDAM_topic:0769 ! Workflows [Term] id: EDAM_data:0950 name: Biological model namespace: data subset: data def: "A biological model which can be represented in mathematical terms." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0771 ! Biological models [Term] id: EDAM_data:2983 name: Pathway or network data namespace: data subset: data def: "Data concerning a specific biological pathway or network." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:2600 ! Pathway or network consider: EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_data:2984 name: Pathway or network report namespace: data subset: data def: "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." [http://edamontology.org] is_a: EDAM_data:2048 ! Report relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_data:2600 name: Pathway or network namespace: data subset: data def: "Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network)." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_data:1883 name: Annotated URI namespace: data subset: data def: "A URI along with annotation describing the data found at the address." [http://edamontology.org] xref: Moby:DescribedLink is_a: EDAM_data:2337 ! Metadata is_a: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:0954 name: Database cross-mapping namespace: data subset: data def: "A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases." [http://edamontology.org] comment: The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. is_a: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:2872 name: ID list namespace: data subset: data def: "A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data." [http://edamontology.org] is_a: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:2765 name: Term ID list namespace: data subset: data def: "One or more terms from one or more controlled vocabularies which are annotations on an entity." [http://edamontology.org] comment: The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. is_a: EDAM_data:2872 ! ID list [Term] id: EDAM_data:1111 name: EMBOSS listfile namespace: data subset: data def: "List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile)." [http://edamontology.org] is_a: EDAM_data:2872 ! ID list [Term] id: EDAM_data:2093 name: Data reference namespace: data subset: data def: "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology." [http://edamontology.org] comment: A list of database accessions or identifiers are usually included. is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2540 name: Data index data namespace: data subset: data def: "Data concerning an index of data." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Database index" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:0955 ! Data index consider: EDAM_data:0956 ! Data index report [Term] id: EDAM_data:0955 name: Data index namespace: data subset: data def: "An index of data of biological relevance." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] id: EDAM_data:3210 !{since=1.1} name: Genome index namespace: data subset: data def: "An index of a genome sequence." [http://edamontology.org] comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. is_a: EDAM_data:0955 ! Data index [Term] id: EDAM_data:0956 name: Data index report namespace: data subset: data def: "A report of an analysis of an index of biological data." [http://edamontology.org] synonym: "Database index annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2048 ! Report relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] id: EDAM_data:2048 name: Report namespace: data subset: data ! alt_id: EDAM_data:0969 ! alt_id: EDAM_data:3037 !{since=beta13} ! Not released def: "A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing. synonym: "Document" EXACT [http://edamontology.org] synonym: "Text" EXACT [http://edamontology.org] synonym: "document" RELATED [http://semanticscience.org/resource/SIO_000148] ! Related external synonym in EDAM without a note is usually almost exact. is_a: EDAM_data:0006 ! Data [Term] id: EDAM_data:1772 name: Score or penalty namespace: data subset: data ! alt_id: EDAM_data:2138 def: "A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty)." [http://edamontology.org] is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2529 name: Molecule report namespace: data subset: data def: "An informative report on a specific molecule." [http://edamontology.org] synonym: "Molecular report" EXACT [http://edamontology.org] is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:0962 name: Small molecule annotation namespace: data subset: data def: "An informative report on a specific chemical compound." [http://edamontology.org] synonym: "Chemical compound annotation" EXACT [http://edamontology.org] synonym: "Small molecule report" EXACT [http://edamontology.org] is_a: EDAM_data:2085 ! Structure report is_a: EDAM_data:2529 ! Molecule report relationship: has_topic EDAM_topic:0154 ! Small molecules [Term] id: EDAM_data:0963 name: Cell line annotation namespace: data subset: data def: "Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on." [http://edamontology.org] synonym: "Organism strain data" EXACT [http://edamontology.org] is_a: EDAM_data:2530 ! Organism annotation [Term] id: EDAM_data:2530 name: Organism annotation namespace: data subset: data def: "An informative report on a specific organism." [http://edamontology.org] is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2307 name: Virus annotation namespace: data subset: data def: "An informative report on a specific virus." [http://edamontology.org] is_a: EDAM_data:2530 ! Organism annotation [Term] id: EDAM_data:2395 name: Fungi annotation namespace: data subset: data def: "An informative report on a specific fungus." [http://edamontology.org] is_a: EDAM_data:2530 ! Organism annotation [Term] id: EDAM_data:0964 name: Scent annotation namespace: data subset: data def: "An informative report about a specific scent." [http://edamontology.org] is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2968 name: Image namespace: data subset: data ! alt_id: EDAM_data:0965 def: "Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type." [http://edamontology.org] synonym: "visual entity" BROAD [http://semanticscience.org/resource/SIO_000079] synonym: "image" NARROW [http://semanticscience.org/resource/SIO_000081] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2884 name: Plot namespace: data subset: data def: "Biological data that is plotted as a graph of some type." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2968 ! Image [Term] id: EDAM_data:2353 name: Ontological data namespace: data subset: data def: "Data concerning an ontology." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:2223 ! Ontology metadata consider: EDAM_data:0582 ! Ontology [Term] id: EDAM_data:2849 name: Abstract namespace: data subset: data def: "An abstract of a scientific article." [http://edamontology.org] is_a: EDAM_data:2857 ! Article metadata [Term] id: EDAM_data:0970 name: Bibliographic reference namespace: data subset: data def: "Bibliographic data that uniquely identifies a scientific article, book or other published material." [http://edamontology.org] comment: A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. synonym: "Reference" EXACT [http://edamontology.org] synonym: "Citation" EXACT [http://edamontology.org] xref: Moby:GCP_SimpleCitation xref: Moby:Publication is_a: EDAM_data:2857 ! Article metadata is_a: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:2526 name: Article data namespace: data subset: data def: "Data concerning the scientific literature." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. is_obsolete: true !{since=beta13} consider: EDAM_data:0971 ! Article [Term] id: EDAM_data:0971 name: Article namespace: data subset: data def: "A body of scientific text, typically a full text article from a scientific journal." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:3068 ! Literature and reference [Term] id: EDAM_data:2857 name: Article metadata namespace: data subset: data def: "Bibliographic data concerning scientific article(s)." [http://edamontology.org] is_a: EDAM_data:2954 ! Article report is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:3068 ! Literature and reference [Term] id: EDAM_data:2954 name: Article report namespace: data subset: data def: "Data concerning or derived from the analysis of a scientific article." [http://edamontology.org] is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:0972 name: Text mining report namespace: data subset: data def: "An abstract of the results of text mining." [http://edamontology.org] comment: A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. is_a: EDAM_data:2954 ! Article report [Term] id: EDAM_data:2143 name: EMBOSS report namespace: data subset: data def: "An application report generated by the EMBOSS suite." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2048 ! Report [Term] id: EDAM_data:2176 name: Cardinality namespace: data subset: data def: "The number of a certain thing." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_data:2527 name: Parameter namespace: data subset: data ! alt_id: EDAM_data:2029 ! alt_id: EDAM_data:1773 ! alt_id: EDAM_data:0961 def: "Typically a simple numerical or string value that controls the operation of a tool." [http://edamontology.org] synonym: "Parameter or primitive" EXACT [http://edamontology.org] synonym: "Tool parameter" EXACT [http://edamontology.org] synonym: "Tool-specific parameter" EXACT [http://edamontology.org] synonym: "Parameter" EXACT [http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter] synonym: "parameter" EXACT [http://semanticscience.org/resource/SIO_000144] !{note="Slightly narrower in the sense of changing the characteristics of a system/function."} is_a: EDAM_data:0006 ! Data [Term] id: EDAM_data:2190 name: Sequence checksum namespace: data subset: data def: "A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing." [http://edamontology.org] synonym: "Hash code" EXACT [http://edamontology.org] synonym: "Hash sum" EXACT [http://edamontology.org] synonym: "Hash" EXACT [http://edamontology.org] synonym: "Hash value" EXACT [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter is_a: EDAM_data:0855 ! Sequence metadata [Term] id: EDAM_data:2192 name: Error namespace: data subset: data def: "Data on an error generated by computer system or tool." [http://edamontology.org] is_a: EDAM_data:0959 ! Job metadata [Term] id: EDAM_data:2249 name: DTD namespace: data subset: data def: "A DTD (document type definition)." [http://edamontology.org] is_a: EDAM_data:2248 ! Schema [Term] id: EDAM_data:2250 name: XML Schema namespace: data subset: data def: "An XML Schema." [http://edamontology.org] synonym: "XSD" EXACT [http://edamontology.org] is_a: EDAM_data:2248 ! Schema [Term] id: EDAM_data:2251 name: Relax-NG schema namespace: data subset: data def: "A relax-NG schema." [http://edamontology.org] is_a: EDAM_data:2248 ! Schema [Term] id: EDAM_data:2252 name: XSLT stylesheet namespace: data subset: data def: "An XSLT stylesheet." [http://edamontology.org] is_a: EDAM_data:2248 ! Schema [Term] id: EDAM_data:1743 name: Atomic coordinate namespace: data subset: data def: "Cartesian coordinate of an atom (in a molecular structure)." [http://edamontology.org] synonym: "Cartesian coordinate" EXACT [http://edamontology.org] is_a: EDAM_data:1917 ! Atomic property [Term] id: EDAM_data:1857 name: Atomic occupancy namespace: data subset: data def: "The fraction of an atom type present at a site in a molecular structure." [http://edamontology.org] comment: The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. xref: WHATIF: PDBx_occupancy is_a: EDAM_data:1917 ! Atomic property [Term] id: EDAM_data:1858 name: Isotropic B factor namespace: data subset: data def: "Isotropic B factor (atomic displacement parameter) for an atom from a PDB file." [http://edamontology.org] xref: WHATIF: PDBx_B_iso_or_equiv is_a: EDAM_data:1917 ! Atomic property [Term] id: EDAM_data:1744 name: Atomic x coordinate namespace: data subset: data def: "Cartesian x coordinate of an atom (in a molecular structure)." [http://edamontology.org] synonym: "Cartesian x coordinate" EXACT [http://edamontology.org] xref: WHATIF: PDBx_Cartn_x is_a: EDAM_data:1743 ! Atomic coordinate ! _atom_site.Cartn_x in PDBML [Term] id: EDAM_data:1745 name: Atomic y coordinate namespace: data subset: data def: "Cartesian y coordinate of an atom (in a molecular structure)." [http://edamontology.org] synonym: "Cartesian y coordinate" EXACT [http://edamontology.org] xref: WHATIF: PDBx_Cartn_y is_a: EDAM_data:1743 ! Atomic coordinate ! _atom_site.Cartn_y in PDBML [Term] id: EDAM_data:1746 name: Atomic z coordinate namespace: data subset: data def: "Cartesian z coordinate of an atom (in a molecular structure)." [http://edamontology.org] synonym: "Cartesian z coordinate" EXACT [http://edamontology.org] xref: WHATIF: PDBx_Cartn_z is_a: EDAM_data:1743 ! Atomic coordinate ! _atom_site.Cartn_z in PDBML [Term] id: EDAM_data:0844 name: Molecular mass namespace: data subset: data def: "Mass of a molecule." [http://edamontology.org] is_a: EDAM_data:2050 ! Molecular property (general) [Term] id: EDAM_data:0845 name: Molecular charge namespace: data subset: data def: "Net charge of a molecule." [http://edamontology.org] is_a: EDAM_data:2050 ! Molecular property (general) ! pdbx_formal_charge in PDBML [Term] id: EDAM_data:0846 name: Chemical formula namespace: data subset: data def: "A specification of a chemical structure." [http://edamontology.org] synonym: "Chemical structure specification" EXACT [http://edamontology.org] is_a: EDAM_data:2050 ! Molecular property (general) [Term] id: EDAM_data:0847 name: QSAR descriptor namespace: data subset: data def: "A QSAR quantitative descriptor (name-value pair) of chemical structure." [http://edamontology.org] comment: QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. is_a: EDAM_data:2050 ! Molecular property (general) [Term] id: EDAM_data:2301 name: SMILES string namespace: data subset: data def: "A specification of a chemical structure in SMILES format." [http://edamontology.org] is_a: EDAM_data:0846 ! Chemical formula ! Many subtypes of the individual descriptors below (not included here) cover all types of protein properties. [Term] id: EDAM_data:1201 name: QSAR descriptor (constitutional) namespace: data subset: data def: "A QSAR constitutional descriptor." [http://edamontology.org] synonym: "QSAR constitutional descriptor" EXACT [http://edamontology.org] is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1202 name: QSAR descriptor (electronic) namespace: data subset: data def: "A QSAR electronic descriptor." [http://edamontology.org] synonym: "QSAR electronic descriptor" EXACT [http://edamontology.org] is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1203 name: QSAR descriptor (geometrical) namespace: data subset: data def: "A QSAR geometrical descriptor." [http://edamontology.org] synonym: "QSAR geometrical descriptor" EXACT [http://edamontology.org] is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1204 name: QSAR descriptor (topological) namespace: data subset: data def: "A QSAR topological descriptor." [http://edamontology.org] synonym: "QSAR topological descriptor" EXACT [http://edamontology.org] is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1205 name: QSAR descriptor (molecular) namespace: data subset: data def: "A QSAR molecular descriptor." [http://edamontology.org] synonym: "QSAR molecular descriptor" EXACT [http://edamontology.org] is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:0848 name: Raw sequence namespace: data subset: data def: "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] comment: Non-sequence characters may be used for example for gaps and translation stop. is_a: EDAM_data:2044 ! Sequence [Term] id: EDAM_data:2201 name: Sequence record full namespace: data subset: data def: "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] xref: SO:2000061 is_a: EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2888 name: Sequence record full (protein) namespace: data subset: data def: "A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] xref: SO:2000061 is_a: EDAM_data:2201 ! Sequence record full is_a: EDAM_data:2886 ! Sequence record (protein) [Term] id: EDAM_data:2889 name: Sequence record full (nucleic acid) namespace: data subset: data def: "A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] xref: SO:2000061 is_a: EDAM_data:2201 ! Sequence record full is_a: EDAM_data:2887 ! Sequence record (nucleic acid) [Term] id: EDAM_data:0849 name: Sequence record namespace: data subset: data ! alt_id: EDAM_data:1220 ! alt_id: EDAM_data:1224 ! alt_id: EDAM_data:1225 ! alt_id: EDAM_data:1226 ! alt_id: EDAM_data:1227 ! alt_id: EDAM_data:1229 ! alt_id: EDAM_data:1230 ! alt_id: EDAM_data:1231 ! alt_id: EDAM_data:1232 def: "A molecular sequence and associated metadata." [http://edamontology.org] is_a: EDAM_data:2044 ! Sequence [Term] id: EDAM_data:2886 name: Sequence record (protein) namespace: data subset: data ! alt_id: EDAM_data:1222 def: "A protein sequence and associated metadata." [http://edamontology.org] synonym: "Protein sequence record" EXACT [http://edamontology.org] is_a: EDAM_data:0849 ! Sequence record is_a: EDAM_data:2976 ! Protein sequence [Term] id: EDAM_data:2887 name: Sequence record (nucleic acid) namespace: data subset: data ! alt_id: EDAM_data:1221 def: "A nucleic acid sequence and associated metadata." [http://edamontology.org] synonym: "Nucleic acid sequence record" EXACT [http://edamontology.org] synonym: "Nucleotide sequence record" EXACT [http://edamontology.org] is_a: EDAM_data:0849 ! Sequence record is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:0850 name: Sequence set namespace: data subset: data def: "A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method." [http://edamontology.org] comment: This concept may be used for arbitrary sequence sets and associated data arising from processing. synonym: "sequence_collection" EXACT [SO:0001260] is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:2974 name: Raw sequence (protein) namespace: data subset: data def: "A raw protein sequence (string of characters)." [http://edamontology.org] is_a: EDAM_data:0848 ! Raw sequence is_a: EDAM_data:2976 ! Protein sequence [Term] id: EDAM_data:2975 name: Raw sequence (nucleic acid) namespace: data subset: data def: "A raw nucleic acid sequence." [http://edamontology.org] is_a: EDAM_data:0848 ! Raw sequence is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:2046 name: Sequence record lite (nucleic acid) namespace: data subset: data def: "A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] is_a: EDAM_data:2043 ! Sequence record lite is_a: EDAM_data:2887 ! Sequence record (nucleic acid) [Term] id: EDAM_data:2047 name: Sequence record lite (protein) namespace: data subset: data def: "A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] is_a: EDAM_data:2043 ! Sequence record lite is_a: EDAM_data:2886 ! Sequence record (protein) [Term] id: EDAM_data:2043 name: Sequence record lite namespace: data subset: data ! alt_id: EDAM_data:1223 def: "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] is_a: EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2173 name: Sequence set (stream) namespace: data subset: data def: "A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing." [http://edamontology.org] comment: This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:2245 name: Sequence set (bootstrapped) namespace: data subset: data def: "A collection of sequences output from a bootstrapping (resampling) procedure." [http://edamontology.org] comment: Bootstrapping is often performed in phylogenetic analysis. is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1233 name: Sequence set (protein) namespace: data subset: data def: "Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1234 name: Sequence set (nucleic acid) namespace: data subset: data def: "Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] is_a: EDAM_data:0850 ! Sequence set is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:1235 name: Sequence cluster namespace: data subset: data def: "A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information." [http://edamontology.org] comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information. is_a: EDAM_data:0850 ! Sequence set relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification relationship: has_topic EDAM_topic:0724 ! Protein families [Term] id: EDAM_data:1236 name: Psiblast checkpoint file namespace: data subset: data def: "A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration." [http://edamontology.org] comment: A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1237 name: HMMER synthetic sequences set namespace: data subset: data def: "Sequences generated by HMMER package in FASTA-style format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1238 name: Proteolytic digest namespace: data subset: data def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses." [http://edamontology.org] is_a: EDAM_data:1233 ! Sequence set (protein) relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:1766 name: CATH domain sequences (ATOM) namespace: data subset: data def: "FASTA sequence database for all CATH domains (based on PDB ATOM records)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1767 name: CATH domain sequences (COMBS) namespace: data subset: data def: "FASTA sequence database for all CATH domains (based on COMBS sequence data)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1239 name: Restriction digest namespace: data subset: data def: "Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease." [http://edamontology.org] xref: SO:0000412 is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:2874 name: Sequence set (polymorphic) namespace: data subset: data def: "A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:1240 name: PCR primers namespace: data subset: data def: "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." [http://edamontology.org] is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:1241 name: vectorstrip cloning vector definition file namespace: data subset: data def: "File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1242 name: Primer3 internal oligo mishybridizing library namespace: data subset: data def: "A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1243 name: Primer3 mispriming library file namespace: data subset: data def: "A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1244 name: primersearch primer pairs sequence record namespace: data subset: data def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1245 name: Sequence cluster (protein) namespace: data subset: data def: "A cluster of protein sequences." [http://edamontology.org] comment: The sequences are typically related, for example a family of sequences. synonym: "Protein sequence cluster" EXACT [http://edamontology.org] is_a: EDAM_data:1233 ! Sequence set (protein) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1246 name: Sequence cluster (nucleic acid) namespace: data subset: data def: "A cluster of nucleotide sequences." [http://edamontology.org] comment: The sequences are typically related, for example a family of sequences. synonym: "Nucleotide sequence cluster" EXACT [http://edamontology.org] is_a: EDAM_data:1234 ! Sequence set (nucleic acid) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1764 name: CATH representative domain sequences (ATOM) namespace: data subset: data def: "FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1765 name: CATH representative domain sequences (COMBS) namespace: data subset: data def: "FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:2198 name: Gene cluster namespace: data subset: data def: "A cluster of similar genes." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1246 ! Sequence cluster (nucleic acid) [Term] id: EDAM_data:1253 name: Sequence information report namespace: data subset: data def: "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2043 ! Sequence record lite consider: EDAM_data:0855 ! Sequence metadata [Term] id: EDAM_data:1254 name: Sequence property namespace: data subset: data def: "An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." [http://edamontology.org] synonym: "Sequence properties report" EXACT [http://edamontology.org] is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:1255 name: Feature record namespace: data subset: data ! alt_id: EDAM_data:1271 ! alt_id: EDAM_data:1275 def: "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence." [http://edamontology.org] comment: This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. synonym: "Sequence features" EXACT [http://edamontology.org] synonym: "Sequence features report" EXACT [http://edamontology.org] synonym: "General sequence features" EXACT [http://edamontology.org] synonym: "sequence_feature" RELATED [SO:0000110] is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:2914 name: Sequence features metadata namespace: data subset: data def: "Metadata on sequence features." [http://edamontology.org] is_a: EDAM_data:0855 ! Sequence metadata [Term] id: EDAM_data:1020 name: Sequence feature key namespace: data subset: data def: "The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key." [http://edamontology.org] comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. synonym: "Sequence feature type" EXACT [http://edamontology.org] synonym: "Sequence feature method" EXACT [http://edamontology.org] is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1021 name: Sequence feature qualifier namespace: data subset: data def: "Typically one of the EMBL or Swiss-Prot feature qualifiers." [http://edamontology.org] comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location. is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1022 name: Sequence feature label namespace: data subset: data def: "Typically an EMBL or Swiss-Prot feature label." [http://edamontology.org] comment: A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. synonym: "Sequence feature name" EXACT [http://edamontology.org] is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1278 name: Genetic map namespace: data subset: data def: "A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies." [http://edamontology.org] comment: A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. synonym: "Linkage map" EXACT [http://edamontology.org] xref: Moby:GeneticMap is_a: EDAM_data:1274 ! Map relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] id: EDAM_data:1283 name: Cytogenetic map namespace: data subset: data ! alt_id: EDAM_data:1287 def: "A map showing banding patterns derived from direct observation of a stained chromosome." [http://edamontology.org] comment: This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. synonym: "Cytologic map" EXACT [http://edamontology.org] synonym: "Cytogenic map" EXACT [http://edamontology.org] synonym: "Chromosome map" EXACT [http://edamontology.org] is_a: EDAM_data:1280 ! Physical map [Term] id: EDAM_data:2870 name: Radiation hybrid map namespace: data subset: data def: "A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome." [http://edamontology.org] comment: The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. synonym: "RH map" EXACT [http://edamontology.org] is_a: EDAM_data:1280 ! Physical map [Term] id: EDAM_data:1279 name: Sequence map namespace: data subset: data def: "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs." [http://edamontology.org] comment: A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. is_a: EDAM_data:1280 ! Physical map [Term] id: EDAM_data:1280 name: Physical map namespace: data subset: data def: "A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them." [http://edamontology.org] comment: Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. is_a: EDAM_data:1274 ! Map [Term] id: EDAM_data:1284 name: DNA transduction map namespace: data subset: data def: "A gene map showing distances between loci based on relative cotransduction frequencies." [http://edamontology.org] is_a: EDAM_data:1278 ! Genetic map [Term] id: EDAM_data:1860 name: QTL map namespace: data subset: data def: "A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers." [http://edamontology.org] synonym: "Quantitative trait locus map" EXACT [http://edamontology.org] is_a: EDAM_data:1278 ! Genetic map [Term] id: EDAM_data:1859 name: Deletion map namespace: data subset: data def: "A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type." [http://edamontology.org] comment: A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. synonym: "Deletion-based cytogenetic map" EXACT [http://edamontology.org] is_a: EDAM_data:1283 ! Cytogenetic map [Term] id: EDAM_data:1863 name: Haplotype map namespace: data subset: data def: "A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation." [http://edamontology.org] xref: Moby:Haplotyping_Study_obj is_a: EDAM_data:1278 ! Genetic map [Term] id: EDAM_data:1285 name: Gene map namespace: data subset: data def: "Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene." [http://edamontology.org] is_a: EDAM_data:1279 ! Sequence map [Term] id: EDAM_data:1286 name: Plasmid map namespace: data subset: data def: "Sequence map of a plasmid (circular DNA)." [http://edamontology.org] is_a: EDAM_data:1279 ! Sequence map [Term] id: EDAM_data:1288 name: Genome map namespace: data subset: data def: "Sequence map of a whole genome." [http://edamontology.org] is_a: EDAM_data:1279 ! Sequence map [Term] id: EDAM_data:1865 name: Map feature namespace: data subset: data def: "A feature which may mapped (positioned) on a genetic or other type of map." [http://edamontology.org] comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. xref: Moby:MapFeature is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1255 ! Feature record consider: EDAM_data:2019 ! Map attribute consider: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:1257 name: Sequence property (protein) namespace: data subset: data def: "A report of general sequence properties derived from protein sequence data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1258 name: Sequence property (nucleic acid) namespace: data subset: data def: "A report of general sequence properties derived from nucleotide sequence data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:1259 name: Sequence complexity namespace: data subset: data def: "A report on sequence complexity, for example low-complexity or repeat regions in sequences." [http://edamontology.org] synonym: "Sequence property (complexity)" EXACT [http://edamontology.org] is_a: EDAM_data:1254 ! Sequence property [Term] id: EDAM_data:1260 name: Sequence ambiguity namespace: data subset: data def: "A report on ambiguity in molecular sequence(s)." [http://edamontology.org] synonym: "Sequence property (ambiguity)" EXACT [http://edamontology.org] is_a: EDAM_data:1254 ! Sequence property [Term] id: EDAM_data:1261 name: Sequence composition namespace: data subset: data def: "A report (typically a table) on character or word composition / frequency of a molecular sequence(s)." [http://edamontology.org] synonym: "Sequence property (composition)" EXACT [http://edamontology.org] is_a: EDAM_data:1254 ! Sequence property [Term] id: EDAM_data:3119 !{since=beta13} name: Sequence features (compositionally-biased regions) namespace: data subset: data def: "A report of regions in a molecular sequence that are biased to certain characters." [http://edamontology.org] is_a: EDAM_data:1261 ! Sequence composition [Term] id: EDAM_data:3085 !{since=beta13} name: Protein sequence composition namespace: data subset: data def: "A report (typically a table) on character or word composition / frequency of protein sequence(s)." [http://edamontology.org] synonym: "Sequence property (protein composition)" EXACT [http://edamontology.org] is_a: EDAM_data:1261 ! Sequence composition [Term] id: EDAM_data:3086 !{since=beta13} name: Nucleic acid sequence composition namespace: data subset: data def: "A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s)." [http://edamontology.org] synonym: "Sequence property (nucleic acid composition)" EXACT [http://edamontology.org] is_a: EDAM_data:1261 ! Sequence composition is_a: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:1262 name: Peptide molecular weight hits namespace: data subset: data def: "A report on peptide fragments of certain molecular weight(s) in one or more protein sequences." [http://edamontology.org] is_a: EDAM_data:1233 ! Sequence set (protein) [Term] id: EDAM_data:1263 name: Sequence composition (base position variability) namespace: data subset: data def: "Report on or plot of third base position variability in a nucleotide sequence." [http://edamontology.org] is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] id: EDAM_data:2157 name: Word composition namespace: data subset: data def: "Word composition data for a molecular sequence." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1268 ! Amino acid word frequencies consider: EDAM_data:1266 ! Sequence composition (base words) [Term] id: EDAM_data:1264 name: Sequence composition table namespace: data subset: data def: "A table of character or word composition / frequency of a molecular sequence." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1261 ! Sequence composition [Term] id: EDAM_data:2166 name: Sequence composition plot namespace: data subset: data def: "A plot of character or word composition / frequency of a molecular sequence." [http://edamontology.org] is_a: EDAM_data:1261 ! Sequence composition [Term] id: EDAM_data:1265 name: Sequence composition (base frequencies) namespace: data subset: data def: "A table of base frequencies of a nucleotide sequence." [http://edamontology.org] is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] id: EDAM_data:1267 name: Amino acid frequencies namespace: data subset: data def: "A table of amino acid frequencies of a protein sequence." [http://edamontology.org] synonym: "Sequence composition (amino acid frequencies)" EXACT [http://edamontology.org] is_a: EDAM_data:3085 ! Protein sequence composition [Term] id: EDAM_data:1266 name: Sequence composition (base words) namespace: data subset: data def: "A table of word composition of a nucleotide sequence." [http://edamontology.org] is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] id: EDAM_data:1268 name: Amino acid word frequencies namespace: data subset: data def: "A table of amino acid word composition of a protein sequence." [http://edamontology.org] synonym: "Sequence composition (amino acid words)" EXACT [http://edamontology.org] is_a: EDAM_data:3085 ! Protein sequence composition [Term] id: EDAM_data:1269 name: DAS sequence feature annotation namespace: data subset: data def: "Annotation of a molecular sequence in DAS format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1978 ! DASGFF [Term] id: EDAM_data:3002 name: Sequence annotation track namespace: data subset: data def: "Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser." [http://edamontology.org] synonym: "Annotation track" EXACT [http://edamontology.org] synonym: "Genome track" EXACT [http://edamontology.org] synonym: "Genomic track" EXACT [http://edamontology.org] synonym: "Genome-browser track" EXACT [http://edamontology.org] synonym: "Genome annotation track" EXACT [http://edamontology.org] is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1270 name: Sequence feature table namespace: data subset: data def: "Annotation of positional sequence features, organized into a standard feature table." [http://edamontology.org] synonym: "Feature table" EXACT [http://edamontology.org] is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1276 name: Nucleic acid features namespace: data subset: data ! alt_id: EDAM_data:1273 def: "Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence)." [http://edamontology.org] comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. synonym: "Nucleic acid feature table" EXACT [http://edamontology.org] synonym: "Feature table (nucleic acid)" EXACT [http://edamontology.org] is_a: EDAM_data:2084 ! Nucleic acid report is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:3139 !{since=beta13} name: Nucleic acid features (STS) namespace: data subset: data def: "A report on sequence tagged sites (STS) in nucleic acid sequences." [http://edamontology.org] comment: Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3122 !{since=beta13} name: Nucleic acid features (difference and change) namespace: data subset: data def: "A report on features in a nucleic acid sequence that indicate changes to or differences between sequences." [http://edamontology.org] is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3123 !{since=beta13} name: Nucleic acid features (expression signal) namespace: data subset: data def: "A report on regions within a nucleic acid sequence containing a signal that alters a biological function." [http://edamontology.org] is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3125 !{since=beta13} name: Nucleic acid features (binding) namespace: data subset: data def: "A report on regions of a nucleic acid sequence that bind some other molecule." [http://edamontology.org] comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3126 !{since=beta13} name: Nucleic acid features (repeats) namespace: data subset: data def: "A report on repetitive elements within a nucleic acid sequence." [http://edamontology.org] comment: This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. is_a: EDAM_data:1299 ! Sequence features (repeats) is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3127 !{since=beta13} name: Nucleic acid features (replication and recombination) namespace: data subset: data def: "A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination." [http://edamontology.org] comment: This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3128 !{since=beta13} name: Nucleic acid features (structure) namespace: data subset: data def: "A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures." [http://edamontology.org] is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3132 !{since=beta13} name: Nucleic acid features (d-loop) namespace: data subset: data def: "A report on displacement loops in a mitochondrial DNA sequence." [http://edamontology.org] comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] id: EDAM_data:3133 !{since=beta13} name: Nucleic acid features (stem loop) namespace: data subset: data def: "A report on stem loops in a DNA sequence." [http://edamontology.org] comment: A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] id: EDAM_data:2882 name: DNA features namespace: data subset: data def: "DNA sequence-specific feature annotation (not in a feature table)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:2883 name: Nucleic acid features (RNA features) namespace: data subset: data def: "Features concerning RNA or regions of DNA that encode an RNA molecule." [http://edamontology.org] synonym: "RNA features" EXACT [http://edamontology.org] is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:3134 !{since=beta13} name: Nucleic acid features (mRNA features) namespace: data subset: data def: "Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules." [http://edamontology.org] comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). synonym: "mRNA features" EXACT [http://edamontology.org] is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) [Term] id: EDAM_data:3137 !{since=beta13} name: Nucleic acid features (non-coding RNA) namespace: data subset: data def: "Features concerning non-coding or functional RNA molecules, including tRNA and rRNA." [http://edamontology.org] synonym: "ncRNA features" EXACT [http://edamontology.org] synonym: "Non-coding RNA features" EXACT [http://edamontology.org] is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) [Term] id: EDAM_data:3138 !{since=beta13} name: Nucleic acid features (transcriptional) namespace: data subset: data def: "Features concerning transcription of DNA into RNA including the regulation of transcription." [http://edamontology.org] comment: This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) [Term] id: EDAM_data:1277 name: Protein features namespace: data subset: data ! alt_id: EDAM_data:1272 def: "Protein sequence-specific feature annotation (positional features of a protein sequence)." [http://edamontology.org] comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. synonym: "Feature table (protein)" EXACT [http://edamontology.org] synonym: "Protein feature table" EXACT [http://edamontology.org] is_a: EDAM_data:1255 ! Feature record is_a: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:1256 name: Sequence features (comparative) namespace: data subset: data def: "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. is_obsolete: true !{since=beta13} consider: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1298 name: Sequence features (motifs) namespace: data subset: data def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." [http://edamontology.org] comment: Use this concept if another, more specific concept is not available. is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:3130 !{since=beta13} name: Protein features (motifs) namespace: data subset: data def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." [http://edamontology.org] comment: Use this concept if another, more specific concept is not available. is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:3131 !{since=beta13} name: Nucleic acid features (motifs) namespace: data subset: data def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences." [http://edamontology.org] comment: Use this concept if another, more specific concept is not available. is_a: EDAM_data:1276 ! Nucleic acid features is_a: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:0858 name: Database hits (secondary) namespace: data subset: data def: "A report of hits from a search of a protein secondary or domain database." [http://edamontology.org] comment: Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'. is_a: EDAM_data:2080 ! Database hits [Term] id: EDAM_data:0901 name: Protein features (domains) namespace: data subset: data def: "Summary of structural domains or 3D folds in a protein or polypeptide chain." [http://edamontology.org] comment: The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. synonym: "Protein domain assignment" EXACT [http://edamontology.org] synonym: "Protein structural domains" EXACT [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_data:3118 !{since=beta13} name: Protein features (topological domains) namespace: data subset: data def: "Summary of topological domains such as cytoplasmic regions in a protein." [http://edamontology.org] synonym: "Protein topological domains" EXACT [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_data:1299 name: Sequence features (repeats) namespace: data subset: data ! alt_id: EDAM_data:1282 def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] comment: The report might include derived data map such as classification, annotation, organization, periodicity etc. synonym: "Repeat sequence map" EXACT [http://edamontology.org] is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:3129 !{since=beta13} name: Protein features (repeats) namespace: data subset: data def: "Location of short repetitive subsequences (repeat sequences) in a protein sequence." [http://edamontology.org] is_a: EDAM_data:1299 ! Sequence features (repeats) is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1281 name: Sequence signature map namespace: data subset: data def: "Image of a sequence with matches to signatures, motifs or profiles." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1290 name: InterPro compact match image namespace: data subset: data def: "Image showing matches between protein sequence(s) and InterPro Entries." [http://edamontology.org] comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1291 name: InterPro detailed match image namespace: data subset: data def: "Image showing detailed information on matches between protein sequence(s) and InterPro Entries." [http://edamontology.org] comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1292 name: InterPro architecture image namespace: data subset: data def: "Image showing the architecture of InterPro domains in a protein sequence." [http://edamontology.org] comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1293 name: SMART protein schematic namespace: data subset: data def: "SMART protein schematic in PNG format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1294 name: GlobPlot domain image namespace: data subset: data def: "Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1564 name: Protein fold recognition report namespace: data subset: data def: "A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s)." [http://edamontology.org] comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0901 ! Protein features (domains) [Term] id: EDAM_data:1300 name: Nucleic acid features (gene and transcript structure) namespace: data subset: data def: "A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc." [http://edamontology.org] synonym: "Gene annotation (structure)" EXACT [http://edamontology.org] is_a: EDAM_data:0916 ! Gene annotation is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3140 !{since=beta13} name: Nucleic acid features (immunoglobulin gene structure) namespace: data subset: data def: "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." [http://edamontology.org] is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:1301 name: Nucleic acid features (mobile genetic elements) namespace: data subset: data def: "A report on a region of a nucleic acid sequence containin mobile genetic elements." [http://edamontology.org] comment: This includes transposons, Plasmids, Bacteriophage elements and Group II introns. synonym: "Nucleic acid features (transposons)" EXACT [http://edamontology.org] is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:1302 name: Nucleic acid features (PolyA signal or site) namespace: data subset: data def: "A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript." [http://edamontology.org] comment: A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. synonym: "PolyA signal" EXACT [http://edamontology.org] synonym: "PolyA site" EXACT [http://edamontology.org] is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:3135 !{since=beta13} name: Nucleic acid features (signal or transit peptide) namespace: data subset: data def: "A report on a coding sequence for a signal or transit peptide." [http://edamontology.org] comment: A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:1303 name: Nucleic acid features (quadruplexes) namespace: data subset: data def: "A report on quadruplex-forming motifs in a nucleotide sequence." [http://edamontology.org] is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] id: EDAM_data:1304 name: Nucleic acid features (CpG island and isochore) namespace: data subset: data def: "A report or plot of CpG rich regions (isochores) in a nucleotide sequence." [http://edamontology.org] is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) [Term] id: EDAM_data:1305 name: Nucleic acid features (restriction sites) namespace: data subset: data def: "Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org] is_a: EDAM_data:3125 ! Nucleic acid features (binding) [Term] id: EDAM_data:1306 name: Nucleic acid features (nucleosome exclusion sequences) namespace: data subset: data def: "A report on nucleosome formation potential or exclusion sequence(s)." [http://edamontology.org] is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination) [Term] id: EDAM_data:1307 name: Nucleic acid features (splice sites) namespace: data subset: data ! alt_id: EDAM_data:0915 def: "A report on splice sites in a nucleotide sequence or alternative RNA splicing events." [http://edamontology.org] synonym: "Nucleic acid report (RNA splice model)" EXACT [http://edamontology.org] synonym: "Nucleic acid report (RNA splicing)" EXACT [http://edamontology.org] is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:1308 name: Nucleic acid features (matrix/scaffold attachment sites) namespace: data subset: data def: "A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence." [http://edamontology.org] is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) [Term] id: EDAM_data:1309 name: Gene features (exonic splicing enhancer) namespace: data subset: data def: "A report on exonic splicing enhancers (ESE) in an exon." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:2397 ! Nucleic acid features (exon) [Term] id: EDAM_data:1310 name: Nucleic acid features (microRNA) namespace: data subset: data def: "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." [http://edamontology.org] is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA) relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_data:2169 name: Nucleic acid features (siRNA) namespace: data subset: data def: "A report on siRNA duplexes in mRNA." [http://edamontology.org] is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA) relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_data:0922 name: Nucleic acid features (primers) namespace: data subset: data def: "Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence." [http://edamontology.org] is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination) relationship: has_topic EDAM_topic:0632 ! Probes and primers [Term] id: EDAM_data:1311 name: Nucleic acid features (operon) namespace: data subset: data def: "A report on operons (operators, promoters and genes) from a bacterial genome." [http://edamontology.org] comment: The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. synonym: "Gene features (operon)" EXACT [http://edamontology.org] is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:1312 name: Gene features (promoter) namespace: data subset: data def: "A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." [http://edamontology.org] is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) [Term] id: EDAM_data:1313 name: Nucleic acid features (coding sequence) namespace: data subset: data ! alt_id: EDAM_data:1317 def: "A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." [http://edamontology.org] synonym: "Gene features (coding sequence)" EXACT [http://edamontology.org] synonym: "Gene features (coding region)" EXACT [http://edamontology.org] synonym: "Gene annotation (translation)" EXACT [http://edamontology.org] is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:1314 name: Gene features (SECIS element) namespace: data subset: data def: "A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:1315 name: Gene features (TFBS) namespace: data subset: data def: "A report on the transcription factor binding sites (TFBS) in a DNA sequence." [http://edamontology.org] is_a: EDAM_data:1312 ! Gene features (promoter) is_a: EDAM_data:3125 ! Nucleic acid features (binding) relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites [Term] id: EDAM_data:2397 name: Nucleic acid features (exon) namespace: data subset: data def: "An informative report on an exon in a nucleotide sequences." [http://edamontology.org] synonym: "Gene features (exon)" EXACT [http://edamontology.org] is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] id: EDAM_data:2754 name: Nucleic acid features (intron) namespace: data subset: data def: "An informative report on an intron in a nucleotide sequences." [http://edamontology.org] synonym: "Gene features (intron)" EXACT [http://edamontology.org] is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:2160 name: Fickett testcode plot namespace: data subset: data def: "A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences." [http://edamontology.org] is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] id: EDAM_data:1289 name: Restriction map namespace: data subset: data def: "Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org] is_a: EDAM_data:1305 ! Nucleic acid features (restriction sites) is_a: EDAM_data:1279 ! Sequence map is_a: EDAM_data:2969 ! Sequence image [Term] id: EDAM_data:1321 name: Protein features (sites) namespace: data subset: data def: "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites." [http://edamontology.org] comment: Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1322 name: Protein features (signal peptides) namespace: data subset: data def: "A report on the location of signal peptides or signal peptide cleavage sites in protein sequences." [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:3120 !{since=beta13} name: Protein features (sequence variants) namespace: data subset: data def: "A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1323 name: Protein features (cleavage sites) namespace: data subset: data def: "A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence." [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:1324 name: Protein features (post-translation modifications) namespace: data subset: data def: "A report on post-translation modifications in a protein sequence, typically describing the specific sites involved." [http://edamontology.org] synonym: "Protein features (post-translation modification sites)" EXACT [http://edamontology.org] synonym: "Post-translation modification" EXACT [http://edamontology.org] is_a: EDAM_data:2191 ! Protein features (chemical modification) [Term] id: EDAM_data:1325 name: Protein features (active sites) namespace: data subset: data def: "A report on catalytic residues (active site) of an enzyme." [http://edamontology.org] synonym: "Enzyme active site" EXACT [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1326 name: Protein features (binding sites) namespace: data subset: data def: "A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:2989 name: Protein features (key folding sites) namespace: data subset: data def: "A report on key residues involved in protein folding." [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1327 name: Protein features (epitopes) namespace: data subset: data def: "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data." [http://edamontology.org] comment: Epitope mapping is commonly done during vaccine design. is_obsolete: true !{since=beta13} consider: EDAM_data:1326 ! Protein features (binding sites) [Term] id: EDAM_data:1328 name: Protein features (nucleic acid binding sites) namespace: data subset: data def: "A report on RNA and DNA-binding proteins and binding sites in protein sequences." [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1329 name: MHC Class I epitopes report namespace: data subset: data def: "A report on epitopes that bind to MHC class I molecules." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1326 ! Protein features (binding sites) [Term] id: EDAM_data:1330 name: MHC Class II epitopes report namespace: data subset: data def: "A report on predicted epitopes that bind to MHC class II molecules." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1326 ! Protein features (binding sites) [Term] id: EDAM_data:1331 name: Protein features (PEST sites) namespace: data subset: data def: "A report or plot of PEST sites in a protein sequence." [http://edamontology.org] comment: 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. is_obsolete: true !{since=beta13} consider: EDAM_data:1323 ! Protein features (cleavage sites) [Term] id: EDAM_data:0857 name: Database hits (sequence) namespace: data subset: data def: "A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits." [http://edamontology.org] comment: The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. is_a: EDAM_data:2080 ! Database hits [Term] id: EDAM_data:0885 name: Database hits (structure) namespace: data subset: data def: "Results (hits) from searching a database of tertiary structure." [http://edamontology.org] comment: This includes alignment and score data. is_a: EDAM_data:2080 ! Database hits [Term] id: EDAM_data:1338 name: Sequence database hits scores list namespace: data subset: data def: "Scores from a sequence database search (for example a BLAST search)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0857 ! Database hits (sequence) [Term] id: EDAM_data:1339 name: Sequence database hits alignments list namespace: data subset: data def: "Alignments from a sequence database search (for example a BLAST search)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0857 ! Database hits (sequence) [Term] id: EDAM_data:1340 name: Sequence database hits evaluation data namespace: data subset: data def: "A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0857 ! Database hits (sequence) [Term] id: EDAM_data:1358 name: Prosite nucleotide pattern namespace: data subset: data def: "A nucleotide regular expression pattern from the Prosite database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:1359 name: Prosite protein pattern namespace: data subset: data def: "A protein regular expression pattern from the Prosite database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:1352 name: Regular expression namespace: data subset: data def: "Regular expression pattern." [http://edamontology.org] is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2070 name: Sequence motif (nucleic acid) namespace: data subset: data def: "A nucleotide sequence motif." [http://edamontology.org] is_a: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:2071 name: Sequence motif (protein) namespace: data subset: data def: "An amino acid sequence motif." [http://edamontology.org] is_a: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:2854 name: Position-specific scoring matrix namespace: data subset: data def: "A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment." [http://edamontology.org] is_a: EDAM_data:1354 ! Sequence profile is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:1361 name: Position frequency matrix namespace: data subset: data def: "A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org] synonym: "PFM" EXACT [http://edamontology.org] is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1362 name: Position weight matrix namespace: data subset: data def: "A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org] comment: Contributions of individual sequences to the matrix might be uneven (weighted). synonym: "PWM" EXACT [http://edamontology.org] is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1363 name: Information content matrix namespace: data subset: data def: "A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position." [http://edamontology.org] synonym: "ICM" EXACT [http://edamontology.org] is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1364 name: Hidden Markov model namespace: data subset: data def: "A hidden Markov model representation of a set or alignment of sequences." [http://edamontology.org] synonym: "HMM" EXACT [http://edamontology.org] is_a: EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:1365 name: Fingerprint namespace: data subset: data def: "One or more fingerprints (sequence classifiers) as used in the PRINTS database." [http://edamontology.org] is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1368 name: Domainatrix signature namespace: data subset: data def: "A protein signature of the type used in the EMBASSY Signature package." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:1371 name: HMMER NULL hidden Markov model namespace: data subset: data def: "NULL hidden Markov model representation used by the HMMER package." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1364 ! Hidden Markov model [Term] id: EDAM_data:1372 name: Protein family signature namespace: data subset: data def: "A protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org] comment: Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1373 name: Protein domain signature namespace: data subset: data def: "A protein domain signature (sequence classifier) from the InterPro database." [http://edamontology.org] comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries. is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1374 name: Protein region signature namespace: data subset: data def: "A protein region signature (sequence classifier) from the InterPro database." [http://edamontology.org] comment: A protein region signature defines a region which cannot be described as a protein family or domain signature. is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1375 name: Protein repeat signature namespace: data subset: data def: "A protein repeat signature (sequence classifier) from the InterPro database." [http://edamontology.org] comment: A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1376 name: Protein site signature namespace: data subset: data def: "A protein site signature (sequence classifier) from the InterPro database." [http://edamontology.org] comment: A protein site signature is a classifier for a specific site in a protein. is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1377 name: Protein conserved site signature namespace: data subset: data def: "A protein conserved site signature (sequence classifier) from the InterPro database." [http://edamontology.org] comment: A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. is_a: EDAM_data:1376 ! Protein site signature [Term] id: EDAM_data:1378 name: Protein active site signature namespace: data subset: data def: "A protein active site signature (sequence classifier) from the InterPro database." [http://edamontology.org] comment: A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. is_a: EDAM_data:1376 ! Protein site signature [Term] id: EDAM_data:1379 name: Protein binding site signature namespace: data subset: data def: "A protein binding site signature (sequence classifier) from the InterPro database." [http://edamontology.org] comment: A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. is_a: EDAM_data:1376 ! Protein site signature [Term] id: EDAM_data:1380 name: Protein post-translational modification signature namespace: data subset: data def: "A protein post-translational modification signature (sequence classifier) from the InterPro database." [http://edamontology.org] comment: A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. is_a: EDAM_data:1376 ! Protein site signature [Term] id: EDAM_data:0861 name: Sequence alignment (words) namespace: data subset: data def: "Alignment of exact matches between subsequences (words) within two or more molecular sequences." [http://edamontology.org] synonym: "Sequence word alignment" EXACT [http://edamontology.org] is_a: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:0863 name: Sequence alignment namespace: data subset: data def: "Alignment of multiple molecular sequences." [http://edamontology.org] synonym: "Sequence alignment" EXACT [http://en.wikipedia.org/wiki/Sequence_alignment] synonym: "sequence alignment" EXACT [http://semanticscience.org/resource/SIO_010066] is_a: EDAM_data:1916 ! Alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_data:0868 name: Sequence profile alignment namespace: data subset: data def: "A profile-profile alignment (each profile typically representing a sequence alignment)." [http://edamontology.org] is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:0869 name: Sequence-profile alignment namespace: data subset: data def: "Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment)." [http://edamontology.org] comment: Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:2366 name: Secondary structure alignment namespace: data subset: data def: "Alignment of the (1D representations of) secondary structure of two or more molecules." [http://edamontology.org] is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:0878 name: Secondary structure alignment (protein) namespace: data subset: data def: "Alignment of the (1D representations of) secondary structure of two or more proteins." [http://edamontology.org] is_a: EDAM_data:2366 ! Secondary structure alignment is_a: EDAM_data:3154 ! Protein alignment [Term] id: EDAM_data:0881 name: Secondary structure alignment (RNA) namespace: data subset: data def: "Alignment of the (1D representations of) secondary structure of two or more RNA molecules." [http://edamontology.org] xref: Moby:RNAStructAlignmentML is_a: EDAM_data:2366 ! Secondary structure alignment [Term] id: EDAM_data:0886 name: Structure alignment namespace: data subset: data def: "Alignment (superimposition) of molecular tertiary (3D) structures." [http://edamontology.org] comment: A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. is_a: EDAM_data:1916 ! Alignment is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] id: EDAM_data:0890 name: Structural (3D) profile alignment namespace: data subset: data def: "A 3D profile-3D profile alignment (each profile representing structures or a structure alignment)." [http://edamontology.org] synonym: "Structural profile alignment" EXACT [http://edamontology.org] is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:0891 name: Sequence-3D profile alignment namespace: data subset: data def: "An alignment of a sequence to a 3D profile (representing structures or a structure alignment)." [http://edamontology.org] synonym: "Sequence-structural profile alignment" EXACT [http://edamontology.org] is_a: EDAM_data:0893 ! Sequence-structure alignment [Term] id: EDAM_data:0893 name: Sequence-structure alignment namespace: data subset: data def: "An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s))." [http://edamontology.org] is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:1381 name: Sequence alignment (pair) namespace: data subset: data def: "Alignment of exactly two molecular sequences." [http://edamontology.org] synonym: "pairwise sequence alignment" RELATED [http://semanticscience.org/resource/SIO_010068] ! Related external synonym in EDAM without a note is usually almost exact. is_a: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1382 name: Sequence alignment (multiple) namespace: data subset: data def: "Alignment of more than two molecular sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1383 name: Sequence alignment (nucleic acid) namespace: data subset: data def: "Alignment of multiple nucleotide sequences." [http://edamontology.org] is_a: EDAM_data:0863 ! Sequence alignment is_a: EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:1384 name: Sequence alignment (protein) namespace: data subset: data def: "Alignment of multiple protein sequences." [http://edamontology.org] is_a: EDAM_data:0863 ! Sequence alignment is_a: EDAM_data:3154 ! Protein alignment [Term] id: EDAM_data:1385 name: Sequence alignment (hybrid) namespace: data subset: data def: "Alignment of multiple molecular sequences of different types." [http://edamontology.org] comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. is_a: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1386 name: Sequence alignment (nucleic acid pair) namespace: data subset: data def: "Alignment of exactly two nucleotide sequences." [http://edamontology.org] is_a: EDAM_data:1381 ! Sequence alignment (pair) is_a: EDAM_data:1383 ! Sequence alignment (nucleic acid) [Term] id: EDAM_data:1387 name: Sequence alignment (protein pair) namespace: data subset: data def: "Alignment of exactly two protein sequences." [http://edamontology.org] is_a: EDAM_data:1381 ! Sequence alignment (pair) is_a: EDAM_data:1384 ! Sequence alignment (protein) [Term] id: EDAM_data:1389 name: Multiple nucleotide sequence alignment namespace: data subset: data def: "Alignment of more than two nucleotide sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1390 name: Multiple protein sequence alignment namespace: data subset: data def: "Alignment of more than two protein sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1388 name: Hybrid sequence alignment (pair) namespace: data subset: data def: "Alignment of exactly two molecular sequences of different types." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1385 ! Sequence alignment (hybrid) [Term] id: EDAM_data:1417 name: Sequence-profile alignment (Domainatrix signature) namespace: data subset: data def: "Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_data:1418 name: Sequence-profile alignment (HMM) namespace: data subset: data def: "Alignment of molecular sequence(s) to a hidden Markov model(s)." [http://edamontology.org] is_a: EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_data:1420 name: Sequence-profile alignment (fingerprint) namespace: data subset: data def: "Alignment of molecular sequences to a protein fingerprint from the PRINTS database." [http://edamontology.org] is_a: EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_data:1479 name: Structure alignment (pair) namespace: data subset: data def: "Alignment (superimposition) of exactly two molecular tertiary (3D) structures." [http://edamontology.org] is_a: EDAM_data:0886 ! Structure alignment [Term] id: EDAM_data:1480 name: Structure alignment (multiple) namespace: data subset: data def: "Alignment (superimposition) of more than two molecular tertiary (3D) structures." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0886 ! Structure alignment [Term] id: EDAM_data:1481 name: Structure alignment (protein) namespace: data subset: data def: "Alignment (superimposition) of protein tertiary (3D) structures." [http://edamontology.org] is_a: EDAM_data:0886 ! Structure alignment is_a: EDAM_data:3154 ! Protein alignment [Term] id: EDAM_data:1482 name: Structure alignment (nucleic acid) namespace: data subset: data def: "Alignment (superimposition) of nucleic acid tertiary (3D) structures." [http://edamontology.org] is_a: EDAM_data:0886 ! Structure alignment is_a: EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:1483 name: Structure alignment (protein pair) namespace: data subset: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures." [http://edamontology.org] is_a: EDAM_data:1481 ! Structure alignment (protein) is_a: EDAM_data:1479 ! Structure alignment (pair) [Term] id: EDAM_data:1484 name: Multiple protein tertiary structure alignment namespace: data subset: data def: "Alignment (superimposition) of more than two protein tertiary (3D) structures." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1481 ! Structure alignment (protein) [Term] id: EDAM_data:1485 name: Structure alignment (protein all atoms) namespace: data subset: data def: "Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] is_a: EDAM_data:1481 ! Structure alignment (protein) [Term] id: EDAM_data:1486 name: Structure alignment (protein C-alpha atoms) namespace: data subset: data def: "Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] comment: C-beta atoms from amino acid side-chains may be considered. is_a: EDAM_data:1481 ! Structure alignment (protein) [Term] id: EDAM_data:1487 name: Pairwise protein tertiary structure alignment (all atoms) namespace: data subset: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1485 ! Structure alignment (protein all atoms) [Term] id: EDAM_data:1488 name: Pairwise protein tertiary structure alignment (C-alpha atoms) namespace: data subset: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] comment: C-beta atoms from amino acid side-chains may be included. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms) [Term] id: EDAM_data:1489 name: Multiple protein tertiary structure alignment (all atoms) namespace: data subset: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1485 ! Structure alignment (protein all atoms) [Term] id: EDAM_data:1490 name: Multiple protein tertiary structure alignment (C-alpha atoms) namespace: data subset: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] comment: C-beta atoms from amino acid side-chains may be included. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms) [Term] id: EDAM_data:1491 name: Structure alignment (nucleic acid pair) namespace: data subset: data def: "Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures." [http://edamontology.org] is_a: EDAM_data:1482 ! Structure alignment (nucleic acid) is_a: EDAM_data:1479 ! Structure alignment (pair) [Term] id: EDAM_data:1492 name: Multiple nucleic acid tertiary structure alignment namespace: data subset: data def: "Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1482 ! Structure alignment (nucleic acid) [Term] id: EDAM_data:1493 name: Structure alignment (RNA) namespace: data subset: data def: "Alignment (superimposition) of RNA tertiary (3D) structures." [http://edamontology.org] is_a: EDAM_data:1482 ! Structure alignment (nucleic acid) [Term] id: EDAM_data:0866 name: Sequence alignment metadata namespace: data subset: data def: "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." [http://edamontology.org] is_a: EDAM_data:0867 ! Sequence alignment report is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:1414 name: Sequence alignment metadata (quality report) namespace: data subset: data def: "Data on molecular sequence alignment quality (estimated accuracy)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:1415 name: Sequence alignment report (site conservation) namespace: data subset: data def: "Data on character conservation in a molecular sequence alignment." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. is_a: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:1416 name: Sequence alignment report (site correlation) namespace: data subset: data def: "Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures." [http://edamontology.org] is_a: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:2242 name: Phylogenetic property values namespace: data subset: data def: "Phylogenetic property values data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0871 ! Phylogenetic character data [Term] id: EDAM_data:1444 name: Phylogenetic character contrasts namespace: data subset: data def: "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." [http://edamontology.org] synonym: "Phylogenetic report (character contrasts)" EXACT [http://edamontology.org] is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] id: EDAM_data:1426 name: Phylogenetic continuous quantitative data namespace: data subset: data def: "Continuous quantitative data that may be read during phylogenetic tree calculation." [http://edamontology.org] synonym: "Quantitative traits" EXACT [http://edamontology.org] synonym: "Phylogenetic continuous quantitative characters" EXACT [http://edamontology.org] is_a: EDAM_data:0871 ! Phylogenetic character data [Term] id: EDAM_data:2873 name: Phylogenetic gene frequencies data namespace: data subset: data def: "Gene frequencies data that may be read during phylogenetic tree calculation." [http://edamontology.org] is_a: EDAM_data:1426 ! Phylogenetic continuous quantitative data [Term] id: EDAM_data:1427 name: Phylogenetic discrete data namespace: data subset: data def: "Character data with discrete states that may be read during phylogenetic tree calculation." [http://edamontology.org] synonym: "Discretely coded characters" EXACT [http://edamontology.org] synonym: "Discrete characters" EXACT [http://edamontology.org] synonym: "Phylogenetic discrete states" EXACT [http://edamontology.org] is_a: EDAM_data:0871 ! Phylogenetic character data [Term] id: EDAM_data:2994 name: Phylogenetic character weights namespace: data subset: data def: "Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted." [http://edamontology.org] is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] id: EDAM_data:1428 name: Phylogenetic character cliques namespace: data subset: data def: "One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny." [http://edamontology.org] synonym: "Phylogenetic report (cliques)" EXACT [http://edamontology.org] is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] id: EDAM_data:1429 name: Phylogenetic invariants namespace: data subset: data def: "Phylogenetic invariants data for testing alternative tree topologies." [http://edamontology.org] synonym: "Phylogenetic report (invariants)" EXACT [http://edamontology.org] is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] id: EDAM_data:2247 name: Phylogenetic consensus tree namespace: data subset: data def: "A consensus phylogenetic tree derived from comparison of multiple trees." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0872 ! Phylogenetic tree [Term] id: EDAM_data:1439 name: DNA substitution model namespace: data subset: data def: "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." [http://edamontology.org] synonym: "Sequence alignment report (DNA substitution model)" EXACT [http://edamontology.org] synonym: "Phylogenetic tree report (DNA substitution model)" EXACT [http://edamontology.org] is_a: EDAM_data:1438 ! Phylogenetic tree report is_a: EDAM_data:0950 ! Biological model is_a: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:1440 name: Phylogenetic tree report (tree shape) namespace: data subset: data def: "Data about the shape of a phylogenetic tree." [http://edamontology.org] is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1441 name: Phylogenetic tree report (tree evaluation) namespace: data subset: data def: "Data on the confidence of a phylogenetic tree." [http://edamontology.org] is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1442 name: Phylogenetic tree report (tree distances) namespace: data subset: data def: "Distances, such as Branch Score distance, between two or more phylogenetic trees." [http://edamontology.org] is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1443 name: Phylogenetic tree report (tree stratigraphic) namespace: data subset: data def: "Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis." [http://edamontology.org] is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1446 name: Comparison matrix (integers) namespace: data subset: data def: "Matrix of integer numbers for sequence comparison." [http://edamontology.org] synonym: "Substitution matrix (integers)" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1447 name: Comparison matrix (floats) namespace: data subset: data def: "Matrix of floating point numbers for sequence comparison." [http://edamontology.org] synonym: "Substitution matrix (floats)" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1448 name: Comparison matrix (nucleotide) namespace: data subset: data def: "Matrix of integer or floating point numbers for nucleotide comparison." [http://edamontology.org] synonym: "Nucleotide substitution matrix" EXACT [http://edamontology.org] is_a: EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1449 name: Comparison matrix (amino acid) namespace: data subset: data def: "Matrix of integer or floating point numbers for amino acid comparison." [http://edamontology.org] synonym: "Amino acid substitution matrix" EXACT [http://edamontology.org] is_a: EDAM_data:2016 ! Amino acid property is_a: EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1450 name: Nucleotide comparison matrix (integers) namespace: data subset: data def: "Matrix of integer numbers for nucleotide comparison." [http://edamontology.org] synonym: "Nucleotide substitution matrix (integers)" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1448 ! Comparison matrix (nucleotide) [Term] id: EDAM_data:1451 name: Nucleotide comparison matrix (floats) namespace: data subset: data def: "Matrix of floating point numbers for nucleotide comparison." [http://edamontology.org] synonym: "Nucleotide substitution matrix (floats)" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1448 ! Comparison matrix (nucleotide) [Term] id: EDAM_data:1452 name: Amino acid comparison matrix (integers) namespace: data subset: data def: "Matrix of integer numbers for amino acid comparison." [http://edamontology.org] synonym: "Amino acid substitution matrix (integers)" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1449 ! Comparison matrix (amino acid) [Term] id: EDAM_data:1453 name: Amino acid comparison matrix (floats) namespace: data subset: data def: "Matrix of floating point numbers for amino acid comparison." [http://edamontology.org] synonym: "Amino acid substitution matrix (floats)" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1449 ! Comparison matrix (amino acid) [Term] id: EDAM_data:1540 name: Protein residue interactions namespace: data subset: data def: "Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups." [http://edamontology.org] synonym: "Residue interaction data" EXACT [http://edamontology.org] synonym: "Atom interaction data" EXACT [http://edamontology.org] is_a: EDAM_data:2599 ! Molecular interaction is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] id: EDAM_data:1543 name: Protein surface report namespace: data subset: data def: "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. synonym: "Protein structure report (surface)" EXACT [http://edamontology.org] is_a: EDAM_data:1542 ! Protein solvent accessibility is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:0875 name: Protein topology namespace: data subset: data def: "Predicted or actual protein topology represented as a string of protein secondary structure elements." [http://edamontology.org] comment: The location and size of the secondary structure elements and intervening loop regions is usually indicated. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0876 ! Protein features (secondary structure) [Term] id: EDAM_data:2081 name: Secondary structure namespace: data subset: data def: "The secondary structure assignment (predicted or real) of a nucleic acid or protein." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:0877 name: Protein features (super-secondary) namespace: data subset: data def: "A report of predicted or actual super-secondary structure of protein sequence(s)." [http://edamontology.org] comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. synonym: "Protein structure report (super-secondary)" EXACT [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:0902 name: Protein architecture report namespace: data subset: data def: "An informative report on architecture (spatial arrangement of secondary structure) of a protein structure." [http://edamontology.org] synonym: "Protein structure report (architecture)" EXACT [http://edamontology.org] synonym: "Protein property (architecture)" EXACT [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:0883 name: Structure namespace: data subset: data def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [http://edamontology.org] synonym: "Structure data" EXACT [http://edamontology.org] comment: The coordinate data may be predicted or real. relationship: has_topic EDAM_topic:0081 ! Structure analysis is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:0884 name: Tertiary structure record namespace: data subset: data def: "An entry from a molecular tertiary (3D) structure database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0883 ! Structure [Term] id: EDAM_data:1546 name: Protein distance matrix namespace: data subset: data def: "A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org] is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1547 name: Protein contact map namespace: data subset: data def: "An amino acid residue contact map for a protein structure." [http://edamontology.org] is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1548 name: Protein residue 3D cluster namespace: data subset: data def: "Report on clusters of contacting residues in protein structures such as a key structural residue network." [http://edamontology.org] is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1549 name: Protein hydrogen bonds namespace: data subset: data def: "Patterns of hydrogen bonding in protein structures." [http://edamontology.org] is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1550 name: Protein non-canonical interactions namespace: data subset: data def: "Non-canonical atomic interactions in protein structures." [http://edamontology.org] synonym: "Protein non-canonical interactions report" EXACT [http://edamontology.org] is_a: EDAM_data:1540 ! Protein residue interactions is_a: EDAM_data:1539 ! Protein structural quality report [Term] id: EDAM_data:1542 name: Protein solvent accessibility namespace: data subset: data def: "Data on the solvent accessible or buried surface area of a protein structure." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:0876 name: Protein features (secondary structure) namespace: data subset: data def: "Secondary structure assignment (predicted or real) of a protein." [http://edamontology.org] comment: The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). synonym: "Protein secondary structure" EXACT [http://edamontology.org] is_a: EDAM_data:2081 ! Secondary structure is_a: EDAM_data:1277 ! Protein features relationship: has_topic EDAM_topic:0694 ! Protein secondary structure [Term] id: EDAM_data:0880 name: RNA secondary structure record namespace: data subset: data def: "An informative report of secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] comment: This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. xref: Moby:RNAStructML is_a: EDAM_data:2081 ! Secondary structure relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] id: EDAM_data:1456 name: Protein features (membrane regions) namespace: data subset: data def: "An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." [http://edamontology.org] comment: This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. synonym: "Transmembrane region report" EXACT [http://edamontology.org] synonym: "Intramembrane region report" EXACT [http://edamontology.org] synonym: "Protein report (membrane protein)" EXACT [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1755 name: Protein atom namespace: data subset: data def: "Data on a single atom from a protein structure." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. synonym: "Atom data" EXACT [http://edamontology.org] synonym: "atom" RELATED [CHEBI:33250] is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1756 name: Protein residue namespace: data subset: data def: "Data on a single amino acid residue position in a protein structure." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. synonym: "Residue" EXACT [http://edamontology.org] is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1459 name: Nucleic acid structure namespace: data subset: data def: "3D coordinate and associated data for a nucleic acid tertiary (3D) structure." [http://edamontology.org] is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis [Term] id: EDAM_data:1460 name: Protein structure namespace: data subset: data def: "3D coordinate and associated data for a protein tertiary (3D) structure." [http://edamontology.org] is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:2814 ! Protein structure analysis relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure [Term] id: EDAM_data:1461 name: Protein-ligand complex namespace: data subset: data def: "The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule." [http://edamontology.org] comment: This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1462 name: Carbohydrate structure namespace: data subset: data def: "3D coordinate and associated data for a carbohydrate (3D) structure." [http://edamontology.org] is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0152 ! Carbohydrates relationship: has_topic EDAM_topic:0153 ! Lipids [Term] id: EDAM_data:2850 name: Lipid structure namespace: data subset: data def: "3D coordinate and associated data for a lipid structure." [http://edamontology.org] is_a: EDAM_data:0883 ! Structure [Term] id: EDAM_data:1463 name: Small molecule structure namespace: data subset: data def: "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." [http://edamontology.org] synonym: "molecular entity" RELATED [CHEBI:23367] is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0154 ! Small molecules [Term] id: EDAM_data:2851 name: Drug structure namespace: data subset: data def: "3D coordinate and associated data for the (3D) structure of a drug." [http://edamontology.org] is_a: EDAM_data:1463 ! Small molecule structure [Term] id: EDAM_data:2852 name: Toxin structure namespace: data subset: data def: "3D coordinate and associated data for the (3D) structure of a toxin." [http://edamontology.org] is_a: EDAM_data:1463 ! Small molecule structure [Term] id: EDAM_data:1464 name: DNA structure namespace: data subset: data def: "3D coordinate and associated data for a DNA tertiary (3D) structure." [http://edamontology.org] is_a: EDAM_data:1459 ! Nucleic acid structure [Term] id: EDAM_data:1465 name: RNA structure record namespace: data subset: data def: "3D coordinate and associated data for an RNA tertiary (3D) structure." [http://edamontology.org] is_a: EDAM_data:1459 ! Nucleic acid structure relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] id: EDAM_data:1466 name: tRNA structure record namespace: data subset: data def: "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." [http://edamontology.org] is_a: EDAM_data:1465 ! RNA structure record [Term] id: EDAM_data:1467 name: Protein chain namespace: data subset: data def: "3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain." [http://edamontology.org] is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1468 name: Protein domain namespace: data subset: data def: "3D coordinate and associated data for the tertiary (3D) structure of a protein domain." [http://edamontology.org] is_a: EDAM_data:1460 ! Protein structure relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_data:2877 name: Protein complex namespace: data subset: data def: "3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another." [http://edamontology.org] is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:2878 name: Protein structural motif namespace: data subset: data def: "3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role." [http://edamontology.org] is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1469 name: Protein structure (all atoms) namespace: data subset: data def: "3D coordinate and associated data for a protein tertiary (3D) structure (all atoms)." [http://edamontology.org] is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1470 name: Protein structure (C-alpha atoms) namespace: data subset: data def: "3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] comment: C-beta atoms from amino acid side-chains may be included. is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1471 name: Protein chain (all atoms) namespace: data subset: data def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1467 ! Protein chain consider: EDAM_data:1469 ! Protein structure (all atoms) [Term] id: EDAM_data:1472 name: Protein chain (C-alpha atoms) namespace: data subset: data def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] comment: C-beta atoms from amino acid side-chains may be included. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1467 ! Protein chain consider: EDAM_data:1470 ! Protein structure (C-alpha atoms) [Term] id: EDAM_data:1473 name: Protein domain (all atoms) namespace: data subset: data def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1468 ! Protein domain consider: EDAM_data:1469 ! Protein structure (all atoms) [Term] id: EDAM_data:1474 name: Protein domain (C-alpha atoms) namespace: data subset: data def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] comment: C-beta atoms from amino acid side-chains may be included. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1468 ! Protein domain consider: EDAM_data:1470 ! Protein structure (C-alpha atoms) [Term] id: EDAM_data:1495 name: DaliLite hit table namespace: data subset: data def: "DaliLite hit table of protein chain tertiary structure alignment data." [http://edamontology.org] comment: The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0887 ! Structure alignment report [Term] id: EDAM_data:1499 name: 3D-1D scoring matrix namespace: data subset: data def: "A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments." [http://edamontology.org] is_a: EDAM_data:0892 ! Protein sequence-structure scoring matrix [Term] id: EDAM_data:0894 name: Amino acid annotation namespace: data subset: data def: "An informative report about a specific amino acid." [http://edamontology.org] is_a: EDAM_data:2016 ! Amino acid property is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:1501 name: Amino acid index namespace: data subset: data def: "A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids." [http://edamontology.org] is_a: EDAM_data:2016 ! Amino acid property is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:1503 name: Amino acid pair-wise contact potentials namespace: data subset: data def: "Statistical protein contact potentials." [http://edamontology.org] is_a: EDAM_data:2016 ! Amino acid property [Term] id: EDAM_data:1502 name: Amino acid index (chemical classes) namespace: data subset: data def: "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." [http://edamontology.org] is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1505 name: Amino acid index (molecular weight) namespace: data subset: data def: "Molecular weights of amino acids." [http://edamontology.org] is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1506 name: Amino acid index (hydropathy) namespace: data subset: data def: "Hydrophobic, hydrophilic or charge properties of amino acids." [http://edamontology.org] is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1507 name: Amino acid index (White-Wimley data) namespace: data subset: data def: "Experimental free energy values for the water-interface and water-octanol transitions for the amino acids." [http://edamontology.org] is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1508 name: Amino acid index (van der Waals radii) namespace: data subset: data def: "Van der Waals radii of atoms for different amino acid residues." [http://edamontology.org] is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1509 name: Enzyme property namespace: data subset: data def: "An informative report on a specific enzyme." [http://edamontology.org] synonym: "Enzyme report" EXACT [http://edamontology.org] synonym: "Protein report (enzyme)" EXACT [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions [Term] id: EDAM_data:1776 name: Protein report (function) namespace: data subset: data def: "Report on general functional properties of specific protein(s)." [http://edamontology.org] comment: For properties that can be mapped to a sequence, use 'Sequence report' instead. is_obsolete: true !{since=beta13} consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:2722 name: Protein features (disordered structure) namespace: data subset: data def: "An informative report about disordered structure in a protein." [http://edamontology.org] synonym: "Protein structure report (disordered structure)" EXACT [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:2147 name: Protein report (transcription factor) namespace: data subset: data def: "An informative report on a transcription factor protein." [http://edamontology.org] comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. synonym: "Transcription factor binding site data" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:2401 name: Protein report (membrane protein) namespace: data subset: data def: "An informative report on a membrane protein." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1456 ! Protein features (membrane regions) [Term] id: EDAM_data:1517 name: Restriction enzyme property namespace: data subset: data ! alt_id: EDAM_data:1510 ! alt_id: EDAM_data:1518 def: "An informative report on a specific restriction enzyme such as enzyme reference data." [http://edamontology.org] comment: This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. synonym: "Restriction enzyme report" EXACT [http://edamontology.org] synonym: "Restriction enzyme pattern data" EXACT [http://edamontology.org] synonym: "Protein report (restriction enzyme)" EXACT [http://edamontology.org] is_a: EDAM_data:1509 ! Enzyme property [Term] id: EDAM_data:1533 name: Protein subcellular localization namespace: data subset: data def: "An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." [http://edamontology.org] synonym: "Protein report (subcellular localization)" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:2191 name: Protein features (chemical modification) namespace: data subset: data def: "Data on a chemical modification of a protein." [http://edamontology.org] synonym: "Protein modification annotation" EXACT [http://edamontology.org] synonym: "protein modification" RELATED [MOD:00000] synonym: "protein modification process" RELATED [GO:0006464] is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:2991 name: Protein torsion angle data namespace: data subset: data def: "Torsion angle data for a protein structure." [http://edamontology.org] synonym: "Torsion angle data" EXACT [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1544 name: Ramachandran plot namespace: data subset: data def: "Phi/psi angle data or a Ramachandran plot of a protein structure." [http://edamontology.org] is_a: EDAM_data:2991 ! Protein torsion angle data [Term] id: EDAM_data:1545 name: Protein dipole moment namespace: data subset: data def: "Data on the net charge distribution (dipole moment) of a protein structure." [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1519 name: Peptide molecular weights namespace: data subset: data ! alt_id: EDAM_data:1535 def: "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents." [http://edamontology.org] comment: The report might include associated data such as frequency of peptide fragment molecular weights. is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1520 name: Peptide hydrophobic moment namespace: data subset: data def: "Report on the hydrophobic moment of a polypeptide sequence." [http://edamontology.org] comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:2970 name: Protein hydropathy data namespace: data subset: data def: "A report on protein properties concerning hydropathy." [http://edamontology.org] synonym: "Protein hydropathy report" EXACT [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1521 name: Protein aliphatic index namespace: data subset: data def: "The aliphatic index of a protein." [http://edamontology.org] comment: The aliphatic index is the relative protein volume occupied by aliphatic side chains. is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:2164 name: Protein sequence properties plot namespace: data subset: data def: "A plot of general physicochemical properties of a protein sequence." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:2165 name: Protein ionization curve namespace: data subset: data def: "A plot of pK versus pH for a protein." [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1522 name: Protein sequence hydropathy plot namespace: data subset: data def: "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc." [http://edamontology.org] comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1523 name: Protein charge plot namespace: data subset: data def: "A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence." [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1524 name: Protein solubility namespace: data subset: data def: "The solubility or atomic solvation energy of a protein sequence or structure." [http://edamontology.org] synonym: "Protein solubility data" EXACT [http://edamontology.org] is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1525 name: Protein crystallizability namespace: data subset: data def: "Data on the crystallizability of a protein sequence." [http://edamontology.org] synonym: "Protein crystallizability data" EXACT [http://edamontology.org] is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1526 name: Protein globularity namespace: data subset: data def: "Data on the stability, intrinsic disorder or globularity of a protein sequence." [http://edamontology.org] synonym: "Protein globularity data" EXACT [http://edamontology.org] is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1527 name: Protein titration curve namespace: data subset: data def: "The titration curve of a protein." [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1528 name: Protein isoelectric point namespace: data subset: data def: "The isoelectric point of one proteins." [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1529 name: Protein pKa value namespace: data subset: data def: "The pKa value of a protein." [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1530 name: Protein hydrogen exchange rate namespace: data subset: data def: "The hydrogen exchange rate of a protein." [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1531 name: Protein extinction coefficient namespace: data subset: data def: "The extinction coefficient of a protein." [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1532 name: Protein optical density namespace: data subset: data def: "The optical density of a protein." [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1534 name: Peptide immunogenicity data namespace: data subset: data def: "An report on allergenicity / immunogenicity of peptides and proteins." [http://edamontology.org] comment: This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. synonym: "Peptide immunogenicity report" EXACT [http://edamontology.org] synonym: "Peptide immunogenicity" EXACT [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:2957 name: Hopp and Woods plot namespace: data subset: data def: "A Hopp and Woods plot of predicted antigenicity of a peptide or protein." [http://edamontology.org] is_a: EDAM_data:1534 ! Peptide immunogenicity data [Term] id: EDAM_data:1536 name: MHC peptide immunogenicity report namespace: data subset: data def: "A report on the immunogenicity of MHC class I or class II binding peptides." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1534 ! Peptide immunogenicity data [Term] id: EDAM_data:2753 name: Carbohydrate conformational map namespace: data subset: data def: "A conformational energy map of the glycosidic linkages in a carbohydrate molecule." [http://edamontology.org] is_a: EDAM_data:2313 ! Carbohydrate structure report [Term] id: EDAM_data:0899 name: Protein features (3D motif) namespace: data subset: data def: "An informative report on the 3D structural motifs in a protein." [http://edamontology.org] comment: This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. synonym: "Protein structure report (3D motif)" EXACT [http://edamontology.org] is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:1537 ! Protein structure report relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces [Term] id: EDAM_data:1539 name: Protein structural quality report namespace: data subset: data def: "Report on the quality of a protein three-dimensional model." [http://edamontology.org] comment: Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. synonym: "Protein structure report (quality evaluation)" EXACT [http://edamontology.org] synonym: "Protein report (structural quality)" EXACT [http://edamontology.org] synonym: "Protein property (structural quality)" EXACT [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:1541 name: Protein flexibility or motion report namespace: data subset: data def: "Informative report on flexibility or motion of a protein structure." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. synonym: "Protein structure report (flexibility or motion)" EXACT [http://edamontology.org] synonym: "Protein property (flexibility or motion)" EXACT [http://edamontology.org] synonym: "Protein flexibility or motion" EXACT [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:2235 name: Raw SCOP domain classification namespace: data subset: data def: "Raw SCOP domain classification data files." [http://edamontology.org] comment: These are the parsable data files provided by SCOP. is_obsolete: true !{since=beta13} consider: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:2236 name: Raw CATH domain classification namespace: data subset: data def: "Raw CATH domain classification data files." [http://edamontology.org] comment: These are the parsable data files provided by CATH. is_obsolete: true !{since=beta13} consider: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:1762 name: CATH domain report namespace: data subset: data def: "Summary of domain classification information for a CATH domain." [http://edamontology.org] comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. is_obsolete: true !{since=beta13} consider: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:1553 name: CATH node namespace: data subset: data def: "Information on a node from the CATH database." [http://edamontology.org] comment: The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. synonym: "CATH classification node report" EXACT [http://edamontology.org] is_a: EDAM_data:3101 ! Protein domain classification node [Term] id: EDAM_data:1554 name: SCOP node namespace: data subset: data def: "Information on a node from the SCOP database." [http://edamontology.org] synonym: "SCOP classification node" EXACT [http://edamontology.org] is_a: EDAM_data:3101 ! Protein domain classification node [Term] id: EDAM_data:3141 !{since=beta13} name: SCOP class namespace: data subset: data def: "Information on a 'class' node from the SCOP database." [http://edamontology.org] is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3142 !{since=beta13} name: SCOP fold namespace: data subset: data def: "Information on a 'fold' node from the SCOP database." [http://edamontology.org] is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3143 !{since=beta13} name: SCOP superfamily namespace: data subset: data def: "Information on a 'superfamily' node from the SCOP database." [http://edamontology.org] is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3144 !{since=beta13} name: SCOP family namespace: data subset: data def: "Information on a 'family' node from the SCOP database." [http://edamontology.org] is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3145 !{since=beta13} name: SCOP protein namespace: data subset: data def: "Information on a 'protein' node from the SCOP database." [http://edamontology.org] is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3146 !{since=beta13} name: SCOP species namespace: data subset: data def: "Information on a 'species' node from the SCOP database." [http://edamontology.org] is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:1555 name: EMBASSY domain classification namespace: data subset: data def: "An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:1556 name: CATH class namespace: data subset: data def: "Information on a protein 'class' node from the CATH database." [http://edamontology.org] is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1557 name: CATH architecture namespace: data subset: data def: "Information on a protein 'architecture' node from the CATH database." [http://edamontology.org] is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1558 name: CATH topology namespace: data subset: data def: "Information on a protein 'topology' node from the CATH database." [http://edamontology.org] is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1559 name: CATH homologous superfamily namespace: data subset: data def: "Information on a protein 'homologous superfamily' node from the CATH database." [http://edamontology.org] is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1560 name: CATH structurally similar group namespace: data subset: data def: "Information on a protein 'structurally similar group' node from the CATH database." [http://edamontology.org] is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1561 name: CATH functional category namespace: data subset: data def: "Information on a protein 'functional category' node from the CATH database." [http://edamontology.org] is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1565 name: Protein-protein interaction namespace: data subset: data ! alt_id: EDAM_data:2712 def: "Data on protein-protein interaction(s)." [http://edamontology.org] comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains). synonym: "Protein structure report (protein complex)" EXACT [http://edamontology.org] is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] id: EDAM_data:1566 name: Protein-ligand interaction namespace: data subset: data def: "Data on protein-ligand (small molecule) interaction(s)." [http://edamontology.org] is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] id: EDAM_data:1567 name: Protein-nucleic acid interaction namespace: data subset: data def: "Data on protein-DNA/RNA interaction(s)." [http://edamontology.org] is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions [Term] id: EDAM_data:2359 name: Domain-domain interaction namespace: data subset: data def: "Data on protein domain-protein domain interaction(s)." [http://edamontology.org] is_a: EDAM_data:1565 ! Protein-protein interaction [Term] id: EDAM_data:2378 name: Protein-motif interaction namespace: data subset: data def: "Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1565 ! Protein-protein interaction [Term] id: EDAM_data:2360 name: Domain-domain interaction (indirect) namespace: data subset: data def: "Data on indirect protein domain-protein domain interaction(s)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2359 ! Domain-domain interaction [Term] id: EDAM_data:2402 name: Protein-drug interaction namespace: data subset: data def: "Informative report on protein-drug interaction(s) including binding affinity data." [http://edamontology.org] is_a: EDAM_data:1566 ! Protein-ligand interaction [Term] id: EDAM_data:2358 name: Domain-nucleic acid interaction namespace: data subset: data def: "Data on protein domain-DNA/RNA interaction(s)." [http://edamontology.org] is_a: EDAM_data:1567 ! Protein-nucleic acid interaction [Term] id: EDAM_data:2025 name: Michaelis Menten plot namespace: data subset: data def: "A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent." [http://edamontology.org] is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_data:2026 name: Hanes Woolf plot namespace: data subset: data def: "A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v)." [http://edamontology.org] is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_data:0909 name: Vmax namespace: data subset: data def: "The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large." [http://edamontology.org] is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_data:0910 name: Km namespace: data subset: data def: "Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction." [http://edamontology.org] is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_data:2720 name: Dinucleotide property namespace: data subset: data def: "Physicochemical property data for one or more dinucleotides." [http://edamontology.org] is_a: EDAM_data:2088 ! DNA base structural data ! [Term] born obsolete ! id: EDAM_data:3149 !{since=beta13} ! name: Nucleic acid property (sequence) ! namespace: data ! subset: data ! def: "A non-positional property of a nucleic acid sequence." [http://edamontology.org] ! synonym: "Nucleic acid sequence property" EXACT [http://edamontology.org] ! is_obsolete: true !{since=beta13} ! consider: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:2985 name: Nucleic acid thermodynamic data namespace: data subset: data def: "A thermodynamic or kinetic property of a nucleic acid molecule." [http://edamontology.org] synonym: "Nucleic acid property (thermodynamic or kinetic)" EXACT [http://edamontology.org] synonym: "Nucleic acid thermodynamic property" EXACT [http://edamontology.org] is_a: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:1583 name: Nucleic acid melting profile namespace: data subset: data def: "Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating." [http://edamontology.org] comment: A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. synonym: "Nucleic acid stability profile" EXACT [http://edamontology.org] is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] id: EDAM_data:1584 name: Nucleic acid enthalpy namespace: data subset: data def: "Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] id: EDAM_data:1585 name: Nucleic acid entropy namespace: data subset: data def: "Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] id: EDAM_data:1586 name: Nucleic acid melting temperature namespace: data subset: data def: "Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2139 ! Nucleic acid melting temperature [Term] id: EDAM_data:2088 name: DNA base structural data namespace: data subset: data def: "Structural data for DNA base pairs or runs of bases, such as energy or angle data." [http://edamontology.org] is_a: EDAM_data:0912 ! Nucleic acid property is_a: EDAM_data:2086 ! Nucleic acid structure report [Term] id: EDAM_data:2167 name: Nucleic acid density plot namespace: data subset: data def: "Density plot (of base composition) for a nucleotide sequence." [http://edamontology.org] is_a: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:1587 name: Nucleic acid stitch profile namespace: data subset: data def: "Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] comment: A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] id: EDAM_data:2958 name: Nucleic acid melting curve namespace: data subset: data def: "A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] comment: Shows the proportion of nucleic acid which are double-stranded versus temperature. is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] id: EDAM_data:2959 name: Nucleic acid probability profile namespace: data subset: data def: "A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] comment: Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] id: EDAM_data:2960 name: Nucleic acid temperature profile namespace: data subset: data def: "A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] comment: Plots melting temperature versus base position. synonym: "Melting map" EXACT [http://edamontology.org] is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] id: EDAM_data:1594 name: Vienna RNA calculated energy namespace: data subset: data def: "RNA calculated energy data generated by the Vienna package." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1584 ! Nucleic acid enthalpy [Term] id: EDAM_data:1588 name: DNA base pair stacking energies data namespace: data subset: data def: "DNA base pair stacking energies data." [http://edamontology.org] is_a: EDAM_data:2088 ! DNA base structural data [Term] id: EDAM_data:1589 name: DNA base pair twist angle data namespace: data subset: data def: "DNA base pair twist angle data." [http://edamontology.org] is_a: EDAM_data:2088 ! DNA base structural data [Term] id: EDAM_data:1590 name: DNA base trimer roll angles data namespace: data subset: data def: "DNA base trimer roll angles data." [http://edamontology.org] is_a: EDAM_data:2088 ! DNA base structural data [Term] id: EDAM_data:1595 name: Base pairing probability matrix dotplot namespace: data subset: data def: "Dotplot of RNA base pairing probability matrix." [http://edamontology.org] comment: Such as generated by the Vienna package. is_a: EDAM_data:2088 ! DNA base structural data [Term] id: EDAM_data:1598 name: Genetic code namespace: data subset: data def: "A genetic code for an organism." [http://edamontology.org] comment: A genetic code need not include detailed codon usage information. is_a: EDAM_data:1597 ! Codon usage table [Term] id: EDAM_data:2865 name: Codon usage bias namespace: data subset: data def: "A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences." [http://edamontology.org] is_a: EDAM_data:0914 ! Codon usage report [Term] id: EDAM_data:1599 name: Codon adaptation index namespace: data subset: data def: "A simple measure of synonymous codon usage bias often used to predict gene expression levels." [http://edamontology.org] synonym: "CAI" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2865 ! Codon usage bias [Term] id: EDAM_data:1600 name: Codon usage bias plot namespace: data subset: data def: "A plot of the synonymous codon usage calculated for windows over a nucleotide sequence." [http://edamontology.org] synonym: "Synonymous codon usage statistic plot" EXACT [http://edamontology.org] is_a: EDAM_data:2865 ! Codon usage bias [Term] id: EDAM_data:1601 name: Nc statistic namespace: data subset: data def: "The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2865 ! Codon usage bias [Term] id: EDAM_data:1602 name: Codon usage fraction difference namespace: data subset: data def: "The differences in codon usage fractions between two codon usage tables." [http://edamontology.org] is_a: EDAM_data:0914 ! Codon usage report [Term] id: EDAM_data:0917 name: Gene classification namespace: data subset: data def: "A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:0927 name: Gene annotation (linkage) namespace: data subset: data def: "An informative report on the linkage of alleles." [http://edamontology.org] is_a: EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:1634 name: Gene annotation (linkage disequilibrium) namespace: data subset: data def: "A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [http://edamontology.org] is_a: EDAM_data:0927 ! Gene annotation (linkage) [Term] id: EDAM_data:0928 name: Gene expression profile namespace: data subset: data def: "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." [http://edamontology.org] synonym: "Gene expression pattern" EXACT [http://edamontology.org] is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2579 name: Expressed gene list namespace: data subset: data def: "A simple summary of expressed genes." [http://edamontology.org] synonym: "Gene annotation (expressed gene list)" EXACT [http://edamontology.org] is_a: EDAM_data:2872 ! ID list [Term] id: EDAM_data:2586 name: Northern blot image namespace: data subset: data def: "An image arising from a Northern Blot experiment." [http://edamontology.org] is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:1636 name: Heat map namespace: data subset: data def: "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." [http://edamontology.org] comment: A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. is_a: EDAM_data:2967 ! Microarray image [Term] id: EDAM_data:2092 name: Nucleic acid features (SNP) namespace: data subset: data def: "Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence." [http://edamontology.org] comment: An SNP is an individual point mutation or substitution of a single nucleotide. synonym: "Single nucleotide polymorphism" EXACT [http://edamontology.org] synonym: "SNP annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_data:2867 name: Nucleic acid features (VNTR) namespace: data subset: data def: "Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence." [http://edamontology.org] comment: VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. synonym: "Variable number of tandem repeat polymorphism" EXACT [http://edamontology.org] synonym: "VNTR annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_data:2868 name: Nucleic acid features (microsatellite) namespace: data subset: data def: "Annotation on a microsatellite polymorphism in a DNA sequence." [http://edamontology.org] comment: A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. synonym: "Microsatellite annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_data:2869 name: Nucleic acid features (RFLP) namespace: data subset: data def: "Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence." [http://edamontology.org] comment: An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. synonym: "RFLP annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_data:1853 name: Chromosome annotation (aberration) namespace: data subset: data def: "A report on a chromosome aberration such as abnormalities in chromosome structure." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0919 ! Gene annotation (chromosome) [Term] id: EDAM_data:1621 name: Pharmacogenomic annotation namespace: data subset: data def: "Data on the influence of genotype on drug response." [http://edamontology.org] comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. is_a: EDAM_data:0920 ! Genotype/phenotype annotation [Term] id: EDAM_data:1622 name: Disease annotation namespace: data subset: data def: "An informative report on a specific disease." [http://edamontology.org] is_a: EDAM_data:0920 ! Genotype/phenotype annotation relationship: has_topic EDAM_topic:0634 ! Disease resources [Term] id: EDAM_data:2533 name: Nucleic acid features (mutation) namespace: data subset: data def: "Annotation on a mutation." [http://edamontology.org] synonym: "Mutation annotation" EXACT [http://edamontology.org] is_a: EDAM_data:0918 ! Nucleic acid features (variation) [Term] id: EDAM_data:2885 name: Nucleic acid features (polymorphism annotation) namespace: data subset: data def: "Annotation on a polymorphism." [http://edamontology.org] synonym: "Polymorphism annotation" EXACT [http://edamontology.org] is_a: EDAM_data:0918 ! Nucleic acid features (variation) [Term] id: EDAM_data:2212 name: Mutation annotation (basic) namespace: data subset: data def: "Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] id: EDAM_data:2213 name: Mutation annotation (prevalence) namespace: data subset: data def: "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] id: EDAM_data:2214 name: Mutation annotation (prognostic) namespace: data subset: data def: "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] id: EDAM_data:2215 name: Mutation annotation (functional) namespace: data subset: data def: "An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] id: EDAM_data:2217 name: Tumor annotation namespace: data subset: data def: "An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on." [http://edamontology.org] is_a: EDAM_data:1622 ! Disease annotation [Term] id: EDAM_data:1852 name: Sequence assembly component namespace: data subset: data def: "A component of a larger sequence assembly." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0925 ! Sequence assembly [Term] id: EDAM_data:0923 name: Experiment annotation (PCR assay data) namespace: data subset: data def: "Data on a PCR assay or electronic / virtual PCR." [http://edamontology.org] synonym: "PCR assay data" EXACT [http://edamontology.org] is_a: EDAM_data:2531 ! Experiment annotation relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_data:3165 !{since=1.0} name: Experiment annotation (sequencing) namespace: data subset: data def: "Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis." [http://edamontology.org] is_a: EDAM_data:2531 ! Experiment annotation relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_data:0924 name: Sequence trace namespace: data subset: data def: "Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores." [http://edamontology.org] comment: This is the raw data produced by a DNA sequencing machine. is_a: EDAM_data:3108 ! Experimental measurement is_a: EDAM_data:2887 ! Sequence record (nucleic acid) [Term] id: EDAM_data:0926 name: Radiation Hybrid (RH) scores namespace: data subset: data def: "Radiation hybrid scores (RH) scores for one or more markers." [http://edamontology.org] comment: Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:2363 name: 2D PAGE data namespace: data subset: data def: "Data concerning two-dimensional polygel electrophoresis." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. is_obsolete: true !{since=beta13} consider: EDAM_data:0942 ! 2D PAGE image consider: EDAM_data:2364 ! Experiment annotation (2D PAGE) [Term] id: EDAM_data:2838 name: Experimental data (proteomics) namespace: data subset: data def: "Data concerning a proteomics experiment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:3147 ! Experiment annotation (mass spectrometry) [Term] id: EDAM_data:2536 name: Mass spectrometry data namespace: data subset: data def: "Data concerning a mass spectrometry experiment." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. is_obsolete: true !{since=beta13} consider: EDAM_data:0943 ! Mass spectrometry spectra consider: EDAM_data:0944 ! Peptide mass fingerprint consider: EDAM_data:3147 ! Experiment annotation (mass spectrometry) [Term] id: EDAM_data:0943 name: Mass spectrometry spectra namespace: data subset: data def: "Spectra from mass spectrometry." [http://edamontology.org] is_a: EDAM_data:3108 ! Experimental measurement relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] id: EDAM_data:0944 name: Peptide mass fingerprint namespace: data subset: data def: "A set of peptide masses (peptide mass fingerprint) from mass spectrometry." [http://edamontology.org] synonym: "Protein fingerprint" EXACT [http://edamontology.org] synonym: "Peak list" EXACT [http://edamontology.org] is_a: EDAM_data:2979 ! Peptide property is_a: EDAM_data:3108 ! Experimental measurement relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:0945 name: Peptide identification namespace: data subset: data def: "Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database." [http://edamontology.org] is_a: EDAM_data:2979 ! Peptide property relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:2537 name: Protein structure raw data namespace: data subset: data def: "Raw data from experimental methods for determining protein structure." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:0937 name: Protein X-ray crystallographic data namespace: data subset: data def: "X-ray crystallography data." [http://edamontology.org] is_a: EDAM_data:2537 ! Protein structure raw data [Term] id: EDAM_data:0938 name: Protein NMR data namespace: data subset: data def: "Protein nuclear magnetic resonance (NMR) raw data." [http://edamontology.org] is_a: EDAM_data:2537 ! Protein structure raw data [Term] id: EDAM_data:0939 name: Protein circular dichroism (CD) spectroscopic data namespace: data subset: data def: "Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data." [http://edamontology.org] is_a: EDAM_data:2537 ! Protein structure raw data [Term] id: EDAM_data:0940 name: Electron microscopy volume map namespace: data subset: data def: "Volume map data from electron microscopy." [http://edamontology.org] synonym: "EM volume map" EXACT [http://edamontology.org] is_a: EDAM_data:3108 ! Experimental measurement relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] id: EDAM_data:0905 name: Protein interaction raw data namespace: data subset: data def: "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:0931 name: Experiment annotation (microarray) namespace: data subset: data ! alt_id: EDAM_data:3114 !{since=beta13} ! Not released def: "Information on a microarray experiment such as conditions, protocol, sample:data relationships etc." [http://edamontology.org] comment: This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. synonym: "Experimental design annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2531 ! Experiment annotation relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:2866 name: Experiment annotation (Northern blot) namespace: data subset: data def: "General annotation on a Northern Blot experiment." [http://edamontology.org] is_a: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:3147 !{since=beta13} name: Experiment annotation (mass spectrometry) namespace: data subset: data def: "General annotation on a mass spectrometry experiment." [http://edamontology.org] is_a: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:0932 name: Oligonucleotide probe data namespace: data subset: data def: "Data on oligonucleotide probes (typically for use with DNA microarrays)." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:2717 ! Oligonucleotide probe annotation [Term] id: EDAM_data:2535 name: Sequence tag profile namespace: data subset: data def: "Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed." [http://edamontology.org] comment: SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. synonym: "Sequencing-based expression profile" EXACT [http://edamontology.org] is_a: EDAM_data:0928 ! Gene expression profile [Term] id: EDAM_data:0933 name: SAGE experimental data namespace: data subset: data def: "Output from a serial analysis of gene expression (SAGE) experiment." [http://edamontology.org] synonym: "Serial analysis of gene expression (SAGE) experimental data" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2535 ! Sequence tag profile [Term] id: EDAM_data:0934 name: MPSS experimental data namespace: data subset: data def: "Massively parallel signature sequencing (MPSS) data." [http://edamontology.org] synonym: "Massively parallel signature sequencing (MPSS) experimental data" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2535 ! Sequence tag profile [Term] id: EDAM_data:0935 name: SBS experimental data namespace: data subset: data def: "Sequencing by synthesis (SBS) data." [http://edamontology.org] synonym: "Sequencing by synthesis (SBS) experimental data" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2535 ! Sequence tag profile [Term] id: EDAM_data:0936 name: Sequence tag profile (with gene assignment) namespace: data subset: data def: "Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers." [http://edamontology.org] is_a: EDAM_data:2535 ! Sequence tag profile [Term] id: EDAM_data:0942 name: 2D PAGE image namespace: data subset: data def: "Two-dimensional gel electrophoresis image." [http://edamontology.org] synonym: "Two-dimensional gel electrophoresis image" EXACT [http://edamontology.org] is_a: EDAM_data:2968 ! Image is_a: EDAM_data:3108 ! Experimental measurement relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] id: EDAM_data:2364 name: Experiment annotation (2D PAGE) namespace: data subset: data def: "An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel." [http://edamontology.org] is_a: EDAM_data:2531 ! Experiment annotation relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] id: EDAM_data:2965 name: 2D PAGE image (annotated) namespace: data subset: data def: "An informative report on a two-dimensional (2D PAGE) gel." [http://edamontology.org] synonym: "2D PAGE image annotation" EXACT [http://edamontology.org] is_a: EDAM_data:0942 ! 2D PAGE image [Term] id: EDAM_data:2372 name: 2D PAGE spot (annotated) namespace: data subset: data def: "An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel." [http://edamontology.org] synonym: "2D PAGE spot annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2965 ! 2D PAGE image (annotated) [Term] id: EDAM_data:1646 name: Molecular weights standard fingerprint namespace: data subset: data def: "Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS." [http://edamontology.org] is_a: EDAM_data:0944 ! Peptide mass fingerprint [Term] id: EDAM_data:2717 name: Oligonucleotide probe annotation namespace: data subset: data def: "General annotation on an oligonucleotide probe." [http://edamontology.org] is_a: EDAM_data:3115 ! Microarray annotation relationship: has_topic EDAM_topic:0632 ! Probes and primers [Term] id: EDAM_data:2966 name: Oligonucleotide probe sets annotation namespace: data subset: data def: "General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set." [http://edamontology.org] is_a: EDAM_data:2717 ! Oligonucleotide probe annotation [Term] id: EDAM_data:1642 name: Affymetrix probe sets library file namespace: data subset: data def: "Affymetrix library file of information about which probes belong to which probe set." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation ! synonym: "CDF file" EXACT [http://edamontology.org] [Term] id: EDAM_data:1643 name: Affymetrix probe sets information library file namespace: data subset: data def: "Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation ! synonym: "GIN file" EXACT [http://edamontology.org] [Term] id: EDAM_data:0856 name: Sequence feature source namespace: data subset: data def: "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived." [http://edamontology.org] comment: This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). is_a: EDAM_data:2042 ! Evidence is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:0859 name: Sequence signature model namespace: data subset: data def: "Data files used by motif or profile methods." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:0946 name: Pathway or network annotation namespace: data subset: data def: "An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_data:2589 name: Hierarchy namespace: data subset: data def: "A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation." [http://edamontology.org] synonym: "Hierarchy annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2987 ! Classification [Term] id: EDAM_data:0904 name: Protein features (mutation) namespace: data subset: data def: "Data on the effect of (typically point) mutation on protein folding, stability, structure and function." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. synonym: "Protein property (mutation)" EXACT [http://edamontology.org] synonym: "Protein report (mutation)" EXACT [http://edamontology.org] synonym: "Protein structure report (mutation)" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:0903 name: Protein folding report namespace: data subset: data def: "A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. synonym: "Protein report (folding)" EXACT [http://edamontology.org] synonym: "Protein property (folding)" EXACT [http://edamontology.org] is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1596 name: Nucleic acid folding report namespace: data subset: data def: "A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. synonym: "Nucleic acid report (folding model)" EXACT [http://edamontology.org] synonym: "Nucleic acid report (folding)" EXACT [http://edamontology.org] is_a: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:1344 name: MEME motif alphabet namespace: data subset: data def: "Alphabet for the motifs (patterns) that MEME will search for." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1345 name: MEME background frequencies file namespace: data subset: data def: "MEME background frequencies file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1346 name: MEME motifs directive file namespace: data subset: data def: "File of directives for ordering and spacing of MEME motifs." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1347 name: Dirichlet distribution namespace: data subset: data def: "Dirichlet distribution used by hidden Markov model analysis programs." [http://edamontology.org] is_a: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1348 name: HMM emission and transition counts namespace: data subset: data def: "Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states." [http://edamontology.org] is_a: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:0947 name: Biological pathway map namespace: data subset: data def: "A map (typically a diagram) of a biological pathway." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1656 name: Pathway or network (metabolic) namespace: data subset: data def: "A report typically including a map (diagram) of a metabolic pathway." [http://edamontology.org] comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1657 name: Pathway or network (genetic information processing) namespace: data subset: data def: "A report typically including a map (diagram) of a genetic information processing pathway." [http://edamontology.org] is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:2961 name: Pathway or network (gene regulation) namespace: data subset: data def: "A report typically including a map (diagram) of a gene regulatory network." [http://edamontology.org] is_a: EDAM_data:2600 ! Pathway or network relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks [Term] id: EDAM_data:1658 name: Pathway or network (environmental information processing) namespace: data subset: data def: "A report typically including a map (diagram) of an environmental information processing pathway." [http://edamontology.org] is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1659 name: Pathway or network (signal transduction) namespace: data subset: data def: "A report typically including a map (diagram) of a signal transduction pathway." [http://edamontology.org] is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1660 name: Pathway or network (cellular process) namespace: data subset: data def: "A report typically including a map (diagram) of a cellular process pathway." [http://edamontology.org] is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1661 name: Pathway or network (disease) namespace: data subset: data def: "A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease." [http://edamontology.org] is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1662 name: Pathway or network (drug structure relationship) namespace: data subset: data def: "A report typically including a map (diagram) of drug structure relationships." [http://edamontology.org] is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1663 name: Pathway or network (protein-protein interaction) namespace: data subset: data def: "A report typically including a map (diagram) of a network of protein interactions." [http://edamontology.org] is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:0951 name: Statistical estimate score namespace: data subset: data def: "A value representing estimated statistical significance of some observed data; typically sequence database hits." [http://edamontology.org] is_a: EDAM_data:1772 ! Score or penalty is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:0865 name: Sequence similarity score namespace: data subset: data def: "A value representing molecular sequence similarity." [http://edamontology.org] is_a: EDAM_data:1772 ! Score or penalty [Term] id: EDAM_data:0888 name: Structure similarity score namespace: data subset: data def: "A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison." [http://edamontology.org] is_a: EDAM_data:1772 ! Score or penalty [Term] id: EDAM_data:2146 name: Threshold namespace: data subset: data def: "A value that serves as a threshold for a tool (usually to control scoring or output)." [http://edamontology.org] is_a: EDAM_data:1772 ! Score or penalty [Term] id: EDAM_data:1667 name: E-value namespace: data subset: data def: "A simple floating point number defining the lower or upper limit of an expectation value (E-value)." [http://edamontology.org] comment: An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. synonym: "Expectation value" EXACT [http://edamontology.org] is_a: EDAM_data:0951 ! Statistical estimate score [Term] id: EDAM_data:1668 name: Z-value namespace: data subset: data def: "The z-value is the number of standard deviations a data value is above or below a mean value." [http://edamontology.org] comment: A z-value might be specified as a threshold for reporting hits from database searches. is_a: EDAM_data:0951 ! Statistical estimate score [Term] id: EDAM_data:1669 name: P-value namespace: data subset: data def: "The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true." [http://edamontology.org] comment: A z-value might be specified as a threshold for reporting hits from database searches. is_a: EDAM_data:0951 ! Statistical estimate score [Term] id: EDAM_data:1412 name: Sequence identity namespace: data subset: data def: "Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences." [http://edamontology.org] is_a: EDAM_data:0865 ! Sequence similarity score [Term] id: EDAM_data:1413 name: Sequence similarity namespace: data subset: data def: "Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension." [http://edamontology.org] comment: Data Type is float probably. is_a: EDAM_data:0865 ! Sequence similarity score [Term] id: EDAM_data:2335 name: Bit score namespace: data subset: data def: "A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system." [http://edamontology.org] comment: Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. is_a: EDAM_data:1413 ! Sequence similarity [Term] id: EDAM_data:1496 name: Molecular similarity score namespace: data subset: data def: "A score reflecting structural similarities of two molecules." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0888 ! Structure similarity score [Term] id: EDAM_data:1497 name: Root-mean-square deviation namespace: data subset: data def: "Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates." [http://edamontology.org] synonym: "RMSD" EXACT [http://edamontology.org] is_a: EDAM_data:0888 ! Structure similarity score [Term] id: EDAM_data:1498 name: Tanimoto similarity score namespace: data subset: data def: "A measure of the similarity between two ligand fingerprints." [http://edamontology.org] comment: A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. is_a: EDAM_data:0888 ! Structure similarity score [Term] id: EDAM_data:1673 name: Swiss-Prot to PDB mapping namespace: data subset: data def: "Cross-mapping of Swiss-Prot codes to PDB identifiers." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0954 ! Database cross-mapping [Term] id: EDAM_data:1674 name: Sequence database cross-references namespace: data subset: data def: "Cross-references from a sequence record to other databases." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:2337 name: Metadata namespace: data subset: data ! alt_id: EDAM_data:2853 def: "Data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Provenance metadata" EXACT [http://edamontology.org] is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2018 name: Annotation namespace: data subset: data def: "A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} consider: EDAM_data:2048 ! Report [Term] id: EDAM_data:0948 name: Data resource definition namespace: data subset: data def: "A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper." [http://edamontology.org] is_a: EDAM_data:1883 ! Annotated URI [Term] id: EDAM_data:0957 name: Database metadata namespace: data subset: data def: "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." [http://edamontology.org] is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:2223 name: Ontology metadata namespace: data subset: data def: "Data concerning a biological ontology." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_data:2193 name: Database entry metadata namespace: data subset: data def: "Basic information on any arbitrary database entry." [http://edamontology.org] is_a: EDAM_data:0957 ! Database metadata [Term] id: EDAM_data:0958 name: Tool metadata namespace: data subset: data def: "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." [http://edamontology.org] is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:2218 name: Server metadata namespace: data subset: data def: "Basic information about a server on the web, such as an SRS server." [http://edamontology.org] is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:0959 name: Job metadata namespace: data subset: data def: "Textual metadata on a submitted or completed job." [http://edamontology.org] xref: Moby:PDGJOB is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:0960 name: User metadata namespace: data subset: data def: "Textual metadata on a software author or end-user, for example a person or other software." [http://edamontology.org] is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:3106 !{since=beta13} name: System metadata namespace: data subset: data def: "Metadata concerning the software, hardware or other aspects of a computer system." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:0583 name: Directory metadata namespace: data subset: data def: "A directory on disk from which files are read." [http://edamontology.org] is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:0953 name: Version information namespace: data subset: data def: "Information on a version of software or data, for example name, version number and release date." [http://edamontology.org] synonym: "Version" EXACT [http://usefulinc.com/ns/doap#Version] synonym: "version identifier" NARROW [http://semanticscience.org/resource/SIO_000653] synonym: "version name or number" NARROW [http://purl.obolibrary.org/obo/IAO_0000129] synonym: "development status" NARROW [http://www.ebi.ac.uk/swo/maturity/SWO_9000061] !{note="Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records."} is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:2724 name: Embryo annotation namespace: data subset: data def: "Annotation on an embryo or concerning embryological development." [http://edamontology.org] is_a: EDAM_data:2530 ! Organism annotation relationship: has_topic EDAM_topic:3065 ! Embryology resources [Term] id: EDAM_data:1664 name: MIRIAM datatype namespace: data subset: data def: "An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources." [http://edamontology.org] comment: A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. is_a: EDAM_data:0948 ! Data resource definition [Term] id: EDAM_data:2875 name: DRCAT resource namespace: data subset: data def: "An entry (resource) from the DRCAT bioinformatics resource catalogue." [http://edamontology.org] is_a: EDAM_data:0948 ! Data resource definition [Term] id: EDAM_data:0952 name: EMBOSS database resource definition namespace: data subset: data def: "Resource definition for an EMBOSS database." [http://edamontology.org] is_a: EDAM_data:0957 ! Database metadata [Term] id: EDAM_data:1675 name: Job status namespace: data subset: data def: "Metadata on the status of a submitted job." [http://edamontology.org] comment: Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). is_a: EDAM_data:0959 ! Job metadata [Term] id: EDAM_data:1678 name: Tool log namespace: data subset: data def: "A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages." [http://edamontology.org] is_a: EDAM_data:0959 ! Job metadata [Term] id: EDAM_data:1677 name: Job type namespace: data subset: data def: "A label (text token) describing the type of job, for example interactive or non-interactive." [http://edamontology.org] is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1679 name: DaliLite log file namespace: data subset: data def: "DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1680 name: STRIDE log file namespace: data subset: data def: "STRIDE log file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1681 name: NACCESS log file namespace: data subset: data def: "NACCESS log file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1682 name: EMBOSS wordfinder log file namespace: data subset: data def: "EMBOSS wordfinder log file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1683 name: EMBOSS domainatrix log file namespace: data subset: data def: "EMBOSS (EMBASSY) domainatrix application log file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1684 name: EMBOSS sites log file namespace: data subset: data def: "EMBOSS (EMBASSY) sites application log file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1685 name: EMBOSS supermatcher error file namespace: data subset: data def: "EMBOSS (EMBASSY) supermatcher error file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1686 name: EMBOSS megamerger log file namespace: data subset: data def: "EMBOSS megamerger log file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1687 name: EMBOSS whichdb log file namespace: data subset: data def: "EMBOSS megamerger log file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1688 name: EMBOSS vectorstrip log file namespace: data subset: data def: "EMBOSS vectorstrip log file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1670 name: Database version information namespace: data subset: data def: "Information on a database (or ontology) version, for example name, version number and release date." [http://edamontology.org] synonym: "Ontology version information" EXACT [http://edamontology.org] is_a: EDAM_data:0953 ! Version information is_a: EDAM_data:0957 ! Database metadata [Term] id: EDAM_data:2090 name: Database entry version information namespace: data subset: data def: "Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on." [http://edamontology.org] is_a: EDAM_data:0953 ! Version information is_a: EDAM_data:2193 ! Database entry metadata [Term] id: EDAM_data:1671 name: Tool version information namespace: data subset: data def: "Information on an application version, for example name, version number and release date." [http://edamontology.org] is_a: EDAM_data:0953 ! Version information is_a: EDAM_data:0958 ! Tool metadata [Term] id: EDAM_data:1771 name: Sequence version information namespace: data subset: data def: "Information on an molecular sequence version." [http://edamontology.org] is_a: EDAM_data:0953 ! Version information is_a: EDAM_data:0855 ! Sequence metadata [Term] id: EDAM_data:2041 name: Genome version information namespace: data subset: data def: "Information on a genome version." [http://edamontology.org] is_a: EDAM_data:0953 ! Version information is_a: EDAM_data:2711 ! Genome metadata [Term] id: EDAM_data:1672 name: CATH version information namespace: data subset: data def: "Information on a version of the CATH database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1670 ! Database version information [Term] id: EDAM_data:1047 name: URI namespace: data subset: data def: "A string of characters that name or otherwise identify a resource on the Internet." [http://edamontology.org] is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2079 name: Search parameter namespace: data subset: data def: "Some simple value controlling a search operation, typically a search of a database." [http://edamontology.org] is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2534 name: Sequence parameter namespace: data subset: data def: "A parameter concerning calculations on molecular sequences." [http://edamontology.org] is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2130 name: Sequence profile type namespace: data subset: data def: "A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc." [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:2023 name: Sequence mask parameter namespace: data subset: data def: "Data used to replace (mask) characters in a molecular sequence." [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:0853 name: DNA sense specification namespace: data subset: data def: "The strand of a DNA sequence (forward or reverse)." [http://edamontology.org] comment: The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. synonym: "DNA strand specification" EXACT [http://edamontology.org] synonym: "Strand" EXACT [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:2126 name: Translation frame specification namespace: data subset: data def: "Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome)." [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:2336 name: Translation phase specification namespace: data subset: data def: "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." [http://edamontology.org] synonym: "Phase" EXACT [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1014 name: Sequence position specification namespace: data subset: data def: "A specification (partial or complete) of one or more positions or regions of a molecular sequence or map." [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:0854 name: Sequence length specification namespace: data subset: data def: "A specification of sequence length(s)." [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:2357 name: Protein signature type namespace: data subset: data def: "A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:0864 name: Sequence alignment parameter namespace: data subset: data def: "Some simple value controlling a sequence alignment (or similar 'match') operation." [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:1120 name: Sequence alignment type namespace: data subset: data def: "A label (text token) describing the type of a sequence alignment." [http://edamontology.org] comment: Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. is_a: EDAM_data:0864 ! Sequence alignment parameter is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1052 name: URL namespace: data subset: data ! alt_id: EDAM_data:1054 ! alt_id: EDAM_data:1168 ! alt_id: EDAM_data:1169 def: "A Uniform Resource Locator (URL)." [http://edamontology.org] xref: Moby:URL xref: Moby:Link is_a: EDAM_data:1047 ! URI [Term] id: EDAM_data:1053 name: URN namespace: data subset: data def: "A Uniform Resource Name (URN)." [http://edamontology.org] is_a: EDAM_data:1047 ! URI [Term] id: EDAM_data:1055 name: LSID namespace: data subset: data def: "A Life Science Identifier (LSID) - a unique identifier of some data." [http://edamontology.org] comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:::[:] synonym: "Life Science Identifier" EXACT [http://edamontology.org] is_a: EDAM_data:1053 ! URN [Term] id: EDAM_data:0968 name: Keyword namespace: data subset: data def: "Keyword(s) or phrase(s) used (typically) for text-searching purposes." [http://edamontology.org] comment: Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. xref: Moby:Global_Keyword xref: Moby:QueryString xref: Moby:Wildcard_Query xref: Moby:BooleanQueryString is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2022 name: Vienna RNA structural data namespace: data subset: data def: "Data used by the Vienna RNA analysis package." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2134 name: Results sort order namespace: data subset: data def: "A control of the order of data that is output, for example the order of sequences in an alignment." [http://edamontology.org] is_a: EDAM_data:2079 ! Search parameter [Term] id: EDAM_data:2135 name: Toggle namespace: data subset: data def: "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2139 name: Nucleic acid melting temperature namespace: data subset: data def: "A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate." [http://edamontology.org] synonym: "Melting temperature" EXACT [http://edamontology.org] is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] id: EDAM_data:2140 name: Concentration namespace: data subset: data def: "The concentration of a chemical compound." [http://edamontology.org] is_a: EDAM_data:2050 ! Molecular property (general) [Term] id: EDAM_data:2151 name: Color namespace: data subset: data def: "Specification of one or more colors." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2152 ! Rendering parameter [Term] id: EDAM_data:2152 name: Rendering parameter namespace: data subset: data def: "A parameter that is used to control rendering (drawing) to a device or image." [http://edamontology.org] synonym: "Graphics parameter" EXACT [http://edamontology.org] synonym: "Graphical parameter" EXACT [http://edamontology.org] is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:3105 !{since=beta13} name: Geotemporal metadata namespace: data subset: data def: "Basic information concerning geographical location or time." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:2156 name: Date namespace: data subset: data def: "A temporal date." [http://edamontology.org] is_a: EDAM_data:3105 ! Geotemporal metadata [Term] id: EDAM_data:1693 name: Number of iterations namespace: data subset: data def: "Number of iterations of an algorithm." [http://edamontology.org] is_a: EDAM_data:2079 ! Search parameter [Term] id: EDAM_data:1694 name: Number of output entities namespace: data subset: data def: "Number of entities (for example database hits, sequences, alignments etc) to write to an output file." [http://edamontology.org] is_a: EDAM_data:2079 ! Search parameter ! Possible values include: 'SC' (score) or 'RF' (rank), pvalue (sort by increasing P-value (probability). i.e. most statistically significant hits given first), count (sort hits by increasing number of submatches (for example HSP) in each hit, score (sort hits in order of increasing score [Term] id: EDAM_data:1695 name: Hit sort order namespace: data subset: data def: "Controls the order of hits (reported matches) in an output file from a database search." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2134 ! Results sort order [Term] id: EDAM_data:0851 name: Sequence mask character namespace: data subset: data def: "A character used to replace (mask) other characters in a molecular sequence." [http://edamontology.org] is_a: EDAM_data:2023 ! Sequence mask parameter [Term] id: EDAM_data:0852 name: Sequence mask type namespace: data subset: data def: "A label (text token) describing the type of sequence masking to perform." [http://edamontology.org] comment: Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. is_a: EDAM_data:2023 ! Sequence mask parameter is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1016 name: Sequence position namespace: data subset: data def: "A position of a single point (base or residue) in a sequence, or part of such a specification." [http://edamontology.org] synonym: "sequence_location" RELATED [SO:0000735] xref: WHATIF: number xref: WHATIF: PDBx_atom_site is_a: EDAM_data:1014 ! Sequence position specification ! _atom_site.id in PDBML [Term] id: EDAM_data:2145 name: Sequence offset namespace: data subset: data def: "An offset for a single-point sequence position." [http://edamontology.org] is_a: EDAM_data:1016 ! Sequence position is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1017 name: Sequence range namespace: data subset: data def: "Specification of range(s) of sequence positions." [http://edamontology.org] is_a: EDAM_data:1014 ! Sequence position specification [Term] id: EDAM_data:2012 name: Map position namespace: data subset: data ! alt_id: EDAM_data:1894 def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval." [http://edamontology.org] comment: This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. synonym: "Locus" EXACT [http://edamontology.org] ! synonym: An ontology concept covering the different types of position/locus RELATED [...] xref: Moby:GCP_MapPoint xref: Moby:GCP_MapPosition xref: Moby:HitPosition xref: Moby:GenePosition xref: Moby:MapPosition xref: Moby:Position xref: Moby:GCP_MapInterval xref: Moby:Locus is_a: EDAM_data:1016 ! Sequence position is_a: EDAM_data:1017 ! Sequence range is_a: EDAM_data:2019 ! Map attribute ! _atom_site.id in PDBML [Term] id: EDAM_data:2216 name: Codon number namespace: data subset: data def: "The number of a codon, for instance, at which a mutation is located." [http://edamontology.org] is_a: EDAM_data:1016 ! Sequence position [Term] id: EDAM_data:1742 name: PDB residue number namespace: data subset: data def: "A residue identifier (a string) from a PDB file." [http://edamontology.org] xref: WHATIF: pdb_number is_a: EDAM_data:1016 ! Sequence position ! PDB_residue_no in PDBML [Term] id: EDAM_data:1856 name: PDB insertion code namespace: data subset: data def: "An insertion code (part of the residue number) for an amino acid residue from a PDB file." [http://edamontology.org] xref: WHATIF: insertion_code is_a: EDAM_data:1016 ! Sequence position ! pdbx_PDB_ins_code in PDBML [Term] id: EDAM_data:1906 name: Quantitative trait locus namespace: data subset: data def: "A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment)." [http://edamontology.org] comment: A QTL sometimes but does not necessarily correspond to a gene. synonym: "QTL" EXACT [http://edamontology.org] xref: Moby:SO_QTL is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2012 ! Map position [Term] id: EDAM_data:1249 name: Sequence length namespace: data subset: data def: "The size (length) of a sequence, subsequence or region in a sequence." [http://edamontology.org] is_a: EDAM_data:0854 ! Sequence length specification [Term] id: EDAM_data:1252 name: Sequence length range namespace: data subset: data def: "Specification of range(s) of length of sequences." [http://edamontology.org] is_a: EDAM_data:0854 ! Sequence length specification [Term] id: EDAM_data:1250 name: Word size namespace: data subset: data def: "Size of a sequence word." [http://edamontology.org] comment: Word size is used for example in word-based sequence database search methods. synonym: "Word length" EXACT [http://edamontology.org] is_a: EDAM_data:1249 ! Sequence length [Term] id: EDAM_data:1251 name: Window size namespace: data subset: data def: "Size of a sequence window." [http://edamontology.org] comment: A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. is_a: EDAM_data:1249 ! Sequence length [Term] id: EDAM_data:2141 name: Window step size namespace: data subset: data def: "Size of the incremental 'step' a sequence window is moved over a sequence." [http://edamontology.org] is_a: EDAM_data:1249 ! Sequence length [Term] id: EDAM_data:1125 name: Comparison matrix type namespace: data subset: data def: "A label (text token) describing the type of a comparison matrix." [http://edamontology.org] comment: For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. example: "blosum" "pam" "gonnet" "id" synonym: "Substitution matrix type" EXACT [http://edamontology.org] is_a: EDAM_data:0864 ! Sequence alignment parameter is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1394 name: Alignment score or penalty namespace: data subset: data def: "A simple floating point number defining the penalty for opening or extending a gap in an alignment." [http://edamontology.org] is_a: EDAM_data:0864 ! Sequence alignment parameter is_a: EDAM_data:1772 ! Score or penalty [Term] id: EDAM_data:1395 name: Score end gaps control namespace: data subset: data def: "Whether end gaps are scored or not." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1396 name: Aligned sequence order namespace: data subset: data def: "Controls the order of sequences in an output sequence alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2134 ! Results sort order [Term] id: EDAM_data:2136 name: Sequence width namespace: data subset: data def: "The width of an output sequence or alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1249 ! Sequence length [Term] id: EDAM_data:2137 name: Gap penalty namespace: data subset: data def: "A penalty for introducing or extending a gap in an alignment." [http://edamontology.org] is_a: EDAM_data:1394 ! Alignment score or penalty [Term] id: EDAM_data:1401 name: Match reward score namespace: data subset: data def: "The score for a 'match' used in various sequence database search applications with simple scoring schemes." [http://edamontology.org] is_a: EDAM_data:1394 ! Alignment score or penalty [Term] id: EDAM_data:1402 name: Mismatch penalty score namespace: data subset: data def: "The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes." [http://edamontology.org] is_a: EDAM_data:1394 ! Alignment score or penalty [Term] id: EDAM_data:1403 name: Drop off score namespace: data subset: data def: "This is the threshold drop in score at which extension of word alignment is halted." [http://edamontology.org] is_a: EDAM_data:1394 ! Alignment score or penalty [Term] id: EDAM_data:1397 name: Gap opening penalty namespace: data subset: data def: "A penalty for opening a gap in an alignment." [http://edamontology.org] is_a: EDAM_data:2137 ! Gap penalty [Term] id: EDAM_data:1398 name: Gap extension penalty namespace: data subset: data def: "A penalty for extending a gap in an alignment." [http://edamontology.org] is_a: EDAM_data:2137 ! Gap penalty [Term] id: EDAM_data:1399 name: Gap separation penalty namespace: data subset: data def: "A penalty for gaps that are close together in an alignment." [http://edamontology.org] is_a: EDAM_data:2137 ! Gap penalty [Term] id: EDAM_data:1400 name: Terminal gap penalty namespace: data subset: data def: "A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1410 ! Terminal gap opening penalty consider: EDAM_data:1411 ! Terminal gap extension penalty [Term] id: EDAM_data:1404 name: Gap opening penalty (integer) namespace: data subset: data def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1397 ! Gap opening penalty [Term] id: EDAM_data:1405 name: Gap opening penalty (float) namespace: data subset: data def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1397 ! Gap opening penalty [Term] id: EDAM_data:1406 name: Gap extension penalty (integer) namespace: data subset: data def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1398 ! Gap extension penalty [Term] id: EDAM_data:1407 name: Gap extension penalty (float) namespace: data subset: data def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1398 ! Gap extension penalty [Term] id: EDAM_data:1408 name: Gap separation penalty (integer) namespace: data subset: data def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1399 ! Gap separation penalty [Term] id: EDAM_data:1409 name: Gap separation penalty (float) namespace: data subset: data def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1399 ! Gap separation penalty [Term] id: EDAM_data:1410 name: Terminal gap opening penalty namespace: data subset: data def: "A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org] is_a: EDAM_data:1397 ! Gap opening penalty [Term] id: EDAM_data:1411 name: Terminal gap extension penalty namespace: data subset: data def: "A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org] is_a: EDAM_data:1398 ! Gap extension penalty [Term] id: EDAM_data:2007 name: UniProt keyword namespace: data subset: data def: "A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org] xref: Moby_namespace:SP_KW xref: http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW is_a: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:1877 name: Synonym namespace: data subset: data def: "An alternative for a word." [http://edamontology.org] synonym: "Alternative name" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:1878 name: Misspelling namespace: data subset: data def: "A common misspelling of a word." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:1879 name: Acronym namespace: data subset: data def: "An abbreviation of a phrase or word." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:1880 name: Misnomer namespace: data subset: data def: "A term which is likely to be misleading of its meaning." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:1591 name: Vienna RNA parameters namespace: data subset: data def: "RNA parameters used by the Vienna package." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1592 name: Vienna RNA structure constraints namespace: data subset: data def: "Structure constraints used by the Vienna package." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1593 name: Vienna RNA concentration data namespace: data subset: data def: "RNA concentration data used by the Vienna package." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1696 name: Drug annotation namespace: data subset: data def: "An informative report on a specific drug." [http://edamontology.org] is_a: EDAM_data:0962 ! Small molecule annotation relationship: has_topic EDAM_topic:0620 ! Drugs and targets [Term] id: EDAM_data:2400 name: Toxin annotation namespace: data subset: data def: "An informative report on a specific toxin." [http://edamontology.org] is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2240 name: Heterogen annotation namespace: data subset: data def: "An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files." [http://edamontology.org] is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2726 name: Inhibitor annotation namespace: data subset: data def: "An informative report on one or more small molecules that are enzyme inhibitors." [http://edamontology.org] is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2396 name: Fungi annotation (anamorph) namespace: data subset: data def: "An informative report on a specific fungus anamorph." [http://edamontology.org] is_a: EDAM_data:2395 ! Fungi annotation [Term] id: EDAM_data:2142 name: EMBOSS graph namespace: data subset: data def: "An image of a graph generated by the EMBOSS suite." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2968 ! Image [Term] id: EDAM_data:1707 name: Phylogenetic tree image namespace: data subset: data def: "An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information." [http://edamontology.org] comment: See also 'Phylogenetic tree' is_a: EDAM_data:2968 ! Image is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1708 name: RNA secondary structure image namespace: data subset: data def: "Image of RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] is_a: EDAM_data:2880 ! Secondary structure image [Term] id: EDAM_data:1709 name: Protein secondary structure image namespace: data subset: data def: "Image of protein secondary structure." [http://edamontology.org] is_a: EDAM_data:2880 ! Secondary structure image is_a: EDAM_data:2956 ! Protein secondary structure report [Term] id: EDAM_data:1710 name: Structure image namespace: data subset: data ! alt_id: EDAM_data:2604 def: "Image of one or more molecular tertiary (3D) structures." [http://edamontology.org] is_a: EDAM_data:2085 ! Structure report is_a: EDAM_data:2968 ! Image [Term] id: EDAM_data:2880 name: Secondary structure image namespace: data subset: data def: "Image of one or more molecular secondary structures." [http://edamontology.org] is_a: EDAM_data:2881 ! Secondary structure report [Term] id: EDAM_data:1711 name: Sequence alignment image namespace: data subset: data def: "Image of two or more aligned molecular sequences possibly annotated with alignment features." [http://edamontology.org] is_a: EDAM_data:2968 ! Image is_a: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:2168 name: Sequence trace image namespace: data subset: data def: "Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases)." [http://edamontology.org] is_a: EDAM_data:2969 ! Sequence image [Term] id: EDAM_data:2969 name: Sequence image namespace: data subset: data def: "Image of a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org] is_a: EDAM_data:2968 ! Image is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:1712 name: Structure image (small molecule) namespace: data subset: data def: "An image of the structure of a small chemical compound." [http://edamontology.org] comment: The molecular identifier and formula are typically included. synonym: "Chemical structure image" EXACT [http://edamontology.org] synonym: "Small molecule structure image" EXACT [http://edamontology.org] is_a: EDAM_data:1710 ! Structure image is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2992 name: Protein structure image namespace: data subset: data def: "An image of protein structure." [http://edamontology.org] synonym: "Structure image (protein)" EXACT [http://edamontology.org] is_a: EDAM_data:1710 ! Structure image is_a: EDAM_data:3153 ! Protein image [Term] id: EDAM_data:3154 !{since=beta13} name: Protein alignment namespace: data subset: data def: "An alignment of protein sequences and/or structures." [http://edamontology.org] is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:3153 !{since=beta13} name: Protein image namespace: data subset: data def: "An image of a protein." [http://edamontology.org] is_a: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:1713 name: Fate map namespace: data subset: data def: " A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development." [http://edamontology.org] is_a: EDAM_data:2724 ! Embryo annotation [Term] id: EDAM_data:2967 name: Microarray image namespace: data subset: data ! alt_id: EDAM_data:1635 def: "An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data." [http://edamontology.org] synonym: "Gene expression image" EXACT [http://edamontology.org] is_a: EDAM_data:2603 ! Microarray data is_a: EDAM_data:2968 ! Image relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:1714 name: Microarray spots image namespace: data subset: data def: "An image of spots from a microarray experiment." [http://edamontology.org] is_a: EDAM_data:2967 ! Microarray image is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:2162 name: Helical wheel namespace: data subset: data def: "An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties." [http://edamontology.org] is_a: EDAM_data:1709 ! Protein secondary structure image [Term] id: EDAM_data:2163 name: Helical net namespace: data subset: data def: "An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix." [http://edamontology.org] comment: Useful for highlighting amphipathicity and other properties. is_a: EDAM_data:1709 ! Protein secondary structure image [Term] id: EDAM_data:2308 name: Virus annotation (taxonomy) namespace: data subset: data def: "An informative report on the taxonomy of a specific virus." [http://edamontology.org] is_a: EDAM_data:2307 ! Virus annotation [Term] id: EDAM_data:0582 name: Ontology namespace: data subset: data ! alt_id: EDAM_data:0829 ! alt_id: EDAM_data:0830 ! alt_id: EDAM_data:0834 ! alt_id: EDAM_data:0836 ! alt_id: EDAM_data:0837 ! alt_id: EDAM_data:0838 ! alt_id: EDAM_data:0839 ! alt_id: EDAM_data:0840 ! alt_id: EDAM_data:2221 def: "An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_data:2858 name: Ontology concept namespace: data subset: data def: "A concept from a biological ontology." [http://edamontology.org] comment: This includes any fields from the concept definition such as concept name, definition, comments and so on. is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_data:0966 name: Ontology term namespace: data subset: data def: "A term (name) from an ontology." [http://edamontology.org] is_a: EDAM_data:0967 ! Ontology concept metadata [Term] id: EDAM_data:0967 name: Ontology concept metadata namespace: data subset: data def: "Data concerning or derived from a concept from a biological ontology." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_data:1715 name: BioPax namespace: data subset: data def: "A term from the BioPax ontology." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1716 name: GO namespace: data subset: data def: "A term definition from The Gene Ontology (GO)." [http://edamontology.org] synonym: "Gene Ontology term" EXACT [http://edamontology.org] xref: Moby:GO_Term xref: Moby:GOTerm xref: Moby:Annotated_GO_Term xref: Moby:Annotated_GO_Term_With_Probability is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1717 name: MeSH namespace: data subset: data def: "A term from the MeSH vocabulary." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1718 name: HGNC namespace: data subset: data def: "A term from the HGNC controlled vocabulary." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1719 name: NCBI taxonomy vocabulary namespace: data subset: data def: "A term from the NCBI taxonomy vocabulary." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1720 name: Plant ontology term namespace: data subset: data def: "A term from the Plant Ontology (PO)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1721 name: UMLS namespace: data subset: data def: "A term from the UMLS vocabulary." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1722 name: FMA namespace: data subset: data def: "A term from Foundational Model of Anatomy." [http://edamontology.org] comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1723 name: EMAP namespace: data subset: data def: "A term from the EMAP mouse ontology." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1724 name: ChEBI namespace: data subset: data def: "A term from the ChEBI ontology." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1725 name: MGED namespace: data subset: data def: "A term from the MGED ontology." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1726 name: myGrid namespace: data subset: data def: "A term from the myGrid ontology." [http://edamontology.org] comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1727 name: GO (biological process) namespace: data subset: data def: "A term definition for a biological process from the Gene Ontology (GO)." [http://edamontology.org] comment: Data Type is an enumerated string. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2858 ! Ontology concept [Term] id: EDAM_data:1728 name: GO (molecular function) namespace: data subset: data def: "A term definition for a molecular function from the Gene Ontology (GO)." [http://edamontology.org] comment: Data Type is an enumerated string. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2858 ! Ontology concept [Term] id: EDAM_data:1729 name: GO (cellular component) namespace: data subset: data def: "A term definition for a cellular component from the Gene Ontology (GO)." [http://edamontology.org] comment: Data Type is an enumerated string. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2858 ! Ontology concept [Term] id: EDAM_data:1730 name: Ontology relation type namespace: data subset: data def: "A relation type defined in an ontology." [http://edamontology.org] is_a: EDAM_data:0967 ! Ontology concept metadata [Term] id: EDAM_data:1731 name: Ontology concept definition namespace: data subset: data def: "The definition of a concept from an ontology." [http://edamontology.org] is_a: EDAM_data:0967 ! Ontology concept metadata [Term] id: EDAM_data:1732 name: Ontology concept comment namespace: data subset: data def: "A comment on a concept from an ontology." [http://edamontology.org] is_a: EDAM_data:0967 ! Ontology concept metadata [Term] id: EDAM_data:1733 name: Ontology concept reference namespace: data subset: data def: "Reference for a concept from an ontology." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:1738 name: doc2loc document information namespace: data subset: data def: "Information on a published article provided by the doc2loc program." [http://edamontology.org] comment: The doc2loc output includes the url, format, type and availability code of a document for every service provider. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0970 ! Bibliographic reference [Term] id: EDAM_data:2177 name: Exactly 1 namespace: data subset: data def: "A single thing." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_data:2178 name: 1 or more namespace: data subset: data def: "One or more things." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_data:2179 name: Exactly 2 namespace: data subset: data def: "Exactly two things." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_data:2180 name: 2 or more namespace: data subset: data def: "Two or more things." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} ! ! Identifier ! [Term] id: EDAM_data:1121 name: BLAST sequence alignment type namespace: identifier subset: identifiers subset: data def: "The type of a BLAST sequence alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1120 ! Sequence alignment type [Term] id: EDAM_data:0974 name: Entity identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a biological entity or phenomenon." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0975 name: Data resource identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a data resource." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0978 name: Discrete entity identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0979 name: Entity feature identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0980 name: Entity collection identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of a collection of discrete biological entities." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0981 name: Phenomenon identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of a physical, observable biological occurrence or event." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:2091 name: Accession namespace: identifier subset: identifiers subset: data ! alt_id: EDAM_data:2862 def: "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." [http://edamontology.org] synonym: "information entity identifier" BROAD [http://semanticscience.org/resource/SIO_000731] synonym: "unique identifier" BROAD [http://semanticscience.org/resource/SIO_000675] is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:2099 name: Name namespace: identifier subset: identifiers subset: data ! alt_id: EDAM_data:2863 def: "A name of a thing, which need not necessarily uniquely identify it." [http://edamontology.org] synonym: "Symbolic name" EXACT [http://edamontology.org] synonym: "name" EXACT [http://usefulinc.com/ns/doap#name] synonym: "name" EXACT [http://semanticscience.org/resource/SIO_000116] synonym: "label" BROAD [http://www.w3.org/2000/01/rdf-schema#label] !{note="Almost exact, but focusing on human readability and not on identification."} is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0976 name: Identifier (typed) namespace: identifier subset: identifiers subset: data def: "An identifier that identifies a particular type of data." [http://edamontology.org] comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:2109 name: Identifier (hybrid) namespace: identifier subset: identifiers subset: data def: "An identifier that is re-used for data objects of fundamentally different types (typically served from a single database)." [http://edamontology.org] comment: This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0977 name: Tool identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a bioinformatics tool, e.g. an application or web service." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:1190 name: Tool name namespace: identifier subset: identifiers subset: data def: "The name of a computer package, application, method or function." [http://edamontology.org] is_a: EDAM_data:0977 ! Tool identifier [Term] id: EDAM_data:1191 name: Tool name (signature) namespace: identifier subset: identifiers subset: data def: "The unique name of a signature (sequence classifier) method." [http://edamontology.org] comment: Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:1192 name: Tool name (BLAST) namespace: identifier subset: identifiers subset: data def: "The name of a BLAST tool." [http://edamontology.org] comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. synonym: "BLAST name" EXACT [http://edamontology.org] is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:1193 name: Tool name (FASTA) namespace: identifier subset: identifiers subset: data def: "The name of a FASTA tool." [http://edamontology.org] comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:1194 name: Tool name (EMBOSS) namespace: identifier subset: identifiers subset: data def: "The name of an EMBOSS application." [http://edamontology.org] is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:1195 name: Tool name (EMBASSY package) namespace: identifier subset: identifiers subset: data def: "The name of an EMBASSY package." [http://edamontology.org] is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:2098 name: Job identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a submitted job." [http://edamontology.org] synonym: "Computation ID" EXACT [http://wsio.org/data_009] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:1676 name: Job ID namespace: identifier subset: identifiers subset: data def: "The (typically numeric) unique identifier of a submitted job." [http://edamontology.org] ! is_a: EDAM_data:2098 ! Job identifier is_obsolete: true !{since=1.0} replaced_by: EDAM_data:2098 ! Job identifier [Term] id: EDAM_data:2118 name: Person identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2101 name: User ID namespace: identifier subset: identifiers subset: data def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] is_a: EDAM_data:2118 ! Person identifier [Term] id: EDAM_data:1689 name: Username namespace: identifier subset: identifiers subset: data def: "A username on a computer system." [http://edamontology.org] is_a: EDAM_data:2101 ! User ID [Term] id: EDAM_data:1690 name: Password namespace: identifier subset: identifiers subset: data def: "A password on a computer system." [http://edamontology.org] is_a: EDAM_data:2101 ! User ID [Term] id: EDAM_data:1691 name: Email address namespace: identifier subset: identifiers subset: data def: "A valid email address of an end-user." [http://edamontology.org] xref: Moby:Email xref: Moby:EmailAddress is_a: EDAM_data:2101 ! User ID [Term] id: EDAM_data:1692 name: Person name namespace: identifier subset: identifiers subset: data def: "The name of a person." [http://edamontology.org] is_a: EDAM_data:2118 ! Person identifier [Term] id: EDAM_data:1881 name: Author ID namespace: identifier subset: identifiers subset: data def: "Information on the authors of a published work." [http://edamontology.org] xref: Moby:Author is_a: EDAM_data:2118 ! Person identifier [Term] id: EDAM_data:1882 name: DragonDB author identifier namespace: identifier subset: identifiers subset: data def: "An identifier representing an author in the DragonDB database." [http://edamontology.org] is_a: EDAM_data:1881 ! Author ID [Term] id: EDAM_data:2596 name: Catalogue identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a catalogue of biological resources." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2779 name: Stock number namespace: identifier subset: identifiers subset: data def: "An identifier of stock from a catalogue of biological resources." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:3022 name: NCBI genetic code ID namespace: identifier subset: identifiers subset: data def: "Identifier of a genetic code in the NCBI list of genetic codes." [http://edamontology.org] regex: "[1-9][0-9]?" example: "16" is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:0982 name: Molecule identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of a molecule." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2529 ! Molecule report [Term] id: EDAM_data:1015 name: Sequence feature ID namespace: identifier subset: identifiers subset: data def: "A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file." [http://edamontology.org] is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:3034 ! Sequence feature identifier [Term] id: EDAM_data:3107 !{since=beta13} name: Sequence feature name namespace: identifier subset: identifiers subset: data def: "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." [http://edamontology.org] is_a: EDAM_data:2099 ! Name is_a: EDAM_data:3034 ! Sequence feature identifier [Term] id: EDAM_data:3034 !{since=beta13} name: Sequence feature identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of molecular sequence feature(s)." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2914 ! Sequence features metadata relationship: is_identifier_of EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1023 name: EMBOSS Uniform Feature Object namespace: data subset: data def: "The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications." [http://edamontology.org] synonym: "UFO" EXACT [http://edamontology.org] is_a: EDAM_data:3034 ! Sequence feature identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1893 name: Locus ID namespace: identifier subset: identifiers subset: data def: "A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [http://edamontology.org] synonym: "Locus name" EXACT [http://edamontology.org] synonym: "Locus identifier" EXACT [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:2012 ! Map position [Term] id: EDAM_data:2340 name: Genome build identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a build of a particular genome." [http://edamontology.org] is_a: EDAM_data:2749 ! Genome identifier [Term] id: EDAM_data:2749 name: Genome identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a particular genome." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2903 name: Genome accession namespace: identifier subset: identifiers subset: data def: "An accession of a particular genome (in a database)." [http://edamontology.org] is_a: EDAM_data:2749 ! Genome identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1025 name: Gene identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." [http://edamontology.org] xref: Moby:GeneAccessionList is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:2795 name: ORF identifier namespace: identifier subset: identifiers subset: data def: "An identifier of an open reading frame." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2727 name: Promoter ID namespace: identifier subset: identifiers subset: data def: "An identifier of a promoter of a gene that is catalogued in a database." [http://edamontology.org] xref: Moby:GeneAccessionList is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2630 name: Mobile genetic element ID namespace: identifier subset: identifiers subset: data def: "An identifier of a mobile genetic element." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2127 name: Genetic code identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a genetic code." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:1598 ! Genetic code [Term] id: EDAM_data:1038 name: Protein domain ID namespace: identifier subset: identifiers subset: data def: "Identifier of a protein structural domain." [http://edamontology.org] comment: This is typically a character or string concatenated with a PDB identifier and a chain identifier. is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:1468 ! Protein domain [Term] id: EDAM_data:2618 name: Protein modification ID namespace: identifier subset: identifiers subset: data def: "Identifier of a protein modification catalogued in a database." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1867 name: Protein fold name namespace: identifier subset: identifiers subset: data def: "The name of a protein fold." [http://edamontology.org] is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2655 name: Cell type identifier namespace: identifier subset: identifiers subset: data def: "A unique identifier of a type or group of cells." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2893 name: Cell type accession namespace: identifier subset: identifiers subset: data def: "Accession of a type or group of cells (catalogued in a database)." [http://edamontology.org] is_a: EDAM_data:2655 ! Cell type identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1869 name: Organism identifier namespace: identifier subset: identifiers subset: data def: "A unique identifier of a (group of) organisms." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2530 ! Organism annotation [Term] id: EDAM_data:2908 name: Organism accession namespace: identifier subset: identifiers subset: data def: "An accession of annotation on a (group of) organisms (catalogued in a database)." [http://edamontology.org] is_a: EDAM_data:1869 ! Organism identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2909 name: Organism name namespace: identifier subset: identifiers subset: data def: "The name of an organism (or group of organisms)." [http://edamontology.org] xref: Moby:Organism_Name xref: Moby:OrganismsLongName xref: Moby:OrganismsShortName xref: Moby:FirstEpithet xref: Moby:InfraspecificEpithet xref: Moby:OccurrenceRecord xref: Moby:BriefOccurrenceRecord is_a: EDAM_data:1869 ! Organism identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1048 name: Database identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a biological or bioinformatics database." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0957 ! Database metadata [Term] id: EDAM_data:1049 name: Directory name namespace: identifier subset: identifiers subset: data def: "The name of a directory." [http://edamontology.org] is_a: EDAM_data:2099 ! Name is_a: EDAM_data:0583 ! Directory metadata [Term] id: EDAM_data:1050 name: File name namespace: identifier subset: identifiers subset: data def: "The name (or part of a name) of a file (of any type)." [http://edamontology.org] is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1051 name: Ontology name namespace: identifier subset: identifiers subset: data def: "Name of an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2338 ! Ontology identifier relationship: is_identifier_of EDAM_data:0582 ! Ontology [Term] id: EDAM_data:2110 name: Molecular property identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a molecular property." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:1062 name: Database entry identifier namespace: identifier subset: identifiers subset: data def: "An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type." [http://edamontology.org] comment: This concept is required for completeness. It should never have child concepts. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:2117 name: Map identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a map of a molecular sequence." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:1274 ! Map [Term] id: EDAM_data:2904 name: Map accession namespace: identifier subset: identifiers subset: data def: "An accession of a map of a molecular sequence (deposited in a database)." [http://edamontology.org] is_a: EDAM_data:2117 ! Map identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1063 name: Sequence identifier namespace: identifier subset: identifiers subset: data def: "An identifier of molecular sequence(s) or entries from a molecular sequence database." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:0855 ! Sequence metadata relationship: is_identifier_of EDAM_data:2044 ! Sequence [Term] id: EDAM_data:2294 name: Sequence variation ID namespace: identifier subset: identifiers subset: data def: "An identifier of an entry from a database of molecular sequence variation." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1064 name: Sequence set ID namespace: identifier subset: identifiers subset: data def: "An identifier of a set of molecular sequence(s)." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1065 name: Sequence signature identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1114 ! Sequence motif identifier consider: EDAM_data:1115 ! Sequence profile ID [Term] id: EDAM_data:1066 name: Sequence alignment ID namespace: identifier subset: identifiers subset: data def: "Identifier of a molecular sequence alignment, for example a record from an alignment database." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1067 name: Phylogenetic distance matrix identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a phylogenetic distance matrix." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:1068 name: Phylogenetic tree ID namespace: identifier subset: identifiers subset: data def: "Identifier of a phylogenetic tree for example from a phylogenetic tree database." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0872 ! Phylogenetic tree [Term] id: EDAM_data:3036 !{since=beta13} name: Matrix identifier namespace: identifier subset: identifiers subset: data def: "An identifier of an array of numerical values, such as a comparison matrix." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2082 ! Matrix [Term] id: EDAM_data:1069 name: Comparison matrix identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a comparison matrix." [http://edamontology.org] synonym: "Substitution matrix identifier" EXACT [http://edamontology.org] is_a: EDAM_data:3036 ! Matrix identifier relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:3035 !{since=beta13} name: Structure identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0883 ! Structure [Term] id: EDAM_data:1070 name: Structure ID namespace: identifier subset: identifiers subset: data def: "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org] is_a: EDAM_data:3035 ! Structure identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1759 name: PDB model number namespace: identifier subset: identifiers subset: data def: "Identifier of a model structure from a PDB file." [http://edamontology.org] synonym: "Model number" EXACT [http://edamontology.org] xref: WHATIF: model_number is_a: EDAM_data:3035 ! Structure identifier ! pdbx_PDB_model_num in PDBML [Term] id: EDAM_data:1071 name: Structural (3D) profile ID namespace: identifier subset: identifiers subset: data def: "Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org] synonym: "Structural profile identifier" EXACT [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0889 ! Structural (3D) profile [Term] id: EDAM_data:1072 name: Structure alignment ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from a database of tertiary structure alignments." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0886 ! Structure alignment [Term] id: EDAM_data:1073 name: Amino acid index ID namespace: identifier subset: identifiers subset: data def: "Identifier of an index of amino acid physicochemical and biochemical property data." [http://edamontology.org] is_a: EDAM_data:3036 ! Matrix identifier is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:2627 name: Molecular interaction ID namespace: identifier subset: identifiers subset: data def: "Identifier of a report of molecular interactions from a database (typically)." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:2599 ! Molecular interaction [Term] id: EDAM_data:1075 name: Protein family identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a protein family." [http://edamontology.org] synonym: "Protein secondary database record identifier" EXACT [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0907 ! Protein family [Term] id: EDAM_data:2910 name: Protein family accession namespace: identifier subset: identifiers subset: data def: "Accession of a protein family (that is deposited in a database)." [http://edamontology.org] is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:1075 ! Protein family identifier [Term] id: EDAM_data:1131 name: Protein family name namespace: identifier subset: identifiers subset: data def: "Name of a protein family." [http://edamontology.org] is_a: EDAM_data:1075 ! Protein family identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2355 name: RNA family identifier namespace: identifier subset: identifiers subset: data def: "Identifier of an RNA family, typically an entry from a RNA sequence classification database." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2354 ! RNA family annotation [Term] id: EDAM_data:2111 name: Codon usage table identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a codon usage table, for example a genetic code." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:1597 ! Codon usage table relationship: is_identifier_of EDAM_data:1598 ! Genetic code [Term] id: EDAM_data:1077 name: Transcription factor identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a transcription factor (or a TF binding site)." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:0989 ! Protein identifier relationship: is_identifier_of EDAM_data:1315 ! Gene features (TFBS) [Term] id: EDAM_data:2911 name: Transcription factor accession namespace: identifier subset: identifiers subset: data def: "Accession of an entry from a database of transcription factors or binding sites." [http://edamontology.org] is_a: EDAM_data:1077 ! Transcription factor identifier is_a: EDAM_data:2907 ! Protein accession is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1078 name: Microarray experiment annotation ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from a database of microarray data." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_data:1079 name: Electron microscopy model ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from a database of electron microscopy data." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0941 ! Electron microscopy model [Term] id: EDAM_data:1080 name: Gene expression report ID namespace: identifier subset: identifiers subset: data ! alt_id: EDAM_data:2708 def: "Accession of a report of gene expression (e.g. a gene expression profile) from a database." [http://edamontology.org] synonym: "Gene expression profile identifier" EXACT [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_data:1081 name: Genotype and phenotype annotation ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from a database of genotypes and phenotypes." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0920 ! Genotype/phenotype annotation [Term] id: EDAM_data:2382 name: Genotype experiment ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from a database of genotype experiment metadata." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:2381 ! Experiment annotation (genotype) [Term] id: EDAM_data:2638 name: PubChem bioassay ID namespace: identifier subset: identifiers subset: data def: "Identifier of an assay from the PubChem database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2639 ! PubChem identifier [Term] id: EDAM_data:1082 name: Pathway or network identifier namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from a database of biological pathways or networks." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:2590 name: Hierarchy identifier namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from a database of biological hierarchies." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2891 ! Biological model accession [Term] id: EDAM_data:2108 name: Reaction ID namespace: identifier subset: identifiers subset: data def: "Identifier of a biological reaction from a database." [http://edamontology.org] is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2978 ! Reaction data [Term] id: EDAM_data:1083 name: Workflow ID namespace: identifier subset: identifiers subset: data def: "Identifier of a biological or biomedical workflow, typically from a database of workflows." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:2972 ! Workflow [Term] id: EDAM_data:1084 name: Data resource definition identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a data type definition from some provider." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2219 name: Database field name namespace: identifier subset: identifiers subset: data def: "The name of a field in a database." [http://edamontology.org] is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1085 name: Biological model identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a mathematical model, typically an entry from a database." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0950 ! Biological model [Term] id: EDAM_data:2891 name: Biological model accession namespace: identifier subset: identifiers subset: data def: "Accession of a mathematical model, typically an entry from a database." [http://edamontology.org] is_a: EDAM_data:1085 ! Biological model identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1086 name: Compound identifier namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from a database of chemicals." [http://edamontology.org] synonym: "Small molecule identifier" EXACT [http://edamontology.org] synonym: "Chemical compound identifier" EXACT [http://edamontology.org] is_a: EDAM_data:0982 ! Molecule identifier relationship: is_identifier_of EDAM_data:0962 ! Small molecule annotation relationship: is_identifier_of EDAM_data:1712 ! Structure image (small molecule) relationship: is_identifier_of EDAM_data:0846 ! Chemical formula [Term] id: EDAM_data:2894 name: Compound accession namespace: identifier subset: identifiers subset: data def: "Accession of an entry from a database of chemicals." [http://edamontology.org] synonym: "Small molecule accession" EXACT [http://edamontology.org] synonym: "Chemical compound accession" EXACT [http://edamontology.org] is_a: EDAM_data:1086 ! Compound identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2338 name: Ontology identifier namespace: identifier subset: identifiers subset: data def: "Any arbitrary identifier of an ontology." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0582 ! Ontology [Term] id: EDAM_data:3025 name: Ontology concept identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2858 ! Ontology concept [Term] id: EDAM_data:1087 name: Ontology concept ID namespace: identifier subset: identifiers subset: data def: "A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] synonym: "Ontology concept ID" EXACT [http://edamontology.org] is_a: EDAM_data:3025 ! Ontology concept identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1088 name: Article ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a scientific article." [http://edamontology.org] is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0971 ! Article [Term] id: EDAM_data:2633 name: Book ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a book." [http://edamontology.org] is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2790 name: Gel identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a two-dimensional (protein) gel." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2791 name: Reference map name (SWISS-2DPAGE) namespace: identifier subset: identifiers subset: data def: "Name of a reference map gel from the SWISS-2DPAGE database." [http://edamontology.org] is_a: EDAM_data:2790 ! Gel identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2373 name: Spot ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a spot from a two-dimensional (protein) gel." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2587 name: Blot ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a blot from a Northern Blot." [http://edamontology.org] is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2379 name: Strain identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] is_a: EDAM_data:1869 ! Organism identifier [Term] id: EDAM_data:2912 name: Strain accession namespace: identifier subset: identifiers subset: data def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] is_a: EDAM_data:2379 ! Strain identifier is_a: EDAM_data:2908 ! Organism accession relationship: is_identifier_of EDAM_data:0963 ! Cell line annotation [Term] id: EDAM_data:2917 name: ConsensusPathDB identifier namespace: identifier subset: identifiers subset: data def: "An identifier of an entity from the ConsensusPathDB database." [http://edamontology.org] is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2776 name: ConsensusPathDB entity ID namespace: identifier subset: identifiers subset: data def: "Identifier of a physical entity from the ConsensusPathDB database." [http://edamontology.org] is_a: EDAM_data:2917 ! ConsensusPathDB identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2777 name: ConsensusPathDB entity name namespace: identifier subset: identifiers subset: data def: "Name of a physical entity from the ConsensusPathDB database." [http://edamontology.org] is_a: EDAM_data:2917 ! ConsensusPathDB identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2639 name: PubChem identifier namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the PubChem database." [http://edamontology.org] is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2367 name: ASTD ID namespace: identifier subset: identifiers subset: data def: "Identifier of an object from the ASTD database." [http://edamontology.org] is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1089 name: FlyBase ID namespace: identifier subset: identifiers subset: data def: "Identifier of an object from the FlyBase database." [http://edamontology.org] regex: "FB[a-zA-Z_0-9]{2}[0-9]{7}" is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2113 name: WormBase identifier namespace: identifier subset: identifiers subset: data def: "Identifier of an object from the WormBase database." [http://edamontology.org] is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2104 name: BioCyc ID namespace: identifier subset: identifiers subset: data def: "Identifier of an object from one of the BioCyc databases." [http://edamontology.org] is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1154 name: KEGG object identifier namespace: identifier subset: identifiers subset: data def: "Unique identifier of an object from one of the KEGG databases (excluding the GENES division)." [http://edamontology.org] is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2380 name: CABRI accession namespace: identifier subset: identifiers subset: data def: "A unique identifier of an item from the CABRI database." [http://edamontology.org] is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2387 name: TAIR accession namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the TAIR database." [http://edamontology.org] is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2610 name: Ensembl ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database." [http://edamontology.org] regex: "ENS[A-Z]*[FPTG][0-9]{11}" is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2620 name: RGD ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the RGD database." [http://edamontology.org] regex: "[0-9]{4,7}" is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2632 name: SGD ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the Saccharomyces genome database (SGD)." [http://edamontology.org] regex: "PWY[a-zA-Z_0-9]{2}\-[0-9]{3}" is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2649 name: PharmGKB ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] regex: "PA[0-9]+" is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2368 name: ASTD ID (exon) namespace: identifier subset: identifiers subset: data def: "Identifier of an exon from the ASTD database." [http://edamontology.org] is_a: EDAM_data:2367 ! ASTD ID [Term] id: EDAM_data:2369 name: ASTD ID (intron) namespace: identifier subset: identifiers subset: data def: "Identifier of an intron from the ASTD database." [http://edamontology.org] is_a: EDAM_data:2367 ! ASTD ID [Term] id: EDAM_data:2370 name: ASTD ID (polya) namespace: identifier subset: identifiers subset: data def: "Identifier of a polyA signal from the ASTD database." [http://edamontology.org] is_a: EDAM_data:2367 ! ASTD ID [Term] id: EDAM_data:2371 name: ASTD ID (tss) namespace: identifier subset: identifiers subset: data def: "Identifier of a transcription start site from the ASTD database." [http://edamontology.org] is_a: EDAM_data:2367 ! ASTD ID [Term] id: EDAM_data:2671 name: Ensembl ID (Homo sapiens) namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division)." [http://edamontology.org] regex: "ENS([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2672 name: Ensembl ID ('Bos taurus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division)." [http://edamontology.org] regex: "ENSBTA([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2673 name: Ensembl ID ('Canis familiaris') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division)." [http://edamontology.org] regex: "ENSCAF([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2674 name: Ensembl ID ('Cavia porcellus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division)." [http://edamontology.org] regex: "ENSCPO([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2675 name: Ensembl ID ('Ciona intestinalis') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division)." [http://edamontology.org] regex: "ENSCIN([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2676 name: Ensembl ID ('Ciona savignyi') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division)." [http://edamontology.org] regex: "ENSCSAV([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2677 name: Ensembl ID ('Danio rerio') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division)." [http://edamontology.org] regex: "ENSDAR([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2678 name: Ensembl ID ('Dasypus novemcinctus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division)." [http://edamontology.org] regex: "ENSDNO([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2679 name: Ensembl ID ('Echinops telfairi') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division)." [http://edamontology.org] regex: "ENSETE([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2680 name: Ensembl ID ('Erinaceus europaeus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division)." [http://edamontology.org] regex: "ENSEEU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2681 name: Ensembl ID ('Felis catus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division)." [http://edamontology.org] regex: "ENSFCA([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2682 name: Ensembl ID ('Gallus gallus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division)." [http://edamontology.org] regex: "ENSGAL([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2683 name: Ensembl ID ('Gasterosteus aculeatus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division)." [http://edamontology.org] regex: "ENSGAC([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2684 name: Ensembl ID ('Homo sapiens') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division)." [http://edamontology.org] regex: "ENSHUM([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2685 name: Ensembl ID ('Loxodonta africana') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division)." [http://edamontology.org] regex: "ENSLAF([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2686 name: Ensembl ID ('Macaca mulatta') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division)." [http://edamontology.org] regex: "ENSMMU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2687 name: Ensembl ID ('Monodelphis domestica') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division)." [http://edamontology.org] regex: "ENSMOD([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2688 name: Ensembl ID ('Mus musculus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division)." [http://edamontology.org] regex: "ENSMUS([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2689 name: Ensembl ID ('Myotis lucifugus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division)." [http://edamontology.org] regex: "ENSMLU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2690 name: Ensembl ID ("Ornithorhynchus anatinus") namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division)." [http://edamontology.org] regex: "ENSOAN([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2691 name: Ensembl ID ('Oryctolagus cuniculus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division)." [http://edamontology.org] regex: "ENSOCU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2692 name: Ensembl ID ('Oryzias latipes') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division)." [http://edamontology.org] regex: "ENSORL([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2693 name: Ensembl ID ('Otolemur garnettii') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division)." [http://edamontology.org] regex: "ENSSAR([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2694 name: Ensembl ID ('Pan troglodytes') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division)." [http://edamontology.org] regex: "ENSPTR([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2695 name: Ensembl ID ('Rattus norvegicus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division)." [http://edamontology.org] regex: "ENSRNO([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2696 name: Ensembl ID ('Spermophilus tridecemlineatus') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division)." [http://edamontology.org] regex: "ENSSTO([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2697 name: Ensembl ID ('Takifugu rubripes') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division)." [http://edamontology.org] regex: "ENSFRU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2698 name: Ensembl ID ('Tupaia belangeri') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division)." [http://edamontology.org] regex: "ENSTBE([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2699 name: Ensembl ID ('Xenopus tropicalis') namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division)." [http://edamontology.org] regex: "ENSXET([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2725 name: Transcript ID (Ensembl) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a gene transcript from the Ensembl database." [http://edamontology.org] synonym: "Ensembl Transcript ID" EXACT [http://edamontology.org] is_a: EDAM_data:2610 ! Ensembl ID is_a: EDAM_data:2769 ! Transcript ID [Term] id: EDAM_data:2597 name: CABRI catalogue name namespace: identifier subset: identifiers subset: data def: "The name of a catalogue of biological resources from the CABRI database." [http://edamontology.org] is_a: EDAM_data:2596 ! Catalogue identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2780 name: Stock number (TAIR) namespace: identifier subset: identifiers subset: data def: "A stock number from The Arabidopsis information resource (TAIR)." [http://edamontology.org] is_a: EDAM_data:2779 ! Stock number [Term] id: EDAM_data:2129 name: File format name namespace: identifier subset: identifiers subset: data def: "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." [http://edamontology.org] is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2131 name: Operating system name namespace: identifier subset: identifiers subset: data def: "Name of a computer operating system such as Linux, PC or Mac." [http://edamontology.org] is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2538 name: Mutation identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a mutation." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2209 name: Mutation ID namespace: identifier subset: identifiers subset: data def: "A unique identifier of a specific mutation catalogued in a database." [http://edamontology.org] is_a: EDAM_data:2538 ! Mutation identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2133 name: Logical operator namespace: identifier subset: identifiers subset: data def: "A logical operator such as OR, AND, XOR, and NOT." [http://edamontology.org] is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1114 name: Sequence motif identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a sequence motif, for example an entry from a motif database." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:1115 name: Sequence profile ID namespace: identifier subset: identifiers subset: data def: "Identifier of a sequence profile." [http://edamontology.org] comment: A sequence profile typically represents a sequence alignment. is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:2660 name: BioNumbers ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:0983 name: Atom identifier namespace: identifier subset: identifiers subset: data def: "Identifier (e.g. character symbol) of a specific atom." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:0984 name: Molecule name namespace: identifier subset: identifiers subset: data def: "Name of a specific molecule." [http://edamontology.org] is_a: EDAM_data:0982 ! Molecule identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2901 name: Molecule accession namespace: identifier subset: identifiers subset: data def: "Accession of a specific molecule (catalogued in a database)." [http://edamontology.org] is_a: EDAM_data:0982 ! Molecule identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:0986 name: Chemical identifier namespace: identifier subset: identifiers subset: data def: "Unique identifier of a chemical compound." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:2119 name: Nucleic acid identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of a nucleic acid molecule." [http://edamontology.org] is_a: EDAM_data:0982 ! Molecule identifier relationship: is_identifier_of EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:0988 name: Peptide identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a peptide chain." [http://edamontology.org] is_a: EDAM_data:0982 ! Molecule identifier [Term] id: EDAM_data:2906 name: Peptide ID namespace: identifier subset: identifiers subset: data def: "Accession of a peptide deposited in a database." [http://edamontology.org] is_a: EDAM_data:0988 ! Peptide identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:1008 name: Polypeptide chain ID namespace: identifier subset: identifiers subset: data def: "Identifier of a polypeptide chain from a protein." [http://edamontology.org] comment: This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA synonym: "Polypeptide chain identifier" EXACT [http://edamontology.org] synonym: "Protein chain identifier" EXACT [http://edamontology.org] synonym: "PDB chain identifier" EXACT [http://edamontology.org] synonym: "Chain identifier" EXACT [http://edamontology.org] synonym: "PDB strand id" EXACT [http://edamontology.org] xref: WHATIF: chain is_a: EDAM_data:0988 ! Peptide identifier relationship: is_identifier_of EDAM_data:1467 ! Protein chain ! pdbx_PDB_strand_id in PDBML [Term] id: EDAM_data:0989 name: Protein identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a protein." [http://edamontology.org] is_a: EDAM_data:0982 ! Molecule identifier relationship: is_identifier_of EDAM_data:0896 ! Protein report [Term] id: EDAM_data:2907 name: Protein accession namespace: identifier subset: identifiers subset: data def: "Accession of a protein deposited in a database." [http://edamontology.org] is_a: EDAM_data:0989 ! Protein identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:1757 name: Atom name namespace: identifier subset: identifiers subset: data def: "Name of an atom." [http://edamontology.org] is_a: EDAM_data:0983 ! Atom identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1748 name: PDB atom name namespace: identifier subset: identifiers subset: data def: "Identifier (a string) of a specific atom from a PDB file for a molecular structure." [http://edamontology.org] xref: WHATIF: atom_type xref: WHATIF: alternate_atom xref: WHATIF: PDBx_auth_atom_id xref: WHATIF: PDBx_type_symbol is_a: EDAM_data:1757 ! Atom name ! pdbx_PDB_atom_name in PDBML [Term] id: EDAM_data:0990 name: Compound name namespace: identifier subset: identifiers subset: data def: "Unique name of a chemical compound." [http://edamontology.org] synonym: "Chemical name" EXACT [http://edamontology.org] is_a: EDAM_data:1086 ! Compound identifier is_a: EDAM_data:0984 ! Molecule name [Term] id: EDAM_data:0991 name: Chemical registry number namespace: identifier subset: identifiers subset: data def: "Unique registry number of a chemical compound." [http://edamontology.org] is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:0992 name: Ligand identifier namespace: identifier subset: identifiers subset: data def: "Code word for a ligand, for example from a PDB file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:0993 name: Drug identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a drug." [http://edamontology.org] is_a: EDAM_data:1086 ! Compound identifier relationship: is_identifier_of EDAM_data:2851 ! Drug structure [Term] id: EDAM_data:2895 name: Drug accession namespace: identifier subset: identifiers subset: data def: "Accession of a drug." [http://edamontology.org] is_a: EDAM_data:0993 ! Drug identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2899 name: Drug name namespace: identifier subset: identifiers subset: data def: "Common name of a drug." [http://edamontology.org] is_a: EDAM_data:0993 ! Drug identifier is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:2576 name: Toxin identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a toxin." [http://edamontology.org] is_a: EDAM_data:1086 ! Compound identifier relationship: is_identifier_of EDAM_data:2852 ! Toxin structure [Term] id: EDAM_data:2896 name: Toxin name namespace: identifier subset: identifiers subset: data def: "Name of a toxin." [http://edamontology.org] is_a: EDAM_data:2576 ! Toxin identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2897 name: Toxin accession namespace: identifier subset: identifiers subset: data def: "Accession of a toxin (catalogued in a database)." [http://edamontology.org] is_a: EDAM_data:2576 ! Toxin identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:0994 name: Amino acid identifier namespace: identifier subset: identifiers subset: data def: "Identifier of an amino acid." [http://edamontology.org] synonym: "Residue identifier" EXACT [http://edamontology.org] is_a: EDAM_data:1086 ! Compound identifier relationship: is_identifier_of EDAM_data:2016 ! Amino acid property [Term] id: EDAM_data:0995 name: Nucleotide identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of a nucleotide." [http://edamontology.org] is_a: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:0996 name: Monosaccharide identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a monosaccharide." [http://edamontology.org] is_a: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:2898 name: Monosaccharide accession namespace: identifier subset: identifiers subset: data def: "Accession of a monosaccharide (catalogued in a database)." [http://edamontology.org] is_a: EDAM_data:0996 ! Monosaccharide identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2812 name: Lipid identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a lipid." [http://edamontology.org] is_a: EDAM_data:0982 ! Molecule identifier relationship: is_identifier_of EDAM_data:2850 ! Lipid structure relationship: is_identifier_of EDAM_data:2879 ! Lipid structure report [Term] id: EDAM_data:2905 name: Lipid accession namespace: identifier subset: identifiers subset: data def: "Accession of an entry from a database of lipids." [http://edamontology.org] is_a: EDAM_data:2812 ! Lipid identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2663 name: Carbohydrate identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a carbohydrate." [http://edamontology.org] is_a: EDAM_data:1086 ! Compound identifier relationship: is_identifier_of EDAM_data:2313 ! Carbohydrate structure report relationship: is_identifier_of EDAM_data:1462 ! Carbohydrate structure [Term] id: EDAM_data:2900 name: Carbohydrate accession namespace: identifier subset: identifiers subset: data def: "Accession of an entry from a database of carbohydrates." [http://edamontology.org] is_a: EDAM_data:2663 ! Carbohydrate identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2605 name: Compound ID (KEGG) namespace: identifier subset: identifiers subset: data def: "Unique identifier of a chemical compound from the KEGG database." [http://edamontology.org] synonym: "KEGG compound ID" EXACT [http://edamontology.org] synonym: "KEGG compound identifier" EXACT [http://edamontology.org] regex: "C[0-9]+" is_a: EDAM_data:2894 ! Compound accession is_a: EDAM_data:1154 ! KEGG object identifier [Term] id: EDAM_data:2580 name: BindingDB Monomer ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a monomer from the BindingDB database." [http://edamontology.org] is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:1172 name: PubChem CID namespace: identifier subset: identifiers subset: data def: "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure." [http://edamontology.org] synonym: "PubChem compound accession identifier" EXACT [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2894 ! Compound accession is_a: EDAM_data:2639 ! PubChem identifier [Term] id: EDAM_data:1173 name: ChemSpider ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the ChemSpider database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:1174 name: ChEBI ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the ChEBI database." [http://edamontology.org] synonym: "ChEBI identifier" EXACT [http://edamontology.org] regex: "CHEBI:[0-9]+" is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2105 name: Compound ID (BioCyc) namespace: identifier subset: identifiers subset: data def: "Identifier of a compound from the BioCyc chemical compounds database." [http://edamontology.org] synonym: "BioCyc compound ID" EXACT [http://edamontology.org] synonym: "BioCyc compound identifier" EXACT [http://edamontology.org] is_a: EDAM_data:2104 ! BioCyc ID is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2622 name: Compound ID (HMDB) namespace: identifier subset: identifiers subset: data def: "Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB)." [http://edamontology.org] synonym: "HMDB ID" EXACT [http://edamontology.org] regex: "HMDB[0-9]{5}" is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2635 name: Compound ID (3DMET) namespace: identifier subset: identifiers subset: data def: "Identifier of a metabolite from the 3DMET database." [http://edamontology.org] synonym: "3DMET ID" EXACT [http://edamontology.org] regex: "B[0-9]{5}" is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2646 name: Compound ID (ChEMBL) namespace: identifier subset: identifiers subset: data def: "Identifier of a small molecular from the ChEMBL database." [http://edamontology.org] synonym: "ChEMBL ID" EXACT [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2658 name: Compound ID (ChemIDplus) namespace: identifier subset: identifiers subset: data def: "Identifier of a chemical from the ChemIDplus database." [http://edamontology.org] synonym: "ChemIDplus ID" EXACT [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:0997 name: Chemical name (ChEBI) namespace: identifier subset: identifiers subset: data def: "Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound." [http://edamontology.org] comment: This is the recommended chemical name for use for example in database annotation. synonym: "ChEBI chemical name" EXACT [http://edamontology.org] is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:0998 name: Chemical name (IUPAC) namespace: identifier subset: identifiers subset: data def: "IUPAC recommended name of a chemical compound." [http://edamontology.org] synonym: "IUPAC chemical name" EXACT [http://edamontology.org] is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:0999 name: Chemical name (INN) namespace: identifier subset: identifiers subset: data def: "International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO)." [http://edamontology.org] synonym: "INN chemical name" EXACT [http://edamontology.org] is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:1000 name: Chemical name (brand) namespace: identifier subset: identifiers subset: data def: "Brand name of a chemical compound." [http://edamontology.org] synonym: "Brand chemical name" EXACT [http://edamontology.org] is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:1001 name: Chemical name (synonymous) namespace: identifier subset: identifiers subset: data def: "Synonymous name of a chemical compound." [http://edamontology.org] synonym: "Synonymous chemical name" EXACT [http://edamontology.org] is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:1002 name: Chemical registry number (CAS) namespace: identifier subset: identifiers subset: data def: "CAS registry number of a chemical compound." [http://edamontology.org] synonym: "CAS chemical registry number" EXACT [http://edamontology.org] is_a: EDAM_data:0991 ! Chemical registry number [Term] id: EDAM_data:1003 name: Chemical registry number (Beilstein) namespace: identifier subset: identifiers subset: data def: "Beilstein registry number of a chemical compound." [http://edamontology.org] synonym: "Beilstein chemical registry number" EXACT [http://edamontology.org] is_a: EDAM_data:0991 ! Chemical registry number [Term] id: EDAM_data:1004 name: Chemical registry number (Gmelin) namespace: identifier subset: identifiers subset: data def: "Gmelin registry number of a chemical compound." [http://edamontology.org] synonym: "Gmelin chemical registry number" EXACT [http://edamontology.org] is_a: EDAM_data:0991 ! Chemical registry number [Term] id: EDAM_data:1005 name: HET group name namespace: identifier subset: identifiers subset: data def: "3-letter code word for a ligand (HET group) from a PDB file, for example ATP." [http://edamontology.org] synonym: "Short ligand name" EXACT [http://edamontology.org] synonym: "Component identifier code" EXACT [http://edamontology.org] is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:2613 name: KEGG Glycan ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND)." [http://edamontology.org] regex: "G[0-9]+" is_a: EDAM_data:2900 ! Carbohydrate accession is_a: EDAM_data:1154 ! KEGG object identifier [Term] id: EDAM_data:2326 name: DrugBank ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a drug from the DrugBank database." [http://edamontology.org] regex: "DB[0-9]{5}" is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:2609 name: Drug ID (KEGG) namespace: identifier subset: identifiers subset: data def: "Unique identifier of a drug from the KEGG Drug database." [http://edamontology.org] regex: "D[0-9]+" is_a: EDAM_data:2895 ! Drug accession is_a: EDAM_data:1154 ! KEGG object identifier [Term] id: EDAM_data:2652 name: Drug ID (PharmGKB) namespace: identifier subset: identifiers subset: data def: "Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] regex: "PA[0-9]+" is_a: EDAM_data:2895 ! Drug accession is_a: EDAM_data:2649 ! PharmGKB ID [Term] id: EDAM_data:2653 name: Drug ID (TTD) namespace: identifier subset: identifiers subset: data def: "Identifier of a drug from the Therapeutic Target Database (TTD)." [http://edamontology.org] regex: "DAP[0-9]+" is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:3102 !{since=beta13} name: CAS number namespace: identifier subset: identifiers subset: data def: "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." [http://edamontology.org] synonym: "CAS registry number" EXACT [http://edamontology.org] is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:3103 !{since=beta13} name: ATC code namespace: identifier subset: identifiers subset: data def: "Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC)." [http://edamontology.org] is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:3104 !{since=beta13} name: UNII namespace: identifier subset: identifiers subset: data def: "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." [http://edamontology.org] synonym: "Unique Ingredient Identifier" EXACT [http://edamontology.org] is_a: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:2578 name: ArachnoServer ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a toxin from the ArachnoServer database." [http://edamontology.org] is_a: EDAM_data:2897 ! Toxin accession [Term] id: EDAM_data:2662 name: T3DB ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database." [http://edamontology.org] regex: "T3D[0-9]+" is_a: EDAM_data:2897 ! Toxin accession [Term] id: EDAM_data:1006 name: Amino acid name namespace: identifier subset: identifiers subset: data def: "String of one or more ASCII characters representing an amino acid." [http://edamontology.org] is_a: EDAM_data:0994 ! Amino acid identifier [Term] id: EDAM_data:2563 name: Amino acid name (single letter) namespace: identifier subset: identifiers subset: data def: "Single letter amino acid identifier, e.g. G." [http://edamontology.org] is_a: EDAM_data:1006 ! Amino acid name [Term] id: EDAM_data:2564 name: Amino acid name (three letter) namespace: identifier subset: identifiers subset: data def: "Three letter amino acid identifier, e.g. GLY." [http://edamontology.org] is_a: EDAM_data:1006 ! Amino acid name [Term] id: EDAM_data:1758 name: PDB residue name namespace: identifier subset: identifiers subset: data def: "Three-letter amino acid residue names as used in PDB files." [http://edamontology.org] xref: WHATIF: type is_a: EDAM_data:2564 ! Amino acid name (three letter) [Term] id: EDAM_data:2565 name: Amino acid name (full name) namespace: identifier subset: identifiers subset: data def: "Full name of an amino acid, e.g. Glycine." [http://edamontology.org] is_a: EDAM_data:1006 ! Amino acid name [Term] id: EDAM_data:1007 name: Nucleotide code namespace: identifier subset: identifiers subset: data def: "String of one or more ASCII characters representing a nucleotide." [http://edamontology.org] is_a: EDAM_data:0995 ! Nucleotide identifier is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:2746 name: MonosaccharideDB ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a monosaccharide from the MonosaccharideDB database." [http://edamontology.org] is_a: EDAM_data:2898 ! Monosaccharide accession [Term] id: EDAM_data:2625 name: LIPID MAPS ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the LIPID MAPS database." [http://edamontology.org] synonym: "LM ID" EXACT [http://edamontology.org] regex: "LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?" is_a: EDAM_data:2905 ! Lipid accession [Term] id: EDAM_data:2665 name: LipidBank ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the LipidBank database." [http://edamontology.org] regex: "[a-zA-Z_0-9]+[0-9]+" is_a: EDAM_data:2905 ! Lipid accession [Term] id: EDAM_data:2664 name: GlycomeDB ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the GlycomeDB database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2900 ! Carbohydrate accession [Term] id: EDAM_data:2752 name: GlycoMap ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2900 ! Carbohydrate accession [Term] id: EDAM_data:2796 name: Linucs ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] is_a: EDAM_data:2900 ! Carbohydrate accession [Term] id: EDAM_data:0987 name: Chromosome name namespace: identifier subset: identifiers subset: data def: "Name of a chromosome." [http://edamontology.org] is_a: EDAM_data:2119 ! Nucleic acid identifier is_a: EDAM_data:0984 ! Molecule name relationship: is_identifier_of EDAM_data:0919 ! Gene annotation (chromosome) [Term] id: EDAM_data:2208 name: Plasmid identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a plasmid in a database." [http://edamontology.org] is_a: EDAM_data:2119 ! Nucleic acid identifier [Term] id: EDAM_data:2718 name: Oligonucleotide ID namespace: identifier subset: identifiers subset: data def: "Identifier of an oligonucleotide from a database." [http://edamontology.org] is_a: EDAM_data:2119 ! Nucleic acid identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2769 name: Transcript ID namespace: identifier subset: identifiers subset: data def: "Identifier of a RNA transcript." [http://edamontology.org] is_a: EDAM_data:2119 ! Nucleic acid identifier is_a: EDAM_data:2901 ! Molecule accession relationship: is_identifier_of EDAM_data:2399 ! Gene annotation (transcript) [Term] id: EDAM_data:2706 name: Chromosome name (BioCyc) namespace: identifier subset: identifiers subset: data def: "Name of a chromosome as used in the BioCyc database." [http://edamontology.org] is_a: EDAM_data:0987 ! Chromosome name [Term] id: EDAM_data:2719 name: dbProbe ID namespace: identifier subset: identifiers subset: data def: "Identifier of an oligonucleotide probe from the dbProbe database." [http://edamontology.org] is_a: EDAM_data:2718 ! Oligonucleotide ID [Term] id: EDAM_data:2721 name: DiProDB ID namespace: identifier subset: identifiers subset: data def: "Identifier of an dinucleotide property from the DiProDB database." [http://edamontology.org] is_a: EDAM_data:2718 ! Oligonucleotide ID [Term] id: EDAM_data:2770 name: HIT ID namespace: identifier subset: identifiers subset: data def: "Identifier of an RNA transcript from the H-InvDB database." [http://edamontology.org] is_a: EDAM_data:2769 ! Transcript ID [Term] id: EDAM_data:2626 name: PeptideAtlas ID namespace: identifier subset: identifiers subset: data def: "Identifier of a peptide from the PeptideAtlas peptide databases." [http://edamontology.org] regex: "PAp[0-9]{8}" is_a: EDAM_data:2906 ! Peptide ID ! pdbx_PDB_strand_id in PDBML [Term] id: EDAM_data:1009 name: Protein name namespace: identifier subset: identifiers subset: data def: "Name of a protein." [http://edamontology.org] is_a: EDAM_data:0989 ! Protein identifier is_a: EDAM_data:0984 ! Molecule name [Term] id: EDAM_data:1010 name: Enzyme identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of an enzyme or record from a database of enzymes." [http://edamontology.org] is_a: EDAM_data:0989 ! Protein identifier relationship: is_identifier_of EDAM_data:1509 ! Enzyme property [Term] id: EDAM_data:2114 name: WormBase wormpep ID namespace: identifier subset: identifiers subset: data def: "Protein identifier used by WormBase database." [http://edamontology.org] regex: "CE[0-9]{5}" is_a: EDAM_data:2907 ! Protein accession is_a: EDAM_data:2113 ! WormBase identifier [Term] id: EDAM_data:2804 name: Protein ID (ConoServer) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a cone snail toxin protein from the ConoServer database." [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2802 name: Protein ID (EcID) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a protein from the EcID database." [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:3029 !{since=beta13} name: Protein ID (EMBL/GenBank/DDBJ) namespace: identifier subset: identifiers subset: data def: "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators." [http://edamontology.org] comment: This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2398 name: Protein ID (Ensembl) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a protein from the Ensembl database." [http://edamontology.org] synonym: "Ensembl protein ID" EXACT [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession is_a: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2713 name: Protein ID (CORUM) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a protein complex from the CORUM database." [http://edamontology.org] synonym: "CORUM complex ID" EXACT [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2715 name: Protein ID (CuticleDB) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a protein from the CuticleDB database." [http://edamontology.org] synonym: "CuticleDB ID" EXACT [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2723 name: Protein ID (DisProt) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a protein from the DisProt database." [http://edamontology.org] synonym: "DisProt ID" EXACT [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2789 name: Protein ID (TopDB) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a membrane protein from the TopDB database." [http://edamontology.org] synonym: "TopDB ID" EXACT [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2792 name: Protein ID (PeroxiBase) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a peroxidase protein from the PeroxiBase database." [http://edamontology.org] synonym: "PeroxiBase ID" EXACT [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2797 name: Protein ID (LGICdb) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a ligand-gated ion channel protein from the LGICdb database." [http://edamontology.org] synonym: "LGICdb ID" EXACT [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2617 name: Signaling Gateway protein ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database." [http://edamontology.org] regex: "A[0-9]{6}" is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2647 name: LGICdb identifier namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database." [http://edamontology.org] regex: "[a-zA-Z_0-9]+" is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2654 name: Target ID (TTD) namespace: identifier subset: identifiers subset: data def: "Identifier of a target protein from the Therapeutic Target Database (TTD)." [http://edamontology.org] regex: "TTDS[0-9]+" is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2756 name: TCID namespace: identifier subset: identifiers subset: data def: "Identifier of a membrane transport proteins from the transport classification database (TCDB)." [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2772 name: HPA antibody id namespace: identifier subset: identifiers subset: data def: "Identifier of a antibody from the HPA database." [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2773 name: IMGT/HLA ID namespace: identifier subset: identifiers subset: data def: "Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database." [http://edamontology.org] is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2764 name: Protein name (UniProt) namespace: identifier subset: identifiers subset: data def: "Official name of a protein as used in the UniProt database." [http://edamontology.org] is_a: EDAM_data:1009 ! Protein name [Term] id: EDAM_data:2775 name: Kinase name namespace: identifier subset: identifiers subset: data def: "The name of a kinase protein." [http://edamontology.org] is_a: EDAM_data:1009 ! Protein name [Term] id: EDAM_data:2321 name: Enzyme ID namespace: identifier subset: identifiers subset: data def: "A unique, persistent identifier of an enzyme." [http://edamontology.org] synonym: "Enzyme accession" EXACT [http://edamontology.org] is_a: EDAM_data:1010 ! Enzyme identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:1012 name: Enzyme name namespace: identifier subset: identifiers subset: data def: "Name of an enzyme." [http://edamontology.org] is_a: EDAM_data:1010 ! Enzyme identifier is_a: EDAM_data:1009 ! Protein name [Term] id: EDAM_data:1011 name: EC number namespace: identifier subset: identifiers subset: data def: "An Enzyme Commission (EC) number of an enzyme." [http://edamontology.org] synonym: "EC code" EXACT [http://edamontology.org] synonym: "EC" EXACT [http://edamontology.org] synonym: "Enzyme Commission number" EXACT [http://edamontology.org] xref: Moby:EC_Number xref: Moby:Annotated_EC_Number regex: "[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+" is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:2107 name: Enzyme ID (BioCyc) namespace: identifier subset: identifiers subset: data def: "Identifier of an enzyme from the BioCyc enzymes database." [http://edamontology.org] synonym: "BioCyc enzyme ID" EXACT [http://edamontology.org] is_a: EDAM_data:2104 ! BioCyc ID is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:2629 name: Enzyme ID (MEROPS) namespace: identifier subset: identifiers subset: data def: "Unique identifier of a peptidase enzyme from the MEROPS database." [http://edamontology.org] synonym: "MEROPS ID" EXACT [http://edamontology.org] regex: "S[0-9]{2}\.[0-9]{3}" is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:2702 name: Enzyme ID (CAZy) namespace: identifier subset: identifiers subset: data def: "Identifier of an enzyme from the CAZy enzymes database." [http://edamontology.org] synonym: "CAZy ID" EXACT [http://edamontology.org] is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:2325 name: REBASE enzyme number namespace: identifier subset: identifiers subset: data def: "Identifier of an enzyme from the REBASE enzymes database." [http://edamontology.org] is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:1013 name: Restriction enzyme name namespace: identifier subset: identifiers subset: data def: "Name of a restriction enzyme." [http://edamontology.org] is_a: EDAM_data:1012 ! Enzyme name relationship: is_identifier_of EDAM_data:1517 ! Restriction enzyme property [Term] id: EDAM_data:1018 name: Nucleic acid feature identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of an nucleic acid feature." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1015 ! Sequence feature ID [Term] id: EDAM_data:1019 name: Protein feature identifier namespace: identifier subset: identifiers subset: data def: "Name or other identifier of a protein feature." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1015 ! Sequence feature ID [Term] id: EDAM_data:2736 name: Sequence feature ID (SwissRegulon) namespace: identifier subset: identifiers subset: data def: "A feature identifier as used in the SwissRegulon database." [http://edamontology.org] comment: This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". is_a: EDAM_data:1015 ! Sequence feature ID [Term] id: EDAM_data:1024 name: Codon name namespace: identifier subset: identifiers subset: data def: "String of one or more ASCII characters representing a codon." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1276 ! Nucleic acid features ! Don't know whether the loci identifiers listed here are 'ordered' or not. [Term] id: EDAM_data:2009 name: Ordered locus name namespace: identifier subset: identifiers subset: data def: "A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1895 name: Locus ID (AGI) namespace: identifier subset: identifiers subset: data def: "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" [http://edamontology.org] synonym: "AGI locus code" EXACT [http://edamontology.org] synonym: "AGI ID" EXACT [http://edamontology.org] synonym: "AGI identifier" EXACT [http://edamontology.org] synonym: "Arabidopsis gene loci number" EXACT [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode regex: "AT[1-5]G[0-9]{5}" is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1896 name: Locus ID (ASPGD) namespace: identifier subset: identifiers subset: data def: "Identifier for loci from ASPGD (Aspergillus Genome Database)." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1897 name: Locus ID (MGG) namespace: identifier subset: identifiers subset: data def: "Identifier for loci from Magnaporthe grisea Database at the Broad Institute." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1898 name: Locus ID (CGD) namespace: identifier subset: identifiers subset: data def: "Identifier for loci from CGD (Candida Genome Database)." [http://edamontology.org] synonym: "CGD locus identifier" EXACT [http://edamontology.org] synonym: "CGDID" EXACT [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGD xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGDID is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1899 name: Locus ID (CMR) namespace: identifier subset: identifiers subset: data def: "Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR xref: http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1900 name: NCBI locus tag namespace: identifier subset: identifiers subset: data def: "Identifier for loci from NCBI database." [http://edamontology.org] synonym: "Locus ID (NCBI)" EXACT [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag xref: Moby_namespace:LocusID is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1901 name: Locus ID (SGD) namespace: identifier subset: identifiers subset: data def: "Identifier for loci from SGD (Saccharomyces Genome Database)." [http://edamontology.org] synonym: "SGDID" EXACT [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGD xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGDID is_a: EDAM_data:1893 ! Locus ID is_a: EDAM_data:2632 ! SGD ID [Term] id: EDAM_data:1902 name: Locus ID (MMP) namespace: identifier subset: identifiers subset: data def: "Identifier of loci from Maize Mapping Project." [http://edamontology.org] xref: Moby_namespace:MMP_Locus is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1903 name: Locus ID (DictyBase) namespace: identifier subset: identifiers subset: data def: "Identifier of locus from DictyBase (Dictyostelium discoideum)." [http://edamontology.org] xref: Moby_namespace:DDB_gene is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1904 name: Locus ID (EntrezGene) namespace: identifier subset: identifiers subset: data def: "Identifier of a locus from EntrezGene database." [http://edamontology.org] xref: Moby_namespace:EntrezGene_EntrezGeneID xref: Moby_namespace:EntrezGene_ID is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1905 name: Locus ID (MaizeGDB) namespace: identifier subset: identifiers subset: data def: "Identifier of locus from MaizeGDB (Maize genome database)." [http://edamontology.org] xref: Moby_namespace:MaizeGDB_Locus is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1908 name: Locus ID (Tropgene) namespace: identifier subset: identifiers subset: data def: "Identifier of a locus from the Tropgene database." [http://edamontology.org] xref: Moby:Tropgene_locus is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:2744 name: Locus ID (PseudoCAP) namespace: identifier subset: identifiers subset: data def: "Identifier of a locus from the PseudoCAP database." [http://edamontology.org] is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:2745 name: Locus ID (UTR) namespace: identifier subset: identifiers subset: data def: "Identifier of a locus from the UTR database." [http://edamontology.org] is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:2794 name: ORF ID namespace: identifier subset: identifiers subset: data def: "Accession of an open reading frame (catalogued in a database)." [http://edamontology.org] is_a: EDAM_data:2795 ! ORF identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1026 name: Gene symbol namespace: identifier subset: identifiers subset: data def: "The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name." [http://edamontology.org] xref: Moby_namespace:Global_GeneSymbol xref: Moby_namespace:Global_GeneCommonName is_a: EDAM_data:2299 ! Gene name [Term] id: EDAM_data:2299 name: Gene name namespace: identifier subset: identifiers subset: data def: "The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol." [http://edamontology.org] is_a: EDAM_data:1025 ! Gene identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2295 name: Gene ID namespace: identifier subset: identifiers subset: data def: "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." [http://edamontology.org] synonym: "Gene code" EXACT [http://edamontology.org] synonym: "Gene accession" EXACT [http://edamontology.org] is_a: EDAM_data:1025 ! Gene identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1891 name: iHOP symbol namespace: identifier subset: identifiers subset: data def: "A unique identifier of a protein or gene used in the iHOP database." [http://edamontology.org] xref: Moby_namespace:iHOPsymbol is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2907 ! Protein accession is_a: EDAM_data:2109 ! Identifier (hybrid) ! Suspect this identifiers more than just genes [Term] id: EDAM_data:1036 name: TIGR identifier namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the TIGR database." [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:1037 name: TAIR accession (gene) namespace: identifier subset: identifiers subset: data def: "Identifier of an gene from the TAIR database." [http://edamontology.org] regex: "Gene:[0-9]{7}" is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2387 ! TAIR accession [Term] id: EDAM_data:2388 name: TAIR accession (At gene) namespace: identifier subset: identifiers subset: data def: "Identifier of an Arabidopsis thaliana gene from the TAIR database." [http://edamontology.org] is_a: EDAM_data:1037 ! TAIR accession (gene) [Term] id: EDAM_data:1806 name: Gene synonym namespace: identifier subset: identifiers subset: data def: "Any name (other than the recommended one) for a gene." [http://edamontology.org] synonym: "Gene name synonym" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1807 name: ORF name namespace: identifier subset: identifiers subset: data def: "The name of an open reading frame attributed by a sequencing project." [http://edamontology.org] is_a: EDAM_data:2795 ! ORF identifier is_a: EDAM_data:2099 ! Name ! GeneFarm gene ID is also given [Term] id: EDAM_data:1892 name: Gene name (GeneFarm) namespace: identifier subset: identifiers subset: data def: "Name of a gene from the GeneFarm database." [http://edamontology.org] xref: Moby_namespace:GENEFARM_GeneName is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1889 name: Gene name (DragonDB) namespace: identifier subset: identifiers subset: data def: "The name of an Antirrhinum Gene from the DragonDB database." [http://edamontology.org] xref: Moby_namespace:DragonDB_Gene is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1890 name: Gene name (Arabidopsis) namespace: identifier subset: identifiers subset: data def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." [http://edamontology.org] xref: Moby_namespace:ArabidopsisGeneSymbol is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1783 name: Gene name (ASPGD) namespace: identifier subset: identifiers subset: data def: "Name of a gene from Aspergillus Genome Database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1784 name: Gene name (CGD) namespace: identifier subset: identifiers subset: data def: "Name of a gene from Candida Genome Database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1785 name: Gene name (dictyBase) namespace: identifier subset: identifiers subset: data def: "Name of a gene from dictyBase database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1786 name: Gene name (EcoGene primary) namespace: identifier subset: identifiers subset: data def: "Primary name of a gene from EcoGene Database." [http://edamontology.org] synonym: "EcoGene primary gene name" EXACT [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1787 name: Gene name (MaizeGDB) namespace: identifier subset: identifiers subset: data def: "Name of a gene from MaizeGDB (maize genes) database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1788 name: Gene name (SGD) namespace: identifier subset: identifiers subset: data def: "Name of a gene from Saccharomyces Genome Database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS is_a: EDAM_data:1026 ! Gene symbol is_a: EDAM_data:2632 ! SGD ID [Term] id: EDAM_data:1789 name: Gene name (TGD) namespace: identifier subset: identifiers subset: data def: "Name of a gene from Tetrahymena Genome Database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1790 name: Gene name (CGSC) namespace: identifier subset: identifiers subset: data def: "Symbol of a gene from E.coli Genetic Stock Center." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1791 name: Gene name (HGNC) namespace: identifier subset: identifiers subset: data def: "Symbol of a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org] synonym: "Official gene name" EXACT [http://edamontology.org] synonym: "Gene name (HUGO)" EXACT [http://edamontology.org] synonym: "HGNC symbol" EXACT [http://edamontology.org] synonym: "HUGO symbol" EXACT [http://edamontology.org] synonym: "HGNC gene symbol" EXACT [http://edamontology.org] synonym: "HUGO gene symbol" EXACT [http://edamontology.org] synonym: "HUGO gene name" EXACT [http://edamontology.org] synonym: "HGNC gene name" EXACT [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene regex: "HGNC:[0-9]{1,5}" is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1792 name: Gene name (MGD) namespace: identifier subset: identifiers subset: data def: "Symbol of a gene from the Mouse Genome Database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD regex: "MGI:[0-9]+" is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1793 name: Gene name (Bacillus subtilis) namespace: identifier subset: identifiers subset: data def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:2103 name: Gene name (KEGG GENES) namespace: identifier subset: identifiers subset: data def: "Name of an entry (gene) from the KEGG GENES database." [http://edamontology.org] synonym: "KEGG GENES entry name" EXACT [http://edamontology.org] xref: Moby_namespace:GeneId regex: "[a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*" is_a: EDAM_data:1026 ! Gene symbol is_a: EDAM_data:1154 ! KEGG object identifier [Term] id: EDAM_data:2296 name: Gene name (AceView) namespace: identifier subset: identifiers subset: data def: "Name of an entry (gene) from the AceView genes database." [http://edamontology.org] synonym: "AceView gene name" EXACT [http://edamontology.org] is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:2300 name: Gene name (NCBI) namespace: identifier subset: identifiers subset: data def: "Name of an entry (gene) from the NCBI genes database." [http://edamontology.org] synonym: "NCBI gene name" EXACT [http://edamontology.org] is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:2740 name: Gene name (Genolist) namespace: identifier subset: identifiers subset: data def: "Name of an entry (gene) from the Genolist genes database." [http://edamontology.org] synonym: "Genolist gene name" EXACT [http://edamontology.org] is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:2743 name: Gene name (HUGO) namespace: identifier subset: identifiers subset: data def: "Name of an entry (gene) from the HUGO database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1791 ! Gene name (HGNC) [Term] id: EDAM_data:2771 name: HIX ID namespace: identifier subset: identifiers subset: data def: "A unique identifier of gene cluster in the H-InvDB database." [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2737 name: FIG ID namespace: identifier subset: identifiers subset: data def: "A unique identifier of gene in the NMPDR database." [http://edamontology.org] comment: A FIG ID consists of four parts: a prefix, genome id, locus type and id number. is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2774 name: Gene ID (JCVI) namespace: identifier subset: identifiers subset: data def: "A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI)." [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2738 name: Gene ID (Xenbase) namespace: identifier subset: identifiers subset: data def: "A unique identifier of gene in the Xenbase database." [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2799 name: Gene ID (MfunGD) namespace: identifier subset: identifiers subset: data def: "A unique identifier of gene in the MfunGD database." [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2739 name: Gene ID (Genolist) namespace: identifier subset: identifiers subset: data def: "A unique identifier of gene in the Genolist database." [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1028 name: Gene identifier (NCBI RefSeq) namespace: identifier subset: identifiers subset: data def: "An NCBI RefSeq unique identifier of a gene." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1027 ! Gene ID (NCBI) [Term] id: EDAM_data:1029 name: Gene identifier (NCBI UniGene) namespace: identifier subset: identifiers subset: data def: "An NCBI UniGene unique identifier of a gene." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1104 ! Sequence cluster ID (UniGene) [Term] id: EDAM_data:1030 name: Gene identifier (Entrez) namespace: identifier subset: identifiers subset: data def: "An Entrez unique identifier of a gene." [http://edamontology.org] regex: "[0-9]+" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1027 ! Gene ID (NCBI) [Term] id: EDAM_data:1886 name: Blattner number namespace: identifier subset: identifiers subset: data def: "The blattner identifier for a gene." [http://edamontology.org] xref: Moby_namespace:Blattner_number is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1027 name: Gene ID (NCBI) namespace: identifier subset: identifiers subset: data def: "An NCBI unique identifier of a gene." [http://edamontology.org] synonym: "Gene identifier (NCBI)" EXACT [http://edamontology.org] synonym: "NCBI gene ID" EXACT [http://edamontology.org] synonym: "NCBI geneid" EXACT [http://edamontology.org] synonym: "Gene identifier (Entrez)" EXACT [http://edamontology.org] synonym: "Entrez gene ID" EXACT [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:1098 ! RefSeq accession [Term] id: EDAM_data:1031 name: Gene ID (CGD) namespace: identifier subset: identifiers subset: data def: "Identifier of a gene or feature from the CGD database." [http://edamontology.org] synonym: "CGD ID" EXACT [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1032 name: Gene ID (DictyBase) namespace: identifier subset: identifiers subset: data def: "Identifier of a gene from DictyBase." [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1033 name: Gene ID (Ensembl) namespace: identifier subset: identifiers subset: data def: "Unique identifier for a gene (or other feature) from the Ensembl database." [http://edamontology.org] synonym: "Ensembl Gene ID" EXACT [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:1034 name: Gene ID (SGD) namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the SGD database." [http://edamontology.org] synonym: "SGD identifier" EXACT [http://edamontology.org] regex: "S[0-9]+" is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2632 ! SGD ID [Term] id: EDAM_data:1885 name: Gene ID (GeneFarm) namespace: identifier subset: identifiers subset: data def: "Identifier of a gene from the GeneFarm database." [http://edamontology.org] xref: Moby_namespace:GENEFARM_GeneID is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1907 name: Gene ID (KOME) namespace: identifier subset: identifiers subset: data def: "Identifier of a gene from the KOME database." [http://edamontology.org] xref: Moby_namespace:GeneId is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1794 name: Gene ID (PlasmoDB) namespace: identifier subset: identifiers subset: data def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1795 name: Gene ID (EcoGene) namespace: identifier subset: identifiers subset: data def: "Identifier of a gene from EcoGene Database." [http://edamontology.org] synonym: "EcoGene Accession" EXACT [http://edamontology.org] synonym: "EcoGene ID" EXACT [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2297 name: Gene ID (ECK) namespace: identifier subset: identifiers subset: data def: "Identifier of an E. coli K-12 gene from EcoGene Database." [http://edamontology.org] synonym: "E. coli K-12 gene identifier" EXACT [http://edamontology.org] synonym: "ECK accession" EXACT [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK is_a: EDAM_data:1795 ! Gene ID (EcoGene) [Term] id: EDAM_data:1796 name: Gene ID (FlyBase) namespace: identifier subset: identifiers subset: data def: "Gene identifier from FlyBase database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1802 name: Gene ID (Gramene) namespace: identifier subset: identifiers subset: data def: "Gene identifier from Gramene database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1803 name: Gene ID (Virginia microbial) namespace: identifier subset: identifiers subset: data def: "Gene identifier from Virginia Bioinformatics Institute microbial database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1804 name: Gene ID (SGN) namespace: identifier subset: identifiers subset: data def: "Gene identifier from Sol Genomics Network." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1805 name: Gene ID (WormBase) namespace: identifier subset: identifiers subset: data def: "Gene identifier used by WormBase database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase regex: "WBGene[0-9]{8}" is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2113 ! WormBase identifier [Term] id: EDAM_data:1035 name: Gene ID (GeneDB) namespace: identifier subset: identifiers subset: data def: "Identifier of a gene from the GeneDB database." [http://edamontology.org] synonym: "GeneDB identifier" EXACT [http://edamontology.org] xref: Moby_namespace:GeneDB regex: "[a-zA-Z_0-9\.-]*" is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2285 name: Gene ID (MIPS) namespace: identifier subset: identifiers subset: data def: "Identifier for genetic elements in MIPS database." [http://edamontology.org] synonym: "MIPS genetic element identifier" EXACT [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2298 name: Gene ID (HGNC) namespace: identifier subset: identifiers subset: data def: "Identifier for a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org] synonym: "HGNC ID" EXACT [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2642 name: Gene ID (miRBase) namespace: identifier subset: identifiers subset: data def: "Identifier for a gene from the miRBase database." [http://edamontology.org] synonym: "miRNA name" EXACT [http://edamontology.org] synonym: "miRNA identifier" EXACT [http://edamontology.org] synonym: "miRNA ID" EXACT [http://edamontology.org] regex: "MI[0-9]{7}" is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2643 name: Gene ID (ZFIN) namespace: identifier subset: identifiers subset: data def: "Identifier for a gene from the Zebrafish information network genome (ZFIN) database." [http://edamontology.org] regex: "ZDB\-GENE\-[0-9]+\-[0-9]+" is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2759 name: Gene ID (VectorBase) namespace: identifier subset: identifiers subset: data def: "Identifier for a gene from the VectorBase database." [http://edamontology.org] synonym: "VectorBase ID" EXACT [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2835 name: Gene ID (VBASE2) namespace: identifier subset: identifiers subset: data def: "Identifier for a gene from the VBASE2 database." [http://edamontology.org] synonym: "VBASE2 ID" EXACT [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1797 name: Gene ID (GeneDB Glossina morsitans) namespace: identifier subset: identifiers subset: data def: "Gene identifier from Glossina morsitans GeneDB database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans is_obsolete: true !{since=beta13} consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1798 name: Gene ID (GeneDB Leishmania major) namespace: identifier subset: identifiers subset: data def: "Gene identifier from Leishmania major GeneDB database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor is_obsolete: true !{since=beta13} consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1799 name: Gene ID (GeneDB Plasmodium falciparum) namespace: identifier subset: identifiers subset: data def: "Gene identifier from Plasmodium falciparum GeneDB database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum is_obsolete: true !{since=beta13} consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1800 name: Gene ID (GeneDB Schizosaccharomyces pombe) namespace: identifier subset: identifiers subset: data def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe is_obsolete: true !{since=beta13} consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1801 name: Gene ID (GeneDB Trypanosoma brucei) namespace: identifier subset: identifiers subset: data def: "Gene identifier from Trypanosoma brucei GeneDB database." [http://edamontology.org] xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei is_obsolete: true !{since=beta13} consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1887 name: Gene ID (MIPS Maize) namespace: identifier subset: identifiers subset: data def: "Identifier for genetic elements in MIPS Maize database." [http://edamontology.org] synonym: "MIPS genetic element identifier (Maize)" EXACT [http://edamontology.org] xref: Moby_namespace:MIPS_GE_Maize is_obsolete: true !{since=beta13} consider: EDAM_data:2285 ! Gene ID (MIPS) [Term] id: EDAM_data:1888 name: Gene ID (MIPS Medicago) namespace: identifier subset: identifiers subset: data def: "Identifier for genetic elements in MIPS Medicago database." [http://edamontology.org] synonym: "MIPS genetic element identifier (Medicago)" EXACT [http://edamontology.org] xref: Moby_namespace:MIPS_GE_Medicago is_obsolete: true !{since=beta13} consider: EDAM_data:2285 ! Gene ID (MIPS) [Term] id: EDAM_data:2751 name: GenomeReviews ID namespace: identifier subset: identifiers subset: data def: "An identifier of a particular genome." [http://edamontology.org] is_a: EDAM_data:2903 ! Genome accession [Term] id: EDAM_data:2786 name: NCBI Genome Project ID namespace: identifier subset: identifiers subset: data def: "An identifier of a genome project assigned by NCBI." [http://edamontology.org] is_a: EDAM_data:2903 ! Genome accession [Term] id: EDAM_data:2787 name: NCBI genome accession namespace: identifier subset: identifiers subset: data def: "A unique identifier of a whole genome assigned by the NCBI." [http://edamontology.org] is_a: EDAM_data:2903 ! Genome accession [Term] id: EDAM_data:2631 name: ACLAME ID namespace: identifier subset: identifiers subset: data def: "An identifier of a mobile genetic element from the Aclame database." [http://edamontology.org] regex: "mge:[0-9]+" is_a: EDAM_data:2630 ! Mobile genetic element ID [Term] id: EDAM_data:2128 name: Genetic code name namespace: identifier subset: identifiers subset: data def: "Informal name for a genetic code, typically an organism name." [http://edamontology.org] is_a: EDAM_data:2127 ! Genetic code identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1039 name: SCOP domain identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a protein domain (or other node) from the SCOP database." [http://edamontology.org] is_a: EDAM_data:1038 ! Protein domain ID relationship: is_identifier_of EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:2700 name: CATH identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a protein domain (or other node) from the CATH database." [http://edamontology.org] is_a: EDAM_data:1038 ! Protein domain ID relationship: is_identifier_of EDAM_data:1553 ! CATH node [Term] id: EDAM_data:2666 name: CDD ID namespace: identifier subset: identifiers subset: data def: "Identifier of a conserved domain from the Conserved Domain Database." [http://edamontology.org] regex: "cd[0-9]{5}" is_a: EDAM_data:1038 ! Protein domain ID [Term] id: EDAM_data:1041 name: SCOP concise classification string (sccs) namespace: identifier subset: identifiers subset: data def: "A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification." [http://edamontology.org] comment: An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. is_a: EDAM_data:1039 ! SCOP domain identifier [Term] id: EDAM_data:1042 name: SCOP sunid namespace: identifier subset: identifiers subset: data def: "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229." [http://edamontology.org] comment: A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. example: "33229" synonym: "sunid" EXACT [http://edamontology.org] synonym: "SCOP unique identifier" EXACT [http://edamontology.org] is_a: EDAM_data:1039 ! SCOP domain identifier [Term] id: EDAM_data:1040 name: CATH domain ID namespace: identifier subset: identifiers subset: data def: "Identifier of a protein domain from CATH." [http://edamontology.org] example: "1nr3A00" synonym: "CATH domain identifier" EXACT [http://edamontology.org] is_a: EDAM_data:2700 ! CATH identifier [Term] id: EDAM_data:1043 name: CATH node ID namespace: identifier subset: identifiers subset: data def: "A code number identifying a node from the CATH database." [http://edamontology.org] example: "3.30.1190.10.1.1.1.1.1" synonym: "CATH code" EXACT [http://edamontology.org] synonym: "CATH node identifier" EXACT [http://edamontology.org] is_a: EDAM_data:2700 ! CATH identifier [Term] id: EDAM_data:2701 name: CATH node ID (family) namespace: identifier subset: identifiers subset: data def: "A code number identifying a family from the CATH database." [http://edamontology.org] example: "2.10.10.10" is_a: EDAM_data:1043 ! CATH node ID relationship: is_identifier_of EDAM_data:1553 ! CATH node [Term] id: EDAM_data:2619 name: RESID ID namespace: identifier subset: identifiers subset: data def: "Identifier of a protein modification catalogued in the RESID database." [http://edamontology.org] regex: "AA[0-9]{4}" is_a: EDAM_data:2618 ! Protein modification ID [Term] id: EDAM_data:2892 name: Cell type name namespace: identifier subset: identifiers subset: data def: "The name of a type or group of cells." [http://edamontology.org] is_a: EDAM_data:2655 ! Cell type identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2656 name: NeuronDB ID namespace: identifier subset: identifiers subset: data def: "A unique identifier of a neuron from the NeuronDB database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2893 ! Cell type accession [Term] id: EDAM_data:2657 name: NeuroMorpho ID namespace: identifier subset: identifiers subset: data def: "A unique identifier of a neuron from the NeuroMorpho database." [http://edamontology.org] regex: "[a-zA-Z_0-9]+" is_a: EDAM_data:2893 ! Cell type accession [Term] id: EDAM_data:1868 name: Taxon namespace: identifier subset: identifiers subset: data def: "The name of a group of organisms belonging to the same taxonomic rank." [http://edamontology.org] comment: For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. synonym: "Taxonomy rank" EXACT [http://edamontology.org] synonym: "Taxonomic rank" EXACT [http://edamontology.org] xref: Moby:BriefTaxonConcept xref: Moby:PotentialTaxon is_a: EDAM_data:2909 ! Organism name [Term] id: EDAM_data:1872 name: Taxonomic classification namespace: identifier subset: identifiers subset: data def: "The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature." [http://edamontology.org] comment: Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. synonym: "Taxonomic name" EXACT [http://edamontology.org] synonym: "Taxonomic information" EXACT [http://edamontology.org] xref: Moby:GCP_Taxon xref: Moby:TaxonName xref: Moby:TaxonTCS xref: Moby:TaxonScientificName xref: Moby:iANT_organism-xml is_a: EDAM_data:2909 ! Organism name [Term] id: EDAM_data:1874 name: Genbank common name namespace: identifier subset: identifiers subset: data def: "Common name for an organism as used in the GenBank database." [http://edamontology.org] is_a: EDAM_data:2909 ! Organism name [Term] id: EDAM_data:1873 name: iHOP organism ID namespace: identifier subset: identifiers subset: data def: "A unique identifier for an organism used in the iHOP database." [http://edamontology.org] xref: Moby_namespace:iHOPorganism is_a: EDAM_data:2908 ! Organism accession [Term] id: EDAM_data:2102 name: KEGG organism code namespace: identifier subset: identifiers subset: data def: "A three-letter code used in the KEGG databases to uniquely identify organisms." [http://edamontology.org] is_a: EDAM_data:2909 ! Organism name is_a: EDAM_data:1154 ! KEGG object identifier [Term] id: EDAM_data:2593 name: BRENDA organism ID namespace: identifier subset: identifiers subset: data def: "A unique identifier for an organism used in the BRENDA database." [http://edamontology.org] is_a: EDAM_data:2908 ! Organism accession [Term] id: EDAM_data:2913 name: Virus identifier namespace: identifier subset: identifiers subset: data def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org] is_a: EDAM_data:1869 ! Organism identifier relationship: is_identifier_of EDAM_data:2307 ! Virus annotation [Term] id: EDAM_data:2785 name: Virus ID namespace: identifier subset: identifiers subset: data def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org] is_a: EDAM_data:2913 ! Virus identifier is_a: EDAM_data:2908 ! Organism accession [Term] id: EDAM_data:2836 name: DPVweb ID namespace: identifier subset: identifiers subset: data def: "A unique identifier for a virus from the DPVweb database." [http://edamontology.org] synonym: "DPVweb virus ID" EXACT [http://edamontology.org] is_a: EDAM_data:2785 ! Virus ID [Term] id: EDAM_data:2784 name: RNAVirusDB ID namespace: identifier subset: identifiers subset: data def: "A unique identifier for a virus from the RNAVirusDB database." [http://edamontology.org] is_a: EDAM_data:2785 ! Virus ID ! Could list (or cross-reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. [Term] id: EDAM_data:1875 name: NCBI taxon namespace: identifier subset: identifiers subset: data def: "The name of a taxon from the NCBI taxonomy database." [http://edamontology.org] is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:2594 name: UniGene taxon namespace: identifier subset: identifiers subset: data def: "The name of a taxon using the controlled vocabulary of the UniGene database." [http://edamontology.org] synonym: "UniGene organism abbreviation" EXACT [http://edamontology.org] is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:2595 name: UTRdb taxon namespace: identifier subset: identifiers subset: data def: "The name of a taxon using the controlled vocabulary of the UTRdb database." [http://edamontology.org] is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:1044 name: Kingdom name namespace: identifier subset: identifiers subset: data def: "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." [http://edamontology.org] is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:1870 name: Genus name namespace: identifier subset: identifiers subset: data def: "The name of a genus of organism." [http://edamontology.org] is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:2732 name: Family name namespace: identifier subset: identifiers subset: data def: "The name of a family of organism." [http://edamontology.org] is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:1045 name: Species name namespace: identifier subset: identifiers subset: data def: "The name of a species (typically a taxonomic group) of organism." [http://edamontology.org] synonym: "Organism species" EXACT [http://edamontology.org] is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:2733 name: Genus name (virus) namespace: identifier subset: identifiers subset: data def: "The name of a genus of viruses." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1870 ! Genus name [Term] id: EDAM_data:2734 name: Family name (virus) namespace: identifier subset: identifiers subset: data def: "The name of a family of viruses." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:2732 ! Family name [Term] id: EDAM_data:2317 name: Cell line name (exact) namespace: identifier subset: identifiers subset: data def: "The name of a cell line." [http://edamontology.org] is_a: EDAM_data:2316 ! Cell line name [Term] id: EDAM_data:2318 name: Cell line name (truncated) namespace: identifier subset: identifiers subset: data def: "The name of a cell line." [http://edamontology.org] is_a: EDAM_data:2316 ! Cell line name [Term] id: EDAM_data:2319 name: Cell line name (no punctuation) namespace: identifier subset: identifiers subset: data def: "The name of a cell line." [http://edamontology.org] is_a: EDAM_data:2316 ! Cell line name [Term] id: EDAM_data:2320 name: Cell line name (assonant) namespace: identifier subset: identifiers subset: data def: "The name of a cell line." [http://edamontology.org] is_a: EDAM_data:2316 ! Cell line name [Term] id: EDAM_data:1056 name: Database name namespace: identifier subset: identifiers subset: data def: "The name of a biological or bioinformatics database." [http://edamontology.org] is_a: EDAM_data:1048 ! Database identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2149 name: Database category name namespace: identifier subset: identifiers subset: data def: "The name of a category of biological or bioinformatics database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:1057 name: Sequence database name namespace: identifier subset: identifiers subset: data def: "The name of a molecular sequence database." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:2735 name: Database name (SwissRegulon) namespace: identifier subset: identifiers subset: data def: "The name of a SwissRegulon database." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:2747 name: Database name (CMD) namespace: identifier subset: identifiers subset: data def: "The name of a subdivision of the Collagen Mutation Database (CMD) database." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:2748 name: Database name (Osteogenesis) namespace: identifier subset: identifiers subset: data def: "The name of a subdivision of the Osteogenesis database." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:1058 name: Enumerated file name namespace: identifier subset: identifiers subset: data def: "The name of a file (of any type) with restricted possible values." [http://edamontology.org] is_a: EDAM_data:1050 ! File name [Term] id: EDAM_data:1059 name: File name extension namespace: identifier subset: identifiers subset: data def: "The extension of a file name." [http://edamontology.org] comment: A file extension is the characters appearing after the final '.' in the file name. is_a: EDAM_data:1050 ! File name [Term] id: EDAM_data:1060 name: File base name namespace: identifier subset: identifiers subset: data def: "The base name of a file." [http://edamontology.org] comment: A file base name is the file name stripped of its directory specification and extension. is_a: EDAM_data:1050 ! File name [Term] id: EDAM_data:1061 name: QSAR descriptor name namespace: identifier subset: identifiers subset: data def: "Name of a QSAR descriptor." [http://edamontology.org] is_a: EDAM_data:2110 ! Molecular property identifier is_a: EDAM_data:2099 ! Name relationship: is_identifier_of EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:2288 name: Sequence identifier (protein) namespace: identifier subset: identifiers subset: data def: "An identifier of protein sequence(s) or protein sequence database entries." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1096 ! Sequence accession (protein) [Term] id: EDAM_data:2289 name: Sequence identifier (nucleic acid) namespace: identifier subset: identifiers subset: data def: "An identifier of nucleotide sequence(s) or nucleotide sequence database entries." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:1093 name: Sequence accession namespace: identifier subset: identifiers subset: data def: "A persistent, unique identifier of a molecular sequence database entry." [http://edamontology.org] synonym: "Sequence accession number" EXACT [http://edamontology.org] is_a: EDAM_data:1063 ! Sequence identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:2154 name: Sequence name namespace: identifier subset: identifiers subset: data def: "Any arbitrary name of a molecular sequence." [http://edamontology.org] is_a: EDAM_data:1063 ! Sequence identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1095 name: EMBOSS Uniform Sequence Address namespace: identifier subset: identifiers subset: data def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [http://edamontology.org] synonym: "EMBOSS USA" EXACT [http://edamontology.org] is_a: EDAM_data:1063 ! Sequence identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2291 name: UniProt ID namespace: identifier subset: identifiers subset: data def: "An identifier of a polypeptide in the UniProt database." [http://edamontology.org] synonym: "UniProt identifier" EXACT [http://edamontology.org] is_a: EDAM_data:1096 ! Sequence accession (protein) relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:1100 name: PIR identifier namespace: identifier subset: identifiers subset: data def: "An identifier of PIR sequence database entry." [http://edamontology.org] synonym: "PIR accession number" EXACT [http://edamontology.org] synonym: "PIR ID" EXACT [http://edamontology.org] is_a: EDAM_data:1096 ! Sequence accession (protein) relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:1101 name: TREMBL accession namespace: identifier subset: identifiers subset: data def: "Identifier of a TREMBL sequence database entry." [http://edamontology.org] is_a: EDAM_data:3021 ! UniProt accession synonym: "TREMBL accession number" EXACT [http://edamontology.org] synonym: "TREMBL ID" EXACT [http://edamontology.org] relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2621 name: TAIR accession (protein) namespace: identifier subset: identifiers subset: data def: "Identifier of a protein sequence from the TAIR database." [http://edamontology.org] regex: "AASequence:[0-9]{10}" is_a: EDAM_data:1096 ! Sequence accession (protein) is_a: EDAM_data:2387 ! TAIR accession relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2290 name: EMBL accession namespace: identifier subset: identifiers subset: data ! alt_id: EDAM_data:1107 def: "An accession number of an entry from the EMBL sequence database." [http://edamontology.org] synonym: "EMBL accession number" EXACT [http://edamontology.org] synonym: "EMBL identifier" EXACT [http://edamontology.org] synonym: "EMBL ID" EXACT [http://edamontology.org] is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID [Term] id: EDAM_data:2292 name: GenBank accession namespace: identifier subset: identifiers subset: data ! alt_id: EDAM_data:1108 def: "Accession number of an entry from the GenBank sequence database." [http://edamontology.org] is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID synonym: "GenBank accession number" EXACT [http://edamontology.org] synonym: "GenBank identifier" EXACT [http://edamontology.org] synonym: "GenBank ID" EXACT [http://edamontology.org] [Term] id: EDAM_data:2916 name: DDBJ accession namespace: identifier subset: identifiers subset: data ! alt_id: EDAM_data:1109 def: "An identifier of an entry from the DDBJ sequence database." [http://edamontology.org] is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID synonym: "DDBJ accession number" EXACT [http://edamontology.org] synonym: "DDBJ identifier" EXACT [http://edamontology.org] synonym: "DDBJ ID" EXACT [http://edamontology.org] [Term] id: EDAM_data:1855 name: Clone ID namespace: identifier subset: identifiers subset: data def: "An identifier of a clone (cloned molecular sequence) from a database." [http://edamontology.org] is_a: EDAM_data:2769 ! Transcript ID [Term] id: EDAM_data:2386 name: EPD ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (promoter) from the EPD database." [http://edamontology.org] synonym: "EPD identifier" EXACT [http://edamontology.org] is_a: EDAM_data:2727 ! Promoter ID [Term] id: EDAM_data:2741 name: ABS ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry (promoter) from the ABS database." [http://edamontology.org] synonym: "ABS identifier" EXACT [http://edamontology.org] is_a: EDAM_data:2727 ! Promoter ID [Term] id: EDAM_data:1096 name: Sequence accession (protein) namespace: identifier subset: identifiers subset: data def: "Accession number of a protein sequence database entry." [http://edamontology.org] synonym: "Protein sequence accession number" EXACT [http://edamontology.org] is_a: EDAM_data:1093 ! Sequence accession relationship: is_identifier_of EDAM_data:2976 ! Protein sequence [Term] id: EDAM_data:1097 name: Sequence accession (nucleic acid) namespace: identifier subset: identifiers subset: data def: "Accession number of a nucleotide sequence database entry." [http://edamontology.org] synonym: "Nucleotide sequence accession number" EXACT [http://edamontology.org] is_a: EDAM_data:1093 ! Sequence accession relationship: is_identifier_of EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:2362 name: Sequence accession (hybrid) namespace: identifier subset: identifiers subset: data def: "Accession number of a nucleotide or protein sequence database entry." [http://edamontology.org] is_a: EDAM_data:1093 ! Sequence accession relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:1098 name: RefSeq accession namespace: identifier subset: identifiers subset: data def: "Accession number of a RefSeq database entry." [http://edamontology.org] regex: "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+" is_a: EDAM_data:2362 ! Sequence accession (hybrid) synonym: "RefSeq ID" EXACT [http://edamontology.org] [Term] id: EDAM_data:2314 name: GI number namespace: identifier subset: identifiers subset: data def: "A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record." [http://edamontology.org] comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. synonym: "NCBI GI number" EXACT [http://edamontology.org] synonym: "gi number" EXACT [http://edamontology.org] is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] id: EDAM_data:2315 name: NCBI version namespace: identifier subset: identifiers subset: data def: "An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number." [http://edamontology.org] comment: Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. synonym: "accession.version" EXACT [http://edamontology.org] synonym: "NCBI accession.version" EXACT [http://edamontology.org] is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] id: EDAM_data:2385 name: RefSeq accession (protein) namespace: identifier subset: identifiers subset: data def: "Accession number of a protein from the RefSeq database." [http://edamontology.org] is_a: EDAM_data:1098 ! RefSeq accession synonym: "RefSeq protein ID" EXACT [http://edamontology.org] [Term] id: EDAM_data:2327 name: GI number (protein) namespace: identifier subset: identifiers subset: data def: "A unique identifier assigned to NCBI protein sequence records." [http://edamontology.org] comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. synonym: "protein gi number" EXACT [http://edamontology.org] synonym: "protein gi" EXACT [http://edamontology.org] is_a: EDAM_data:2314 ! GI number [Term] id: EDAM_data:1099 name: UniProt accession (extended) namespace: identifier subset: identifiers subset: data def: "Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number." [http://edamontology.org] regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+" example: "Q7M1G0" "P43353-2" "P01012.107" ! is_a: EDAM_data:3021 ! UniProt accession ! relationship: is_identifier_of EDAM_format:1208 ! Protein sequence ! now 'protein' format ! relationship: is_identifier_of EDAM_data:0849 ! Sequence record is_obsolete: true !{since=1.0} consider: EDAM_data:3021 ! UniProt accession [Term] id: EDAM_data:3021 name: UniProt accession namespace: identifier subset: identifiers subset: data def: "Accession number of a UniProt (protein sequence) database entry." [http://edamontology.org] regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]" example: "P43353" "Q7M1G0" "Q9C199" "A5A6J6" synonym: "UniProtKB accession number" EXACT [http://edamontology.org] synonym: "UniProtKB entry accession" EXACT [http://edamontology.org] synonym: "UniProt accession number" EXACT [http://edamontology.org] synonym: "Swiss-Prot accession" EXACT [http://edamontology.org] is_a: EDAM_data:2291 ! UniProt ID relationship: is_identifier_of EDAM_data:0849 ! Sequence record ! Of protein/peptide (feature) record? Also of a class of protein molecules? [Term] id: EDAM_data:2392 name: UniParc accession namespace: identifier subset: identifiers subset: data def: "Accession number of a UniParc (protein sequence) database entry." [http://edamontology.org] synonym: "UniParc ID" EXACT [http://edamontology.org] synonym: "UPI" EXACT [http://edamontology.org] regex: "UPI[A-F0-9]{10}" is_a: EDAM_data:2291 ! UniProt ID [Term] id: EDAM_data:2915 name: Gramene identifier namespace: identifier subset: identifiers subset: data def: "Identifier of a Gramene database entry." [http://edamontology.org] is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] id: EDAM_data:1102 name: Gramene primary identifier namespace: identifier subset: identifiers subset: data def: "Primary identifier of a Gramene database entry." [http://edamontology.org] synonym: "Gramene primary ID" EXACT [http://edamontology.org] is_a: EDAM_data:2915 ! Gramene identifier [Term] id: EDAM_data:2293 name: Gramene secondary identifier namespace: identifier subset: identifiers subset: data def: "Secondary (internal) identifier of a Gramene database entry." [http://edamontology.org] synonym: "Gramene secondary ID" EXACT [http://edamontology.org] synonym: "Gramene internal ID" EXACT [http://edamontology.org] synonym: "Gramene internal identifier" EXACT [http://edamontology.org] is_a: EDAM_data:2915 ! Gramene identifier [Term] id: EDAM_data:2384 name: IPI protein ID namespace: identifier subset: identifiers subset: data def: "Identifier of a protein entry catalogued in the International Protein Index (IPI) database." [http://edamontology.org] regex: "IPI[0-9]{8}" is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] id: EDAM_data:2728 name: EST accession namespace: identifier subset: identifiers subset: data def: "Identifier of an EST sequence." [http://edamontology.org] is_a: EDAM_data:1855 ! Clone ID [Term] id: EDAM_data:1103 name: EMBL/GenBank/DDBJ ID namespace: identifier subset: identifiers subset: data def: "Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases." [http://edamontology.org] is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2389 name: UniSTS accession namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the UniSTS database." [http://edamontology.org] is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2390 name: UNITE accession namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the UNITE database." [http://edamontology.org] is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2391 name: UTR accession namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the UTR database." [http://edamontology.org] is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2393 name: mFLJ/mKIAA number namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the Rouge or HUGE databases." [http://edamontology.org] is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2781 name: REDIdb ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the RNA editing database (REDIdb)." [http://edamontology.org] is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2729 name: COGEME EST ID namespace: identifier subset: identifiers subset: data def: "Identifier of an EST sequence from the COGEME database." [http://edamontology.org] is_a: EDAM_data:2728 ! EST accession [Term] id: EDAM_data:2730 name: COGEME unisequence ID namespace: identifier subset: identifiers subset: data def: "Identifier of a unisequence from the COGEME database." [http://edamontology.org] comment: A unisequence is a single sequence assembled from ESTs. is_a: EDAM_data:2728 ! EST accession [Term] id: EDAM_data:2798 name: MaizeDB ID namespace: identifier subset: identifiers subset: data def: "Identifier of an EST sequence from the MaizeDB database." [http://edamontology.org] is_a: EDAM_data:2728 ! EST accession [Term] id: EDAM_data:1105 name: dbEST accession namespace: identifier subset: identifiers subset: data def: "Identifier of a dbEST database entry." [http://edamontology.org] synonym: "dbEST ID" EXACT [http://edamontology.org] is_a: EDAM_data:2292 ! GenBank accession is_a: EDAM_data:2728 ! EST accession [Term] id: EDAM_data:2704 name: Clone ID (IMAGE) namespace: identifier subset: identifiers subset: data def: "A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence)." [http://edamontology.org] synonym: "I.M.A.G.E. cloneID" EXACT [http://edamontology.org] synonym: "IMAGE cloneID" EXACT [http://edamontology.org] is_a: EDAM_data:1855 ! Clone ID [Term] id: EDAM_data:2803 name: Clone ID (RefSeq) namespace: identifier subset: identifiers subset: data def: "A unique identifier of a cDNA molecule catalogued in the RefSeq database." [http://edamontology.org] is_a: EDAM_data:1855 ! Clone ID is_a: EDAM_data:1098 ! RefSeq accession [Term] id: EDAM_data:1110 name: EMBOSS sequence type namespace: identifier subset: identifiers subset: data def: "The EMBOSS type of a molecular sequence." [http://edamontology.org] comment: See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1094 ! Sequence type [Term] id: EDAM_data:1106 name: dbSNP ID namespace: identifier subset: identifiers subset: data def: "Identifier of a dbSNP database entry." [http://edamontology.org] synonym: "dbSNP identifier" EXACT [http://edamontology.org] is_a: EDAM_data:2294 ! Sequence variation ID [Term] id: EDAM_data:2805 name: GeneSNP ID namespace: identifier subset: identifiers subset: data def: "Identifier of a GeneSNP database entry." [http://edamontology.org] is_a: EDAM_data:2294 ! Sequence variation ID [Term] id: EDAM_data:1112 name: Sequence cluster ID namespace: identifier subset: identifiers subset: data def: "An identifier of a cluster of molecular sequence(s)." [http://edamontology.org] is_a: EDAM_data:1064 ! Sequence set ID relationship: is_identifier_of EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:2346 name: Sequence cluster ID (UniRef) namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the UniRef database." [http://edamontology.org] synonym: "UniRef entry accession" EXACT [http://edamontology.org] synonym: "UniRef cluster id" EXACT [http://edamontology.org] is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:1113 name: Sequence cluster ID (COG) namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the COG database." [http://edamontology.org] synonym: "COG ID" EXACT [http://edamontology.org] is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:1104 name: Sequence cluster ID (UniGene) namespace: identifier subset: identifiers subset: data def: "A unique identifier of an entry (gene cluster) from the NCBI UniGene database." [http://edamontology.org] synonym: "UniGene ID" EXACT [http://edamontology.org] synonym: "UniGene identifier" EXACT [http://edamontology.org] synonym: "UniGene cluster ID" EXACT [http://edamontology.org] synonym: "UniGene cluster id" EXACT [http://edamontology.org] is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:2220 name: Sequence cluster ID (SYSTERS) namespace: identifier subset: identifiers subset: data def: "Unique identifier of a sequence cluster from the SYSTERS database." [http://edamontology.org] synonym: "SYSTERS cluster ID" EXACT [http://edamontology.org] is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:2612 name: Sequence cluster ID (CluSTr) namespace: identifier subset: identifiers subset: data def: "Unique identifier of a sequence cluster from the CluSTr database." [http://edamontology.org] synonym: "CluSTr cluster ID" EXACT [http://edamontology.org] synonym: "CluSTr ID" EXACT [http://edamontology.org] regex: "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?" is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:2347 name: Sequence cluster ID (UniRef100) namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the UniRef100 database." [http://edamontology.org] synonym: "UniRef100 entry accession" EXACT [http://edamontology.org] synonym: "UniRef100 cluster id" EXACT [http://edamontology.org] is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) [Term] id: EDAM_data:2348 name: Sequence cluster ID (UniRef90) namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the UniRef90 database." [http://edamontology.org] synonym: "UniRef90 entry accession" EXACT [http://edamontology.org] synonym: "UniRef90 cluster id" EXACT [http://edamontology.org] is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) [Term] id: EDAM_data:2349 name: Sequence cluster ID (UniRef50) namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the UniRef50 database." [http://edamontology.org] synonym: "UniRef50 entry accession" EXACT [http://edamontology.org] synonym: "UniRef50 cluster id" EXACT [http://edamontology.org] is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) [Term] id: EDAM_data:2761 name: UTRSite ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs." [http://edamontology.org] is_a: EDAM_data:1114 ! Sequence motif identifier [Term] id: EDAM_data:1116 name: ELM ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the ELMdb database of protein functional sites." [http://edamontology.org] is_a: EDAM_data:1114 ! Sequence motif identifier [Term] id: EDAM_data:1117 name: Prosite accession number namespace: identifier subset: identifiers subset: data def: "Accession number of an entry from the Prosite database." [http://edamontology.org] synonym: "Prosite ID" EXACT [http://edamontology.org] regex: "PS[0-9]{5}" is_a: EDAM_data:1114 ! Sequence motif identifier [Term] id: EDAM_data:2714 name: CDD PSSM-ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a position-specific scoring matrix from the CDD database." [http://edamontology.org] is_a: EDAM_data:1115 ! Sequence profile ID [Term] id: EDAM_data:1118 name: HMMER hidden Markov model ID namespace: identifier subset: identifiers subset: data def: "Unique identifier or name of a HMMER hidden Markov model." [http://edamontology.org] is_a: EDAM_data:1115 ! Sequence profile ID relationship: is_identifier_of EDAM_data:1364 ! Hidden Markov model [Term] id: EDAM_data:1119 name: JASPAR profile ID namespace: identifier subset: identifiers subset: data def: "Unique identifier or name of a profile from the JASPAR database." [http://edamontology.org] is_a: EDAM_data:1115 ! Sequence profile ID [Term] id: EDAM_data:2150 name: Sequence profile name namespace: identifier subset: identifiers subset: data def: "Name of a sequence profile." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1115 ! Sequence profile ID [Term] id: EDAM_data:1123 name: TreeBASE study accession number namespace: identifier subset: identifiers subset: data def: "Accession number of an entry from the TreeBASE database." [http://edamontology.org] is_a: EDAM_data:1068 ! Phylogenetic tree ID [Term] id: EDAM_data:1124 name: TreeFam accession number namespace: identifier subset: identifiers subset: data def: "Accession number of an entry from the TreeFam database." [http://edamontology.org] is_a: EDAM_data:1068 ! Phylogenetic tree ID [Term] id: EDAM_data:1126 name: Comparison matrix name namespace: identifier subset: identifiers subset: data def: "Unique name or identifier of a comparison matrix." [http://edamontology.org] comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. synonym: "Substitution matrix name" EXACT [http://edamontology.org] is_a: EDAM_data:1069 ! Comparison matrix identifier is_a: EDAM_data:2099 ! Name relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1127 name: PDB ID namespace: identifier subset: identifiers subset: data def: "An identifier of an entry from the PDB database." [http://edamontology.org] synonym: "PDB identifier" EXACT [http://edamontology.org] synonym: "PDBID" EXACT [http://edamontology.org] regex: "[a-zA-Z_0-9]{4}" is_a: EDAM_data:1070 ! Structure ID [Term] id: EDAM_data:2667 name: MMDB ID namespace: identifier subset: identifiers subset: data def: "An identifier of an entry from the MMDB database." [http://edamontology.org] synonym: "MMDB accession" EXACT [http://edamontology.org] regex: "[0-9]{1,5}" is_a: EDAM_data:1070 ! Structure ID [Term] id: EDAM_data:2793 name: SISYPHUS ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the SISYPHUS database of tertiary structure alignments." [http://edamontology.org] is_a: EDAM_data:1072 ! Structure alignment ID [Term] id: EDAM_data:1128 name: AAindex ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the AAindex database." [http://edamontology.org] is_a: EDAM_data:1073 ! Amino acid index ID [Term] id: EDAM_data:1074 name: Protein interaction ID namespace: identifier subset: identifiers subset: data def: "Identifier of a report of protein interactions from a protein interaction database (typically)." [http://edamontology.org] is_a: EDAM_data:2627 ! Molecular interaction ID [Term] id: EDAM_data:2628 name: BioGRID interaction ID namespace: identifier subset: identifiers subset: data def: "A unique identifier of an interaction from the BioGRID database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2627 ! Molecular interaction ID [Term] id: EDAM_data:2636 name: MatrixDB interaction ID namespace: identifier subset: identifiers subset: data def: "A unique identifier of an interaction from the MatrixDB database." [http://edamontology.org] regex: "([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)" is_a: EDAM_data:2627 ! Molecular interaction ID [Term] id: EDAM_data:1129 name: BIND accession number namespace: identifier subset: identifiers subset: data def: "Accession number of an entry from the BIND database." [http://edamontology.org] is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:1130 name: IntAct accession number namespace: identifier subset: identifiers subset: data def: "Accession number of an entry from the IntAct database." [http://edamontology.org] regex: "EBI\-[0-9]+" is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:2302 name: STRING ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the STRING database of protein-protein interactions." [http://edamontology.org] is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:2615 name: MINT ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the MINT database of protein-protein interactions." [http://edamontology.org] regex: "MINT\-[0-9]{1,5}" is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:2616 name: DIP ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the DIP database of protein-protein interactions." [http://edamontology.org] regex: "DIP[\:\-][0-9]{3}[EN]" is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:2668 name: iRefIndex ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the iRefIndex database of protein-protein interactions." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:1076 name: Codon usage table name namespace: identifier subset: identifiers subset: data def: "Unique name of a codon usage table." [http://edamontology.org] is_a: EDAM_data:2111 ! Codon usage table identifier is_a: EDAM_data:2099 ! Name relationship: is_identifier_of EDAM_data:1597 ! Codon usage table relationship: is_identifier_of EDAM_data:1598 ! Genetic code [Term] id: EDAM_data:2356 name: RFAM accession namespace: identifier subset: identifiers subset: data def: "Stable accession number of an entry (RNA family) from the RFAM database." [http://edamontology.org] is_a: EDAM_data:2355 ! RNA family identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2606 name: RFAM name namespace: identifier subset: identifiers subset: data def: "Name (not necessarily stable) an entry (RNA family) from the RFAM database." [http://edamontology.org] is_a: EDAM_data:2355 ! RNA family identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2766 name: HAMAP ID namespace: identifier subset: identifiers subset: data def: "Name of a protein family from the HAMAP database." [http://edamontology.org] is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1132 name: InterPro entry name namespace: identifier subset: identifiers subset: data def: "Name of an InterPro entry, usually indicating the type of protein matches for that entry." [http://edamontology.org] is_a: EDAM_data:1131 ! Protein family name relationship: is_identifier_of EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1133 name: InterPro accession namespace: identifier subset: identifiers subset: data def: "Primary accession number of an InterPro entry." [http://edamontology.org] comment: Every InterPro entry has a unique accession number to provide a persistent citation of database records. synonym: "InterPro primary accession number" EXACT [http://edamontology.org] synonym: "InterPro primary accession" EXACT [http://edamontology.org] regex: "IPR[0-9]{6}" example: "IPR015590" is_a: EDAM_data:2910 ! Protein family accession relationship: is_identifier_of EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1134 name: InterPro secondary accession namespace: identifier subset: identifiers subset: data def: "Secondary accession number of an InterPro entry." [http://edamontology.org] synonym: "InterPro secondary accession number" EXACT [http://edamontology.org] is_a: EDAM_data:1133 ! InterPro accession relationship: is_identifier_of EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1135 name: Gene3D ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the Gene3D database." [http://edamontology.org] is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1136 name: PIRSF ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the PIRSF database." [http://edamontology.org] regex: "PIRSF[0-9]{6}" is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1137 name: PRINTS code namespace: identifier subset: identifiers subset: data def: "The unique identifier of an entry in the PRINTS database." [http://edamontology.org] regex: "PR[0-9]{5}" is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1138 name: Pfam accession number namespace: identifier subset: identifiers subset: data def: "Accession number of a Pfam entry." [http://edamontology.org] regex: "PF[0-9]{5}" is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2758 name: Pfam clan ID namespace: identifier subset: identifiers subset: data def: "Accession number of a Pfam clan." [http://edamontology.org] regex: "CL[0-9]{4}" is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2757 name: Pfam domain name namespace: identifier subset: identifiers subset: data def: "Name of a domain from the Pfam database." [http://edamontology.org] regex: "PF[0-9]{5}" is_a: EDAM_data:1131 ! Protein family name [Term] id: EDAM_data:2782 name: SMART domain name namespace: identifier subset: identifiers subset: data def: "Name of a domain from the SMART database." [http://edamontology.org] is_a: EDAM_data:1131 ! Protein family name [Term] id: EDAM_data:1139 name: SMART accession number namespace: identifier subset: identifiers subset: data def: "Accession number of an entry from the SMART database." [http://edamontology.org] regex: "SM[0-9]{5}" is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1140 name: Superfamily hidden Markov model number namespace: identifier subset: identifiers subset: data def: "Unique identifier (number) of a hidden Markov model from the Superfamily database." [http://edamontology.org] is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1141 name: TIGRFam ID namespace: identifier subset: identifiers subset: data def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org] synonym: "TIGRFam accession number" EXACT [http://edamontology.org] is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1142 name: ProDom accession number namespace: identifier subset: identifiers subset: data def: "A ProDom domain family accession number." [http://edamontology.org] comment: ProDom is a protein domain family database. regex: "PD[0-9]+" is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2614 name: TCDB ID namespace: identifier subset: identifiers subset: data def: "A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins." [http://edamontology.org] comment: OBO file for regular expression. synonym: "TC number" EXACT [http://edamontology.org] regex: "[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+" is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2731 name: Protein family ID (GeneFarm) namespace: identifier subset: identifiers subset: data def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org] synonym: "GeneFarm family ID" EXACT [http://edamontology.org] is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2783 name: Protein family ID (PANTHER) namespace: identifier subset: identifiers subset: data def: "Accession number of an entry (family) from the PANTHER database." [http://edamontology.org] synonym: "Panther family ID" EXACT [http://edamontology.org] is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1143 name: TRANSFAC accession number namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the TRANSFAC database." [http://edamontology.org] is_a: EDAM_data:2911 ! Transcription factor accession [Term] id: EDAM_data:2716 name: DBD ID namespace: identifier subset: identifiers subset: data def: "Identifier of a predicted transcription factor from the DBD database." [http://edamontology.org] is_a: EDAM_data:2911 ! Transcription factor accession [Term] id: EDAM_data:2742 name: AraC-XylS ID namespace: identifier subset: identifiers subset: data def: "Identifier of a transcription factor from the AraC-XylS database." [http://edamontology.org] is_a: EDAM_data:2911 ! Transcription factor accession [Term] id: EDAM_data:2755 name: Transcription factor name namespace: identifier subset: identifiers subset: data def: "The name of a transcription factor." [http://edamontology.org] is_a: EDAM_data:1077 ! Transcription factor identifier is_a: EDAM_data:1009 ! Protein name [Term] id: EDAM_data:1144 name: ArrayExpress accession number namespace: identifier subset: identifiers subset: data def: "Accession number of an entry from the ArrayExpress database." [http://edamontology.org] synonym: "ArrayExpress experiment ID" EXACT [http://edamontology.org] regex: "[AEP]-[a-zA-Z_0-9]{4}-[0-9]+" is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] id: EDAM_data:1145 name: PRIDE experiment accession number namespace: identifier subset: identifiers subset: data def: "PRIDE experiment accession number." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] id: EDAM_data:2710 name: CleanEx dataset code namespace: identifier subset: identifiers subset: data def: "An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database." [http://edamontology.org] is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] id: EDAM_data:1146 name: EMDB ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the EMDB electron microscopy database." [http://edamontology.org] is_a: EDAM_data:1079 ! Electron microscopy model ID [Term] id: EDAM_data:1147 name: GEO accession number namespace: identifier subset: identifiers subset: data def: "Accession number of an entry from the GEO database." [http://edamontology.org] regex: "o^GDS[0-9]+" is_a: EDAM_data:1080 ! Gene expression report ID [Term] id: EDAM_data:1148 name: GermOnline ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the GermOnline database." [http://edamontology.org] is_a: EDAM_data:1080 ! Gene expression report ID [Term] id: EDAM_data:1149 name: EMAGE ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the EMAGE database." [http://edamontology.org] is_a: EDAM_data:1080 ! Gene expression report ID [Term] id: EDAM_data:2709 name: CleanEx entry name namespace: identifier subset: identifiers subset: data def: "An identifier of a gene expression profile from the CleanEx database." [http://edamontology.org] is_a: EDAM_data:1080 ! Gene expression report ID [Term] id: EDAM_data:1150 name: Disease ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from a database of disease." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:1622 ! Disease annotation [Term] id: EDAM_data:1151 name: HGVbase ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the HGVbase database." [http://edamontology.org] is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID [Term] id: EDAM_data:1152 name: HIVDB identifier namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the HIVDB database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:1153 name: OMIM ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the OMIM database." [http://edamontology.org] regex: "[*#+%^]?[0-9]{6}" is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID [Term] id: EDAM_data:2611 name: ICD identifier namespace: identifier subset: identifiers subset: data def: "An identifier of a disease from the International Classification of Diseases (ICD) database." [http://edamontology.org] regex: "[A-Z][0-9]+(\.[-[0-9]+])?" is_a: EDAM_data:1150 ! Disease ID relationship: is_identifier_of EDAM_data:1622 ! Disease annotation [Term] id: EDAM_data:2800 name: Orpha number namespace: identifier subset: identifiers subset: data def: "An identifier of a disease from the Orpha database." [http://edamontology.org] is_a: EDAM_data:1150 ! Disease ID relationship: is_identifier_of EDAM_data:1622 ! Disease annotation [Term] id: EDAM_data:2651 name: Disease ID (PharmGKB) namespace: identifier subset: identifiers subset: data def: "Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] regex: "PA[0-9]+" is_a: EDAM_data:1150 ! Disease ID is_a: EDAM_data:2649 ! PharmGKB ID [Term] id: EDAM_data:2383 name: EGA accession namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the EGA database." [http://edamontology.org] is_a: EDAM_data:2382 ! Genotype experiment ID [Term] id: EDAM_data:2342 name: Pathway or network name namespace: identifier subset: identifiers subset: data def: "The name of a biological pathway or network." [http://edamontology.org] is_a: EDAM_data:1082 ! Pathway or network identifier [Term] id: EDAM_data:2365 name: Pathway or network accession namespace: identifier subset: identifiers subset: data def: "A persistent, unique identifier of a biological pathway or network (typically a database entry)." [http://edamontology.org] is_a: EDAM_data:1082 ! Pathway or network identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2637 name: cPath ID namespace: identifier subset: identifiers subset: data def: "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database." [http://edamontology.org] comment: These identifiers are unique within the cPath database, however, they are not stable between releases. regex: "[0-9]+" is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2659 name: Pathway ID (SMPDB) namespace: identifier subset: identifiers subset: data def: "Identifier of a pathway from the Small Molecule Pathway Database (SMPDB)." [http://edamontology.org] regex: "SMP[0-9]{5}" is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2837 name: Pathway ID (BioSystems) namespace: identifier subset: identifiers subset: data def: "Identifier of a pathway from the BioSystems pathway database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2650 name: Pathway ID (PharmGKB) namespace: identifier subset: identifiers subset: data def: "Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] regex: "PA[0-9]+" is_a: EDAM_data:2365 ! Pathway or network accession is_a: EDAM_data:2649 ! PharmGKB ID [Term] id: EDAM_data:2345 name: Pathway ID (ConsensusPathDB) namespace: identifier subset: identifiers subset: data def: "Identifier of a pathway from the ConsensusPathDB pathway database." [http://edamontology.org] is_a: EDAM_data:2917 ! ConsensusPathDB identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2343 name: Pathway ID (KEGG) namespace: identifier subset: identifiers subset: data def: "Identifier of a pathway from the KEGG pathway database." [http://edamontology.org] synonym: "KEGG pathway ID" EXACT [http://edamontology.org] regex: "[a-zA-Z_0-9]{2,3}[0-9]{5}" is_a: EDAM_data:2365 ! Pathway or network accession is_a: EDAM_data:1154 ! KEGG object identifier [Term] id: EDAM_data:2344 name: Pathway ID (NCI-Nature) namespace: identifier subset: identifiers subset: data def: "Identifier of a pathway from the NCI-Nature pathway database." [http://edamontology.org] regex: "[a-zA-Z_0-9]+" is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1155 name: Pathway ID (reactome) namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the Reactome database." [http://edamontology.org] synonym: "Reactome ID" EXACT [http://edamontology.org] regex: "REACT_[0-9]+(\.[0-9]+)?" is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1156 name: Pathway ID (aMAZE) namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the aMAZE database." [http://edamontology.org] synonym: "aMAZE ID" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:1082 ! Pathway or network identifier [Term] id: EDAM_data:1157 name: Pathway ID (BioCyc) namespace: identifier subset: identifiers subset: data def: "Identifier of an pathway from the BioCyc biological pathways database." [http://edamontology.org] synonym: "BioCyc pathway ID" EXACT [http://edamontology.org] is_a: EDAM_data:2365 ! Pathway or network accession is_a: EDAM_data:2104 ! BioCyc ID [Term] id: EDAM_data:1158 name: Pathway ID (INOH) namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the INOH database." [http://edamontology.org] synonym: "INOH identifier" EXACT [http://edamontology.org] is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1159 name: Pathway ID (PATIKA) namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the PATIKA database." [http://edamontology.org] synonym: "PATIKA ID" EXACT [http://edamontology.org] is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1160 name: Pathway ID (CPDB) namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB." [http://edamontology.org] comment: This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. synonym: "CPDB ID" EXACT [http://edamontology.org] is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1161 name: Pathway ID (Panther) namespace: identifier subset: identifiers subset: data def: "Identifier of a biological pathway from the Panther Pathways database." [http://edamontology.org] synonym: "Panther Pathways ID" EXACT [http://edamontology.org] regex: "PTHR[0-9]{5}" is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2645 name: Pathway ID (Unipathway) namespace: identifier subset: identifiers subset: data def: "Identifier of a biological pathway from the Unipathway database." [http://edamontology.org] synonym: "upaid" EXACT [http://edamontology.org] regex: "UPA[0-9]{5}" is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2670 name: Pathway ID (DQCS) namespace: identifier subset: identifiers subset: data def: "Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS)." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2591 name: Brite hierarchy ID namespace: identifier subset: identifiers subset: data def: "Identifier of an entry from the Brite database of biological hierarchies." [http://edamontology.org] is_a: EDAM_data:2891 ! Biological model accession [Term] id: EDAM_data:1162 name: MIRIAM identifier namespace: identifier subset: identifiers subset: data def: "Unique identifier of a MIRIAM data resource." [http://edamontology.org] comment: This is the identifier used internally by MIRIAM for a data type. regex: "MIR:[0-9]{8}" example: "MIR:00100005" is_a: EDAM_data:2902 ! Data resource definition accession relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype [Term] id: EDAM_data:1163 name: MIRIAM data type name namespace: identifier subset: identifiers subset: data def: "The name of a data type from the MIRIAM database." [http://edamontology.org] is_a: EDAM_data:2253 ! Data resource definition name relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype [Term] id: EDAM_data:2253 name: Data resource definition name namespace: identifier subset: identifiers subset: data def: "The name of a data type." [http://edamontology.org] is_a: EDAM_data:1084 ! Data resource definition identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2902 name: Data resource definition accession namespace: identifier subset: identifiers subset: data def: "Accession of a data definition (catalogued in a database)." [http://edamontology.org] is_a: EDAM_data:1084 ! Data resource definition identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1164 name: MIRIAM URI namespace: identifier subset: identifiers subset: data def: "The URI (URL or URN) of a data entity from the MIRIAM database." [http://edamontology.org] comment: A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. example: "urn:miriam:pubmed:16333295" "urn:miriam:obo.go:GO%3A0045202" !{note="'urn:miriam:pubmed:16333295' is the MIRIAM URI of the publication about MIRIAM, whereas 'urn:miriam:obo.go:GO%3A0045202' refers to GO"} is_a: EDAM_data:2902 ! Data resource definition accession is_a: EDAM_data:1047 ! URI relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype [Term] id: EDAM_data:1165 name: MIRIAM data type primary name namespace: identifier subset: identifiers subset: data def: "The primary name of a data type from the MIRIAM database." [http://edamontology.org] comment: The primary name of a MIRIAM data type is taken from a controlled vocabulary. example: "UniProt" "Enzyme Nomenclature" !{note="A protein entity has the data type 'UniProt', an enzyme has the type 'Enzyme Nomenclature' etc."} is_a: EDAM_data:1163 ! MIRIAM data type name [Term] id: EDAM_data:1166 name: MIRIAM data type synonymous name namespace: identifier subset: identifiers subset: data def: "A synonymous name of a data type from the MIRIAM database." [http://edamontology.org] comment: A synonymous name for a MIRIAM data type taken from a controlled vocabulary. is_a: EDAM_data:1163 ! MIRIAM data type name [Term] id: EDAM_data:2106 name: Reaction ID (BioCyc) namespace: identifier subset: identifiers subset: data def: "Identifier of a biological reaction from the BioCyc reactions database." [http://edamontology.org] is_a: EDAM_data:2108 ! Reaction ID is_a: EDAM_data:2104 ! BioCyc ID relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids [Term] id: EDAM_data:2309 name: Reaction ID (SABIO-RK) namespace: identifier subset: identifiers subset: data def: "Identifier of a biological reaction from the SABIO-RK reactions database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2108 ! Reaction ID [Term] id: EDAM_data:2648 name: Reaction kinetics ID (SABIO-RK) namespace: identifier subset: identifiers subset: data def: "Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2309 ! Reaction ID (SABIO-RK) [Term] id: EDAM_data:2608 name: Reaction ID (KEGG) namespace: identifier subset: identifiers subset: data def: "Identifier of a biological reaction from the KEGG reactions database." [http://edamontology.org] regex: "R[0-9]+" is_a: EDAM_data:2108 ! Reaction ID is_a: EDAM_data:1154 ! KEGG object identifier [Term] id: EDAM_data:2641 name: Reaction ID (MACie) namespace: identifier subset: identifiers subset: data def: "Identifier of an enzyme reaction mechanism from the MACie database." [http://edamontology.org] synonym: "MACie entry number" EXACT [http://edamontology.org] regex: "M[0-9]{4}" is_a: EDAM_data:2108 ! Reaction ID [Term] id: EDAM_data:2644 name: Reaction ID (Rhea) namespace: identifier subset: identifiers subset: data def: "Identifier of an enzyme-catalysed reaction from the Rhea database." [http://edamontology.org] regex: "[0-9]{5}" is_a: EDAM_data:2108 ! Reaction ID [Term] id: EDAM_data:1167 name: Taverna workflow ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a Taverna workflow." [http://edamontology.org] is_a: EDAM_data:1083 ! Workflow ID [Term] id: EDAM_data:1170 name: Biological model name namespace: identifier subset: identifiers subset: data def: "Name of a biological (mathematical) model." [http://edamontology.org] is_a: EDAM_data:1085 ! Biological model identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1171 name: BioModel ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the BioModel database." [http://edamontology.org] regex: "(BIOMD|MODEL)[0-9]{10}" is_a: EDAM_data:2891 ! Biological model accession [Term] id: EDAM_data:2669 name: ModelDB ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of an entry from the ModelDB database." [http://edamontology.org] regex: "[0-9]+" is_a: EDAM_data:2891 ! Biological model accession [Term] id: EDAM_data:2339 name: Ontology concept name namespace: identifier subset: identifiers subset: data def: "The name of a concept in an ontology." [http://edamontology.org] is_a: EDAM_data:3025 ! Ontology concept identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1175 name: BioPax concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from the BioPax ontology." [http://edamontology.org] is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1176 name: GO concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from The Gene Ontology." [http://edamontology.org] synonym: "GO concept identifier" EXACT [http://edamontology.org] regex: "[0-9]{7}" "GO:[0-9]{7}" is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1177 name: MeSH concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from the MeSH vocabulary." [http://edamontology.org] is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1178 name: HGNC concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from the HGNC controlled vocabulary." [http://edamontology.org] is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1179 name: NCBI taxonomy ID namespace: identifier subset: identifiers subset: data def: "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." [http://edamontology.org] regex: "[1-9][0-9]{0,8}" example: "9662" "3483" "182682" synonym: "NCBI taxonomy identifier" EXACT [http://edamontology.org] synonym: "NCBI tax ID" EXACT [http://edamontology.org] is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1180 name: Plant Ontology concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from the Plant Ontology (PO)." [http://edamontology.org] is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1181 name: UMLS concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from the UMLS vocabulary." [http://edamontology.org] is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1182 name: FMA concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from Foundational Model of Anatomy." [http://edamontology.org] comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. regex: "FMA:[0-9]+" is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1183 name: EMAP concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from the EMAP mouse ontology." [http://edamontology.org] is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1184 name: ChEBI concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from the ChEBI ontology." [http://edamontology.org] is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1185 name: MGED concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from the MGED ontology." [http://edamontology.org] is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1186 name: myGrid concept ID namespace: identifier subset: identifiers subset: data def: "An identifier of a concept from the myGrid ontology." [http://edamontology.org] comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:2705 name: GO concept ID (cellular compartment) namespace: identifier subset: identifiers subset: data def: "An identifier of a 'cellular compartment' concept from the Gene Ontology." [http://edamontology.org] synonym: "GO concept identifier (cellular compartment)" EXACT [http://edamontology.org] regex: "[0-9]{7}" "GO:[0-9]{7}" is_a: EDAM_data:1176 ! GO concept ID [Term] id: EDAM_data:2582 name: GO concept ID (biological process) namespace: identifier subset: identifiers subset: data def: "An identifier of a 'biological process' concept from the the Gene Ontology." [http://edamontology.org] regex: "[0-9]{7}" "GO:[0-9]{7}" is_a: EDAM_data:1176 ! GO concept ID [Term] id: EDAM_data:2583 name: GO concept ID (molecular function) namespace: identifier subset: identifiers subset: data def: "An identifier of a 'molecular function' concept from the the Gene Ontology." [http://edamontology.org] regex: "[0-9]{7}" "GO:[0-9]{7}" is_a: EDAM_data:1176 ! GO concept ID [Term] id: EDAM_data:2581 name: GO concept name namespace: identifier subset: identifiers subset: data def: "The name of a concept from the GO ontology." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2339 ! Ontology concept name [Term] id: EDAM_data:3026 name: GO concept name (biological process) namespace: identifier subset: identifiers subset: data def: "The name of a concept for a biological process from the GO ontology." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2339 ! Ontology concept name [Term] id: EDAM_data:3027 name: GO concept name (molecular function) namespace: identifier subset: identifiers subset: data def: "The name of a concept for a molecular function from the GO ontology." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2339 ! Ontology concept name [Term] id: EDAM_data:2584 name: GO concept name (cellular component) namespace: identifier subset: identifiers subset: data def: "The name of a concept for a cellular component from the GO ontology." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2339 ! Ontology concept name ! Different biological types of signature are listed below. Bioinformatics types (motif, profile, HMM etc) are given elsewhere [Term] id: EDAM_data:1187 name: PubMed ID namespace: identifier subset: identifiers subset: data def: "PubMed unique identifier of an article." [http://edamontology.org] synonym: "PMID" EXACT [http://edamontology.org] regex: "[1-9][0-9]{0,8}" example: "4963447" is_a: EDAM_data:1088 ! Article ID [Term] id: EDAM_data:1188 name: Digital Object Identifier namespace: identifier subset: identifiers subset: data def: "Digital Object Identifier (DOI) of a published article." [http://edamontology.org] regex: "(doi\:)?[0-9]{2}\.[0-9]{4}/.*" is_a: EDAM_data:1088 ! Article ID [Term] id: EDAM_data:1189 name: Medline UI namespace: identifier subset: identifiers subset: data def: "Medline UI (unique identifier) of an article." [http://edamontology.org] comment: The use of Medline UI has been replaced by the PubMed unique identifier. synonym: "Medline unique identifier" EXACT [http://edamontology.org] is_a: EDAM_data:1088 ! Article ID [Term] id: EDAM_data:2634 name: ISBN namespace: identifier subset: identifiers subset: data def: "The International Standard Book Number (ISBN) is for identifying printed books." [http://edamontology.org] regex: "(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)" is_a: EDAM_data:2633 ! Book ID [Term] id: EDAM_data:2374 name: Spot serial number namespace: identifier subset: identifiers subset: data def: "Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database." [http://edamontology.org] is_a: EDAM_data:2373 ! Spot ID [Term] id: EDAM_data:2375 name: Spot ID (HSC-2DPAGE) namespace: identifier subset: identifiers subset: data def: "Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database." [http://edamontology.org] is_a: EDAM_data:2373 ! Spot ID [Term] id: EDAM_data:2588 name: BlotBase blot ID namespace: identifier subset: identifiers subset: data def: "Unique identifier of a blot from a Northern Blot from the BlotBase database." [http://edamontology.org] is_a: EDAM_data:2587 ! Blot ID [Term] id: EDAM_data:1046 name: Strain name namespace: identifier subset: identifiers subset: data def: "The name of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] is_a: EDAM_data:2909 ! Organism name is_a: EDAM_data:2379 ! Strain identifier [Term] id: EDAM_data:2778 name: CCAP strain number namespace: identifier subset: identifiers subset: data def: "The number of a strain of algae and protozoa from the CCAP database." [http://edamontology.org] is_a: EDAM_data:2912 ! Strain accession [Term] id: EDAM_data:2316 name: Cell line name namespace: identifier subset: identifiers subset: data def: "The name of a cell line." [http://edamontology.org] is_a: EDAM_data:1046 ! Strain name [Term] id: EDAM_data:2112 name: FlyBase primary identifier namespace: identifier subset: identifiers subset: data def: "Primary identifier of an object from the FlyBase database." [http://edamontology.org] is_a: EDAM_data:1089 ! FlyBase ID [Term] id: EDAM_data:2174 name: FlyBase secondary identifier namespace: identifier subset: identifiers subset: data def: "Secondary identifier of an object from the FlyBase database." [http://edamontology.org] comment: Secondary identifier are used to handle entries that were merged with or split from other entries in the database. is_a: EDAM_data:1089 ! FlyBase ID [Term] id: EDAM_data:1091 name: WormBase name namespace: identifier subset: identifiers subset: data def: "Name of an object from the WormBase database, usually a human-readable name." [http://edamontology.org] is_a: EDAM_data:2113 ! WormBase identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1092 name: WormBase class namespace: identifier subset: identifiers subset: data def: "Class of an object from the WormBase database." [http://edamontology.org] comment: A WormBase class describes the type of object such as 'sequence' or 'protein'. is_a: EDAM_data:2113 ! WormBase identifier [Term] id: EDAM_data:2254 name: OBO file format name namespace: identifier subset: identifiers subset: data def: "Name of an OBO file format such as OBO-XML, plain and so on." [http://edamontology.org] is_a: EDAM_data:2129 ! File format name ! ! Format ! [Term] id: EDAM_format:2350 name: Format (typed) namespace: format subset: formats def: "A broad class of format distinguished by the scientific nature of the data that is identified." [http://edamontology.org] comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. is_a: EDAM_format:1915 ! Format [Term] id: EDAM_format:2330 name: Textual format namespace: format subset: formats def: "Textual format." [http://edamontology.org] comment: Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or very precisely not plain-textual). synonym: "Tabular format" NARROW [http://edamontology.org, http://filext.com/file-extension/TSV] !{note="Many textual formats used in bioinformatics are tabular (tab-separated values, TSV)."} synonym: "Plain text" NARROW [http://edamontology.org] synonym: "TXT" NARROW [http://filext.com/file-extension/TXT] synonym: "Text File" NARROW [http://filext.com/file-extension/TXT] synonym: "TSV" NARROW [http://filext.com/file-extension/TSV] synonym: "Tab-Separated Values" NARROW [http://filext.com/file-extension/TSV] is_a: EDAM_format:1915 ! Format [Term] id: EDAM_format:2331 name: HTML namespace: format subset: formats def: "HTML format." [http://edamontology.org] synonym: "Hypertext Markup Language" EXACT [http://edamontology.org, http://filext.com/file-extension/HTML] synonym: "HTML" EXACT [http://filext.com/file-extension/HTML] !{note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."} synonym: "HTM" EXACT [http://filext.com/file-extension/HTM] !{note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."} is_a: EDAM_format:1915 ! Format relationship: is_format_of EDAM_data:2048 ! Report [Term] id: EDAM_format:2332 name: XML namespace: format subset: formats def: "eXtensible Markup Language (XML) format." [http://edamontology.org] comment: Data in XML format can be serialised into text, or binary format. synonym: "Extensible Markup Language" EXACT [http://edamontology.org, http://filext.com/file-extension/XML] synonym: "XML" EXACT [http://filext.com/file-extension/XML] !{note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."} is_a: EDAM_format:1915 ! Format [Term] id: EDAM_format:2333 name: Binary format namespace: format subset: formats def: "Binary format." [http://edamontology.org] comment: Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. is_a: EDAM_format:1915 ! Format [Term] id: EDAM_format:2376 name: RDF namespace: format subset: formats def: "Resource Description Framework (RDF) format." [http://edamontology.org] comment: Data in RDF format can be serialised into XML, textual, or binary format. is_a: EDAM_format:1915 ! Format [Term] id: EDAM_format:2921 name: Sequence variation annotation format namespace: format subset: formats def: "Format of sequence variation annotation." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0918 ! Nucleic acid features (variation) [Term] id: EDAM_format:2919 name: Sequence annotation track format namespace: format subset: formats def: "Format of a sequence annotation track." [http://edamontology.org] is_a: EDAM_format:1920 ! Sequence feature annotation format relationship: is_format_of EDAM_data:3002 ! Sequence annotation track [Term] id: EDAM_format:2352 name: BioXSD namespace: format subset: formats def: "BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more)." [http://edamontology.org] synonym: "BioXSD XML format" EXACT [http://edamontology.org] xref: http://bioxsd.org !{documentation=true} is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:1919 ! Sequence record format is_a: EDAM_format:1920 ! Sequence feature annotation format is_a: EDAM_format:2555 ! Alignment format (XML) is_a: EDAM_format:2332 ! XML relationship: is_format_of EDAM_data:2044 ! Sequence relationship: is_format_of EDAM_data:1255 ! Feature record relationship: is_format_of EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_format:2848 name: Bibliographic reference format namespace: format subset: formats def: "Format of a bibliographic reference." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0970 ! Bibliographic reference relationship: is_format_of EDAM_data:2849 ! Abstract [Term] id: EDAM_format:2334 name: URI format namespace: format subset: formats def: "Typical textual representation of a URI." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:1047 ! URI [Term] id: EDAM_format:1918 name: Atomic data format namespace: format subset: formats def: "Data format for an individual atom." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_format:1475 ! PDB database entry format [Term] id: EDAM_format:1919 name: Sequence record format namespace: format subset: formats def: "Data format for a molecular sequence record." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_format:1920 name: Sequence feature annotation format namespace: format subset: formats def: "Data format for molecular sequence feature information." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1255 ! Feature record [Term] id: EDAM_format:1921 name: Alignment format namespace: format subset: formats def: "Data format for molecular sequence alignment information." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_format:2920 name: Alignment format (pair only) namespace: format subset: formats def: "Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences." [http://edamontology.org] is_a: EDAM_format:1921 ! Alignment format relationship: is_format_of EDAM_data:1381 ! Sequence alignment (pair) [Term] id: EDAM_format:2006 name: Phylogenetic tree format namespace: format subset: formats def: "Data format for a phylogenetic tree." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0872 ! Phylogenetic tree [Term] id: EDAM_format:2033 name: Tertiary structure format namespace: format subset: formats def: "Data format for a molecular tertiary structure." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:3167 name: Experiment annotation format namespace: format subset: formats def: "Data format for annotation on a laboratory experiment." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:2034 name: Biological model format namespace: format subset: formats def: "Data format for a biological model." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0950 ! Biological model [Term] id: EDAM_format:2014 name: Sequence-profile alignment format namespace: format subset: formats def: "Data format for a sequence-profile alignment." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_format:2562 name: Amino acid identifier format namespace: format subset: formats def: "Text format (representation) of amino acid residues." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_data:0994 ! Amino acid identifier [Term] id: EDAM_format:2017 name: Amino acid index format namespace: format subset: formats def: "Data format for an amino acid index." [http://edamontology.org] is_a: EDAM_format:3033 ! Matrix format relationship: is_format_of EDAM_data:1501 ! Amino acid index [Term] id: EDAM_format:2020 name: Article format namespace: format subset: formats def: "Data format for a full-text scientific article." [http://edamontology.org] synonym: "Literature format" EXACT [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0971 ! Article [Term] id: EDAM_format:2021 name: Text mining report format namespace: format subset: formats def: "Data format for an abstract (report) from text mining." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0972 ! Text mining report [Term] id: EDAM_format:2027 name: Enzyme kinetics report format namespace: format subset: formats def: "Data format for reports on enzyme kinetics." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_format:2030 name: Small molecule report format namespace: format subset: formats def: "Format of a report on a chemical compound." [http://edamontology.org] synonym: "Chemical compound annotation format" EXACT [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_format:2031 name: Gene annotation format namespace: format subset: formats def: "Format of a report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0916 ! Gene annotation [Term] id: EDAM_format:2032 name: Workflow format namespace: format subset: formats def: "Format of a workflow." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2972 ! Workflow [Term] id: EDAM_format:2035 name: Chemical formula format namespace: format subset: formats def: "Text format of a chemical formula." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0846 ! Chemical formula [Term] id: EDAM_format:2036 name: Phylogenetic character data format namespace: format subset: formats def: "Format of raw (unplotted) phylogenetic data." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0871 ! Phylogenetic character data [Term] id: EDAM_format:3097 !{since=beta13} name: Protein domain classification format namespace: format subset: formats def: "Format of data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_format:3098 !{since=beta13} name: Raw SCOP domain classification format namespace: format subset: formats def: "Format of raw SCOP domain classification data files." [http://edamontology.org] comment: These are the parsable data files provided by SCOP. is_a: EDAM_format:3097 ! Protein domain classification format [Term] id: EDAM_format:3099 !{since=beta13} name: Raw CATH domain classification format namespace: format subset: formats def: "Format of raw CATH domain classification data files." [http://edamontology.org] comment: These are the parsable data files provided by CATH. is_a: EDAM_format:3097 ! Protein domain classification format [Term] id: EDAM_format:3100 !{since=beta13} name: CATH domain report format namespace: format subset: formats def: "Format of summary of domain classification information for a CATH domain." [http://edamontology.org] comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. is_a: EDAM_format:3097 ! Protein domain classification format [Term] id: EDAM_format:2045 name: Electron microscopy model format namespace: format subset: formats def: "Annotation format for electron microscopy models." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:2049 name: Phylogenetic tree report (tree distances) format namespace: format subset: formats def: "Format for phylogenetic tree distance data." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1442 ! Phylogenetic tree report (tree distances) [Term] id: EDAM_format:2051 name: Polymorphism report format namespace: format subset: formats def: "Format for sequence polymorphism data." [http://edamontology.org] is_obsolete: true !{since=1.0} ! is_a: EDAM_format:2350 ! Format (typed) ! relationship: is_format_of EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_format:2052 name: Protein family report format namespace: format subset: formats def: "Format for reports on a protein family." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0907 ! Protein family [Term] id: EDAM_format:2054 name: Protein interaction format namespace: format subset: formats def: "Format for protein interaction data." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0906 ! Protein interaction [Term] id: EDAM_format:2055 name: Sequence assembly format namespace: format subset: formats def: "Format for sequence assembly data." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0925 ! Sequence assembly [Term] id: EDAM_format:2056 name: Microarray experiment data format namespace: format subset: formats def: "Format for microarray experimental data." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_format:2058 name: Gene expression report format namespace: format subset: formats def: "Format for a report on gene expression." [http://edamontology.org] is_a: EDAM_format:2031 ! Gene annotation format relationship: is_format_of EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_format:2059 name: Genotype and phenotype annotation format namespace: format subset: formats def: "Format of a report on genotype / phenotype information." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0920 ! Genotype/phenotype annotation [Term] id: EDAM_format:2060 name: Map format namespace: format subset: formats def: "Format of a map of (typically one) molecular sequence annotated with features." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1274 ! Map [Term] id: EDAM_format:2061 name: Nucleic acid features (primers) format namespace: format subset: formats def: "Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0922 ! Nucleic acid features (primers) [Term] id: EDAM_format:2062 name: Protein report format namespace: format subset: formats def: "Format of a report of general information about a specific protein." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0896 ! Protein report [Term] id: EDAM_format:3033 !{since=beta13} name: Matrix format namespace: format subset: formats def: "Format of a matrix (array) of numerical values." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2082 ! Matrix [Term] id: EDAM_format:2064 name: 3D-1D scoring matrix format namespace: format subset: formats def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [http://edamontology.org] is_a: EDAM_format:3033 ! Matrix format relationship: is_format_of EDAM_data:1499 ! 3D-1D scoring matrix [Term] id: EDAM_format:2065 name: Protein structure report (quality evaluation) format namespace: format subset: formats def: "Format of a report on the quality of a protein three-dimensional model." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1539 ! Protein structural quality report [Term] id: EDAM_format:2066 name: Database hits (sequence) format namespace: format subset: formats def: "Format of a report on sequence hits and associated data from searching a sequence database." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0857 ! Database hits (sequence) [Term] id: EDAM_format:2067 name: Sequence distance matrix format namespace: format subset: formats def: "Format of a matrix of genetic distances between molecular sequences." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0870 ! Sequence distance matrix [Term] id: EDAM_format:2068 name: Sequence motif format namespace: format subset: formats def: "Format of a sequence motif." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1353 ! Sequence motif [Term] id: EDAM_format:2069 name: Sequence profile format namespace: format subset: formats def: "Format of a sequence profile." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1354 ! Sequence profile [Term] id: EDAM_format:2074 name: Dirichlet distribution format namespace: format subset: formats def: "Data format of a dirichlet distribution." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1347 ! Dirichlet distribution [Term] id: EDAM_format:2075 name: HMM emission and transition counts format namespace: format subset: formats def: "Data format for the emission and transition counts of a hidden Markov model." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1348 ! HMM emission and transition counts [Term] id: EDAM_format:2077 name: Protein secondary structure format namespace: format subset: formats def: "Format for secondary structure (predicted or real) of a protein molecule." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0876 ! Protein features (secondary structure) [Term] id: EDAM_format:2076 name: RNA secondary structure format namespace: format subset: formats def: "Format for secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0880 ! RNA secondary structure record [Term] id: EDAM_format:2078 name: Sequence range format namespace: format subset: formats def: "Format used to specify range(s) of sequence positions." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1017 ! Sequence range [Term] id: EDAM_format:2155 name: Sequence features (repeats) format namespace: format subset: formats def: "Format used for map of repeats in molecular (typically nucleotide) sequences." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1299 ! Sequence features (repeats) [Term] id: EDAM_format:2158 name: Nucleic acid features (restriction sites) format namespace: format subset: formats def: "Format used for report on restriction enzyme recognition sites in nucleotide sequences." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1305 ! Nucleic acid features (restriction sites) [Term] id: EDAM_format:2159 name: Gene features (coding region) format namespace: format subset: formats def: "Format used for report on coding regions in nucleotide sequences." [http://edamontology.org] is_a: EDAM_format:2031 ! Gene annotation format relationship: is_format_of EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] id: EDAM_format:2170 name: Sequence cluster format namespace: format subset: formats def: "Format used for clusters of molecular sequences." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_format:2195 name: Ontology format namespace: format subset: formats def: "Format used for ontologies." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0582 ! Ontology [Term] id: EDAM_format:2210 name: Strain data format namespace: format subset: formats def: "Format of a report on organism strain data / cell line." [http://edamontology.org] is_obsolete: true !{since=1.0} ! is_a: EDAM_format:2350 ! Format (typed) ! relationship: is_format_of EDAM_data:0963 ! Cell line annotation [Term] id: EDAM_format:2542 name: Protein features (domains) format namespace: format subset: formats def: "Format of a report on protein features (domain composition)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:2571 name: Raw sequence format namespace: format subset: formats def: "Format of a raw molecular sequence (i.e. the alphabet used)." [http://edamontology.org] synonym: "Symbol sequence" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0848 ! Raw sequence [Term] id: EDAM_format:1734 name: PubMed citation namespace: format subset: formats def: "Format of bibliographic reference as used by the PubMed database." [http://edamontology.org] is_a: EDAM_format:2848 ! Bibliographic reference format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1735 name: Medline Display Format namespace: format subset: formats def: "Format for abstracts of scientific articles from the Medline database." [http://edamontology.org] comment: Bibliographic reference information including citation information is included xref: Moby:PubMed-MEDLINE is_a: EDAM_format:2848 ! Bibliographic reference format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1736 name: CiteXplore-core namespace: format subset: formats def: "CiteXplore 'core' citation format including title, journal, authors and abstract." [http://edamontology.org] is_a: EDAM_format:2848 ! Bibliographic reference format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1737 name: CiteXplore-all namespace: format subset: formats def: "CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references." [http://edamontology.org] is_a: EDAM_format:2848 ! Bibliographic reference format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1747 name: PDB atom record format namespace: format subset: formats def: "Format of an ATOM record (describing data for an individual atom) from a PDB file." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_format:1476 ! PDB format [Term] id: EDAM_format:2551 name: Sequence record format (text) namespace: format subset: formats def: "Data format for a molecular sequence record." [http://edamontology.org] is_a: EDAM_format:1919 ! Sequence record format [Term] id: EDAM_format:2552 name: Sequence record format (XML) namespace: format subset: formats def: "Data format for a molecular sequence record." [http://edamontology.org] is_a: EDAM_format:1919 ! Sequence record format [Term] id: EDAM_format:2203 name: Sequence record lite format namespace: format subset: formats def: "Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment." [http://edamontology.org] is_a: EDAM_format:1919 ! Sequence record format relationship: is_format_of EDAM_data:2043 ! Sequence record lite [Term] id: EDAM_format:2202 name: Sequence record full format namespace: format subset: formats def: "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] is_a: EDAM_format:1919 ! Sequence record format relationship: is_format_of EDAM_data:2201 ! Sequence record full [Term] id: EDAM_format:2057 name: Sequence trace format namespace: format subset: formats def: "Format for sequence trace data (i.e. including base call information)." [http://edamontology.org] is_a: EDAM_format:1919 ! Sequence record format relationship: is_format_of EDAM_data:0924 ! Sequence trace [Term] id: EDAM_format:1923 name: acedb namespace: format subset: formats def: "ACEDB sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1924 name: clustal sequence format namespace: format subset: formats def: "Clustalw output format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1982 ! clustal [Term] id: EDAM_format:1925 name: codata namespace: format subset: formats def: "Codata entry format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1928 name: experiment namespace: format subset: formats def: "Staden experiment file format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1934 name: fitch namespace: format subset: formats def: "Fitch program format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1935 name: gcg namespace: format subset: formats def: "GCG sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1938 name: GFF2-seq namespace: format subset: formats def: "GFF feature file format with sequence in the header." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:1974 ! GFF2 [Term] id: EDAM_format:1939 name: GFF3-seq namespace: format subset: formats def: "GFF3 feature file format with sequence." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:1975 ! GFF3 [Term] id: EDAM_format:1941 name: hennig86 namespace: format subset: formats def: "Hennig86 output sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1942 name: ig namespace: format subset: formats def: "Intelligenetics sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1943 name: igstrict namespace: format subset: formats def: "Intelligenetics sequence format (strict version)." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1944 name: jackknifer namespace: format subset: formats def: "Jackknifer interleaved and non-interleaved sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1945 name: mase namespace: format subset: formats def: "Mase program sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1946 name: mega-seq namespace: format subset: formats def: "Mega interleaved and non-interleaved sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1947 name: msf namespace: format subset: formats def: "GCG MSF (multiple sequence file) file format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1949 name: nexus-seq namespace: format subset: formats def: "Nexus/paup interleaved sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1950 name: pdbatom namespace: format subset: formats def: "PDB sequence format (ATOM lines)." [http://edamontology.org] comment: pdb format in EMBOSS. is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1951 name: pdbatomnuc namespace: format subset: formats def: "PDB nucleotide sequence format (ATOM lines)." [http://edamontology.org] comment: pdbnuc format in EMBOSS. is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1952 name: pdbseqresnuc namespace: format subset: formats def: "PDB nucleotide sequence format (SEQRES lines)." [http://edamontology.org] comment: pdbnucseq format in EMBOSS. is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1953 name: pdbseqres namespace: format subset: formats def: "PDB sequence format (SEQRES lines)." [http://edamontology.org] comment: pdbseq format in EMBOSS. is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1955 name: phylip sequence format namespace: format subset: formats def: "Phylip interleaved sequence format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1997 ! phylip [Term] id: EDAM_format:1956 name: phylipnon sequence format namespace: format subset: formats def: "Phylip non-interleaved sequence format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1998 ! phylipnon [Term] id: EDAM_format:1957 name: raw namespace: format subset: formats def: "Raw sequence format with no non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2330 ! Textual format ! For now, identical to genpept [Term] id: EDAM_format:1958 name: refseqp namespace: format subset: formats def: "Refseq protein entry sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1959 name: selex sequence format namespace: format subset: formats def: "Selex sequence format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2000 ! selex [Term] id: EDAM_format:1960 name: Staden format namespace: format subset: formats def: "Staden suite sequence format." [http://edamontology.org] xref: http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html !{documentation=true} xref: http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden !{documentation=true} is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1961 name: stockholm namespace: format subset: formats def: "Stockholm multiple sequence alignment format (used by Pfam and Rfam)." [http://edamontology.org] xref: http://en.wikipedia.org/wiki/Stockholm_format !{documentation=true} is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1962 name: strider namespace: format subset: formats def: "DNA strider output sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1964 name: text namespace: format subset: formats def: "Plain text sequence format (essentially unformatted)." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1965 name: treecon sequence format namespace: format subset: formats def: "Treecon output sequence format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2005 ! treecon-seq [Term] id: EDAM_format:1966 name: asn1 sequence format namespace: format subset: formats def: "NCBI ASN.1 sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1969 name: debug-seq namespace: format subset: formats def: "EMBOSS debugging trace sequence format of full internal data content." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1970 name: jackknifernon namespace: format subset: formats def: "Jackknifer output sequence non-interleaved format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1971 name: meganon sequence format namespace: format subset: formats def: "Mega non-interleaved output sequence format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1992 ! meganon [Term] id: EDAM_format:1973 name: nexusnon namespace: format subset: formats def: "Nexus/paup non-interleaved sequence format." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1967 name: das namespace: format subset: formats def: "DAS sequence (XML) format (any type)." [http://edamontology.org] synonym: "das sequence format" EXACT [http://edamontology.org] is_a: EDAM_format:2552 ! Sequence record format (XML) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1968 name: dasdna namespace: format subset: formats def: "DAS sequence (XML) format (nucleotide-only)." [http://edamontology.org] comment: The use of this format is deprecated. is_a: EDAM_format:2552 ! Sequence record format (XML) is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2546 name: FASTA-like namespace: format subset: formats def: "A format resembling FASTA format." [http://edamontology.org] comment: This concept may be used for the many non-standard FASTA-like formats. is_a: EDAM_format:2203 ! Sequence record lite format [Term] id: EDAM_format:2200 ! This is the one used for annotation in eSysbio name: FASTA-like (text) namespace: format subset: formats def: "A text format resembling FASTA format." [http://edamontology.org] comment: This concept may also be used for the many non-standard FASTA-like formats. synonym: "DNA and Protein Sequence Alignment" NARROW [http://filext.com/file-extension/FASTA] is_a: EDAM_format:2546 ! FASTA-like is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2310 name: FASTA-HTML namespace: format subset: formats def: "FASTA format wrapped in HTML elements." [http://edamontology.org] is_a: EDAM_format:2546 ! FASTA-like is_a: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1929 name: FASTA format namespace: format subset: formats def: "FASTA format including NCBI-style IDs." [http://edamontology.org] ! Is it different from 1972? synonym: "FASTA" EXACT [http://edamontology.org] synonym: "FASTA sequence format" EXACT [http://edamontology.org] is_a: EDAM_format:2200 ! FASTA-like (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1926 name: dbid namespace: format subset: formats def: "Fasta format variant with database name before ID." [http://edamontology.org] is_a: EDAM_format:2200 ! FASTA-like (text) [Term] id: EDAM_format:1940 name: giFASTA format namespace: format subset: formats def: "FASTA sequence format including NCBI-style GIs." [http://edamontology.org] is_a: EDAM_format:2200 ! FASTA-like (text) [Term] id: EDAM_format:1954 name: Pearson format namespace: format subset: formats def: "Plain old FASTA sequence format (unspecified format for IDs)." [http://edamontology.org] is_a: EDAM_format:2200 ! FASTA-like (text) [Term] id: EDAM_format:1972 name: NCBI format namespace: format subset: formats def: "NCBI FASTA sequence format with NCBI-style IDs." [http://edamontology.org] comment: There are several variants of this. is_a: EDAM_format:2200 ! FASTA-like (text) [Term] id: EDAM_format:2543 name: EMBL-like format namespace: format subset: formats def: "A format resembling EMBL entry (plain text) format." [http://edamontology.org] comment: This concept may be used for the many non-standard EMBL-like formats. is_a: EDAM_format:2202 ! Sequence record full format [Term] id: EDAM_format:2559 name: GenBank-like format namespace: format subset: formats def: "A format resembling GenBank entry (plain text) format." [http://edamontology.org] comment: This concept may be used for the non-standard GenBank-like formats. is_a: EDAM_format:2202 ! Sequence record full format [Term] id: EDAM_format:2547 name: uniprotkb-like format namespace: format subset: formats def: "A sequence format resembling uniprotkb entry format." [http://edamontology.org] is_a: EDAM_format:2202 ! Sequence record full format is_a: EDAM_format:2206 ! Sequence feature table format (text) [Term] id: EDAM_format:1948 name: nbrf namespace: format subset: formats def: "NBRF/PIR entry sequence format." [http://edamontology.org] is_a: EDAM_format:2202 ! Sequence record full format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2181 name: EMBL-like (text) namespace: format subset: formats def: "A text format resembling EMBL entry format." [http://edamontology.org] comment: This concept may be used for the many non-standard EMBL-like text formats. is_a: EDAM_format:2543 ! EMBL-like format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2558 name: EMBL-like (XML) namespace: format subset: formats def: "An XML format resembling EMBL entry format." [http://edamontology.org] comment: This concept may be used for the any non-standard EMBL-like XML formats. is_a: EDAM_format:2543 ! EMBL-like format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2311 name: EMBL-HTML namespace: format subset: formats def: "EMBL entry format wrapped in HTML elements." [http://edamontology.org] is_a: EDAM_format:2543 ! EMBL-like format is_a: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1927 name: EMBL format namespace: format subset: formats def: "EMBL entry format." [http://edamontology.org] synonym: "EMBL sequence format" EXACT [http://edamontology.org] synonym: "EMBL" EXACT [http://edamontology.org] is_a: EDAM_format:2181 ! EMBL-like (text) is_a: EDAM_format:2206 ! Sequence feature table format (text) [Term] id: EDAM_format:2186 name: geneseq namespace: format subset: formats def: "Geneseq sequence format." [http://edamontology.org] is_a: EDAM_format:2181 ! EMBL-like (text) [Term] id: EDAM_format:2204 name: EMBL format (XML) namespace: format subset: formats def: "An XML format for EMBL entries." [http://edamontology.org] comment: This is a placeholder for other more specific concepts. It should not normally be used for annotation. is_a: EDAM_format:2558 ! EMBL-like (XML) [Term] id: EDAM_format:2183 name: EMBLXML namespace: format subset: formats def: "XML format for EMBL entries." [http://edamontology.org] is_a: EDAM_format:2204 ! EMBL format (XML) [Term] id: EDAM_format:2184 name: cdsxml namespace: format subset: formats def: "XML format for EMBL entries." [http://edamontology.org] is_a: EDAM_format:2204 ! EMBL format (XML) [Term] id: EDAM_format:2185 name: insdxml namespace: format subset: formats def: "XML format for EMBL entries." [http://edamontology.org] is_a: EDAM_format:2204 ! EMBL format (XML) [Term] id: EDAM_format:2205 name: GenBank-like format (text) namespace: format subset: formats def: "A text format resembling GenBank entry (plain text) format." [http://edamontology.org] comment: This concept may be used for the non-standard GenBank-like text formats. is_a: EDAM_format:2559 ! GenBank-like format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2532 name: GenBank-HTML namespace: format subset: formats def: "Genbank entry format wrapped in HTML elements." [http://edamontology.org] is_a: EDAM_format:2559 ! GenBank-like format is_a: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1936 name: GenBank format namespace: format subset: formats def: "Genbank entry format." [http://edamontology.org] is_a: EDAM_format:2205 ! GenBank-like format (text) is_a: EDAM_format:2206 ! Sequence feature table format (text) ! For now, identical to refseqp [Term] id: EDAM_format:1937 name: genpept namespace: format subset: formats def: "Genpept protein entry format." [http://edamontology.org] is_a: EDAM_format:2205 ! GenBank-like format (text) [Term] id: EDAM_format:2187 name: uniprotkb-like (text) namespace: format subset: formats def: "A text sequence format resembling uniprotkb entry format." [http://edamontology.org] is_a: EDAM_format:2547 ! uniprotkb-like format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1963 name: Swiss-Prot format namespace: format subset: formats def: "Swiss-Prot entry sequence format." [http://edamontology.org] is_a: EDAM_format:2187 ! uniprotkb-like (text) [Term] id: EDAM_format:2188 name: uniprot namespace: format subset: formats def: "UniProt entry sequence format." [http://edamontology.org] is_a: EDAM_format:2187 ! uniprotkb-like (text) [Term] id: EDAM_format:2189 name: ipi namespace: format subset: formats def: "ipi sequence format." [http://edamontology.org] is_a: EDAM_format:2187 ! uniprotkb-like (text) [Term] id: EDAM_format:1628 name: ABI namespace: format subset: formats def: "A format of raw sequence read data from an Applied Biosystems sequencing machine." [http://edamontology.org] is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:1629 name: mira namespace: format subset: formats def: "Format of MIRA sequence trace information file." [http://edamontology.org] is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2545 name: FASTQ-like format namespace: format subset: formats def: "A format resembling FASTQ short read format." [http://edamontology.org] comment: This concept may be used for non-standard FASTQ short read-like formats. is_a: EDAM_format:2057 ! Sequence trace format [Term] id: EDAM_format:2572 name: BAM namespace: format subset: formats def: "BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [http://edamontology.org] xref: http://samtools.sourceforge.net/SAM-1.3.pdf !{documentation=true} is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:1921 ! Alignment format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:2573 name: SAM namespace: format subset: formats def: "Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [http://edamontology.org] comment: The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. xref: http://samtools.sourceforge.net/SAM-1.3.pdf !{documentation=true} is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2920 ! Alignment format (pair only) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2182 name: FASTQ-like format (text) namespace: format subset: formats def: "A text format resembling FASTQ short read format." [http://edamontology.org] comment: This concept may be used for non-standard FASTQ short read-like formats. is_a: EDAM_format:2545 ! FASTQ-like format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1930 name: FASTQ namespace: format subset: formats def: "FASTQ short read format ignoring quality scores." [http://edamontology.org] is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1931 name: FASTQ-illumina namespace: format subset: formats def: "FASTQ Illumina 1.3 short read format." [http://edamontology.org] is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1932 name: FASTQ-sanger namespace: format subset: formats def: "FASTQ short read format with phred quality." [http://edamontology.org] is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1933 name: FASTQ-solexa namespace: format subset: formats def: "FASTQ Solexa/Illumina 1.0 short read format." [http://edamontology.org] is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:2548 name: Sequence feature table format namespace: format subset: formats def: "Format for a sequence feature table." [http://edamontology.org] is_a: EDAM_format:1920 ! Sequence feature annotation format relationship: is_format_of EDAM_data:1255 ! Feature record [Term] id: EDAM_format:1979 name: debug-feat namespace: format subset: formats def: "EMBOSS debugging trace feature format of full internal data content." [http://edamontology.org] is_a: EDAM_format:1920 ! Sequence feature annotation format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2206 name: Sequence feature table format (text) namespace: format subset: formats def: "Text format for a sequence feature table." [http://edamontology.org] is_a: EDAM_format:2548 ! Sequence feature table format [Term] id: EDAM_format:2553 name: Sequence feature table format (XML) namespace: format subset: formats def: "XML format for a sequence feature table." [http://edamontology.org] is_a: EDAM_format:2548 ! Sequence feature table format [Term] id: EDAM_format:2305 name: GFF namespace: format subset: formats def: "GFF feature format (of indeterminate version)." [http://edamontology.org] is_a: EDAM_format:2206 ! Sequence feature table format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1976 name: pir namespace: format subset: formats def: "PIR feature format." [http://edamontology.org] is_a: EDAM_format:2206 ! Sequence feature table format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1977 name: swiss feature namespace: format subset: formats def: "Swiss-Prot feature format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1963 ! Swiss-Prot format [Term] id: EDAM_format:1980 name: EMBL feature namespace: format subset: formats def: "EMBL feature format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1927 ! EMBL format [Term] id: EDAM_format:1981 name: GenBank feature namespace: format subset: formats def: "Genbank feature format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1936 ! GenBank format [Term] id: EDAM_format:1974 name: GFF2 namespace: format subset: formats def: "General Feature Format (GFF) of sequence features." [http://edamontology.org] xref: http://www.sanger.ac.uk/resources/software/gff/spec.html !{documentation=true} is_a: EDAM_format:2305 ! GFF [Term] id: EDAM_format:1975 name: GFF3 namespace: format subset: formats def: "Generic Feature Format version 3 (GFF3) of sequence features." [http://edamontology.org] xref: http://sequenceontology.org/resources/gff3.html !{documentation=true} is_a: EDAM_format:2305 ! GFF [Term] id: EDAM_format:2306 name: GTF namespace: format subset: formats def: "Gene Transfer Format (GTF), a restricted version of GFF." [http://edamontology.org] xref: http://mblab.wustl.edu/GTF22.html !{documentation=true} xref: http://genome.ucsc.edu/FAQ/FAQformat#format4 !{documentation=true} is_a: EDAM_format:2305 ! GFF [Term] id: EDAM_format:1978 name: DASGFF namespace: format subset: formats def: "DAS GFF (XML) feature format." [http://edamontology.org] synonym: "DASGFF feature" EXACT [http://edamontology.org] synonym: "das feature" EXACT [http://edamontology.org] is_a: EDAM_format:2553 ! Sequence feature table format (XML) is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2554 name: Alignment format (text) namespace: format subset: formats def: "Text format for molecular sequence alignment information." [http://edamontology.org] is_a: EDAM_format:1921 ! Alignment format [Term] id: EDAM_format:2555 name: Alignment format (XML) namespace: format subset: formats def: "XML format for molecular sequence alignment information." [http://edamontology.org] is_a: EDAM_format:1921 ! Alignment format [Term] id: EDAM_format:1982 name: clustal namespace: format subset: formats def: "Clustalw format for (aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1983 name: debug namespace: format subset: formats def: "EMBOSS alignment format for debugging trace of full internal data content." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1984 name: FASTA-aln namespace: format subset: formats def: "Fasta format for (aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2200 ! FASTA-like (text) [Term] id: EDAM_format:2922 name: markx0 variant namespace: format subset: formats def: "Some variant of Pearson MARKX alignment format." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1985 name: markx0 namespace: format subset: formats def: "Pearson MARKX0 alignment format." [http://edamontology.org] is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1986 name: markx1 namespace: format subset: formats def: "Pearson MARKX1 alignment format." [http://edamontology.org] is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1987 name: markx10 namespace: format subset: formats def: "Pearson MARKX10 alignment format." [http://edamontology.org] is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1988 name: markx2 namespace: format subset: formats def: "Pearson MARKX2 alignment format." [http://edamontology.org] is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1989 name: markx3 namespace: format subset: formats def: "Pearson MARKX3 alignment format." [http://edamontology.org] is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1990 name: match namespace: format subset: formats def: "Alignment format for start and end of matches between sequence pairs." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2923 name: mega variant namespace: format subset: formats def: "Some variant of Mega format for (typically aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1991 name: mega namespace: format subset: formats def: "Mega format for (typically aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2923 ! mega variant [Term] id: EDAM_format:1992 name: meganon namespace: format subset: formats def: "Mega non-interleaved format for (typically aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2923 ! mega variant [Term] id: EDAM_format:1993 name: msf alignment format namespace: format subset: formats def: "MSF format for (aligned) sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1947 ! msf [Term] id: EDAM_format:1994 name: nexus alignment format namespace: format subset: formats def: "Nexus/paup format for (aligned) sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1949 ! nexus-seq [Term] id: EDAM_format:1995 name: nexusnon alignment format namespace: format subset: formats def: "Nexus/paup non-interleaved format for (aligned) sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:1973 ! nexusnon [Term] id: EDAM_format:1996 name: pair namespace: format subset: formats def: "EMBOSS simple sequence pair alignment format." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:2924 name: phylip variant namespace: format subset: formats def: "Some variant of Phylip format for (aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1997 name: phylip namespace: format subset: formats def: "Phylip format for (aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2924 ! phylip variant [Term] id: EDAM_format:1998 name: phylipnon namespace: format subset: formats def: "Phylip non-interleaved format for (aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2924 ! phylip variant [Term] id: EDAM_format:1999 name: score namespace: format subset: formats def: "Alignment format for score values for pairs of sequences." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2000 name: selex namespace: format subset: formats def: "SELEX format for (aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2001 name: simple namespace: format subset: formats def: "EMBOSS simple multiple alignment format." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2002 name: srs namespace: format subset: formats def: "Simple multiple sequence (alignment) format for SRS." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2003 name: srspair namespace: format subset: formats def: "Simple sequence pair (alignment) format for SRS." [http://edamontology.org] is_a: EDAM_format:2920 ! Alignment format (pair only) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2004 name: tcoffee namespace: format subset: formats def: "TCOFFEE program alignment format." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2005 name: treecon-seq namespace: format subset: formats def: "Treecon format for (aligned) sequences." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1391 name: hmmer-aln namespace: format subset: formats def: "FASTA-style format for multiple sequences aligned by HMMER package to an HMM." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1392 name: dialign namespace: format subset: formats def: "Multiple sequences aligned by DIALIGN package." [http://edamontology.org] is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1393 name: daf namespace: format subset: formats def: "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family." [http://edamontology.org] comment: The format is clustal-like and includes annotation of domain family classification information. is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2556 name: Phylogenetic tree format (text) namespace: format subset: formats def: "Text format for a phylogenetic tree." [http://edamontology.org] is_a: EDAM_format:2006 ! Phylogenetic tree format [Term] id: EDAM_format:2557 name: Phylogenetic tree format (XML) namespace: format subset: formats def: "XML format for a phylogenetic tree." [http://edamontology.org] is_a: EDAM_format:2006 ! Phylogenetic tree format [Term] id: EDAM_format:1435 name: phylip tree namespace: format subset: formats def: "Phylogenetic tree data format used by the PHYLIP program." [http://edamontology.org] is_a: EDAM_format:2556 ! Phylogenetic tree format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1425 name: Phylip tree raw namespace: format subset: formats def: "Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted." [http://edamontology.org] is_a: EDAM_format:2556 ! Phylogenetic tree format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1424 name: Clustalw dendrogram namespace: format subset: formats def: "Dendrogram (tree file) format generated by Clustalw." [http://edamontology.org] is_a: EDAM_format:2556 ! Phylogenetic tree format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1436 name: treebase namespace: format subset: formats def: "The format of an entry from the TreeBASE database of phylogenetic data." [http://edamontology.org] is_a: EDAM_format:2556 ! Phylogenetic tree format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1437 name: treefam namespace: format subset: formats def: "The format of an entry from the TreeFam database of phylogenetic data." [http://edamontology.org] is_a: EDAM_format:2556 ! Phylogenetic tree format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1910 name: newick namespace: format subset: formats def: "Phylogenetic tree Newick (text) format." [http://edamontology.org] xref: Moby:Newick_Text is_a: EDAM_format:2556 ! Phylogenetic tree format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1911 name: treecon namespace: format subset: formats def: "Phylogenetic tree TreeCon (text) format." [http://edamontology.org] xref: Moby:TreeCon is_a: EDAM_format:2556 ! Phylogenetic tree format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1912 name: nexus namespace: format subset: formats def: "Phylogenetic tree Nexus (text) format." [http://edamontology.org] xref: Moby:Nexus_Text is_a: EDAM_format:2556 ! Phylogenetic tree format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1475 name: PDB database entry format namespace: format subset: formats def: "Format of an entry (or part of an entry) from the PDB database." [http://edamontology.org] synonym: "PDB entry" EXACT [http://edamontology.org] is_a: EDAM_format:2033 ! Tertiary structure format [Term] id: EDAM_format:1476 name: PDB format namespace: format subset: formats def: "Entry format of PDB database in PDB format." [http://edamontology.org] synonym: "PDB" EXACT [http://edamontology.org] xref: Moby:PDB-formatted-text xref: Moby:PDB-Text is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1477 name: mmCIF namespace: format subset: formats def: "Entry format of PDB database in mmCIF format." [http://edamontology.org] synonym: "mmcif" EXACT [http://edamontology.org] xref: Moby:mmCIF-Text xref: Moby:mmCIF_Text is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1478 name: PDBML namespace: format subset: formats def: "Entry format of PDB database in PDBML (XML) format." [http://edamontology.org] is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2013 name: Biological pathway or network format namespace: format subset: formats def: "Data format for a biological pathway or network." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2600 ! Pathway or network [Term] id: EDAM_format:3166 name: Biological pathway or network report format namespace: format subset: formats def: "Data format for a report of information derived from a biological pathway or network." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_format:2585 name: SBML namespace: format subset: formats def: "Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation." [http://edamontology.org] xref: http://sbml.org !{documentation=true} is_a: EDAM_format:2034 ! Biological model format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3155 !{since=1.0} name: SBRML namespace: format subset: formats def: "Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models." [http://edamontology.org] xref: http://www.comp-sys-bio.org/tiki-index.php?page=SBRML !{documentation=true} is_a: EDAM_format:3166 ! Biological pathway or network report format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3156 !{since=1.0} name: BioPAX namespace: format subset: formats def: "BioPAX is an exchange format for pathway data, with its data model defined in OWL." [http://edamontology.org] xref: http://www.biopax.org !{documentation=true} is_a: EDAM_format:2013 ! Biological pathway or network format is_a: EDAM_format:2197 ! OWL [Term] id: EDAM_format:3157 !{since=1.0} name: EBI Application Result XML namespace: format subset: formats def: "EBI Application Result XML is a format returned by sequence similarity search Web services at EBI." [http://edamontology.org] xref: http://www.ebi.ac.uk/schema/ApplicationResult.xsd !{documentation=true} is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2920 ! Alignment format (pair only) is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3158 !{since=1.0} name: PSI MI XML (MIF) namespace: format subset: formats def: "XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI." [http://edamontology.org] xref: http://psidev.sourceforge.net/mi/xml/doc/user !{documentation=true} is_a: EDAM_format:2054 ! Protein interaction format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3159 !{since=1.0} name: phyloXML namespace: format subset: formats def: "phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data." [http://edamontology.org] xref: http://www.phyloxml.org !{documentation=true} is_a: EDAM_format:2557 ! Phylogenetic tree format (XML) is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3160 !{since=1.0} name: NeXML namespace: format subset: formats def: "NeXML is a standardised XML format for rich phyloinformatic data." [http://edamontology.org] xref: http://www.nexml.org !{documentation=true} is_a: EDAM_format:2557 ! Phylogenetic tree format (XML) ! And more is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3161 !{since=1.0} name: MAGE-ML namespace: format subset: formats def: "MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org] xref: http://www.mged.org/Workgroups/MAGE/mage-ml.html !{documentation=true} is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2056 ! Microarray experiment data format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3162 !{since=1.0} name: MAGE-TAB namespace: format subset: formats def: "MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org] xref: http://www.mged.org/mage-tab !{documentation=true} is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2056 ! Microarray experiment data format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3163 !{since=1.0} name: GCDML namespace: format subset: formats def: "GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC)." [http://edamontology.org] xref: http://gcdml.gensc.org !{documentation=true} is_a: EDAM_format:3167 ! Experiment annotation format is_a: EDAM_format:2332 ! XML relationship: is_format_of EDAM_data:3165 ! Experiment annotation (sequencing) [Term] id: EDAM_format:3164 !{since=1.0} name: GTrack namespace: format subset: formats def: "GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG)." [http://edamontology.org] xref: http://www.gtrack.no !{documentation=true} is_a: EDAM_format:2919 ! Sequence annotation track format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1666 name: BioModel mathematical model format namespace: format subset: formats def: "Format of mathematical models from the BioModel database." [http://edamontology.org] comment: Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1647 name: KEGG PATHWAY entry format namespace: format subset: formats def: "The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1648 name: MetaCyc entry format namespace: format subset: formats def: "The format of an entry from the MetaCyc metabolic pathways database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1649 name: HumanCyc entry format namespace: format subset: formats def: "The format of a report from the HumanCyc metabolic pathways database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1650 name: INOH entry format namespace: format subset: formats def: "The format of an entry from the INOH signal transduction pathways database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1651 name: PATIKA entry format namespace: format subset: formats def: "The format of an entry from the PATIKA biological pathways database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1652 name: Reactome entry format namespace: format subset: formats def: "The format of an entry from the reactome biological pathways database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1653 name: aMAZE entry format namespace: format subset: formats def: "The format of an entry from the aMAZE biological pathways and molecular interactions database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1654 name: CPDB entry format namespace: format subset: formats def: "The format of an entry from the CPDB database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1655 name: Panther Pathways entry format namespace: format subset: formats def: "The format of an entry from the Panther Pathways database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2341 name: NCI-Nature pathway entry format namespace: format subset: formats def: "The format of an entry from the NCI-Nature pathways database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2015 name: Sequence-profile alignment (HMM) format namespace: format subset: formats def: "Data format for a sequence-HMM profile alignment." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2014 ! Sequence-profile alignment format [Term] id: EDAM_format:1419 name: Sequence-MEME profile alignment namespace: format subset: formats def: "Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package." [http://edamontology.org] is_a: EDAM_format:2014 ! Sequence-profile alignment format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1421 name: HMMER profile alignment (sequences versus HMMs) namespace: format subset: formats def: "Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database." [http://edamontology.org] is_a: EDAM_format:2014 ! Sequence-profile alignment format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1422 name: HMMER profile alignment (HMM versus sequences) namespace: format subset: formats def: "Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database." [http://edamontology.org] is_a: EDAM_format:2014 ! Sequence-profile alignment format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1504 name: aaindex namespace: format subset: formats def: "Amino acid index format used by the AAindex database." [http://edamontology.org] is_a: EDAM_format:2017 ! Amino acid index format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1739 name: pmc namespace: format subset: formats def: "Article format of the PubMed Central database." [http://edamontology.org] is_a: EDAM_format:2020 ! Article format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2194 name: medline namespace: format subset: formats def: "Abstract format used by MedLine database." [http://edamontology.org] is_a: EDAM_format:2020 ! Article format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1740 name: iHOP text mining abstract format namespace: format subset: formats def: "iHOP abstract format." [http://edamontology.org] is_a: EDAM_format:2021 ! Text mining report format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1741 name: Oscar3 namespace: format subset: formats def: "Text mining abstract format from the Oscar 3 application." [http://edamontology.org] comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. is_a: EDAM_format:2021 ! Text mining report format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1582 name: findkm namespace: format subset: formats def: "A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax)." [http://edamontology.org] is_a: EDAM_format:2027 ! Enzyme kinetics report format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1697 name: KEGG LIGAND entry format namespace: format subset: formats def: "The format of an entry from the KEGG LIGAND chemical database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1698 name: KEGG COMPOUND entry format namespace: format subset: formats def: "The format of an entry from the KEGG COMPOUND database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1699 name: KEGG PLANT entry format namespace: format subset: formats def: "The format of an entry from the KEGG PLANT database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1700 name: KEGG GLYCAN entry format namespace: format subset: formats def: "The format of an entry from the KEGG GLYCAN database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1706 name: KEGG DRUG entry format namespace: format subset: formats def: "The format of an entry from the KEGG DRUG database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1701 name: PubChem entry format namespace: format subset: formats def: "The format of an entry from PubChem." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1702 name: ChemSpider entry format namespace: format subset: formats def: "The format of an entry from a database of chemical structures and property predictions." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1703 name: ChEBI entry format namespace: format subset: formats def: "The format of an entry from Chemical Entities of Biological Interest (ChEBI)." [http://edamontology.org] comment: ChEBI includes an ontological classification defining relations between entities or classes of entities. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1704 name: MSDchem ligand dictionary entry format namespace: format subset: formats def: "The format of an entry from the MSDchem ligand dictionary." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1705 name: HET group dictionary entry format namespace: format subset: formats def: "The format of an entry from the HET group dictionary (HET groups from PDB files)." [http://edamontology.org] is_a: EDAM_format:2030 ! Small molecule report format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1808 name: GeneIlluminator gene report format namespace: format subset: formats def: "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service." [http://edamontology.org] comment: This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. xref: Moby:GI_Gene is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1809 name: BacMap gene card format namespace: format subset: formats def: "Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database." [http://edamontology.org] xref: Moby:BacMapGeneCard is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1810 name: ColiCard report format namespace: format subset: formats def: "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [http://edamontology.org] xref: Moby:ColiCard is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2328 name: PseudoCAP gene report format namespace: format subset: formats def: "Format of a report on a gene from the PseudoCAP database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2329 name: GeneCards gene report format namespace: format subset: formats def: "Format of a report on a gene from the GeneCards database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1603 name: Ensembl gene report format namespace: format subset: formats def: "Entry format of Ensembl genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1604 name: DictyBase gene report format namespace: format subset: formats def: "Entry format of DictyBase genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1605 name: CGD gene report format namespace: format subset: formats def: "Entry format of Candida Genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1606 name: DragonDB gene report format namespace: format subset: formats def: "Entry format of DragonDB genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1607 name: EcoCyc gene report format namespace: format subset: formats def: "Entry format of EcoCyc genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1608 name: FlyBase gene report format namespace: format subset: formats def: "Entry format of FlyBase genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1609 name: Gramene gene report format namespace: format subset: formats def: "Entry format of Gramene genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1610 name: KEGG GENES gene report format namespace: format subset: formats def: "Entry format of KEGG GENES genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1611 name: MaizeGDB gene report format namespace: format subset: formats def: "Entry format of the Maize genetics and genomics database (MaizeGDB)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1612 name: MGD gene report format namespace: format subset: formats def: "Entry format of the Mouse Genome Database (MGD)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1613 name: RGD gene report format namespace: format subset: formats def: "Entry format of the Rat Genome Database (RGD)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1614 name: SGD gene report format namespace: format subset: formats def: "Entry format of the Saccharomyces Genome Database (SGD)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1615 name: GeneDB gene report format namespace: format subset: formats def: "Entry format of the Sanger GeneDB genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1616 name: TAIR gene report format namespace: format subset: formats def: "Entry format of The Arabidopsis Information Resource (TAIR) genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1617 name: WormBase gene report format namespace: format subset: formats def: "Entry format of the WormBase genomes database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1618 name: ZFIN gene report format namespace: format subset: formats def: "Entry format of the Zebrafish Information Network (ZFIN) genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1619 name: TIGR gene report format namespace: format subset: formats def: "Entry format of the TIGR genome database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1782 name: NCBI gene report format namespace: format subset: formats def: "Entry (gene) format of the NCBI database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1665 name: Taverna workflow format namespace: format subset: formats def: "Format of Taverna workflows." [http://edamontology.org] is_a: EDAM_format:2032 ! Workflow format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:1196 name: smiles namespace: format subset: formats def: "Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation." [http://edamontology.org] is_a: EDAM_format:2035 ! Chemical formula format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1197 name: inchi namespace: format subset: formats def: "Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation." [http://edamontology.org] is_a: EDAM_format:2035 ! Chemical formula format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1198 name: mf namespace: format subset: formats def: "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound." [http://edamontology.org] comment: The general MF query format consists of a series of valid atomic symbols, with an optional number or range. is_a: EDAM_format:2035 ! Chemical formula format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1199 name: inchikey namespace: format subset: formats def: "The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound." [http://edamontology.org] comment: An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. is_a: EDAM_format:2035 ! Chemical formula format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1200 name: smarts namespace: format subset: formats def: "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." [http://edamontology.org] is_a: EDAM_format:1196 ! smiles [Term] id: EDAM_format:2037 name: Phylogenetic continuous quantitative character format namespace: format subset: formats def: "Format of phylogenetic continuous quantitative character data." [http://edamontology.org] is_a: EDAM_format:2036 ! Phylogenetic character data format relationship: is_format_of EDAM_data:1426 ! Phylogenetic continuous quantitative data [Term] id: EDAM_format:1431 name: Phylogenetic property values format namespace: format subset: formats def: "Format of phylogenetic property data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2036 ! Phylogenetic character data format [Term] id: EDAM_format:2038 name: Phylogenetic discrete states format namespace: format subset: formats def: "Format of phylogenetic discrete states data." [http://edamontology.org] is_a: EDAM_format:2036 ! Phylogenetic character data format relationship: is_format_of EDAM_data:1427 ! Phylogenetic discrete data [Term] id: EDAM_format:2039 name: Phylogenetic tree report (cliques) format namespace: format subset: formats def: "Format of phylogenetic cliques data." [http://edamontology.org] is_a: EDAM_format:2036 ! Phylogenetic character data format relationship: is_format_of EDAM_data:1428 ! Phylogenetic character cliques [Term] id: EDAM_format:2040 name: Phylogenetic tree report (invariants) format namespace: format subset: formats def: "Format of phylogenetic invariants data." [http://edamontology.org] is_a: EDAM_format:2036 ! Phylogenetic character data format relationship: is_format_of EDAM_data:1429 ! Phylogenetic invariants [Term] id: EDAM_format:1430 name: phylip continuous quantitative characters namespace: format subset: formats def: "PHYLIP file format for continuous quantitative character data." [http://edamontology.org] is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1432 name: phylip character frequencies namespace: format subset: formats def: "PHYLIP file format for phylogenetics character frequency data." [http://edamontology.org] is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2243 name: phylip property values namespace: format subset: formats def: "PHYLIP file format for phylogenetic property data." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2036 ! Phylogenetic character data format [Term] id: EDAM_format:1433 name: phylip discrete states namespace: format subset: formats def: "Format of PHYLIP discrete states data." [http://edamontology.org] is_a: EDAM_format:2038 ! Phylogenetic discrete states format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1434 name: phylip cliques namespace: format subset: formats def: "Format of PHYLIP cliques data." [http://edamontology.org] is_a: EDAM_format:2039 ! Phylogenetic tree report (cliques) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1645 name: EMDB entry format namespace: format subset: formats def: "Format of an entry from the Electron Microscopy DataBase (EMDB)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1445 name: phylip tree distance namespace: format subset: formats def: "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." [http://edamontology.org] is_a: EDAM_format:2049 ! Phylogenetic tree report (tree distances) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1620 name: dbSNP polymorphism report format namespace: format subset: formats def: "Entry format for the dbSNP database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1570 name: InterPro entry format namespace: format subset: formats def: "Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences." [http://edamontology.org] comment: This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1571 name: InterPro entry abstract format namespace: format subset: formats def: "Entry format for the textual abstract of signatures in an InterPro entry and its protein matches." [http://edamontology.org] comment: References are included and a functional inference is made where possible. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1572 name: Gene3D entry format namespace: format subset: formats def: "Entry format for the Gene3D protein secondary database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1573 name: PIRSF entry format namespace: format subset: formats def: "Entry format for the PIRSF protein secondary database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1574 name: PRINTS entry format namespace: format subset: formats def: "Entry format for the PRINTS protein secondary database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1575 name: Panther Families and HMMs entry format namespace: format subset: formats def: "Entry format for the Panther library of protein families and subfamilies." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1576 name: Pfam entry format namespace: format subset: formats def: "Entry format for the Pfam protein secondary database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1577 name: SMART entry format namespace: format subset: formats def: "Entry format for the SMART protein secondary database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1578 name: Superfamily entry format namespace: format subset: formats def: "Entry format for the Superfamily protein secondary database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1579 name: TIGRFam entry format namespace: format subset: formats def: "Entry format for the TIGRFam protein secondary database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1580 name: ProDom entry format namespace: format subset: formats def: "Entry format for the ProDom protein domain classification database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1581 name: FSSP entry format namespace: format subset: formats def: "Entry format for the FSSP database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1568 name: BIND entry format namespace: format subset: formats def: "Entry format for the BIND database of protein interaction." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1569 name: IntAct entry format namespace: format subset: formats def: "Entry format for the IntAct database of protein interaction." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2560 name: STRING entry format namespace: format subset: formats def: "Entry format for the STRING database of protein interaction." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2303 name: STRING entry format (HTML) namespace: format subset: formats def: "Entry format (HTML) for the STRING database of protein interaction." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2304 name: STRING entry format (XML) namespace: format subset: formats def: "Entry format (XML) for the STRING database of protein interaction." [http://edamontology.org] is_a: EDAM_format:2054 ! Protein interaction format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2561 name: Sequence assembly format (text) namespace: format subset: formats def: "Text format for sequence assembly data." [http://edamontology.org] is_a: EDAM_format:2055 ! Sequence assembly format [Term] id: EDAM_format:1630 name: CAF namespace: format subset: formats def: "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." [http://edamontology.org] xref: http://www.sanger.ac.uk/resources/software/caf/ !{documentation=true} is_a: EDAM_format:2561 ! Sequence assembly format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1631 name: exp namespace: format subset: formats def: "Sequence assembly project file EXP format." [http://edamontology.org] is_a: EDAM_format:2561 ! Sequence assembly format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1632 name: SCF namespace: format subset: formats def: "Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata." [http://edamontology.org] xref: http://staden.sourceforge.net/manual/formats_unix_2.html !{documentation=true} is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:1633 name: PHD namespace: format subset: formats def: "PHD sequence trace format to store serialised chromatogram data (reads)." [http://edamontology.org] xref: http://www.bioperl.org/wiki/PHD_sequence_format !{documentation=true} is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1640 name: ArrayExpress entry format namespace: format subset: formats def: "Entry format for the ArrayExpress microarrays database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1641 name: affymetrix-exp namespace: format subset: formats def: "Affymetrix data file format for information about experimental conditions and protocols." [http://edamontology.org] synonym: "Affymetrix experimental conditions data file format" EXACT [http://edamontology.org] is_a: EDAM_format:2056 ! Microarray experiment data format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1638 name: cel namespace: format subset: formats def: "Format of Affymetrix data file of information about (raw) expression levels of the individual probes." [http://edamontology.org] synonym: "Affymetrix probe raw data format" EXACT [http://edamontology.org] is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2330 ! Textual format relationship: is_format_of EDAM_data:3110 ! Raw microarray data [Term] id: EDAM_format:1644 name: CHP namespace: format subset: formats def: "Format of Affymetrix data file of information about (normalised) expression levels of the individual probes." [http://edamontology.org] synonym: "Affymetrix probe normalised data format" EXACT [http://edamontology.org] is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2330 ! Textual format relationship: is_format_of EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_format:1637 name: dat namespace: format subset: formats def: "Format of Affymetrix data file of raw image data." [http://edamontology.org] synonym: "Affymetrix image data file format" EXACT [http://edamontology.org] is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2330 ! Textual format relationship: is_format_of EDAM_data:1714 ! Microarray spots image [Term] id: EDAM_format:1623 name: OMIM entry format namespace: format subset: formats def: "Format of an entry from the OMIM database of genotypes and phenotypes." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1624 name: HGVbase entry format namespace: format subset: formats def: "Format of a record from the HGVbase database of genotypes and phenotypes." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1625 name: HIVDB entry format namespace: format subset: formats def: "Format of a record from the HIVDB database of genotypes and phenotypes." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1626 name: KEGG DISEASE entry format namespace: format subset: formats def: "Format of an entry from the KEGG DISEASE database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1861 name: PlasMapper TextMap namespace: format subset: formats def: "Map of a plasmid (circular DNA) in PlasMapper TextMap format." [http://edamontology.org] xref: Moby:PlasMapperTextMap is_a: EDAM_format:2060 ! Map format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1627 name: Primer3 primer namespace: format subset: formats def: "Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program." [http://edamontology.org] is_a: EDAM_format:2061 ! Nucleic acid features (primers) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2063 name: Protein report (enzyme) format namespace: format subset: formats def: "Format of a report of general information about a specific enzyme." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:1511 name: IntEnz enzyme report format namespace: format subset: formats def: "Format of an entry from IntEnz (The Integrated Relational Enzyme Database)." [http://edamontology.org] comment: IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1512 name: BRENDA enzyme report format namespace: format subset: formats def: "Format of an entry from the BRENDA enzyme database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2322 name: BioCyc enzyme report format namespace: format subset: formats def: "Format of an entry from the BioCyc enzyme database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2323 name: ENZYME enzyme report format namespace: format subset: formats def: "Format of an entry from the Enzyme nomenclature database (ENZYME)." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1513 name: KEGG REACTION enzyme report format namespace: format subset: formats def: "Format of an entry from the KEGG REACTION database of biochemical reactions." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1514 name: KEGG ENZYME enzyme report format namespace: format subset: formats def: "Format of an entry from the KEGG ENZYME database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1515 name: REBASE proto enzyme report format namespace: format subset: formats def: "Format of an entry from the proto section of the REBASE enzyme database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1516 name: REBASE withrefm enzyme report format namespace: format subset: formats def: "Format of an entry from the withrefm section of the REBASE enzyme database." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1500 name: Domainatrix 3D-1D scoring matrix format namespace: format subset: formats def: "Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} [Term] id: EDAM_format:1551 name: Pcons report format namespace: format subset: formats def: "Format of output of the Pcons Model Quality Assessment Program (MQAP)." [http://edamontology.org] comment: Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1552 name: ProQ report format namespace: format subset: formats def: "Format of output of the ProQ protein model quality predictor." [http://edamontology.org] comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1341 name: InterPro hits format namespace: format subset: formats def: "Results format for searches of the InterPro database." [http://edamontology.org] is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1342 name: InterPro protein view report format namespace: format subset: formats def: "Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries." [http://edamontology.org] comment: The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. is_a: EDAM_format:1341 ! InterPro hits format [Term] id: EDAM_format:1343 name: InterPro match table format namespace: format subset: formats def: "Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry." [http://edamontology.org] comment: The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. is_a: EDAM_format:1341 ! InterPro hits format [Term] id: EDAM_format:1332 name: FASTA search results format namespace: format subset: formats def: "Format of results of a sequence database search using FASTA." [http://edamontology.org] comment: This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1333 name: BLAST results namespace: format subset: formats def: "Format of results of a sequence database search using some variant of BLAST." [http://edamontology.org] comment: This includes score data, alignment data and summary table. is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1334 name: mspcrunch namespace: format subset: formats def: "Format of results of a sequence database search using some variant of MSPCrunch." [http://edamontology.org] is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1335 name: smith-waterman namespace: format subset: formats def: "Format of results of a sequence database search using some variant of Smith Waterman." [http://edamontology.org] is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1336 name: dhf namespace: format subset: formats def: "Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information." [http://edamontology.org] comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1337 name: lhf namespace: format subset: formats def: "Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information." [http://edamontology.org] comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database. is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1423 name: phylip distance matrix namespace: format subset: formats def: "Format of PHYLIP phylogenetic distance matrix data." [http://edamontology.org] comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). is_a: EDAM_format:2067 ! Sequence distance matrix format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1360 name: meme-motif namespace: format subset: formats def: "A motif in the format generated by the MEME program." [http://edamontology.org] is_a: EDAM_format:2068 ! Sequence motif format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1356 name: prosite-pattern namespace: format subset: formats def: "Format of a regular expression pattern from the Prosite database." [http://edamontology.org] is_a: EDAM_format:2068 ! Sequence motif format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1357 name: EMBOSS sequence pattern namespace: format subset: formats def: "Format of an EMBOSS sequence pattern." [http://edamontology.org] is_a: EDAM_format:2068 ! Sequence motif format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2072 name: Hidden Markov model format namespace: format subset: formats def: "Format of a hidden Markov model." [http://edamontology.org] is_a: EDAM_format:2069 ! Sequence profile format relationship: is_format_of EDAM_data:1364 ! Hidden Markov model [Term] id: EDAM_format:1367 name: jaspar namespace: format subset: formats def: "A profile (sequence classifier) in the format used in the JASPAR database." [http://edamontology.org] is_a: EDAM_format:2069 ! Sequence profile format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1366 name: prosite-profile namespace: format subset: formats def: "Sequence profile (sequence classifier) format used in the PROSITE database." [http://edamontology.org] is_a: EDAM_format:2069 ! Sequence profile format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1369 name: MEME background Markov model namespace: format subset: formats def: "Format of the model of random sequences used by MEME." [http://edamontology.org] is_a: EDAM_format:2072 ! Hidden Markov model format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1370 name: hmmer namespace: format subset: formats def: "Format of a hidden Markov model representation used by the HMMER package." [http://edamontology.org] is_a: EDAM_format:2072 ! Hidden Markov model format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1349 name: HMMER Dirichlet prior namespace: format subset: formats def: "Dirichlet distribution HMMER format." [http://edamontology.org] is_a: EDAM_format:2074 ! Dirichlet distribution format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1350 name: MEME Dirichlet prior namespace: format subset: formats def: "Dirichlet distribution MEME format." [http://edamontology.org] is_a: EDAM_format:2074 ! Dirichlet distribution format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1351 name: HMMER emission and transition namespace: format subset: formats def: "Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model." [http://edamontology.org] is_a: EDAM_format:2075 ! HMM emission and transition counts format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1454 name: dssp namespace: format subset: formats def: "Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins)." [http://edamontology.org] comment: The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. is_a: EDAM_format:2077 ! Protein secondary structure format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1455 name: hssp namespace: format subset: formats def: "Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins)." [http://edamontology.org] is_a: EDAM_format:2077 ! Protein secondary structure format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1457 name: Vienna RNA secondary structure namespace: format subset: formats def: "Format of RNA secondary structure (in bracket notation) with free energy values, generated by the Vienna program." [http://edamontology.org] synonym: "Dot-bracket format" EXACT [http://edamontology.org] is_a: EDAM_format:2076 ! RNA secondary structure format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1458 name: Vienna local RNA secondary structure namespace: format subset: formats def: "Format of local RNA secondary structure components with free energy values, generated by the Vienna program." [http://edamontology.org] is_a: EDAM_format:1457 ! Vienna RNA secondary structure is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1248 name: EMBL feature location namespace: format subset: formats def: "Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database." [http://edamontology.org] synonym: "Feature location" EXACT [http://edamontology.org] is_a: EDAM_format:2078 ! Sequence range format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1295 name: quicktandem namespace: format subset: formats def: "Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program)." [http://edamontology.org] is_a: EDAM_format:2155 ! Sequence features (repeats) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1296 name: Sanger inverted repeats namespace: format subset: formats def: "Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program)." [http://edamontology.org] is_a: EDAM_format:2155 ! Sequence features (repeats) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1297 name: EMBOSS repeat namespace: format subset: formats def: "Report format for tandem repeats in a sequence (an EMBOSS report format)." [http://edamontology.org] is_a: EDAM_format:2155 ! Sequence features (repeats) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1318 name: restrict namespace: format subset: formats def: "Report format for restriction enzyme recognition sites used by EMBOSS restrict program." [http://edamontology.org] is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1319 name: restover namespace: format subset: formats def: "Report format for restriction enzyme recognition sites used by EMBOSS restover program." [http://edamontology.org] is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1320 name: REBASE restriction sites namespace: format subset: formats def: "Report format for restriction enzyme recognition sites used by REBASE database." [http://edamontology.org] is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1316 name: est2genome namespace: format subset: formats def: "Format of a report on exon-intron structure generated by EMBOSS est2genome." [http://edamontology.org] is_a: EDAM_format:2159 ! Gene features (coding region) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2171 name: Sequence cluster format (protein) namespace: format subset: formats def: "Format used for clusters of protein sequences." [http://edamontology.org] is_a: EDAM_format:2170 ! Sequence cluster format [Term] id: EDAM_format:2172 name: Sequence cluster format (nucleic acid) namespace: format subset: formats def: "Format used for clusters of nucleotide sequences." [http://edamontology.org] is_a: EDAM_format:2170 ! Sequence cluster format [Term] id: EDAM_format:1247 name: COG sequence cluster format namespace: format subset: formats def: "Format of an entry from the COG database of clusters of (related) protein sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2175 name: Gene cluster format namespace: format subset: formats ! alt_id: EDAM_format:2918 def: "Format used for clusters of genes." [http://edamontology.org] is_obsolete: true !{since=beta13} consider: EDAM_format:2172 ! Sequence cluster format (nucleic acid) [Term] id: EDAM_format:1228 name: UniGene entry format namespace: format subset: formats def: "Format of an entry from UniGene." [http://edamontology.org] comment: A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1639 name: affymetrix namespace: format subset: formats def: "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [http://edamontology.org] is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2172 ! Sequence cluster format (nucleic acid) [Term] id: EDAM_format:2196 name: OBO format namespace: format subset: formats def: "OBO ontology format." [http://edamontology.org] is_a: EDAM_format:2195 ! Ontology format [Term] id: EDAM_format:2549 name: OBO namespace: format subset: formats def: "OBO ontology text format." [http://edamontology.org] is_a: EDAM_format:2196 ! OBO format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2197 name: OWL namespace: format subset: formats def: "OWL ontology format." [http://edamontology.org] is_a: EDAM_format:2195 ! Ontology format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2550 name: OBO-XML namespace: format subset: formats def: "OBO ontology XML format." [http://edamontology.org] is_a: EDAM_format:2196 ! OBO format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2211 name: CIP strain data format namespace: format subset: formats def: "Format for a report of strain data as used for CIP database entries." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1760 name: CATH chain report format namespace: format subset: formats def: "Format of CATH domain classification information for a polypeptide chain." [http://edamontology.org] comment: The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1761 name: CATH PDB report format namespace: format subset: formats def: "Format of CATH domain classification information for a protein PDB file." [http://edamontology.org] comment: The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1563 name: SMART domain assignment report format namespace: format subset: formats def: "Format of SMART domain assignment data." [http://edamontology.org] comment: The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:3000 name: AB1 namespace: format subset: formats def: "AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence." [http://www.fileinfo.com/extension/ab1, http://edamontology.org] comment: AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). is_a: EDAM_format:2333 ! Binary format is_a: EDAM_format:2057 ! Sequence trace format [Term] id: EDAM_format:3001 name: ACE namespace: format subset: formats def: "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." [http://edamontology.org] xref: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt !{documentation=true} is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2055 ! Sequence assembly format [Term] id: EDAM_format:3003 name: BED namespace: format subset: formats def: "Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser." [http://edamontology.org] comment: BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). xref: http://genome.ucsc.edu/FAQ/FAQformat#format1 !{documentation=true} is_a: EDAM_format:2919 ! Sequence annotation track format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3004 name: bigBed namespace: format subset: formats def: "bigBed format for large sequence annotation tracks, similar to textual BED format." [http://edamontology.org] xref: http://genome.ucsc.edu/FAQ/FAQformat#format1.5 !{documentation=true} is_a: EDAM_format:2919 ! Sequence annotation track format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:3005 name: WIG namespace: format subset: formats def: "Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser." [http://edamontology.org] xref: http://genome.ucsc.edu/goldenPath/help/wiggle.html !{documentation=true} is_a: EDAM_format:2919 ! Sequence annotation track format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3006 name: bigWig namespace: format subset: formats def: "bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format." [http://edamontology.org] xref: http://genome.ucsc.edu/FAQ/FAQformat#format6.1 !{documentation=true} is_a: EDAM_format:2919 ! Sequence annotation track format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:3007 name: PSL namespace: format subset: formats def: "PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track." [http://edamontology.org] xref: http://genome.ucsc.edu/FAQ/FAQformat#format2 !{documentation=true} is_a: EDAM_format:2919 ! Sequence annotation track format is_a: EDAM_format:2920 ! Alignment format (pair only) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3008 name: MAF namespace: format subset: formats def: "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth." [http://edamontology.org] comment: Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. xref: http://genome.ucsc.edu/FAQ/FAQformat#format5 !{documentation=true} is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2919 ! Sequence annotation track format [Term] id: EDAM_format:3009 name: 2bit namespace: format subset: formats def: "2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'." [http://edamontology.org] xref: http://jcomeau.freeshell.org/www/genome/2bitformat.html !{documentation=true} xref: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD !{documentation=true} is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:3010 name: .nib namespace: format subset: formats def: ".nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'." [http://edamontology.org] xref: http://genome.ucsc.edu/FAQ/FAQformat#format8 !{documentation=true} is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:2094 name: pure namespace: format subset: formats def: "Alphabet for molecular sequence with possible unknown positions but without non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2095 name: unpure namespace: format subset: formats def: "Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2096 name: unambiguous sequence namespace: format subset: formats def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters." [http://edamontology.org] is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2566 name: completely unambiguous namespace: format subset: formats def: "Alphabet for a molecular sequence without any unknown positions or ambiguity characters." [http://edamontology.org] is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2097 name: ambiguous namespace: format subset: formats def: "Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters." [http://edamontology.org] is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1207 name: nucleotide namespace: format subset: formats def: "Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] comment: Non-sequence characters may be used for example for gaps. synonym: "Nucleotide sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence] is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1208 name: protein namespace: format subset: formats def: "Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] comment: Non-sequence characters may be used for gaps and translation stop. synonym: "Amino acid sequence" EXACT [http://edamontology.org] synonym: "Amino acid sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence] is_a: EDAM_format:2571 ! Raw sequence format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1206 name: unambiguous pure namespace: format subset: formats def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2094 ! pure is_a: EDAM_format:2096 ! unambiguous sequence [Term] id: EDAM_format:2567 name: completely unambiguous pure namespace: format subset: formats def: "Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2094 ! pure is_a: EDAM_format:2566 ! completely unambiguous [Term] id: EDAM_format:1209 name: consensus namespace: format subset: formats def: "Alphabet for the consensus of two or more molecular sequences." [http://edamontology.org] is_a: EDAM_format:2097 ! ambiguous is_a: EDAM_format:2095 ! unpure [Term] id: EDAM_format:1210 name: pure nucleotide namespace: format subset: formats def: "Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2094 ! pure is_a: EDAM_format:1207 ! nucleotide [Term] id: EDAM_format:1211 name: unambiguous pure nucleotide namespace: format subset: formats def: "Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters ." [http://edamontology.org] is_a: EDAM_format:1207 ! nucleotide is_a: EDAM_format:1206 ! unambiguous pure [Term] id: EDAM_format:2568 name: completely unambiguous pure nucleotide namespace: format subset: formats def: "Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters ." [http://edamontology.org] is_a: EDAM_format:1207 ! nucleotide is_a: EDAM_format:2567 ! completely unambiguous pure [Term] id: EDAM_format:1212 name: dna namespace: format subset: formats def: "Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] synonym: "DNA sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence] is_a: EDAM_format:1207 ! nucleotide [Term] id: EDAM_format:1213 name: rna namespace: format subset: formats def: "Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] synonym: "RNA sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence] is_a: EDAM_format:1207 ! nucleotide [Term] id: EDAM_format:1214 name: unambiguous pure dna namespace: format subset: formats def: "Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] is_a: EDAM_format:1206 ! unambiguous pure is_a: EDAM_format:1212 ! dna [Term] id: EDAM_format:2569 name: completely unambiguous pure dna namespace: format subset: formats def: "Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2567 ! completely unambiguous pure is_a: EDAM_format:1212 ! dna [Term] id: EDAM_format:1215 name: pure dna namespace: format subset: formats def: "Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] is_a: EDAM_format:1210 ! pure nucleotide is_a: EDAM_format:1212 ! dna [Term] id: EDAM_format:1216 name: unambiguous pure rna sequence namespace: format subset: formats def: "Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] is_a: EDAM_format:1206 ! unambiguous pure is_a: EDAM_format:1213 ! rna [Term] id: EDAM_format:2570 name: completely unambiguous pure rna sequence namespace: format subset: formats def: "Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2567 ! completely unambiguous pure is_a: EDAM_format:1213 ! rna [Term] id: EDAM_format:1217 name: pure rna namespace: format subset: formats def: "Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] is_a: EDAM_format:1210 ! pure nucleotide is_a: EDAM_format:1213 ! rna [Term] id: EDAM_format:1218 name: unambiguous pure protein namespace: format subset: formats def: "Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] is_a: EDAM_format:1206 ! unambiguous pure is_a: EDAM_format:1208 ! protein [Term] id: EDAM_format:2607 name: completely unambiguous pure protein namespace: format subset: formats def: "Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2567 ! completely unambiguous pure is_a: EDAM_format:1208 ! protein [Term] id: EDAM_format:1219 name: pure protein namespace: format subset: formats def: "Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2094 ! pure is_a: EDAM_format:1208 ! protein [Term] id: EDAM_format:3011 name: genePred namespace: format subset: formats def: "genePred table format for gene prediction tracks." [http://edamontology.org] comment: genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. xref: http://genome.ucsc.edu/FAQ/FAQformat#format9 !{documentation=true} is_a: EDAM_format:2919 ! Sequence annotation track format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3012 name: pgSnp namespace: format subset: formats def: "Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser." [http://edamontology.org] ! UCSC-specific,but also for custom tracks & useful xref: http://genome.ucsc.edu/FAQ/FAQformat#format10 !{documentation=true} is_a: EDAM_format:2919 ! Sequence annotation track format is_a: EDAM_format:2330 ! Textual format ! [Term] ! id: EDAM_format:todo if desired (but then we could include 100 ucsc db tables) At least, this one is used also in IGV (for importing genome cytobands) ! name: Cytoband format ! namespace: format ! subset: formats ! def: "Cytoband format for chromosome cytobands." [http://edamontology.org] ! comment: Reflects a UCSC Browser DB table. ! xref: http://www.broadinstitute.org/software/igv/Cytoband !{documentation=true} [Term] id: EDAM_format:3013 name: axt namespace: format subset: formats def: "axt format of alignments, typically produced from BLASTZ." [http://edamontology.org] xref: http://genome.ucsc.edu/goldenPath/help/axt.html !{documentation=true} is_a: EDAM_format:2920 ! Alignment format (pair only) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3014 name: LAV namespace: format subset: formats def: "LAV format of alignments generated by BLASTZ and LASTZ." [http://genome.ucsc.edu/goldenPath/help/axt.html] ! Can be used by UCSC and Galaxy xref: http://www.bx.psu.edu/miller_lab/dist/lav_format.html !{documentation=true} is_a: EDAM_format:2920 ! Alignment format (pair only) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3015 name: Pileup namespace: format subset: formats def: "Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s)." [http://edamontology.org] xref: http://samtools.sourceforge.net/pileup.shtml !{documentation=true} is_a: EDAM_format:2920 ! Alignment format (pair only) is_a: EDAM_format:2330 ! Textual format ! and of track? (encoded as points, but could be 'function', like wig) [Term] id: EDAM_format:3016 name: VCF namespace: format subset: formats def: "Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org] xref: http://vcftools.sourceforge.net/specs.html !{documentation=true} is_a: EDAM_format:2921 ! Sequence variation annotation format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3017 name: SRF namespace: format subset: formats def: "Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive." [http://edamontology.org, http://srf.sourceforge.net/ShortSequenceFormatDec18th_v_1_3.htm] xref: http://srf.sourceforge.net/ !{documentation=true} is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:3018 name: ZTR namespace: format subset: formats def: "ZTR format for storing chromatogram data from DNA sequencing instruments." [http://staden.sourceforge.net/manual/formats_unix_12.html, http://edamontology.org] xref: http://staden.sourceforge.net/manual/formats_unix_12.html !{documentation=true} is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:3019 name: GVF namespace: format subset: formats def: "Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation." [http://edamontology.org] xref: http://sequenceontology.org/gvf.html !{documentation=true} is_a: EDAM_format:1975 ! GFF3 ! is_format_of (1255, Sequence feature annotation) is defined in parent (+ here has special tags for a particular class of seqfeatures: variation (indels,polymphs,structvar)) [Term] id: EDAM_format:3020 name: BCF namespace: format subset: formats def: "BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org] xref: http://samtools.sourceforge.net/mpileup.shtml !{documentation=true, note="BCF described on this site"} is_a: EDAM_format:2921 ! Sequence variation annotation format is_a: EDAM_format:2333 ! Binary format