diff --git a/releases/EDAM.obo b/releases/EDAM.obo index a1f742c..665b1ef 100644 --- a/releases/EDAM.obo +++ b/releases/EDAM.obo @@ -1,23 +1,23 @@ format-version: 1.2 -date: 17:06:2011 10:32 -data-version: Beta12 +date: 15:01:2011 15:01 +data-version: Beta13 subsetdef: topic "Topic" subsetdef: data "Data" subsetdef: format "Format" subsetdef: identifier "Identifier" subsetdef: operation "Operation" ! Use for mapping to "global" id space(s) e.g.: -! idspace: EDAM http://purl.org/edam/ "EDAM terms" -! NEXT term number is 0003029 +! idspace: EDAM http://purl.org/edam/ "EDAM concepts" +! NEXT term number is 0003155 ! xref: WHATIF: CorrectedPDBasXML ! xref:http://www.geneontology.org/doc/GO.xrf_abbs: FB ! xref:Moby:GI_Gene ! xref: Moby_namespace:iHOPorganism ! xref: SO:0000348 ! xref: BioCatalogue:Protein Multiple Alignment ! xref: GO:0006464 ! protein modification process -! regex: Regular expression for validating a "data<-identifier" instance. +! regex: Regular expression for validating a "data<-identifier" value. ! spec: URL of format specification for a "format" term -! seealso: Ontology term ID of term in external ontology for fine-grained annotation +! seealso: Ontology concept ID of concept in external ontology for 'fine-grained' annotation ! {cardinality=1, minCardinality=1, maxCardinality=1} @@ -25,12 +25,17 @@ subsetdef: operation "Operation" ! Relations ! [Typedef] -id: in_topic -name: in_topic +id: has_topic +name: has_topic def: "'Data' or 'Operation' is within the scope of a 'Topic'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true +inverse_of: is_topic_of +domain: EDAM:0000004 ! Operation +domain: EDAM:0000006 ! Data +range: EDAM:0000003 ! Topic +! Note: second 'domain' line is not visible in OBOEdit [Typedef] id: has_input @@ -39,6 +44,9 @@ def: "An 'Operation' consumes a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true +inverse_of: is_input_of +domain: EDAM:0000004 ! Operation +range: EDAM:0000006 ! Data [Typedef] id: has_output @@ -47,6 +55,41 @@ def: "An 'Operation' produces a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true +inverse_of: is_output_of +domain: EDAM:0000004 ! Operation +range: EDAM:0000006 ! Data + +[Typedef] +id: has_format +name: has_format +def: "'Data' has a certain 'Format'." [EDAM:EBI] +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +inverse_of: is_format_of +domain: EDAM:0000006 ! Data +range: EDAM:0001915 ! Format + +[Typedef] +id: has_identifier +name: has_identifier +def: "'Data' is identified by an 'Identifier'." [EDAM:EBI] +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +inverse_of: is_identifier_of +domain: EDAM:0000006 ! Data +range: EDAM:0000842 ! Identifier + +! For annotating tools +[Typedef] +id: has_operation +name: has_operation +def: "A tool has an 'Operation'." [EDAM:EBI] +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +range: EDAM:0000004 ! Operation [Typedef] id: is_format_of @@ -55,6 +98,9 @@ def: "A data 'Format' is a format of a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true +inverse_of: has_format +domain: EDAM:0001915 ! Format +range: EDAM:0000006 ! Data [Typedef] id: is_identifier_of @@ -63,9 +109,59 @@ def: "A data 'Identifier' is an identifier of a certain type of 'Data'." [EDAM:E is_anti_symmetric: true is_cyclic: false is_transitive: true +inverse_of: has_identifier +domain: EDAM:0000842 ! Identifier +range: EDAM:0000006 ! Data + +[Typedef] +id: is_topic_of +name: is_topic_of +def: "'Topic' is_topic_of 'Data' or 'Operation'." [EDAM:EBI] +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +inverse_of: has_topic +domain: EDAM:0000003 ! Topic +range: EDAM:0000003 ! Topic + +[Typedef] +id: is_input_of +name: is_input_of +def: "'Data' is an input of an 'Operation'." [EDAM:EBI] +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +inverse_of: has_input +domain: EDAM:0000006 ! Data +range: EDAM:0000004 ! Operation + +[Typedef] +id: is_output_of +name: is_output_of +def: "'Data' is an output of an 'Operation'." [EDAM:EBI] +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +inverse_of: has_output +domain: EDAM:0000006 ! Data +range: EDAM:0000004 ! Operation + + +[Typedef] +id: regex +name: regex +is_metadata_tag: true +[Typedef] +id: spec +name: spec +is_metadata_tag: true +[Typedef] +id: seealso +name: seealso +is_metadata_tag: true ! @@ -76,7 +172,7 @@ is_transitive: true id: EDAM:0000003 name: Topic namespace: topic -def: "A general bioinformatics subject or category, such as a field of study, data, processing, analysis or technology." [EDAM:EBI "EMBRACE definition"] +def: "A broad category within bioinformatics that covers one or (typically) a combination of fields of study, types of data, processing, analysis or technology." [EDAM:EBI "EMBRACE definition"] subset: topic [Term] @@ -90,9 +186,21 @@ subset: operation id: EDAM:0000006 name: Data namespace: data +alt_id: EDAM:0003030 def: "A type of data in common use in bioinformatics." [EDAM:EBI "EMBRACE definition"] subset: data + +[Term] +id: EDAM:0003031 +name: Core data +namespace: data +def: "A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation." [EDAM:EBI "EMBRACE definition"] +comment: Core data entities typically have a format and may be identified by an accession number. +subset: data +is_a: EDAM:0000006 ! Data + + [Term] id: EDAM:0001915 name: Format @@ -104,17 +212,20 @@ subset: format id: EDAM:0000842 name: Identifier namespace: identifier -def: "A label that identifies (typically uniquely) something such as data, a resource or a biological entity." [EDAM:EBI "EMBRACE definition"] -comment: This term is used for datatypes with the sole purpose of identification. It is not used for datatypes which contain other fields not related to identification. +alt_id: EDAM:0002860 +alt_id: EDAM:0002861 +alt_id: EDAM:0002926 +def: "A short numerical or textual label that identifies (typically uniquely) something such as data, a resource or a biological entity." [EDAM:EBI "EMBRACE definition"] +comment: This term is used for datatypes with the sole purpose of identification. It is not used for datatypes which contain other fields not related to identification. Identifiers typically are enumerated string (a string with one of a limited set of values) or are strings that are conformant to a regular expression. An ID is not necessarily stable or persistent over time, for example between different versions of a database. subset: identifier +is_a: EDAM:0000006 ! Data [Term] id: EDAM:0000002 name: Biological entity namespace: entity -def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things or an observable phenonema or occurence." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0000006 ! Data +def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things or an observable phenomenon or occurrence." [EDAM:EBI "EMBRACE definition"] is_obsolete: true @@ -143,8 +254,7 @@ is_obsolete: true id: EDAM:0000012 name: Phenomenon namespace: entity -def: "An observable biological occurence or event with a physical basis." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0000006 ! Data +def: "An observable biological occurrence or event with a physical basis." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] @@ -152,7 +262,6 @@ id: EDAM:0000009 name: Discrete entity namespace: entity def: "Any biological thing with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0000006 ! Data is_obsolete: true [Term] @@ -160,7 +269,6 @@ id: EDAM:0000010 name: Entity feature namespace: entity def: "A physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0000006 ! Data is_obsolete: true [Term] @@ -168,7 +276,6 @@ id: EDAM:0000011 name: Entity collection namespace: entity def: "A collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] -! relationship: has_attribute EDAM:0000006 ! Data is_obsolete: true [Term] @@ -732,7 +839,7 @@ is_obsolete: true id: EDAM:0000073 name: Metabolic pathway namespace: entity -def: "A group of related chemical (enzyme catalysed) reactions occuring within a cell." [EDAM:EBI "EMBRACE definition"] +def: "A group of related chemical (enzyme catalysed) reactions occurring within a cell." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] @@ -761,6 +868,7 @@ is_obsolete: true id: EDAM:0000076 name: Undefined namespace: topic +alt_id: EDAM:0000580 def: "Debugging." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true @@ -769,99 +877,153 @@ is_obsolete: true id: EDAM:0002807 name: Tool topic namespace: topic -def: "A topic concerning primarily bioinformatics tools, typically the broad function or purpose of a software tool." [EDAM:EBI "EMBRACE definition"] +def: "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000003 ! Topic + [Term] -id: EDAM:0002808 -name: Data topic +id: EDAM:0002809 +name: Study topic namespace: topic -def: "A topic concerning primarily bioinformatics data, typically the broad category of content of a data resource." [EDAM:EBI "EMBRACE definition"] +def: "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000003 ! Topic + [Term] -id: EDAM:0002809 -name: Study topic +id: EDAM:0003071 +name: Biological data resources namespace: topic -def: "A topic concerning primarily a general area of bioinformatics study that is not better modelled in as a tool or data topic, typically the broad category of content of bioinformatics journals or conference proceedings." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002808 +def: "A topic concerning primarily a specific type of bioinformatics data, typically the broad category of content of a digital archives of biological data, including databanks, databases proper, web portals and other data resources." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000003 ! Topic +synonym: "Biological databases" EXACT [] +synonym: "Biological data resource" EXACT [] +is_a: EDAM:0000003 ! Topic + [Term] id: EDAM:0000077 -name: Nucleic acids +name: Nucleic acid analysis namespace: topic -def: "The study of nucleic acids." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0003046 +def: "Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis." [EDAM:EBI "EMBRACE definition"] subset: topic +synonym: "Nucleic acids" EXACT [] +synonym: "Nucleic acid informatics" EXACT [] +synonym: "Nucleic acid bioinformatics" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002839 name: Molecules namespace: topic -def: "The study of specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true [Term] id: EDAM:0000078 -name: Proteins +name: Protein analysis namespace: topic -def: "The study of proteins." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000586 +def: "Processing and analysis of protein data, typically molecular sequence and structural data." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000586 ! Proteins +synonym: "Protein informatics" EXACT [] +synonym: "Protein bioinformatics" EXACT [] +synonym: "Proteins" EXACT [] +is_a: EDAM:0000003 ! Topic + +[Term] +id: EDAM:0002225 +name: Protein databases +namespace: topic +def: "Data resources concerning proteins." [EDAM:EBI "EMBRACE definition"] +subset: topic +synonym: "Protein data resources" EXACT [] +is_a: EDAM:0003071 ! Biological data resources +is_a: EDAM:0000078 ! Protein analysis + [Term] id: EDAM:0000079 name: Metabolites namespace: topic -def: "The study of the reactants or products of metabolism, typically small molecules such as including vitamins, polyols, nucleotides and amino acids." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources (typically structural data) concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." [EDAM:EBI "EMBRACE definition"] comment: This concept excludes macromolecules such as proteins and nucleic acids. subset: topic is_a: EDAM:0000154 ! Small molecules [Term] id: EDAM:0000080 +name: Sequence analysis +namespace: topic alt_id: EDAM:0002228 alt_id: EDAM:0000584 -name: Sequence -namespace: topic -def: "The study of molecular sequences (mononmer composition of polymers) and related data such as alignments and motifs." [EDAM:EBI "EMBRACE definition"] +def: "Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] subset: topic +synonym: "Sequences" EXACT [] xref: BioCatalogue:Sequence Analysis is_a: EDAM:0000003 ! Topic + +[Term] +id: EDAM:0003041 +name: Sequence databases +namespace: topic +def: "Data resources concerning molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] +subset: topic +synonym: "Sequence data" EXACT [] +synonym: "Sequence data resource" EXACT [] +synonym: "Sequence data resources" EXACT [] +is_a: EDAM:0003071 ! Biological data resources +is_a: EDAM:0000080 ! Sequence analysis + [Term] id: EDAM:0000081 +name: Structure analysis +namespace: topic +alt_id: EDAM:0000693 alt_id: EDAM:0002827 alt_id: EDAM:0000585 -name: Structure -namespace: topic -def: "The study of molecular secondary or tertiary (3D) structures and related data such as alignments and structural motifs." [EDAM:EBI "EMBRACE definition"] +def: "Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids." [EDAM:EBI "EMBRACE definition"] +comment: This includes related concepts such as structural properties, alignments and structural motifs. subset: topic -synonym: "Structure analysis" EXACT [] +synonym: "Structural bioinformatics" EXACT [] +synonym: "Computation structural biology" EXACT [] is_a: EDAM:0000003 ! Topic + +[Term] +id: EDAM:0003038 +name: Structure databases +namespace: topic +alt_id: EDAM:0003059 +def: "Data resources concerning molecular secondary or tertiary (3D) structural information, typically of proteins and nucleic acids." [EDAM:EBI "EMBRACE definition"] +subset: topic +synonym: "Structure data resources" EXACT [] +is_a: EDAM:0003071 ! Biological data resources +is_a: EDAM:0000081 ! Structure analysis + + [Term] id: EDAM:0000082 name: Structure prediction namespace: topic -def: "Study concerning the prediction of molecular (secondary or tertiary) structure." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000171 +def: "Resources concerning the prediction of molecular (secondary or tertiary) structure." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000081 ! Structure +is_a: EDAM:0000081 ! Structure analysis [Term] id: EDAM:0000083 name: Alignment namespace: topic -def: "Study concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000182 ! Sequence alignment @@ -870,30 +1032,44 @@ consider: EDAM:0000184 ! Threading [Term] id: EDAM:0000084 +alt_id: EDAM:0000192 +alt_id: EDAM:0000193 name: Phylogenetics namespace: topic -def: "The study of evolutionary relationships amongst organisms." [EDAM:EBI "EMBRACE definition"] -comment: Phylogenetics involves phylogenetic tree construction, typically from molecular sequence or morphological data. It can be used to analyse the genetic basis of heredity and variation, gene transfer, mode of selection / evolution etc. +alt_id: EDAM:0000636 +def: "Resources concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc." [EDAM:EBI "EMBRACE definition"] +comment: This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data. subset: topic xref: BioCatalogue:Phylogeny xref: BioCatalogue:Statistical Robustness +synonym: "Phylogenetic simulation" EXACT [] +synonym: "Phylogenetic clocks, dating and stratigraphy" EXACT [] is_a: EDAM:0000003 ! Topic + + + + + + + [Term] id: EDAM:0000200 +alt_id: EDAM:0000206 name: Microarrays namespace: topic -def: "The study of microarrays, for example, to process microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning microarrays, for example, to process microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Microarrays -is_a: EDAM:0000003 ! Topic +synonym: "DNA microarrays" EXACT [] +is_a: EDAM:0000607 ! Laboratory resources [Term] id: EDAM:0000121 -alt_id: EDAM:0000764 name: Proteomics namespace: topic -def: "The study of experimental methods for studying the whole proteomes of organisms." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000764 +def: "Informatics resources concerning the study of whole proteomes of organisms." [EDAM:EBI "EMBRACE definition"] comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues). subset: topic synonym: "Protein expression" EXACT [] @@ -901,472 +1077,340 @@ xref: BioCatalogue:Proteomics is_a: EDAM:0000003 ! Topic + + + [Term] id: EDAM:0000085 name: Functional genomics namespace: topic -def: "The study of gene or protein functions and their interactions." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the study of gene or protein functions and their interactions." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000622 ! Genomics +is_a: EDAM:0000622 ! Genomics [Term] id: EDAM:0000122 name: Structural genomics namespace: topic -def: "Determine or study the three dimensional structure for all (available) proteins in a given organism." [EDAM:EBI "EMBRACE definition"] +def: "Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0002226 ! Structure determination +xref: BioCatalogue:Structural Genomics +is_a: EDAM:0002226 ! Structure determination +is_a: EDAM:0000622 ! Genomics + + -[Term] -id: EDAM:0000086 -name: Model organisms -namespace: topic -def: "The study of a model organism." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000621 ! Organism [Term] -id: EDAM:0000087 -name: Health and disease +id: EDAM:0003061 +name: Documentation and help namespace: topic -def: "The study of health and disease, particularly in humans." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning documentation and getting help." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000634 ! Disease -consider: EDAM:0000803 ! Human disease +is_a: EDAM:0003068 ! Literature and reference + + [Term] -id: EDAM:0000088 -name: Literature and documentation +id: EDAM:0003047 +name: Molecular biology reference namespace: topic -def: "The study of the bioinformatics literature, bibliographic data and documentation." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning general molecular biology information extracted from the literature." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue: Document Discovery xref: BioCatalogue: Literature retrieval -is_a: EDAM:0000003 ! Topic +is_a: EDAM:0000606 ! Literature data resources + [Term] id: EDAM:0000089 name: Ontologies namespace: topic -def: "The study of ontologies of biological or bioinformatics concepts (terms and relations), controlled vocabularies, structured glossary or other related resource." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002255 +def: "Resources concerning ontologies of biological or bioinformatics concepts (terms and relations), controlled vocabularies, structured glossary or other related resource." [EDAM:EBI "EMBRACE definition"] comment: This includes the annotation of entities (typically biological database entries) with terms from a controlled vocabulary. subset: topic synonym: "Ontology" EXACT [] xref: BioCatalogue:Ontology xref: BioCatalogue:Ontology Lookup -is_a: EDAM:0002829 ! Ontologies and nomenclature +is_a: EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0000090 -name: Data retrieval +alt_id: EDAM:0000155 +alt_id: EDAM:0002274 +alt_id: EDAM:0000165 +name: Data search and retrieval namespace: topic -def: "Study concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [EDAM:EBI "EMBRACE definition"] +comment: This includes, for example, search, query and retrieval of molecular sequences and associated data. subset: topic +synonym: "Data retrieval" EXACT [] +xref: BioCatalogue:Sequence Retrieval xref: BioCatalogue:Data Retrieval xref: BioCatalogue:Identifier Retrieval xref: BioCatalogue:Image Retrieval +xref: BioCatalogue:Structure Retrieval is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0000091 name: Data handling namespace: topic -def: "The study of the generic management of biological data including basic handling of files and databases, datatypes and workflows." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002282 +def: "Resources for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Data types, processing and visualisation" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0000092 -name: Data rendering and visualisation +name: Data visualisation namespace: topic -def: "The plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [EDAM:EBI "EMBRACE definition"] +def: "Resources for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [EDAM:EBI "EMBRACE definition"] subset: topic +synonym: "Data rendering and visualisation" EXACT [] +synonym: "Data rendering" EXACT [] +synonym: "Data plotting" EXACT [] is_a: EDAM:0000091 ! Data handling -[Term] -id: EDAM:0002282 -name: Datatypes, workflows and data handling -namespace: topic -def: "The study of handling biological data in a generic sense, including datatypes, data identifiers, data management, workflows etc." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000769 ! Workflows -consider: EDAM:0000770 ! Data types and objects [Term] id: EDAM:0002258 name: Chemoinformatics namespace: topic -def: "The application of information technology to chemistry." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources for the application of information technology to chemistry." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Cheminformatics" EXACT [] synonym: "Chemical informatics" EXACT [] synonym: "Computational chemistry" EXACT [] xref: BioCatalogue:Chemoinformatics -is_a: EDAM:0002841 ! Informatics +is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002269 name: Biostatistics namespace: topic -def: "The application of statistical methods to biological problems." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources for the application of statistical methods to biological problems." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Biometry" EXACT [] synonym: "Biometrics" EXACT [] xref: BioCatalogue:Biostatistics -is_obsolete: true -consider: EDAM:0000091 ! Data handling +is_a: EDAM:0000091 ! Data handling [Term] -id: EDAM:0000094 -name: Nucleic acid physicochemistry +id: EDAM:0003077 +alt_id: EDAM:0001779 +name: Data acquisition and deposition namespace: topic -def: "The study of the physical or chemical properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the acquisition and deposition of biological data." [EDAM:EBI "EMBRACE definition"] +synonym: "Database submission" EXACT [] subset: topic -is_a: EDAM:0000077 ! Nucleic acids +is_a: EDAM:0000091 ! Data handling + [Term] -id: EDAM:0000095 -name: Nucleic acid features +id: EDAM:0000094 +name: Nucleic acid thermodynamics namespace: topic -def: "The study of the positional features of nucleic acids." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000614 +alt_id: EDAM:0000104 +def: "Informatics resources concerning the study of the thermodynamic properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"] +comment: This includes the study of thermal and conformational properties including DNA or DNA/RNA denaturation (melting). subset: topic -is_obsolete: true -consider: EDAM:0000747 ! Nucleic acid functional sites +synonym: "Nucleic acid physicochemistry" EXACT [] +synonym: "Nucleic acid properties" EXACT [] +synonym: "Nucleic acid denaturation" EXACT [] +synonym: "DNA melting" EXACT [] +is_a: EDAM:0000640 ! Nucleic acid sequence analysis + + [Term] id: EDAM:0000097 -alt_id: EDAM:0002833 -name: Nucleic acid structure +name: Nucleic acid structure analysis namespace: topic -def: "The study of nucleic acid (secondary or tertiary) structural data such as whole structures, structural features and associated annotation." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000699 +alt_id: EDAM:0000106 +def: "The processing and analysis of nucleic acid (secondary or tertiary) structural data." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000077 ! Nucleic acids -is_a: EDAM:0000081 ! Structure +is_a: EDAM:0000081 ! Structure analysis +is_a: EDAM:0000077 ! Nucleic acid analysis + [Term] -id: EDAM:0000098 -name: DNA +id: EDAM:0003039 +name: Nucleic acid structure namespace: topic -def: "The study of DNA." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002833 +def: "Data resources concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000654 ! DNA +is_a: EDAM:0003038 ! Structure databases + [Term] id: EDAM:0000099 name: RNA namespace: topic -def: "The study of RNA." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000653 +def: "Informatics resources concerning RNA sequences and structures." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM: EDAM:0000653 ! RNA +is_a: EDAM:0003042 ! Nucleic acid sequences + [Term] id: EDAM:0000100 name: Nucleic acid restriction namespace: topic -def: "The study of restriction enzymes and their cleavage sites." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000640 ! Nucleic acid sequences -is_a: EDAM:0000821 ! Enzymes - -[Term] -id: EDAM:0000104 -name: Nucleic acid denaturation -namespace: topic -def: "The study of DNA or DNA/RNA denaturation (melting) including thermal and conformational properties." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "DNA melting" EXACT [] -is_a: EDAM:0000094 ! Nucleic acid physicochemistry - -[Term] -id: EDAM:0000105 -name: Nucleic acid sequence features -namespace: topic -def: "The study of positional features in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000747 ! Nucleic acid functional sites +is_a: EDAM:0000640 ! Nucleic acid sequence analysis +is_a: EDAM:0000821 ! Enzymes and reactions -[Term] -id: EDAM:0000106 -name: Nucleic acid structural features -namespace: topic -def: "The study of positional features in nucleic acid structures." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000097 ! Nucleic acid structure [Term] id: EDAM:0000107 -name: Codon usage +name: Codon usage analysis namespace: topic -def: "The study of codon usage in nucleotide sequence(s)." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000640 ! Nucleic acid sequences +is_a: EDAM:0000110 ! Transcription [Term] id: EDAM:0000109 name: Gene finding namespace: topic -def: "Study that aims to identify, predict, model or analyse genes or gene structure in DNA sequences." [EDAM:EBI "EMBRACE definition"] +def: "Resources that aim to identify, predict, model or analyse genes or gene structure in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. subset: topic synonym: "Gene prediction" EXACT [] xref: BioCatalogue:Gene Prediction -is_a: EDAM:0002816 ! Genes +is_a: EDAM:0003073 ! Nucleic acid feature detection [Term] id: EDAM:0000110 name: Transcription namespace: topic -def: "The study of the transcription of DNA into mRNA and transcription regulation including transcription factors and regulatory motifs, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"] -comment: This includes promoters, enhancers, silencers and boundary elements / insulators. +def: "Informatics resources concerning the transcription of DNA into mRNA." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Transcription Factors -is_a: EDAM:0000197 ! Gene expression and regulation +is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0000108 name: Translation namespace: topic -def: "The study of the translation of mRNA into protein." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the translation of mRNA into protein." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000197 ! Gene expression and regulation +is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0000111 name: Promoters namespace: topic -def: "The study of promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene)." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins)." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Promoter Prediction -is_a: EDAM:0000110 ! Transcription +is_obsolete: true +consider: EDAM:0000749 ! Transcription factors and regulatory sites [Term] id: EDAM:0000112 name: Nucleic acid folding namespace: topic -def: "The study of the folding (in 3D space) of nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the folding (in 3D space) of nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000173 ! Nucleic acid structure prediction [Term] -id: EDAM:0000113 -name: Functional RNA -namespace: topic -def: "The study of functional or non-coding RNA." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000659 ! Functional RNA - -[Term] id: EDAM:0000114 -name: RNA splicing -namespace: topic -def: "The study of RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [EDAM:EBI "EMBRACE definition"] -comment: This includes splice sites, splicing patterns and alternatives, etc. -subset: topic -is_a: EDAM:0000653 ! RNA -is_a: EDAM:0000197 ! Gene expression and regulation -is_a: EDAM:0000630 ! Gene structure - -[Term] -id: EDAM:0000115 -name: tRNA -namespace: topic -def: "The study of transfer RNA (tRNA)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000663 ! tRNA - -[Term] -id: EDAM:0000116 -name: rRNA +name: Gene structure and RNA splicing namespace: topic -def: "The study of ribosomal RNA (rRNA)." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000750 +def: "Informatics resources concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [EDAM:EBI "EMBRACE definition"] +comment: This includes splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. subset: topic -is_obsolete: true -consider: EDAM:0000660 ! rRNA - -[Term] -id: EDAM:0000117 -name: microRNA -namespace: topic -def: "The study of microRNA (miRNA)." [EDAM:EBI "EMBRACE definition"] -comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. -subset: topic -is_obsolete: true -consider: EDAM:0000661 ! miRNA - -[Term] -id: EDAM:0000118 -name: siRNA -namespace: topic -def: "The study of small interfering (silencing) RNA (siRNA)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000662 ! siRNA +synonym: "RNA splicing" EXACT [] +synonym: "Gene structure" EXACT [] +is_a: EDAM:0003062 ! Genetic organisation +is_a: EDAM:0000747 ! Nucleic acid sites and features -[Term] -id: EDAM:0000119 -name: piRNA -namespace: topic -def: "The study of piwi-interacting RNA (piRNA)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000659 ! Functional RNA sequence -[Term] -id: EDAM:0000120 -name: snoRNA -namespace: topic -def: "The study of small nucleolar RNA (snoRNAs)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000665 ! snoRNA [Term] id: EDAM:0000123 -name: Protein physicochemistry +name: Protein properties namespace: topic -def: "The study of the physical and biochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000615 +def: "Informatics resources for the study of the physical and biochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000586 ! Proteins +synonym: "Protein physicochemistry" EXACT [] +is_a: EDAM:0000639 ! Protein sequence analysis -[Term] -id: EDAM:0000124 -name: Protein features -namespace: topic -def: "The study of the positional features of protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000748 ! Protein functional sites [Term] id: EDAM:0001775 -name: Protein function +name: Protein function analysis namespace: topic -def: "The study of protein function." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0003057 +def: "Informatics resources for the study of protein function." [EDAM:EBI "EMBRACE definition"] subset: topic -xref: BioCatalogue:Function Prediction -is_a: EDAM:0000586 ! Proteins +is_a: EDAM:0000078 ! Protein analysis -[Term] -id: EDAM:0000127 -name: Protein domains -namespace: topic -def: "The study of protein structural domains." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000736 ! Protein domains [Term] id: EDAM:0000128 name: Protein interactions namespace: topic -def: "The study of protein-protein, protein-DNA/RNA and protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000587 +def: "Informatics resources concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Interaction -is_a: EDAM:0000586 ! Proteins +is_a: EDAM:0001775 ! Protein function analysis +is_a: EDAM:0002225 ! Protein databases -[Term] -id: EDAM:0000129 -name: Protein classification -namespace: topic -def: "The study of the classification of proteins (from sequence or structural data)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000595 ! Protein classification [Term] id: EDAM:0000130 -name: Protein folding, stability and design -namespace: topic -def: "The study of protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation and the implications for protein design." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000586 ! Proteins - -[Term] -id: EDAM:0000131 -name: Transmembrane proteins +name: Protein folding and stability namespace: topic -def: "The study of a protein or region of a protein that spans a membrane." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000820 ! Membrane protein +is_a: EDAM:0002814 ! Protein structure analysis [Term] id: EDAM:0002232 name: Lipoproteins namespace: topic -def: "The study of lipoproteins (protein-lipid assemblies)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000635 ! Specific protein - -[Term] -id: EDAM:0000132 -name: Enzymes -namespace: topic -def: "The study of proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning lipoproteins (protein-lipid assemblies)." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000821 ! Enzymes +is_a: EDAM:0000635 ! Specific protein resources [Term] id: EDAM:0000137 name: Protein hydropathy namespace: topic -def: "The study of the hydrophobic, hydrophilic and charge properties of a protein." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000123 ! Protein physicochemistry - -[Term] -id: EDAM:0000138 -name: Protein sequence features -namespace: topic -def: "Predict, identify or analyse features in protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources for the study of the hydrophobic, hydrophilic and charge properties of a protein." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000748 ! Protein functional sites - -[Term] -id: EDAM:0000139 -name: Protein structural features -namespace: topic -def: "Predict, identify or analyse protein structural features." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000166 ! Protein structural motifs +is_a: EDAM:0000123 ! Protein properties [Term] id: EDAM:0000140 name: Protein targeting and localization namespace: topic -def: "The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000588 +def: "Informatics resources for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000586 ! Proteins +is_a: EDAM:0002276 ! Protein function prediction +is_a: EDAM:0002225 ! Protein databases -[Term] -id: EDAM:0002124 -name: Protein secondary structure analysis -namespace: topic -def: "Handle and analyse protein secondary structure." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000694 ! Protein secondary structure [Term] id: EDAM:0000143 name: Protein structure comparison namespace: topic -def: "Study concerning the comparison of two or more protein structures." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the comparison of two or more protein structures." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that are exclusively for protein structure. subset: topic is_obsolete: true @@ -1377,52 +1421,39 @@ consider: EDAM:0001770 ! Structure comparison id: EDAM:0002280 name: Nucleic acid structure comparison namespace: topic -def: "The study of the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that are exclusively for nucleic acid structures. subset: topic is_obsolete: true -consider: EDAM:0000097 ! Nucleic acid structure +consider: EDAM:0000097 ! Nucleic acid structure analysis consider: EDAM:0001770 ! Structure comparison [Term] id: EDAM:0000144 -name: Protein residue interactions +name: Protein residue interaction analysis namespace: topic -def: "The study of inter-atomic or inter-residue interactions in protein (3D) structures." [EDAM:EBI "EMBRACE definition"] +def: "The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000694 ! Protein secondary structure +synonym: "Protein residue interactions" EXACT [] +is_a: EDAM:0002814 ! Protein structure analysis -[Term] -id: EDAM:0000145 -name: Molecular flexibility and motion -namespace: topic -def: "The study of flexibility and motion in protein and other molecular structures." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000176 ! Molecular dynamics -[Term] -id: EDAM:0000146 -name: Protein surfaces -namespace: topic -def: "The study of the surface of a protein structure, including biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"] -comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. -subset: topic -is_a: EDAM:0000698 ! Protein tertiary structure [Term] id: EDAM:0002276 name: Protein function prediction namespace: topic -def: "Study concerning the prediction of functional properties of a protein." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the prediction of functional properties of a protein." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Function Prediction -is_a: EDAM:0001775 ! Protein function +is_a: EDAM:0001775 ! Protein function analysis [Term] id: EDAM:0000147 name: Protein-protein interactions namespace: topic -def: "The study of protein-protein interactions, protein complexes, protein functional coupling etc." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000719 +def: "Informatics resources concerning protein-protein interactions, protein complexes, protein functional coupling etc." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000128 ! Protein interactions @@ -1430,7 +1461,8 @@ is_a: EDAM:0000128 ! Protein interactions id: EDAM:0000148 name: Protein-ligand interactions namespace: topic -def: "The study of protein-ligand (small molecule) interactions." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000717 +def: "Informatics resources concerning protein-ligand (small molecule) interactions." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Ligand Interaction is_a: EDAM:0000128 ! Protein interactions @@ -1439,26 +1471,28 @@ is_a: EDAM:0000128 ! Protein interactions id: EDAM:0000149 name: Protein-nucleic acid interactions namespace: topic -def: "The study of protein-DNA/RNA interactions." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000718 +def: "Informatics resources concerning protein-DNA/RNA interactions." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000128 ! Protein interactions [Term] id: EDAM:0000150 -name: Protein rational design +name: Protein design namespace: topic -def: "The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000130 ! Protein folding, stability and design +is_a: EDAM:0000172 ! Protein structure prediction + [Term] id: EDAM:0000151 name: G protein-coupled receptors (GPCR) namespace: topic -def: "The study of G-protein coupled receptors (GPCRs)." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning G-protein coupled receptors (GPCRs)." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true -consider: EDAM:0000820 ! Membrane protein +consider: EDAM:0000820 ! Membrane proteins [Term] id: EDAM:0002278 @@ -1472,114 +1506,112 @@ consider: EDAM:0000178 ! Protein secondary structure prediction [Term] id: EDAM:0000152 -alt_id: EDAM:0000695 name: Carbohydrates namespace: topic -def: "The study of carbohydrates, typically including structural information." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000695 +def: "Informatics resources concerning carbohydrates, typically including structural information." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000081 ! Structure +is_a: EDAM:0003038 ! Structure databases [Term] id: EDAM:0000153 -alt_id: EDAM:0002624 name: Lipids namespace: topic -def: "The study of lipids and their structures." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002624 +def: "Informatics resources concerning lipids and their structures." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000081 ! Structure +is_a: EDAM:0003038 ! Structure databases [Term] id: EDAM:0000154 -alt_id: EDAM:0000696 name: Small molecules namespace: topic -def: "The study of small molecules of biological significance." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000696 +def: "Informatics resources concerning small molecules of biological significance, typically including structural information." [EDAM:EBI "EMBRACE definition"] comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. subset: topic -is_a: EDAM:0000081 ! Structure - -[Term] -id: EDAM:0000155 -name: Sequence search and retrieval -namespace: topic -def: "Search or query a database and retrieve molecular sequences and associated data." [EDAM:EBI "EMBRACE definition"] -subset: topic -xref: BioCatalogue:Sequence Retrieval -is_obsolete: true -consider: EDAM:0000090 ! Data retrieval +is_a: EDAM:0003038 ! Structure databases + + [Term] id: EDAM:0000156 name: Sequence editing namespace: topic -def: "Create, edit, change or convert a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] +def: "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true -consider: EDAM:0000080 ! Sequence +consider: EDAM:0000080 ! Sequence analysis consider: EDAM:0000091 ! Data handling [Term] id: EDAM:0000157 -name: Sequence composition +name: Sequence composition analysis namespace: topic -def: "Analyse the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [EDAM:EBI "EMBRACE definition"] +def: "Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000080 ! Sequence +is_a: EDAM:0000080 ! Sequence analysis + + + + [Term] id: EDAM:0000158 +alt_id: EDAM:0000161 +alt_id: EDAM:0000162 name: Sequence motifs namespace: topic -def: "The study of conserved patterns (motifs) in molecular sequences." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Motifs" EXACT [] -is_a: EDAM:0000080 ! Sequence +is_a: EDAM:0000594 ! Sequence classification + [Term] id: EDAM:0000188 name: Sequence profiles and HMMs namespace: topic -def: "The study of sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000744 +alt_id: EDAM:0000746 +alt_id: EDAM:0001763 +def: "Resources concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. subset: topic -is_a: EDAM:0000080 ! Sequence -is_a: EDAM:0000182 ! Sequence alignment +is_a: EDAM:0000594 ! Sequence classification [Term] id: EDAM:0000159 +alt_id: EDAM:0002260 +alt_id: EDAM:0002261 name: Sequence comparison namespace: topic -def: "Study concerning the comparison of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the comparison of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. subset: topic -is_a: EDAM:0000080 ! Sequence +xref: BioCatalogue:Protein Sequence Similarity +xref: BioCatalogue:Nucleotide Sequence Similarity +is_a: EDAM:0000080 ! Sequence analysis + [Term] id: EDAM:0000160 -name: Sequence features +name: Sequence sites and features namespace: topic -def: "The study of the positional features of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000600 +def: "Data resources concerning the positional features, such as functional and other key sites, in molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000080 ! Sequence +is_a: EDAM:0003041 ! Sequence databases -[Term] -id: EDAM:0000161 -name: Protein sequence motifs -namespace: topic -def: "The study of conserved patterns (motifs) in protein sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -xref: BioCatalogue:Motifs -is_obsolete: true -consider: EDAM:0000158 ! Sequence motifs [Term] -id: EDAM:0000162 -name: Nucleic acid sequence motifs +id: EDAM:0003072 +name: Sequence feature detection namespace: topic -def: "The study of conserved patterns (motifs) in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the detection of the positional features, such as functional and other key sites, in molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000158 ! Sequence motifs +is_a: EDAM:0000080 ! Sequence analysis + [Term] id: EDAM:0000163 @@ -1592,112 +1624,87 @@ is_obsolete: true consider: EDAM:0000159 ! Sequence comparison [Term] -id: EDAM:0000164 -alt_id: EDAM:0000594 -name: Sequence clustering +id: EDAM:0003052 +name: Sequence clusters and classification namespace: topic -def: "The study of molecular sequences that have been compared and grouped together on the basis of similarity." [EDAM:EBI "EMBRACE definition"] -comment: This includes systems that generate, process, analyse or store sequence clusters. +def: "Data resources concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity." [EDAM:EBI "EMBRACE definition"] +comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. subset: topic -is_a: EDAM:0000159 ! Sequence comparison -is_a: EDAM:0002230 ! Classification +synonym: "Sequence clusters" EXACT [] +synonym: "Sequence families" EXACT [] +is_a: EDAM:0003041 ! Sequence databases -[Term] -id: EDAM:0002260 -name: Protein sequence comparison -namespace: topic -def: "Compare two or more protein sequences." [EDAM:EBI "EMBRACE definition"] -comment: Use this term for methods that are exclusively for protein sequences. -subset: topic -xref: BioCatalogue:Protein Sequence Similarity -is_obsolete: true -consider: EDAM:0000159 ! Sequence comparison -consider: EDAM:0000639 ! Protein sequences [Term] -id: EDAM:0002261 -name: Nucleic acid sequence comparison +id: EDAM:0000164 +name: Sequence clustering namespace: topic -def: "Compare two or more nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -comment: Use this term for methods that are exclusively for nucleotide sequences. +def: "Resources concerning the comparison and grouping together of molecular sequences on the basis of their similarities." [EDAM:EBI "EMBRACE definition"] +comment: This includes systems that generate, process and analyse sequence clusters. subset: topic -xref: BioCatalogue:Nucleotide Sequence Similarity -is_obsolete: true -consider: EDAM:0000159 ! Sequence comparison -consider: EDAM:0000640 ! Nucleic acid sequences +is_a: EDAM:0000159 ! Sequence comparison + [Term] -id: EDAM:0000165 -name: Structure search and retrieval +id: EDAM:0000594 +name: Sequence classification namespace: topic -def: "Search or query a database and retrieve molecular structures." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the classification of molecular sequences based on some measure of their similarity." [EDAM:EBI "EMBRACE definition"] +comment: Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. subset: topic -xref: BioCatalogue:Structure Retrieval -is_obsolete: true -consider: EDAM:0000081 ! Structure -consider: EDAM:0000090 ! Data retrieval +is_a: EDAM:0000080 ! Sequence analysis + + + [Term] id: EDAM:0000166 -name: Protein structural motifs +name: Protein structural motifs and surfaces namespace: topic -def: "The study of (3D) structural features or common 3D motifs within protein structures." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000139 +alt_id: EDAM:0000170 +alt_id: EDAM:0000146 +alt_id: EDAM:0000589 +def: "Resources concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"] +comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. subset: topic +synonym: "Protein structural features" EXACT [] +synonym: "Protein surfaces" EXACT [] +synonym: "Protein structural motifs" EXACT [] +synonym: "Structural motifs" EXACT [] is_a: EDAM:0000698 ! Protein tertiary structure [Term] id: EDAM:0000167 name: Structural (3D) profiles namespace: topic -def: "Generate, manipulate, analyse or use some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000599 +def: "The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Structural profiles" EXACT [] is_a: EDAM:0001770 ! Structure comparison [Term] id: EDAM:0001770 +alt_id: EDAM:0000168 +alt_id: EDAM:0000169 name: Structure comparison namespace: topic -def: "Study concerning the comparison of two or more molecular structures." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the comparison of two or more molecular structures." [EDAM:EBI "EMBRACE definition"] +comment: This might involve comparison of secondary or tertiary (3D) structural information. subset: topic -is_a: EDAM:0000081 ! Structure +is_a: EDAM:0000081 ! Structure analysis [Term] id: EDAM:0002844 name: Structural clustering namespace: topic -def: "The study of molecular structures that have been compared and grouped together on the basis of similarity; generate, process, analyse or store structural clusters." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Structure classification" EXACT [] is_a: EDAM:0001770 ! Structure comparison -is_a: EDAM:0002230 ! Classification -[Term] -id: EDAM:0000170 -name: Structural features and motifs -namespace: topic -def: "The study of structural features and common motifs of molecular structures." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000166 ! Protein structural motifs - -[Term] -id: EDAM:0000168 -name: Secondary structure comparison -namespace: topic -def: "The study of the comparison of two or more protein secondary structures." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000694 ! Protein secondary structure -[Term] -id: EDAM:0000169 -name: Tertiary structure comparison -namespace: topic -def: "Study concerning the comparison of two or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0001770 ! Structure comparison -is_a: EDAM:0000698 ! Protein tertiary structure [Term] id: EDAM:0002271 @@ -1709,42 +1716,45 @@ subset: topic is_obsolete: true consider: EDAM:0001770 ! Structure comparison -[Term] -id: EDAM:0000171 -name: Tertiary structure prediction -namespace: topic -def: "Predict protein or nucleic acid tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000082 ! Structure prediction [Term] id: EDAM:0000172 name: Protein structure prediction namespace: topic -def: "Study concerning the prediction of secondary or tertiary structure or other structural features of protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Structure Prediction is_a: EDAM:0000082 ! Structure prediction +is_a: EDAM:0002814 ! Protein structure analysis [Term] id: EDAM:0000173 name: Nucleic acid structure prediction namespace: topic -def: "Study concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000181 +def: "Resources concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Nucleic acid folding" EXACT [] +synonym: "RNA/DNA structure prediction" EXACT [] xref: BioCatalogue:Nucleotide Structure Prediction xref: BioCatalogue:Nucleotide Secondary Structure xref: BioCatalogue:Nucleotide Tertiary Structure is_a: EDAM:0000082 ! Structure prediction -is_a: EDAM:0000097 ! Nucleic acid structure +is_a: EDAM:0000097 ! Nucleic acid structure analysis + +[Term] +id: EDAM:0002953 +name: Nucleic acid design +namespace: topic +def: "Resources for the design of nucleic acid sequences with specific conformations." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000174 name: Ab initio structure prediction namespace: topic -def: "Study concerning the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [EDAM:EBI "EMBRACE definition"] +def: "Resources for the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "de novo protein structure prediction" EXACT [] is_a: EDAM:0000082 ! Structure prediction @@ -1753,32 +1763,37 @@ is_a: EDAM:0000082 ! Structure prediction id: EDAM:0002275 name: Molecular modelling namespace: topic -def: "Study concering the construction or analysis of models of a molecules properties or behaviour. " [EDAM:EBI "EMBRACE definition"] +def: "Resources for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. " [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000082 ! Structure prediction +is_a: EDAM:0000172 ! Protein structure prediction [Term] id: EDAM:0000175 name: Homology modelling namespace: topic -def: "The modelling of the three-dimensional structure of a protein using known sequence and structural data." [EDAM:EBI "EMBRACE definition"] +def: "Resources for the modelling of the three-dimensional structure of a protein using known sequence and structural data." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Comparative modelling" EXACT [] is_a: EDAM:0002275 ! Molecular modelling [Term] id: EDAM:0000176 +alt_id: EDAM:0000145 name: Molecular dynamics namespace: topic -def: "The study of the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [EDAM:EBI "EMBRACE definition"] +comment: This includes resources concerning flexibility and motion in protein and other molecular structures. subset: topic +synonym: "Molecular motions" EXACT [] +synonym: "Molecular flexibility" EXACT [] is_a: EDAM:0002275 ! Molecular modelling [Term] id: EDAM:0000177 name: Molecular docking namespace: topic -def: "Modelling of the structure of a protein in complex with a small molecule or another macromolecule." [EDAM:EBI "EMBRACE definition"] +def: "Resources for modelling the structure of proteins in complex with small molecules or other macromolecules." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002275 ! Molecular modelling @@ -1786,140 +1801,92 @@ is_a: EDAM:0002275 ! Molecular modelling id: EDAM:0000178 name: Protein secondary structure prediction namespace: topic -def: "Study concerning the prediction of secondary or supersecondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the prediction of secondary or supersecondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Secondary Structure is_a: EDAM:0000172 ! Protein structure prediction -is_a: EDAM:0000694 ! Protein secondary structure [Term] id: EDAM:0000179 name: Protein tertiary structure prediction namespace: topic -def: "Study concerning the prediction of tertiary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the prediction of tertiary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Tertiary Structure is_a: EDAM:0000172 ! Protein structure prediction -is_a: EDAM:0000698 ! Protein tertiary structure [Term] id: EDAM:0000180 name: Protein fold recognition namespace: topic -def: "Study concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000172 ! Protein structure prediction -[Term] -id: EDAM:0000181 -name: RNA structure prediction -namespace: topic -def: "Predict or design secondary or tertiary structure of RNA." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0000182 -alt_id: EDAM:0000187 name: Sequence alignment namespace: topic -def: "Study concerning the generation or analysis of alignments of molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] -comment: This includes the generation of alignments (the identification of equivalent sites) and the analysis of alignments. +alt_id: EDAM:0002283 +alt_id: EDAM:0000185 +alt_id: EDAM:0000186 +alt_id: EDAM:0000187 +alt_id: EDAM:0000596 +alt_id: EDAM:0000189 +def: "Resources concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] +comment: This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. subset: topic xref: BioCatalogue:Protein Sequence Alignment xref: BioCatalogue:Nucleotide Sequence Alignment +xref: BioCatalogue:Protein Pairwise Alignment +xref: BioCatalogue:Nucleotide Pairwise Alignment +xref: BioCatalogue:Protein Multiple Alignment +xref: BioCatalogue:Nucleotide Multiple Alignment is_a: EDAM:0000159 ! Sequence comparison +is_a: EDAM:0003041 ! Sequence databases -[Term] -id: EDAM:0002283 -name: Sequence profile alignment -namespace: topic -def: "The study of the alignment (equivalence between sites) of sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000183 -alt_id: EDAM:0000597 -alt_id: EDAM:0000190 +alt_id: EDAM:0002272 +alt_id: EDAM:0002273 name: Structure alignment namespace: topic -def: "Study concerning the generation or analysis of alignments (superimposition) of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000597 +alt_id: EDAM:0000190 +def: "Resources concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +comment: This includes the generation, storage, analysis, rendering etc. of structure alignments. subset: topic synonym: "Structure alignment generation" EXACT [] is_a: EDAM:0001770 ! Structure comparison +is_a: EDAM:0003038 ! Structure databases [Term] id: EDAM:0000184 name: Threading namespace: topic -def: "Study concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Sequence-structure alignment" EXACT [] -is_a: EDAM:0000175 ! Homology modelling +is_a: EDAM:0000180 ! Protein fold recognition -[Term] -id: EDAM:0000185 -name: Pairwise sequence alignment -namespace: topic -def: "Align exactly two molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] -subset: topic -xref: BioCatalogue:Protein Pairwise Alignment -xref: BioCatalogue:Nucleotide Pairwise Alignment -is_obsolete: true -consider: EDAM:0000182 ! Sequence alignment -[Term] -id: EDAM:0000186 -name: Multiple sequence alignment -namespace: topic -def: "Align two or more molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] -subset: topic -xref: BioCatalogue:Protein Multiple Alignment -xref: BioCatalogue:Nucleotide Multiple Alignment -is_obsolete: true -consider: EDAM:0000182 ! Sequence alignment - -[Term] -id: EDAM:0000189 -name: Structure-based sequence alignment -namespace: topic -def: "Study concerning the alignment of molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000182 ! Sequence alignment - - -[Term] -id: EDAM:0002272 -name: Multiple structure alignment -namespace: topic -def: "Align (superimpose) two or more molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000183 ! Structure alignment - -[Term] -id: EDAM:0002273 -name: Pairwise structure alignment -namespace: topic -def: "Align (superimpose) exactly two molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000183 ! Structure alignment [Term] id: EDAM:0000191 name: Phylogeny reconstruction namespace: topic -def: "Study concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] +comment: Currently too specific for the topic branch (but might be unobsoleted). subset: topic xref: BioCatalogue:Tree Inference xref: BioCatalogue:Evolutionary Distance Measurements is_a: EDAM:0000084 ! Phylogenetics + + [Term] id: EDAM:0002257 name: Phylogeny visualisation @@ -1930,28 +1897,12 @@ xref: BioCatalogue:Tree Display is_obsolete: true consider: EDAM:0000084 ! Phylogenetics -[Term] -id: EDAM:0000192 -name: Phylogenetic simulation -namespace: topic -def: "Simulate DNA sequence evolution, a phylogenetic tree or the underlying data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000084 ! Phylogenetics - -[Term] -id: EDAM:0000193 -name: Phylogenetic clocks, dating and stratigraphy -namespace: topic -def: "Estimate or use molecular clock and stratigraphic (age) data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000084 ! Phylogenetics [Term] id: EDAM:0000194 name: Phylogenomics namespace: topic -def: "The study of integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000084 ! Phylogenetics is_a: EDAM:0000622 ! Genomics @@ -1960,25 +1911,28 @@ is_a: EDAM:0000622 ! Genomics id: EDAM:0002842 name: High-throughput sequencing namespace: topic -def: "The study of parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Next-generation sequencing" EXACT [] -is_a: EDAM:0000102 ! Sequencing and mapping +is_obsolete: true +consider: EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0000195 -name: Polymerase chain reaction +name: Virtual PCR namespace: topic -def: "Study concerning the polymerase chain reaction (PCR)." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning simulated polymerase chain reaction (PCR)." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "PCR" EXACT [] -is_a: EDAM:0000102 ! Sequencing and mapping +synonym: "Polymerase chain reaction" EXACT [] +is_obsolete: true +consider: EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000196 name: Sequence assembly namespace: topic -def: "Study concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000102 ! Sequencing and mapping @@ -1987,155 +1941,129 @@ is_a: EDAM:0000102 ! Sequencing and mapping id: EDAM:0000133 name: Two-dimensional gel electrophoresis namespace: topic -def: "The study of two-dimensional gel electrophoresis image and related data." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000765 +def: "Resources concerning two-dimensional gel electrophoresis image and related data." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000121 ! Proteomics +is_obsolete: true +consider: EDAM:0000121 ! Proteomics + + + [Term] id: EDAM:0000134 name: Mass spectrometry namespace: topic -def: "The study of mass spectrometry and related data." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000766 +def: "Resources concerning mass spectrometry and related data." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000121 ! Proteomics +is_obsolete: true +consider: EDAM:0000121 ! Proteomics + [Term] id: EDAM:0000135 name: Protein microarrays namespace: topic -def: "The study of protein microarray data." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000121 ! Proteomics -is_a: EDAM:0000200 ! Microarrays - -[Term] -id: EDAM:0000101 -name: Comparative genomics -namespace: topic -def: "Resources to study (typically compare) the structure or function of multiple genomes." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning protein microarray data." [EDAM:EBI "EMBRACE definition"] subset: topic -xref: BioCatalogue:Comparative Genomics is_obsolete: true -consider: EDAM:0000797 ! Comparative genomics +consider: EDAM:0000121 ! Proteomics +consider: EDAM:0000200 ! Microarrays + [Term] id: EDAM:0000102 name: Sequencing and mapping namespace: topic -def: "Study concerning the determination and mapping of complete nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the determination and mapping of complete (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000003 ! Topic +is_a: EDAM:0000640 ! Nucleic acid sequence analysis + [Term] id: EDAM:0000197 -alt_id: EDAM:0000631 -alt_id: EDAM:0000204 -name: Gene expression and regulation +name: Gene expression resources namespace: topic -def: "The study of gene expression and regulation (genetic information that is used in the synthesis of a protein)." [EDAM:EBI "EMBRACE definition"] -comment: This involves analysis of microarray data, northern blots, gene-indexed expression profiles etc. +def: "Data resources concerning primarily raw or processed gene expression (typically microarray) data." [EDAM:EBI "EMBRACE definition"] +comment: This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein. subset: topic -is_a: EDAM:0002816 ! Genes +is_a: EDAM:0002816 ! Gene resources +is_a: EDAM:0000203 ! Transcriptomics -[Term] -id: EDAM:0000198 -name: Pathways and networks -namespace: topic -def: "The study of biological pathways and networks." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000602 ! Pathways, networks and models [Term] -id: EDAM:0000199 -name: Mutation and polymorphism +id: EDAM:0003062 +name: Genetic organisation namespace: topic -def: "The study of DNA sequence variation (mutation and polymorphism) data." [EDAM:EBI "EMBRACE definition"] +def: "Data resources concerning the structural and functional organisation of genes and other genetic elements." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000640 ! Nucleic acid sequences -is_a: EDAM:0000625 ! Genotype and phenotype +is_a: EDAM:0002816 ! Gene resources + + [Term] -id: EDAM:0000202 -name: Pharmacoinformatics +id: EDAM:0000204 +name: Gene regulation resources namespace: topic -def: "The application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0003049 +alt_id: EDAM:0000631 +def: "Data resources concerning primarily the regulation of gene expression." [EDAM:EBI "EMBRACE definition"] subset: topic -synonym: "Computational pharmacology" EXACT [] -is_a: EDAM:0002841 ! Informatics +is_a: EDAM:0002816 ! Gene resources [Term] -id: EDAM:0000203 -name: Gene expression profiling +id: EDAM:0000199 +name: Genetic variation namespace: topic -def: "Study concerning the analysis of mRNA expression levels, by identifying, quantifying or comparing mRNA transcripts or interpreting (in functional terms) gene expression data." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000626 +def: "Resources concerning DNA sequence variation (mutation and polymorphism) data." [EDAM:EBI "EMBRACE definition"] subset: topic -synonym: "Transcriptomics" EXACT [] -is_a: EDAM:0000197 ! Gene expression and regulation +synonym: "Mutation and polymorphism" EXACT [] +synonym: "DNA variation" EXACT [] +is_a: EDAM:0000625 ! Genotype and phenotype resources +is_a: EDAM:0003041 ! Sequence databases +is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] -id: EDAM:0000205 -name: EST and cDNA +id: EDAM:0000202 +name: Pharmacoinformatics namespace: topic -def: "The study of expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000197 ! Gene expression and regulation -consider: EDAM:0000655 ! mRNA, EST or cDNA +synonym: "Computational pharmacology" EXACT [] +is_a: EDAM:0002258 ! Chemoinformatics [Term] -id: EDAM:0002274 -name: Pathway search and retrieval +id: EDAM:0000203 +name: Transcriptomics namespace: topic -def: "Search or query a database and retrieve a biological pathway or associated data." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the analysis of mRNA expression levels, by identifying, quantifying or comparing mRNA transcripts or interpreting (in functional terms) gene expression data." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000602 ! Pathways, networks and models +synonym: "Gene expression profiling" EXACT [] +synonym: "Expression profiling" EXACT [] +is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002277 name: SNPs namespace: topic -def: "The study of single nucleotide polymorphisms (SNP) and associated data." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning single nucleotide polymorphisms (SNP) and associated data." [EDAM:EBI "EMBRACE definition"] comment: A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. subset: topic -is_a: EDAM:0000199 ! Mutation and polymorphism - -[Term] -id: EDAM:0000136 -name: Raw structural data analysis -namespace: topic -def: "The study of raw data from X-ray crystallography or nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy, typically to model a protein structure." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0002275 ! Molecular modelling +is_a: EDAM:0000199 ! Genetic variation [Term] -id: EDAM:0000206 -name: DNA microarrays -namespace: topic -def: "The study of DNA microarrays." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000200 ! Microarrays - -[Term] -id: EDAM:0000207 -name: DNA microarray probes -namespace: topic -def: "The study of DNA microarray probes." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000632 ! Molecular probes or primers - -[Term] id: EDAM:0000208 name: Pharmacogenomics namespace: topic -def: "The study of the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [EDAM:EBI "EMBRACE definition"] subset: topic +synonym: "Pharmacogenetics" EXACT [] is_a: EDAM:0000202 ! Pharmacoinformatics is_a: EDAM:0000622 ! Genomics @@ -2143,8 +2071,8 @@ is_a: EDAM:0000622 ! Genomics id: EDAM:0000209 name: Drug design namespace: topic -def: "Study concerning the design of drugs or potential drug compounds." [EDAM:EBI "EMBRACE definition"] -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. +def: "Informatics resources concerning the design of drugs or potential drug compounds." [EDAM:EBI "EMBRACE definition"] +comment: This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. subset: topic is_a: EDAM:0000202 ! Pharmacoinformatics @@ -2152,110 +2080,113 @@ is_a: EDAM:0000202 ! Pharmacoinformatics id: EDAM:0000210 name: Fish namespace: topic -def: "The study of fish or data concerning fish." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a fish, a group of fish or all fish. subset: topic -is_a: EDAM:0002820 ! Vertebrate +is_a: EDAM:0002820 ! Vertebrates [Term] id: EDAM:0000211 -name: Fly +name: Flies namespace: topic -def: "The study of flies or data concerning flies." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a fly, a group of flies or all flies. subset: topic -is_a: EDAM:0002819 ! Invertebrate +synonym: "Fly" EXACT [] +is_a: EDAM:0002819 ! Invertebrates [Term] -id: EDAM:0000212 -name: Model organisms (microbes) +id: EDAM:0003048 +name: Mammals namespace: topic -def: "The study of microbial model organism." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0001811 ! Prokaryote +is_a: EDAM:0002820 ! Vertebrates + [Term] id: EDAM:0000213 -name: Mouse or rat +name: Mice or rats namespace: topic -def: "The study of mice or rats or data concerning them." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a group of mice / rats or all mice / rats. subset: topic -is_a: EDAM:0002820 ! Vertebrate +synonym: "Mouse or rat" EXACT [] +is_a: EDAM:0003048 ! Mammals + [Term] -id: EDAM:0000214 -name: Model organisms (plants) +id: EDAM:0000215 +name: Worms namespace: topic -def: "The study of plants model organisms." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +comment: The resource may be specific to a worm, a group of worms or all worms. subset: topic -is_obsolete: true -consider: EDAM:0000780 ! Plant +synonym: "Worm" EXACT [] +is_a: EDAM:0002819 ! Invertebrates + [Term] -id: EDAM:0000215 -name: Worm +id: EDAM:0000217 +name: Literature analysis namespace: topic -def: "The study of worms or data concerning worms." [EDAM:EBI "EMBRACE definition"] -comment: The resource may be specific to a worm, a group of worms or all worms. +alt_id: EDAM:0000088 +alt_id: EDAM:0003058 +def: "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002819 ! Invertebrate +xref: BioCatalogue: Document Discovery +xref: BioCatalogue: Literature retrieval +synonym: "Literature search and analysis" EXACT [] +synonym: "Literature sources" EXACT [] +is_a: EDAM:0003068 ! Literature and reference + [Term] -id: EDAM:0000216 -name: Model organisms (yeast) +id: EDAM:0000606 +name: Literature data resources namespace: topic -def: "The study of yeast model organisms." [EDAM:EBI "EMBRACE definition"] +def: "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0002817 ! Yeast +is_a: EDAM:0003068 ! Literature and reference +is_a: EDAM:0003071 ! Biological data resources + [Term] -id: EDAM:0000217 -name: Literature search +id: EDAM:0003068 +name: Literature and reference namespace: topic -def: "Query the biomedical and informatics literature." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the scientific literature, reference information and documentation." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000088 ! Literature and documentation +is_a: EDAM:0000003 ! Topic + [Term] id: EDAM:0000218 name: Text mining namespace: topic -def: "Study concerning the analysis of the biomedical and informatics literature." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning the analysis of the biomedical and informatics literature." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Text data mining" EXACT [] xref: BioCatalogue:Text Mining xref: BioCatalogue:Document Similarity xref: BioCatalogue:Document Clustering xref: BioCatalogue:Named Entity Recognition -is_a: EDAM:0000088 ! Literature and documentation - - -[Term] -id: EDAM:0002255 -name: Ontology lookup -namespace: topic -def: "Query a biomedical ontology, for example to look-up terms." [EDAM:EBI "EMBRACE definition"] -subset: topic -xref: BioCatalogue:Ontology Lookup -is_obsolete: true -consider: EDAM:0000089 ! Ontologies +is_a: EDAM:0000217 ! Literature analysis [Term] id: EDAM:0000219 +alt_id: EDAM:0002256 name: Annotation namespace: topic -def: "Study concerning the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] +def: "Resources for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000089 ! Ontologies +synonym: "Ontology annotation" EXACT [] xref: BioCatalogue:Genome Annotation xref: BioCatalogue:Ontology Annotation +is_a: EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0000221 @@ -2276,65 +2207,9 @@ subset: topic xref: BioCatalogue:Genome Annotation is_obsolete: true consider: EDAM:0000219 ! Annotation -consider: EDAM:0000643 ! Genomes +consider: EDAM:0000621 ! Genome, proteome and model organisms -[Term] -id: EDAM:0002256 -name: Ontology annotation -namespace: topic -def: "Annotate a biomedical ontology, for example add new terms." [EDAM:EBI "EMBRACE definition"] -subset: topic -xref: BioCatalogue:Ontology Annotation -is_obsolete: true -consider: EDAM:0000219 ! Annotation - -[Term] -id: EDAM:0001779 -name: Database submission -namespace: topic -def: "Submit an object to a database." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000091 ! Data handling - -[Term] -id: EDAM:0002286 -name: File format handling -namespace: topic -def: "Handle file formatting tasks, for example file format conversion, transformation or validation." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000091 ! Data handling - -[Term] -id: EDAM:0002267 -name: Biological model construction -namespace: topic -def: "Construct a biological model." [EDAM:EBI "EMBRACE definition"] -subset: topic -xref: BioCatalogue:Model Creation -is_obsolete: true -consider: EDAM:0000771 ! Biological models - - -[Term] -id: EDAM:0002268 -name: Biological model analysis -namespace: topic -def: "The study of a biological model." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000771 ! Biological models - - -[Term] -id: EDAM:0002231 -name: Phenotype and disease -namespace: resource -def: "An information resource for biological genotypes, phenotypes and/or diseases." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000625 ! Genotype and phenotype [Term] id: EDAM:0002230 @@ -2342,13 +2217,14 @@ name: Classification namespace: topic def: "Resources that help to identify, group, or name things in a structured way according to some schema based on observable relationships." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000003 ! Topic +is_obsolete: true +consider: EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0002829 -name: Ontologies and nomenclature +name: Ontologies, nomenclature and classification namespace: topic -def: "Resources and study on conceptualisation and naming." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning conceptualisation, categorisation and naming, or that help to identify, group, or name things in a structured way according to some schema based on observable relationships." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000003 ! Topic @@ -2357,128 +2233,91 @@ is_a: EDAM:0000003 ! Topic id: EDAM:0002811 name: Nomenclature namespace: topic -def: "An information resource for biological nomenclature (naming)." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000619 +def: "Informatics resources concerning biological nomenclature (naming), symbols and terminology." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002829 ! Ontologies and nomenclature +is_a: EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0002229 -name: Cell biology informatics +name: Cell biology resources namespace: topic -def: "Study of the informatics of cellular biology and cell culture." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning cells, such as key genes and proteins involved in the cell cycle." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002841 ! Informatics +is_a: EDAM:0003070 ! Biological science resources + [Term] -id: EDAM:0002227 -name: Genetics +id: EDAM:0003064 +name: Developmental biology resources namespace: topic -def: "An information resource for genetics." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning how organisms grow and develop." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000622 ! Genomics +is_a: EDAM:0003070 ! Biological science resources [Term] -id: EDAM:0000580 -name: Undefined +id: EDAM:0003067 +name: Anatomy resources namespace: topic -def: "Debugging." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the structures of living organisms." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true +is_a: EDAM:0003070 ! Biological science resources + + [Term] -id: EDAM:0002226 -name: Structure determination +id: EDAM:0003065 +name: Embryology resources namespace: topic -def: "The study of experimental methods for biomolecular structure determination." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage." [EDAM:EBI "EMBRACE definition"] subset: topic -xref: BioCatalogue:Structural Genomics -synonym: "Structural genomics" EXACT [] -is_a: EDAM:0000081 ! Structure +is_a: EDAM:0003064 ! Developmental biology resources + [Term] -id: EDAM:0000586 -alt_id: EDAM:0002225 -name: Proteins +id: EDAM:0003053 +name: Genetics namespace: topic -def: "The study of proteins." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002227 +def: "Informatics resources concerning the study of genes, genetic variation and heredity in living organisms." [EDAM:EBI "EMBRACE definition"] subset: topic +synonym: "Genetics data resources" EXACT [] is_a: EDAM:0000003 ! Topic -[Term] -id: EDAM:0000587 -name: Protein interaction -namespace: resource -def: "The study of protein interactions." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000128 ! Protein interactions - - -[Term] -id: EDAM:0000588 -name: Protein localization -namespace: resource -def: "A database concerning protein localization." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000140 ! Protein targeting and localization - -[Term] -id: EDAM:0000589 -name: Protein structural motif -namespace: resource -def: "The study of protein structural motifs." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000166 ! Protein structural motifs [Term] -id: EDAM:0000591 -name: Proteome annotation -namespace: resource -def: "The study of annotation for an entire proteome." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000644 ! Proteome - -[Term] -id: EDAM:0000592 -name: Molecular motions -namespace: resource -def: "The study of molecular motions." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000145 ! Molecular flexibility and motion - -[Term] -id: EDAM:0000593 -name: NMR +id: EDAM:0002226 +name: Structure determination namespace: topic -def: "The study of raw NMR data." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000136 +def: "Informatics resources concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, including the assignment or modelling of molecular structure from such data." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002226 ! Structure determination +synonym: "Structural determination" EXACT [] +synonym: "Structural assignment" EXACT [] +synonym: "Structure assignment" EXACT [] +synonym: "Raw structural data analysis" EXACT [] +is_a: EDAM:0000081 ! Structure analysis + + [Term] id: EDAM:0000595 name: Protein classification namespace: topic -def: "Study concerning the classification of proteins (from sequence or structural data)." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000129 +def: "Resources concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000586 ! Proteins -is_a: EDAM:0002230 ! Classification - - -[Term] -id: EDAM:0000596 -name: Sequence alignment -namespace: resource -def: "The study of molecular sequence alignments." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000182 ! Sequence alignment - +is_a: EDAM:0000078 ! Protein analysis +is_a: EDAM:0002829 ! Ontologies, nomenclature and classification +is_a: EDAM:0000594 ! Sequence classification [Term] id: EDAM:0000598 name: Sequence motif or profile namespace: topic -def: "The study of sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [EDAM:EBI "EMBRACE definition"] +comment: This includes comparison, discovery, recognition etc. of sequence motifs. subset: topic is_obsolete: true consider: EDAM:0000158 ! Sequence motifs @@ -2486,133 +2325,144 @@ consider: EDAM:0000188 ! Sequence profiles and HMMs [Term] -id: EDAM:0000599 -name: Structural (3D) profile -namespace: resource -def: "The study of one or more structural (3D) profiles or templates derived from a molecular structure or structural alignment of a particular type." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000167 ! Structural (3D) profiles - - -[Term] -id: EDAM:0000600 -name: Functional sites -namespace: topic -def: "The study of functional sites in molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000160 ! Sequence features - - -[Term] id: EDAM:0000601 -alt_id: EDAM:0000142 name: Protein modifications namespace: topic -def: "The study of protein chemical modifications, e.g. post-translational modifications." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000142 +def: "Informatics resources concerning protein chemical modifications, e.g. post-translational modifications." [EDAM:EBI "EMBRACE definition"] comment: EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of term GO:0006464) and/or the Protein Modifications ontology (children of term MOD:00000) subset: topic xref: GO:0006464 ! protein modification process synonym: "Protein post-translation modification" EXACT [] -is_a: EDAM:0000586 ! Proteins +is_a: EDAM:0000123 ! Protein properties +is_a: EDAM:0002225 ! Protein databases seealso: GO:0006464 ! protein modification process seealso: MOD:00000 ! protein modification [Term] id: EDAM:0000602 -alt_id: EDAM:0002259 name: Pathways, networks and models namespace: topic -def: "Study concerning biological pathways, networks and other models, including the holistic analysis and modelling of biological systems (systems biology)." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000198 +alt_id: EDAM:0000755 +def: "Data resources concerning biological pathways, networks and other models." [EDAM:EBI "EMBRACE definition"] subset: topic -synonym: "Systems biology" EXACT [] xref: BioCatalogue:Pathways xref: BioCatalogue:Pathway Retrieval +is_a: EDAM:0002259 ! Systems biology +is_a: EDAM:0003071 ! Biological data resources + + +[Term] +id: EDAM:0003075 +name: Biological system modelling +namespace: topic +def: "Resources for modelling biological systems in mathematical terms." [EDAM:EBI "EMBRACE definition"] +subset: topic +xref: BioCatalogue:Model Analysis +xref: BioCatalogue:Model Execution +is_a: EDAM:0002259 ! Systems biology + +[Term] +id: EDAM:0003076 +name: Network or pathway analysis +namespace: topic +def: "The processing (including construction) and analysis of biological networks and pathways." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0002259 ! Systems biology + + +[Term] +id: EDAM:0002259 +name: Systems biology +namespace: topic +def: "Informatics resources concerning the holistic modelling and analysis of biological systems and the interactions therein." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Systems Biology is_a: EDAM:0000003 ! Topic -[Term] -id: EDAM:0000603 -name: Proteomics -namespace: resource -def: "A proteomics database." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000121 ! Proteomics [Term] id: EDAM:0000605 name: Informatics namespace: topic -def: "A database concerning biological data management and modelling, including datatypes, workflows and models." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002841 +def: "A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000091 ! Data handling -[Term] -id: EDAM:0000606 -name: Literature -namespace: resource -def: "A biological or biomedical literature database." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000088 ! Literature and documentation [Term] id: EDAM:0000607 name: Laboratory resources namespace: topic -def: "Biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." [EDAM:EBI "EMBRACE definition"] +def: "Data resources concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000003 ! Topic +is_a: EDAM:0003071 ! Biological data resources [Term] id: EDAM:0000608 -name: Cell lines and culture +name: Cell culture resources namespace: topic -def: "The study of general cell culture or data on a specific cell lines." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning general cell culture or data on a specific cell lines." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002229 ! Cell biology informatics +is_a: EDAM:0000607 ! Laboratory resources [Term] -id: EDAM:0000609 -name: Cell cycle -namespace: resource -def: "The study of the cell cycle including key genes and proteins." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000612 ! Cell cycle and development +id: EDAM:0000610 +name: Ecoinformatics +namespace: topic +def: "Informatics resources concerning the application of information technology to the ecological and environmental sciences." [EDAM:EBI "EMBRACE definition"] +subset: topic +synonym: "Computational ecology" EXACT [] +synonym: "Ecological informatics" EXACT [] +is_a: EDAM:0000003 ! Topic + [Term] -id: EDAM:0002841 -name: Informatics +id: EDAM:0003063 +name: Medical informatics resources namespace: topic -def: "A sub-discipline of bioinformatics; the application of information technology to a specialised biological area." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000087 +def: "Informatics resources for the application of information technology to health, disease and biomedicine." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000003 ! Topic +synonym: "Health and disease" EXACT [] +synonym: "Healthcare informatics" EXACT [] +synonym: "Health informatics" EXACT [] +synonym: "Clinical informatics" EXACT [] +synonym: "Biomedical informatics" EXACT [] +is_a: EDAM:0000607 ! Laboratory resources [Term] -id: EDAM:0000610 -name: Ecoinformatics +id: EDAM:0003050 +name: Biodiversity namespace: topic -def: "The application of information technology to the ecological and environmental sciences." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet." [EDAM:EBI "EMBRACE definition"] subset: topic -synonym: "Computational ecology" EXACT [] -is_a: EDAM:0002841 ! Informatics +synonym: "Biodiversity data resource" EXACT [] +synonym: "Biodiversity data resources" EXACT [] +is_a: EDAM:0000610 ! Ecoinformatics + [Term] id: EDAM:0002840 name: Toxicoinformatics namespace: topic -def: "The study of the adverse effects of chemical substances on living organisms." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the adverse effects of chemical substances on living organisms." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002841 ! Informatics +synonym: "Computational toxicology" EXACT [] +is_a: EDAM:0002258 ! Chemoinformatics [Term] id: EDAM:0002661 name: Toxins and targets namespace: topic -def: "Study concerning structural and associated data for toxic chemical substances." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning structural and associated data for toxic chemical substances." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002840 ! Toxicoinformatics is_a: EDAM:0000154 ! Small molecules @@ -2621,586 +2471,469 @@ is_a: EDAM:0000154 ! Small molecules id: EDAM:0000611 name: Electron microscopy namespace: topic -def: "The study of electron microscopy data." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning electron microscopy data." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002226 ! Structure determination +is_obsolete: true +consider: EDAM:0002226 ! Structure determination [Term] id: EDAM:0002828 name: X-ray crystallography namespace: topic -def: "The study of X-ray crystallography data." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning X-ray crystallography data." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002226 ! Structure determination +is_obsolete: true +consider: EDAM:0002226 ! Structure determination + +[Term] +id: EDAM:0000593 +name: NMR +namespace: topic +def: "Resources concerning raw NMR data." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0002226 ! Structure determination + [Term] id: EDAM:0000612 -name: Cell cycle and development +name: Cell cycle namespace: topic -def: "The study of the cell cycle including key genes and proteins, tissue development and embryology." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000609 +def: "Resources concerning the cell cycle including key genes and proteins." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002229 ! Cell biology informatics +is_obsolete: true +consider: EDAM:0002229 ! Cell biology resources [Term] id: EDAM:0000613 -alt_id: EDAM:0000604 name: Peptides and amino acids namespace: topic -def: "The study of amino acid or peptide physicochemical, biochemical or structural property data." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000604 +def: "Informatics resources concerning the physicochemical, biochemical or structural properties of amino acids or peptides." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000586 ! Proteins - - -[Term] -id: EDAM:0000614 -name: Nucleic acid physicochemical property -namespace: resource -def: "The study of nucleic acid physicochemical and biochemical property data." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000094 ! Nucleic acid physicochemistry +is_a: EDAM:0000154 ! Small molecules -[Term] -id: EDAM:0000615 -name: Protein physicochemical property -namespace: resource -def: "The study of protein physicochemical and biochemical property data." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000123 ! Protein physicochemistry [Term] id: EDAM:0000616 -name: Organelles +name: Organelle genes and proteins namespace: topic -def: "The study of a specific organelle, or organelles in general." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002229 ! Cell biology informatics - +is_a: EDAM:0003078 ! Gene and protein resources [Term] id: EDAM:0000617 -name: Ribosomes +name: Ribosomal genes and proteins namespace: topic -def: "The study of ribosome-specific data." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning ribosomes, typically of ribosome-related genes and proteins." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000616 ! Organelles - +synonym: "Ribosome genes and proteins" EXACT [] +is_a: EDAM:0000616 ! Organelle genes and proteins -[Term] -id: EDAM:0000619 -name: Biochemical nomenclature -namespace: resource -def: "The study of biochemical nomenclature, symbols or terminology." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0002811 ! Nomenclature [Term] id: EDAM:0000621 -name: Organism +name: Genome, proteome and model organisms namespace: topic -def: "The study of a specific organism (e.g. a model organism) or group of organisms, either describing the organism(s) itself or data associated with it." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000086 +alt_id: EDAM:0000591 +alt_id: EDAM:0000643 +alt_id: EDAM:0000800 +alt_id: EDAM:0000795 +def: "Informatics resources concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms." [EDAM:EBI "EMBRACE definition"] +comment: General information on or more organisms, genomes (including molecular sequences and map, genes and annotation) and proteomes may be included. subset: topic -is_a: EDAM:0000003 ! Topic +synonym: "Genome map" EXACT [] +is_a: EDAM:0000622 ! Genomics +is_a: EDAM:0000121 ! Proteomics +is_a: EDAM:0000625 ! Genotype and phenotype resources [Term] id: EDAM:0000622 -alt_id: EDAM:0000093 -alt_id: EDAM:0000794 name: Genomics namespace: topic -def: "The study of of whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000093 +alt_id: EDAM:0000794 +def: "Informatics resources concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Genomics xref: BioCatalogue:Functional Genomics is_a: EDAM:0000003 ! Topic + [Term] id: EDAM:0002816 -name: Genes +name: Gene resources namespace: topic -def: "The study of of genes." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000630 +def: "Informatics resource (typically a database) primarily focussed on genes." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000003 ! Topic -is_a: EDAM:0000654 ! DNA +synonym: "Gene database" EXACT [] +synonym: "Gene resource" EXACT [] +is_a: EDAM:0003071 ! Biological data resources +is_a: EDAM:0003053 ! Genetics + + +[Term] +id: EDAM:0003054 +name: Molecular genetics +namespace: topic +def: "Resources concerning the structure and function of genes at a molecular level." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0003053 ! Genetics + + +[Term] +id: EDAM:0003055 +name: Quantitative genetics +namespace: topic +def: "Resources concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0003053 ! Genetics + + +[Term] +id: EDAM:0003056 +name: Population genetics +namespace: topic +def: "Resources concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0003053 ! Genetics + + [Term] id: EDAM:0000623 -name: Gene family or system +name: Genes, gene family or system namespace: topic -def: "The study of a particular gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] +def: "Data resources concerning particular gene(s), gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002816 ! Genes -is_a: EDAM:0000722 ! Nucleic acid classification +is_a: EDAM:0003052 ! Sequence clusters and classification +is_a: EDAM:0002816 ! Gene resources + + [Term] id: EDAM:0000624 name: Chromosomes namespace: topic -def: "The study of chromosomes." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning chromosomes." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000654 ! DNA +is_a: EDAM:0003062 ! Genetic organisation + + [Term] id: EDAM:0000625 -name: Genotype and phenotype +name: Genotype and phenotype resources namespace: topic -def: "The study of genotypes and / or phenotypes especially concerning variations (mutation) and disease." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002231 +def: "Informatics resources concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000003 ! Topic +is_a: EDAM:0002816 ! Gene resources [Term] -id: EDAM:0000627 -name: DNA methylation -namespace: resource -def: "The study of DNA methylation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000654 ! DNA +id: EDAM:0003078 +name: Gene and protein resources +namespace: topic +def: "Data resources concerning specific genes and their encoded proteins or a related group of such genes and proteins." [EDAM:EBI "EMBRACE definition"] +subset: topic +synonym: "Genes and proteins resources" EXACT [] +is_a: EDAM:0000635 ! Specific protein resources +is_a: EDAM:0000623 ! Genes, gene family or system + [Term] -id: EDAM:0000628 -name: DNA replication -namespace: resource -def: "The study of DNA replication." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000654 ! DNA +id: EDAM:0003070 +name: Biological science resources +namespace: topic +alt_id: EDAM:0003066 +def: "Informatics resources concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." [EDAM:EBI "EMBRACE definition"] +subset: topic +synonym: "Phenotype resource" EXACT [] +is_a: EDAM:0003071 ! Biological data resources + [Term] id: EDAM:0000629 name: Gene expression and microarray namespace: topic -def: "The study of gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true -consider: EDAM:0000197 ! Gene expression and regulation +consider: EDAM:0000197 ! Gene expression resources +consider: EDAM:0000200 ! Microarrays [Term] -id: EDAM:0000630 -name: Gene structure +id: EDAM:0000634 +name: Disease resources namespace: topic -def: "The study of gene structure, including introns, exons, splicing, gene fusion etc." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning diseases." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002816 ! Genes +is_a: EDAM:0000625 ! Genotype and phenotype resources [Term] -id: EDAM:0000633 -name: Immunological -namespace: resource -def: "A database concerning immunology in general, including immune processes, immunity related proteins and peptide ligands etc." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000804 ! Immunoinformatics - - -[Term] -id: EDAM:0000634 -alt_id: EDAM:0002813 -name: Disease +id: EDAM:0002813 +name: Disease genes and proteins namespace: topic -def: "Study of diseases." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000819 +def: "Informatics resources concerning the genes, gene variations and proteins involved in one or more specific diseases." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000625 ! Genotype and phenotype +is_a: EDAM:0000634 ! Disease resources +is_a: EDAM:0003078 ! Gene and protein resources [Term] id: EDAM:0000635 -name: Specific protein +name: Specific protein resources namespace: topic -def: "The study of a particular protein or group of proteins." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning a particular protein, protein family or other group of proteins." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000586 ! Proteins +synonym: "Specific protein" EXACT [] +is_a: EDAM:0002225 ! Protein databases [Term] -id: EDAM:0000636 -name: Phylogenetics -namespace: resource -def: "The study of phylogeny; phylogenetic trees, gene transfer, mode of selection / evolution etc." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000084 ! Phylogenetics - -[Term] id: EDAM:0000637 name: Taxonomy namespace: topic -def: "The study of organism classification, identification and naming." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning organism classification, identification and naming." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002829 ! Ontologies and nomenclature -is_a: EDAM:0002230 ! Classification +is_a: EDAM:0002829 ! Ontologies, nomenclature and classification + [Term] id: EDAM:0000639 +name: Protein sequence analysis +namespace: topic alt_id: EDAM:0000125 +def: "Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] +subset: topic +xref: BioCatalogue:Protein Sequence Analysis +is_a: EDAM:0000080 ! Sequence analysis +is_a: EDAM:0000078 ! Protein analysis + +[Term] +id: EDAM:0003043 name: Protein sequences namespace: topic -def: "The study of protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Data resources concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000080 ! Sequence -is_a: EDAM:0000586 ! Proteins -is_a: EDAM:0000080 ! Sequence xref: BioCatalogue:Protein Sequence Analysis +is_a: EDAM:0003041 ! Sequence databases +is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000640 +name: Nucleic acid sequence analysis +namespace: topic alt_id: EDAM:0000096 +def: "Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] +subset: topic +xref: BioCatalogue:Nucleotide Sequence Analysis +is_a: EDAM:0000080 ! Sequence analysis +is_a: EDAM:0000077 ! Nucleic acid analysis + +[Term] +id: EDAM:0003042 name: Nucleic acid sequences namespace: topic -def: "The study of nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] +def: "Data resources concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] subset: topic -xref: BioCatalogue:Nucleotide Sequence Analysis -is_a: EDAM:0000080 ! Sequence -is_a: EDAM:0000080 ! Sequence -is_a: EDAM:0000077 ! Nucleic acids +is_a: EDAM:0003041 ! Sequence databases [Term] id: EDAM:0000641 -name: Repeat sequence -alt_id: EDAM:0002262 +name: Repeat sequences namespace: topic -def: "The study of the repetitive nature of molecular sequences." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002262 +def: "Resources concerning the repetitive nature of molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: topic +synonym: "Repeat sequence" EXACT [] xref: BioCatalogue:Repeats -is_a: EDAM:0000157 ! Sequence composition +is_a: EDAM:0000157 ! Sequence composition analysis +is_a: EDAM:0003041 ! Sequence databases [Term] id: EDAM:0000642 -alt_id: EDAM:0002263 -name: Low complexity sequence +name: Low complexity sequences namespace: topic -def: "The study of the (character) complexity of molecular sequences, particularly regions of low complexity." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002263 +def: "Resources concerning the (character) complexity of molecular sequences, particularly regions of low complexity." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000157 ! Sequence composition - -[Term] -id: EDAM:0000626 -name: Polymorphism -namespace: resource -def: "The study of gene polymorphism, polymorphic sequences etc." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000199 ! Mutation and polymorphism +is_a: EDAM:0000157 ! Sequence composition analysis +is_a: EDAM:0003041 ! Sequence databases -[Term] -id: EDAM:0000643 -alt_id: EDAM:0000800 -name: Genomes -namespace: topic -def: "The study of a specific genome including molecular sequences and map, genes and annotation." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "Genome map" EXACT [] -is_a: EDAM:0000654 ! DNA [Term] id: EDAM:0000644 name: Proteome namespace: topic -def: "Information on a specific proteome including protein sequences and annotation." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning a specific proteome including protein sequences and annotation." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000639 ! Protein sequences +is_obsolete: true +consider: EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0000646 name: BLAST -namespace: resource +namespace: resources def: "A BLAST-format database of sequences." [EDAM:EBI "EMBRACE definition"] is_obsolete: true -consider: EDAM:0000080 ! Sequence +consider: EDAM:0003041 ! Sequence database -[Term] -id: EDAM:0000653 -name: RNA -namespace: topic -def: "The study of RNA." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000077 ! Nucleic acids [Term] id: EDAM:0000654 name: DNA namespace: topic -def: "The study of DNA, typically DNA sequence analysis or processes such as methylation and replication." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000098 +alt_id: EDAM:0000666 +alt_id: EDAM:0000627 +alt_id: EDAM:0000628 +def: "Resources concerning DNA sequences and structure, including processes such as methylation and replication." [EDAM:EBI "EMBRACE definition"] comment: The DNA sequences might be coding or non-coding sequences. subset: topic -is_a: EDAM:0000077 ! Nucleic acids +is_a: EDAM:0003042 ! Nucleic acid sequences + + [Term] id: EDAM:0000655 name: mRNA, EST or cDNA namespace: topic -def: "The study of mRNA, EST or cDNA sequences." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000205 +def: "Resources concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Transcriptome" EXACT [] -is_a: EDAM:0000653 ! RNA -is_a: EDAM:0000197 ! Gene expression and regulation +is_a: EDAM:0000099 ! RNA [Term] id: EDAM:0000659 name: Functional RNA namespace: topic -def: "The study of one or more functional or non-coding RNA sequences." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000113 +alt_id: EDAM:0000119 +alt_id: EDAM:0000664 +alt_id: EDAM:0000665 +alt_id: EDAM:0000120 +def: "Resources concerning functional or non-coding RNA sequences." [EDAM:EBI "EMBRACE definition"] +comment: For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). subset: topic -is_a: EDAM:0000653 ! RNA +is_a: EDAM:0000099 ! RNA [Term] -id: EDAM:0000660 -name: rRNA +id: EDAM:0003060 +name: Regulatory RNA namespace: topic -def: "The study of one or more ribosomal RNA (rRNA) sequences." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000661 +alt_id: EDAM:0000662 +alt_id: EDAM:0000117 +alt_id: EDAM:0000118 +def: "Resources concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA)." [EDAM:EBI "EMBRACE definition"] +comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. subset: topic -is_a: EDAM:0000659 ! Functional RNA sequence +is_a: EDAM:0000659 ! Functional RNA -[Term] -id: EDAM:0000661 -name: miRNA -namespace: topic -def: "The study of one or more microRNA (miRNA) sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -synonym: "microRNA" EXACT [] -is_a: EDAM:0000659 ! Functional RNA sequence [Term] -id: EDAM:0000662 -name: siRNA +id: EDAM:0000660 +name: rRNA namespace: topic -def: "The study of one or more small interfering RNA (siRNA) sequences." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000116 +def: "Resources concerning one or more ribosomal RNA (rRNA) sequences." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000659 ! Functional RNA sequence +is_a: EDAM:0000659 ! Functional RNA + [Term] id: EDAM:0000663 name: tRNA namespace: topic -def: "The study of one or more transfer RNA (tRNA) sequences." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000115 +def: "Resources concerning one or more transfer RNA (tRNA) sequences." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000659 ! Functional RNA sequence +is_a: EDAM:0000659 ! Functional RNA [Term] -id: EDAM:0000664 -name: snRNA -namespace: topic -def: "The study of one or more small nuclear RNA (snRNA) sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000659 ! Functional RNA sequence - - -[Term] -id: EDAM:0000665 -name: snoRNA -namespace: topic -def: "The study of one or more small nucleolar RNA (snoRNA) sequences." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000664 ! snRNA sequence - -[Term] -id: EDAM:0000666 -name: rDNA +id: EDAM:0002814 +name: Protein structure analysis namespace: topic -def: "The study of one or more ribosomal DNA (rDNA) sequences." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000126 +alt_id: EDAM:0000590 +def: "Resources concerning protein secondary or tertiary structural data and/or associated annotation." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000654 ! DNA - -[Term] -id: EDAM:0000669 -name: Eukaryote genome -namespace: resource -def: "Information on a specific eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0002818 ! Eukaryote -consider: EDAM:0000643 0000669 ! Genome - - -[Term] -id: EDAM:0000670 -name: Prokaryote genome -namespace: resource -def: "Information on a specific prokaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0001811 ! Prokaryote -consider: EDAM:0000643 ! Genomes - -[Term] -id: EDAM:0000671 -name: Viral genome -namespace: resource -def: "Information on a specific viral genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000781 ! Virus -consider: EDAM:0000643 ! Genomes - -[Term] -id: EDAM:0000675 -name: Unicellular eukaryote genome -namespace: resource -def: "Information on a specific unicellular eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0002821 ! Unicellular eukaryote -consider: EDAM:0000643 ! Genomes - -[Term] -id: EDAM:0000676 -name: Fungal genome -namespace: resource -def: "Information on a specific fungal genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000782 ! Fungal -consider: EDAM:0000643 ! Genomes - -[Term] -id: EDAM:0000677 -name: Plant genome -namespace: resource -def: "Information on a specific plant genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000780 ! Plant -consider: EDAM:0000643 ! Genomes - -[Term] -id: EDAM:0000678 -name: Invertebrate genome -namespace: resource -def: "Information on a specific invertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0002819 ! Invertebrate -consider: EDAM:0000643 ! Genomes - -[Term] -id: EDAM:0000679 -name: Vertebrate genome -namespace: resource -def: "Information on a specific vertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0002820 ! Vertebrate -consider: EDAM:0000643 ! Genomes - -[Term] -id: EDAM:0000682 -name: Yeast genome -namespace: resource -def: "Information on a specific yeast genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0002817 ! Yeast -consider: EDAM:0000643 ! Genomes - - -[Term] -id: EDAM:0000687 -name: Human genome -namespace: resource -def: "Information on the human genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0002815 ! Human -consider: EDAM:0000643 ! Genomes - -[Term] -id: EDAM:0000691 -name: Prokaryote proteome -namespace: resource -def: "Information on a specific prokaryote proteome including molecular sequences and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000644 ! Proteome -consider: EDAM:0001811 ! Prokaryote +is_a: EDAM:0000078 ! Protein analysis +is_a: EDAM:0000081 ! Structure analysis [Term] -id: EDAM:0000692 -name: Human proteome -namespace: resource -def: "Information on the human proteome including molecular sequences and annotation." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000644 ! Proteome -consider: EDAM:0002815 ! Human - -[Term] -id: EDAM:0002814 -alt_id: EDAM:0000126 -alt_id: EDAM:0000590 +id: EDAM:0003040 name: Protein structure namespace: topic -def: "The study of protein secondary or tertiary structural data and/or associated annotation." [EDAM:EBI "EMBRACE definition"] +def: "Data resources concerning protein secondary or tertiary structural data and/or associated annotation." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000586 ! Proteins -is_a: EDAM:0000081 ! Structure - -[Term] -id: EDAM:0000693 -name: Tertiary structure -namespace: resource -def: "The study of molecular tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000081 0000693 ! Structure +is_a: EDAM:0003038 ! Structure databases +is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000694 name: Protein secondary structure namespace: topic -def: "The study of protein secondary structure or secondary structure alignments." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002124 +def: "Data resources concerning protein secondary structure or secondary structure alignments." [EDAM:EBI "EMBRACE definition"] +comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. subset: topic -is_a: EDAM:0002814 ! Protein structure +synonym: "Protein secondary structure analysis" EXACT [] +is_a: EDAM:0003040 ! Protein structure [Term] id: EDAM:0000698 -alt_id: EDAM:0002125 name: Protein tertiary structure namespace: topic -def: "The study of protein tertiary structures." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002125 +def: "Data resources concerning protein tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002814 ! Protein structure - -[Term] -id: EDAM:0000699 -name: Nucleic acid structure -namespace: resource -def: "The study of nucleic acid secondary or tertiary structure." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000097 ! Nucleic acid 0000698structure - -[Term] -id: EDAM:0000700 -name: Protein domain structure -namespace: resource -def: "A database or other collection of tertiary structures of protein domains." [EDAM:EBI "EMBRACE definition"] -synonym: "Domain structure library" EXACT [] -is_obsolete: true -consider: EDAM:0000736 ! Protein domains +is_a: EDAM:0003040 ! Protein structure -[Term] -id: EDAM:0000703 -name: CATH domain structure -namespace: resource -def: "A collection of tertiary structures of protein domains defined in CATH." [EDAM:EBI "EMBRACE definition"] -synonym: "CATH structure library" EXACT [] -is_obsolete: true -consider: EDAM:0000736 ! Protein domains [Term] id: EDAM:0000697 name: RNA structure and alignment namespace: topic -def: "The study of RNA secondary or tertiary structure and alignments." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning RNA secondary or tertiary structure and alignments." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000097 ! Nucleic acid structure +synonym: "RNA structure" EXACT [] +synonym: "RNA structure alignment" EXACT [] +synonym: "RNA alignment" EXACT [] is_a: EDAM:0000183 ! Structure alignment -is_a: EDAM:0000653 ! RNA [Term] id: EDAM:0002826 name: Protein structure alignment namespace: topic -def: "The study of protein secondary or tertiary structure alignments." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning protein secondary or tertiary structure alignments." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002814 ! Protein structure is_a: EDAM:0000183 ! Structure alignment +is_a: EDAM:0002814 ! Protein structure analysis [Term] id: EDAM:0000620 name: Drugs and targets namespace: topic -def: "The study of the structures of drugs, drug target, their interactions and binding affinities." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the structures of drugs, drug target, their interactions and binding affinities." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000154 ! Small molecules is_a: EDAM:0000202 ! Pharmacoinformatics @@ -3211,101 +2944,81 @@ name: Scents namespace: topic def: "A database about scents." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000154 ! Small molecules - - -[Term] -id: EDAM:0000717 -name: Protein-ligand interaction -namespace: resource -def: "The study of protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000148 ! Protein-ligand interactions - -[Term] -id: EDAM:0000718 -name: Protein-nucleic acid interaction -namespace: resource -def: "The study of protein-nucleic acid interactions." [EDAM:EBI "EMBRACE definition"] is_obsolete: true -consider: EDAM:0000149 ! Protein-nucleic acid interactions - +consider: EDAM:0000154 ! Small molecules -[Term] -id: EDAM:0000719 -name: Protein-protein interaction -namespace: resource -def: "The study of protein-protein interactions; protein complexes, protein functional coupling etc." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000147 ! Protein-protein interactions [Term] id: EDAM:0000722 name: Nucleic acid classification namespace: topic -def: "The study of nucleic acid classification (typically sequence classification)." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning nucleic acid classification (typically sequence classification)." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0002230 ! Classification -is_a: EDAM:0000077 ! Nucleic acids +is_a: EDAM:0002829 ! Ontologies, nomenclature and classification +is_a: EDAM:0000077 ! Nucleic acid analysis +is_a: EDAM:0000594 ! Sequence classification [Term] id: EDAM:0000723 name: Protein structure classification -namespace: resource -def: "The study of protein structural classifications." [EDAM:EBI "EMBRACE definition"] +namespace: resources +def: "Resources concerning protein structural classifications." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0001770 ! Structure comparison -consider: EDAM:0000736 ! Protein domains +consider: EDAM:0000736 ! Protein domains and folds [Term] id: EDAM:0000724 name: Protein families namespace: topic -def: "The study of protein sequences that are classified into groups or families." [EDAM:EBI "EMBRACE definition"] +def: "Data resources concerning primarily proteins that have been classified as members of a protein family (or other grouping)." [EDAM:EBI "EMBRACE definition"] comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. subset: topic synonym: "Protein sequence classification" EXACT [] synonym: "Protein secondary" EXACT [] -is_a: EDAM:0000595 ! Protein classification - +is_a: EDAM:0003052 ! Sequence clusters and classification +is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000736 -name: Protein domains +name: Protein domains and folds namespace: topic -def: "The study of protein tertiary structural domains and their classification." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000703 +alt_id: EDAM:0000700 +alt_id: EDAM:0000127 +def: "Resources concerning protein tertiary structural domains and folds." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Domains is_a: EDAM:0000698 ! Protein tertiary structure -is_a: EDAM:0000595 ! Protein classification +is_a: EDAM:0000724 ! Protein families + [Term] id: EDAM:0000740 name: Nucleic acid sequence alignment namespace: topic -def: "The study of nucleotide sequence alignments." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning nucleotide sequence alignments." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000182 ! Sequence alignment -is_a: EDAM:0000640 ! Nucleic acid sequences +is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0000741 name: Protein sequence alignment namespace: topic -def: "The study of protein sequence alignments." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning protein sequence alignments." [EDAM:EBI "EMBRACE definition"] comment: A sequence profile typically represents a sequence alignment. -comment: A HMM typically represents a sequence alignment. subset: topic is_a: EDAM:0000182 ! Sequence alignment -is_a: EDAM:0000639 ! Protein sequences +is_a: EDAM:0000639 ! Protein sequence analysis [Term] id: EDAM:0000742 name: Sequence motif or profile (nucleotide) -namespace: resource -def: "The study of nucleotide sequence motifs, or sequence profiles derived from an nucleic acid sequence alignment." [EDAM:EBI "EMBRACE definition"] +namespace: resources +def: "Resources concerning nucleotide sequence motifs, or sequence profiles derived from an nucleic acid sequence alignment." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000158 ! Sequence motifs @@ -3313,164 +3026,186 @@ consider: EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0000743 name: Sequence motif or profile (protein) -namespace: resource -def: "The study of protein sequence motifs, or sequence profiles derived from an protein sequence alignment." [EDAM:EBI "EMBRACE definition"] +namespace: resources +def: "Resources concerning protein sequence motifs, or sequence profiles derived from an protein sequence alignment." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000158 ! Sequence motifs + [Term] -id: EDAM:0000744 -name: Sequence profile library -namespace: resource -def: "A library of sequence profiles." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000188 ! Sequence profiles and HMMs +id: EDAM:0000747 +name: Nucleic acid sites and features +namespace: topic +alt_id: EDAM:0000105 +alt_id: EDAM:0000095 +def: "Data resources concerning positional features such as functional sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +subset: topic +synonym: "Nucleic acid functional sites" EXACT [] +synonym: "Nucleic acid features" EXACT [] +is_a: EDAM:0000160 ! Sequence sites and features +is_a: EDAM:0003042 ! Nucleic acid sequences [Term] -id: EDAM:0000746 -name: HMM sequence profile library -namespace: resource -def: "A library of hidden Markov models." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM: ! Sequence profiles and HMMs +id: EDAM:0003073 +name: Nucleic acid feature detection +namespace: topic +def: "Resources concerning the detection of positional features such as functional sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000640 ! Nucleic acid sequence analysis +is_a: EDAM:0003072 ! Sequence feature detection -[Term] -id: EDAM:0001763 -name: CATH HMM library -namespace: resource -def: "A library of hidden Markov models for CATH domain." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000188 ! Sequence profiles and HMMs [Term] -id: EDAM:0000747 -name: Nucleic acid functional sites +id: EDAM:0000748 +name: Protein sites and features namespace: topic -def: "The study of functional sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000124 +alt_id: EDAM:0000138 +def: "Data resources concerning positional features such as functional sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000600 ! Functional sites -is_a: EDAM:0000640 ! Nucleic acid sequences +synonym: "Protein functional sites" EXACT [] +synonym: "Protein sequence features" EXACT [] +is_a: EDAM:0000160 ! Sequence sites and features +is_a: EDAM:0003043 ! Protein sequences + [Term] -id: EDAM:0000748 -name: Protein functional sites +id: EDAM:0003074 +name: Protein feature detection namespace: topic -def: "The study of functional sites in protein sequences." [EDAM:EBI "EMBRACE definition"] -comment: This includes promoters, transcription factor binding sites etc. +def: "Resources concerning the detection, identification and analysis of positional protein sequence features, such as functional sites." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000600 ! Functional sites -is_a: EDAM:0001775 ! Protein function -is_a: EDAM:0000639 ! Protein sequences +is_a: EDAM:0000639 ! Protein sequence analysis +is_a: EDAM:0003072 ! Sequence feature detection + [Term] id: EDAM:0000749 -name: Transcription regulatory sites -namespace: resource -def: "The study of transcription regulatory sites database in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000110 ! Transcription +name: Transcription factors and regulatory sites +namespace: topic +alt_id: EDAM:0000811 +def: "Resources concerning transcription factors; proteins that bind to DNA and control transcription of DNA to mRNA, either promoting (as an activator) or blocking (as a repressor) the binding to DNA of RNA polymerase, and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +comment: This includes promoters, enhancers, silencers and boundary elements / insulators. This includes sequence and structural information, binding profiles etc, and may also include the transcription factor binding site in DNA. +synonym: "Transcriptional regulatory sites" EXACT [] +synonym: "Transcription factors" EXACT [] +synonym: "Transcription factor and binding site" EXACT [] +is_a: EDAM:0000204 ! Gene regulation resources +is_a: EDAM:0000110 ! Transcription +is_a: EDAM:0000635 ! Specific protein resources +is_a: EDAM:0000747 ! Nucleic acid sites and features +is_a: EDAM:0003062 ! Genetic organisation +is_a: EDAM:0003073 ! Nucleic acid feature detection + -[Term] -id: EDAM:0000750 -name: Splice sites -namespace: resource -def: "The study of splice sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000114 ! RNA splicing [Term] id: EDAM:0000751 -name: Phosphorylation +name: Phosphorylation sites namespace: topic -def: "The study of protein phosphorylation and phosphorylation sites in protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning protein phosphorylation and phosphorylation sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000601 ! Protein modifications +is_a: EDAM:0000748 ! Protein sites and features [Term] id: EDAM:0000753 name: Metabolic pathways namespace: topic -def: "The study of metabolic pathways." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning metabolic pathways." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000602 ! Pathways, networks and models [Term] id: EDAM:0000754 -name: Signalling pathways +name: Signaling pathways namespace: topic -def: "The study of signalling pathways." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning signaling pathways." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000602 ! Pathways, networks and models [Term] -id: EDAM:0002846 -name: Gene regulatory networks +id: EDAM:0003044 +name: Protein interaction networks namespace: topic -def: "The study of gene regulatory networks." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning protein-protein interaction networks." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000602 ! Pathways, networks and models -is_a: EDAM:0000197 ! Gene expression and regulation +is_a: EDAM:0000147 ! Protein-protein interactions [Term] -id: EDAM:0000755 -name: KEGG PATHWAY +id: EDAM:0000771 +name: Biological models namespace: topic -def: "KEGG PATHWAY database of biological pathways." [EDAM:EBI "EMBRACE definition"] -comment: KEGG (Kyoto Encyclopedia of Genes and Genomes) PATHWAY contains pathway maps for metabolism, genetic information processing, environmental information processing, cellular processes, human diseases. The KEGG PATHWAY maps are manually drawn and representing knowledge on molecular interactions and reaction networks. +alt_id: EDAM:0002267 +alt_id: EDAM:0002268 +def: "Informatics resources concerning mathematical or other models of biological processes." [EDAM:EBI "EMBRACE definition"] +comment: This includes databases of models and methods to construct or analyse a model. subset: topic -is_obsolete: true -consider: EDAM:0000602 ! Pathways, networks and models - -[Term] -id: EDAM:0000765 -name: Two-dimensional gel electrophoresis -namespace: resource -def: "The study of two-dimensional gel electrophoresis image and related data." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000133 ! Two-dimensional gel electrophoresis +xref: BioCatalogue:Model Creation +is_a: EDAM:0000602 ! Pathways, networks and models [Term] -id: EDAM:0000766 -name: Mass spectrometry -namespace: resource -def: "The study of mass spectrometry data." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000134 ! Mass spectrometry +id: EDAM:0002846 +name: Gene regulatory networks +namespace: topic +def: "Informatics resources concerning gene regulatory networks." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000602 ! Pathways, networks and models +is_a: EDAM:0000204 ! Gene regulation resources + [Term] id: EDAM:0000767 -alt_id: EDAM:0000141 -name: Peptide identification and proteolysis +name: Protein and peptide identification namespace: topic -def: "The study of peptide (e.g. digest product) identification, typically from proteomics experiments such as mass spectrometry and protein microarrays, including proteolysis and mass calculations on a protein." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000603 +def: "Informatics resources concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays." [EDAM:EBI "EMBRACE definition"] +comment: This includes the results of any methods that separate, characterize and identify expressed proteins. subset: topic -is_a: EDAM:0000613 ! Peptides and amino acids +synonym: "Peptide identification and proteolysis" EXACT [] +synonym: "Proteomics data" EXACT [] +synonym: "Proteomics data resources" EXACT [] is_a: EDAM:0000121 ! Proteomics -is_a: EDAM:0000821 ! Enzymes +is_a: EDAM:0000639 ! Protein sequence analysis +is_a: EDAM:0002225 ! Protein databases + + +[Term] +id: EDAM:0000141 +name: Protein cleavage sites and proteolysis +namespace: topic +def: "Resources concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000639 ! Protein sequence analysis + + + [Term] id: EDAM:0000769 name: Workflows namespace: topic -def: "Study concerning biological or biomedical analytical workflows or pipelines." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning biological or biomedical analytical workflows or pipelines." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0000220 +name: Data processing and validation +namespace: topic +alt_id: EDAM:0002286 alt_id: EDAM:0002270 alt_id: EDAM:0002834 -name: Data file processing -namespace: topic -def: "Study concerning basic manipulations of files or reports of generic biological data." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning basic manipulations of files or reports of generic biological data." [EDAM:EBI "EMBRACE definition"] comment: This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. subset: topic synonym: "Report handling" EXACT [] synonym: "File handling" EXACT [] +synonym: "Data file handling" EXACT [] synonym: "Report processing" EXACT [] is_a: EDAM:0000091 ! Data handling @@ -3478,234 +3213,212 @@ is_a: EDAM:0000091 ! Data handling id: EDAM:0000770 name: Data types and objects namespace: topic -def: "The study of structuring data into basic types and (computational) objects." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning structuring data into basic types and (computational) objects." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000091 ! Data handling [Term] -id: EDAM:0000771 -name: Biological models +id: EDAM:0000632 +name: Probes and primers namespace: topic -def: "The study of mathematical or other biological models." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000207 +def: "Resources concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR)." [EDAM:EBI "EMBRACE definition"] subset: topic -xref: BioCatalogue:Model Analysis -xref: BioCatalogue:Model Execution -is_a: EDAM:0000602 ! Pathways, networks and models +is_a: EDAM:0000607 ! Laboratory resources +is_a: EDAM:0003041 ! Sequence databases + [Term] -id: EDAM:0000632 -name: Molecular probes or primers +id: EDAM:0003032 +name: Primer or probe design namespace: topic -def: "The study of molecular probes (e.g. a DNA microarray probe) or primers (e.g. for PCR)." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning the design of primers for PCR and DNA amplification or the design of molecular probes." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000080 ! Sequence -is_a: EDAM:0000200 ! Microarrays -is_a: EDAM:0000195 ! Polymerase chain reaction +is_a: EDAM:0000080 ! Sequence analysis + + [Term] id: EDAM:0000779 -name: Mitochondria +name: Mitochondrial genes and proteins namespace: topic -def: "The study of mitochondrial genes and proteins." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning mitochondria, typically of mitochondrial genes and proteins." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000616 ! Organelles +synonym: "Mitochondria genes and proteins" EXACT [] +is_a: EDAM:0000616 ! Organelle genes and proteins [Term] id: EDAM:0002818 -name: Eukaryote +name: Eukaryotes namespace: topic -def: "The study of eukaryotes or data concerning eukaryotes." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000669 +def: "Informatics resources concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. subset: topic -is_a: EDAM:0000621 ! Organism +synonym: "Eukaryote" EXACT [] +is_a: EDAM:0000621 ! Genome, proteome and model organisms [Term] id: EDAM:0002821 -name: Unicellular eukaryote +name: Unicellular eukaryotes namespace: topic -def: "The study of unicellular eukaryotes or data concerning unicellular eukaryotes." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000675 +def: "Informatics resources concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. subset: topic -is_a: EDAM:0002818 ! Eukaryote +synonym: "Unicellular eukaryote" EXACT [] +is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0002819 -name: Invertebrate +name: Invertebrates namespace: topic -def: "The study of invertebrates or data concerning invertebrates." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000678 +def: "Informatics resources concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. subset: topic -is_a: EDAM:0002818 ! Eukaryote +is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0002820 -name: Vertebrate +name: Vertebrates namespace: topic -def: "The study of vertebrates or data concerning vertebrates." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000679 +def: "Informatics resources concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. subset: topic -is_a: EDAM:0002818 ! Eukaryote +synonym: "Vertebrate" EXACT [] +is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0002815 -name: Human +name: Humans namespace: topic -def: "The study of humans or data concerning humans." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000692 +alt_id: EDAM:0000687 +def: "Informatics resources concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a human, a group of humans or all humans. subset: topic -is_a: EDAM:0002820 ! Vertebrate +synonym: "Human" EXACT [] +is_a: EDAM:0003048 ! Mammals [Term] id: EDAM:0000780 -name: Plant +name: Plants namespace: topic -def: "The study of plants or data concerning plants." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000677 +alt_id: EDAM:0000785 +alt_id: EDAM:0000784 +alt_id: EDAM:0000214 +def: "Informatics resources concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a plant, a group of plants or all plants. subset: topic -is_a: EDAM:0002818 ! Eukaryote +synonym: "Plant" EXACT [] +is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0000781 -alt_id: EDAM:0000790 -name: Virus +name: Viruses namespace: topic -def: "The study of viruses or data concerning viruses." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000790 +alt_id: EDAM:0000671 +alt_id: EDAM:0000791 +def: "Informatics resources concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a virus, a group of viruses or all viruses. subset: topic -is_a: EDAM:0000621 ! Organism +synonym: "Virus" EXACT [] +is_a: EDAM:0000621 ! Genome, proteome and model organisms [Term] id: EDAM:0000782 -name: Fungal +name: Fungi namespace: topic -def: "The study of fungis and molds or data concerning fungis and molds." [EDAM:EBI "EMBRACE definition"] -comment: The resource may be specific to a fungus, a group of fungi or all fugi. +alt_id: EDAM:0000792 +alt_id: EDAM:0000793 +alt_id: EDAM:0000676 +def: "Informatics resources concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] +comment: The resource may be specific to a fungus, a group of fungi or all fungi. +synonym: "Fungal" EXACT [] subset: topic -is_a: EDAM:0002818 ! Eukaryote +is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0000783 -name: Pathogen +name: Pathogens namespace: topic -def: "The study of pathogens or data concerning pathogens." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a pathogen, a group of pathogens or all pathogens. subset: topic -is_a: EDAM:0000621 ! Organism +synonym: "Pathogen" EXACT [] +is_a: EDAM:0000621 ! Genome, proteome and model organisms [Term] id: EDAM:0001811 -name: Prokaryote +name: Prokaryotes and archae namespace: topic -def: "A database concerning specific bacteria or archae." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000691 +alt_id: EDAM:0000670 +alt_id: EDAM:0000212 +def: "Informatics resources concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. subset: topic -is_a: EDAM:0000621 ! Organism - -[Term] -id: EDAM:0000784 -name: Plant (general) -namespace: topic -def: "Study concerning plants in general, or aspects that might apply to any plant." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000780 ! Plant - - -[Term] -id: EDAM:0000785 -name: Plant-specific -namespace: resource -def: "A database for a specific plant or groups of plants." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000780 ! Plant - +synonym: "Prokaryote and archae" EXACT [] +is_a: EDAM:0000621 ! Genome, proteome and model organisms [Term] id: EDAM:0000786 name: Arabidopsis -namespace: resource -def: "The study of Arabidopsis-specific data." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000780 ! Plant - +namespace: topic +def: "Informatics resources concerning Arabidopsis-specific data." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000780 ! Plants [Term] id: EDAM:0000787 name: Rice -namespace: resource -def: "The study of rice-specific data." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000780 ! Plant +namespace: topic +def: "Informatics resources concerning rice-specific data." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000780 ! Plants -[Term] -id: EDAM:0000791 -name: Virus-specific -namespace: resource -def: "The study of data specific to a virus or group of viruses; sequence and structural data, interactions of viral proteins etc." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000781 ! Virus [Term] id: EDAM:0002817 name: Yeast namespace: topic -def: "Study concerning yeast." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_a: EDAM:0000782 ! Fungal - - -[Term] -id: EDAM:0000792 -name: Fungal (general) -namespace: topic -def: "Study concerning fungi in general, i.e. aspects that might apply to all fungi." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000682 +alt_id: EDAM:0000216 +def: "Informatics resources concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] subset: topic -is_obsolete: true -consider: EDAM:0000782 ! Fungal - -[Term] -id: EDAM:0000793 -name: Fungi-specific -namespace: resource -def: "The study of data specific to a fungus, group of fungi." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000782 ! Fungal - - -[Term] -id: EDAM:0000795 -name: Genome annotation -namespace: resource -def: "Annotation on a specific genome sequence." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000643 ! Genomes +is_a: EDAM:0000782 ! Fungi [Term] id: EDAM:0000796 -alt_id: EDAM:0000103 name: Genetic mapping and linkage namespace: topic -def: "Study that aims to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000103 +def: "Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Genetic linkage" EXACT [] synonym: "Linkage mapping" EXACT [] is_a: EDAM:0000102 ! Sequencing and mapping +relationship: has_topic EDAM:0003053 ! Genetics + [Term] id: EDAM:0000797 name: Comparative genomics namespace: topic -def: "The study (typically comparison) of the structure or function of multiple genomes." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000101 +def: "Informatics resources for the study (typically comparison) of the structure or function of multiple genomes." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Comparative Genomics is_a: EDAM:0000622 ! Genomics @@ -3715,111 +3428,96 @@ is_a: EDAM:0000622 ! Genomics id: EDAM:0000798 name: Mobile genetic elements namespace: topic -def: "The study of mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000654 ! DNA +is_a: EDAM:0003062 ! Genetic organisation [Term] id: EDAM:0000801 name: Human genes -namespace: resource -def: "The study of human genes." [EDAM:EBI "EMBRACE definition"] +namespace: resources +def: "Resources concerning human genes." [EDAM:EBI "EMBRACE definition"] is_obsolete: true -consider: EDAM:0000803 ! Human disease +consider: EDAM:0000623 ! Genes, gene family or system + [Term] id: EDAM:0000803 name: Human disease namespace: topic -def: "The study of human diseases, typically describing the genes, mutations and proteins implicated in disease." [EDAM:EBI "EMBRACE definition"] +def: "Resources concerning human diseases, typically describing the genes, mutations and proteins implicated in disease." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000634 ! Disease +is_obsolete: true +consider: EDAM:0000634 ! Disease resources [Term] id: EDAM:0000804 -alt_id: EDAM:0000201 name: Immunoinformatics namespace: topic -def: "The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide and so on." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000201 +alt_id: EDAM:0000633 +def: "Informatics resources for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Computational immunology" EXACT [] -synonym: "Immunology" EXACT [] -is_a: EDAM:0002841 ! Informatics +is_a: EDAM:0000003 ! Topics [Term] id: EDAM:0002830 -name: Immune-related proteins and peptides +name: Immunity genes, immunoproteins and antigens namespace: topic -def: "Study concerning immunity-related proteins and peptide ligands." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources concerning immunity-related genes, proteins and their ligands." [EDAM:EBI "EMBRACE definition"] comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." subset: topic +synonym: "Immunoproteins and immunopeptides" EXACT [] is_a: EDAM:0000804 ! Immunoinformatics -is_a: EDAM:0000635 ! Specific protein -is_a: EDAM:0000613 ! Peptides and amino acids +is_a: EDAM:0003078 ! Gene and protein resources -[Term] -id: EDAM:0000805 -name: Cancer gene -namespace: resource -def: "The study of genes implicated in cancer." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0002640 ! Cancer - -[Term] -id: EDAM:0000811 -name: Transcription factor and binding site -namespace: topic -def: "The study of transcription factors and transcription factor binding sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -comment: This includes sequence and structural information, binding profiles etc. -subset: topic -is_a: EDAM:0000110 ! Transcription -is_a: EDAM:0000635 ! Specific protein [Term] id: EDAM:0002847 name: Disease (specific) namespace: topic -def: "Resources dedicated to one or more specific diseases (not diseases in general)." [EDAM:EBI "EMBRACE definition"] +def: "Informatics resources dedicated to one or more specific diseases (not diseases in general)." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true -consider: EDAM:0000634 ! Disease +consider: EDAM:0000634 ! Disease resources [Term] id: EDAM:0002640 -name: Cancer +name: Cancer resources namespace: topic -def: "A resource dedicated to the study of cancer, for example, genes implicated in cancer." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000805 +def: "Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000634 ! Disease - +is_a: EDAM:0000634 ! Disease resources -[Term] -id: EDAM:0000819 -name: Disease-associated protein -namespace: topic -def: "The study of disease-associated proteins." [EDAM:EBI "EMBRACE definition"] -subset: topic -is_obsolete: true -consider: EDAM:0000634 ! Disease [Term] id: EDAM:0000820 -name: Membrane protein +name: Membrane proteins namespace: topic -def: "The study of membrane proteins." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000131 +def: "Informatics resources concerning a protein or region of a protein that spans a membrane." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000635 ! Specific protein +synonym: "Transmembrane proteins" EXACT [] +is_a: EDAM:0000635 ! Specific protein resources [Term] id: EDAM:0000821 -name: Enzymes +name: Enzymes and reactions namespace: topic -def: "The study of enzymes, enzyme-catalysed reactions and their kinetics, enzyme nomenclature etc." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000132 +def: "Informatics resources concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." [EDAM:EBI "EMBRACE definition"] subset: topic -is_a: EDAM:0000635 ! Specific protein +is_a: EDAM:0000635 ! Specific protein resources + + +! ! Operation +! + [Term] id: EDAM:0000223 @@ -3846,6 +3544,8 @@ name: Analysis and processing namespace: operation def: "Process (read and / or write) data of a specific type, for example applying analytical methods." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "Calculation" EXACT [] +synonym: "Computation" EXACT [] is_a: EDAM:0000004 ! Operation relationship: has_input EDAM:0000006 ! Data {minCardinality=0} relationship: has_output EDAM:0000006 ! Data {minCardinality=0} @@ -3894,7 +3594,7 @@ subset: operation is_a: EDAM:0002505 ! Text processing relationship: has_input EDAM:0000971 ! Article {minCardinality=1} relationship: has_output EDAM:0002954 ! Article report -relationship: in_topic EDAM:0000088 ! Literature and documentation +relationship: has_topic EDAM:0000217 ! Literature analysis [Term] id: EDAM:0002993 @@ -3902,10 +3602,7 @@ name: Molecular interaction data processing namespace: operation def: "Process (read and / or write) molecular interaction data." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_output EDAM:0002599 ! Molecular interaction data {minCardinality=0} -relationship: has_input EDAM:0002599 ! Molecular interaction data {minCardinality=0} -relationship: in_topic EDAM:0000128 ! Protein interactions +is_obsolete: true [Term] @@ -3914,8 +3611,7 @@ name: Molecular interaction analysis namespace: operation def: "Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002993 ! Molecular interaction data processing -relationship: has_output EDAM:0002599 ! Molecular interaction data {minCardinality=1} +is_obsolete: true [Term] id: EDAM:0002949 @@ -3923,10 +3619,19 @@ name: Protein interaction analysis namespace: operation def: "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002948 ! Molecular interaction analysis is_a: EDAM:0002405 ! Protein interaction data processing -relationship: has_output EDAM:0000906 ! Protein interaction report {minCardinality=1} -relationship: in_topic EDAM:0000128 ! Protein interactions +relationship: has_output EDAM:0000906 ! Protein report (interaction) {minCardinality=1} +relationship: has_topic EDAM:0000128 ! Protein interactions + + +[Term] +id: EDAM:0003096 +name: Editing +namespace: operation +def: "Edit, convert or otherwise change a data entity, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] +subset: operation +is_a: EDAM:0000004 ! Operation + [Term] @@ -3951,7 +3656,7 @@ is_a: EDAM:0000004 ! Operation id: EDAM:0002997 name: Protein comparison namespace: operation -def: "Compare two or more proteins to identify similarities." [EDAM:EBI "EMBRACE definition"] +def: "Compare two or more proteins (or some aspect) to identify similarities." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002424 ! Comparison @@ -3963,34 +3668,42 @@ def: "Compare two or more nucleic acids to identify similarities." [EDAM:EBI "EM subset: operation is_a: EDAM:0002424 ! Comparison - - - - [Term] id: EDAM:0002990 name: Classification namespace: operation -def: "Classify molecular sequences, structures or other biological data." [EDAM:EBI "EMBRACE definition"] +def: "Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation -relationship: has_output EDAM:0002987 ! Classification data {minCardinality=1} +relationship: has_output EDAM:0002987 ! Classification {minCardinality=1} [Term] id: EDAM:0002995 name: Sequence classification namespace: operation -def: "Classify molecular sequences." [EDAM:EBI "EMBRACE definition"] +def: "Assign molecular sequence(s) to a group or category." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002990 ! Classification is_a: EDAM:0002403 ! Sequence analysis [Term] +id: EDAM:0003093 +name: Sequence screening +namespace: operation +def: "Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries." [EDAM:EBI "EMBRACE definition"] +subset: operation +is_a: EDAM:0002995 ! Sequence classification + + + + + +[Term] id: EDAM:0002996 name: Structure classification namespace: operation -def: "Classify molecular structures." [EDAM:EBI "EMBRACE definition"] +def: "Assign molecular structure(s) to a group or category." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002990 ! Classification is_a: EDAM:0002480 ! Structure analysis @@ -4011,7 +3724,7 @@ namespace: operation def: "Model or simulate some biological entity or system." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation -relationship: in_topic EDAM:0002275 ! Molecular modelling +relationship: has_topic EDAM:0002275 ! Molecular modelling [Term] @@ -4041,7 +3754,7 @@ def: "Map properties to positions on an biological entity (typically a molecular comment: This is a broad concept and is used a placeholder for other, more specific terms. subset: operation is_a: EDAM:0000004 ! Operation -relationship: in_topic EDAM:0000102 ! Sequencing and mapping +relationship: has_topic EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0002430 @@ -4049,7 +3762,8 @@ name: Design namespace: operation def: "Design a biological entity (typically a molecular sequence or structure) with specific properties." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000004 ! Operation +is_obsolete: true +consider: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) [Term] @@ -4070,7 +3784,7 @@ subset: operation synonym: "Database retrieval" EXACT [] is_a: EDAM:0000004 ! Operation relationship: has_output EDAM:0000006 ! Data {minCardinality=0} -relationship: in_topic EDAM:0000090 ! Data retrieval +relationship: has_topic EDAM:0000090 ! Data search and retrieval [Term] id: EDAM:0002501 @@ -4079,9 +3793,9 @@ namespace: operation def: "Process (read and / or write) nucleic acid sequence or structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002525 ! Nucleic acid data {minCardinality=0} -relationship: has_output EDAM:0002525 ! Nucleic acid data {minCardinality=0} -relationship: in_topic EDAM:0000077 ! Nucleic acids +relationship: has_input EDAM:0002084 ! Nucleic acid report {minCardinality=0} +relationship: has_output EDAM:0002084 ! Nucleic acid report {minCardinality=0} +relationship: has_topic EDAM:0000077 ! Nucleic acid analysis [Term] @@ -4091,9 +3805,9 @@ namespace: operation def: "Process (read and / or write) protein sequence or structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002524 ! Protein data {minCardinality=0} -relationship: has_output EDAM:0002524 ! Protein data {minCardinality=0} -relationship: in_topic EDAM:0000586 ! Proteins +relationship: has_input EDAM:0000896 ! Protein report {minCardinality=0} +relationship: has_output EDAM:0000896 ! Protein report {minCardinality=0} +relationship: has_topic EDAM:0000078 ! Protein analysis [Term] @@ -4115,7 +3829,7 @@ subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0001916 ! Alignment {minCardinality=0} relationship: has_output EDAM:0001916 ! Alignment {minCardinality=0} -relationship: in_topic EDAM:0000083 ! Alignment + [Term] @@ -4125,10 +3839,10 @@ namespace: operation def: "Process (read and / or write) an index of (typically a file of) biological data." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Database index processing" EXACT [] -is_a: EDAM:0002409 ! Data file processing +is_a: EDAM:0002409 ! File processing relationship: has_input EDAM:0000955 ! Data index {minCardinality=0} relationship: has_output EDAM:0000955 ! Data index {minCardinality=0} -relationship: in_topic EDAM:0000220 ! Data file processing +relationship: has_topic EDAM:0000220 ! Data processing and validation [Term] id: EDAM:0002504 @@ -4136,40 +3850,22 @@ name: Structural data processing namespace: operation def: "Process (read and / or write) molecular structural data." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002053 ! Structural data {minCardinality=0} -relationship: has_output EDAM:0002053 ! Structural data {minCardinality=0} -relationship: in_topic EDAM:0000081 ! Structure - -[Term] -id: EDAM:0002484 -name: Structure processing -namespace: operation -def: "Process (read and / or write) one or more molecular structures (secondary or tertiary)." [EDAM:EBI "EMBRACE definition"] -subset: operation is_obsolete: true -consider: EDAM:0002504 ! Structural data processing +consider: EDAM:0002465 ! Structure processing [Term] -id: EDAM:0002431 -name: Structure analysis -namespace: operation -def: "Analyse one or more molecular structures." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002480 ! Structure analysis - -[Term] id: EDAM:0002403 name: Sequence analysis namespace: operation +alt_id: EDAM:0002477 def: "Analyse one or more known molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "Sequence analysis (general)" EXACT [] is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} relationship: has_output EDAM:0002955 ! Sequence report {minCardinality=1} -relationship: in_topic EDAM:0000080 ! Sequence +relationship: has_topic EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0002408 @@ -4187,10 +3883,10 @@ name: Sequence motif processing namespace: operation def: "Process (read and / or write) molecular sequence motifs." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002503 ! Sequence data processing +is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0001353 ! Sequence motif {minCardinality=0} relationship: has_output EDAM:0001353 ! Sequence motif {minCardinality=0} -relationship: in_topic EDAM:0000158 ! Sequence motifs +relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] @@ -4199,40 +3895,19 @@ name: Physicochemical property data processing namespace: operation def: "Process (read and / or write) data on the physicochemical property of a molecule." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002087 ! Molecular property {minCardinality=0} -relationship: has_output EDAM:0002087 ! Molecular property {minCardinality=0} - -[Term] -id: EDAM:0002418 -name: Nucleic acid structure analysis -namespace: operation -def: "Analyse nucleic acid structural data." [EDAM:EBI "EMBRACE definition"] -subset: operation is_obsolete: true -consider: EDAM:0002481 ! Nucleic acid structure analysis - +consider: EDAM:0002420 ! Analysis and processing -[Term] -id: EDAM:0002458 -name: Protein structure analysis -namespace: operation -def: "Analyse protein structural data." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002406 ! Protein structure analysis [Term] id: EDAM:0002414 -name: Protein function data processing +name: Protein function analysis namespace: operation -def: "Process (read and / or write) protein functional data." [EDAM:EBI "EMBRACE definition"] +def: "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." [EDAM:EBI "EMBRACE definition"] +comment: This is a broad concept and is used a placeholder for other, more specific terms. subset: operation is_a: EDAM:0002502 ! Protein data processing -! is_obsolete: true -! consider: EDAM:0001777 ! Protein function prediction -! consider: EDAM:0001778 ! Protein function comparison -relationship: has_output EDAM:0001776 ! Protein report (function) +relationship: has_output EDAM:0000896 ! Protein report [Term] id: EDAM:0000258 @@ -4244,7 +3919,7 @@ is_a: EDAM:0002463 ! Sequence alignment processing is_a: EDAM:0002946 ! Alignment analysis relationship: has_input EDAM:0000292 ! Sequence alignment {minCardinality=1} ! Extends cardinality constraint on parent. relationship: has_output EDAM:0000867 ! Sequence alignment report {minCardinality=1} -relationship: in_topic EDAM:0000182 ! Sequence alignment +relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] @@ -4257,7 +3932,7 @@ is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002502 ! Protein data processing is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_input EDAM:0001384 ! Sequence alignment (protein) {minCardinality=1} -relationship: in_topic EDAM:0000741 ! Protein sequence alignment +relationship: has_topic EDAM:0000741 ! Protein sequence alignment [Term] id: EDAM:0002507 @@ -4269,7 +3944,7 @@ is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002501 ! Nucleic acid data processing is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_input EDAM:0001383 ! Sequence alignment (nucleic acid) {minCardinality=1} -relationship: in_topic EDAM:0000740 ! Nucleic acid sequence alignment +relationship: has_topic EDAM:0000740 ! Nucleic acid sequence alignment [Term] id: EDAM:0002416 @@ -4278,21 +3953,22 @@ namespace: operation def: "Analyse known protein secondary structure data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002444 ! Protein secondary structure processing +synonym: "Secondary structure analysis (protein)" EXACT [] relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} relationship: has_output EDAM:0002956 ! Protein secondary structure report -relationship: in_topic EDAM:0000694 ! Protein secondary structure +relationship: has_topic EDAM:0000694 ! Protein secondary structure [Term] id: EDAM:0000270 -name: Transmembrane protein data processing +name: Transmembrane protein analysis namespace: operation -def: "Process (read and / or write) data on transmembrane proteins and domains / regions." [EDAM:EBI "EMBRACE definition"] +def: "Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions." [EDAM:EBI "EMBRACE definition"] comment: Use this (or child) term for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). subset: operation is_a: EDAM:0002502 ! Protein data processing -relationship: has_output EDAM:0001456 ! Protein report (membrane protein) -relationship: in_topic EDAM:0000820 ! Membrane protein +relationship: has_output EDAM:0001456 ! Protein features (membrane regions) +relationship: has_topic EDAM:0000820 ! Membrane proteins [Term] @@ -4305,7 +3981,8 @@ is_a: EDAM:0002423 ! Prediction, detection and recognition is_a: EDAM:0002480 ! Structure analysis is_a: EDAM:0002426 ! Modelling and simulation relationship: has_output EDAM:0000883 ! Structure -relationship: in_topic EDAM:0000082 ! Structure prediction +relationship: has_topic EDAM:0000082 ! Structure prediction +relationship: has_topic EDAM:0000176 ! Molecular dynamics [Term] @@ -4317,7 +3994,7 @@ subset: operation is_a: EDAM:0002423 ! Prediction, detection and recognition is_a: EDAM:0002465 ! Structure processing relationship: has_output EDAM:0000883 ! Structure -relationship: in_topic EDAM:0000082 ! Structure prediction +relationship: has_topic EDAM:0000082 ! Structure prediction [Term] @@ -4327,64 +4004,64 @@ namespace: operation def: "Process (read and / or write) protein interaction data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002502 ! Protein data processing -is_a: EDAM:0002993 ! Molecular interaction data processing -relationship: has_input EDAM:0000906 ! Protein interaction report {minCardinality=0} -relationship: has_output EDAM:0000906 ! Protein interaction report {minCardinality=0} -relationship: in_topic EDAM:0000128 ! Protein interactions +relationship: has_input EDAM:0000906 ! Protein report (interaction) {minCardinality=0} +relationship: has_output EDAM:0000906 ! Protein report (interaction) {minCardinality=0} +relationship: has_topic EDAM:0000128 ! Protein interactions [Term] id: EDAM:0002521 -name: DNA map data processing +name: Map data processing namespace: operation def: "Process (read and / or write) a DNA map of some type." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "DNA map data processing" EXACT [] is_a: EDAM:0002501 ! Nucleic acid data processing -is_a: EDAM:0002429 ! Mapping and assembly relationship: has_input EDAM:0001274 ! Map {minCardinality=0} relationship: has_output EDAM:0001274 ! Map {minCardinality=0} -relationship: in_topic EDAM:0000796 ! Genetic mapping and linkage +relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0002520 name: DNA mapping namespace: operation -def: "Generate a DNA map of some type." [EDAM:EBI "EMBRACE definition"] +def: "Generate a map of a DNA sequence annotated with positional or non-positional features of some type." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002521 ! DNA map data processing +is_a: EDAM:0002521 ! Map data processing +is_a: EDAM:0002429 ! Mapping and assembly relationship: has_output EDAM:0001274 ! Map {minCardinality=1} -relationship: in_topic EDAM:0000796 ! Genetic mapping and linkage +relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0000282 name: Genetic mapping namespace: operation -def: "Map genetic markers in DNA sequences to determine a genetic (linkage) map for a DNA molecule (typically a chromosome)." [EDAM:EBI "EMBRACE definition"] +def: "Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances." [EDAM:EBI "EMBRACE definition"] comment: Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. subset: operation synonym: "Genetic map generation" EXACT [] synonym: "Linkage mapping" EXACT [] is_a: EDAM:0002520 ! DNA mapping relationship: has_output EDAM:0001278 ! Genetic map {minCardinality=1} -relationship: in_topic EDAM:0000796 ! Genetic mapping and linkage +relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0002944 name: Physical mapping namespace: operation -def: "Map genetic markers onto a physical map of a DNA sequence." [EDAM:EBI "EMBRACE definition"] +def: "Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002520 ! DNA mapping relationship: has_output EDAM:0001280 ! Physical map {minCardinality=1} -relationship: in_topic EDAM:0000102 ! Sequencing and mapping +relationship: has_topic EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0002871 name: Sequence tagged site (STS) mapping namespace: operation -def: "The construction of a physical DNA map (sequence map) from analysis of sequence tagged sites (STS)." [EDAM:EBI "EMBRACE definition"] +def: "Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS)." [EDAM:EBI "EMBRACE definition"] comment: An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. subset: operation synonym: "Sequence mapping" EXACT [] @@ -4398,9 +4075,9 @@ namespace: operation def: "Analyse genetic linkage." [EDAM:EBI "EMBRACE definition"] comment: For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. subset: operation -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) +is_a: EDAM:0002478 ! Nucleic acid sequence analysis relationship: has_output EDAM:0000927 ! Gene annotation (linkage) -relationship: in_topic EDAM:0000796 ! Genetic mapping and linkage +relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0002493 @@ -4408,10 +4085,9 @@ name: Codon usage data processing namespace: operation def: "Process (read and / or write) codon usage data." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0002927 ! Codon usage data {minCardinality=0} -relationship: has_output EDAM:0002927 ! Codon usage data {minCardinality=0} -relationship: in_topic EDAM:0000107 ! Codon usage +is_obsolete: true +consider: EDAM:0000286 ! Codon usage analysis + [Term] @@ -4420,10 +4096,8 @@ name: Sequence data processing namespace: operation def: "Process (read and / or write) molecular sequence data." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002925 ! Sequence data {minCardinality=0} -relationship: has_output EDAM:0002925 ! Sequence data {minCardinality=0} -relationship: in_topic EDAM:0000080 ! Sequence +is_obsolete: true +consider: EDAM:0002446 ! Sequence processing [Term] @@ -4432,11 +4106,10 @@ name: Sequence alignment processing namespace: operation def: "Process (read and / or write) a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002503 ! Sequence data processing is_a: EDAM:0002951 ! Alignment processing relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=0} relationship: has_output EDAM:0000863 ! Sequence alignment {minCardinality=0} -relationship: in_topic EDAM:0000182 ! Sequence alignment +relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0002952 @@ -4444,11 +4117,10 @@ name: Structure alignment processing namespace: operation def: "Process (read and / or write) a molecular tertiary (3D) structure alignment." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002504 ! Structural data processing is_a: EDAM:0002951 ! Alignment processing relationship: has_input EDAM:0000886 ! Structure alignment {minCardinality=0} relationship: has_output EDAM:0000886 ! Structure alignment {minCardinality=0} -relationship: in_topic EDAM:0000183 ! Structure alignment +relationship: has_topic EDAM:0000183 ! Structure alignment [Term] @@ -4462,7 +4134,7 @@ is_a: EDAM:0002463 ! Sequence alignment processing is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002928 ! Alignment relationship: has_output EDAM:0000863 ! Sequence alignment {minCardinality=1} -relationship: in_topic EDAM:0000182 ! Sequence alignment +relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000293 @@ -4470,8 +4142,8 @@ name: Hybrid sequence alignment namespace: operation def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000292 ! Sequence alignment -relationship: has_output EDAM:0001385 ! Sequence alignment (hybrid) {minCardinality=1} +is_obsolete: true +consider: EDAM:0000292 ! Sequence alignment [Term] id: EDAM:0000294 @@ -4480,20 +4152,21 @@ namespace: operation def: "Align molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000292 ! Sequence alignment -relationship: in_topic EDAM:0000189 ! Structure-based sequence alignment +relationship: has_topic EDAM:0000182 ! Sequence alignment + [Term] id: EDAM:0002480 name: Structure analysis namespace: operation +alt_id: EDAM:0002431 def: "Analyse known molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002465 ! Structure processing -is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} relationship: has_output EDAM:0002085 ! Structure report {minCardinality=1} -relationship: in_topic EDAM:0000081 ! Structure +relationship: has_topic EDAM:0000081 ! Structure analysis [Term] id: EDAM:0002931 @@ -4502,10 +4175,9 @@ namespace: operation def: "Compare two or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002424 ! Comparison -is_a: EDAM:0002482 ! Secondary structure data processing relationship: has_input EDAM:0002081 ! Secondary structure {minCardinality=2} relationship: has_output EDAM:0002881 ! Secondary structure report {minCardinality=1} -relationship: in_topic EDAM:0000169 ! Tertiary structure comparison +relationship: has_topic EDAM:0001770 ! Structure comparison [Term] id: EDAM:0002483 @@ -4515,7 +4187,7 @@ def: "Compare two or more molecular tertiary structures." [EDAM:EBI "EMBRACE def subset: operation is_a: EDAM:0002424 ! Comparison is_a: EDAM:0002480 ! Structure analysis -relationship: in_topic EDAM:0000169 ! Tertiary structure comparison +relationship: has_topic EDAM:0001770 ! Structure comparison [Term] @@ -4528,7 +4200,7 @@ is_a: EDAM:0002928 ! Alignment is_a: EDAM:0002483 ! Structure comparison is_a: EDAM:0002952 ! Structure alignment processing relationship: has_output EDAM:0000886 ! Structure alignment {minCardinality=1} -relationship: in_topic EDAM:0000183 ! Structure alignment +relationship: has_topic EDAM:0000183 ! Structure alignment [Term] id: EDAM:0002413 @@ -4536,10 +4208,10 @@ name: Sequence profile processing namespace: operation def: "Process (read and / or write) some type of sequence profile." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002503 ! Sequence data processing +is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0001354 ! Sequence profile {minCardinality=0} relationship: has_output EDAM:0001354 ! Sequence profile {minCardinality=0} -relationship: in_topic EDAM:0000188 ! Sequence profiles and HMMs +relationship: has_topic EDAM:0000188 ! Sequence profiles and HMMs [Term] id: EDAM:0002411 @@ -4547,10 +4219,10 @@ name: Structural (3D) profile processing namespace: operation def: "Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002504 ! Structural data processing +is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=0} relationship: has_output EDAM:0000889 ! Structural (3D) profile {minCardinality=0} -relationship: in_topic EDAM:0000167 ! Structural (3D) profiles +relationship: has_topic EDAM:0000167 ! Structural (3D) profiles [Term] @@ -4562,12 +4234,11 @@ comment: Methods use some type of mapping between sequence and fold, for example subset: operation synonym: "Protein domain prediction" EXACT [] synonym: "Protein fold prediction" EXACT [] -is_a: EDAM:0002479 ! Sequence analysis (protein) -is_a: EDAM:0000474 ! Structure prediction (protein) +is_a: EDAM:0000414 ! Protein feature detection (from sequence) +is_a: EDAM:0000474 ! Protein structure prediction is_a: EDAM:0002997 ! Protein comparison -is_a: EDAM:0002996 ! Structure classification relationship: has_output EDAM:0000901 ! Protein features (domains) {minCardinality=1} -relationship: in_topic EDAM:0000184 ! Threading +relationship: has_topic EDAM:0000184 ! Threading [Term] id: EDAM:0002246 @@ -4575,8 +4246,7 @@ name: Demonstration namespace: operation def: "An operation performing purely illustrative (pedagogical) purposes." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000004 ! Operation -relationship: in_topic EDAM:0000088 ! Literature and documentation +is_obsolete: true [Term] id: EDAM:0002505 @@ -4585,8 +4255,8 @@ namespace: operation def: "Process (read and / or write) text." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0000969 ! Text {minCardinality=0} -relationship: has_output EDAM:0000969 ! Text {minCardinality=0} +relationship: has_input EDAM:0002048 ! Report {minCardinality=0} +relationship: has_output EDAM:0002048 ! Report {minCardinality=0} [Term] id: EDAM:0000306 @@ -4596,18 +4266,20 @@ def: "Process and analyse text (typically the biomedical and informatics literat subset: operation synonym: "Text data mining" EXACT [] is_a: EDAM:0002947 ! Article analysis -relationship: has_input EDAM:0000969 ! Text {minCardinality=0} +relationship: has_input EDAM:0002048 ! Report {minCardinality=0} relationship: has_output EDAM:0000972 ! Text mining report +relationship: has_topic EDAM:0000218 ! Text mining [Term] id: EDAM:0002419 name: Primer and probe design namespace: operation -def: "Design oligonucleotide primers or probes." [EDAM:EBI "EMBRACE definition"] +def: "Predict oligonucleotide primers or probes." [EDAM:EBI "EMBRACE definition"] subset: operation -! is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -is_a: EDAM:0002953 ! Nucleic acid design -relationship: in_topic EDAM:0000632 ! Molecular probes or primers +is_a: EDAM:0003095 ! Nucleic acid design +is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) +synonym: "Primer and probe prediction" EXACT [] +relationship: has_topic EDAM:0003032 ! Primer or probe design [Term] id: EDAM:0000310 @@ -4618,9 +4290,9 @@ comment: Typically, contigs (for example ESTs and genomic DNA fragments) are ali subset: operation is_a: EDAM:0002429 ! Mapping and assembly is_a: EDAM:0002446 ! Sequence processing -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) +is_a: EDAM:0002478 ! Nucleic acid sequence analysis relationship: has_output EDAM:0000925 ! Sequence assembly -relationship: in_topic EDAM:0000196 ! Sequence assembly +relationship: has_topic EDAM:0000196 ! Sequence assembly [Term] id: EDAM:0002432 @@ -4629,19 +4301,21 @@ namespace: operation def: "Process (read and / or write) microarray data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true -consider: EDAM:0002495 ! Gene expression (microarray) data processing +consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0002495 -name: Gene expression (microarray) data processing +name: Gene expression data processing namespace: operation def: "Process (read and / or write) gene expression (typically microarray) data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002603 ! Microarray data {minCardinality=0} -relationship: has_output EDAM:0002603 ! Microarray data {minCardinality=0} -relationship: in_topic EDAM:0000197 ! Gene expression and regulation -relationship: in_topic EDAM:0000200 ! Microarrays +synonym: "Gene expression (microarray) data processing" EXACT [] +synonym: "Microarray data processing" EXACT [] +relationship: has_input EDAM:0003117 ! Microarray hybridisation data {minCardinality=0} +relationship: has_output EDAM:0003117 ! Microarray hybridisation data {minCardinality=0} +relationship: has_topic EDAM:0000197 ! Gene expression resources +relationship: has_topic EDAM:0000200 ! Microarrays [Term] @@ -4651,7 +4325,7 @@ namespace: operation def: "Analyse raw microarray data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true -consider: EDAM:0002495 ! Gene expression (microarray) data processing +consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0000311 @@ -4660,10 +4334,10 @@ namespace: operation def: "Standardize or normalize microarray data." [EDAM:EBI "EMBRACE definition"] comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. subset: operation -is_a: EDAM:0002495 ! Gene expression (microarray) data processing +is_a: EDAM:0002495 ! Gene expression data processing is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_input EDAM:0002603 ! Microarray data {minCardinality=1} -relationship: has_output EDAM:0002603 ! Microarray data {minCardinality=1} +relationship: has_input EDAM:0003117 ! Microarray hybridisation data {minCardinality=1} +relationship: has_output EDAM:0003117 ! Microarray hybridisation data {minCardinality=1} [Term] id: EDAM:0000318 @@ -4679,24 +4353,27 @@ consider: EDAM:0002406 ! Protein structure analysis id: EDAM:0002406 name: Protein structure analysis namespace: operation +alt_id: EDAM:0002458 def: "Analyse protein tertiary structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002480 ! Structure analysis is_a: EDAM:0002459 ! Structure processing (protein) +synonym: "Structure analysis (protein)" EXACT [] relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=1} -relationship: has_output EDAM:0001537 ! Protein structure report {minCardinality=1} +relationship: has_output EDAM:0000897 ! Protein property [Term] id: EDAM:0002481 name: Nucleic acid structure analysis namespace: operation +alt_id: EDAM:0002418 def: "Analyse nucleic acid tertiary structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002480 ! Structure analysis is_a: EDAM:0002519 ! Structure processing (nucleic acid) relationship: has_input EDAM:0001459 ! Nucleic acid structure {minCardinality=1} -relationship: has_output EDAM:0002086 ! Nucleic acid structure report {minCardinality=1} +relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=1} [Term] id: EDAM:0000324 @@ -4705,9 +4382,8 @@ namespace: operation def: "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002443 ! Phylogenetic tree processing -is_a: EDAM:0002423 ! Prediction, detection and recognition relationship: has_input EDAM:0000872 ! Phylogenetic tree {minCardinality=1} -relationship: has_output EDAM:0001438 ! Phylogenetic report {minCardinality=1} +relationship: has_output EDAM:0001438 ! Phylogenetic tree report {minCardinality=1} [Term] id: EDAM:0002438 @@ -4716,9 +4392,22 @@ namespace: operation def: "Generate, analyse or handle a biological pathway or network." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing -relationship: has_input EDAM:0002983 ! Pathway or network data {minCardinality=0} -relationship: has_output EDAM:0002983 ! Pathway or network data {minCardinality=0} -relationship: in_topic EDAM:0000602 ! Pathways, networks and models +relationship: has_input EDAM:0002600 ! Pathway or network {minCardinality=0} +relationship: has_output EDAM:0002600 ! Pathway or network {minCardinality=0} +relationship: has_topic EDAM:0000602 ! Pathways, networks and models + +[Term] +id: EDAM:0003083 +name: Pathway or network rendering +namespace: operation +def: "Render (visualise) a biological pathway or network." [EDAM:EBI "EMBRACE definition"] +subset: operation +is_a: EDAM:0002438 ! Pathway or network processing +is_a: EDAM:0000337 ! Plotting and rendering +relationship: has_input EDAM:0002600 ! Pathway or network {minCardinality=1} +relationship: has_topic EDAM:0000602 ! Pathways, networks and models + + [Term] @@ -4733,29 +4422,30 @@ relationship: has_output EDAM:0002984 ! Pathway or network report {minCardinalit [Term] id: EDAM:0002415 -name: Protein folding modelling +name: Protein folding analysis namespace: operation -def: "Analyse (typically by modelling) protein folding." [EDAM:EBI "EMBRACE definition"] +def: "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." [EDAM:EBI "EMBRACE definition"] +comment: This is a broad concept and is used a placeholder for other, more specific terms. subset: operation +synonym: "Protein folding modelling" EXACT [] is_a: EDAM:0002502 ! Protein data processing is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_output EDAM:0000903 ! Protein report (folding) {minCardinality=1} -relationship: in_topic EDAM:0000130 ! Protein folding, stability and design +relationship: has_output EDAM:0000903 ! Protein folding report {minCardinality=1} +relationship: has_topic EDAM:0000130 ! Protein folding and stability [Term] id: EDAM:0000331 -name: Protein mutation modelling +name: Protein modelling (mutation) namespace: operation -def: "Predict the effect of point mutation on protein folding, stability, structure and function." [EDAM:EBI "EMBRACE definition"] +def: "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function." [EDAM:EBI "EMBRACE definition"] comment: Methods might predict silent or pathological mutations. subset: operation -is_a: EDAM:0002502 ! Protein data processing -is_a: EDAM:0002426 ! Modelling and simulation +is_a: EDAM:0000477 ! Protein modelling is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0000904 ! Protein report (mutation) -relationship: in_topic EDAM:0000130 ! Protein folding, stability and design -relationship: in_topic EDAM:0000199 ! Mutation and polymorphism +synonym: "Protein mutation modelling" EXACT [] +relationship: has_topic EDAM:0000130 ! Protein folding and stability +relationship: has_topic EDAM:0000199 ! Genetic variation [Term] id: EDAM:0000332 @@ -4764,21 +4454,22 @@ namespace: operation def: "Design molecules that elicit an immune response (immunogens)." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true -consider: EDAM:0000559 ! Peptide immunogen design +consider: EDAM:0000559 ! Peptide immunogen prediction and optimisation [Term] id: EDAM:0002409 -name: Data file processing +name: File processing namespace: operation def: "Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Report handling" EXACT [] synonym: "File handling" EXACT [] +synonym: "Data file processing" EXACT [] is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000006 ! Data {minCardinality=0} relationship: has_output EDAM:0000006 ! Data {minCardinality=0} -relationship: in_topic EDAM:0000220 ! Data file processing +relationship: has_topic EDAM:0000220 ! Data processing and validation [Term] @@ -4790,40 +4481,63 @@ subset: operation synonym: "Visualisation" EXACT [] is_a: EDAM:0000004 ! Operation relationship: has_input EDAM:0000006 ! Data {minCardinality=1} -relationship: has_output EDAM:0002968 ! Image or plot {minCardinality=0} -relationship: in_topic EDAM:0000092 ! Data rendering and visualisation +relationship: has_output EDAM:0002968 ! Image {minCardinality=0} +relationship: has_topic EDAM:0000092 ! Data visualisation [Term] id: EDAM:0002121 name: Sequence file processing namespace: operation -def: "Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file creation or concatenation, removal or ordering of sequences." [EDAM:EBI "EMBRACE definition"] +def: "Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002446 ! Sequence processing -is_a: EDAM:0002409 ! Data file processing +is_a: EDAM:0002409 ! File processing [Term] -id: EDAM:0002122 +id: EDAM:0003081 name: Sequence alignment editing namespace: operation +def: "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] +subset: operation +is_a: EDAM:0002122 ! Sequence alignment file processing +is_a: EDAM:0003096 ! Editing + +[Term] +id: EDAM:0002122 +name: Sequence alignment file processing +namespace: operation def: "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002409 ! Data file processing +is_a: EDAM:0002409 ! File processing is_a: EDAM:0002463 ! Sequence alignment processing relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=1} relationship: has_output EDAM:0000863 ! Sequence alignment {minCardinality=1} + + + + [Term] -id: EDAM:0002234 +id: EDAM:0003080 name: Structure editing namespace: operation -def: "Perform basic operations on a file of molecular tertiary structural data." [EDAM:EBI "EMBRACE definition"] +def: "Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002409 ! Data file processing +is_a: EDAM:0002234 ! Structure file processing +is_a: EDAM:0003096 ! Editing +relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} + +[Term] +id: EDAM:0002234 +name: Structure file processing +namespace: operation +def: "Perform basic (non-analytical) operations on a file of molecular tertiary structural data." [EDAM:EBI "EMBRACE definition"] +subset: operation +is_a: EDAM:0002409 ! File processing is_a: EDAM:0002465 ! Structure processing -relationship: has_input EDAM:0000883 ! Structure -relationship: has_output EDAM:0000883 ! Structure + + [Term] id: EDAM:0002120 @@ -4831,7 +4545,7 @@ name: Listfile processing namespace: operation def: "Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses)." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002409 ! Data file processing +is_a: EDAM:0002409 ! File processing relationship: has_input EDAM:0001111 ! EMBOSS listfile relationship: has_output EDAM:0001111 ! EMBOSS listfile @@ -4843,8 +4557,8 @@ namespace: operation def: "Prepare or load a user-specified data file so that it is available for use." [EDAM:EBI "EMBRACE definition"] subset: operation xref: WHATIF:UploadPDB -is_a: EDAM:0002409 ! Data file processing -relationship: has_input EDAM:0002860 ! Identifier {minCardinality=1} +is_a: EDAM:0002409 ! File processing +relationship: has_input EDAM:0000842 ! Identifier {minCardinality=1} [Term] id: EDAM:0000335 @@ -4852,7 +4566,7 @@ name: File reformatting namespace: operation def: "Reformat a file of data (or equivalent entity in memory)." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002409 ! Data file processing +is_a: EDAM:0002409 ! File processing [Term] @@ -4861,7 +4575,7 @@ name: File validation namespace: operation def: "Test and validate the format and content of a data file." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002409 ! Data file processing +is_a: EDAM:0002409 ! File processing is_a: EDAM:0002428 ! Validation and standardisation @@ -4883,7 +4597,7 @@ namespace: operation def: "Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000224 ! Search and retrieval -relationship: has_input EDAM:0002860 ! Identifier {minCardinality=1} +relationship: has_input EDAM:0000842 ! Identifier {minCardinality=1} [Term] id: EDAM:0000343 @@ -4896,12 +4610,16 @@ consider: EDAM:0002421 ! Database search [Term] id: EDAM:0000304 -name: Data retrieval (documentation) +name: Data retrieval (metadata and documentation) namespace: operation -def: "Search for and retrieve information on databases or tools." [EDAM:EBI "EMBRACE definition"] +def: "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described." [EDAM:EBI "EMBRACE definition"] +comment: This includes documentation, general information and other metadata on entities such as databases, database entries and tools. subset: operation +synonym: "Data retrieval (documentation)" EXACT [] +synonym: "Data retrieval (metadata)" EXACT [] +relationship: has_output EDAM:0002337 ! Metadata {minCardinality=1} is_a: EDAM:0002422 ! Data retrieval -relationship: in_topic EDAM:0000088 ! Literature and documentation + [Term] id: EDAM:0000225 @@ -4909,8 +4627,8 @@ name: Data retrieval (database cross-reference) namespace: operation def: "Search database to retrieve all relevant references to a particular entity or entry." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002422 ! Data retrieval -relationship: has_output EDAM:0002093 ! Data reference {minCardinality=0} +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0001813 @@ -4928,7 +4646,7 @@ relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} id: EDAM:0001814 name: Structure retrieval namespace: operation -def: "Query a tertiary structure data resource (typically a database) and retrieve structures and / pr annotation." [EDAM:EBI "EMBRACE definition"] +def: "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation." [EDAM:EBI "EMBRACE definition"] comment: This includes direct retrieval methods but not those that perform calculations on the sequence or structure. subset: operation xref: WHATIF:DownloadPDB @@ -4945,9 +4663,8 @@ namespace: operation def: "Query a profile data resource and retrieve one or more profile(s) and / or associated annotation." [EDAM:EBI "EMBRACE definition"] comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. subset: operation -is_a: EDAM:0002422 ! Data retrieval -is_a: EDAM:0002413 ! Sequence profile processing -relationship: in_topic EDAM:0000188 ! Sequence profiles and HMMs +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] @@ -4956,10 +4673,8 @@ name: Data retrieval (codon usage table) namespace: operation def: "Retrieve a codon usage table and / or associated annotation." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002422 ! Data retrieval -is_a: EDAM:0002433 ! Codon usage table processing -relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=0} -relationship: in_topic EDAM:0000107 ! Codon usage +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002264 @@ -4967,10 +4682,8 @@ name: Data retrieval (pathway or network) namespace: operation def: "Query a biological pathways database and retrieve annotation on one or more pathways." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002422 ! Data retrieval -is_a: EDAM:0002438 ! Pathway or network processing -relationship: has_output EDAM:0002600 ! Pathway or network {minCardinality=0} -relationship: in_topic EDAM:0000602 ! Pathways, networks and models +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] @@ -4979,8 +4692,8 @@ name: Data retrieval (identifier) namespace: operation def: "Query a database and retrieve one or more data identifiers." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002422 ! Data retrieval -relationship: has_output EDAM:0002860 ! Identifier {minCardinality=0} +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002224 @@ -4989,9 +4702,8 @@ namespace: operation def: "Query an ontology and retrieve concepts or relations." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Ontology retrieval" EXACT [] -is_a: EDAM:0002422 ! Data retrieval -relationship: has_output EDAM:0002858 ! Ontology concept {minCardinality=0} -relationship: in_topic EDAM:0000089 ! Ontologies +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002222 @@ -5000,10 +4712,8 @@ namespace: operation def: "Search and retrieve documentation on a bioinformatics ontology." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Ontology information retrieval" EXACT [] -is_a: EDAM:0002422 ! Data retrieval -relationship: has_output EDAM:0002223 ! Ontology metadata {minCardinality=0} -relationship: in_topic EDAM:0000088 ! Literature and documentation -relationship: in_topic EDAM:0000089 ! Ontologies +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002468 @@ -5011,10 +4721,8 @@ name: Data retrieval (phylogenetic tree) namespace: operation def: "Retrieve a phylogenetic tree from a data resource." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002422 ! Data retrieval -is_a: EDAM:0002443 ! Phylogenetic tree processing -relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=0} -relationship: in_topic EDAM:0000084 ! Phylogenetics +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0000257 @@ -5022,9 +4730,8 @@ name: Data retrieval (sequence alignment) namespace: operation def: "Display basic information about a sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002463 ! Sequence alignment processing -is_a: EDAM:0002422 ! Data retrieval -relationship: has_output EDAM:0000866 ! Sequence alignment metadata {minCardinality=0} +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002473 @@ -5033,9 +4740,8 @@ namespace: operation def: "Retrieve information on a specific genotype or phenotype." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Genotype and phenotype information retrieval" EXACT [] -is_a: EDAM:0002422 ! Data retrieval -relationship: has_output EDAM:0000920 ! Genotype and phenotype annotation {minCardinality=0} -relationship: in_topic EDAM:0000625 ! Genotype and phenotype +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002472 @@ -5044,9 +4750,8 @@ namespace: operation def: "Retrieve information on a specific gene." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Gene information retrieval" EXACT [] -is_a: EDAM:0002422 ! Data retrieval -relationship: has_output EDAM:0000916 ! Gene annotation {minCardinality=0} -relationship: in_topic EDAM:0002816 ! Genes +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002471 @@ -5055,9 +4760,8 @@ namespace: operation def: "Retrieve information on an RNA family." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "RNA family information retrieval" EXACT [] -is_a: EDAM:0002422 ! Data retrieval -relationship: has_output EDAM:0002354 ! RNA family annotation {minCardinality=0} -relationship: in_topic EDAM:0000197 ! Gene expression and regulation +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] @@ -5067,9 +4771,8 @@ namespace: operation def: "Retrieve information on a protein family." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Protein family information retrieval" EXACT [] -is_a: EDAM:0002422 ! Data retrieval -relationship: has_output EDAM:0000907 ! Protein family annotation {minCardinality=0} -relationship: in_topic EDAM:0000595 ! Protein classification +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002469 @@ -5077,9 +4780,8 @@ name: Data retrieval (protein interaction annotation) namespace: operation def: "Retrieve information on a protein interaction." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002422 ! Data retrieval -is_a: EDAM:0002405 ! Protein interaction data processing -relationship: has_output EDAM:0000906 ! Protein interaction report {minCardinality=0} +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002467 @@ -5088,9 +4790,8 @@ namespace: operation def: "Retrieve information on a protein." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Protein information retrieval" EXACT [] -is_a: EDAM:0002422 ! Data retrieval -is_a: EDAM:0002502 ! Protein data processing -relationship: has_output EDAM:0000896 ! Protein report {minCardinality=0} +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0000280 @@ -5099,33 +4800,32 @@ namespace: operation def: "Retrieve information on restriction enzymes or restriction enzyme sites." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Restriction enzyme information retrieval" EXACT [] -is_a: EDAM:0002467 ! Data retrieval (protein annotation) -relationship: has_output EDAM:0001517 ! Protein report (restriction enzyme) {minCardinality=0} -relationship: in_topic EDAM:0000100 ! Nucleic acid restriction +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0000515 -name: Data retrieval (tool annotation) +name: Data retrieval (tool metadata) namespace: operation def: "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Tool information retrieval" EXACT [] -is_a: EDAM:0002422 ! Data retrieval (documentation) +synonym: "Data retrieval (tool annotation)" EXACT [] +is_a: EDAM:0000304 ! Data retrieval (metadata and documentation) relationship: has_output EDAM:0000958 ! Tool metadata {minCardinality=0} -relationship: in_topic EDAM:0000088 ! Literature and documentation [Term] id: EDAM:0000516 -name: Data retrieval (database annotation) +name: Data retrieval (database metadata) namespace: operation def: "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Database information retrieval" EXACT [] -is_a: EDAM:0002422 ! Data retrieval (documentation) +synonym: "Data retrieval (database annotation)" EXACT [] +is_a: EDAM:0000304 ! Data retrieval (metadata and documentation) relationship: has_output EDAM:0000957 ! Database metadata {minCardinality=0} -relationship: in_topic EDAM:0000088 ! Literature and documentation [Term] @@ -5163,7 +4863,7 @@ def: "Query the biomedical and informatics literature." [EDAM:EBI "EMBRACE defin subset: operation is_a: EDAM:0002421 ! Database search relationship: has_output EDAM:0000970 ! Bibliographic reference {minCardinality=0} -relationship: in_topic EDAM:0000088 ! Literature and documentation +relationship: has_topic EDAM:0000217 ! Literature analysis [Term] id: EDAM:0000338 @@ -5173,9 +4873,9 @@ def: "Search a sequence database by sequence comparison and retrieve similar seq comment: This excludes direct retrieval methods (e.g. the dbfetch program). subset: operation is_a: EDAM:0002421 ! Database search -is_a: EDAM:0002995 ! Sequence classification +is_a: EDAM:0002403 ! Sequence analysis relationship: has_output EDAM:0000857 ! Database hits (sequence) {minCardinality=0} -relationship: in_topic EDAM:0000159 ! Sequence comparison +relationship: has_topic EDAM:0000159 ! Sequence comparison [Term] @@ -5187,7 +4887,7 @@ subset: operation is_a: EDAM:0002421 ! Database search is_a: EDAM:0002996 ! Structure classification relationship: has_output EDAM:0000885 ! Database hits (structure) {minCardinality=0} -relationship: in_topic EDAM:0000081 ! Structure +relationship: has_topic EDAM:0000081 ! Structure analysis [Term] id: EDAM:0000340 @@ -5198,9 +4898,9 @@ comment: Methods might use fingerprints, profiles, hidden Markov models, sequenc subset: operation synonym: "Protein sequence classification" EXACT [] is_a: EDAM:0002421 ! Database search -is_a: EDAM:0002995 ! Sequence classification +is_a: EDAM:0003093 ! Sequence screening relationship: has_output EDAM:0000858 ! Database hits (secondary) {minCardinality=0} -relationship: in_topic EDAM:0000595 ! Protein classification +relationship: has_topic EDAM:0000595 ! Protein classification [Term] id: EDAM:0000341 @@ -5210,10 +4910,9 @@ def: "Screen a sequence against a motif or pattern database." [EDAM:EBI "EMBRACE subset: operation is_a: EDAM:0002421 ! Database search is_a: EDAM:0000239 ! Sequence motif recognition -! is_a: EDAM:0002403 ! Sequence analysis -is_a: EDAM:0002995 ! Sequence classification +is_a: EDAM:0003093 ! Sequence screening relationship: has_output EDAM:0001298 ! Sequence features (motifs) {minCardinality=0} -relationship: in_topic EDAM:0000158 ! Sequence motifs +relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0000342 @@ -5223,7 +4922,7 @@ def: "Search a database of sequence profiles with a query sequence." [EDAM:EBI " subset: operation is_a: EDAM:0002421 ! Database search is_a: EDAM:0000300 ! Sequence-profile alignment -is_a: EDAM:0002995 ! Sequence classification +is_a: EDAM:0003093 ! Sequence screening relationship: has_output EDAM:0001298 ! Sequence features (motifs) [Term] @@ -5234,8 +4933,9 @@ def: "Search a sequence database and retrieve sequences that are similar to a qu subset: operation synonym: "Sequence similarity search" EXACT [] is_a: EDAM:0000338 ! Sequence database search -is_a: EDAM:0002403 ! Sequence analysis -relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} +is_a: EDAM:0003093 ! Sequence screening +is_a: EDAM:0002451 ! Sequence comparison + [Term] @@ -5247,7 +4947,7 @@ subset: operation is_a: EDAM:0000338 ! Sequence database search is_a: EDAM:0000239 ! Sequence motif recognition relationship: has_input EDAM:0001353 ! Sequence motif {minCardinality=1} -relationship: in_topic EDAM:0000158 ! Sequence motifs +relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] @@ -5257,8 +4957,8 @@ namespace: operation def: "Search a sequence database and retrieve sequences of a given amino acid composition." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000338 ! Sequence database search -relationship: has_input EDAM:0001267 ! Sequence composition (amino acid frequencies) -relationship: in_topic EDAM:0000157 ! Sequence composition +relationship: has_input EDAM:0001267 ! Amino acid frequencies +relationship: has_topic EDAM:0000157 ! Sequence composition analysis [Term] @@ -5302,7 +5002,7 @@ subset: operation synonym: "Sequence similarity search (local alignment-based methods) " EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000493 ! Pairwise sequence alignment (local) -relationship: in_topic EDAM:0000182 ! Sequence alignment +relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000353 @@ -5314,7 +5014,7 @@ subset: operation synonym: "Sequence similarity search (global alignment-based methods)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000494 ! Pairwise sequence alignment (global) -relationship: in_topic EDAM:0000182 ! Sequence alignment +relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000354 @@ -5325,7 +5025,7 @@ comment: STSs are genetic markers that are easily detected by the polymerase cha subset: operation synonym: "Sequence similarity search (primer sequences)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) -relationship: in_topic EDAM:0000195 ! Polymerase chain reaction +relationship: has_topic EDAM:0003032 ! Primer or probe design [Term] id: EDAM:0000355 @@ -5337,8 +5037,8 @@ synonym: "Protein fingerprinting" EXACT [] synonym: "Peptide mass fingerprinting" EXACT [] is_a: EDAM:0000349 ! Sequence database search (by physicochemical property) relationship: has_input EDAM:0000944 ! Peptide mass fingerprint -relationship: in_topic EDAM:0000123 ! Protein physicochemistry -relationship: in_topic EDAM:0000767 ! Peptide identification and proteolysis +relationship: has_topic EDAM:0000123 ! Protein properties +relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] @@ -5348,7 +5048,7 @@ namespace: operation def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000349 ! Sequence database search (by physicochemical property) -relationship: in_topic EDAM:0000123 ! Protein physicochemistry +relationship: has_topic EDAM:0000123 ! Protein properties [Term] id: EDAM:0000357 @@ -5384,8 +5084,8 @@ def: "Search a tertiary structure database and retrieve structures with a sequen subset: operation synonym: "Structure retrieval by sequence" EXACT [] is_a: EDAM:0000339 ! Structure database search -is_a: EDAM:0002403 ! Sequence analysis -relationship: in_topic EDAM:0000159 ! Sequence comparison +is_a: EDAM:0002451 ! Sequence comparison +is_a: EDAM:0003093 ! Sequence screening [Term] id: EDAM:0000360 @@ -5396,8 +5096,8 @@ subset: operation synonym: "Structure retrieval by structure" EXACT [] synonym: "Structural similarity search" EXACT [] is_a: EDAM:0000339 ! Structure database search -relationship: in_topic EDAM:0001770 ! Structure comparison -relationship: in_topic EDAM:0001770 ! Structure comparison +relationship: has_topic EDAM:0001770 ! Structure comparison +relationship: has_topic EDAM:0001770 ! Structure comparison [Term] id: EDAM:0000226 @@ -5408,7 +5108,7 @@ comment: This is a broad concept and is used a placeholder for other, more speci subset: operation is_a: EDAM:0000004 ! Operation relationship: has_input EDAM:0000582 ! Ontology -relationship: in_topic EDAM:0000089 ! Ontologies +relationship: has_topic EDAM:0000089 ! Ontologies [Term] @@ -5449,7 +5149,7 @@ namespace: operation def: "Annotate a DNA map of some type with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000226 ! Annotation -is_a: EDAM:0002521 ! DNA map data processing +is_a: EDAM:0002521 ! Map data processing relationship: has_input EDAM:0001274 ! Map {minCardinality=1} relationship: has_output EDAM:0001274 ! Map {minCardinality=1} @@ -5478,75 +5178,77 @@ relationship: has_output EDAM:0000956 ! Data index report {minCardinality=1} [Term] -id: EDAM:0002477 -name: Sequence analysis (general) +id: EDAM:0002478 +name: Nucleic acid sequence analysis namespace: operation -def: "Analyse a molecular sequence (using methods that might be applicable to nucleic acid or protein sequences)." [EDAM:EBI "EMBRACE definition"] +def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [EDAM:EBI "EMBRACE definition"] subset: operation -is_obsolete: true -consider: EDAM:0002403 ! Sequence analysis +is_a: EDAM:0002403 ! Sequence analysis +is_a: EDAM:0002448 ! Sequence processing (nucleic acid) +relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=1} +relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis [Term] -id: EDAM:0002478 -name: Sequence analysis (nucleic acid) +id: EDAM:0003095 +name: Nucleic acid design namespace: operation -def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [EDAM:EBI "EMBRACE definition"] +def: "Design (or predict) nucleic acid sequences with specific chemical or physical properties." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002403 ! Sequence analysis -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=1} -relationship: in_topic EDAM:0000640 ! Nucleic acid sequences +is_a: EDAM:0002478 ! Nucleic acid sequence analysis + + + [Term] id: EDAM:0002479 -name: Sequence analysis (protein) +name: Protein sequence analysis namespace: operation -def: "Analyse a protein sequence (using methods that might be applicable to protein sequences)." [EDAM:EBI "EMBRACE definition"] +def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002403 ! Sequence analysis -is_a: EDAM:0002502 ! Protein data processing +is_a: EDAM:0002447 ! Sequence processing (protein) +synonym: "Sequence analysis (protein)" EXACT [] relationship: has_input EDAM:0002976 ! Protein sequence {minCardinality=1} -relationship: in_topic EDAM:0000639 ! Protein sequences +relationship: has_topic EDAM:0000639 ! Protein sequence analysis + + [Term] id: EDAM:0002446 name: Sequence processing namespace: operation +alt_id: EDAM:0002449 def: "Process (read and / or write) one or more molecular sequences and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002503 ! Sequence data processing +synonym: "Sequence processing (general)" EXACT [] +is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=0} relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} - +relationship: has_topic EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0002447 name: Sequence processing (protein) namespace: operation -def: "Process (read and / or write) a protein sequence (using methods that are only applicable to protein sequences)." [EDAM:EBI "EMBRACE definition"] +def: "Process (read and / or write) a protein sequence and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: operation -is_obsolete: true -consider: EDAM:0002446 ! Sequence processing +is_a: EDAM:0002446 ! Sequence processing +is_a: EDAM:0002502 ! Protein data processing +relationship: has_input EDAM:0002976 ! Protein sequence {minCardinality=0} +relationship: has_output EDAM:0002976 ! Protein sequence {minCardinality=0} [Term] id: EDAM:0002448 name: Sequence processing (nucleic acid) namespace: operation -def: "Process (read and / or write) a nucleotide sequence (using methods that are only applicable to nucleic acid sequences)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0002446 ! Sequence processing - -[Term] -id: EDAM:0002449 -name: Sequence processing (general) -namespace: operation -def: "Process (read and / or write) a sequence (using methods that might be applicable to nucleic acid or protein sequences)." [EDAM:EBI "EMBRACE definition"] +def: "Process (read and / or write) a nucleotide sequence and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: operation -is_obsolete: true -consider: EDAM:0002446 ! Sequence processing +is_a: EDAM:0002446 ! Sequence processing +is_a: EDAM:0002501 ! Nucleic acid data processing +relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=0} +relationship: has_output EDAM:0002977 ! Nucleic acid sequence {minCardinality=0} [Term] id: EDAM:0000229 @@ -5572,8 +5274,8 @@ namespace: operation def: "Generate a nucleic acid sequence by some means." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000230 ! Sequence generation -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: in_topic EDAM:0000640 ! Nucleic acid sequences +is_a: EDAM:0002448 ! Sequence processing (nucleic acid) +relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis [Term] @@ -5583,8 +5285,8 @@ namespace: operation def: "Generate a protein sequence by some means." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000230 ! Sequence generation -is_a: EDAM:0002502 ! Protein data processing -relationship: in_topic EDAM:0000639 ! Protein sequences +is_a: EDAM:0002447 ! Sequence processing (protein) +relationship: has_topic EDAM:0000639 ! Protein sequence analysis [Term] id: EDAM:0000231 @@ -5593,6 +5295,7 @@ namespace: operation def: "Edit or change a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002121 ! Sequence file processing +is_a: EDAM:0003096 ! Editing [Term] id: EDAM:0002511 @@ -5601,7 +5304,7 @@ namespace: operation def: "Edit or change a nucleic acid sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000231 ! Sequence editing -is_a: EDAM:0002501 ! Nucleic acid data processing +is_a: EDAM:0002448 ! Sequence processing (nucleic acid) [Term] id: EDAM:0002512 @@ -5610,7 +5313,7 @@ namespace: operation def: "Edit or change a protein sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000231 ! Sequence editing -is_a: EDAM:0002502 ! Protein data processing +is_a: EDAM:0002447 ! Sequence processing (protein) [Term] @@ -5620,7 +5323,7 @@ namespace: operation def: "Merge two or more (typically overlapping) molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence splicing" EXACT [] -is_a: EDAM:0002121 ! Sequence file processing +is_a: EDAM:0000231 ! Sequence editing [Term] id: EDAM:0000233 @@ -5628,7 +5331,7 @@ name: Sequence conversion namespace: operation def: "Convert a molecular sequence from one type to another." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002121 ! Sequence file processing +is_a: EDAM:0000231 ! Sequence editing [Term] id: EDAM:0001780 @@ -5638,30 +5341,32 @@ def: "Submit a molecular sequence to a database." [EDAM:EBI "EMBRACE definition" subset: operation is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} -relationship: in_topic EDAM:0000091 ! Data handling +relationship: has_topic EDAM:0000091 ! Data handling [Term] id: EDAM:0000234 name: Sequence complexity calculation namespace: operation +alt_id: EDAM:0000373 +alt_id: EDAM:0000374 def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000236 ! Sequence composition calculation -! is_a: EDAM:0002403 ! Sequence analysis -relationship: has_output EDAM:0001259 ! Sequence property (complexity) {minCardinality=1} -relationship: in_topic EDAM:0000642 ! Low complexity sequence +relationship: has_output EDAM:0001259 ! Sequence complexity {minCardinality=1} +relationship: has_topic EDAM:0000642 ! Low complexity sequences [Term] id: EDAM:0000235 name: Sequence ambiguity calculation namespace: operation +alt_id: EDAM:0000375 +alt_id: EDAM:0000376 def: "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000236 ! Sequence composition calculation -! is_a: EDAM:0002403 ! Sequence analysis -relationship: has_output EDAM:0001260 ! Sequence property (ambiguity) {minCardinality=1} -relationship: in_topic EDAM:0000157 ! Sequence composition +relationship: has_output EDAM:0001260 ! Sequence ambiguity {minCardinality=1} +relationship: has_topic EDAM:0000157 ! Sequence composition analysis [Term] @@ -5684,9 +5389,9 @@ namespace: operation def: "Calculate character or word composition or frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002403 ! Sequence analysis -relationship: has_output EDAM:0001261 ! Sequence property (composition) -relationship: in_topic EDAM:0000157 ! Sequence composition -relationship: in_topic EDAM:0000157 ! Sequence composition +relationship: has_output EDAM:0001261 ! Sequence composition +relationship: has_topic EDAM:0000157 ! Sequence composition analysis +relationship: has_topic EDAM:0000157 ! Sequence composition analysis [Term] @@ -5697,7 +5402,7 @@ def: "Find and/or analyse repeat sequences in (typically nucleotide) sequences." comment: Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. subset: operation is_a: EDAM:0002403 ! Sequence analysis -relationship: in_topic EDAM:0000641 ! Repeat sequence +relationship: has_topic EDAM:0000641 ! Repeat sequences [Term] id: EDAM:0000290 @@ -5707,7 +5412,7 @@ def: "Compare two or more molecular sequences, identify and remove redundant seq subset: operation is_a: EDAM:0000291 ! Sequence clustering relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} -relationship: in_topic EDAM:0000164 ! Sequence clustering +relationship: has_topic EDAM:0000164 ! Sequence clustering [Term] @@ -5718,28 +5423,31 @@ def: "Compare two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002424 ! Comparison +relationship: has_input EDAM:0002044 ! Sequence {minCardinality=2} relationship: has_output EDAM:0002955 ! Sequence report -relationship: in_topic EDAM:0000159 ! Sequence comparison +relationship: has_topic EDAM:0000159 ! Sequence comparison [Term] id: EDAM:0002508 -name: Sequence comparison (nucleic acid) +name: Nucleic acid sequence comparison namespace: operation def: "Compare two or more nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "Sequence comparison (nucleic acid)" EXACT [] is_a: EDAM:0002451 ! Sequence comparison -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) +is_a: EDAM:0002478 ! Nucleic acid sequence analysis is_a: EDAM:0002998 ! Nucleic acid comparison [Term] id: EDAM:0002509 -name: Sequence comparison (protein) +name: Protein sequence comparison namespace: operation def: "Compare two or more protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "Sequence comparison (protein)" EXACT [] is_a: EDAM:0002451 ! Sequence comparison -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0002479 ! Protein sequence analysis is_a: EDAM:0002997 ! Protein comparison [Term] @@ -5749,7 +5457,7 @@ namespace: operation def: "Find exact character or word matches between molecular sequences without full sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002451 ! Sequence comparison -relationship: has_output EDAM:0000861 ! Sequence word alignment {minCardinality=1} +relationship: has_output EDAM:0000861 ! Sequence alignment (words) {minCardinality=1} [Term] id: EDAM:0000289 @@ -5760,7 +5468,7 @@ subset: operation synonym: "Phylogenetic distance matrix generation" EXACT [] is_a: EDAM:0002451 ! Sequence comparison relationship: has_output EDAM:0000870 ! Sequence distance matrix -relationship: in_topic EDAM:0000084 ! Phylogenetics +relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] @@ -5769,9 +5477,8 @@ name: Vector sequence detection namespace: operation def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002508 ! Sequence comparison (nucleic acid) -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -! is_a: EDAM:0002423 ! Prediction, detection and recognition +is_a: EDAM:0002508 ! Nucleic acid sequence comparison +is_a: EDAM:0000415 ! Nucleic acid feature detection [Term] id: EDAM:0002233 @@ -5780,8 +5487,7 @@ namespace: operation def: "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000291 ! Sequence clustering -! is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: in_topic EDAM:0000164 ! Sequence clustering +relationship: has_topic EDAM:0000164 ! Sequence clustering [Term] id: EDAM:0000317 @@ -5801,10 +5507,9 @@ namespace: operation def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [EDAM:EBI "EMBRACE definition"] comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. subset: operation -is_a: EDAM:0002508 ! Sequence comparison (nucleic acid) -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -! is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: in_topic EDAM:0000102 ! Sequencing and mapping +is_a: EDAM:0002508 ! Nucleic acid sequence comparison +is_a: EDAM:0000415 ! Nucleic acid feature detection +relationship: has_topic EDAM:0000102 ! Sequencing and mapping [Term] @@ -5814,8 +5519,9 @@ namespace: operation def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. subset: operation -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: in_topic EDAM:0000110 ! Transcription +is_obsolete: true +consider: EDAM:0000438 ! Transcription regulatory element prediction + [Term] id: EDAM:0000281 @@ -5824,11 +5530,8 @@ namespace: operation def: "Identify genetic markers in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. subset: operation -! is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -is_a: EDAM:0002429 ! Mapping and assembly -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -relationship: in_topic EDAM:0000796 ! Genetic mapping and linkage +is_obsolete: true +consider: EDAM:0000415 ! Nucleic acid feature detection [Term] @@ -5854,9 +5557,9 @@ namespace: operation def: "Generate digest fragments for a nucleotide sequence containing restriction sites." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002513 ! Sequence generation (nucleic acid) -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) +is_a: EDAM:0000262 ! Nucleic acid property calculation relationship: has_output EDAM:0001239 ! Restriction digest -relationship: in_topic EDAM:0000100 ! Nucleic acid restriction +relationship: has_topic EDAM:0000100 ! Nucleic acid restriction [Term] @@ -5866,9 +5569,9 @@ namespace: operation def: "Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002514 ! Sequence generation (protein) -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001238 ! Proteolytic digest -relationship: in_topic EDAM:0000767 ! Peptide identification and proteolysis +relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0000367 @@ -5904,7 +5607,7 @@ namespace: operation def: "Create (or remove) restriction sites in sequences, for example using silent mutations." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002511 ! Sequence editing (nucleic acid) -relationship: in_topic EDAM:0000100 ! Nucleic acid restriction +relationship: has_topic EDAM:0000100 ! Nucleic acid restriction [Term] id: EDAM:0000371 @@ -5913,7 +5616,7 @@ namespace: operation def: "Translate a DNA sequence into protein." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000233 ! Sequence conversion -relationship: in_topic EDAM:0000108 ! Translation +relationship: has_topic EDAM:0000108 ! Translation [Term] @@ -5923,7 +5626,7 @@ namespace: operation def: "Transcribe a nucleotide sequence into mRNA sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000233 ! Sequence conversion -relationship: in_topic EDAM:0000110 ! Transcription +relationship: has_topic EDAM:0000110 ! Transcription [Term] @@ -5933,46 +5636,7 @@ namespace: operation def: "Back-translate a protein sequence into DNA." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000233 ! Sequence conversion -relationship: in_topic EDAM:0000108 ! Translation - - -[Term] -id: EDAM:0000373 -name: Sequence complexity calculation (protein) -namespace: operation -def: "Calculate protein sequence complexity." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000234 ! Sequence complexity calculation - - -[Term] -id: EDAM:0000374 -name: Sequence complexity calculation (nucleic acid) -namespace: operation -def: "Calculate nucleotide sequence complexity, for example to find low-complexity regions in sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000234 ! Sequence complexity calculation - -[Term] -id: EDAM:0000375 -name: Sequence ambiguity calculation (nucleic acid) -namespace: operation -def: "Calculate ambiguity in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000235 ! Sequence ambiguity calculation - - -[Term] -id: EDAM:0000376 -name: Sequence ambiguity calculation (protein) -namespace: operation -def: "Calculate ambiguity in a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000235 ! Sequence ambiguity calculation +relationship: has_topic EDAM:0000108 ! Translation [Term] @@ -5982,7 +5646,8 @@ namespace: operation def: "Calculate base frequency or word composition of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000236 ! Sequence composition calculation -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) +is_a: EDAM:0000262 ! Nucleic acid property calculation + [Term] id: EDAM:0000378 @@ -5991,7 +5656,7 @@ namespace: operation def: "Calculate amino acid frequency or word composition of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000236 ! Sequence composition calculation -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0003088 ! Protein property calculation (from sequence) [Term] id: EDAM:0002284 @@ -6000,17 +5665,16 @@ namespace: operation def: "Calculate a density plot (of base composition) for a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000377 ! Sequence composition calculation (nucleic acid) -is_a: EDAM:0002515 ! Sequence rendering (nucleic acid) [Term] id: EDAM:0000379 name: Repeat sequence detection namespace: operation +alt_id: EDAM:0002450 def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000237 ! Repeat sequence analysis -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -! is_a: EDAM:0002423 ! Prediction, detection and recognition +is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001299 ! Sequence features (repeats) @@ -6023,14 +5687,6 @@ subset: operation is_a: EDAM:0000237 ! Repeat sequence analysis is_a: EDAM:0000236 ! Sequence composition calculation -[Term] -id: EDAM:0002450 -name: Repeat sequence rendering -namespace: operation -def: "Visualise repeats in molecular sequences." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000379 ! Repeat sequence detection [Term] id: EDAM:0000490 @@ -6049,8 +5705,8 @@ namespace: operation def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." [EDAM:EBI "EMBRACE definition"] comment: For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. subset: operation -is_a: EDAM:0000241 ! Transcription regulatory sequence analysis -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) +is_a: EDAM:0000438 ! Transcription regulatory element prediction +is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001315 ! Gene features (TFBS) [Term] @@ -6062,7 +5718,6 @@ comment: Motifs and patterns might be conserved or over-represented (occur with subset: operation synonym: "Motif discovery" EXACT [] is_a: EDAM:0000253 ! Sequence feature detection -! is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002404 ! Sequence motif processing relationship: has_output EDAM:0001298 ! Sequence features (motifs) @@ -6073,7 +5728,6 @@ namespace: operation def: "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence motif detection" EXACT [] -! is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002404 ! Sequence motif processing is_a: EDAM:0000253 ! Sequence feature detection relationship: has_output EDAM:0001298 ! Sequence features (motifs) @@ -6090,50 +5744,41 @@ is_a: EDAM:0002404 ! Sequence motif processing relationship: has_output EDAM:0001298 ! Sequence features (motifs) -[Term] -id: EDAM:0000381 -name: Sequence motif recognition (nucleic acid) -namespace: operation -def: "Find (scan for) known motifs, patterns and regular expressions in nucleotide sequence(s)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000239 ! Sequence motif recognition -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) - - -[Term] -id: EDAM:0000382 -name: Sequence motif recognition (protein) -namespace: operation -def: "Find (scan for) known motifs, patterns and regular expressions in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0000239 ! Sequence motif recognition -is_a: EDAM:0000414 ! Sequence feature detection (protein) [Term] id: EDAM:0002123 -name: Small molecule property processing +name: Small molecule data processing namespace: operation def: "Process (read and / or write) physicochemical property data for small molecules." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002417 ! Physicochemical property data processing -relationship: has_input EDAM:0002601 ! Small molecule data {minCardinality=0} -relationship: has_output EDAM:0002601 ! Small molecule data {minCardinality=0} -relationship: in_topic EDAM:0000154 ! Small molecules +is_obsolete: true +consider: EDAM:0002420 ! Analysis and processing [Term] id: EDAM:0000250 name: Protein property calculation namespace: operation -def: "Calculate (or predict) the physicochemical property data of proteins." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002933 +def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [EDAM:EBI "EMBRACE definition"] +comment: This includes methods to render and visualise the properties of a protein sequence. subset: operation -is_a: EDAM:0002417 ! Physicochemical property data processing -is_a: EDAM:0002479 ! Sequence analysis (protein) +synonym: "Protein property rendering" EXACT [] is_a: EDAM:0002502 ! Protein data processing is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_input EDAM:0000897 ! Protein property {minCardinality=0} relationship: has_output EDAM:0000897 ! Protein property {minCardinality=0} -relationship: in_topic EDAM:0000123 ! Protein physicochemistry +relationship: has_topic EDAM:0000123 ! Protein properties + +[Term] +id: EDAM:0003088 +name: Protein property calculation (from sequence) +namespace: operation +def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [EDAM:EBI "EMBRACE definition"] +subset: operation +is_a: EDAM:0000250 ! Protein property calculation +is_a: EDAM:0002479 ! Protein sequence analysis + [Term] @@ -6142,12 +5787,9 @@ name: Nucleic acid property processing namespace: operation def: "Process (read and / or write) physicochemical property data of nucleic acids." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002417 ! Physicochemical property data processing -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000912 ! Nucleic acid property {minCardinality=0} -relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=0} -relationship: in_topic EDAM:0000094 ! Nucleic acid physicochemistry +is_obsolete: true +consider: EDAM:0000262 ! Nucleic acid property calculation + [Term] id: EDAM:0000334 @@ -6155,9 +5797,9 @@ name: Enzyme kinetics calculation namespace: operation def: "Calculate Km, Vmax and derived data for an enzyme reaction." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000250 ! Protein property calculation +is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0002024 ! Enzyme kinetics data {minCardinality=1} -relationship: in_topic EDAM:0000821 ! Enzymes +relationship: has_topic EDAM:0000821 ! Enzymes and reactions [Term] id: EDAM:0000398 @@ -6165,10 +5807,9 @@ name: Protein molecular weight calculation namespace: operation def: "Calculate the molecular weight of a protein sequence or fragments." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000250 ! Protein property calculation -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001519 ! Peptide molecular weights {minCardinality=1} -relationship: in_topic EDAM:0000767 ! Peptide identification and proteolysis +relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] @@ -6196,8 +5837,7 @@ name: Protein extinction coefficient calculation namespace: operation def: "Predict extinction coefficients or optical density of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000250 ! Protein property calculation -! is_a: EDAM:0002423 ! Prediction, detection and recognition +is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001531 ! Protein extinction coefficient {minCardinality=1} @@ -6207,9 +5847,9 @@ name: Protein pH-dependent property calculation namespace: operation def: "Calculate pH-dependent properties from pKa calculations of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000250 ! Protein property calculation +is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0000897 ! Protein property -relationship: in_topic EDAM:0000137 ! Protein hydropathy +relationship: has_topic EDAM:0000137 ! Protein hydropathy [Term] id: EDAM:0000401 @@ -6226,12 +5866,10 @@ namespace: operation def: "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins." [EDAM:EBI "EMBRACE definition"] comment: This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. subset: operation -is_a: EDAM:0002414 ! Protein function data processing is_a: EDAM:0002492 ! Protein interaction prediction -is_a: EDAM:0000250 ! Protein property calculation -! is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_output EDAM:0001534 ! Peptide immunogenicity report {minCardinality=1} -relationship: in_topic EDAM:0000804 ! Immunoinformatics +is_a: EDAM:0003088 ! Protein property calculation (from sequence) +relationship: has_output EDAM:0001534 ! Peptide immunogenicity {minCardinality=1} +relationship: has_topic EDAM:0000804 ! Immunoinformatics [Term] @@ -6241,7 +5879,6 @@ namespace: operation def: "Generate a Hopp and Woods plot of antigenicity of a protein." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000252 ! Peptide immunogenicity prediction -is_a: EDAM:0002516 ! Sequence rendering (protein) [Term] @@ -6251,7 +5888,6 @@ namespace: operation def: "Plot a protein titration curve." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000400 ! Protein pH-dependent property calculation -! is_a: EDAM:0002933 ! Protein property rendering relationship: has_output EDAM:0001527 ! Protein titration curve {minCardinality=1} @@ -6281,7 +5917,6 @@ namespace: operation def: "Calculate hydrophobic or hydrophilic / charged regions of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -is_a: EDAM:0002516 ! Sequence rendering (protein) [Term] id: EDAM:0000406 @@ -6300,7 +5935,6 @@ def: "Calculate the hydrophobic moment of a peptide sequence and recognize amphi comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -is_a: EDAM:0002516 ! Sequence rendering (protein) relationship: has_output EDAM:0001520 ! Peptide hydrophobic moment {minCardinality=1} [Term] @@ -6310,8 +5944,7 @@ namespace: operation def: "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -! is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_output EDAM:0001526 ! Protein globularity data {minCardinality=1} +relationship: has_output EDAM:0001526 ! Protein globularity {minCardinality=1} [Term] id: EDAM:0000409 @@ -6320,8 +5953,7 @@ namespace: operation def: "Predict the solubility or atomic solvation energy of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -! is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_output EDAM:0001524 ! Protein solubility data {minCardinality=1} +relationship: has_output EDAM:0001524 ! Protein solubility {minCardinality=1} [Term] id: EDAM:0000410 @@ -6330,8 +5962,7 @@ namespace: operation def: "Predict crystallizability of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -! is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_output EDAM:0001525 ! Protein crystallizability data {minCardinality=1} +relationship: has_output EDAM:0001525 ! Protein crystallizability {minCardinality=1} [Term] @@ -6341,9 +5972,8 @@ namespace: operation def: "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000262 ! Nucleic acid property calculation -! is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_output EDAM:0002985 ! Nucleic acid thermodynamic property {minCardinality=1} -relationship: in_topic EDAM:0000104 ! Nucleic acid denaturation +relationship: has_output EDAM:0002985 ! Nucleic acid thermodynamic data {minCardinality=1} + [Term] @@ -6354,21 +5984,18 @@ def: "Calculate and plot a DNA or DNA/RNA melting profile." [EDAM:EBI "EMBRACE d comment: A melting profile is used to visualise and analyse partly melted DNA conformations. subset: operation is_a: EDAM:0000262 ! Nucleic acid property calculation -! is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -is_a: EDAM:0002515 ! Sequence rendering (nucleic acid) relationship: has_output EDAM:0001583 ! Nucleic acid melting profile {minCardinality=1} -relationship: in_topic EDAM:0000104 ! Nucleic acid denaturation [Term] id: EDAM:0000262 name: Nucleic acid property calculation namespace: operation -def: "Calculate or extract a property of nucleic acid structure such as conformational parameters or properties." [EDAM:EBI "EMBRACE definition"] +def: "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000261 ! Nucleic acid property processing +is_a: EDAM:0002478 ! Nucleic acid sequence analysis relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=1} -relationship: in_topic EDAM:0000097 ! Nucleic acid structure + [Term] @@ -6377,12 +6004,12 @@ name: RNA secondary structure processing namespace: operation def: "Process (read and / or write) RNA secondary structure data." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002482 ! Secondary structure data processing +is_a: EDAM:0002482 ! Secondary structure processing is_a: EDAM:0002501 ! Nucleic acid data processing relationship: has_input EDAM:0000880 ! RNA secondary structure {minCardinality=0} relationship: has_output EDAM:0000880 ! RNA secondary structure {minCardinality=0} -relationship: in_topic EDAM:0000097 ! Nucleic acid structure -relationship: in_topic EDAM:0000653 ! RNA +relationship: has_topic EDAM:0000097 ! Nucleic acid structure analysis +relationship: has_topic EDAM:0000697 ! RNA structure and alignment [Term] @@ -6395,7 +6022,7 @@ is_a: EDAM:0002465 ! Structure processing is_a: EDAM:0002501 ! Nucleic acid data processing relationship: has_input EDAM:0001459 ! Nucleic acid structure {minCardinality=0} relationship: has_output EDAM:0001459 ! Nucleic acid structure {minCardinality=0} -relationship: in_topic EDAM:0000097 ! Nucleic acid structure +relationship: has_topic EDAM:0000097 ! Nucleic acid structure analysis [Term] @@ -6404,10 +6031,10 @@ name: Structure processing (RNA) namespace: operation def: "Process (read and / or write) RNA tertiary structure data." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002519 ! Structure processing (nucleic acid) -relationship: has_input EDAM:0001465 ! RNA structure {minCardinality=0} -relationship: has_output EDAM:0001465 ! RNA structure {minCardinality=0} -relationship: in_topic EDAM:0000653 ! RNA +is_obsolete: true +consider: EDAM:0002519 ! Structure processing (nucleic acid) + + [Term] id: EDAM:0000278 @@ -6417,10 +6044,9 @@ def: "Predict RNA secondary structure (for example knots, pseudoknots, alternati comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). subset: operation is_a: EDAM:0002439 ! RNA secondary structure processing -is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) +is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0000880 ! RNA secondary structure {minCardinality=1} -relationship: in_topic EDAM:0000173 ! Nucleic acid structure prediction +relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0002441 @@ -6428,8 +6054,7 @@ name: RNA structure prediction namespace: operation def: "Predict RNA tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002440 ! Structure processing (RNA) -is_a: EDAM:0000475 ! Structure prediction (nucleic acid) +is_a: EDAM:0000475 ! Nucleic acid structure prediction relationship: has_output EDAM:0001465 ! RNA structure {minCardinality=1} @@ -6439,32 +6064,33 @@ name: DNA structure prediction namespace: operation def: "Predict DNA tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000475 ! Structure prediction (nucleic acid) +is_a: EDAM:0000475 ! Nucleic acid structure prediction relationship: has_output EDAM:0001464 ! DNA structure {minCardinality=1} [Term] id: EDAM:0000279 -name: Nucleic acid folding +name: Nucleic acid folding analysis namespace: operation -def: "Analyse or model RNA/DNA folding." [EDAM:EBI "EMBRACE definition"] +def: "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002426 ! Modelling and simulation is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_output EDAM:0001596 ! Nucleic acid report (folding model) -relationship: in_topic EDAM:0000173 ! Nucleic acid structure prediction +synonym: "Nucleic acid folding" EXACT [] +synonym: "Nucleic acid folding modelling" EXACT [] +relationship: has_output EDAM:0001596 ! Nucleic acid folding report +relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0000461 name: Nucleic acid curvature calculation namespace: operation -def: "Calculate curvature and flexibility / stiffness of a nuclotide sequence." [EDAM:EBI "EMBRACE definition"] +def: "Calculate curvature and flexibility / stiffness of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] comment: This includes properties such as. subset: operation is_a: EDAM:0000262 ! Nucleic acid property calculation -! is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=1} -relationship: in_topic EDAM:0000640 ! Nucleic acid sequences +relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0001768 @@ -6473,7 +6099,7 @@ namespace: operation def: "Identify folding families of related RNAs." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true -consider: EDAM:0000483 ! Structured RNA design +consider: EDAM:0000483 ! Structured RNA prediction and optimisation [Term] id: EDAM:0001769 @@ -6481,40 +6107,44 @@ name: Nucleic acid folding energy calculation namespace: operation def: "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000279 ! Nucleic acid folding +is_a: EDAM:0000279 ! Nucleic acid folding analysis [Term] -id: EDAM:0002455 -name: Quadruplex structure prediction +id: EDAM:0001777 +name: Protein function prediction namespace: operation -def: "Predict quadruplex (4 stranded) structures in DNA." [EDAM:EBI "EMBRACE definition"] +def: "Predict general functional properties of a protein." [EDAM:EBI "EMBRACE definition"] +comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. subset: operation -is_a: EDAM:0002442 ! DNA structure prediction -! is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_output EDAM:0002086 ! Nucleic acid structure report {minCardinality=1} +is_a: EDAM:0002414 ! Protein function analysis +is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) +relationship: has_topic EDAM:0002276 ! Protein function prediction + [Term] -id: EDAM:0001777 -name: Protein function prediction +id: EDAM:0003084 +name: Protein function prediction (from sequence) namespace: operation -def: "Predict general functional properties of a protein." [EDAM:EBI "EMBRACE definition"] +def: "Predict general (non-positional) functional properties of a protein from analysing its sequence." [EDAM:EBI "EMBRACE definition"] comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. subset: operation -is_a: EDAM:0002414 ! Protein function data processing +is_a: EDAM:0001777 ! Protein function prediction +is_a: EDAM:0002479 ! Protein sequence analysis is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: in_topic EDAM:0002276 ! Protein function prediction +relationship: has_topic EDAM:0002276 ! Protein function prediction + [Term] id: EDAM:0001778 name: Protein function comparison namespace: operation -def: "Compare the general functional properties of two or more proteins." [EDAM:EBI "EMBRACE definition"] +def: "Compare the functional properties of two or more proteins." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002414 ! Protein function data processing +is_a: EDAM:0002414 ! Protein function analysis is_a: EDAM:0002997 ! Protein comparison -relationship: in_topic EDAM:0001775 ! Protein function +relationship: has_topic EDAM:0001775 ! Protein function analysis [Term] id: EDAM:0000413 @@ -6533,7 +6163,7 @@ subset: operation is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002423 ! Prediction, detection and recognition relationship: has_output EDAM:0001255 ! Sequence features {minCardinality=1} -relationship: in_topic EDAM:0000160 ! Sequence features +relationship: has_topic EDAM:0003072 ! Sequence feature detection [Term] @@ -6543,9 +6173,10 @@ namespace: operation def: "Process (read and / or write) a sequence feature table." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0001270 ! Feature table {minCardinality=0} -relationship: has_output EDAM:0001270 ! Feature table {minCardinality=0} -relationship: in_topic EDAM:0000160 ! Sequence features +relationship: has_input EDAM:0001270 ! Sequence feature table {minCardinality=0} +relationship: has_input EDAM:0002201 ! Sequence record full {minCardinality=0} +relationship: has_output EDAM:0001255 ! Sequence features {minCardinality=0} +relationship: has_topic EDAM:0000160 ! Sequence sites and features [Term] id: EDAM:0000254 @@ -6553,10 +6184,8 @@ name: Data retrieval (feature table) namespace: operation def: "Extract a sequence feature table from a sequence database entry." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002453 ! Feature table processing -is_a: EDAM:0002422 ! Data retrieval -relationship: has_input EDAM:0000849 ! Sequence record {minCardinality=1} -relationship: has_output EDAM:0001270 ! Feature table {minCardinality=0} +is_obsolete: true +consider: EDAM:0002422 ! Data retrieval [Term] @@ -6566,10 +6195,9 @@ namespace: operation def: "Query the features (in a feature table) of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002453 ! Feature table processing -relationship: has_input EDAM:0001270 ! Feature table {minCardinality=0} +relationship: has_input EDAM:0001270 ! Sequence feature table {minCardinality=0} relationship: has_input EDAM:0002201 ! Sequence record full {minCardinality=0} -relationship: has_output EDAM:0001275 ! General sequence features - +relationship: has_output EDAM:0001255 ! Sequence features [Term] id: EDAM:0000256 @@ -6579,33 +6207,86 @@ def: "Compare the feature tables of two or more molecular sequences." [EDAM:EBI subset: operation is_a: EDAM:0002453 ! Feature table processing is_a: EDAM:0002424 ! Comparison -relationship: has_input EDAM:0001270 ! Feature table {minCardinality=0} +relationship: has_input EDAM:0001270 ! Sequence feature table {minCardinality=0} relationship: has_input EDAM:0002201 ! Sequence record full {minCardinality=0} + + +[Term] +id: EDAM:0003092 +name: Protein feature detection +namespace: operation +def: "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures." [EDAM:EBI "EMBRACE definition"] +subset: operation +is_a: EDAM:0002502 ! Protein data processing +is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) +relationship: has_output EDAM:0001277 ! Protein features {minCardinality=1} +relationship: has_topic EDAM:0003074 ! Protein feature detection + + + [Term] id: EDAM:0000414 -name: Sequence feature detection (protein) +name: Protein feature detection (from sequence) namespace: operation -def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions." [EDAM:EBI "EMBRACE definition"] +def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." [EDAM:EBI "EMBRACE definition"] comment: Methods typically involve scanning for known motifs, patterns and regular expressions. subset: operation +synonym: "Sequence feature detection (protein)" EXACT [] +is_a: EDAM:0003092 ! Protein feature detection is_a: EDAM:0000253 ! Sequence feature detection -is_a: EDAM:0002479 ! Sequence analysis (protein) -relationship: has_output EDAM:0001277 ! Protein features {minCardinality=1} -relationship: in_topic EDAM:0000748 ! Protein functional sites +is_a: EDAM:0002479 ! Protein sequence analysis + + + +[Term] +id: EDAM:0003090 +name: Protein feature detection (from structure) +namespace: operation +def: "Predict, recognise and identify positional features in proteins from analysing protein structure." [EDAM:EBI "EMBRACE definition"] +subset: operation +is_a: EDAM:0003092 ! Protein feature detection +is_a: EDAM:0002406 ! Protein structure analysis + + + + +[Term] +id: EDAM:0003087 +name: Protein site detection +namespace: operation +alt_id: EDAM:0000382 +def: "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." [EDAM:EBI "EMBRACE definition"] +subset: operation +synonym: "name: Sequence motif recognition (protein)" EXACT [] +is_a: EDAM:0000414 ! Protein feature detection (from sequence) +is_a: EDAM:0000239 ! Sequence motif recognition + + [Term] id: EDAM:0000415 -name: Sequence feature detection (nucleic acid) +name: Nucleic acid feature detection namespace: operation -def: "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000381 +def: "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions." [EDAM:EBI "EMBRACE definition"] comment: Methods typically involve scanning for known motifs, patterns and regular expressions. subset: operation -is_a: EDAM:0000253 ! Sequence feature detection -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) +synonym: "Sequence feature detection (nucleic acid)" EXACT [] +is_a: EDAM:0000239 ! Sequence motif recognition +is_a: EDAM:0002478 ! Nucleic acid sequence analysis +is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM:0001276 ! Nucleic acid features {minCardinality=1} -relationship: in_topic EDAM:0000747 ! Nucleic acid functional sites +relationship: has_topic EDAM:0003073 ! Nucleic acid feature detection + + + + + + + + [Term] id: EDAM:0000416 @@ -6614,21 +6295,21 @@ namespace: operation def: "Predict antigenic determinant sites (epitopes) in protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Epitope mapping is commonly done during vaccine design. subset: operation -is_a: EDAM:0000414 ! Sequence feature detection (protein) +is_a: EDAM:0003087 ! Protein site detection is_a: EDAM:0002429 ! Mapping and assembly -relationship: has_output EDAM:0001327 ! Protein features (epitopes) -relationship: in_topic EDAM:0000804 ! Immunoinformatics +relationship: has_output EDAM:0001326 ! Protein features (binding sites) +relationship: has_topic EDAM:0000804 ! Immunoinformatics [Term] id: EDAM:0000417 -name: Protein post-translation modification prediction +name: Protein post-translation modification site prediction namespace: operation def: "Predict post-translation modification sites in protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. subset: operation -is_a: EDAM:0000414 ! Sequence feature detection (protein) -relationship: has_output EDAM:0001324 ! Protein features (post-translation modification sites) -relationship: in_topic EDAM:0000601 ! Protein modifications +is_a: EDAM:0003087 ! Protein site detection +relationship: has_output EDAM:0001324 ! Protein features (post-translation modifications) +relationship: has_topic EDAM:0000601 ! Protein modifications [Term] id: EDAM:0002489 @@ -6638,10 +6319,9 @@ def: "Predict the subcellular localization of a protein sequence." [EDAM:EBI "EM comment: The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. subset: operation synonym: "Protein targeting prediction" EXACT [] -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0003084 ! Protein function prediction (from sequence) is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0001533 ! Protein report (subcellular localization) -relationship: in_topic EDAM:0000140 ! Protein targeting and localization +relationship: has_topic EDAM:0000140 ! Protein targeting and localization [Term] id: EDAM:0000418 @@ -6650,20 +6330,21 @@ namespace: operation def: "Detect or predict signal peptides and signal peptide cleavage sites in protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. subset: operation -is_a: EDAM:0000414 ! Sequence feature detection (protein) +is_a: EDAM:0003087 ! Protein site detection is_a: EDAM:0002489 ! Protein subcellular localization prediction relationship: has_output EDAM:0001322 ! Protein features (signal peptides) -relationship: in_topic EDAM:0000140 ! Protein targeting and localization +relationship: has_topic EDAM:0000140 ! Protein targeting and localization [Term] id: EDAM:0000419 -name: Ligand-binding and active site prediction (from sequence) +name: Binding site prediction (from sequence) namespace: operation def: "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000414 ! Sequence feature detection (protein) -is_a: EDAM:0002575 ! Ligand-binding and active site prediction +synonym: "Ligand-binding and active site prediction (from sequence)" EXACT [] +is_a: EDAM:0003087 ! Protein site detection +is_a: EDAM:0002575 ! Binding site prediction [Term] @@ -6672,9 +6353,7 @@ name: Protein-nucleic acid binding prediction namespace: operation def: "Predict RNA and DNA-binding binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -! is_a: EDAM:0000414 ! Sequence feature detection (protein) -! is_a: EDAM:0000389 ! Protein-nucleic acid binding site data analysis -is_a: EDAM:0000419 ! Ligand-binding and active site prediction (from sequence) +is_a: EDAM:0000419 ! Binding site prediction (from sequence) relationship: has_output EDAM:0001326 ! Protein features (binding sites) {minCardinality=0} [Term] @@ -6683,19 +6362,19 @@ name: Protein folding site prediction namespace: operation def: "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000414 ! Sequence feature detection (protein) -is_a: EDAM:0002415 ! Protein folding modelling +is_a: EDAM:0003087 ! Protein site detection +is_a: EDAM:0002415 ! Protein folding analysis relationship: has_output EDAM:0002989 ! Protein features (key folding sites) {minCardinality=1} [Term] id: EDAM:0000422 name: Protein cleavage site prediction namespace: operation -def: "Dectect or predict cleavage sites (enzymatic or chemical) in protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Detect or predict cleavage sites (enzymatic or chemical) in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000414 ! Sequence feature detection (protein) +is_a: EDAM:0003087 ! Protein site detection relationship: has_output EDAM:0001323 ! Protein features (cleavage sites) -relationship: in_topic EDAM:0000767 ! Peptide identification and proteolysis +relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0000423 @@ -6739,10 +6418,9 @@ namespace: operation def: "Detect, predict and identify genes or components of genes in DNA sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Gene finding" EXACT [] -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -! is_a: EDAM:0002423 ! Prediction, detection and recognition +is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001300 ! Nucleic acid features (gene structure) -relationship: in_topic EDAM:0000109 ! Gene finding +relationship: has_topic EDAM:0000109 ! Gene finding [Term] @@ -6770,8 +6448,8 @@ name: Transposon prediction namespace: operation def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_output EDAM:0001301 ! Nucleic acid features (transposons) +is_a: EDAM:0000415 ! Nucleic acid feature detection +relationship: has_output EDAM:0001301 ! Nucleic acid features (mobile genetic elements) [Term] id: EDAM:0000428 @@ -6779,30 +6457,35 @@ name: PolyA signal detection namespace: operation def: "Detect polyA signals in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_output EDAM:0001302 ! Nucleic acid features (PolyA signal) +is_a: EDAM:0000415 ! Nucleic acid feature detection +relationship: has_output EDAM:0001302 ! Nucleic acid features (PolyA signal or site) [Term] id: EDAM:0000429 name: Quadruplex formation site detection namespace: operation +alt_id: EDAM:0002455 def: "Detect quadruplex-forming motifs in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -comment: Quadruplex structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. +comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. subset: operation -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) +is_a: EDAM:0000415 ! Nucleic acid feature detection +synonym: "Quadruplex structure prediction" EXACT [] relationship: has_output EDAM:0001303 ! Nucleic acid features (quadruplexes) -relationship: in_topic EDAM:0000173 ! Nucleic acid structure prediction +relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0000430 -name: CpG island and isochores detection +name: CpG island and isochore detection namespace: operation +alt_id: EDAM:0000576 def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences." [EDAM:EBI "EMBRACE definition"] -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. +comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. subset: operation -is_a: EDAM:0000377 ! Sequence composition calculation (nucleic acid) -relationship: has_output EDAM:0001304 ! Sequence composition (CpG island and isochore) -relationship: in_topic EDAM:0000157 ! Sequence composition +synonym: "CpG island and isochores detection" EXACT [] +synonym: "CpG island and isochores rendering" EXACT [] +is_a: EDAM:0000415 ! Nucleic acid feature detection +relationship: has_output EDAM:0001304 ! Nucleic acid features (CpG island and isochore) +relationship: has_topic EDAM:0000157 ! Sequence composition analysis [Term] @@ -6811,9 +6494,9 @@ name: Restriction site recognition namespace: operation def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) +is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001305 ! Nucleic acid features (restriction sites) -relationship: in_topic EDAM:0000100 ! Nucleic acid restriction +relationship: has_topic EDAM:0000100 ! Nucleic acid restriction [Term] id: EDAM:0000433 @@ -6822,9 +6505,9 @@ namespace: operation def: "Identify, predict or analyse splice sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might require a pre-mRNA or genomic DNA sequence. subset: operation -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) +is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001307 ! Nucleic acid features (splice sites) -relationship: in_topic EDAM:0000114 ! RNA splicing +relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing [Term] id: EDAM:0000453 @@ -6841,7 +6524,7 @@ name: Nucleosome formation or exclusion sequence prediction namespace: operation def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) +is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001306 ! Nucleic acid features (nucleosome exclusion sequences) @@ -6870,7 +6553,7 @@ namespace: operation def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000425 ! Whole gene prediction -relationship: in_topic EDAM:0000663 ! tRNA +relationship: has_topic EDAM:0000663 ! tRNA [Term] id: EDAM:0000436 @@ -6879,7 +6562,7 @@ namespace: operation def: "Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000426 ! Gene component prediction -relationship: has_output EDAM:0001313 ! Gene features (coding region) +relationship: has_output EDAM:0001313 ! Nucleic acid features (coding sequence) [Term] @@ -6890,7 +6573,7 @@ def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [EDA comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. subset: operation is_a: EDAM:0000426 ! Gene component prediction -relationship: has_output EDAM:0001314 ! Gene features (SECIS element) +relationship: has_output EDAM:0001300 ! Nucleic acid features (gene structure) [Term] id: EDAM:0000438 @@ -6900,7 +6583,9 @@ def: "Identify or predict transcription regulatory motifs, patterns, elements or comment: This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. subset: operation is_a: EDAM:0000426 ! Gene component prediction -is_a: EDAM:0000241 ! Transcription regulatory sequence analysis +relationship: has_topic EDAM:0000110 ! Transcription +relationship: has_topic EDAM:0000749 ! Transcription factors and regulatory sites + [Term] id: EDAM:0000439 @@ -6909,7 +6594,7 @@ namespace: operation def: "Predict translation initiation sites, possibly by searching a database of sites." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000436 ! Coding region prediction -relationship: in_topic EDAM:0000108 ! Translation +relationship: has_topic EDAM:0000108 ! Translation [Term] id: EDAM:0000440 @@ -6920,7 +6605,6 @@ comment: Methods might recognize CG content, CpG islands, splice sites, polyA si subset: operation is_a: EDAM:0000438 ! Transcription regulatory element prediction relationship: has_output EDAM:0001312 ! Gene features (promoter) -relationship: in_topic EDAM:0000111 ! Promoters [Term] id: EDAM:0000441 @@ -6951,7 +6635,7 @@ comment: Trans-regulatory elements regulate genes distant from the gene from whi subset: operation synonym: "Functional RNA identification" EXACT [] is_a: EDAM:0000438 ! Transcription regulatory element prediction -relationship: in_topic EDAM:0000659 ! Functional RNA +relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] @@ -6982,8 +6666,8 @@ def: "Identify or predict exonic splicing enhancers (ESE) in exons." [EDAM:EBI " comment: An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. subset: operation is_a: EDAM:0000440 ! Promoter prediction -relationship: has_output EDAM:0001309 ! Gene features (exonic splicing enhancer) -relationship: in_topic EDAM:0000114 ! RNA splicing +relationship: has_output EDAM:0002397 ! Nucleic acid features (exon) +relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing [Term] id: EDAM:0002008 @@ -6993,18 +6677,17 @@ def: "Identify or predict siRNA duplexes in RNA." [EDAM:EBI "EMBRACE definition" subset: operation is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) relationship: has_output EDAM:0002169 ! Nucleic acid features (siRNA) -relationship: in_topic EDAM:0000662 ! siRNA +relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] id: EDAM:0000465 -name: siRNA assay design +name: siRNA binding specificity prediction namespace: operation -def: "Design an siRNA sequence and assess binding specificity, for example for a functional assay." [EDAM:EBI "EMBRACE definition"] +def: "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) -is_a: EDAM:0002430 ! Design -relationship: in_topic EDAM:0000662 ! siRNA +relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] @@ -7015,7 +6698,7 @@ def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA subset: operation is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) relationship: has_output EDAM:0001310 ! Nucleic acid features (microRNA) -relationship: in_topic EDAM:0000661 ! miRNA + [Term] @@ -7034,7 +6717,7 @@ name: Sequence alignment conversion namespace: operation def: "Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence)." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002122 ! Sequence alignment editing +is_a: EDAM:0003081 ! Sequence alignment editing [Term] @@ -7049,7 +6732,7 @@ is_a: EDAM:0000258 ! Sequence alignment analysis [Term] id: EDAM:0000448 -name: Sequence alignment conservation analysis +name: Sequence alignment analysis (conservation) namespace: operation def: "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. @@ -7059,7 +6742,7 @@ relationship: has_output EDAM:0001415 ! Sequence alignment report (site conserva [Term] id: EDAM:0000449 -name: Sequence alignment correlation analysis +name: Sequence alignment analysis (site correlation) namespace: operation def: "Analyse correlations between sites in a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. @@ -7069,42 +6752,41 @@ relationship: has_output EDAM:0001416 ! Sequence alignment report (site correlat [Term] id: EDAM:0000450 -name: Chimeric sequence detection +name: Sequence alignment analysis (chimeric sequence detection) namespace: operation def: "Detects chimeric sequences (chimeras) from a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. subset: operation is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) -! is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: in_topic EDAM:0000195 ! Polymerase chain reaction +relationship: has_topic EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000451 -name: Recombination detection +name: Sequence alignment analysis (recombination detection) namespace: operation def: "Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. subset: operation is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) -! is_a: EDAM:0002423 ! Prediction, detection and recognition + [Term] id: EDAM:0000452 -name: Indel detection +name: Sequence alignment analysis (indel detection) namespace: operation def: "Identify insertion, deletion and duplication events from a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. subset: operation is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) -! is_a: EDAM:0002423 ! Prediction, detection and recognition + [Term] id: EDAM:0000457 name: Nucleic acid stitch profile plotting namespace: operation def: "Calculate and plot a DNA or DNA/RNA stitch profile." [EDAM:EBI "EMBRACE definition"] -comment: A stich profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. +comment: A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. subset: operation is_a: EDAM:0000456 ! Nucleic acid melting profile plotting relationship: has_output EDAM:0001587 ! Nucleic acid stitch profile @@ -7143,11 +6825,11 @@ name: Protein secondary structure processing namespace: operation def: "Process (read and / or write) protein secondary structure data." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002482 ! Secondary structure data processing +is_a: EDAM:0002482 ! Secondary structure processing is_a: EDAM:0002502 ! Protein data processing relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=0} relationship: has_output EDAM:0000876 ! Protein features (secondary structure) {minCardinality=0} -relationship: in_topic EDAM:0000694 ! Protein secondary structure +relationship: has_topic EDAM:0000694 ! Protein secondary structure [Term] id: EDAM:0000319 @@ -7158,7 +6840,7 @@ subset: operation is_a: EDAM:0002444 ! Protein secondary structure processing is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} -relationship: in_topic EDAM:0000136 ! Raw structural data analysis +relationship: has_topic EDAM:0002226 ! Structure determination [Term] id: EDAM:0000267 @@ -7167,11 +6849,12 @@ namespace: operation def: "Predict secondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. subset: operation +synonym: "Secondary structure prediction (protein)" EXACT [] is_a: EDAM:0002444 ! Protein secondary structure processing -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0000414 ! Protein feature detection (from sequence) is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} -relationship: in_topic EDAM:0000178 ! Protein secondary structure prediction +relationship: has_topic EDAM:0000178 ! Protein secondary structure prediction [Term] id: EDAM:0000268 @@ -7181,7 +6864,7 @@ def: "Predict super-secondary structure of protein sequence(s)." [EDAM:EBI "EMBR comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. subset: operation is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_output EDAM:0000877 ! Protein structure report (super-secondary) +relationship: has_output EDAM:0000877 ! Protein features (super-secondary) [Term] id: EDAM:0000534 @@ -7190,7 +6873,7 @@ namespace: operation def: "Assign secondary structure from protein coordinate data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000319 ! Protein secondary structure assignment -is_a: EDAM:0002406 ! Protein structure analysis +is_a: EDAM:0003090 ! Protein feature detection (from structure) [Term] id: EDAM:0000535 @@ -7259,9 +6942,9 @@ name: Transmembrane protein prediction namespace: operation def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000270 ! Transmembrane protein data processing +is_a: EDAM:0000270 ! Transmembrane protein analysis is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_output EDAM:0001456 ! Protein structure report (membrane protein) {minCardinality=1} +relationship: has_output EDAM:0001456 ! Protein features (membrane regions) {minCardinality=1} [Term] id: EDAM:0002456 @@ -7272,7 +6955,7 @@ subset: operation synonym: "G protein-coupled receptor (GPCR) classification" EXACT [] is_a: EDAM:0000473 ! GPCR analysis is_a: EDAM:0002995 ! Sequence classification -relationship: has_output EDAM:0000907 ! Protein family annotation {minCardinality=1} +relationship: has_output EDAM:0000907 ! Protein family {minCardinality=1} [Term] @@ -7282,10 +6965,9 @@ namespace: operation def: "Predict G-protein coupled receptor (GPCR) coupling selectivity." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000473 ! GPCR analysis -! is_a: EDAM:0002423 ! Prediction, detection and recognition is_a: EDAM:0002492 ! Protein interaction prediction -is_a: EDAM:0000250 ! Protein property calculation -relationship: has_output EDAM:0001776 ! Protein report (function) {minCardinality=1} +is_a: EDAM:0003088 ! Protein property calculation (from sequence) +relationship: has_output EDAM:0000896 ! Protein report {minCardinality=1} [Term] @@ -7295,9 +6977,9 @@ namespace: operation def: "Analyse G-protein coupled receptor proteins (GPCRs)." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "G protein-coupled receptor (GPCR) analysis" EXACT [] -is_a: EDAM:0000270 ! Transmembrane protein data processing -relationship: has_output EDAM:0001456 ! Protein report (membrane protein) -relationship: in_topic EDAM:0000820 ! Membrane protein +is_a: EDAM:0000270 ! Transmembrane protein analysis +relationship: has_output EDAM:0001456 ! Protein features (membrane regions) +relationship: has_topic EDAM:0000820 ! Membrane proteins [Term] @@ -7312,56 +6994,56 @@ is_a: EDAM:0000473 ! GPCR analysis [Term] id: EDAM:0000474 -name: Structure prediction (protein) +name: Protein structure prediction namespace: operation def: "Predict tertiary structure (backbone and side-chain conformation) of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -synonym: "Protein structure prediction" EXACT [] is_a: EDAM:0000271 ! Structure prediction is_a: EDAM:0002459 ! Structure processing (protein) -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0002479 ! Protein sequence analysis is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM:0001460 ! Protein structure {minCardinality=1} -relationship: in_topic EDAM:0000179 ! Protein tertiary structure prediction +relationship: has_topic EDAM:0000179 ! Protein tertiary structure prediction [Term] id: EDAM:0000475 -name: Structure prediction (nucleic acid) +name: Nucleic acid structure prediction namespace: operation def: "Predict tertiary structure of DNA or RNA." [EDAM:EBI "EMBRACE definition"] comment: Methods might identify thermodynamically stable or evolutionarily conserved structures. subset: operation is_a: EDAM:0000271 ! Structure prediction is_a: EDAM:0002519 ! Structure processing (nucleic acid) -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) +is_a: EDAM:0002478 ! Nucleic acid sequence analysis is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM:0001459 ! Nucleic acid structure {minCardinality=1} -relationship: in_topic EDAM:0000173 ! Nucleic acid structure prediction +relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0000476 name: Ab initio structure prediction namespace: operation -def: "Predict tertiary structure of protein sequence(s) without homologues of known structure." [EDAM:EBI "EMBRACE definition"] +def: "Predict tertiary structure of protein sequence(s) without homologs of known structure." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000474 ! Structure prediction (protein) -relationship: in_topic EDAM:0000174 ! Ab initio structure prediction +is_a: EDAM:0000474 ! Protein structure prediction +relationship: has_topic EDAM:0000174 ! Ab initio structure prediction [Term] id: EDAM:0000477 name: Protein modelling namespace: operation -def: "Build a three-dimensional protein model based on known (for example homologues) structures." [EDAM:EBI "EMBRACE definition"] +def: "Build a three-dimensional protein model based on known (for example homologs) structures." [EDAM:EBI "EMBRACE definition"] comment: The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. subset: operation synonym: "Comparative modelling" EXACT [] synonym: "Homology modelling" EXACT [] synonym: "Homology structure modelling" EXACT [] synonym: "Protein structure comparative modelling" EXACT [] -is_a: EDAM:0000474 ! Structure prediction (protein) +is_a: EDAM:0002406 ! Protein structure analysis +is_a: EDAM:0000474 ! Protein structure prediction is_a: EDAM:0002426 ! Modelling and simulation -relationship: in_topic EDAM:0000175 ! Homology modelling +relationship: has_topic EDAM:0000175 ! Homology modelling [Term] @@ -7371,12 +7053,11 @@ namespace: operation def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [EDAM:EBI "EMBRACE definition"] comment: This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. subset: operation -is_a: EDAM:0002459 ! Structure processing (protein) -is_a: EDAM:0002426 ! Modelling and simulation +is_a: EDAM:0000477 ! Protein modelling is_a: EDAM:0002492 ! Protein interaction prediction relationship: has_output EDAM:0001461 ! Protein-ligand complex {minCardinality=0} relationship: has_output EDAM:0002877 ! Protein complex {minCardinality=0} -relationship: in_topic EDAM:0000177 ! Molecular docking +relationship: has_topic EDAM:0000177 ! Molecular docking [Term] @@ -7391,8 +7072,8 @@ is_a: EDAM:0000303 ! Protein fold recognition is_a: EDAM:0002928 ! Alignment relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=1} relationship: has_output EDAM:0000893 ! Sequence-structure alignment {minCardinality=1} -relationship: in_topic EDAM:0000175 ! Homology modelling -relationship: in_topic EDAM:0000184 ! Threading +relationship: has_topic EDAM:0000175 ! Homology modelling +relationship: has_topic EDAM:0000184 ! Threading [Term] @@ -7426,7 +7107,7 @@ id: EDAM:0001841 name: Rotamer likelihood prediction namespace: operation def: "Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure." [EDAM:WHATIF "EMBRACE definition"] -comment: Output typically includes, for each residue position, the likelihoods for the 20 aminoacid types with estimated reliability of the 20 likelihoods. +comment: Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. subset: operation xref: WHATIF:ShowLikelyRotamers xref: WHATIF:ShowLikelyRotamers100 @@ -7451,20 +7132,20 @@ subset: operation synonym: "Virtual ligand screening" EXACT [] is_a: EDAM:0000478 ! Protein docking relationship: has_output EDAM:0001461 ! Protein-ligand complex {minCardinality=1} -relationship: in_topic EDAM:0000148 ! Protein-ligand interactions +relationship: has_topic EDAM:0000148 ! Protein-ligand interactions [Term] id: EDAM:0000483 -name: Structured RNA design +name: Structured RNA prediction and optimisation namespace: operation -def: "Predict or design RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection." [EDAM:EBI "EMBRACE definition"] +def: "Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "RNA inverse folding" EXACT [] synonym: "Nucleic acid folding family identification" EXACT [] -is_a: EDAM:0000278 ! RNA secondary structure prediction -is_a: EDAM:0002441 ! RNA structure prediction -is_a: EDAM:0002953 ! Nucleic acid design +is_a: EDAM:0003095 ! Nucleic acid design +is_a: EDAM:0002425 ! Optimisation and refinement relationship: has_output EDAM:0001234 ! Sequence set (nucleic acid) +relationship: has_topic EDAM:0002953 ! Nucleic acid design [Term] id: EDAM:0000273 @@ -7474,7 +7155,7 @@ def: "Analyse experimental protein-protein interaction data from for example yea subset: operation is_a: EDAM:0002949 ! Protein interaction analysis relationship: has_input EDAM:0000905 ! Protein interaction raw data -relationship: in_topic EDAM:0000147 ! Protein-protein interactions +relationship: has_topic EDAM:0000147 ! Protein-protein interactions [Term] id: EDAM:0002492 @@ -7484,7 +7165,7 @@ def: "Predict the interactions of proteins with other molecules." [EDAM:EBI "EMB subset: operation is_a: EDAM:0002405 ! Protein interaction data processing is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0000906 ! Protein interaction report {minCardinality=1} +relationship: has_output EDAM:0000906 ! Protein report (interaction) {minCardinality=1} [Term] id: EDAM:0002464 @@ -7494,7 +7175,7 @@ def: "Identify or predict protein-protein interactions, interfaces, binding site subset: operation is_a: EDAM:0002492 ! Protein interaction prediction relationship: has_output EDAM:0001565 ! Protein-protein interaction {minCardinality=1} -relationship: in_topic EDAM:0000147 ! Protein-protein interactions +relationship: has_topic EDAM:0000147 ! Protein-protein interactions [Term] @@ -7504,7 +7185,7 @@ namespace: operation def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002464 ! Protein-protein interaction prediction -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0003084 ! Protein function prediction (from sequence) [Term] id: EDAM:0000275 @@ -7513,7 +7194,8 @@ namespace: operation def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002464 ! Protein-protein interaction prediction -is_a: EDAM:0002406 ! Protein structure analysis +is_a: EDAM:0003090 ! Protein feature detection (from structure) + [Term] @@ -7523,20 +7205,21 @@ namespace: operation def: "Process (read and / or write) a network of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002405 ! Protein interaction data processing +is_a: EDAM:0002438 ! Pathway or network processing relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=0} relationship: has_output EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=0} -relationship: in_topic EDAM:0000147 ! Protein-protein interactions +relationship: has_topic EDAM:0003044 ! Protein interaction networks [Term] id: EDAM:0000333 -name: Protein-nucleic acid binding site design +name: Zinc finger protein domain prediction and optimisation namespace: operation -def: "Design zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases)." [EDAM:EBI "EMBRACE definition"] +def: "Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000420 ! Protein-nucleic acid binding prediction -is_a: EDAM:0002430 ! Design +is_a: EDAM:0002425 ! Optimisation and refinement relationship: has_output EDAM:0001567 ! Protein-nucleic acid interaction -relationship: in_topic EDAM:0000150 ! Protein rational design +relationship: has_topic EDAM:0000150 ! Protein design [Term] @@ -7547,6 +7230,7 @@ def: "Analyse a network of protein interactions." [EDAM:EBI "EMBRACE definition" subset: operation is_a: EDAM:0002445 ! Protein interaction network processing is_a: EDAM:0002949 ! Protein interaction analysis +is_a: EDAM:0002497 ! Pathway or network analysis relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=1} relationship: has_output EDAM:0002984 ! Pathway or network report @@ -7556,27 +7240,28 @@ name: Protein interaction network comparison namespace: operation def: "Compare two or more networks of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002445 ! Protein interaction network processing -is_a: EDAM:0002997 ! Protein comparison +is_a: EDAM:0000276 ! Protein interaction network analysis +is_a: EDAM:0001778 ! Protein function comparison relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=2} -relationship: has_output EDAM:0002984 ! Pathway or network report + [Term] id: EDAM:0000484 name: SNP detection namespace: operation def: "Find single nucleotide polymorphisms (SNPs) between sequences." [EDAM:EBI "EMBRACE definition"] -comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated nonsynonymous SNPs etc. +comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. subset: operation synonym: "Single nucleotide polymorphism detection" EXACT [] -is_a: EDAM:0000281 ! Genetic marker identification -relationship: has_output EDAM:0002885 ! Polymorphism annotation +is_a: EDAM:0002508 ! Nucleic acid sequence comparison +is_a: EDAM:0002508 ! Nucleic acid sequence comparison +relationship: has_output EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0000485 name: Radiation Hybrid Mapping namespace: operation -def: "Map genetic markers using radiation hybrid scores onto a DNA physical map, using provided radiation hybrid (RH) scores for one or more markers." [EDAM:EBI "EMBRACE definition"] +def: "Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002944 ! Physical mapping relationship: has_output EDAM:0002870 ! Radiation hybrid map {minCardinality=1} @@ -7616,15 +7301,19 @@ relationship: has_output EDAM:0001634 ! Gene annotation (linkage disequilibrium) [Term] id: EDAM:0000286 -name: Codon usage data analysis +name: Codon usage analysis namespace: operation -def: "Analyse existing codon usage data, from processing molecular sequences or a codon usage table." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002494 +def: "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002493 ! Codon usage data processing -is_a: EDAM:0002420 ! Analysis and processing -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0002927 ! Codon usage data {minCardinality=1} -relationship: has_output EDAM:0000914 ! Codon usage report {minCardinality=1} +synonym: "synon: Codon usage table analysis" EXACT [] +synonym: "synon: Codon usage data analysis" EXACT [] +is_a: EDAM:0002501 ! Nucleic acid data processing +relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=0} +relationship: has_input EDAM:0001597 ! Codon usage table {minCardinality=0} +relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=0} +relationship: has_output EDAM:0000914 ! Codon usage report {minCardinality=0} +relationship: has_topic EDAM:0000107 ! Codon usage analysis [Term] @@ -7633,7 +7322,7 @@ name: Codon usage table processing namespace: operation def: "Process (read and / or write) a codon usage table." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002493 ! Codon usage data processing +is_a: EDAM:0000286 ! Codon usage analysis relationship: has_input EDAM:0001597 ! Codon usage table {minCardinality=0} relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=0} @@ -7643,10 +7332,9 @@ name: Base position variability plotting namespace: operation def: "Identify and plot third base position variability in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000286 ! Codon usage data analysis -is_a: EDAM:0002515 ! Sequence rendering (nucleic acid) +is_a: EDAM:0000286 ! Codon usage analysis relationship: has_output EDAM:0001263 ! Sequence composition (base position variability) {minCardinality=1} -relationship: in_topic EDAM:0000109 ! Gene finding +relationship: has_topic EDAM:0000109 ! Gene finding [Term] @@ -7655,7 +7343,7 @@ name: Genetic code prediction namespace: operation def: "Predict genetic code from analysis of codon usage data." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000286 ! Codon usage data analysis +is_a: EDAM:0000286 ! Codon usage analysis is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM:0001598 ! Genetic code {minCardinality=1} @@ -7665,7 +7353,7 @@ name: Codon usage bias calculation namespace: operation def: "Calculate codon usage bias." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000286 ! Codon usage data analysis +is_a: EDAM:0000286 ! Codon usage analysis relationship: has_output EDAM:0002865 ! Codon usage bias {minCardinality=1} [Term] @@ -7681,20 +7369,12 @@ relationship: has_output EDAM:0001600 ! Codon usage bias plot {minCardinality=1} id: EDAM:0002964 name: Codon usage fraction calculation namespace: operation -def: "Calculate the differences in codon usage fractions between two codon usage tables." [EDAM:EBI "EMBRACE definition"] +def: "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000285 ! Codon usage table comparison +is_a: EDAM:0000286 ! Codon usage analysis relationship: has_output EDAM:0001602 ! Codon usage fraction difference {minCardinality=1} -[Term] -id: EDAM:0002494 -name: Codon usage table analysis -namespace: operation -def: "Analyse one or more codon usage tables." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002433 ! Codon usage table processing -is_a: EDAM:0000286 ! Codon usage data analysis -relationship: has_input EDAM:0001597 ! Codon usage table {minCardinality=1} + [Term] id: EDAM:0000284 @@ -7711,7 +7391,7 @@ name: Codon usage table comparison namespace: operation def: "Compare two or more codon usage tables." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002494 ! Codon usage table analysis +is_a: EDAM:0002433 ! Codon usage table processing is_a: EDAM:0002998 ! Nucleic acid comparison [Term] @@ -7739,7 +7419,7 @@ name: Sequence alignment refinement namespace: operation def: "Refine an existing sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002122 ! Sequence alignment editing +is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002425 ! Optimisation and refinement @@ -7803,7 +7483,7 @@ def: "Align multiple sequences using relative gap costs calculated from neighbor comment: This is supposed to give a more biologically meaningful alignment than standard alignments. subset: operation is_a: EDAM:0000492 ! Multiple sequence alignment -relationship: in_topic EDAM:0000084 ! Phylogenetics +relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] @@ -7812,12 +7492,11 @@ name: Secondary structure alignment namespace: operation def: "Align molecular secondary structure (represented as a 1D string)." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002482 ! Secondary structure data processing +is_a: EDAM:0002482 ! Secondary structure processing is_a: EDAM:0002931 ! Secondary structure comparison is_a: EDAM:0000294 ! Structure-based sequence alignment -relationship: has_input EDAM:0002081 ! Secondary structure {minCardinality=2} relationship: has_output EDAM:0002366 ! Secondary structure alignment {minCardinality=1} -relationship: in_topic EDAM:0000189 ! Structure-based sequence alignment +relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] @@ -7828,6 +7507,7 @@ def: "Align protein secondary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000500 ! Secondary structure alignment is_a: EDAM:0002488 ! Protein secondary structure comparison +synonym: "Secondary structure alignment (protein)" EXACT [] relationship: has_output EDAM:0000878 ! Secondary structure alignment (protein) {minCardinality=1} [Term] @@ -7838,6 +7518,7 @@ def: "Align RNA secondary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002439 ! RNA secondary structure processing is_a: EDAM:0000500 ! Secondary structure alignment +synonym: "Secondary structure alignment (RNA)" EXACT [] relationship: has_input EDAM:0000880 ! RNA secondary structure {minCardinality=2} relationship: has_output EDAM:0000881 ! Secondary structure alignment (RNA) {minCardinality=1} @@ -7864,14 +7545,15 @@ name: Protein secondary structure comparison namespace: operation def: "Compare protein secondary structures." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002444 ! Protein secondary structure processing +is_a: EDAM:0002416 ! Protein secondary structure analysis is_a: EDAM:0002931 ! Secondary structure comparison is_a: EDAM:0002997 ! Protein comparison +synonym: "Secondary structure comparison (protein)" EXACT [] relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=2} [Term] id: EDAM:0002487 -name: Structure comparison (protein) +name: Protein structure comparison namespace: operation def: "Compare protein tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Methods might identify structural neighbors, find structural similarities or define a structural core. @@ -7879,16 +7561,19 @@ subset: operation is_a: EDAM:0002459 ! Structure processing (protein) is_a: EDAM:0002483 ! Structure comparison is_a: EDAM:0002997 ! Protein comparison +synonym: "Structure comparison (protein)" EXACT [] relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=2} -relationship: has_output EDAM:0001537 ! Protein structure report {minCardinality=1} +relationship: has_output EDAM:0000897 ! Protein property + [Term] id: EDAM:0002518 -name: Structure comparison (nucleic acid) +name: Nucleic acid structure comparison namespace: operation def: "Compare nucleic acid tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "Structure comparison (nucleic acid)" EXACT [] is_a: EDAM:0002483 ! Structure comparison is_a: EDAM:0002481 ! Nucleic acid structure analysis is_a: EDAM:0002998 ! Nucleic acid comparison @@ -7899,9 +7584,8 @@ name: Structure alignment (protein) namespace: operation def: "Align protein tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000295 ! Structure alignment -is_a: EDAM:0002487 ! Structure comparison (protein) -relationship: has_output EDAM:0001481 ! Structure alignment (protein) {minCardinality=1} +is_obsolete: true +consider: EDAM:0000295 ! Structure alignment [Term] id: EDAM:0000506 @@ -7909,11 +7593,8 @@ name: Structure alignment (RNA) namespace: operation def: "Align RNA tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000295 ! Structure alignment -is_a: EDAM:0002440 ! Structure processing (RNA) -is_a: EDAM:0002518 ! Structure comparison (nucleic acid) -relationship: has_input EDAM:0001465 ! RNA structure {minCardinality=2} -relationship: has_output EDAM:0001493 ! Structure alignment (RNA) {minCardinality=1} +is_obsolete: true +consider: EDAM:0000295 ! Structure alignment [Term] id: EDAM:0000507 @@ -8031,7 +7712,7 @@ is_a: EDAM:0002411 ! Structural (3D) profile processing is_a: EDAM:0002928 ! Alignment relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=2} relationship: has_output EDAM:0000890 ! Structural (3D) profile alignment {minCardinality=1} -relationship: in_topic EDAM:0000183 ! Structure alignment +relationship: has_topic EDAM:0000183 ! Structure alignment [Term] id: EDAM:0000513 @@ -8063,33 +7744,35 @@ is_a: EDAM:0002928 ! Alignment is_a: EDAM:0002403 ! Sequence analysis relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=2} relationship: has_output EDAM:0000891 ! Sequence-3D profile alignment {minCardinality=1} -relationship: in_topic EDAM:0000184 ! Threading +relationship: has_topic EDAM:0000184 ! Threading [Term] id: EDAM:0000308 name: PCR primer design namespace: operation -def: "Design oligonucleotide primers for PCR and DNA amplification etc." [EDAM:EBI "EMBRACE definition"] +def: "Design or predict oligonucleotide primers for PCR and DNA amplification etc." [EDAM:EBI "EMBRACE definition"] comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. subset: operation +synonym: "PCR primer prediction" EXACT [] is_a: EDAM:0002419 ! Primer and probe design relationship: has_input EDAM:0002977 ! Nucleic acid sequence relationship: has_output EDAM:0001240 ! PCR primers {minCardinality=0} -relationship: in_topic EDAM:0000195 ! Polymerase chain reaction -relationship: in_topic EDAM:0000632 ! Molecular probes or primers +relationship: has_topic EDAM:0003032 ! Primer or probe design [Term] id: EDAM:0000309 name: Microarray probe design namespace: operation -def: "Design and optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [EDAM:EBI "EMBRACE definition"] +def: "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "Microarray probe prediction" EXACT [] is_a: EDAM:0002419 ! Primer and probe design +is_a: EDAM:0002425 ! Optimisation and refinement relationship: has_input EDAM:0002977 ! Nucleic acid sequence -relationship: has_output EDAM:0000932 ! Oligonucleotide probe data {minCardinality=1} -relationship: in_topic EDAM:0000200 ! Microarrays -relationship: in_topic EDAM:0000632 ! Molecular probes or primers +relationship: has_output EDAM:0002717 ! Oligonucleotide probe annotation {minCardinality=1} +relationship: has_topic EDAM:0000200 ! Microarrays +relationship: has_topic EDAM:0003032 ! Primer or probe design [Term] @@ -8098,23 +7781,23 @@ name: Virtual PCR namespace: operation def: "Perform in-silico (virtual) PCR." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: in_topic EDAM:0000195 ! Polymerase chain reaction +is_a: EDAM:0002478 ! Nucleic acid sequence analysis +relationship: has_topic EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000517 name: PCR primer design (for large scale sequencing) namespace: operation -def: "Design primers for large scale sequencing." [EDAM:EBI "EMBRACE definition"] +def: "Predict primers for large scale sequencing." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design -relationship: in_topic EDAM:0000102 ! Sequencing and mapping +relationship: has_topic EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0000518 name: PCR primer design (for genotyping polymorphisms) namespace: operation -def: "Design primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [EDAM:EBI "EMBRACE definition"] +def: "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design @@ -8122,17 +7805,17 @@ is_a: EDAM:0000308 ! PCR primer design id: EDAM:0000519 name: PCR primer design (for gene transcription profiling) namespace: operation -def: "Design primers for gene transcription profiling." [EDAM:EBI "EMBRACE definition"] +def: "Predict primers for gene transcription profiling." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design -relationship: in_topic EDAM:0000203 ! Gene expression profiling +relationship: has_topic EDAM:0000203 ! Transcriptomics [Term] id: EDAM:0000520 name: PCR primer design (for conserved primers) namespace: operation -def: "Design primers that are conserved across multiple genomes or species." [EDAM:EBI "EMBRACE definition"] +def: "Predict primers that are conserved across multiple genomes or species." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design @@ -8140,16 +7823,16 @@ is_a: EDAM:0000308 ! PCR primer design id: EDAM:0000521 name: PCR primer design (based on gene structure) namespace: operation -def: "Design primers based on gene structure, promoters, exon-exon junctions etc." [EDAM:EBI "EMBRACE definition"] +def: "Predict primers based on gene structure, promoters, exon-exon junctions etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design -relationship: in_topic EDAM:0000109 ! Gene finding +relationship: has_topic EDAM:0000109 ! Gene finding [Term] id: EDAM:0000522 name: PCR primer design (for methylation PCRs) namespace: operation -def: "Design primers for methylation PCRs." [EDAM:EBI "EMBRACE definition"] +def: "Predict primers for methylation PCRs." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design @@ -8204,11 +7887,11 @@ name: Gene expression profile processing namespace: operation def: "Process (read and / or write) a gene expression profile." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002495 ! Gene expression (microarray) data processing +is_a: EDAM:0002495 ! Gene expression data processing relationship: has_input EDAM:0000928 ! Gene expression profile {minCardinality=0} relationship: has_output EDAM:0000928 ! Gene expression profile {minCardinality=0} -relationship: in_topic EDAM:0000203 ! Gene expression profiling -relationship: in_topic EDAM:0000206 ! DNA microarrays +relationship: has_topic EDAM:0000203 ! Transcriptomics +relationship: has_topic EDAM:0000200 ! Microarrays [Term] @@ -8240,8 +7923,8 @@ subset: operation is_a: EDAM:0002438 ! Pathway or network processing relationship: has_input EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=0} relationship: has_output EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=0} -relationship: in_topic EDAM:0000197 ! Gene expression and regulation -relationship: in_topic EDAM:0002846 ! Gene regulatory networks +relationship: has_topic EDAM:0000197 ! Gene expression resources +relationship: has_topic EDAM:0002846 ! Gene regulatory networks [Term] @@ -8265,6 +7948,19 @@ is_a: EDAM:0002496 ! Gene regulatory network processing is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=1} + +[Term] +id: EDAM:0003094 +name: Protein interaction network prediction +namespace: operation +def: "Predict a network of protein interactions." [EDAM:EBI "EMBRACE definition"] +subset: operation +is_a: EDAM:0002445 ! Protein interaction network processing +relationship: has_output EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=1} + + + + [Term] id: EDAM:0000316 name: Functional profiling @@ -8282,19 +7978,20 @@ namespace: operation def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002499 ! Splicing modelling -relationship: in_topic EDAM:0000114 ! RNA splicing +relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing [Term] id: EDAM:0002499 -name: Splicing modelling +name: Splicing analysis namespace: operation -def: "Characterize or model alternative splicing events from analysis of sequence data." [EDAM:EBI "EMBRACE definition"] +def: "Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) +synonym: "Splicing modelling" EXACT [] +is_a: EDAM:0002508 ! Nucleic acid sequence comparison is_a: EDAM:0002426 ! Modelling and simulation is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) -relationship: has_output EDAM:0000915 ! Nucleic acid report (RNA splice model) {minCardinality=1} -relationship: in_topic EDAM:0000114 ! RNA splicing +relationship: has_output EDAM:0001307 ! Nucleic acid features (splice sites) {minCardinality=1} +relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing [Term] id: EDAM:0000313 @@ -8303,7 +8000,7 @@ namespace: operation def: "Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000315 ! Gene expression profile comparison -relationship: has_output EDAM:0000929 ! Gene annotation (expression) +relationship: has_output EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0000314 @@ -8323,13 +8020,13 @@ def: "Compare gene expression profiles or patterns." [EDAM:EBI "EMBRACE definiti subset: operation is_a: EDAM:0000532 ! Gene expression profile analysis is_a: EDAM:0002998 ! Nucleic acid comparison -relationship: has_output EDAM:0000929 ! Gene annotation (expression) +relationship: has_output EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0002436 name: Gene expression profile annotation namespace: operation -def: "Annotate a gene expression profile, typically with terms from an ontology of gene functions, in order to interpret it." [EDAM:EBI "EMBRACE definition"] +def: "Annotate a gene expression profile with terms from an ontology of gene functions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000532 ! Gene expression profile analysis is_a: EDAM:0000226 ! Annotation @@ -8361,7 +8058,7 @@ relationship: has_output EDAM:0002984 ! Pathway or network report id: EDAM:0000527 name: Tag mapping namespace: operation -def: "Make tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data." [EDAM:EBI "EMBRACE definition"] +def: "Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology terms." [EDAM:EBI "EMBRACE definition"] comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. subset: operation synonym: "Tag to gene assignment" EXACT [] @@ -8377,7 +8074,6 @@ subset: operation synonym: "Serial analysis of gene expression data processing" EXACT [] is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing -! consider: EDAM:0000312 ! Sequencing-based expression profile data processing [Term] @@ -8389,7 +8085,7 @@ subset: operation synonym: "Massively parallel signature sequencing data processing" EXACT [] is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing -! consider: EDAM:0000312 ! Sequencing-based expression profile data processing + [Term] id: EDAM:0000530 @@ -8400,14 +8096,14 @@ subset: operation synonym: "Sequencing by synthesis data processing" EXACT [] is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing -! consider: EDAM:0000312 ! Sequencing-based expression profile data processing + [Term] id: EDAM:0000531 name: Heat map generation namespace: operation def: "Generate a heat map of gene expression from microarray data." [EDAM:EBI "EMBRACE definition"] -comment: The heat map usually uses a colouring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. +comment: The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. subset: operation is_a: EDAM:0000571 ! Microarray data rendering relationship: has_output EDAM:0001636 ! Heat map {minCardinality=1} @@ -8417,6 +8113,7 @@ relationship: has_output EDAM:0001636 ! Heat map {minCardinality=1} id: EDAM:0002934 name: Microarray cluster textual view rendering def: "Visualise gene clusters with gene names." [EDAM:EBI "EMBRACE definition"] +subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8426,8 +8123,7 @@ name: Microarray wave graph rendering namespace: operation synonym: "Microarray cluster temporal graph rendering" EXACT [] def: "Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis." [EDAM:EBI "EMBRACE definition"] -comment: This view can be rendered as a pie graph. -comment: The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different colour shades. +comment: This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8438,6 +8134,7 @@ name: Microarray dendrograph rendering synonym: "Microarray checks view rendering" EXACT [] synonym: "Microarray view rendering" EXACT [] def: "Generate a dendrograph of raw, preprocessed or clustered microarray data." [EDAM:EBI "EMBRACE definition"] +subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8446,6 +8143,7 @@ id: EDAM:0002937 name: Microarray proximity map rendering synonym: "Microarray distance map rendering" EXACT [] def: "Generate a plot of distances (distance matrix) between genes." [EDAM:EBI "EMBRACE definition"] +subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8454,7 +8152,8 @@ id: EDAM:0002938 name: Microarray tree or dendrogram view rendering synonym: "Microarray matrix tree plot rendering" EXACT [] synonym: "Microarray 2-way dendrogram rendering" EXACT [] -def: "Visualise clustered gene expression data using a gene tree, array tree and colour coded band of gene expression." [EDAM:EBI "EMBRACE definition"] +def: "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." [EDAM:EBI "EMBRACE definition"] +subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8462,6 +8161,7 @@ is_a: EDAM:0000571 ! Microarray data rendering id: EDAM:0002939 name: Microarray principal component rendering def: "Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values." [EDAM:EBI "EMBRACE definition"] +subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8469,6 +8169,7 @@ is_a: EDAM:0000571 ! Microarray data rendering id: EDAM:0002940 name: Microarray scatter plot rendering def: "Generate a scatter plot of microarray data, typically after principal component analysis." [EDAM:EBI "EMBRACE definition"] +subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8476,6 +8177,7 @@ is_a: EDAM:0000571 ! Microarray data rendering id: EDAM:0002941 name: Whole microarray graph view rendering def: "Visualise gene expression data where each band (or line graph) corresponds to a sample." [EDAM:EBI "EMBRACE definition"] +subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8483,6 +8185,7 @@ is_a: EDAM:0000571 ! Microarray data rendering id: EDAM:0002942 name: Microarray tree-map rendering def: "Visualise gene expression data after hierarchical clustering for representing hierarchical relationships." [EDAM:EBI "EMBRACE definition"] +subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8490,6 +8193,7 @@ is_a: EDAM:0000571 ! Microarray data rendering id: EDAM:0002943 name: Microarray Box-Whisker plot rendering def: "Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles." [EDAM:EBI "EMBRACE definition"] +subset: operation is_a: EDAM:0000571 ! Microarray data rendering @@ -8503,21 +8207,23 @@ is_a: EDAM:0002465 ! Structure processing is_a: EDAM:0002502 ! Protein data processing relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=0} relationship: has_output EDAM:0001460 ! Protein structure {minCardinality=0} -relationship: in_topic EDAM:0000698 ! Protein tertiary structure +relationship: has_topic EDAM:0000698 ! Protein tertiary structure [Term] id: EDAM:0000243 -name: Protein structural property calculation +name: Protein property calculation (from structure) namespace: operation -def: "Calculate or extract a property of protein structure." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0003089 +def: "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." [EDAM:EBI "EMBRACE definition"] comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. subset: operation is_a: EDAM:0002406 ! Protein structure analysis is_a: EDAM:0000250 ! Protein property calculation +synonym: "Protein structural property calculation" EXACT [] relationship: has_output EDAM:0000897 ! Protein property {minCardinality=0} -relationship: in_topic EDAM:0000123 ! Protein physicochemistry -relationship: in_topic EDAM:0002814 ! Protein structure +relationship: has_topic EDAM:0000123 ! Protein properties +relationship: has_topic EDAM:0002814 ! Protein structure analysis [Term] id: EDAM:0000244 @@ -8526,10 +8232,10 @@ namespace: operation def: "Analyse flexibility and motion in protein structure." [EDAM:EBI "EMBRACE definition"] comment: Use this term for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. subset: operation -is_a: EDAM:0002406 ! Protein structure analysis +is_a: EDAM:0000243 ! Protein property calculation (from structure) is_a: EDAM:0002476 ! Molecular dynamics simulation -relationship: has_output EDAM:0001541 ! Protein structure report (flexibility or motion) {minCardinality=1} -relationship: in_topic EDAM:0000145 ! Molecular flexibility and motion +relationship: has_output EDAM:0001541 ! Protein flexibility or motion report {minCardinality=1} + [Term] id: EDAM:0000245 @@ -8539,10 +8245,9 @@ def: "Identify or screen for 3D structural motifs in protein structure(s)." [EDA comment: This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. subset: operation synonym: "Protein structural feature identification" EXACT [] -is_a: EDAM:0002406 ! Protein structure analysis -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0000899 ! Protein structure report (3D motif) {minCardinality=1} -relationship: in_topic EDAM:0000166 ! Protein structural motifs +is_a: EDAM:0003090 ! Protein feature detection (from structure) +relationship: has_output EDAM:0000899 ! Protein features (3D motif) {minCardinality=1} +relationship: has_topic EDAM:0000166 ! Protein structural motifs and surfaces [Term] id: EDAM:0000246 @@ -8550,10 +8255,9 @@ name: Protein domain recognition namespace: operation def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002406 ! Protein structure analysis -is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) +is_a: EDAM:0003090 ! Protein feature detection (from structure) relationship: has_output EDAM:0000901 ! Protein features (domains) {minCardinality=1} -relationship: in_topic EDAM:0000736 ! Protein domains +relationship: has_topic EDAM:0000736 ! Protein domains and folds [Term] @@ -8563,7 +8267,7 @@ namespace: operation def: "Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002406 ! Protein structure analysis -relationship: has_output EDAM:0000902 ! Protein structure report (architecture) {minCardinality=1} +relationship: has_output EDAM:0000902 ! Protein architecture report {minCardinality=1} [Term] @@ -8573,10 +8277,8 @@ namespace: operation def: "Compare the architecture of two or more protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000247 ! Protein architecture analysis -is_a: EDAM:0002487 ! Structure comparison (protein) is_a: EDAM:0002488 ! Protein secondary structure comparison -is_a: EDAM:0002997 ! Protein comparison -relationship: has_output EDAM:0000902 ! Protein structure report (architecture) {minCardinality=1} +relationship: has_output EDAM:0000902 ! Protein architecture report {minCardinality=1} [Term] id: EDAM:0002475 @@ -8586,7 +8288,8 @@ def: "Identify the architecture of a protein structure." [EDAM:EBI "EMBRACE defi subset: operation is_a: EDAM:0000247 ! Protein architecture analysis is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM:0000902 ! Protein structure report (architecture) {minCardinality=1} +is_a: EDAM:0002996 ! Structure classification +relationship: has_output EDAM:0000902 ! Protein architecture report {minCardinality=1} [Term] id: EDAM:0000248 @@ -8602,23 +8305,21 @@ xref: WHATIF: SymShellOneXML xref: WHATIF: SymShellTwoXML xref: WHATIF: SymShellFiveXML xref: WHATIF: SymShellTenXML -is_a: EDAM:0000243 ! Protein structural property calculation +is_a: EDAM:0000243 ! Protein property calculation (from structure) relationship: has_output EDAM:0001540 ! Protein residue interactions {minCardinality=1} -relationship: in_topic EDAM:0000144 ! Protein residue interactions +relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis [Term] id: EDAM:0000272 -name: Protein residue interaction prediction +name: Residue interaction prediction namespace: operation def: "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods usually involve multiple sequence alignment analysis. subset: operation -is_a: EDAM:0000474 ! Structure prediction (protein) -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0000243 ! Protein property calculation (from structure) is_a: EDAM:0002506 ! Sequence alignment analysis (protein) -! is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: in_topic EDAM:0000144 ! Protein residue interactions +relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis [Term] @@ -8627,8 +8328,8 @@ name: Torsion angle calculation namespace: operation def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000243 ! Protein structural property calculation -relationship: has_output EDAM:0002991 ! Torsion angle data +is_a: EDAM:0000243 ! Protein property calculation (from structure) +relationship: has_output EDAM:0002991 ! Protein torsion angle data [Term] id: EDAM:0000320 @@ -8638,7 +8339,7 @@ def: "Assign a protein tertiary structure (3D coordinates) from raw experimental subset: operation is_a: EDAM:0002459 ! Structure processing (protein) relationship: has_output EDAM:0001460 ! Protein structure {minCardinality=1} -relationship: in_topic EDAM:0000136 ! Raw structural data analysis +relationship: has_topic EDAM:0002226 ! Structure determination [Term] @@ -8649,40 +8350,36 @@ def: "Evaluate the quality or correctness a protein three-dimensional model." [E comment: Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. subset: operation xref: WHATIF: UseFileDB -is_a: EDAM:0002406 ! Protein structure analysis is_a: EDAM:0000477 ! Protein modelling is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_output EDAM:0001539 ! Protein structure report (quality evaluation) {minCardinality=1} -relationship: in_topic EDAM:0002275 ! Molecular modelling -relationship: in_topic EDAM:0000175 ! Homology modelling -relationship: in_topic EDAM:0000179 ! Protein tertiary structure prediction +relationship: has_output EDAM:0001539 ! Protein structural quality report {minCardinality=1} +relationship: has_topic EDAM:0002275 ! Molecular modelling +relationship: has_topic EDAM:0000175 ! Homology modelling +relationship: has_topic EDAM:0000179 ! Protein tertiary structure prediction [Term] id: EDAM:0000322 name: Protein model refinement namespace: operation -def: "Refine a model of protein structure to reduce steric clashes, volume irregularities etc." [EDAM:EBI "EMBRACE definition"] +def: "Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc." [EDAM:EBI "EMBRACE definition"] comment: The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. subset: operation xref: WHATIF: CorrectedPDBasXML -is_a: EDAM:0002406 ! Protein structure analysis -is_a: EDAM:0000477 ! Protein modelling -is_a: EDAM:0002428 ! Validation and standardisation +is_a: EDAM:0000321 ! Protein model evaluation is_a: EDAM:0002425 ! Optimisation and refinement -relationship: in_topic EDAM:0002275 ! Molecular modelling -relationship: in_topic EDAM:0000175 ! Homology modelling + [Term] id: EDAM:0002239 name: 3D-1D scoring matrix generation namespace: operation def: "Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data." [EDAM:EBI "EMBRACE definition"] -comment: A 3D-1D scoring matrix scores the probability of amino acids occuring in different structural environments. +comment: A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. subset: operation -is_a: EDAM:0000243 ! Protein structural property calculation -is_a: EDAM:0002479 ! Sequence analysis (protein) +is_a: EDAM:0000243 ! Protein property calculation (from structure) +is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001499 ! 3D-1D scoring matrix {minCardinality=1} -relationship: in_topic EDAM:0000167 ! Structural (3D) profiles +relationship: has_topic EDAM:0000167 ! Structural (3D) profiles [Term] @@ -8692,8 +8389,8 @@ namespace: operation def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000250 ! Protein property calculation -relationship: has_output EDAM:0002970 ! Protein hydropathy report {minCardinality=1} -relationship: in_topic EDAM:0000137 ! Protein hydropathy +relationship: has_output EDAM:0002970 ! Protein hydropathy data {minCardinality=1} +relationship: has_topic EDAM:0000137 ! Protein hydropathy [Term] @@ -8703,7 +8400,7 @@ namespace: operation def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002574 ! Protein hydropathy calculation -is_a: EDAM:0000243 ! Protein structural property calculation +is_a: EDAM:0000243 ! Protein property calculation (from structure) [Term] @@ -8712,9 +8409,9 @@ name: Protein solvent accessibility calculation namespace: operation def: "Calculate solvent accessible or buried surface areas in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000243 ! Protein structural property calculation +is_a: EDAM:0000243 ! Protein property calculation (from structure) relationship: has_output EDAM:0001542 ! Protein solvent accessibility -relationship: in_topic EDAM:0000137 ! Protein hydropathy +relationship: has_topic EDAM:0000137 ! Protein hydropathy [Term] id: EDAM:0001850 @@ -8723,7 +8420,7 @@ namespace: operation def: "Assign cysteine bonding state and disulfide bond partners in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000534 ! Protein secondary structure assignment (from coordinate data) -relationship: in_topic EDAM:0000144 ! Protein residue interactions +relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis [Term] id: EDAM:0000385 @@ -8740,7 +8437,7 @@ name: Protein dipole moment calculation namespace: operation def: "Calculate whether a protein structure has an unusually large net charge (dipole moment)." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000250 ! Protein property calculation +is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001545 ! Protein dipole moment {minCardinality=1} [Term] @@ -8750,21 +8447,21 @@ namespace: operation def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000384 ! Protein solvent accessibility calculation -relationship: has_output EDAM:0001543 ! Protein structure report (surface) {minCardinality=1} -relationship: in_topic EDAM:0000146 ! Protein surfaces +relationship: has_output EDAM:0001543 ! Protein surface report {minCardinality=1} +relationship: has_topic EDAM:0000166 ! Protein structural motifs and surfaces [Term] id: EDAM:0001816 name: Surface rendering namespace: operation -def: "Calculate the positions of dots that are homogeneously distributed over the surface of the molecule." [EDAM:WHATIF "EMBRACE definition"] -comment: A dot has three coordinates (x,y,z) and (typically) a colour. +def: "Calculate the positions of dots that are homogeneously distributed over the surface of a molecule." [EDAM:WHATIF "EMBRACE definition"] +comment: A dot has three coordinates (x,y,z) and (typically) a color. subset: operation xref: WHATIF:GetSurfaceDots -is_a: EDAM:0000387 ! Protein surface and interior calculation +is_a: EDAM:0002462 ! Protein surface calculation is_a: EDAM:0000570 ! Structure rendering -relationship: has_input EDAM:0001543 ! Protein structure report (surface) + [Term] @@ -8913,23 +8610,25 @@ is_a: EDAM:0001850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM:0002575 -name: Ligand-binding and active site prediction +name: Binding site prediction namespace: operation def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "Ligand-binding and active site prediction" EXACT [] is_a: EDAM:0002492 ! Protein interaction prediction relationship: has_output EDAM:0001325 ! Protein features (active sites) {minCardinality=0} relationship: has_output EDAM:0001326 ! Protein features (binding sites) {minCardinality=0} -relationship: in_topic EDAM:0000148 ! Protein-ligand interactions +relationship: has_topic EDAM:0000148 ! Protein-ligand interactions [Term] id: EDAM:0000388 -name: Ligand-binding and active site prediction (from structure) +name: Binding site prediction (from structure) namespace: operation def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "Ligand-binding and active site prediction (from structure)" EXACT [] is_a: EDAM:0000245 ! Protein structural motif recognition -is_a: EDAM:0002575 ! Ligand-binding and active site prediction +is_a: EDAM:0002575 ! Binding site prediction [Term] @@ -8940,7 +8639,7 @@ def: "Analyse RNA or DNA-binding sites in protein structure." [EDAM:EBI "EMBRACE subset: operation is_a: EDAM:0002949 ! Protein interaction analysis relationship: has_input EDAM:0001567 ! Protein-nucleic acid interaction -relationship: in_topic EDAM:0000149 ! Protein-nucleic acid interactions +relationship: has_topic EDAM:0000149 ! Protein-nucleic acid interactions [Term] id: EDAM:0000390 @@ -8953,22 +8652,12 @@ relationship: has_output EDAM:0000901 ! Protein features (domains) {minCardinali [Term] -id: EDAM:0001833 -name: Residue contact calculation -namespace: operation -def: "Calculate contacts between an amino acid (side chain and / or main chain atoms) and other residues or atoms." [EDAM:WHATIF "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000248 ! Residue interaction calculation - -[Term] id: EDAM:0000391 name: Protein distance matrix calculation namespace: operation def: "Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000248 ! Residue interaction calculation -! is_a: EDAM:0000243 ! Protein structural property calculation relationship: has_output EDAM:0001546 ! Protein distance matrix {minCardinality=1} [Term] @@ -9017,11 +8706,11 @@ comment: A HET group usually corresponds to ligands, lipids, but might also (not subset: operation xref: WHATIF: HETGroupNames is_a: EDAM:0001838 ! Residue contact calculation (residue-ligand) -! is_a: EDAM:0002423 ! Prediction, detection and recognition [Term] id: EDAM:0002950 +alt_id: EDAM:0001833 name: Residue contact calculation namespace: operation def: "Calculate contacts between residues and some other group in a protein structure." [EDAM:WHATIF "EMBRACE definition"] @@ -9039,8 +8728,7 @@ xref: WHATIF:ShowLigandContacts xref: WHATIF:ShowDrugContacts xref: WHATIF:ShowDrugContactsShort is_a: EDAM:0002950 ! Residue contact calculation -! is_a: EDAM:0002405 ! Protein interaction data processing -is_a: EDAM:0000388 ! Ligand-binding and active site prediction (from structure) +is_a: EDAM:0000388 ! Binding site prediction (from structure) [Term] @@ -9095,8 +8783,7 @@ subset: operation xref: WHATIF:HasMetalContacts xref: WHATIF:HasMetalContactsPlus is_a: EDAM:0002950 ! Residue contact calculation -! is_a: EDAM:0002405 ! Protein interaction data processing -is_a: EDAM:0000388 ! Ligand-binding and active site prediction (from structure) +is_a: EDAM:0000388 ! Binding site prediction (from structure) [Term] @@ -9126,7 +8813,6 @@ namespace: operation def: "Calculate a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000249 ! Torsion angle calculation -! is_a: EDAM:0002933 ! Protein property rendering relationship: has_output EDAM:0001544 ! Ramachandran plot {minCardinality=1} @@ -9138,7 +8824,7 @@ def: "Analyse (typically to validate) a Ramachandran plot of a protein structure subset: operation is_a: EDAM:0001844 ! Dihedral angle validation relationship: has_input EDAM:0001544 ! Ramachandran plot {minCardinality=1} -relationship: has_output EDAM:0001539 ! Protein structure report (quality evaluation) +relationship: has_output EDAM:0001539 ! Protein structural quality report [Term] id: EDAM:0001825 @@ -9207,7 +8893,7 @@ def: "Calculate non-canonical atomic interactions in protein structures." [EDAM: subset: operation is_a: EDAM:0000248 ! Residue interaction calculation is_a: EDAM:0000321 ! Protein model evaluation -relationship: has_output EDAM:0001550 ! Protein non-canonical interactions report {minCardinality=1} +relationship: has_output EDAM:0001550 ! Protein non-canonical interactions {minCardinality=1} [Term] id: EDAM:0001913 @@ -9246,11 +8932,9 @@ def: "Detect 'bumps' between residues in a structure, i.e. those with pairs of a subset: operation xref: WHATIF:ShowBumps is_a: EDAM:0000395 ! Residue non-canonical interaction detection -! is_a: EDAM:0002423 ! Prediction, detection and recognition -! Operation [Term] id: EDAM:0002443 @@ -9261,20 +8945,19 @@ subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000872 ! Phylogenetic tree {minCardinality=0} relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=0} -relationship: in_topic EDAM:0000084 ! Phylogenetics +relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] id: EDAM:0000550 -name: Phylogenetic modelling +name: Sequence alignment analysis (phylogenetic modelling) namespace: operation def: "Identify a plausible model of DNA substitution that explains a DNA sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) is_a: EDAM:0002426 ! Modelling and simulation -! is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_output EDAM:0001439 ! Phylogenetic report (DNA substitution model) -relationship: in_topic EDAM:0000084 ! Phylogenetics +relationship: has_output EDAM:0001439 ! DNA substitution model +relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] @@ -9298,8 +8981,8 @@ synonym: "Phylogenetic tree generation" EXACT [] is_a: EDAM:0002443 ! Phylogenetic tree processing is_a: EDAM:0002995 ! Sequence classification relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=1} -relationship: in_topic EDAM:0000080 ! Sequence -relationship: in_topic EDAM:0000191 ! Phylogeny reconstruction +relationship: has_topic EDAM:0000080 ! Sequence analysis +relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] @@ -9319,6 +9002,7 @@ namespace: operation def: "Edit a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002443 ! Phylogenetic tree processing +is_a: EDAM:0003096 ! Editing relationship: has_input EDAM:0000872 ! Phylogenetic tree {minCardinality=1} relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=1} @@ -9331,7 +9015,7 @@ def: "Analyse the shape (topology) of a phylogenetic tree." [EDAM:EBI "EMBRACE d subset: operation synonym: "Phylogenetic tree topology analysis" EXACT [] is_a: EDAM:0000324 ! Phylogenetic tree analysis -relationship: has_output EDAM:0001440 ! Phylogenetic report (tree shape) {minCardinality=1} +relationship: has_output EDAM:0001440 ! Phylogenetic tree report (tree shape) {minCardinality=1} [Term] id: EDAM:0000552 @@ -9341,7 +9025,7 @@ def: "Apply bootstrapping or other measures to estimate confidence of a phylogen subset: operation is_a: EDAM:0000324 ! Phylogenetic tree analysis is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_output EDAM:0001441 ! Phylogenetic report (tree evaluation) {minCardinality=1} +relationship: has_output EDAM:0001441 ! Phylogenetic tree report (tree evaluation) {minCardinality=1} [Term] @@ -9351,9 +9035,8 @@ namespace: operation def: "Predict families of genes and gene function based on their position in a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000324 ! Phylogenetic tree analysis -! is_a: EDAM:0002423 ! Prediction, detection and recognition relationship: has_output EDAM:0000916 ! Gene annotation -relationship: in_topic EDAM:0000194 ! Phylogenomics +relationship: has_topic EDAM:0000194 ! Phylogenomics [Term] id: EDAM:0000538 @@ -9400,7 +9083,7 @@ def: "Phylogenetic tree construction from gene frequency data." [EDAM:EBI "EMBRA subset: operation is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) relationship: has_input EDAM:0002873 ! Phylogenetic gene frequencies data {minCardinality=1} -relationship: in_topic EDAM:0000197 ! Gene expression and regulation +relationship: has_topic EDAM:0000197 ! Gene expression resources [Term] @@ -9410,8 +9093,7 @@ namespace: operation def: "Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: in_topic EDAM:0000199 ! Mutation and polymorphism +relationship: has_topic EDAM:0000199 ! Genetic variation [Term] id: EDAM:0000544 @@ -9430,7 +9112,7 @@ def: "Infer a phylogenetic tree by comparing orthologous sequences in different comment: A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. subset: operation is_a: EDAM:0000540 ! Phylogenetic tree construction (from molecular sequences) -relationship: in_topic EDAM:0000194 ! Phylogenomics +relationship: has_topic EDAM:0000194 ! Phylogenomics [Term] id: EDAM:0000545 @@ -9478,7 +9160,7 @@ is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM:0000555 -name: Consensus phylogenetic tree construction +name: Phylogenetic tree construction (consensus) namespace: operation def: "Compare two or more phylogenetic trees to produce a consensus tree." [EDAM:EBI "EMBRACE definition"] comment: Methods typically test for topological similarity between trees using for example a congruence index. @@ -9494,7 +9176,6 @@ namespace: operation def: "Compare two or more phylogenetic trees to detect subtrees or supertrees." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000325 ! Phylogenetic tree comparison -! is_a: EDAM:0002423 ! Prediction, detection and recognition [Term] @@ -9504,7 +9185,7 @@ namespace: operation def: "Compare two or more phylogenetic trees to calculate distances between trees." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000325 ! Phylogenetic tree comparison -relationship: has_output EDAM:0001442 ! Phylogenetic report (tree distances) {minCardinality=1} +relationship: has_output EDAM:0001442 ! Phylogenetic tree report (tree distances) {minCardinality=1} [Term] id: EDAM:0000558 @@ -9521,7 +9202,7 @@ name: Protein folding simulation namespace: operation def: "Simulate the folding of a protein." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002415 ! Protein folding modelling +is_a: EDAM:0002415 ! Protein folding analysis [Term] @@ -9530,7 +9211,7 @@ name: Protein folding pathway prediction namespace: operation def: "Predict the folding pathway(s) or non-native structural intermediates of a protein." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002415 ! Protein folding modelling +is_a: EDAM:0002415 ! Protein folding analysis is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) @@ -9541,56 +9222,49 @@ namespace: operation def: "Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:ProlineMutationValue -is_a: EDAM:0000331 ! Protein mutation modelling +is_a: EDAM:0000331 ! Protein modelling (mutation) [Term] id: EDAM:0000330 name: Protein SNP mapping namespace: operation -def: "Map single nucleotide polymorphisms (SNPs) on protein structure(s)." [EDAM:EBI "EMBRACE definition"] +def: "Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s)." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000331 ! Protein mutation modelling -relationship: has_output EDAM:0002885 ! Polymorphism annotation -relationship: in_topic EDAM:0002277 ! SNPs +is_a: EDAM:0000331 ! Protein modelling (mutation) +relationship: has_output EDAM:0002885 ! Nucleic acid features (polymorphism annotation) +relationship: has_topic EDAM:0002277 ! SNPs [Term] id: EDAM:0000559 -name: Peptide immunogen design +name: Peptide immunogen prediction and optimisation namespace: operation -def: "Design peptide ligands that elicit an immunological response." [EDAM:EBI "EMBRACE definition"] +def: "Predict and optimise peptide ligands that elicit an immunological response." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002479 ! Sequence analysis (protein) -is_a: EDAM:0002430 ! Design +is_a: EDAM:0000252 ! Peptide immunogenicity prediction +is_a: EDAM:0002425 ! Optimisation and refinement relationship: has_output EDAM:0001460 ! Protein structure -relationship: in_topic EDAM:0000150 ! Protein rational design -relationship: in_topic EDAM:0000804 ! Immunoinformatics +relationship: has_topic EDAM:0000150 ! Protein design +relationship: has_topic EDAM:0000804 ! Immunoinformatics + -[Term] -id: EDAM:0002953 -name: Nucleic acid design -namespace: operation -def: "Design a nucleic acid molecule with certain properties." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -is_a: EDAM:0002430 ! Design -relationship: has_output EDAM:0002977 ! Nucleic acid sequence -relationship: in_topic EDAM:0000804 ! Immunoinformatics [Term] id: EDAM:0000560 -name: DNA vaccine design +name: DNA vaccine prediction and optimisation namespace: operation -def: "Design DNA to elicit (via DNA vaccination) an immunological response." [EDAM:EBI "EMBRACE definition"] +def: "Predict or optimise DNA to elicit (via DNA vaccination) an immunological response." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002953 ! Nucleic acid design -relationship: in_topic EDAM:0000804 ! Immunoinformatics +is_a: EDAM:0003095 ! Nucleic acid design +is_a: EDAM:0002425 ! Optimisation and refinement +relationship: has_topic EDAM:0000804 ! Immunoinformatics +relationship: has_topic EDAM:0002953 ! Nucleic acid design [Term] id: EDAM:0000561 name: Sequence reformatting namespace: operation -def: "Reformat a molecular sequence." [EDAM:EBI "EMBRACE definition"] +def: "Reformat (a file or other report of) molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000335 ! File reformatting is_a: EDAM:0002121 ! Sequence file processing @@ -9599,14 +9273,14 @@ is_a: EDAM:0002121 ! Sequence file processing id: EDAM:0000562 name: Sequence alignment reformatting namespace: operation -def: "Reformat a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] +def: "Reformat (a file or other report of) molecular sequence alignment(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000335 ! File reformatting is_a: EDAM:0002122 ! Sequence alignment editing [Term] id: EDAM:0000563 -name: Codon usage table reformating +name: Codon usage table reformatting namespace: operation def: "Reformat a codon usage table." [EDAM:EBI "EMBRACE definition"] subset: operation @@ -9620,21 +9294,11 @@ relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=1} id: EDAM:0001848 name: Structure reformatting namespace: operation -def: "Reformat a file of tertiary structure data." [EDAM:WHATIF "EMBRACE definition"] +def: "Reformat (a file or other report of) tertiary structure data." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF: PDBasXML +is_a: EDAM:0002234 ! Structure file processing is_a: EDAM:0000335 ! File reformatting -is_a: EDAM:0002234 ! Structure editing - -[Term] -id: EDAM:0002933 -name: Protein property rendering -namespace: operation -def: "Visualise, format or render the properties of a protein sequence." [EDAM:EBI "EMBRACE definition"] -subset: operation -is_obsolete: true -consider: EDAM:0000250 ! Protein property calculation - [Term] @@ -9646,17 +9310,18 @@ subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} -relationship: has_output EDAM:0002969 ! Sequence image or plot {minCardinality=1} +relationship: has_output EDAM:0002969 ! Sequence image {minCardinality=1} [Term] id: EDAM:0002515 name: Sequence rendering (nucleic acid) namespace: operation def: "Visualise, format or render a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] +comment: Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. subset: operation is_a: EDAM:0000564 ! Sequence rendering -is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: in_topic EDAM:0000640 ! Nucleic acid sequences +is_a: EDAM:0002448 ! Sequence processing (nucleic acid) +relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis [Term] @@ -9664,10 +9329,10 @@ id: EDAM:0002516 name: Sequence rendering (protein) namespace: operation def: "Visualise, format or render a protein sequence." [EDAM:EBI "EMBRACE definition"] +comment: Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. subset: operation is_a: EDAM:0000564 ! Sequence rendering -! is_a: EDAM:0002933 ! Protein property rendering -is_a: EDAM:0002502 ! Protein data processing +is_a: EDAM:0002447 ! Sequence processing (protein) [Term] id: EDAM:0000565 @@ -9678,7 +9343,7 @@ subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002463 ! Sequence alignment processing relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=1} -relationship: has_output EDAM:0001711 ! Sequence alignment image or plot {minCardinality=1} +relationship: has_output EDAM:0001711 ! Sequence alignment image {minCardinality=1} [Term] id: EDAM:0002452 @@ -9686,10 +9351,10 @@ name: Sequence cluster processing namespace: operation def: "Process (read and / or write) a sequence cluster." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002503 ! Sequence data processing +is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0001235 ! Sequence cluster {minCardinality=0} relationship: has_output EDAM:0001235 ! Sequence cluster {minCardinality=0} -relationship: in_topic EDAM:0000164 ! Sequence clustering +relationship: has_topic EDAM:0000164 ! Sequence clustering [Term] @@ -9744,7 +9409,7 @@ relationship: has_output EDAM:0002162 ! Helical wheel {minCardinality=1} [Term] id: EDAM:0002486 -name: Toplogy diagram rendering +name: Topology diagram rendering namespace: operation def: "Render a topology diagram of protein secondary structure." [EDAM:EBI "EMBRACE definition"] subset: operation @@ -9758,29 +9423,33 @@ namespace: operation def: "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000569 ! Protein secondary structure rendering -is_a: EDAM:0000270 ! Transmembrane protein data processing -relationship: has_input EDAM:0001456 ! Protein structure report (membrane protein) {minCardinality=1} +is_a: EDAM:0000270 ! Transmembrane protein analysis +relationship: has_input EDAM:0001456 ! Protein features (membrane regions) {minCardinality=1} relationship: has_output EDAM:0002992 ! Protein structure image [Term] id: EDAM:0002482 -name: Secondary structure data processing +name: Secondary structure processing namespace: operation def: "Process (read and / or write) a molecular secondary structure." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002504 ! Structural data processing -relationship: has_input EDAM:0002973 ! Secondary structure data {minCardinality=0} -relationship: has_output EDAM:0002973 ! Secondary structure data {minCardinality=0} +is_a: EDAM:0002420 ! Analysis and processing +relationship: has_input EDAM:0002081 ! Secondary structure {minCardinality=0} +relationship: has_output EDAM:0002081 ! Secondary structure {minCardinality=0} +relationship: has_topic EDAM:0000081 ! Structure analysis + [Term] id: EDAM:0002465 name: Structure processing namespace: operation +alt_id: EDAM:0002484 def: "Process (read and / or write) a molecular tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0002504 ! Structural data processing +is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000883 ! Structure {minCardinality=0} relationship: has_output EDAM:0000883 ! Structure {minCardinality=0} +relationship: has_topic EDAM:0000081 ! Structure analysis [Term] id: EDAM:0000570 @@ -9802,8 +9471,8 @@ def: "Visualise microarray data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002435 ! Gene expression profile processing -relationship: has_input EDAM:0002603 ! Microarray data {minCardinality=1} -relationship: has_output EDAM:0002967 ! Microarray image or plot {minCardinality=1} +relationship: has_input EDAM:0003117 ! Microarray hybridisation data {minCardinality=1} +relationship: has_output EDAM:0002967 ! Microarray image {minCardinality=1} [Term] id: EDAM:0000572 @@ -9811,18 +9480,19 @@ name: Protein interaction network rendering namespace: operation def: "Identify and analyse networks of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000337 ! Plotting and rendering +is_a: EDAM:0003083 ! Pathway or network rendering is_a: EDAM:0002445 ! Protein interaction network processing relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=1} [Term] id: EDAM:0000573 -name: DNA map rendering +name: Map rendering namespace: operation def: "Render and visualise a DNA map." [EDAM:EBI "EMBRACE definition"] subset: operation +synonym: "DNA map rendering" EXACT [] is_a: EDAM:0002515 ! Sequence rendering (nucleic acid) -is_a: EDAM:0002521 ! DNA map data processing +is_a: EDAM:0002521 ! Map data processing relationship: has_input EDAM:0001274 ! Map {minCardinality=1} [Term] @@ -9836,23 +9506,13 @@ consider: EDAM:0000564 ! Sequence rendering [Term] -id: EDAM:0000576 -name: CpG island and isochores rendering -namespace: operation -def: "Visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence." [EDAM:EBI "EMBRACE definition"] -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. -subset: operation -is_obsolete: true -consider: EDAM:0000430 ! CpG island and isochores detection - -[Term] id: EDAM:0000577 name: DNA linear map rendering namespace: operation def: "Draw a linear maps of DNA." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true -consider: EDAM:0000573 ! DNA map rendering +consider: EDAM:0000573 ! Map rendering [Term] id: EDAM:0000578 @@ -9860,7 +9520,7 @@ name: DNA circular map rendering namespace: operation def: "Draw a circular maps of DNA, for example a plasmid map." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000573 ! DNA map rendering +is_a: EDAM:0000573 ! Map rendering [Term] id: EDAM:0000579 @@ -9868,8 +9528,8 @@ name: Operon rendering namespace: operation def: "Visualise operon structure etc." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000573 ! DNA map rendering -relationship: in_topic EDAM:0000109 ! Gene finding +is_a: EDAM:0000573 ! Map rendering +relationship: has_topic EDAM:0000109 ! Gene finding [Term] @@ -9878,7 +9538,7 @@ name: Restriction map rendering namespace: operation def: "Visualise restriction maps in DNA sequences." [EDAM:EBI "EMBRACE definition"] subset: operation -is_a: EDAM:0000573 ! DNA map rendering +is_a: EDAM:0000573 ! Map rendering is_a: EDAM:0000431 ! Restriction site recognition relationship: has_output EDAM:0001289 ! Restriction map @@ -9934,23 +9594,6 @@ subset: data is_obsolete: true consider: EDAM:0000582 ! Ontology -[Term] -id: EDAM:0000829 -name: BioPax ontology -namespace: data -def: "BioPax ontology of biological pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology - -[Term] -id: EDAM:0000830 -name: Gene Ontology -namespace: data -def: "The Gene Ontology (GO) is a controlled vocabulary for gene and gene product attributes in any organism." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology [Term] id: EDAM:0000831 @@ -9961,6 +9604,7 @@ subset: data is_obsolete: true consider: EDAM:0000582 ! Ontology + [Term] id: EDAM:0000832 name: HGNC vocabulary @@ -9970,14 +9614,6 @@ subset: data is_obsolete: true consider: EDAM:0000582 ! Ontology -[Term] -id: EDAM:0000834 -name: Plant Ontology -namespace: data -def: "Controlled vocabularies for botanical terms for morphological and anatomical structures (organ, tissue and cell types and their relationships) and terms describing (i) whole plant growth stages and (ii) plant structure developmental stages." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology [Term] id: EDAM:0000835 @@ -9988,107 +9624,31 @@ subset: data is_obsolete: true consider: EDAM:0000582 ! Ontology -[Term] -id: EDAM:0000836 -name: FMA ontology -namespace: data -def: "Ontology for phenotypic structure (anatomy) of the human body." [EDAM:EBI "EMBRACE definition"] -comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. -subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology - -[Term] -id: EDAM:0000837 -name: EMAP ontology -namespace: data -def: "Mouse anatomical terms organized into 26 developmental stages (Theiler Stages TS1-TS26) for whole embryo anatomical structures that are present from fertilization through to birth." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology - -[Term] -id: EDAM:0000838 -name: ChEBI ontology -namespace: data -def: "Dictionary of terms for chemical entities of biological interest (from ChEBI database), specifically small chemical compounds." [EDAM:EBI "EMBRACE definition"] -comment: 'Chemical entity' refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc identifiable as a separately distinguishable entity. The entities covered are either natural, or synthetic products used to intervene in the processes of living organisms. -subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology -[Term] -id: EDAM:0000839 -name: MGED ontology -namespace: data -def: "Terms for the standardized description of a microarray experiment." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology -[Term] -id: EDAM:0000840 -name: myGrid ontology -namespace: data -def: "Terms describing the bioinformatics research domain and services." [EDAM:EBI "EMBRACE definition"] -comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides terms for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. -subset: data -is_obsolete: true -consider: EDAM:0000582 ! Ontology +! ! Data +! + [Term] id: EDAM:0000841 name: Undefined namespace: data -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true - -[Term] -id: EDAM:0002860 -name: Identifier -namespace: data -def: "A short numerical or textual label that identifies a thing." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0002926 ! Identifier data - - -[Term] -id: EDAM:0002861 -name: ID -namespace: data -def: "A short string value or number that is an identifier of a thing, typically an object (entry) from a database." [EDAM:EBI "EMBRACE definition"] -comment: Identifiers typically are enumerated string (a string with one of a limited set of values) or are strings that are conformant to a regular expression. An ID is not necessarily stable or persistent over time, for example between different versions of a database. -subset: data -is_a: EDAM:0002860 ! Identifier - - -[Term] -id: EDAM:0002862 -name: Accession -namespace: data -def: "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0002861 ! ID - -[Term] -id: EDAM:0002863 -name: Name -namespace: data -def: "A name of a thing, which need not necessarily uniquely identify it." [EDAM:EBI "EMBRACE definition"] +def: "Debugging." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002860 ! Identifier +is_obsolete: true + [Term] id: EDAM:0002100 -alt_id: EDAM:0002864 name: Type namespace: data +alt_id: EDAM:0002864 def: "A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter or primitive +is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0001866 @@ -10151,22 +9711,14 @@ is_obsolete: true consider: EDAM:0002100 ! Type [Term] -id: EDAM:0002806 -name: Core data -namespace: data -def: "Primary ." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000006 ! Data - -[Term] id: EDAM:0002524 name: Protein data namespace: data def: "Data concerning one or more protein molecules." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002528 ! Molecular data +is_obsolete: true +consider: EDAM:0000896 ! Protein report [Term] id: EDAM:0002525 @@ -10175,7 +9727,8 @@ namespace: data def: "Data concerning one or more nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002528 ! Molecular data +is_obsolete: true +consider: EDAM:0002084 ! Nucleic acid report [Term] id: EDAM:0002248 @@ -10183,7 +9736,7 @@ name: Schema namespace: data def: "A data schema for organising or transforming data of some type." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000006 ! Data +is_a: EDAM:0003031 ! Core data [Term] @@ -10195,34 +9748,14 @@ subset: data is_obsolete: true consider: EDAM:0000006 ! Data -[Term] -id: EDAM:0002048 -name: Report -namespace: data -def: "An informative record that collates information on a particular subject or entity, such as data derived from analysis of primary (e.g. sequence or structure) data. This is typically a database entry or the output of a tool." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. -subset: data -is_obsolete: true -consider: EDAM:0002018 ! Metadata and annotation - - -[Term] -id: EDAM:0002926 -name: Identifier data -namespace: data -def: "Something that identifies other data or metadata concerning such an identifier." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. -subset: data -is_a: EDAM:0000006 ! Data [Term] id: EDAM:0002767 -name: Identifier metadata +name: Identifier with metadata namespace: data -def: "Basic information concerning an identifier of data. For example, provenance of a gene symbol, as opposed to information about the gene itself." [EDAM:EBI "EMBRACE definition"] +def: "Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002926 ! Identifier data -is_a: EDAM:0002018 ! Metadata and annotation +is_a: EDAM:0000842 ! Identifier [Term] id: EDAM:0002768 @@ -10231,36 +9764,36 @@ namespace: data def: "Annotation about a gene symbol." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002767 ! Identifier metadata +consider: EDAM:0002767 ! Identifier with metadata [Term] id: EDAM:0002087 name: Molecular property namespace: data -def: "A physical (e.g. structural) or chemical property of a molecule or part of a molecule." [EDAM:EBI "EMBRACE definition"] +def: "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Physicochemical property" EXACT [] -is_a: EDAM:0002529 ! Molecular report +is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0001917 -name: General atomic property +name: Atomic property namespace: data def: "Data for an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "General atomic property" EXACT [] is_a: EDAM:0002087 ! Molecular property -! relationship: is_attribute_of EDAM:0000014 ! Atom [Term] id: EDAM:0002050 -name: General molecular property +name: Molecular property (general) namespace: data def: "General data for a molecule." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "General molecular property" EXACT [] is_a: EDAM:0002087 ! Molecular property -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity [Term] @@ -10270,7 +9803,10 @@ namespace: data def: "Data concerning molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0000006 ! Data +is_obsolete: true +consider: EDAM:0002044 ! Sequence +consider: EDAM:0002955 ! Sequence report + [Term] id: EDAM:0002044 @@ -10279,8 +9815,8 @@ namespace: data def: "One or more molecular sequences, possibly with associated annotation." [EDAM:EBI "EMBRACE definition"] comment: This term is a placeholder of terms for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. subset: data -is_a: EDAM:0002925 ! Sequence data -relationship: in_topic EDAM:0000080 ! Sequence +relationship: has_topic EDAM:0000080 ! Sequence analysis +is_a: EDAM:0003031 ! Core data [Term] @@ -10290,7 +9826,6 @@ namespace: data def: "One or more protein sequences, possibly with associated annotation." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002044 ! Sequence -is_a: EDAM:0002524 ! Protein data [Term] id: EDAM:0002977 @@ -10299,7 +9834,6 @@ namespace: data def: "One or more nucleic acid sequences, possibly with associated annotation." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002044 ! Sequence -is_a: EDAM:0002525 ! Nucleic acid data [Term] id: EDAM:0002955 @@ -10308,8 +9842,7 @@ namespace: data def: "An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence-derived report" EXACT [] -is_a: EDAM:0002018 ! Metadata and annotation -is_a: EDAM:0002925 ! Sequence data +is_a: EDAM:0002048 ! Report [Term] @@ -10320,6 +9853,8 @@ def: "Basic or general information concerning molecular sequences." [EDAM:EBI "E comment: This is used for such things as a report including the sequence identifier, type and length. subset: data is_a: EDAM:0001254 ! Sequence property +is_a: EDAM:0002955 ! Sequence report +is_a: EDAM:0002337 ! Metadata [Term] id: EDAM:0002522 @@ -10328,20 +9863,20 @@ namespace: data def: "Data concerning a map of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0000006 ! Data -! consider: EDAM:0001274 ! Map -! consider: EDAM:0002019 ! Map attribute +is_obsolete: true +consider: EDAM:0001274 ! Map +consider: EDAM:0002019 ! Map attribute [Term] id: EDAM:0001274 name: Map namespace: data -def: "A map of (typically one) molecular sequence annotated with positional or non-positional features." [EDAM:EBI "EMBRACE definition"] +def: "A map of (typically one) DNA sequence annotated with positional or non-positional features." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002522 ! Map data -relationship: in_topic EDAM:0000643 ! Genomes - +synonym: "DNA map" EXACT [] +relationship: has_topic EDAM:0000102 ! Sequencing and mapping +is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0001864 @@ -10360,7 +9895,9 @@ name: Map attribute namespace: data def: "An attribute of a molecular map (genetic or physical)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002522 ! Map data +is_a: EDAM:0002337 ! Metadata +relationship: has_topic EDAM:0000102 ! Sequencing and mapping + [Term] id: EDAM:0002080 @@ -10387,8 +9924,8 @@ namespace: data def: "Data concerning specific or conserved pattern in molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002925 ! Sequence data -relationship: in_topic EDAM:0000158 ! Sequence motifs +is_obsolete: true +consider: EDAM:0001353 ! Sequence motif [Term] id: EDAM:0001353 @@ -10396,8 +9933,8 @@ name: Sequence motif namespace: data def: "Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002981 ! Sequence motif data - +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0002762 @@ -10405,7 +9942,8 @@ name: Sequence motif metadata namespace: data def: "Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002981 ! Sequence motif data +is_a: EDAM:0002337 ! Metadata +relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0002982 @@ -10414,8 +9952,8 @@ namespace: data def: "Data concerning models representing a (typically multiple) sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002925 ! Sequence data -relationship: in_topic EDAM:0000188 ! Sequence profiles and HMMs +is_obsolete: true +consider: EDAM:0001354 ! Sequence profile [Term] id: EDAM:0001354 @@ -10423,7 +9961,8 @@ name: Sequence profile namespace: data def: "Some type of statistical model representing a (typically multiple) sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002982 ! Sequence profile data +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000188 ! Sequence profiles and HMMs [Term] id: EDAM:0002788 @@ -10431,8 +9970,8 @@ name: Sequence profile metadata namespace: data def: "Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002982 ! Sequence profile data -is_a: EDAM:0002018 ! Metadata and annotation +is_a: EDAM:0002337 ! Metadata +relationship: has_topic EDAM:0000188 ! Sequence profiles and HMMs [Term] id: EDAM:0001355 @@ -10441,7 +9980,7 @@ namespace: data def: "An entry (sequence classifier and associated data) from the InterPro database." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "InterPro entry" EXACT [] -is_a: EDAM:0002980 ! Protein classification data +is_a: EDAM:0000907 ! Protein family [Term] id: EDAM:0002161 @@ -10449,7 +9988,7 @@ name: Sequence similarity plot namespace: data def: "A plot of sequence similarities identified from word-matching or character comparison." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001711 ! Sequence alignment image or plot +is_a: EDAM:0000867 ! Sequence alignment report [Term] id: EDAM:0000862 @@ -10466,10 +10005,9 @@ namespace: data def: "Data concerning an alignment of two or more molecular sequences, structures or derived data." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. subset: data -is_a: EDAM:0000006 ! Data -! is_obsolete: true -! consider: EDAM:0001916 ! Alignment -! consider: EDAM:0002083 ! Alignment report +is_obsolete: true +consider: EDAM:0001916 ! Alignment +consider: EDAM:0002083 ! Alignment report [Term] @@ -10478,7 +10016,7 @@ name: Alignment namespace: data def: "An alignment of molecular sequences, structures or profiles derived from them." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002539 ! Alignment data +is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002083 @@ -10487,15 +10025,14 @@ namespace: data def: "An informative report about a molecular alignment of some type, including alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002539 ! Alignment data +is_a: EDAM:0002048 ! Report [Term] id: EDAM:0002711 name: Genome metadata namespace: data -def: "A report of general information about a genome as a whole." [EDAM:EBI "EMBRACE definition"] +def: "Provenance metadata or other general information concerning a genome as a whole." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation is_a: EDAM:0000855 ! Sequence metadata @@ -10545,7 +10082,7 @@ namespace: data def: "An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0000006 ! Data +is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002855 @@ -10574,17 +10111,18 @@ def: "Distances (values representing similarity) between a group of molecular st subset: data is_a: EDAM:0002855 ! Distance matrix + +! Phylogenetic character data! Also molecular sequences, microsatellites), polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments [Term] id: EDAM:0002523 -name: Phylogenetic data +name: Phylogenetic raw data namespace: data def: "Data concerning phylogeny, typically of molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0000006 ! Data -! consider: EDAM:0000872 ! Phylogenetic tree -! consider: EDAM:0001438 ! Phylogenetic report -! consider: EDAM:0000871 ! Phylogenetic character data! Also molecular sequences, microsatellites), polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments +synonym: "Phylogenetic data" EXACT [] +is_a: EDAM:0003031 ! Core data + [Term] id: EDAM:0000871 @@ -10592,7 +10130,7 @@ name: Phylogenetic character data namespace: data def: "Data from which a phylogenetic tree may be generated." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002523 ! Phylogenetic data +is_a: EDAM:0002523 ! Phylogenetic raw data [Term] id: EDAM:0000872 @@ -10604,30 +10142,20 @@ subset: data xref: Moby:Tree xref: Moby:phylogenetic_tree xref: Moby:myTree -is_a: EDAM:0002523 ! Phylogenetic data -is_a: EDAM:0000950 ! Biological model -relationship: in_topic EDAM:0000084 ! Phylogenetics +relationship: has_topic EDAM:0000084 ! Phylogenetics +is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0001438 -name: Phylogenetic report +name: Phylogenetic tree report namespace: data +alt_id: EDAM:0000873 def: "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Phylogenetic tree-derived report" EXACT [] -is_a: EDAM:0002523 ! Phylogenetic data -is_a: EDAM:0002018 ! Metadata and annotation - -[Term] -id: EDAM:0000873 -name: Phylogenetic tree-derived report -namespace: data -def: "A report of annotation on or data derived from a phylogenetic tree or from comparing two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0001438 ! Phylogenetic report +is_a: EDAM:0002048 ! Report [Term] @@ -10640,6 +10168,7 @@ subset: data synonym: "Substitution matrix" EXACT [] is_a: EDAM:0002082 ! Matrix + [Term] id: EDAM:0002053 name: Structural data @@ -10647,7 +10176,10 @@ namespace: data def: "Data concerning molecular structural data." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0000006 ! Data +is_obsolete: true +consider: EDAM:0000883 ! Structure +consider: EDAM:0002085 ! Structure report + [Term] id: EDAM:0002085 @@ -10656,8 +10188,7 @@ namespace: data def: "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Structure-derived report" EXACT [] -is_a: EDAM:0002053 ! Structural data -is_a: EDAM:0002018 ! Metadata and annotation +is_a: EDAM:0002048 ! Report [Term] id: EDAM:0002973 @@ -10665,7 +10196,9 @@ name: Secondary structure data namespace: data def: "Data concerning molecular secondary structure data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002053 ! Structural data +is_obsolete: true +consider: EDAM:0002081 ! Secondary structure +consider: EDAM:0002881 ! Secondary structure report [Term] @@ -10675,14 +10208,14 @@ namespace: data def: "An informative report on general information, properties or features of one or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Secondary structure-derived report" EXACT [] -is_a: EDAM:0002973 ! Secondary structure data -is_a: EDAM:0002018 ! Metadata and annotation +is_a: EDAM:0002048 ! Report + [Term] id: EDAM:0002956 name: Protein secondary structure report namespace: data -def: "An informative report on general information, properties or features of one or more protein secondary structures." [EDAM:EBI "EMBRACE definition"] +def: "An informative report about the properties or features of one or more protein secondary structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002881 ! Secondary structure report @@ -10710,7 +10243,8 @@ namespace: data def: "Some type of structural (3D) profile or template (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "3D profile" EXACT [] -is_a: EDAM:0002053 ! Structural data +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000167 ! Structural (3D) profiles [Term] id: EDAM:0000892 @@ -10727,18 +10261,19 @@ namespace: data def: "Data concerning a specific type of molecule." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0000006 ! Data -! consider: EDAM:0002524 ! Protein data -! consider: EDAM:0002525 ! Nucleic acid data -! consider: EDAM:0002601 ! Small molecule data +synonym: "Molecule-specific data" EXACT [] +is_obsolete: true +consider: EDAM:0002529 ! Molecule report + [Term] id: EDAM:0002599 -name: Molecular interaction data +name: Molecular interaction namespace: data -def: "An informative report concerning the interaction of two or more molecules (or parts of molecules)." [EDAM:EBI "EMBRACE definition"] +def: "Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000006 ! Data +synonym: "Molecular interaction data" EXACT [] +is_a: EDAM:0003031 ! Core data [Term] @@ -10748,23 +10283,26 @@ namespace: data def: "Data concerning one or more small molecules." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002528 ! Molecular data +is_obsolete: true +consider: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002016 -name: Amino acid data +name: Amino acid property namespace: data -def: "Data concerning one, more or all amino acids." [EDAM:EBI "EMBRACE definition"] +def: "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002601 ! Small molecule data +synonym: "Amino acid data" EXACT [] +is_a: EDAM:0002087 ! Molecular property [Term] id: EDAM:0002979 -name: Peptide data +name: Peptide property namespace: data def: "Data concerning small peptides." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002601 ! Small molecule data +synonym: "Peptide data" EXACT [] +is_a: EDAM:0002087 ! Molecular property [Term] @@ -10773,17 +10311,20 @@ name: Peptide annotation namespace: data def: "An informative report about a specific peptide." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule report -relationship: in_topic EDAM:0000613 ! Peptides and amino acids +is_a: EDAM:0000962 ! Small molecule annotation +is_a: EDAM:0002979 ! Peptide property +relationship: has_topic EDAM:0000613 ! Peptides and amino acids [Term] id: EDAM:0002399 name: Gene annotation (transcript) namespace: data -def: "An informative report on a specific gene transcript." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002703 +def: "An informative report on a specific gene transcript, clone or EST." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene transcript annotation" EXACT [] +synonym: "Gene annotation (clone or EST)" EXACT [] is_a: EDAM:0000916 ! Gene annotation @@ -10791,19 +10332,19 @@ is_a: EDAM:0000916 ! Gene annotation id: EDAM:0000896 name: Protein report namespace: data -def: "An informative report about one or more specific protein molecules, derived from analysis of primary (sequence or structural) data." [EDAM:EBI "EMBRACE definition"] +def: "An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene product annotation" EXACT [] -is_a: EDAM:0002529 ! Molecular report -is_a: EDAM:0002524 ! Protein data -relationship: in_topic EDAM:0000586 ! Proteins +is_a: EDAM:0002529 ! Molecule report +relationship: has_topic EDAM:0000078 ! Protein analysis + [Term] id: EDAM:0000897 name: Protein property namespace: data -def: "A physicochemical property (primarily non-positional data) of a protein sequence or structure." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. +def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model." [EDAM:EBI "EMBRACE definition"] +comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Protein physicochemical property" EXACT [] is_a: EDAM:0000896 ! Protein report @@ -10814,14 +10355,40 @@ is_a: EDAM:0002087 ! Molecular property id: EDAM:0001537 name: Protein structure report namespace: data -def: "Annotation on or information derived from one or more specific protein 3D structure(s)." [EDAM:EBI "EMBRACE definition"] +def: "Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains." [EDAM:EBI "EMBRACE definition"] subset: data +alt_id: EDAM:0000898 +alt_id: EDAM:0001538 +alt_id: EDAM:0002377 +synonym: "Protein structure report (domain)" EXACT [] synonym: "Protein structure-derived report" EXACT [] synonym: "Protein structural property" EXACT [] synonym: "Protein report (structure)" EXACT [] +synonym: "Protein property (structural)" EXACT [] is_a: EDAM:0000896 ! Protein report is_a: EDAM:0002085 ! Structure report -relationship: in_topic EDAM:0002814 ! Protein structure + + +[Term] +id: EDAM:0003151 +name: Protein property (physicochemical) +namespace: data +def: "A report of primarily non-positional data describing intrinsic physicochemical properties of a protein molecule." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "Protein physicochemical property" EXACT [] +is_obsolete: true +consider: EDAM:0000897 ! Protein property + + +[Term] +id: EDAM:0003152 +name: Protein property (sequence) +namespace: data +def: "A non-positional property of a protein sequence." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "Protein sequence property" EXACT [] +is_obsolete: true +consider: EDAM:0000897 ! Protein property [Term] @@ -10841,69 +10408,54 @@ subset: data is_a: EDAM:0002085 ! Structure report -[Term] -id: EDAM:0000898 -name: Protein structure-derived report -namespace: data -def: "A report of information derived from one or more specific protein 3D structure(s)." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0001537 ! Protein structure report -consider: EDAM:0000897 ! Protein property - - -[Term] -id: EDAM:0001538 -name: Protein structural property -namespace: data -def: "Structural information derived from analysis of a specific protein 3D structure." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0001537 ! Protein structure report [Term] id: EDAM:0002987 -name: Classification data +name: Classification namespace: data -def: "Data concerning the classification of molecular sequences, structures or other entities." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. +def: "Data concerning a classification of molecular sequences, structures or other entities." [EDAM:EBI "EMBRACE definition"] +comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. subset: data -is_a: EDAM:0000006 ! Data -relationship: in_topic EDAM:0002230 ! Classification +synonym: "Classification data" EXACT [] +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0003028 -name: Taxonomic data +name: Taxonomy namespace: data def: "Data concerning the classification, identification and naming of organisms." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002987 ! Classification data -relationship: in_topic EDAM:0002230 ! Classification +synonym: "Taxonomic data" EXACT [] +is_a: EDAM:0002987 ! Classification +relationship: has_topic EDAM:0000637 ! Taxonomy [Term] id: EDAM:0002986 -name: Nucleic acid classification data +name: Nucleic acid classification namespace: data def: "Data concerning the classification of nucleic acid sequences or structures." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002525 ! Nucleic acid data -is_a: EDAM:0002987 ! Classification data -relationship: in_topic EDAM:0000722 ! Nucleic acid classification +synonym: "Nucleic acid classification data" EXACT [] +is_a: EDAM:0002084 ! Nucleic acid report +is_a: EDAM:0002987 ! Classification +relationship: has_topic EDAM:0000722 ! Nucleic acid classification [Term] id: EDAM:0002980 -name: Protein classification data +name: Protein classification namespace: data def: "Data concerning the classification of protein sequences or structures." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002524 ! Protein data -is_a: EDAM:0002987 ! Classification data -relationship: in_topic EDAM:0000595 ! Protein classification +synonym: "Protein classification data" EXACT [] +is_a: EDAM:0000896 ! Protein report +is_a: EDAM:0002987 ! Classification +relationship: has_topic EDAM:0000595 ! Protein classification [Term] id: EDAM:0000900 @@ -10911,29 +10463,38 @@ name: Protein domain classification namespace: data def: "Data concerning the classification of the sequences and/or structures of protein structural domain(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002980 ! Protein classification data -! relationship: is_attribute_of EDAM:0000065 ! Protein domain -relationship: in_topic EDAM:0000736 ! Protein domains +is_a: EDAM:0002980 ! Protein classification +relationship: has_topic EDAM:0000736 ! Protein domains and folds + +[Term] +id: EDAM:0003101 +name: Protein domain classification node +namespace: data +def: "A node from a classification of protein structural domain(s)." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0000900 ! Protein domain classification + [Term] id: EDAM:0000906 -name: Protein interaction report +name: Protein interaction namespace: data -def: "An informative report on one or more predicted or actual protein-protein, protein-DNA/RNA or protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] +def: "An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation -is_a: EDAM:0002599 ! Molecular interaction data -relationship: in_topic EDAM:0000128 ! Protein interactions +synonym: "Protein report (interaction)" EXACT [] +is_a: EDAM:0002599 ! Molecular interaction +is_a: EDAM:0000896 ! Protein report +relationship: has_topic EDAM:0000128 ! Protein interactions [Term] id: EDAM:0000907 -name: Protein family annotation +name: Protein family namespace: data -def: "An informative report on a specific protein family or other group of classified protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "An informative report on a specific protein family or other group of classified proteins." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation -is_a: EDAM:0002980 ! Protein classification data -relationship: in_topic EDAM:0000724 ! Protein families +synonym: "Protein family annotation" EXACT [] +is_a: EDAM:0002980 ! Protein classification +relationship: has_topic EDAM:0000724 ! Protein families [Term] @@ -10942,17 +10503,21 @@ name: RNA family annotation namespace: data def: "An informative report on a specific RNA family or other group of classified RNA sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation -is_a: EDAM:0002986 ! Nucleic acid classification data +is_a: EDAM:0002986 ! Nucleic acid classification [Term] id: EDAM:0002978 name: Reaction data namespace: data -def: "Data concerning a biochemical reaction." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000908 +def: "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. +synonym: "Reaction annotation" EXACT [] +synonym: "Enzyme kinetics annotation" EXACT [] subset: data -is_a: EDAM:0000006 ! Data +is_a: EDAM:0003031 ! Core data + + [Term] id: EDAM:0002024 @@ -10969,8 +10534,7 @@ name: Nucleotide base annotation namespace: data def: "An informative report about a specific nucleotide base." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule report - +is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002116 @@ -10980,7 +10544,6 @@ def: "An informative report on a trinucleotide sequence that encodes an amino ac subset: data is_obsolete: true consider: EDAM:0001276 ! Nucleic acid features -! relationship: is_attribute_of EDAM:0000050 ! Codon [Term] id: EDAM:0002084 @@ -10988,15 +10551,14 @@ name: Nucleic acid report namespace: data def: "An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002529 ! Molecular report -is_a: EDAM:0002525 ! Nucleic acid data +is_a: EDAM:0002529 ! Molecule report [Term] id: EDAM:0000912 name: Nucleic acid property namespace: data -def: "A report on the physicochemical properties (primarily non-positional data) of a nucleic acid sequence or structure." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. +def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] +comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Nucleic acid physicochemical property" EXACT [] is_a: EDAM:0002084 ! Nucleic acid report @@ -11007,24 +10569,16 @@ is_a: EDAM:0002087 ! Molecular property id: EDAM:0002086 name: Nucleic acid structure report namespace: data -def: "Annotation on or information derived from one or more specific nucleic acid 3D structure(s)." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000913 +def: "A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s)." [EDAM:EBI "EMBRACE definition"] +comment: This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. subset: data synonym: "Nucleic acid structural property" EXACT [] +synonym: "Nucleic acid property (structural)" EXACT [] is_a: EDAM:0000912 ! Nucleic acid property is_a: EDAM:0002085 ! Structure report -[Term] -id: EDAM:0000913 -name: Nucleic acid structural property -namespace: data -def: "A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule such as stiffness, curvature, twist/roll data or other conformational parameters or properties." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. -subset: data -is_obsolete: true -consider: EDAM:0002086 ! Nucleic acid structure report -consider: EDAM:0000912 ! Nucleic acid property - [Term] id: EDAM:0002927 @@ -11033,17 +10587,20 @@ namespace: data def: "Data concerning codon usage." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0000006 ! Data +is_obsolete: true +consider: EDAM:0001597 ! Codon usage table +consider: EDAM:0000914 ! Codon usage report + [Term] id: EDAM:0001597 name: Codon usage table namespace: data def: "Table of codon usage data calculated from one or more nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] -comment: A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from a codon usage table. +comment: A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. subset: data -is_a: EDAM:0002927 ! Codon usage data - +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000107 ! Codon usage analysis [Term] id: EDAM:0000914 @@ -11052,19 +10609,102 @@ namespace: data def: "Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0002927 ! Codon usage data +is_a: EDAM:0002048 ! Report +relationship: has_topic EDAM:0000107 ! Codon usage analysis + +[Term] +id: EDAM:0002603 +name: Microarray data +namespace: data +alt_id: EDAM:0002541 +def: "Image or hybridisation data for a microarray, typically a study of gene expression." [EDAM:EBI "EMBRACE definition"] +comment: This is a broad data type and is used a placeholder for other, more specific types. See also EDAM:0000931 ! Experiment annotation (microarray) +subset: data +synonym: "Gene expression data" EXACT [] +is_a: EDAM:0003031 ! Core data + + [Term] -id: EDAM:0002541 -name: Gene expression data +id: EDAM:0003110 +name: Raw microarray data namespace: data -def: "Data concerning gene expression." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. +def: "Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment." [EDAM:EBI "EMBRACE definition"] +comment: Such data as found in Affymetrix CEL or GPR files. subset: data -is_a: EDAM:0000006 ! Data -! is_obsolete: true -! consider: EDAM:0000929 ! Gene annotation (expression) -! consider: EDAM:0000928 ! Gene expression profile +is_a: EDAM:0003117 ! Microarray hybridisation data +is_a: EDAM:0003108 ! Experimental measurement + + +[Term] +id: EDAM:0003111 +name: Processed microarray data +namespace: data +alt_id: EDAM:0000929 +def: "Data generated from processing and analysis of probe set data from a microarray experiment." [EDAM:EBI "EMBRACE definition"] +comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. +subset: data +synonym: "Microarray probe set data" EXACT [] +synonym: "Gene expression report" EXACT [] +synonym: "Gene annotation (expression)" EXACT [] +is_a: EDAM:0003117 ! Microarray hybridisation data +is_a: EDAM:0000928 ! Gene expression profile +relationship: has_topic EDAM:0000197 ! Gene expression resources + + +[Term] +id: EDAM:0003117 +name: Microarray hybridisation data +namespace: data +def: "Data concerning the hybridisations measured during a microarray experiment." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0002603 ! Microarray data +relationship: has_topic EDAM:0000197 ! Gene expression resources + +[Term] +id: EDAM:0003112 +name: Normalised microarray data +namespace: data +def: "The final processed (normalised) data for a set of hybridisations in a microarray experiment." [EDAM:EBI "EMBRACE definition"] +comment: This combines data from all hybridisations. +subset: data +synonym: "Gene expression matrix" EXACT [] +synonym: "Gene expression data matrix" EXACT [] +is_a: EDAM:0003117 ! Microarray hybridisation data + +[Term] +id: EDAM:0003113 +name: Sample annotation +namespace: data +def: "Annotation on a biological sample, for example experimental factors and their values." [EDAM:EBI "EMBRACE definition"] +comment: This might include compound and dose in a dose response experiment. +subset: data +is_a: EDAM:0000931 ! Experiment annotation (microarray) + + + + + + +[Term] +id: EDAM:0003115 +name: Microarray annotation +namespace: data +def: "Annotation on the array itself used in a microarray experiment." [EDAM:EBI "EMBRACE definition"] +comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. +subset: data +is_a: EDAM:0000931 ! Experiment annotation (microarray) + + +[Term] +id: EDAM:0003116 +name: Microarray protocol annotation +namespace: data +def: "Annotation on laboratory and/or data processing protocols used in an microarray experiment." [EDAM:EBI "EMBRACE definition"] +comment: This might describe e.g. the normalisation methods used to process the raw data. +subset: data +is_a: EDAM:0000931 ! Experiment annotation (microarray) + [Term] id: EDAM:0002763 @@ -11080,36 +10720,38 @@ consider: EDAM:0000916 ! Gene annotation id: EDAM:0000916 name: Gene annotation namespace: data +alt_id: EDAM:0002394 +alt_id: EDAM:0002361 def: "An informative report on a particular locus, gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] -comment: This might include the gene name, description, summary and so on. +comment: This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). subset: data synonym: "Gene report" EXACT [] -synonym: "Gene family annotation" EXACT [] +synonym: "Gene annotation (functional)" EXACT [] xref: Moby:gene xref: Moby:GeneInfo xref: Moby_namespace:Human_Readable_Description -is_a: EDAM:0002986 ! Nucleic acid classification data is_a: EDAM:0001276 ! Nucleic acid features -relationship: in_topic EDAM:0000623 ! Gene family or system +relationship: has_topic EDAM:0000623 ! Genes, gene family or system [Term] -id: EDAM:0002703 -name: Gene annotation (clone or EST) +id: EDAM:0003148 +name: Gene family annotation namespace: data -def: "An informative report on a particular clone or EST." [EDAM:EBI "EMBRACE definition"] +def: "An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation +is_a: EDAM:0002986 ! Nucleic acid classification is_a: EDAM:0000916 ! Gene annotation [Term] id: EDAM:0000918 -name: Sequence variation annotation +name: Nucleic acid features (variation) namespace: data -def: "Report on a mutation in a molecular sequence such as single base nucleotide subsitutions, deletions and insertions." [EDAM:EBI "EMBRACE definition"] +def: "A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000920 ! Genotype and phenotype annotation -relationship: in_topic EDAM:0000199 ! Mutation and polymorphism +synonym: "Sequence variation annotation" EXACT [] +is_a: EDAM:0003122 ! Nucleic acid features (difference and change) +relationship: has_topic EDAM:0000199 ! Genetic variation [Term] @@ -11120,7 +10762,7 @@ def: "An informative report on a specific chromosome." [EDAM:EBI "EMBRACE defini comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. subset: data is_a: EDAM:0000916 ! Gene annotation -relationship: in_topic EDAM:0000624 ! Chromosomes +relationship: has_topic EDAM:0000624 ! Chromosomes [Term] id: EDAM:0002602 @@ -11128,34 +10770,39 @@ name: Genotype and phenotype data namespace: data def: "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000006 ! Data +is_obsolete: true +consider: EDAM:0000920 ! Genotype/phenotype annotation + [Term] id: EDAM:0000920 name: Genotype/phenotype annotation namespace: data -def: "An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific trait or phenotype." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002890 +def: "An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation -is_a: EDAM:0002602 ! Genotype and phenotype data +is_a: EDAM:0002048 ! Report + [Term] -id: EDAM:0002890 -name: Phenotype annotation +id: EDAM:0002531 +name: Experiment annotation namespace: data -def: "An informative report on a specific physical characteristic of an organism, influenced by genetic and environmental factors." [EDAM:EBI "EMBRACE definition"] +def: "Annotation on a wet lab experiment, such as experimental conditions." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation -is_a: EDAM:0002602 ! Genotype and phenotype data +is_a: EDAM:0002048 ! Report [Term] -id: EDAM:0002531 -name: Experiment annotation +id: EDAM:0003109 +name: Experimental measurement annotation namespace: data -def: "Annotation on a wet lab experiment." [EDAM:EBI "EMBRACE definition"] +def: "Annotation on the result of a wet lab experiment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation -is_a: EDAM:0002028 ! Experimental data +is_obsolete: true +consider: EDAM:0003108 ! Experimental measurement +consider: EDAM:0002531 ! Experiment annotation + + [Term] @@ -11181,10 +10828,26 @@ is_a: EDAM:0001234 ! Sequence set (nucleic acid) id: EDAM:0002028 name: Experimental data namespace: data -def: "Raw data resulting from or used in a laboratory experiment." [EDAM:EBI "EMBRACE definition"] +def: "Raw data from or annotation on laboratory experiments." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data -is_a: EDAM:0000006 ! Data +synonym: "Experimental measurement data" EXACT [] +is_obsolete: true +consider: EDAM:0003108 ! Experimental measurement +consider: EDAM:0002531 ! Experiment annotation + +[Term] +id: EDAM:0003108 +name: Experimental measurement +namespace: data +def: "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware." [EDAM:EBI "EMBRACE definition"] +comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. +subset: data +synonym: "Raw experimental data" EXACT [] +synonym: "Experimental measurement data" EXACT [] +is_a: EDAM:0003031 ! Core data + + [Term] @@ -11193,17 +10856,17 @@ name: Evidence namespace: data def: "Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter or primitive +is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0000941 -name: Experiment annotation (electron microscopy model) +name: Electron microscopy model namespace: data def: "Annotation on a structural 3D model (volume map) from electron microscopy." [EDAM:EBI "EMBRACE definition"] comment: This might include the location in the model of the known features of a particular macromolecule. subset: data -is_a: EDAM:0002531 ! Experiment annotation -relationship: in_topic EDAM:0000611 ! Electron microscopy +is_a: EDAM:0000940 ! Electron microscopy volume map +relationship: has_topic EDAM:0002226 ! Structure determination [Term] id: EDAM:0002971 @@ -11211,8 +10874,9 @@ name: Workflow data namespace: data def: "Data concerning a computational workflow." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000006 ! Data -relationship: in_topic EDAM:0000769 ! Workflows +is_obsolete: true +consider: EDAM:0000949 ! Workflow metadata +consider: EDAM:0002972 ! Workflow [Term] @@ -11221,8 +10885,9 @@ name: Workflow metadata namespace: data def: "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002971 ! Workflow data -is_a: EDAM:0002018 ! Metadata and annotation +is_a: EDAM:0002337 ! Metadata +relationship: has_topic EDAM:0000769 ! Workflows + [Term] id: EDAM:0002972 @@ -11230,16 +10895,18 @@ name: Workflow namespace: data def: "A computational workflow." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002971 ! Workflow data +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000769 ! Workflows + [Term] id: EDAM:0000950 name: Biological model namespace: data -def: "A biological model, typically represented as a human readable report and / or in mathematical terms." [EDAM:EBI "EMBRACE definition"] +def: "A biological model which can be represented in mathematical terms." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000006 ! Data -relationship: in_topic EDAM:0000771 ! Biological models +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000771 ! Biological models [Term] id: EDAM:0002983 @@ -11247,8 +10914,9 @@ name: Pathway or network data namespace: data def: "Data concerning a specific biological pathway or network." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000006 ! Data -relationship: in_topic EDAM:0000602 ! Pathways, networks and models +is_obsolete: true +consider: EDAM:0002600 ! Pathway or network +consider: EDAM:0002984 ! Pathway or network report [Term] @@ -11257,7 +10925,8 @@ name: Pathway or network report namespace: data def: "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002983 ! Pathway or network data +is_a: EDAM:0002048 ! Report +relationship: has_topic EDAM:0000602 ! Pathways, networks and models [Term] id: EDAM:0002600 @@ -11265,18 +10934,19 @@ name: Pathway or network namespace: data def: "Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002983 ! Pathway or network data -is_a: EDAM:0000950 ! Biological model +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000602 ! Pathways, networks and models + [Term] id: EDAM:0001883 -name: URI metadata +name: Annotated URI namespace: data def: "A URI along with annotation describing the data found at the address." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby:DescribedLink +is_a: EDAM:0002337 ! Metadata is_a: EDAM:0002093 ! Data reference -is_a: EDAM:0002018 ! Metadata and annotation [Term] @@ -11299,14 +10969,12 @@ is_a: EDAM:0002093 ! Data reference [Term] id: EDAM:0002765 -name: Annotation +name: Term ID list namespace: data def: "One or more terms from one or more controlled vocabularies which are annotations on an entity." [EDAM:EBI "EMBRACE definition"] comment: The terms are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. subset: data -is_a: EDAM:0002018 ! Metadata and annotation is_a: EDAM:0002872 ! ID list -is_a: EDAM:0002353 ! Ontological data [Term] id: EDAM:0001111 @@ -11321,10 +10989,10 @@ is_a: EDAM:0002872 ! ID list id: EDAM:0002093 name: Data reference namespace: data -def: "Reference to a dataset/database (or a cross-reference between two datasets/databases), typically entries in a biological database or ontology." [EDAM:EBI "EMBRACE definition"] +def: "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology." [EDAM:EBI "EMBRACE definition"] comment: A list of database accessions or identifiers are usually included. subset: data -is_a: EDAM:0000006 ! Data +is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002540 @@ -11334,9 +11002,9 @@ def: "Data concerning an index of data." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Database index" EXACT [] -is_a: EDAM:0000006 ! Data -! consider: EDAM:0000955 ! Data index -! consider: EDAM:0000956 ! Data index report +is_obsolete: true +consider: EDAM:0000955 ! Data index +consider: EDAM:0000956 ! Data index report [Term] id: EDAM:0000955 @@ -11344,7 +11012,9 @@ name: Data index namespace: data def: "An index of data of biological relevance." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002540 ! Data index data +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000220 ! Data processing and validation + [Term] id: EDAM:0000956 @@ -11353,58 +11023,56 @@ namespace: data def: "A report of an analysis of an index of biological data." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Database index annotation" EXACT [] -is_a: EDAM:0002540 ! Data index data - -[Term] -id: EDAM:0002018 -name: Metadata and annotation -namespace: data -def: "Data concerning or describing some other data or entity, as distinct from the primary data that is being described. This is typically an informative record that collates information (annotation) on a particular thing, and is often derived from analysis of primary (e.g. sequence or structure) data." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. -subset: data -is_a: EDAM:0000006 ! Data +is_a: EDAM:0002048 ! Report +relationship: has_topic EDAM:0000220 ! Data processing and validation [Term] -id: EDAM:0002853 -name: Core metadata +id: EDAM:0002048 +name: Report namespace: data -def: "Data concerning or describing some core data as distinct from the primary data that is being described. Typically an informative record derived from analysis of the core data." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000969 +alt_id: EDAM:0003037 +def: "A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself." [EDAM:EBI "EMBRACE definition"] +comment: This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing. subset: data -is_obsolete: true -consider: EDAM:0000006 ! Data +synonym: "Text" EXACT [] +synonym: "Textual data" EXACT [] +synonym: "Document" EXACT [] +is_a: EDAM:0000006 ! Data [Term] id: EDAM:0001772 -alt_id: EDAM:0002138 name: Score or penalty namespace: data +alt_id: EDAM:0002138 def: "A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter or primitive +is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0002529 -name: Molecular report +name: Molecule report namespace: data def: "An informative report on a specific molecule." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation -is_a: EDAM:0002528 ! Molecular data +synonym: "Molecular report" EXACT [] +is_a: EDAM:0002048 ! Report [Term] id: EDAM:0000962 -name: Small molecule report +name: Small molecule annotation namespace: data def: "An informative report on a specific chemical compound." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Chemical compound annotation" EXACT [] +synonym: "Small molecule report" EXACT [] is_a: EDAM:0002085 ! Structure report -is_a: EDAM:0002529 ! Molecular report -is_a: EDAM:0002601 ! Small molecule data -relationship: in_topic EDAM:0000154 ! Small molecules +is_a: EDAM:0002529 ! Molecule report +relationship: has_topic EDAM:0000154 ! Small molecules + [Term] id: EDAM:0000963 @@ -11421,8 +11089,7 @@ name: Organism annotation namespace: data def: "An informative report on a specific organism." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation - +is_a: EDAM:0002048 ! Report [Term] id: EDAM:0002307 @@ -11446,26 +11113,19 @@ name: Scent annotation namespace: data def: "An informative report about a specific scent." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule report -relationship: in_topic EDAM:0000618 ! Scents +is_a: EDAM:0000962 ! Small molecule annotation -[Term] -id: EDAM:0002968 -name: Image or plot -namespace: data -def: "Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0000006 ! Data [Term] -id: EDAM:0000965 +id: EDAM:0002968 name: Image namespace: data -def: "Biological or biomedical image data that may be rendered, for example displayed on screen." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000965 +def: "Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0002968 ! Image or plot +is_a: EDAM:0003031 ! Core data + [Term] id: EDAM:0002884 @@ -11474,7 +11134,7 @@ namespace: data def: "Biological data that is plotted as a graph of some type." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002968 ! Image or plot +consider: EDAM:0002968 ! Image [Term] id: EDAM:0002353 @@ -11483,18 +11143,10 @@ namespace: data def: "Data concerning an ontology." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0000006 ! Data -! is_obsolete: true -! consider: EDAM:0002223 ! Ontology metadata +is_obsolete: true +consider: EDAM:0002223 ! Ontology metadata +consider: EDAM:0000582 ! Ontology -[Term] -id: EDAM:0002603 -name: Microarray data -namespace: data -def: "Data concerning microarrays." [EDAM:EBI "EMBRACE definition"] -comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. -subset: data -is_a: EDAM:0002028 ! Experimental data [Term] id: EDAM:0002849 @@ -11510,7 +11162,7 @@ id: EDAM:0000970 name: Bibliographic reference namespace: data def: "Bibliographic data that uniquely identifies a scientific article, book or other published material." [EDAM:EBI "EMBRACE definition"] -comment: A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if availabile. +comment: A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. subset: data synonym: "Reference" EXACT [] synonym: "Citation" EXACT [] @@ -11527,8 +11179,8 @@ namespace: data def: "Data concerning the scientific literature." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. subset: data -is_a: EDAM:0000006 ! Data -! consider: EDAM:0000971 ! Article +is_obsolete: true +consider: EDAM:0000971 ! Article [Term] id: EDAM:0000971 @@ -11536,8 +11188,8 @@ name: Article namespace: data def: "A body of scientific text, typically a full text article from a scientific journal." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002526 ! Article data - +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0003068 ! Literature data resources [Term] id: EDAM:0002857 @@ -11546,6 +11198,9 @@ namespace: data def: "Bibliographic data concerning scientific article(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002954 ! Article report +is_a: EDAM:0002337 ! Metadata +relationship: has_topic EDAM:0003068 ! Literature data resources + [Term] id: EDAM:0002954 @@ -11553,8 +11208,8 @@ name: Article report namespace: data def: "Data concerning or derived from the analysis of a scientific article." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002526 ! Article data -is_a: EDAM:0002018 ! Metadata and annotation +is_a: EDAM:0002048 ! Report + [Term] id: EDAM:0000972 @@ -11565,14 +11220,6 @@ comment: A text mining abstract will typically include an annotated a list of wo subset: data is_a: EDAM:0002954 ! Article report -[Term] -id: EDAM:0000969 -name: Text -namespace: data -def: "A report of free (essentially unformatted) text." [EDAM:EBI "EMBRACE definition"] -comment: This term can be used for any free-form comments and annotations. -subset: data -is_a: EDAM:0002527 ! Parameter or primitive [Term] @@ -11582,7 +11229,7 @@ namespace: data def: "An application report generated by the EMBOSS suite." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002018 ! Metadata and annotation +consider: EDAM:0002048 ! Report [Term] id: EDAM:0002176 @@ -11595,11 +11242,17 @@ is_obsolete: true [Term] id: EDAM:0002527 -alt_id: EDAM:0002029 -name: Parameter or primitive +name: Parameter namespace: data -def: "Data with a very simple structure, typically a simple numerical or string value that controls the operation of or is output by a tool." [EDAM:EBI "EMBRACE definition"] -subset: data +alt_id: EDAM:0002029 +alt_id: EDAM:0001773 +alt_id: EDAM:0000961 +def: "Typically a simple numerical or string value that controls the operation of a tool." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "Parameter or primitive" EXACT [] +synonym: "Tool parameter" EXACT [] +synonym: "Tool-specific parameter" EXACT [] +synonym: "Generic parameter" EXACT [] is_a: EDAM:0000006 ! Data @@ -11668,8 +11321,7 @@ namespace: data def: "Cartesian coordinate of an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Cartesian coordinate" EXACT [] -is_a: EDAM:0001917 ! General atomic property -! relationship: is_attribute_of EDAM:0000014 ! Atom +is_a: EDAM:0001917 ! Atomic property [Term] @@ -11680,7 +11332,7 @@ def: "The fraction of an atom type present at a site in a molecular structure." comment: The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. subset: data xref: WHATIF: PDBx_occupancy -is_a: EDAM:0001917 ! General atomic property +is_a: EDAM:0001917 ! Atomic property [Term] @@ -11690,7 +11342,7 @@ namespace: data def: "Isotropic B factor (atomic displacement parameter) for an atom from a PDB file." [EDAM:EBI "EMBRACE definition"] subset: data xref: WHATIF: PDBx_B_iso_or_equiv -is_a: EDAM:0001917 ! General atomic property +is_a: EDAM:0001917 ! Atomic property [Term] id: EDAM:0001744 @@ -11701,7 +11353,6 @@ subset: data synonym: "Cartesian x coordinate" EXACT [] xref: WHATIF: PDBx_Cartn_x is_a: EDAM:0001743 ! Atomic coordinate -! relationship: is_attribute_of EDAM:0000014 ! Atom ! _atom_site.Cartn_x in PDBML [Term] @@ -11713,7 +11364,6 @@ subset: data synonym: "Cartesian y coordinate" EXACT [] xref: WHATIF: PDBx_Cartn_y is_a: EDAM:0001743 ! Atomic coordinate -! relationship: is_attribute_of EDAM:0000014 ! Atom ! _atom_site.Cartn_y in PDBML [Term] @@ -11725,7 +11375,6 @@ subset: data synonym: "Cartesian z coordinate" EXACT [] xref: WHATIF: PDBx_Cartn_z is_a: EDAM:0001743 ! Atomic coordinate -! relationship: is_attribute_of EDAM:0000014 ! Atom ! _atom_site.Cartn_z in PDBML [Term] @@ -11734,8 +11383,7 @@ name: Molecular mass namespace: data def: "Mass of a molecule." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002050 ! General molecular property -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity +is_a: EDAM:0002050 ! Molecular property (general) [Term] id: EDAM:0000845 @@ -11743,8 +11391,7 @@ name: Molecular charge namespace: data def: "Net charge of a molecule." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002050 ! General molecular property -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity +is_a: EDAM:0002050 ! Molecular property (general) ! pdbx_formal_charge in PDBML @@ -11755,8 +11402,7 @@ namespace: data def: "A specification of a chemical structure." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Chemical structure specification" EXACT [] -is_a: EDAM:0002050 ! General molecular property -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity +is_a: EDAM:0002050 ! Molecular property (general) [Term] @@ -11766,8 +11412,7 @@ namespace: data def: "A QSAR quantitative descriptor (name-value pair) of chemical structure." [EDAM:EBI "EMBRACE definition"] comment: QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. subset: data -is_a: EDAM:0002050 ! General molecular property -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity +is_a: EDAM:0002050 ! Molecular property (general) [Term] id: EDAM:0002301 @@ -11776,7 +11421,6 @@ namespace: data def: "A specification of a chemical structure in SMILES format." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000846 ! Chemical formula -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity ! Many subtypes of the individual descriptors below (not included here) cover all types of protein properties. @@ -11788,7 +11432,6 @@ def: "A QSAR constitutional descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR constitutional descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity [Term] @@ -11799,7 +11442,6 @@ def: "A QSAR electronic descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR electronic descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity [Term] @@ -11810,7 +11452,6 @@ def: "A QSAR geometrical descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR geometrical descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity [Term] @@ -11821,7 +11462,6 @@ def: "A QSAR topological descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR topological descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity [Term] @@ -11832,7 +11472,6 @@ def: "A QSAR molecular descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR molecular descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity [Term] id: EDAM:0000848 @@ -11878,6 +11517,15 @@ is_a: EDAM:0002887 ! Sequence record (nucleic acid) id: EDAM:0000849 name: Sequence record namespace: data +alt_id: EDAM:0001220 +alt_id: EDAM:0001224 +alt_id: EDAM:0001225 +alt_id: EDAM:0001226 +alt_id: EDAM:0001227 +alt_id: EDAM:0001229 +alt_id: EDAM:0001230 +alt_id: EDAM:0001231 +alt_id: EDAM:0001232 def: "A molecular sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002044 ! Sequence @@ -11885,9 +11533,9 @@ is_a: EDAM:0002044 ! Sequence [Term] id: EDAM:0002886 -alt_id: EDAM:0001222 name: Sequence record (protein) namespace: data +alt_id: EDAM:0001222 def: "A protein sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein sequence record" EXACT [] @@ -11896,9 +11544,9 @@ is_a: EDAM:0002976 ! Protein sequence [Term] id: EDAM:0002887 -alt_id: EDAM:0001221 name: Sequence record (nucleic acid) namespace: data +alt_id: EDAM:0001221 def: "A nucleic acid sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Nucleic acid sequence record" EXACT [] @@ -11958,115 +11606,11 @@ is_a: EDAM:0002886 ! Sequence record (protein) id: EDAM:0002043 name: Sequence record lite namespace: data +alt_id: EDAM:0001223 def: "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000849 ! Sequence record -[Term] -id: EDAM:0001220 -name: General sequence record -namespace: data -def: "A report in a general sequence format (nucleotide or protein)." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000849 ! Sequence record - -[Term] -id: EDAM:0001223 -name: FASTA record -namespace: data -def: "A sequence record in FASTA format." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001929 ! FASTA sequence format - - -[Term] -id: EDAM:0001224 -name: RefSeq sequence record -namespace: data -def: "A record from RefSeq." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001958 ! refseqp - -[Term] -id: EDAM:0001225 -name: DDBJ nucleotide sequence record -namespace: data -def: "An entry from DDBJ." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001936 ! GenBank sequence format - - -[Term] -id: EDAM:0001226 -name: EMBL nucleotide sequence record -namespace: data -def: "An entry from EMBL." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001936 ! GenBank sequence format - -[Term] -id: EDAM:0001227 -name: GenBank nucleotide sequence record -namespace: data -def: "An entry from GenBank." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001936 ! GenBank sequence format - - -[Term] -id: EDAM:0001229 -name: dbEST nucleotide sequence record -namespace: data -def: "An entry from dbEST." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001936 ! GenBank sequence format - - -[Term] -id: EDAM:0001230 -name: UniProt protein sequence record -namespace: data -def: "An entry from UniProt/Swiss-Prot." [EDAM:EBI "EMBRACE definition"] -subset: data -synonym: "Swiss-Prot entry" EXACT [] -is_obsolete: true -consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001963 ! swiss sequence format - - -[Term] -id: EDAM:0001231 -name: TREMBL protein sequence record -namespace: data -def: "An entry from TREMBL." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001963 ! swiss sequence format - - -[Term] -id: EDAM:0001232 -name: PIR protein sequence record -namespace: data -def: "An entry from PIR." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001948 ! nbrf [Term] id: EDAM:0002173 @@ -12095,7 +11639,6 @@ namespace: data def: "Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000850 ! Sequence set -! is_a: EDAM:0002976 ! Protein sequence [Term] @@ -12116,8 +11659,8 @@ def: "A set of sequences that have been clustered or otherwise classified as bel comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information. subset: data is_a: EDAM:0000850 ! Sequence set -relationship: in_topic EDAM:0000164 ! Sequence clustering -relationship: in_topic EDAM:0000724 ! Protein families +relationship: has_topic EDAM:0003052 ! Sequence clusters and classification +relationship: has_topic EDAM:0000724 ! Protein families [Term] @@ -12147,7 +11690,7 @@ namespace: data def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001233 ! Sequence set (protein) - +relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0001766 @@ -12172,7 +11715,7 @@ consider: EDAM:0000850 ! Sequence set id: EDAM:0001239 name: Restriction digest namespace: data -def: "Restriction digest fragments from digesting a ucleotide sequence with restriction sites using a restriction endonuclease." [EDAM:EBI "EMBRACE definition"] +def: "Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease." [EDAM:EBI "EMBRACE definition"] subset: data xref: SO:0000412 is_a: EDAM:0001234 ! Sequence set (nucleic acid) @@ -12184,7 +11727,8 @@ name: Sequence set (polymorphic) namespace: data def: "A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001234 ! Sequence set (nucleic acid) +is_obsolete: true +consider: EDAM:0001234 ! Sequence set (nucleic acid) [Term] id: EDAM:0001240 @@ -12226,7 +11770,7 @@ consider: EDAM:0000850 ! Sequence set id: EDAM:0001244 name: primersearch primer pairs sequence record namespace: data -def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application,." [EDAM:EBI "EMBRACE definition"] +def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set @@ -12281,7 +11825,8 @@ name: Gene cluster namespace: data def: "A cluster of similar genes." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001246 ! Sequence cluster (nucleic acid) +is_obsolete: true +consider: EDAM:0001246 ! Sequence cluster (nucleic acid) [Term] id: EDAM:0001253 @@ -12290,7 +11835,7 @@ namespace: data def: "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0000883 ! Sequence record lite +consider: EDAM:0002043 ! Sequence record lite consider: EDAM:0000855 ! Sequence metadata [Term] @@ -12307,28 +11852,34 @@ is_a: EDAM:0002955 ! Sequence report id: EDAM:0001255 name: Sequence features namespace: data +alt_id: EDAM:0001271 +alt_id: EDAM:0001275 def: "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence." [EDAM:EBI "EMBRACE definition"] +comment: This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. subset: data +synonym: "Sequence features report" EXACT [] +synonym: "General sequence features" EXACT [] is_a: EDAM:0002955 ! Sequence report + [Term] id: EDAM:0002914 name: Sequence features metadata namespace: data -def: "Metadata on sequence featutures." [EDAM:EBI "EMBRACE definition"] +def: "Metadata on sequence features." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000855 ! Sequence metadata -! is_a: EDAM:0002955 ! Sequence report [Term] id: EDAM:0001020 name: Sequence feature key namespace: data -def: "Typically one of the EMBL or Swiss-Prot sequence feature keys." [EDAM:EBI "EMBRACE definition"] +def: "The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key." [EDAM:EBI "EMBRACE definition"] comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. subset: data synonym: "Sequence feature type" EXACT [] +synonym: "Sequence feature method" EXACT [] is_a: EDAM:0002914 ! Sequence feature metadata @@ -12361,13 +11912,13 @@ subset: data synonym: "Linkage map" EXACT [] xref: Moby:GeneticMap is_a: EDAM:0001274 ! Map -relationship: in_topic EDAM:0000796 ! Genetic mapping and linkage +relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0001283 -alt_id: EDAM:0001287 name: Cytogenetic map namespace: data +alt_id: EDAM:0001287 def: "A map showing banding patterns derived from direct observation of a stained chromosome." [EDAM:EBI "EMBRACE definition"] comment: This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. subset: data @@ -12391,7 +11942,7 @@ is_a: EDAM:0001280 ! Physical map id: EDAM:0001279 name: Sequence map namespace: data -def: "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measuresd in base pairs." [EDAM:EBI "EMBRACE definition"] +def: "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs." [EDAM:EBI "EMBRACE definition"] comment: A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. subset: data is_a: EDAM:0001280 ! Physical map @@ -12504,30 +12055,66 @@ consider: EDAM:0000912 ! Nucleic acid property [Term] id: EDAM:0001259 -name: Sequence property (complexity) +name: Sequence complexity namespace: data def: "A report on sequence complexity, for example low-complexity or repeat regions in sequences." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Sequence property (complexity)" EXACT [] is_a: EDAM:0001254 ! Sequence property [Term] id: EDAM:0001260 -name: Sequence property (ambiguity) +name: Sequence ambiguity namespace: data def: "A report on ambiguity in molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Sequence property (ambiguity)" EXACT [] is_a: EDAM:0001254 ! Sequence property [Term] id: EDAM:0001261 -name: Sequence property (composition) +name: Sequence composition namespace: data def: "A report (typically a table) on character or word composition / frequency of a molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Sequence property (composition)" EXACT [] is_a: EDAM:0001254 ! Sequence property + +[Term] +id: EDAM:0003119 +name: Sequence features (compositionally-biased regions) +namespace: data +def: "A report of regions in a molecular sequence that are biased to certain characters." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001261 ! Sequence composition + + + + +[Term] +id: EDAM:0003085 +name: Protein sequence composition +namespace: data +def: "A report (typically a table) on character or word composition / frequency of protein sequence(s)." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "Sequence property (protein composition)" EXACT [] +is_a: EDAM:0001261 ! Sequence composition + +[Term] +id: EDAM:0003086 +name: Nucleic acid sequence composition +namespace: data +def: "A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s)." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "Sequence property (nucleic acid composition)" EXACT [] +is_a: EDAM:0001261 ! Sequence composition +is_a: EDAM:0000912 ! Nucleic acid property + + + [Term] id: EDAM:0001262 name: Peptide molecular weight hits @@ -12542,7 +12129,7 @@ name: Sequence composition (base position variability) namespace: data def: "Report on or plot of third base position variability in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001261 ! Sequence property (composition) +is_a: EDAM:0003086 ! Nucleic acid sequence composition [Term] @@ -12552,7 +12139,7 @@ namespace: data def: "Word composition data for a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0001268 ! Sequence composition (amino acid words) +consider: EDAM:0001268 ! Amino acid word frequencies consider: EDAM:0001266 ! Sequence composition (base words) [Term] @@ -12562,7 +12149,7 @@ namespace: data def: "A table of character or word composition / frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0001261 ! Sequence property (composition) +consider: EDAM:0001261 ! Sequence composition [Term] id: EDAM:0002166 @@ -12570,8 +12157,7 @@ name: Sequence composition plot namespace: data def: "A plot of character or word composition / frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001261 ! Sequence property (composition) -is_a: EDAM:0002969 ! Sequence image or plot +is_a: EDAM:0001261 ! Sequence composition [Term] id: EDAM:0001265 @@ -12579,17 +12165,18 @@ name: Sequence composition (base frequencies) namespace: data def: "A table of base frequencies of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001261 ! Sequence property (composition) -is_a: EDAM:0000912 ! Nucleic acid property +is_a: EDAM:0003086 ! Nucleic acid sequence composition + [Term] id: EDAM:0001267 -name: Sequence composition (amino acid frequencies) +name: Amino acid frequencies namespace: data def: "A table of amino acid frequencies of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001261 ! Sequence property (composition) -is_a: EDAM:0000897 ! Protein property +synonym: "Sequence composition (amino acid frequencies)" EXACT [] +is_a: EDAM:0003085 ! Protein sequence composition + [Term] id: EDAM:0001266 @@ -12597,16 +12184,18 @@ name: Sequence composition (base words) namespace: data def: "A table of word composition of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001261 ! Sequence property (composition) +is_a: EDAM:0003086 ! Nucleic acid sequence composition [Term] id: EDAM:0001268 -name: Sequence composition (amino acid words) +name: Amino acid word frequencies namespace: data def: "A table of amino acid word composition of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001261 ! Sequence property (composition) +synonym: "Sequence composition (amino acid words)" EXACT [] +is_a: EDAM:0003085 ! Protein sequence composition + [Term] @@ -12630,63 +12219,115 @@ synonym: "Genome track" EXACT [] synonym: "Genomic track" EXACT [] synonym: "Genome-browser track" EXACT [] synonym: "Genome annotation track" EXACT [] -is_a: EDAM:0001270 ! Feature table +is_a: EDAM:0001255 ! Sequence features [Term] id: EDAM:0001270 -name: Feature table +name: Sequence feature table namespace: data def: "Annotation of positional sequence features, organized into a standard feature table." [EDAM:EBI "EMBRACE definition"] +synonym: "Feature table" EXACT [] +is_a: EDAM:0001255 ! Sequence feature annotation + + +[Term] +id: EDAM:0001276 +name: Nucleic acid features +namespace: data +alt_id: EDAM:0001273 +def: "Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence)." [EDAM:EBI "EMBRACE definition"] +comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. subset: data +synonym: "Nucleic acid feature table" EXACT [] +synonym: "Feature table (nucleic acid)" EXACT [] +is_a: EDAM:0002084 ! Nucleic acid report is_a: EDAM:0001255 ! Sequence features [Term] -id: EDAM:0001271 -name: Sequence features report +id: EDAM:0003139 +name: Nucleic acid features (STS) namespace: data -def: "Annotation of positional sequence features that are not organized into a standard feature table, but which are in a human-readable report." [EDAM:EBI "EMBRACE definition"] -comment: Is a source of sequence feature table information although internal conversion would be required. +def: "A report on sequence tagged sites (STS) in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] +comment: Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. subset: data -is_obsolete: true -consider: EDAM:0001255 ! Sequence features +is_a: EDAM:0001276 ! Nucleic acid features [Term] -id: EDAM:0001272 -name: Feature table (protein) +id: EDAM:0003122 +name: Nucleic acid features (difference and change) namespace: data -def: "Protein sequence feature annotation in any known sequence feature table format." [EDAM:EBI "EMBRACE definition"] +def: "A report on features in a nucleic acid sequence that indicate changes to or differences between sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001270 ! Feature table -is_a: EDAM:0001277 ! Protein features +is_a: EDAM:0001276 ! Nucleic acid features [Term] -id: EDAM:0001273 -name: Feature table (nucleic acid) +id: EDAM:0003123 +name: Nucleic acid features (expression signal) namespace: data -def: "Nucleotide sequence feature annotation in any known sequence feature table format." [EDAM:EBI "EMBRACE definition"] +def: "A report on regions within a nucleic acid sequence containing a signal that alters a biological function." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001270 ! Feature table is_a: EDAM:0001276 ! Nucleic acid features + [Term] -id: EDAM:0001275 -name: General sequence features +id: EDAM:0003125 +name: Nucleic acid features (binding) namespace: data -def: "General sequence feature annotation (positional features) that is applicable to a nucleotide or protein sequence." [EDAM:EBI "EMBRACE definition"] +def: "A report on regions of a nucleic acid sequence that bind some other molecule." [EDAM:EBI "EMBRACE definition"] +comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). subset: data -is_a: EDAM:0001255 ! Sequence features +is_a: EDAM:0001276 ! Nucleic acid features + [Term] -id: EDAM:0001276 -name: Nucleic acid features +id: EDAM:0003126 +name: Nucleic acid features (repeats) namespace: data -def: "Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence)." [EDAM:EBI "EMBRACE definition"] +def: "A report on repetitive elements within a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] +comment: This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. subset: data -is_a: EDAM:0002084 ! Nucleic acid report -is_a: EDAM:0001255 ! Sequence features +is_a: EDAM:0001299 ! Sequence features (repeats) +is_a: EDAM:0001276 ! Nucleic acid features + + +[Term] +id: EDAM:0003127 +name: Nucleic acid features (replication and recombination) +namespace: data +def: "A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination." [EDAM:EBI "EMBRACE definition"] +comment: This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. +subset: data +is_a: EDAM:0001276 ! Nucleic acid features + +[Term] +id: EDAM:0003128 +name: Nucleic acid features (structure) +namespace: data +def: "A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001276 ! Nucleic acid features + +[Term] +id: EDAM:0003132 +name: Nucleic acid features (d-loop) +namespace: data +def: "A report on displacement loops in a mitochondrial DNA sequence." [EDAM:EBI "EMBRACE definition"] +comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. +subset: data +is_a: EDAM:0003128 ! Nucleic acid features (structure) + +[Term] +id: EDAM:0003133 +name: Nucleic acid features (stem loop) +namespace: data +def: "A report on stem loops in a DNA sequence." [EDAM:EBI "EMBRACE definition"] +comment: A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. +subset: data +is_a: EDAM:0003128 ! Nucleic acid features (structure) + [Term] id: EDAM:0002882 @@ -12699,22 +12340,58 @@ consider: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0002883 -name: RNA features +name: Nucleic acid features (RNA features) namespace: data -def: "RNA sequence-specific feature annotation (not in a feature table)." [EDAM:EBI "EMBRACE definition"] +def: "Features concerning RNA or regions of DNA that encode an RNA molecule." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001276 ! Nucleic acid features +synonym: "RNA features" EXACT [] +is_a: EDAM:0001300 ! Nucleic acid features (gene structure) + +[Term] +id: EDAM:0003134 +name: Nucleic acid features (mRNA features) +namespace: data +def: "Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules." [EDAM:EBI "EMBRACE definition"] +comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). +subset: data +synonym: "mRNA features" EXACT [] +is_a: EDAM:0002883 ! Nucleic acid features (RNA features) + + +[Term] +id: EDAM:0003137 +name: Nucleic acid features (non-coding RNA) +namespace: data +def: "Features concerning non-coding or functional RNA molecules, including tRNA and rRNA." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "ncRNA features" EXACT [] +synonym: "Non-coding RNA features" EXACT [] +is_a: EDAM:0002883 ! Nucleic acid features (RNA features) + +[Term] +id: EDAM:0003138 +name: Nucleic acid features (transcriptional) +namespace: data +def: "Features concerning transcription of DNA into RNA including the regulation of transcription." [EDAM:EBI "EMBRACE definition"] +comment: This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. +subset: data +is_a: EDAM:0002883 ! Nucleic acid features (RNA features) + [Term] id: EDAM:0001277 name: Protein features namespace: data +alt_id: EDAM:0001272 def: "Protein sequence-specific feature annotation (positional features of a protein sequence)." [EDAM:EBI "EMBRACE definition"] +comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. subset: data +synonym: "Feature table (protein)" EXACT [] +synonym: "Protein feature table" EXACT [] is_a: EDAM:0001255 ! Sequence features is_a: EDAM:0000896 ! Protein report + [Term] id: EDAM:0001256 name: Sequence features (comparative) @@ -12722,7 +12399,8 @@ namespace: data def: "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data -is_a: EDAM:0001275 ! General sequence features +is_obsolete: true +consider: EDAM:0001255 ! Sequence features [Term] @@ -12730,18 +12408,38 @@ id: EDAM:0001298 name: Sequence features (motifs) namespace: data def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." [EDAM:EBI "EMBRACE definition"] -comment: Motifs typically correspond to functional regions +comment: Use this term if another, more specific term is not available. +subset: data +is_a: EDAM:0001255 ! Sequence features + +[Term] +id: EDAM:0003130 +name: Protein features (motifs) +namespace: data +def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." [EDAM:EBI "EMBRACE definition"] +comment: Use this term if another, more specific term is not available. +subset: data +is_a: EDAM:0001277 ! Protein features +is_a: EDAM:0001298 ! Sequence features (motifs) + +[Term] +id: EDAM:0003131 +name: Nucleic acid features (motifs) +namespace: data +def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] +comment: Use this term if another, more specific term is not available. subset: data -is_a: EDAM:0001275 ! General sequence features +is_a: EDAM:0001276 ! Nucleic acid features +is_a: EDAM:0001298 ! Sequence features (motifs) + [Term] id: EDAM:0000858 name: Database hits (secondary) namespace: data def: "A report of hits from a search of a protein secondary or domain database." [EDAM:EBI "EMBRACE definition"] -comment: Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. +comment: Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See terms under 'Protein features'. subset: data -is_a: EDAM:0000901 ! Protein features (domains) is_a: EDAM:0002080 ! Database hits @@ -12749,23 +12447,51 @@ is_a: EDAM:0002080 ! Database hits id: EDAM:0000901 name: Protein features (domains) namespace: data -def: "Summary of structural domains or folds in a protein or polypeptide chain." [EDAM:EBI "EMBRACE definition"] +def: "Summary of structural domains or 3D folds in a protein or polypeptide chain." [EDAM:EBI "EMBRACE definition"] comment: The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. subset: data synonym: "Protein domain assignment" EXACT [] +synonym: "Protein structural domains" EXACT [] is_a: EDAM:0001277 ! Protein features -! relationship: is_attribute_of EDAM:0000025 ! Polypeptide -relationship: in_topic EDAM:0000736 ! Protein domains +relationship: has_topic EDAM:0000736 ! Protein domains and folds + +[Term] +id: EDAM:0003118 +name: Protein features (topological domains) +namespace: data +def: "Summary of topological domains such as cytoplasmic regions in a protein." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "Protein topological domains" EXACT [] +is_a: EDAM:0001277 ! Protein features +relationship: has_topic EDAM:0000736 ! Protein domains and folds + + + + [Term] id: EDAM:0001299 name: Sequence features (repeats) namespace: data +alt_id: EDAM:0001282 def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] comment: The report might include derived data map such as classification, annotation, organization, periodicity etc. subset: data -is_a: EDAM:0001275 ! General sequence features +synonym: "Repeat sequence map" EXACT [] +is_a: EDAM:0001255 ! Sequence features + + +[Term] +id: EDAM:0003129 +name: Protein features (repeats) +namespace: data +def: "Location of short repetitive subsequences (repeat sequences) in a protein sequence." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001299 ! Sequence features (repeats) +is_a: EDAM:0001277 ! Protein features + + [Term] id: EDAM:0001281 @@ -12838,41 +12564,65 @@ is_obsolete: true consider: EDAM:0000901 ! Protein features (domains) [Term] -id: EDAM:0001282 -name: Repeat sequence map -namespace: data -def: "Image of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0001299 ! Sequence features (repeats) - -[Term] id: EDAM:0001300 -name: Nucleic acid features (gene structure) +name: Nucleic acid features (gene and transcript structure) namespace: data -def: "A report on predicted or actual gene structure and features such as promoters, coding regions, splice sites etc." [EDAM:EBI "EMBRACE definition"] +def: "A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene annotation (structure)" EXACT [] is_a: EDAM:0000916 ! Gene annotation is_a: EDAM:0001276 ! Nucleic acid features +[Term] +id: EDAM:0003140 +name: Nucleic acid features (immunoglobulin gene structure) +namespace: data +def: "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001300 ! Nucleic acid features (gene structure) + + + [Term] id: EDAM:0001301 -name: Nucleic acid features (transposons) +name: Nucleic acid features (mobile genetic elements) namespace: data -def: "A report on transposons, retrotransposons / retrotransposition signatures etc." [EDAM:EBI "EMBRACE definition"] +def: "A report on a region of a nucleic acid sequence containin mobile genetic elements." [EDAM:EBI "EMBRACE definition"] +comment: This includes transposons, Plasmids, Bacteriophage elements and Group II introns. subset: data +synonym: "Nucleic acid features (transposons)" EXACT [] is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0001302 -name: Nucleic acid features (PolyA signal) +name: Nucleic acid features (PolyA signal or site) namespace: data -def: "A report on polyA signals in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] +def: "A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript." [EDAM:EBI "EMBRACE definition"] +comment: A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. subset: data -is_a: EDAM:0001276 ! Nucleic acid features +synonym: "PolyA signal" EXACT [] +synonym: "PolyA site" EXACT [] +is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) + + + + +[Term] +id: EDAM:0003135 +name: Nucleic acid features (signal or transit peptide) +namespace: data +def: "A report on a coding sequence for a signal or transit peptide." [EDAM:EBI "EMBRACE definition"] +comment: A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. +subset: data +is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) + + + + + + [Term] id: EDAM:0001303 @@ -12880,16 +12630,15 @@ name: Nucleic acid features (quadruplexes) namespace: data def: "A report on quadruplex-forming motifs in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features - +is_a: EDAM:0003128 ! Nucleic acid features (structure) [Term] id: EDAM:0001304 -name: Sequence composition (CpG island and isochore) +name: Nucleic acid features (CpG island and isochore) namespace: data -def: "A report or plot of CpG rich regions in a nucleotide sequence, fractional GC content or variation of GC content, methylation status of CpG islands, isochores in a DNA sequence etc." [EDAM:EBI "EMBRACE definition"] +def: "A report or plot of CpG rich regions (isochores) in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001261 ! Sequence property (composition) +is_a: EDAM:0003138 ! Nucleic acid features (transcriptional) [Term] id: EDAM:0001305 @@ -12897,7 +12646,7 @@ name: Nucleic acid features (restriction sites) namespace: data def: "Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features +is_a: EDAM:0003125 ! Nucleic acid features (binding) [Term] id: EDAM:0001306 @@ -12905,15 +12654,18 @@ name: Nucleic acid features (nucleosome exclusion sequences) namespace: data def: "A report on nucleosome formation potential or exclusion sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features +is_a: EDAM:0003127 ! Nucleic acid features (replication and recombination) [Term] id: EDAM:0001307 name: Nucleic acid features (splice sites) namespace: data -def: "A report on splice sites in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0000915 +def: "A report on splice sites in a nucleotide sequence or alternative RNA splicing events." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features +synonym: "Nucleic acid report (RNA splice model)" EXACT [] +synonym: "Nucleic acid report (RNA splicing)" EXACT [] +is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) [Term] @@ -12922,7 +12674,7 @@ name: Nucleic acid features (matrix/scaffold attachment sites) namespace: data def: "A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features +is_a: EDAM:0003138 ! Nucleic acid features (transcriptional) [Term] @@ -12931,7 +12683,8 @@ name: Gene features (exonic splicing enhancer) namespace: data def: "A report on exonic splicing enhancers (ESE) in an exon." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002397 ! Gene features (exon) +is_obsolete: true +consider: EDAM:0002397 ! Nucleic acid features (exon) [Term] @@ -12940,7 +12693,8 @@ name: Nucleic acid features (microRNA) namespace: data def: "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features +is_a: EDAM:0003137 ! Nucleic acid features (non-coding RNA) +relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] id: EDAM:0002169 @@ -12948,7 +12702,8 @@ name: Nucleic acid features (siRNA) namespace: data def: "A report on siRNA duplexes in mRNA." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features +is_a: EDAM:0003137 ! Nucleic acid features (non-coding RNA) +relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] id: EDAM:0000922 @@ -12956,34 +12711,39 @@ name: Nucleic acid features (primers) namespace: data def: "Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001276 ! Nucleic acid features -relationship: in_topic EDAM:0000632 ! Molecular probes or primers +is_a: EDAM:0003127 ! Nucleic acid features (replication and recombination) +relationship: has_topic EDAM:0000632 ! Probes and primers [Term] id: EDAM:0001311 -name: Gene features (operon) +name: Nucleic acid features (operon) namespace: data def: "A report on operons (operators, promoters and genes) from a bacterial genome." [EDAM:EBI "EMBRACE definition"] comment: The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. subset: data +synonym: "Gene features (operon)" EXACT [] is_a: EDAM:0001300 ! Nucleic acid features (gene structure) - [Term] id: EDAM:0001312 name: Gene features (promoter) namespace: data def: "A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001300 ! Nucleic acid features (gene structure) +is_a: EDAM:0003138 ! Nucleic acid features (transcriptional) + [Term] id: EDAM:0001313 -name: Gene features (coding region) +name: Nucleic acid features (coding sequence) namespace: data -def: "A report or plot on protein-coding regions (CDS or exon) in a nucleotide sequences. Or translation initiation sites, protein coding genes, exon-intron structure, open reading frames etc." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0001317 +def: "A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001300 ! Nucleic acid features (gene structure) +synonym: "Gene features (coding sequence)" EXACT [] +synonym: "Gene features (coding region)" EXACT [] +synonym: "Gene annotation (translation)" EXACT [] +is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) [Term] id: EDAM:0001314 @@ -12991,7 +12751,8 @@ name: Gene features (SECIS element) namespace: data def: "A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001300 ! Nucleic acid features (gene structure) +is_obsolete: true +consider: EDAM:0001300 ! Nucleic acid features (gene structure) [Term] @@ -13001,32 +12762,26 @@ namespace: data def: "A report on the transcription factor binding sites (TFBS) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001312 ! Gene features (promoter) -relationship: in_topic EDAM:0000811 ! Transcription factor and binding site - +is_a: EDAM:0003125 ! Nucleic acid features (binding) +relationship: has_topic EDAM:0000749 ! Transcription factors and regulatory sites [Term] id: EDAM:0002397 -name: Gene features (exon) +name: Nucleic acid features (exon) namespace: data def: "An informative report on an exon in a nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001313 ! Gene features (coding region) +synonym: "Gene features (exon)" EXACT [] +is_a: EDAM:0001313 ! Nucleic acid features (coding sequence) [Term] id: EDAM:0002754 -name: Gene features (intron) +name: Nucleic acid features (intron) namespace: data def: "An informative report on an intron in a nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001313 ! Gene features (coding region) - -[Term] -id: EDAM:0001317 -name: Gene annotation (translation) -namespace: data -def: "A report on a nucleotide sequence with its coding regions and/or translation." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0000916 ! Gene annotation +synonym: "Gene features (intron)" EXACT [] +is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) [Term] @@ -13035,8 +12790,7 @@ name: Fickett testcode plot namespace: data def: "A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001317 ! Gene annotation (translation) -is_a: EDAM:0002969 ! Sequence image or plot +is_a: EDAM:0001313 ! Nucleic acid features (coding sequence) [Term] @@ -13046,15 +12800,18 @@ namespace: data def: "Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001305 ! Nucleic acid features (restriction sites) -is_a: EDAM:0002969 ! Sequence image or plot +is_a: EDAM:0001279 ! Sequence map +is_a: EDAM:0002969 ! Sequence image [Term] id: EDAM:0001321 name: Protein features (sites) namespace: data -def: "A report on predicted or actual key residue positions (sites) in a protein sequence, such as binding or functional sites." [EDAM:EBI "EMBRACE definition"] +def: "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites." [EDAM:EBI "EMBRACE definition"] +comment: Use this term for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. subset: data -is_a: EDAM:0001277 ! Protein features +is_obsolete: true +consider: EDAM:0001277 ! Protein features [Term] id: EDAM:0001322 @@ -13062,7 +12819,16 @@ name: Protein features (signal peptides) namespace: data def: "A report on the location of signal peptides or signal peptide cleavage sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001321 ! Protein features (sites) +is_a: EDAM:0001277 ! Protein features + +[Term] +id: EDAM:0003120 +name: Protein features (sequence variants) +namespace: data +def: "A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001277 ! Protein features + [Term] @@ -13071,33 +12837,37 @@ name: Protein features (cleavage sites) namespace: data def: "A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001321 ! Protein features (sites) +is_a: EDAM:0001277 ! Protein features +relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0001324 -name: Protein features (post-translation modification sites) +name: Protein features (post-translation modifications) namespace: data -def: "A report on post-translation modification sites in a protein sequence." [EDAM:EBI "EMBRACE definition"] +def: "A report on post-translation modifications in a protein sequence, typically describing the specific sites involved." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001321 ! Protein features (sites) +synonym: "Protein features (post-translation modification sites)" EXACT [] +synonym: "Post-translation modification" EXACT [] +is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001325 name: Protein features (active sites) namespace: data -def: "A report on catalytic residues (active site) of a protein." [EDAM:EBI "EMBRACE definition"] +def: "A report on catalytic residues (active site) of an enzyme." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001321 ! Protein features (sites) - +synonym: "Enzyme active site" EXACT [] +is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001326 name: Protein features (binding sites) namespace: data -def: "A report on ligand-binding (non-catalytic) residues of a protein." [EDAM:EBI "EMBRACE definition"] +def: "A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001321 ! Protein features (sites) +is_a: EDAM:0001277 ! Protein features + [Term] id: EDAM:0002989 @@ -13105,7 +12875,9 @@ name: Protein features (key folding sites) namespace: data def: "A report on key residues involved in protein folding." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001321 ! Protein features (sites) +is_a: EDAM:0001277 ! Protein features + + [Term] id: EDAM:0001327 @@ -13114,7 +12886,8 @@ namespace: data def: "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data." [EDAM:EBI "EMBRACE definition"] comment: Epitope mapping is commonly done during vaccine design. subset: data -is_a: EDAM:0001326 ! Protein features (binding sites) +is_obsolete: true +consider: EDAM:0001326 ! Protein features (binding sites) [Term] id: EDAM:0001328 @@ -13122,7 +12895,7 @@ name: Protein features (nucleic acid binding sites) namespace: data def: "A report on RNA and DNA-binding proteins and binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001326 ! Protein features (binding sites) +is_a: EDAM:0001277 ! Protein features [Term] @@ -13132,7 +12905,7 @@ namespace: data def: "A report on epitopes that bind to MHC class I molecules." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0001327 ! Protein features (epitopes) +consider: EDAM:0001326 ! Protein features (binding sites) [Term] @@ -13142,7 +12915,7 @@ namespace: data def: "A report on predicted epitopes that bind to MHC class II molecules." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0001327 ! Protein features (epitopes) +consider: EDAM:0001326 ! Protein features (binding sites) [Term] id: EDAM:0001331 @@ -13151,13 +12924,14 @@ namespace: data def: "A report or plot of PEST sites in a protein sequence." [EDAM:EBI "EMBRACE definition"] comment: 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. subset: data -is_a: EDAM:0001323 ! Protein features (cleavage sites) +is_obsolete: true +consider: EDAM:0001323 ! Protein features (cleavage sites) [Term] id: EDAM:0000857 name: Database hits (sequence) namespace: data -def: "A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignmnets for the hits." [EDAM:EBI "EMBRACE definition"] +def: "A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits." [EDAM:EBI "EMBRACE definition"] comment: The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. subset: data is_a: EDAM:0002080 ! Database hits @@ -13225,7 +12999,7 @@ name: Regular expression namespace: data def: "Regular expression pattern." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter or primitive +is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0002070 @@ -13234,21 +13008,19 @@ namespace: data def: "A nucleotide sequence motif." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001353 ! Sequence motif -is_a: EDAM:0002525 ! Nucleic acid data [Term] id: EDAM:0002071 name: Sequence motif (protein) namespace: data -def: "A protein sequence motif." [EDAM:EBI "EMBRACE definition"] +def: "An amino acid sequence motif." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001353 ! Sequence motif -is_a: EDAM:0002524 ! Protein data [Term] id: EDAM:0002854 -name: Position matrix +name: Position-specific scoring matrix namespace: data def: "A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: data @@ -13263,7 +13035,7 @@ namespace: data def: "A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "PFM" EXACT [] -is_a: EDAM:0002854 ! Position matrix +is_a: EDAM:0002854 ! Position-specific scoring matrix [Term] @@ -13274,7 +13046,7 @@ def: "A profile (typically representing a sequence alignment) that is weighted m comment: Contributions of individual sequences to the matrix might be uneven (weighted). subset: data synonym: "PWM" EXACT [] -is_a: EDAM:0002854 ! Position matrix +is_a: EDAM:0002854 ! Position-specific scoring matrix [Term] @@ -13284,7 +13056,7 @@ namespace: data def: "A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "ICM" EXACT [] -is_a: EDAM:0002854 ! Position matrix +is_a: EDAM:0002854 ! Position-specific scoring matrix [Term] @@ -13302,7 +13074,7 @@ name: Fingerprint namespace: data def: "One or more fingerprints (sequence classifiers) as used in the PRINTS database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002854 ! Position matrix +is_a: EDAM:0002854 ! Position-specific scoring matrix [Term] @@ -13406,11 +13178,12 @@ is_a: EDAM:0001376 ! Protein site signature [Term] id: EDAM:0000861 -name: Sequence word alignment +name: Sequence alignment (words) namespace: data def: "Alignment of exact matches between subsequences (words) within two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001916 ! Alignment +synonym: "Sequence word alignment" EXACT [] +is_a: EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0000863 @@ -13419,7 +13192,7 @@ namespace: data def: "Alignment of multiple molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001916 ! Alignment -relationship: in_topic EDAM:0000182 ! Sequence alignment +relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000868 @@ -13456,7 +13229,7 @@ namespace: data def: "Alignment of the (1D representations of) secondary structure of two or more proteins." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002366 ! Secondary structure alignment -is_a: EDAM:0000896 ! Protein report +is_a: EDAM:0003154 ! Protein alignment [Term] id: EDAM:0000881 @@ -13476,7 +13249,7 @@ def: "Alignment (superimposition) of molecular tertiary (3D) structures." [EDAM: comment: A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. subset: data is_a: EDAM:0001916 ! Alignment -relationship: in_topic EDAM:0000183 ! Structure alignment +relationship: has_topic EDAM:0000183 ! Structure alignment [Term] id: EDAM:0000890 @@ -13539,7 +13312,7 @@ namespace: data def: "Alignment of multiple protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000863 ! Sequence alignment -is_a: EDAM:0000896 ! Protein report +is_a: EDAM:0003154 ! Protein alignment [Term] @@ -13590,7 +13363,7 @@ consider: EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0001388 -name: Pairwise hybrid sequence alignment +name: Hybrid sequence alignment (pair) namespace: data def: "Alignment of exactly two molecular sequences of different types." [EDAM:EBI "EMBRACE definition"] subset: data @@ -13627,17 +13400,16 @@ is_a: EDAM:0000869 ! Sequence-profile alignment [Term] id: EDAM:0001479 -name: Tertiary structure alignment (pair) +name: Structure alignment (pair) namespace: data def: "Alignment (superimposition) of exactly two molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0000886 ! Structure alignment +is_a: EDAM:0000886 ! Structure alignment [Term] id: EDAM:0001480 -name: Tertiary structure alignment (multiple) +name: Structure alignment (multiple) namespace: data def: "Alignment (superimposition) of more than two molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data @@ -13652,7 +13424,7 @@ namespace: data def: "Alignment (superimposition) of protein tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000886 ! Structure alignment -is_a: EDAM:0000896 ! Protein report +is_a: EDAM:0003154 ! Protein alignment [Term] id: EDAM:0001482 @@ -13665,12 +13437,12 @@ is_a: EDAM:0002084 ! Nucleic acid report [Term] id: EDAM:0001483 -name: Pairwise protein tertiary structure alignment +name: Structure alignment (protein pair) namespace: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001481 ! Structure alignment (protein) +is_a: EDAM:0001481 ! Structure alignment (protein) +is_a: EDAM:0001479 ! Structure alignment (pair) [Term] id: EDAM:0001484 @@ -13741,12 +13513,12 @@ consider: EDAM:0001486 ! Structure alignment (protein C-alpha atoms) [Term] id: EDAM:0001491 -name: Pairwise nucleic acid tertiary structure alignment +name: Structure alignment (nucleic acid pair) namespace: data def: "Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data -is_obsolete: true -consider: EDAM:0001482 ! Structure alignment (nucleic acid) +is_a: EDAM:0001482 ! Structure alignment (nucleic acid) +is_a: EDAM:0001479 ! Structure alignment (pair) [Term] id: EDAM:0001492 @@ -13773,6 +13545,7 @@ namespace: data def: "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000867 ! Sequence alignment report +is_a: EDAM:0002337 ! Metadata [Term] @@ -13815,11 +13588,12 @@ consider: EDAM:0000871 ! Phylogenetic character data [Term] id: EDAM:0001444 -name: Phylogenetic report (character contrasts) +name: Phylogenetic character contrasts namespace: data def: "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic report +synonym: "Phylogenetic report (character contrasts)" EXACT [] +is_a: EDAM:0002523 ! Phylogenetic raw data [Term] id: EDAM:0001426 @@ -13857,23 +13631,25 @@ name: Phylogenetic character weights namespace: data def: "Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002523 ! Phylogenetic data +is_a: EDAM:0002523 ! Phylogenetic raw data [Term] id: EDAM:0001428 -name: Phylogenetic report (cliques) +name: Phylogenetic character cliques namespace: data def: "One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic report +synonym: "Phylogenetic report (cliques)" EXACT [] +is_a: EDAM:0002523 ! Phylogenetic raw data [Term] id: EDAM:0001429 -name: Phylogenetic report (invariants) +name: Phylogenetic invariants namespace: data def: "Phylogenetic invariants data for testing alternative tree topologies." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic report +synonym: "Phylogenetic report (invariants)" EXACT [] +is_a: EDAM:0002523 ! Phylogenetic raw data [Term] @@ -13887,47 +13663,49 @@ consider: EDAM:0000872 ! Phylogenetic tree [Term] id: EDAM:0001439 -name: Phylogenetic report (DNA substitution model) +name: DNA substitution model namespace: data def: "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic report +synonym: "Sequence alignment report (DNA substitution model)" EXACT [] +synonym: "Phylogenetic tree report (DNA substitution model)" EXACT [] +is_a: EDAM:0001438 ! Phylogenetic tree report is_a: EDAM:0000950 ! Biological model is_a: EDAM:0000867 ! Sequence alignment report [Term] id: EDAM:0001440 -name: Phylogenetic report (tree shape) +name: Phylogenetic tree report (tree shape) namespace: data def: "Data about the shape of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic report +is_a: EDAM:0001438 ! Phylogenetic tree report [Term] id: EDAM:0001441 -name: Phylogenetic report (tree evaluation) +name: Phylogenetic tree report (tree evaluation) namespace: data def: "Data on the confidence of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic report +is_a: EDAM:0001438 ! Phylogenetic tree report [Term] id: EDAM:0001442 -name: Phylogenetic report (tree distances) +name: Phylogenetic tree report (tree distances) namespace: data def: "Distances, such as Branch Score distance, between two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic report +is_a: EDAM:0001438 ! Phylogenetic tree report [Term] id: EDAM:0001443 -name: Phylogenetic report (tree stratigraphic) +name: Phylogenetic tree report (tree stratigraphic) namespace: data def: "Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001438 ! Phylogenetic report +is_a: EDAM:0001438 ! Phylogenetic tree report [Term] id: EDAM:0001446 @@ -13965,7 +13743,7 @@ namespace: data def: "Matrix of integer or floating point numbers for amino acid comparison." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Amino acid substitution matrix" EXACT [] -is_a: EDAM:0002016 ! Amino acid data +is_a: EDAM:0002016 ! Amino acid property is_a: EDAM:0000874 ! Comparison matrix [Term] @@ -14020,21 +13798,20 @@ def: "Data on inter-atomic or inter-residue contacts, distances and interactions subset: data synonym: "Residue interaction data" EXACT [] synonym: "Atom interaction data" EXACT [] -is_a: EDAM:0002599 ! Molecular interaction data -is_a: EDAM:0001537 ! Protein structure report -is_a: EDAM:0000897 ! Protein property -! relationship: is_attribute_of EDAM:0000008 ! Protein residue group - +is_a: EDAM:0002599 ! Molecular interaction +is_a: EDAM:0000906 ! Protein interaction +relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis [Term] id: EDAM:0001543 -name: Protein structure report (surface) +name: Protein surface report namespace: data def: "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data +synonym: "Protein structure report (surface)" EXACT [] is_a: EDAM:0001542 ! Protein solvent accessibility -! relationship: is_attribute_of EDAM:0000008 ! Protein +is_a: EDAM:0001537 ! Protein structure report [Term] @@ -14053,24 +13830,29 @@ name: Secondary structure namespace: data def: "The secondary structure assignment (predicted or real) of a nucleic acid or protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002973 ! Secondary structure data +is_a: EDAM:0003031 ! Core data + [Term] id: EDAM:0000877 -name: Protein structure report (super-secondary) +name: Protein features (super-secondary) namespace: data def: "A report of predicted or actual super-secondary structure of protein sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. subset: data +synonym: "Protein structure report (super-secondary)" EXACT [] +is_a: EDAM:0001277 ! Protein features is_a: EDAM:0001537 ! Protein structure report - [Term] id: EDAM:0000902 -name: Protein structure report (architecture) +name: Protein architecture report namespace: data def: "An informative report on architecture (spatial arrangement of secondary structure) of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Protein structure report (architecture)" EXACT [] +synonym: "Protein property (architecture)" EXACT [] +is_a: EDAM:0000897 ! Protein property is_a: EDAM:0001537 ! Protein structure report [Term] @@ -14080,9 +13862,8 @@ namespace: data def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [EDAM:EBI "EMBRACE definition"] comment: The coordinate data may be predicted or real. subset: data -is_a: EDAM:0002053 ! Structural data -relationship: in_topic EDAM:0000081 ! Structure -! relationship: is_attribute_of EDAM:0000013 ! Molecular entity +relationship: has_topic EDAM:0000081 ! Structure analysis +is_a: EDAM:0003031 ! Core data [Term] @@ -14102,7 +13883,6 @@ namespace: data def: "A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001540 ! Protein residue interactions -! relationship: is_attribute_of EDAM:0000008 ! Protein residue group [Term] @@ -14112,7 +13892,6 @@ namespace: data def: "An amino acid residue contact map for a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001540 ! Protein residue interactions -! relationship: is_attribute_of EDAM:0000008 ! Protein residue group [Term] id: EDAM:0001548 @@ -14121,7 +13900,6 @@ namespace: data def: "Report on clusters of contacting residues in protein structures such as a key structural residue network." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001540 ! Protein residue interactions -! relationship: is_attribute_of EDAM:0000008 ! Protein residue group [Term] id: EDAM:0001549 @@ -14130,17 +13908,16 @@ namespace: data def: "Patterns of hydrogen bonding in protein structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001540 ! Protein residue interactions -! relationship: is_attribute_of EDAM:0000008 ! Protein residue group [Term] id: EDAM:0001550 -name: Protein non-canonical interactions report +name: Protein non-canonical interactions namespace: data def: "Non-canonical atomic interactions in protein structures." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Protein non-canonical interactions report" EXACT [] is_a: EDAM:0001540 ! Protein residue interactions -is_a: EDAM:0001539 ! Protein structure report (quality evaluation) -! relationship: is_attribute_of EDAM:0000008 ! Protein residue group +is_a: EDAM:0001539 ! Protein structural quality report [Term] id: EDAM:0001542 @@ -14150,20 +13927,18 @@ def: "Data on the solvent accessible or buried surface area of a protein structu comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This term covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. subset: data is_a: EDAM:0001540 ! Protein residue interactions -! relationship: is_attribute_of EDAM:0000008 ! Protein [Term] id: EDAM:0000876 name: Protein features (secondary structure) namespace: data -def: "The secondary structure assignment (predicted or real) of a protein." [EDAM:EBI "EMBRACE definition"] -comment: The location and size of the secondary structure elements and intervening loop regions is typically given. +def: "Secondary structure assignment (predicted or real) of a protein." [EDAM:EBI "EMBRACE definition"] +comment: The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). subset: data synonym: "Protein secondary structure" EXACT [] is_a: EDAM:0002081 ! Secondary structure is_a: EDAM:0001277 ! Protein features -! relationship: is_attribute_of EDAM:0000025 ! Polypeptide -relationship: in_topic EDAM:0000694 ! Protein secondary structure +relationship: has_topic EDAM:0000694 ! Protein secondary structure [Term] @@ -14175,19 +13950,20 @@ comment: This includes thermodynamically stable or evolutionarily conserved stru subset: data xref: Moby:RNAStructML is_a: EDAM:0002081 ! Secondary structure -relationship: in_topic EDAM:0000697 ! RNA structure and alignment +relationship: has_topic EDAM:0000697 ! RNA structure and alignment [Term] id: EDAM:0001456 -name: Protein report (membrane protein) +name: Protein features (membrane regions) namespace: data -def: "An informative report on a membrane protein, typically describing physicochemical properties of the secondary structure elements." [EDAM:EBI "EMBRACE definition"] +def: "An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." [EDAM:EBI "EMBRACE definition"] comment: This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. subset: data synonym: "Transmembrane region report" EXACT [] -is_a: EDAM:0000896 ! Protein report -! relationship: is_attribute_of EDAM:0000040 ! Transmembrane protein +synonym: "Intramembrane region report" EXACT [] +synonym: "Protein report (membrane protein)" EXACT [] +is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001755 @@ -14198,7 +13974,6 @@ comment: This is a broad data type and is used a placeholder for other, more spe subset: data synonym: "Atom data" EXACT [] is_a: EDAM:0001460 ! Protein structure -! relationship: is_attribute_of EDAM:0000014 ! Atom [Term] id: EDAM:0001756 @@ -14209,7 +13984,6 @@ comment: This is a broad data type and is used a placeholder for other, more spe subset: data synonym: "Residue" EXACT [] is_a: EDAM:0001460 ! Protein structure -! relationship: is_attribute_of EDAM:0000064 ! Protein residue [Term] id: EDAM:0001459 @@ -14218,9 +13992,7 @@ namespace: data def: "3D coordinate and associated data for a nucleic acid tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000883 ! Structure -is_a: EDAM:0002525 ! Nucleic acid data -! relationship: is_attribute_of EDAM:0000024 ! Nucleic acid -relationship: in_topic EDAM:0000097 ! Nucleic acid structure +relationship: has_topic EDAM:0000097 ! Nucleic acid structure analysis [Term] @@ -14230,13 +14002,8 @@ namespace: data def: "3D coordinate and associated data for a protein tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000883 ! Structure -is_a: EDAM:0002524 ! Protein data -! relationship: is_attribute_of EDAM:0000065 ! Protein domain -! relationship: is_attribute_of EDAM:0000025 ! Polypeptide -! relationship: is_attribute_of EDAM:0000044 ! Protein-protein complex -! relationship: is_attribute_of EDAM:0000037 ! Protein -relationship: in_topic EDAM:0002814 ! Protein structure -relationship: in_topic EDAM:0000698 ! Protein tertiary structure +relationship: has_topic EDAM:0002814 ! Protein structure analysis +relationship: has_topic EDAM:0000698 ! Protein tertiary structure [Term] @@ -14244,7 +14011,7 @@ id: EDAM:0001461 name: Protein-ligand complex namespace: data def: "The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule." [EDAM:EBI "EMBRACE definition"] -comment: This includes interactions of proteins with atoms, ions and small molecules or macromoluleces such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. +comment: This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. subset: data is_a: EDAM:0001460 ! Protein structure @@ -14256,10 +14023,8 @@ namespace: data def: "3D coordinate and associated data for a carbohydrate (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000883 ! Structure -! relationship: is_attribute_of EDAM:0000026 ! Polysaccharide -! relationship: is_attribute_of EDAM:0000023 ! Monosaccharide -relationship: in_topic EDAM:0000152 ! Carbohydrates -relationship: in_topic EDAM:0000153 ! Lipids +relationship: has_topic EDAM:0000152 ! Carbohydrates +relationship: has_topic EDAM:0000153 ! Lipids [Term] id: EDAM:0002850 @@ -14276,8 +14041,7 @@ namespace: data def: "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000883 ! Structure -is_a: EDAM:0002601 ! Small molecule data -relationship: in_topic EDAM:0000154 ! Small molecules +relationship: has_topic EDAM:0000154 ! Small molecules [Term] id: EDAM:0002851 @@ -14286,7 +14050,6 @@ namespace: data def: "3D coordinate and associated data for the (3D) structure of a drug." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001463 ! Small molecule structure -! relationship: is_attribute_of EDAM:0000020 ! Drug [Term] id: EDAM:0002852 @@ -14295,7 +14058,6 @@ namespace: data def: "3D coordinate and associated data for the (3D) structure of a toxin." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001463 ! Small molecule structure -! relationship: is_attribute_of EDAM:0002577 ! Toxin [Term] @@ -14305,7 +14067,6 @@ namespace: data def: "3D coordinate and associated data for a DNA tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001459 ! Nucleic acid structure -! relationship: is_attribute_of EDAM:0000028 ! DNA [Term] id: EDAM:0001465 @@ -14314,8 +14075,7 @@ namespace: data def: "3D coordinate and associated data for an RNA tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001459 ! Nucleic acid structure -! relationship: is_attribute_of EDAM:0000029 ! RNA -relationship: in_topic EDAM:0000697 ! RNA structure and alignment +relationship: has_topic EDAM:0000697 ! RNA structure and alignment [Term] @@ -14325,7 +14085,6 @@ namespace: data def: "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001465 ! RNA structure -! relationship: is_attribute_of EDAM:0000029 ! RNA [Term] id: EDAM:0001467 @@ -14334,7 +14093,6 @@ namespace: data def: "3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001460 ! Protein structure -! relationship: is_attribute_of EDAM:0000025 ! Polypeptide [Term] id: EDAM:0001468 @@ -14343,26 +14101,23 @@ namespace: data def: "3D coordinate and associated data for the tertiary (3D) structure of a protein domain." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001460 ! Protein structure -! relationship: is_attribute_of EDAM:0000065 ! Protein domain -relationship: in_topic EDAM:0000736 ! Protein domains +relationship: has_topic EDAM:0000736 ! Protein domains and folds [Term] id: EDAM:0002877 name: Protein complex namespace: data -def: "3D coordinate and associated data for a multiprotein complex; two or more polypeptides chains in a stable, functional association with one another." [EDAM:EBI "EMBRACE definition"] +def: "3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001460 ! Protein structure -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0002878 name: Protein structural motif namespace: data -def: "3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but tpyically those forming a feature with a structural or functional role." [EDAM:EBI "EMBRACE definition"] +def: "3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001460 ! Protein structure -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001469 @@ -14390,7 +14145,6 @@ subset: data is_obsolete: true consider: EDAM:0001467 ! Protein chain consider: EDAM:0001469 ! Protein structure (all atoms) -! relationship: is_attribute_of EDAM:0000025 ! Polypeptide [Term] id: EDAM:0001472 @@ -14402,7 +14156,6 @@ subset: data is_obsolete: true consider: EDAM:0001467 ! Protein chain consider: EDAM:0001470 ! Protein structure (C-alpha atoms) -! relationship: is_attribute_of EDAM:0000025 ! Polypeptide [Term] id: EDAM:0001473 @@ -14413,7 +14166,6 @@ subset: data is_obsolete: true consider: EDAM:0001468 ! Protein domain consider: EDAM:0001469 ! Protein structure (all atoms) -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001474 @@ -14425,7 +14177,6 @@ subset: data is_obsolete: true consider: EDAM:0001468 ! Protein domain consider: EDAM:0001470 ! Protein structure (C-alpha atoms) -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] @@ -14454,8 +14205,9 @@ name: Amino acid annotation namespace: data def: "An informative report about a specific amino acid." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002016 ! Amino acid data -is_a: EDAM:0000962 ! Small molecule report +is_a: EDAM:0002016 ! Amino acid property +is_a: EDAM:0000962 ! Small molecule annotation + [Term] @@ -14464,7 +14216,8 @@ name: Amino acid index namespace: data def: "A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002016 ! Amino acid data +is_a: EDAM:0002016 ! Amino acid property +is_a: EDAM:0002082 ! Matrix [Term] id: EDAM:0001503 @@ -14472,7 +14225,7 @@ name: Amino acid pair-wise contact potentials namespace: data def: "Statistical protein contact potentials." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002016 ! Amino acid data +is_a: EDAM:0002016 ! Amino acid property [Term] id: EDAM:0001502 @@ -14518,13 +14271,14 @@ is_a: EDAM:0001501 ! Amino acid index [Term] id: EDAM:0001509 -name: Protein report (enzyme) +name: Enzyme property namespace: data def: "An informative report on a specific enzyme." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Enzyme report" EXACT [] -is_a: EDAM:0000896 ! Protein report -relationship: in_topic EDAM:0000821 ! Enzymes +synonym: "Protein report (enzyme)" EXACT [] +is_a: EDAM:0000897 ! Protein property +relationship: has_topic EDAM:0000821 ! Enzymes and reactions [Term] id: EDAM:0001776 @@ -14533,33 +14287,22 @@ namespace: data def: "Report on general functional properties of specific protein(s)." [EDAM:EBI "EMBRACE definition"] comment: For properties that can be mapped to a sequence, use 'Sequence report' instead. subset: data -is_a: EDAM:0000896 ! Protein report - +is_obsolete: true +consider: EDAM:0000896 ! Protein report -[Term] -id: EDAM:0002377 -name: Protein structure report (domain) -namespace: data -def: "An informative report about a specific protein domain." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0001537 ! Protein structure report -[Term] -id: EDAM:0002712 -name: Protein structure report (protein complex) -namespace: data -def: "An informative report about a specific protein complex (of multiple polypeptide chains)." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0001537 ! Protein structure report [Term] id: EDAM:0002722 -name: Protein structure report (disordered protein) +name: Protein features (disordered structure) namespace: data -def: "An informative report about a disordered protein." [EDAM:EBI "EMBRACE definition"] +def: "An informative report about disordered structure in a protein." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Protein structure report (disordered structure)" EXACT [] +is_a: EDAM:0001277 ! Protein features is_a: EDAM:0001537 ! Protein structure report + [Term] id: EDAM:0002147 name: Protein report (transcription factor) @@ -14568,7 +14311,8 @@ def: "An informative report on a transcription factor protein." [EDAM:EBI "EMBRA comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. subset: data synonym: "Transcription factor binding site data" EXACT [] -is_a: EDAM:0000896 ! Protein report +is_obsolete: true +consider: EDAM:0000896 ! Protein report [Term] @@ -14578,59 +14322,52 @@ namespace: data def: "An informative report on a membrane protein." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0001456 ! Protein report (membrane protein) +consider: EDAM:0001456 ! Protein features (membrane regions) -[Term] -id: EDAM:0001510 -name: Restriction enzyme report -namespace: data -def: "An informative report on a specific restriction enzyme." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0001517 ! Protein report (restriction enzyme) [Term] id: EDAM:0001517 -name: Protein report (restriction enzyme) +name: Restriction enzyme property namespace: data -def: "Reference data on one or more restriction enzymes such as name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references etc." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0001510 +alt_id: EDAM:0001518 +def: "An informative report on a specific restriction enzyme such as enzyme reference data." [EDAM:EBI "EMBRACE definition"] +comment: This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. subset: data -is_a: EDAM:0001509 ! Protein report (enzyme) - -[Term] -id: EDAM:0001518 -name: Restriction enzyme pattern data -namespace: data -def: "Data on one or more 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." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0001517 ! Protein report (restriction enzyme) +synonym: "Restriction enzyme report" EXACT [] +synonym: "Restriction enzyme pattern data" EXACT [] +synonym: "Protein report (restriction enzyme)" EXACT [] +is_a: EDAM:0001509 ! Enzyme property [Term] id: EDAM:0001533 -name: Protein report (subcellular localization) +name: Protein subcellular localization namespace: data def: "An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001776 ! Protein report (function) +synonym: "Protein report (subcellular localization)" EXACT [] +is_obsolete: true +consider: EDAM:0000896 ! Protein report [Term] id: EDAM:0002191 -name: Protein modification annotation +name: Protein features (checmical modification) namespace: data def: "Data on a chemical modification of a protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000897 ! Protein property +synonym: "Protein modification annotation" EXACT [] +is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0002991 -name: Torsion angle data +name: Protein torsion angle data namespace: data def: "Torsion angle data for a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Torsion angle data" EXACT [] is_a: EDAM:0000897 ! Protein property -! relationship: is_attribute_of EDAM:0000008 ! Protein [Term] @@ -14639,9 +14376,7 @@ name: Ramachandran plot namespace: data def: "Phi/psi angle data or a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002991 ! Torsion angle data -is_a: EDAM:0002968 ! Image or plot -! relationship: is_attribute_of EDAM:0000008 ! Protein +is_a: EDAM:0002991 ! Protein torsion angle data [Term] id: EDAM:0001545 @@ -14650,14 +14385,15 @@ namespace: data def: "Data on the net charge distribution (dipole moment) of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property -! relationship: is_attribute_of EDAM:0000008 ! Protein [Term] id: EDAM:0001519 name: Peptide molecular weights namespace: data +alt_id: EDAM:0001535 def: "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents." [EDAM:EBI "EMBRACE definition"] +comment: The report might include associated data such as frequency of peptide fragment molecular weights. subset: data is_a: EDAM:0000897 ! Protein property @@ -14669,14 +14405,15 @@ namespace: data def: "Report on the hydrophobic moment of a polypeptide sequence." [EDAM:EBI "EMBRACE definition"] comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: data -is_a: EDAM:0002970 ! Protein hydropathy report +is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0002970 -name: Protein hydropathy report +name: Protein hydropathy data namespace: data def: "A report on protein properties concerning hydropathy." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Protein hydropathy report" EXACT [] is_a: EDAM:0000897 ! Protein property [Term] @@ -14686,7 +14423,7 @@ namespace: data def: "The aliphatic index of a protein." [EDAM:EBI "EMBRACE definition"] comment: The aliphatic index is the relative protein volume occupied by aliphatic side chains. subset: data -is_a: EDAM:0002970 ! Protein hydropathy report +is_a: EDAM:0002970 ! Protein hydropathy data [Term] @@ -14705,7 +14442,6 @@ namespace: data def: "A plot of pK versus pH for a protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property -is_a: EDAM:0002968 ! Image or plot [Term] id: EDAM:0001522 @@ -14714,8 +14450,7 @@ namespace: data def: "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc." [EDAM:EBI "EMBRACE definition"] comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: data -is_a: EDAM:0002970 ! Protein hydropathy report -is_a: EDAM:0002969 ! Sequence image or plot +is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0001523 @@ -14724,31 +14459,33 @@ namespace: data def: "A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property -is_a: EDAM:0002969 ! Sequence image or plot [Term] id: EDAM:0001524 -name: Protein solubility data +name: Protein solubility namespace: data def: "The solubility or atomic solvation energy of a protein sequence or structure." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002970 ! Protein hydropathy report +synonym: "Protein solubility data" EXACT [] +is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0001525 -name: Protein crystallizability data +name: Protein crystallizability namespace: data def: "Data on the crystallizability of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002970 ! Protein hydropathy report +synonym: "Protein crystallizability data" EXACT [] +is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0001526 -name: Protein globularity data +name: Protein globularity namespace: data def: "Data on the stability, intrinsic disorder or globularity of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002970 ! Protein hydropathy report +synonym: "Protein globularity data" EXACT [] +is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0001527 @@ -14803,11 +14540,13 @@ is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001534 -name: Peptide immunogenicity report +name: Peptide immunogenicity data namespace: data def: "An report on allergenicity / immunogenicity of peptides and proteins." [EDAM:EBI "EMBRACE definition"] comment: This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. subset: data +synonym: "Peptide immunogenicity report" EXACT [] +synonym: "Peptide immunogenicity" EXACT [] is_a: EDAM:0000897 ! Protein property @@ -14817,15 +14556,7 @@ name: Hopp and Woods plot namespace: data def: "A Hopp and Woods plot of predicted antigenicity of a peptide or protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001534 ! Peptide immunogenicity report - -[Term] -id: EDAM:0001535 -name: Peptide fragment molecular weight frequencies -namespace: data -def: "Frequency of peptide fragment molecular weights found in proteins." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0001519 ! Peptide molecular weights +is_a: EDAM:0001534 ! Peptide immunogenicity data [Term] id: EDAM:0001536 @@ -14833,7 +14564,8 @@ name: MHC peptide immunogenicity report namespace: data def: "A report on the immunogenicity of MHC class I or class II binding peptides." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001534 ! Peptide immunogenicity report +is_obsolete: true +consider: EDAM:0001534 ! Peptide immunogenicity data [Term] @@ -14846,33 +14578,42 @@ is_a: EDAM:0002313 ! Carbohydrate structure report [Term] id: EDAM:0000899 -name: Protein structure report (3D motif) +name: Protein features (3D motif) namespace: data -def: "An informative report on a protein 3D structural motif." [EDAM:EBI "EMBRACE definition"] +def: "An informative report on the 3D structural motifs in a protein." [EDAM:EBI "EMBRACE definition"] comment: This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. subset: data +synonym: "Protein structure report (3D motif)" EXACT [] +is_a: EDAM:0001277 ! Protein features is_a: EDAM:0001537 ! Protein structure report -relationship: in_topic EDAM:0000166 ! Protein structural motifs +relationship: has_topic EDAM:0000166 ! Protein structural motifs and surfaces [Term] id: EDAM:0001539 -name: Protein structure report (quality evaluation) +name: Protein structural quality report namespace: data def: "Report on the quality of a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] comment: Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. subset: data +synonym: "Protein structure report (quality evaluation)" EXACT [] +synonym: "Protein report (structural quality)" EXACT [] +synonym: "Protein property (structural quality)" EXACT [] +is_a: EDAM:0000897 ! Protein property is_a: EDAM:0001537 ! Protein structure report [Term] id: EDAM:0001541 -name: Protein structure report (flexibility or motion) +name: Protein flexibility or motion report namespace: data def: "Informative report on flexibility or motion of a protein structure." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data +synonym: "Protein structure report (flexibility or motion)" EXACT [] +synonym: "Protein property (flexibility or motion)" EXACT [] +synonym: "Protein flexibility or motion" EXACT [] +is_a: EDAM:0000897 ! Protein property is_a: EDAM:0001537 ! Protein structure report -! relationship: is_attribute_of EDAM:0000008 ! Protein [Term] id: EDAM:0002235 @@ -14881,8 +14622,8 @@ namespace: data def: "Raw SCOP domain classification data files." [EDAM:EBI "EMBRACE definition"] comment: These are the parsable data files provided by SCOP. subset: data -is_a: EDAM:0000900 ! Protein domain classification -! relationship: is_attribute_of EDAM:0000223 ! Undefined +is_obsolete: true +consider: EDAM:0000900 ! Protein domain classification [Term] @@ -14892,8 +14633,8 @@ namespace: data def: "Raw CATH domain classification data files." [EDAM:EBI "EMBRACE definition"] comment: These are the parsable data files provided by CATH. subset: data -is_a: EDAM:0000900 ! Protein domain classification -! relationship: is_attribute_of EDAM:0000223 ! Undefined +is_obsolete: true +consider: EDAM:0000900 ! Protein domain classification [Term] @@ -14903,8 +14644,8 @@ namespace: data def: "Summary of domain classification information for a CATH domain." [EDAM:EBI "EMBRACE definition"] comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. subset: data -is_a: EDAM:0000900 ! Protein domain classification -! relationship: is_attribute_of EDAM:0000025 ! Protein domain +is_obsolete: true +consider: EDAM:0000900 ! Protein domain classification [Term] @@ -14915,8 +14656,7 @@ def: "Information on a node from the CATH database." [EDAM:EBI "EMBRACE definiti comment: The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. subset: data synonym: "CATH classification node report" EXACT [] -is_a: EDAM:0000900 ! Protein domain classification -! relationship: is_attribute_of EDAM:0000065 ! Protein domain +is_a: EDAM:0003101 ! Protein domain classification node [Term] @@ -14926,8 +14666,60 @@ namespace: data def: "Information on a node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "SCOP classification node" EXACT [] -is_a: EDAM:0000900 ! Protein domain classification -! relationship: is_attribute_of EDAM:0000065 ! Protein domain +is_a: EDAM:0003101 ! Protein domain classification node + + +[Term] +id: EDAM:0003141 +name: SCOP class +namespace: data +def: "Information on a 'class' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001554 ! SCOP node + +[Term] +id: EDAM:0003142 +name: SCOP fold +namespace: data +def: "Information on a 'fold' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001554 ! SCOP node + +[Term] +id: EDAM:0003143 +name: SCOP superfamily +namespace: data +def: "Information on a 'superfamily' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001554 ! SCOP node + +[Term] +id: EDAM:0003144 +name: SCOP family +namespace: data +def: "Information on a 'family' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001554 ! SCOP node + +[Term] +id: EDAM:0003145 +name: SCOP protein +namespace: data +def: "Information on a 'protein' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001554 ! SCOP node + +[Term] +id: EDAM:0003146 +name: SCOP species +namespace: data +def: "Information on a 'species' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0001554 ! SCOP node + + + + [Term] id: EDAM:0001555 @@ -14937,72 +14729,68 @@ def: "An EMBASSY domain classification file (DCF) of classification and other da subset: data is_obsolete: true consider: EDAM:0000900 ! Protein domain classification -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001556 name: CATH class namespace: data -def: "Information on a protein domain 'class' from the CATH database." [EDAM:EBI "EMBRACE definition"] +def: "Information on a protein 'class' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001557 name: CATH architecture namespace: data -def: "Information on a protein domain 'architecture' from the CATH database." [EDAM:EBI "EMBRACE definition"] +def: "Information on a protein 'architecture' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001558 name: CATH topology namespace: data -def: "Information on a protein domain 'topology' from the CATH database." [EDAM:EBI "EMBRACE definition"] +def: "Information on a protein 'topology' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001559 name: CATH homologous superfamily namespace: data -def: "Information on a protein domain 'homologous superfamily' from the CATH database." [EDAM:EBI "EMBRACE definition"] +def: "Information on a protein 'homologous superfamily' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001560 name: CATH structurally similar group namespace: data -def: "Information on a protein domain 'structurally similar group' from the CATH database." [EDAM:EBI "EMBRACE definition"] +def: "Information on a protein 'structurally similar group' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001561 name: CATH functional category namespace: data -def: "Information on a protein domain 'functional category' from the CATH database." [EDAM:EBI "EMBRACE definition"] +def: "Information on a protein 'functional category' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node -! relationship: is_attribute_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001565 name: Protein-protein interaction namespace: data +alt_id: EDAM:0002712 def: "Data on protein-protein interaction(s)." [EDAM:EBI "EMBRACE definition"] +comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains). subset: data -is_a: EDAM:0000906 ! Protein interaction report -relationship: in_topic EDAM:0000147 ! Protein-protein interactions +synonym: "Protein structure report (protein complex)" EXACT [] +is_a: EDAM:0000906 ! Protein report (interaction) +relationship: has_topic EDAM:0000147 ! Protein-protein interactions [Term] @@ -15011,8 +14799,8 @@ name: Protein-ligand interaction namespace: data def: "Data on protein-ligand (small molecule) interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000906 ! Protein interaction report -relationship: in_topic EDAM:0000148 ! Protein-ligand interactions +is_a: EDAM:0000906 ! Protein report (interaction) +relationship: has_topic EDAM:0000148 ! Protein-ligand interactions [Term] id: EDAM:0001567 @@ -15020,8 +14808,8 @@ name: Protein-nucleic acid interaction namespace: data def: "Data on protein-DNA/RNA interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000906 ! Protein interaction report -relationship: in_topic EDAM:0000149 ! Protein-nucleic acid interactions +is_a: EDAM:0000906 ! Protein report (interaction) +relationship: has_topic EDAM:0000149 ! Protein-nucleic acid interactions [Term] @@ -15038,7 +14826,8 @@ name: Protein-motif interaction namespace: data def: "Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001565 ! Protein-protein interaction +is_obsolete: true +consider: EDAM:0001565 ! Protein-protein interaction [Term] id: EDAM:0002360 @@ -15066,16 +14855,6 @@ def: "Data on protein domain-DNA/RNA interaction(s)." [EDAM:EBI "EMBRACE definit subset: data is_a: EDAM:0001567 ! Protein-nucleic acid interaction -[Term] -id: EDAM:0000908 -name: Reaction annotation -namespace: data -def: "General annotation on the kinetics of enzyme-catalysed reaction(s)." [EDAM:EBI "EMBRACE definition"] -subset: data -synonym: "Enzyme kinetics annotation" EXACT [] -is_a: EDAM:0002024 ! Enzyme kinetics data -is_a: EDAM:0002018 ! Metadata and annotation - [Term] id: EDAM:0002025 @@ -15084,7 +14863,6 @@ namespace: data def: "A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002024 ! Enzyme kinetics data -is_a: EDAM:0002968 ! Image or plot [Term] @@ -15094,7 +14872,6 @@ namespace: data def: "A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002024 ! Enzyme kinetics data -is_a: EDAM:0002968 ! Image or plot [Term] @@ -15123,15 +14900,29 @@ subset: data is_a: EDAM:0002088 ! DNA base structural data + +[Term] +id: EDAM:0003149 +name: Nucleic acid property (sequence) +namespace: data +def: "A non-positional property of a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "Nucleic acid sequence property" EXACT [] +is_obsolete: true +consider: EDAM:0000912 ! Nucleic acid property + [Term] id: EDAM:0002985 -name: Nucleic acid thermodynamic property +name: Nucleic acid thermodynamic data namespace: data -def: "A thermodynamic property of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] +def: "A thermodynamic or kinetic property of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Nucleic acid property (thermodynamic or kinetic)" EXACT [] +synonym: "Nucleic acid thermodynamic property" EXACT [] is_a: EDAM:0000912 ! Nucleic acid property + [Term] id: EDAM:0001583 name: Nucleic acid melting profile @@ -15140,7 +14931,7 @@ def: "Data on the dissociation characteristics of a double-stranded nucleic acid comment: A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. subset: data synonym: "Nucleic acid stability profile" EXACT [] -is_a: EDAM:0002985 ! Nucleic acid thermodynamic property +is_a: EDAM:0002985 ! Nucleic acid thermodynamic data [Term] id: EDAM:0001584 @@ -15148,9 +14939,7 @@ name: Nucleic acid enthalpy namespace: data def: "Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002985 ! Nucleic acid thermodynamic property -! relationship: is_attribute_of EDAM:0000028 ! DNA -! relationship: is_attribute_of EDAM:0000043 ! RNA/DNA hybrid +is_a: EDAM:0002985 ! Nucleic acid thermodynamic data [Term] id: EDAM:0001585 @@ -15158,9 +14947,7 @@ name: Nucleic acid entropy namespace: data def: "Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002985 ! Nucleic acid thermodynamic property -! relationship: is_attribute_of EDAM:0000028 ! DNA -! relationship: is_attribute_of EDAM:0000043 ! RNA/DNA hybrid +is_a: EDAM:0002985 ! Nucleic acid thermodynamic data [Term] @@ -15170,7 +14957,7 @@ namespace: data def: "Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002139 ! Melting temperature +consider: EDAM:0002139 ! Nucleic acid melting temperature [Term] @@ -15180,6 +14967,7 @@ namespace: data def: "Structural data for DNA base pairs or runs of bases, such as energy or angle data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000912 ! Nucleic acid property +is_a: EDAM:0002086 ! Nucleic acid structure report [Term] @@ -15189,7 +14977,6 @@ namespace: data def: "Density plot (of base composition) for a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000912 ! Nucleic acid property -is_a: EDAM:0002969 ! Sequence image or plot [Term] @@ -15281,7 +15068,8 @@ namespace: data def: "A genetic code for an organism." [EDAM:EBI "EMBRACE definition"] comment: A genetic code need not include detailed codon usage information. subset: data -is_a: EDAM:0000914 ! Codon usage report +is_a: EDAM:0001597 ! Codon usage table + [Term] id: EDAM:0002865 @@ -15311,7 +15099,6 @@ def: "A plot of the synonymous codon usage calculated for windows over a nucleot subset: data synonym: "Synonymous codon usage statistic plot" EXACT [] is_a: EDAM:0002865 ! Codon usage bias -is_a: EDAM:0002968 ! Image or plot [Term] @@ -15339,7 +15126,7 @@ namespace: data def: "A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002394 ! Gene annotation (functional) +consider: EDAM:0000916 ! Gene annotation [Term] id: EDAM:0000927 @@ -15351,16 +15138,6 @@ is_a: EDAM:0000916 ! Gene annotation [Term] -id: EDAM:0002394 -name: Gene annotation (functional) -alt_id: EDAM:0002361 -namespace: data -def: "An informative report on the function of a gene, typically a report about the gene and its encoded protein, including a functional classification of the gene sequence along according to the encoded proteins." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0000916 ! Gene annotation -is_a: EDAM:0001776 ! Protein report (function) - -[Term] id: EDAM:0001634 name: Gene annotation (linkage disequilibrium) namespace: data @@ -15368,15 +15145,9 @@ def: "A report on linkage disequilibrium; the non-random association of alleles subset: data is_a: EDAM:0000927 ! Gene annotation (linkage) -[Term] -id: EDAM:0000929 -name: Gene annotation (expression) -namespace: data -def: "An informative report concerning or derived from primary (experimental) gene expression or gene regulation data." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0002541 ! Gene expression data -is_a: EDAM:0000916 ! Gene annotation -relationship: in_topic EDAM:0000197 ! Gene expression and regulation + + + [Term] id: EDAM:0000928 @@ -15385,94 +15156,90 @@ namespace: data def: "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene expression pattern" EXACT [] -is_a: EDAM:0002541 ! Gene expression data -relationship: in_topic EDAM:0000197 ! Gene expression and regulation +is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002579 -name: Gene annotation (expressed gene list) +name: Expressed gene list namespace: data def: "A simple summary of expressed genes." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000929 ! Gene annotation (expression) +synonym: "Gene annotation (expressed gene list)" EXACT [] +is_a: EDAM:0002872 ! ID list [Term] id: EDAM:0002586 name: Northern blot image namespace: data -def: "General annotation on (the results of) a Northern Blot experiment." [EDAM:EBI "EMBRACE definition"] +def: "An image arising from a Northern Blot experiment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001635 ! Gene expression image -is_a: EDAM:0002028 ! Experimental data +is_a: EDAM:0003108 ! Experimental measurement -[Term] -id: EDAM:0001635 -name: Gene expression image -namespace: data -def: "An image, for example an interactive digital image (image map) for visualising gene-expression data." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0000929 ! Gene annotation (expression) -is_a: EDAM:0002968 ! Image or plot [Term] id: EDAM:0001636 name: Heat map namespace: data def: "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." [EDAM:EBI "EMBRACE definition"] -comment: A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell colour represents the level of expression of a gene that context. +comment: A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. subset: data -is_a: EDAM:0002967 ! Microarray image or plot +is_a: EDAM:0002967 ! Microarray image [Term] id: EDAM:0002092 -name: SNP annotation +name: Nucleic acid features (SNP) namespace: data def: "Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: An SNP is an individual point mutation or substitution of a single nucleotide. subset: data synonym: "Single nucleotide polymorphism" EXACT [] -is_a: EDAM:0002885 ! Polymorphism annotation +synonym: "SNP annotation" EXACT [] +is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) + [Term] id: EDAM:0002867 -name: VNTR annotation +name: Nucleic acid features (VNTR) namespace: data def: "Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. subset: data synonym: "Variable number of tandem repeat polymorphism" EXACT [] -is_a: EDAM:0002885 ! Polymorphism annotation +synonym: "VNTR annotation" EXACT [] +is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0002868 -name: Microsatellite annotation +name: Nucleic acid features (microsatellite) namespace: data def: "Annotation on a microsatellite polymorphism in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. subset: data -is_a: EDAM:0002885 ! Polymorphism annotation +synonym: "Microsatellite annotation" EXACT [] +is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0002869 -name: RFLP annotation +name: Nucleic acid features (RFLP) namespace: data def: "Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. subset: data -is_a: EDAM:0002885 ! Polymorphism annotation +synonym: "RFLP annotation" EXACT [] +is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0001853 name: Chromosome annotation (aberration) namespace: data -def: "A report on a chromosome aberration such as abornmalities in chromosome structure." [EDAM:EBI "EMBRACE definition"] +def: "A report on a chromosome aberration such as abnormalities in chromosome structure." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0000919 ! Gene annotation (chromosome) +consider: EDAM:0000919 ! Nucleic acid features (chromosome) [Term] @@ -15491,24 +15258,27 @@ name: Disease annotation namespace: data def: "An informative report on a specific disease." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002890 ! Phenotype annotation -relationship: in_topic EDAM:0000634 ! Disease +is_a: EDAM:0000920 ! Genotype/phenotype annotation +relationship: has_topic EDAM:0000634 ! Disease resources + [Term] id: EDAM:0002533 -name: Mutation annotation +name: Nucleic acid features (mutation) namespace: data def: "Annotation on a mutation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000918 ! Sequence variation annotation +synonym: "Mutation annotation" EXACT [] +is_a: EDAM:0000918 ! Nucleic acid features (variation) [Term] id: EDAM:0002885 -name: Polymorphism annotation +name: Nucleic acid features (polymorphism annotation) namespace: data def: "Annotation on a polymorphism." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000918 ! Sequence variation annotation +synonym: "Polymorphism annotation" EXACT [] +is_a: EDAM:0000918 ! Nucleic acid features (variation) [Term] @@ -15518,7 +15288,7 @@ namespace: data def: "Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002533 ! Mutation annotation +consider: EDAM:0002533 ! Nucleic acid features (mutation) [Term] @@ -15528,7 +15298,7 @@ namespace: data def: "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002533 ! Mutation annotation +consider: EDAM:0002533 ! Nucleic acid features (mutation) [Term] @@ -15538,7 +15308,7 @@ namespace: data def: "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002533 ! Mutation annotation +consider: EDAM:0002533 ! Nucleic acid features (mutation) [Term] @@ -15548,13 +15318,13 @@ namespace: data def: "An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002533 ! Mutation annotation +consider: EDAM:0002533 ! Nucleic acid features (mutation) [Term] id: EDAM:0002217 name: Tumor annotation namespace: data -def: "An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic typem, and so on." [EDAM:EBI "EMBRACE definition"] +def: "An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001622 ! Disease annotation @@ -15570,11 +15340,13 @@ consider: EDAM:0000925 ! Sequence assembly [Term] id: EDAM:0000923 -name: PCR assay data +name: Experiment annotation (PCR assay data) namespace: data def: "Data on a PCR assay or electronic / virtual PCR." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002028 ! Experimental data +synonym: "PCR assay data" EXACT [] +is_a: EDAM:0002531 ! Experiment annotation +relationship: has_topic EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000924 @@ -15583,7 +15355,7 @@ namespace: data def: "A molecular sequence (reads) with associated sequencing metadata (such as base-call quality scores or raw sequencing data)." [EDAM:EBI "EMBRACE definition"] comment: This is the raw data produced by a DNA sequencing machine. subset: data -is_a: EDAM:0002028 ! Experimental data +is_a: EDAM:0003108 ! Experimental measurement is_a: EDAM:0002887 ! Sequence record (nucleic acid) [Term] @@ -15593,7 +15365,7 @@ namespace: data def: "Radiation hybrid scores (RH) scores for one or more markers." [EDAM:EBI "EMBRACE definition"] comment: Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. subset: data -is_a: EDAM:0002028 ! Experimental data +is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0002363 @@ -15602,8 +15374,9 @@ namespace: data def: "Data concerning two-dimensional polygel electrophoresis." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data -is_a: EDAM:0002028 ! Experimental data - +is_obsolete: true +consider: EDAM:0000942 ! 2D PAGE image +consider: EDAM:0002364 ! Experiment annotation (2D PAGE) [Term] id: EDAM:0002838 @@ -15612,7 +15385,7 @@ namespace: data def: "Data concerning a proteomics experiment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002536 ! Mass spectrometry data +consider: EDAM:0003147 ! Experiment annotation (mass spectrometry) [Term] @@ -15622,8 +15395,10 @@ namespace: data def: "Data concerning a mass spectrometry experiment." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data -is_a: EDAM:0002028 ! Experimental data - +is_obsolete: true +consider: EDAM:0000943 ! Mass spectrometry spectra +consider: EDAM:0000944 ! Peptide mass fingerprint +consider: EDAM:0003147 ! Experiment annotation (mass spectrometry) [Term] id: EDAM:0000943 @@ -15631,8 +15406,8 @@ name: Mass spectrometry spectra namespace: data def: "Spectra from mass spectrometry." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002536 ! Mass spectrometry data -relationship: in_topic EDAM:0000134 ! Mass spectrometry +is_a: EDAM:0003108 ! Experimental measurement +relationship: has_topic EDAM:0000121 ! Proteomics [Term] @@ -15643,9 +15418,9 @@ def: "A set of peptide masses (peptide mass fingerprint) from mass spectrometry. subset: data synonym: "Protein fingerprint" EXACT [] synonym: "Peak list" EXACT [] -is_a: EDAM:0002536 ! Mass spectrometry data -is_a: EDAM:0002979 ! Peptide data -relationship: in_topic EDAM:0000767 ! Peptide identification and proteolysis +is_a: EDAM:0002979 ! Peptide property +is_a: EDAM:0003108 ! Experimental measurement +relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0000945 @@ -15653,9 +15428,8 @@ name: Peptide identification namespace: data def: "Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002536 ! Mass spectrometry data -is_a: EDAM:0002979 ! Peptide data -relationship: in_topic EDAM:0000767 ! Peptide identification and proteolysis +is_a: EDAM:0002979 ! Peptide property +relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] @@ -15665,8 +15439,7 @@ namespace: data def: "Raw data from experimental methods for determining protein structure." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data -is_a: EDAM:0002028 ! Experimental data -is_a: EDAM:0002524 ! Protein data +is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0000937 @@ -15700,8 +15473,8 @@ namespace: data def: "Volume map data from electron microscopy." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "EM volume map" EXACT [] -is_a: EDAM:0002028 ! Experimental data -relationship: in_topic EDAM:0000611 ! Electron microscopy +is_a: EDAM:0003108 ! Experimental measurement +relationship: has_topic EDAM:0002226 ! Structure determination [Term] @@ -15711,16 +15484,19 @@ namespace: data def: "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data -is_a: EDAM:0002028 ! Experimental data +is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0000931 name: Experiment annotation (microarray) namespace: data -def: "Information on one or more microarray experiments (conditions, protocol etc)." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0003114 +def: "Information on a microarray experiment such as conditions, protocol, sample:data relationships etc." [EDAM:EBI "EMBRACE definition"] +comment: This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. subset: data +synonym: "Experimental design annotation" EXACT [] is_a: EDAM:0002531 ! Experiment annotation -relationship: in_topic EDAM:0000197 ! Gene expression and regulation +relationship: has_topic EDAM:0000197 ! Gene expression resources [Term] id: EDAM:0002866 @@ -15731,13 +15507,24 @@ subset: data is_a: EDAM:0002531 ! Experiment annotation [Term] +id: EDAM:0003147 +name: Experiment annotation (mass spectrometry) +namespace: data +def: "General annotation on a mass spectrometry experiment." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0002531 ! Experiment annotation + + +[Term] id: EDAM:0000932 name: Oligonucleotide probe data namespace: data def: "Data on oligonucleotide probes (typically for use with DNA microarrays)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002028 ! Experimental data -relationship: in_topic EDAM:0000632 ! Molecular probes or primers +is_obsolete: true +consider: EDAM:0002717 ! Oligonucleotide probe annotation + + [Term] @@ -15748,7 +15535,6 @@ def: "Output from a serial analysis of gene expression (SAGE), massively paralle comment: SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. subset: data synonym: "Sequencing-based expression profile" EXACT [] -is_a: EDAM:0002028 ! Experimental data is_a: EDAM:0000928 ! Gene expression profile @@ -15799,9 +15585,9 @@ namespace: data def: "Two-dimensional gel electrophoresis image." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Two-dimensional gel electrophoresis image" EXACT [] -is_a: EDAM:0002363 ! 2D PAGE data -is_a: EDAM:0002968 ! Image or plot -relationship: in_topic EDAM:0000133 ! Two-dimensional gel electrophoresis +is_a: EDAM:0002968 ! Image +is_a: EDAM:0003108 ! Experimental measurement +relationship: has_topic EDAM:0000121 ! Proteomics [Term] id: EDAM:0002364 @@ -15809,24 +15595,27 @@ name: Experiment annotation (2D PAGE) namespace: data def: "An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002363 ! 2D PAGE data is_a: EDAM:0002531 ! Experiment annotation +relationship: has_topic EDAM:0000121 ! Proteomics [Term] id: EDAM:0002965 -name: 2D PAGE image annotation +name: 2D PAGE image (annotated) namespace: data def: "An informative report on a two-dimensional (2D PAGE) gel." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002363 ! 2D PAGE data +synonym: "2D PAGE image annotation" EXACT [] +is_a: EDAM:0000942 ! 2D PAGE image + [Term] id: EDAM:0002372 -name: 2D PAGE spot annotation +name: 2D PAGE spot (annotated) namespace: data def: "An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002965 ! 2D PAGE image annotation +synonym: "2D PAGE spot annotation" EXACT [] +is_a: EDAM:0002965 ! 2D PAGE image (annotated) [Term] id: EDAM:0001646 @@ -15842,8 +15631,10 @@ name: Oligonucleotide probe annotation namespace: data def: "General annotation on an oligonucleotide probe." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000932 ! Oligonucleotide probe data -is_a: EDAM:0002018 ! Metadata and annotation +is_a: EDAM:0003115 ! Microarray annotation +relationship: has_topic EDAM:0000632 ! Probes and primers + + [Term] id: EDAM:0002966 @@ -15851,8 +15642,8 @@ name: Oligonucleotide probe sets annotation namespace: data def: "General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000932 ! Oligonucleotide probe data -is_a: EDAM:0002018 ! Metadata and annotation +is_a: EDAM:0002717 ! Oligonucleotide probe annotation + [Term] id: EDAM:0001642 @@ -15879,10 +15670,12 @@ consider: EDAM:0002966 ! Oligonucleotide probe sets annotation id: EDAM:0000856 name: Sequence feature source namespace: data -def: "How the annotation of a sequence feature (in EMBL or Swiss-Prot database) was derived." [EDAM:EBI "EMBRACE definition"] -comment: This might be the name and version of a software tool, or 'curated' to indicate a manual annotation (made by a human). +def: "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived." [EDAM:EBI "EMBRACE definition"] +comment: This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). subset: data is_a: EDAM:0002042 ! Evidence +is_a: EDAM:0002914 ! Sequence feature metadata + [Term] id: EDAM:0000859 @@ -15905,52 +15698,50 @@ consider: EDAM:0002984 ! Pathway or network report [Term] id: EDAM:0002589 -name: Hierarchy annotation -namespace: data -def: "An informative report about a specific biological hierarchy." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0002987 ! Classification data - -[Term] -id: EDAM:0000915 -name: Nucleic acid report (RNA splice model) +name: Hierarchy namespace: data -def: "A model of alternative RNA splicing events." [EDAM:EBI "EMBRACE definition"] +def: "A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000950 ! Biological model -is_a: EDAM:0002084 ! Nucleic acid report +synonym: "Hierarchy annotation" EXACT [] +is_a: EDAM:0002987 ! Classification [Term] id: EDAM:0000904 -name: Protein report (mutation) +name: Protein features (mutation) namespace: data def: "Data on the effect of (typically point) mutation on protein folding, stability, structure and function." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data -is_a: EDAM:0000950 ! Biological model -is_a: EDAM:0000896 ! Protein report +synonym: "Protein property (mutation)" EXACT [] +synonym: "Protein report (mutation)" EXACT [] +synonym: "Protein structure report (mutation)" EXACT [] +is_obsolete: true +consider: EDAM:0000896 ! Protein report [Term] id: EDAM:0000903 -name: Protein report (folding) +name: Protein folding report namespace: data -def: "A report on a model of protein folding, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc." [EDAM:EBI "EMBRACE definition"] +def: "A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data -is_a: EDAM:0000950 ! Biological model -is_a: EDAM:0000896 ! Protein report +synonym: "Protein report (folding)" EXACT [] +synonym: "Protein property (folding)" EXACT [] +is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001596 -name: Nucleic acid report (folding model) +name: Nucleic acid folding report namespace: data -def: "A report on a RNA/DNA folding model, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." [EDAM:EBI "EMBRACE definition"] +def: "A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data -is_a: EDAM:0000950 ! Biological model -is_a: EDAM:0002084 ! Nucleic acid report +synonym: "Nucleic acid report (folding model)" EXACT [] +synonym: "Nucleic acid report (folding)" EXACT [] +is_a: EDAM:0000912 ! Nucleic acid property + [Term] id: EDAM:0001344 @@ -16029,7 +15820,7 @@ namespace: data def: "A report typically including a map (diagram) of a gene regulatory network." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002600 ! Pathway or network -relationship: in_topic EDAM:0002846 ! Gene regulatory networks +relationship: has_topic EDAM:0002846 ! Gene regulatory networks [Term] @@ -16090,7 +15881,7 @@ namespace: data def: "A value representing estimated statistical significance of some observed data; typically sequence database hits." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001772 ! Score or penalty - +is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0000865 @@ -16222,40 +16013,38 @@ subset: data is_obsolete: true consider: EDAM:0002093 ! Data reference -[Term] -id: EDAM:0001023 -name: EMBOSS Uniform Feature Object -namespace: data -def: "The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"] -subset: data -is_a: EDAM:0002093 ! Data reference [Term] -id: EDAM:0001095 -name: EMBOSS Uniform Sequence Address +id: EDAM:0002337 +name: Metadata namespace: data -def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0002853 +def: "Data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing." [EDAM:EBI "EMBRACE definition"] +comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -synonym: "USA" EXACT [] -is_a: EDAM:0002093 ! Data reference +synonym: "Provenance metadata" EXACT [] +is_a: EDAM:0002048 ! Report + [Term] -id: EDAM:0002337 -name: Provenance data +id: EDAM:0002018 +name: Annotation namespace: data -def: "Data on the origin, source, history, ownership or location of some thing." [EDAM:EBI "EMBRACE definition"] +def: "A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data -is_a: EDAM:0000006 ! Data -is_a: EDAM:0002018 ! Metadata and annotation +is_obsolete: true +consider: EDAM:0002048 ! Report + + [Term] id: EDAM:0000948 -name: Data definition +name: Data resource definition namespace: data -def: "A definition of a data resource or type of data, including metadata and links to the resource or data proper." [EDAM:EBI "EMBRACE definition"] +def: "A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002093 ! Data reference +is_a: EDAM:0001883 ! Annotated URI [Term] id: EDAM:0000957 @@ -16263,17 +16052,17 @@ name: Database metadata namespace: data def: "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Provenance data +is_a: EDAM:0003106 ! System metadata [Term] id: EDAM:0002223 name: Ontology metadata namespace: data -def: "Data concerning or derived from a biological ontology." [EDAM:EBI "EMBRACE definition"] +def: "Data concerning a biological ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002018 ! Metadata and annotation -is_a: EDAM:0002353 ! Ontological data +is_a: EDAM:0002337 ! Metadata +relationship: has_topic EDAM:0000089 ! Ontologies [Term] id: EDAM:0002193 @@ -16281,7 +16070,7 @@ name: Database entry metadata namespace: data def: "Basic information on any arbitrary database entry." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Provenance data +is_a: EDAM:0000957 ! Database metadata [Term] @@ -16290,7 +16079,7 @@ name: Tool metadata namespace: data def: "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Provenance data +is_a: EDAM:0003106 ! System metadata [Term] @@ -16299,7 +16088,7 @@ name: Server metadata namespace: data def: "Basic information about a server on the web, such as an SRS server." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Provenance data +is_a: EDAM:0003106 ! System metadata [Term] @@ -16309,7 +16098,7 @@ namespace: data def: "Textual metadata on a submitted or completed job." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby:PDGJOB -is_a: EDAM:0002337 ! Provenance data +is_a: EDAM:0003106 ! System metadata [Term] id: EDAM:0000960 @@ -16317,7 +16106,15 @@ name: User metadata namespace: data def: "Textual metadata on a software author or end-user, for example a person or other software." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Provenance data +is_a: EDAM:0003106 ! System metadata + +[Term] +id: EDAM:0003106 +name: System metadata +namespace: data +def: "Metadata concerning the software, hardware or other aspects of a computer system." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0002337 ! Metadata [Term] @@ -16326,7 +16123,7 @@ name: Directory metadata namespace: data def: "A directory on disk from which files are read." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Provenance data +is_a: EDAM:0003106 ! System metadata [Term] id: EDAM:0000953 @@ -16334,7 +16131,7 @@ name: Version information namespace: data def: "Information on a version of software or data, for example name, version number and release date." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002337 ! Provenance data +is_a: EDAM:0002337 ! Metadata [Term] id: EDAM:0002724 @@ -16343,6 +16140,7 @@ namespace: data def: "Annotation on an embryo or concerning embryological development." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002530 ! Organism annotation +relationship: has_topic EDAM:0003065 ! Embryology resources [Term] id: EDAM:0001664 @@ -16351,8 +16149,8 @@ namespace: data def: "An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources." [EDAM:EBI "EMBRACE definition"] comment: A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. subset: data -is_a: EDAM:0000948 ! Data definition -is_a: EDAM:0001883 ! URI metadata +is_a: EDAM:0000948 ! Data resource definition + [Term] id: EDAM:0002875 @@ -16360,7 +16158,7 @@ name: DRCAT resource namespace: data def: "An entry (resource) from the DRCAT bioinformatics resource catalogue." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000948 ! Data definition +is_a: EDAM:0000948 ! Data resource definition [Term] @@ -16562,17 +16360,9 @@ name: URI namespace: data def: "A string of characters that name or otherwise identify a resource on the Internet." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter or primitive +is_a: EDAM:0002527 ! Parameter -[Term] -id: EDAM:0000961 -name: Generic parameter -namespace: data -def: "Some simple value controlling an operation common to diverse tools." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0002527 ! Parameter or primitive [Term] id: EDAM:0002079 @@ -16580,18 +16370,9 @@ name: Search parameter namespace: data def: "Some simple value controlling a search operation, typically a search of a database." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter or primitive +is_a: EDAM:0002527 ! Parameter -[Term] -id: EDAM:0001773 -name: Tool-specific parameter -namespace: data -def: "Some simple value(s) controlling an operation specific to a single (or few) tools only." [EDAM:EBI "EMBRACE definition"] -comment: This term should be used in preference to introducing many tool-specific terms into the ontology. It should never have child terms. -subset: data -is_obsolete: true -consider: EDAM:0002527 ! Parameter or primitive [Term] id: EDAM:0002534 @@ -16599,7 +16380,7 @@ name: Sequence parameter namespace: data def: "A parameter concerning calculations on molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter or primitive +is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0002130 @@ -16627,7 +16408,10 @@ namespace: data def: "The strand of a DNA sequence (forward or reverse)." [EDAM:EBI "EMBRACE definition"] comment: The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. subset: data +synonym: "DNA strand specification" EXACT [] +synonym: "Strand" EXACT [] is_a: EDAM:0002534 ! Sequence parameter +is_a: EDAM:0002914 ! Sequence feature metadata [Term] @@ -16636,7 +16420,7 @@ name: Translation frame specification namespace: data def: "Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002534 ! Sequence parameter +is_a: EDAM:0002534 ! Sequence parameter3 [Term] @@ -16645,7 +16429,9 @@ name: Translation phase specification namespace: data def: "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." [EDAM:EBI "EMBRACE definition"] subset: data +synonym: "Phase" EXACT [] is_a: EDAM:0002534 ! Sequence parameter +is_a: EDAM:0002914 ! Sequence feature metadata [Term] @@ -16693,16 +16479,22 @@ subset: data is_a: EDAM:0000864 ! Sequence alignment parameter is_a: EDAM:0002100 ! Type + + [Term] id: EDAM:0001052 name: URL namespace: data +alt_id: EDAM:0001054 +alt_id: EDAM:0001168 +alt_id: EDAM:0001169 def: "A Uniform Resource Locator (URL)." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby:URL xref: Moby:Link is_a: EDAM:0001047 ! URI + [Term] id: EDAM:0001053 name: URN @@ -16711,14 +16503,6 @@ def: "A Uniform Resource Name (URN)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001047 ! URI -[Term] -id: EDAM:0001054 -name: URL of database entry -namespace: data -def: "A URL of an entry, record or field from a biological or biomedical database." [EDAM:EBI "EMBRACE definition"] -subset: data -is_obsolete: true -consider: EDAM:0001052 ! URL [Term] id: EDAM:0001055 @@ -16741,7 +16525,7 @@ xref: Moby:Global_Keyword xref: Moby:QueryString xref: Moby:Wildcard_Query xref: Moby:BooleanQueryString -is_a: EDAM:0002527 ! Parameter or primitive +is_a: EDAM:0002527 ! Parameter [Term] @@ -16751,7 +16535,7 @@ namespace: data def: "Data used by the Vienna RNA analysis package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002527 ! Parameter or primitive +consider: EDAM:0002527 ! Parameter [Term] @@ -16769,18 +16553,17 @@ namespace: data def: "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002527 ! Parameter or primitive +consider: EDAM:0002527 ! Parameter [Term] id: EDAM:0002139 -name: Melting temperature +name: Nucleic acid melting temperature namespace: data def: "A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002985 ! Nucleic acid thermodynamic property -! relationship: is_attribute_of EDAM:0000028 ! DNA -! relationship: is_attribute_of EDAM:0000043 ! RNA/DNA hybrid +synonym: "Melting temperature" EXACT [] +is_a: EDAM:0002985 ! Nucleic acid thermodynamic data [Term] @@ -16789,13 +16572,13 @@ name: Concentration namespace: data def: "The concentration of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002050 ! General molecular property +is_a: EDAM:0002050 ! Molecular property (general) [Term] id: EDAM:0002151 -name: Colour +name: Color namespace: data -def: "Specification of one or more colours." [EDAM:EBI "EMBRACE definition"] +def: "Specification of one or more colors." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002152 ! Rendering parameter @@ -16809,8 +16592,16 @@ def: "A parameter that is used to control rendering (drawing) to a device or ima subset: data synonym: "Graphics parameter" EXACT [] synonym: "Graphical parameter" EXACT [] -is_a: EDAM:0002527 ! Parameter or primitive +is_a: EDAM:0002527 ! Parameter + +[Term] +id: EDAM:0003105 +name: Geotemporal metadata +namespace: data +def: "Basic information concerning geographical location or time." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0002337 ! Metadata [Term] id: EDAM:0002156 @@ -16818,8 +16609,7 @@ name: Date namespace: data def: "A temporal date." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002527 ! Parameter or primitive -is_a: EDAM:0002337 ! Provenance data +is_a: EDAM:0003105 ! Geotemporal metadata [Term] @@ -16879,7 +16669,6 @@ subset: data xref: WHATIF: number xref: WHATIF: PDBx_atom_site is_a: EDAM:0001014 ! Sequence position specification -! relationship: is_attribute_of EDAM:0000010 ! Entity feature ! _atom_site.id in PDBML [Term] @@ -16889,7 +16678,7 @@ namespace: data def: "An offset for a single-point sequence position." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001016 ! Sequence position -! relationship: is_attribute_of EDAM:0000010 ! Entity feature +is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0001017 @@ -16898,13 +16687,12 @@ namespace: data def: "Specification of range(s) of sequence positions." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001014 ! Sequence position specification -! relationship: is_attribute_of EDAM:0000010 ! Entity feature [Term] id: EDAM:0002012 -alt_id: EDAM:0001894 name: Map position namespace: data +alt_id: EDAM:0001894 def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval." [EDAM:EBI "EMBRACE definition"] comment: This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. subset: data @@ -16939,7 +16727,6 @@ def: "A residue identifier (a string) from a PDB file." [EDAM:EBI "EMBRACE defin subset: data xref: WHATIF: pdb_number is_a: EDAM:0001016 ! Sequence position -! relationship: is_attribute_of EDAM:0000064 ! Protein residue ! PDB_residue_no in PDBML [Term] @@ -16964,7 +16751,6 @@ synonym: "QTL" EXACT [] xref: Moby:SO_QTL is_obsolete: true consider: EDAM:0002012 ! Map position -! relationship: is_attribute_of EDAM:0000010 ! Entity feature [Term] id: EDAM:0001249 @@ -17040,7 +16826,7 @@ namespace: data def: "Whether end gaps are scored or not." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002527 ! Parameter or primitive +consider: EDAM:0002527 ! Parameter [Term] @@ -17265,7 +17051,7 @@ namespace: data def: "RNA parameters used by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002527 ! Parameter or primitive +consider: EDAM:0002527 ! Parameter [Term] id: EDAM:0001592 @@ -17274,7 +17060,7 @@ namespace: data def: "Structure constraints used by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002527 ! Parameter or primitive +consider: EDAM:0002527 ! Parameter [Term] @@ -17284,7 +17070,7 @@ namespace: data def: "RNA concentration data used by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002527 ! Parameter or primitive +consider: EDAM:0002527 ! Parameter [Term] id: EDAM:0001696 @@ -17292,8 +17078,8 @@ name: Drug annotation namespace: data def: "An informative report on a specific drug." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule report -relationship: in_topic EDAM:0000620 ! Drugs and targets +is_a: EDAM:0000962 ! Small molecule annotation +relationship: has_topic EDAM:0000620 ! Drugs and targets [Term] id: EDAM:0002400 @@ -17301,7 +17087,7 @@ name: Toxin annotation namespace: data def: "An informative report on a specific toxin." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule report +is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002240 @@ -17309,7 +17095,7 @@ name: Heterogen annotation namespace: data def: "An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule report +is_a: EDAM:0000962 ! Small molecule annotation [Term] @@ -17318,7 +17104,7 @@ name: Inhibitor annotation namespace: data def: "An informative report on one or more small molecules that are enzyme inhibitors." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0000962 ! Small molecule report +is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002396 @@ -17335,7 +17121,7 @@ namespace: data def: "An image of a graph generated by the EMBOSS suite." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -consider: EDAM:0002968 ! Image or plot +consider: EDAM:0002968 ! Image [Term] @@ -17345,8 +17131,8 @@ namespace: data def: "An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information." [EDAM:EBI "EMBRACE definition"] comment: See also 'Phylogenetic tree' subset: data -is_a: EDAM:0002968 ! Image or plot -is_a: EDAM:0001438 ! Phylogenetic report +is_a: EDAM:0002968 ! Image +is_a: EDAM:0001438 ! Phylogenetic tree report [Term] @@ -17368,13 +17154,13 @@ is_a: EDAM:0002956 ! Protein secondary structure report [Term] id: EDAM:0001710 -alt_id: EDAM:0002604 name: Structure image namespace: data +alt_id: EDAM:0002604 def: "Image of one or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002085 ! Structure report -is_a: EDAM:0002968 ! Image or plot +is_a: EDAM:0002968 ! Image [Term] id: EDAM:0002880 @@ -17386,11 +17172,11 @@ is_a: EDAM:0002881 ! Secondary structure report [Term] id: EDAM:0001711 -name: Sequence alignment image or plot +name: Sequence alignment image namespace: data def: "Image of two or more aligned molecular sequences possibly annotated with alignment features." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002968 ! Image or plot +is_a: EDAM:0002968 ! Image is_a: EDAM:0000867 ! Sequence alignment report @@ -17400,37 +17186,59 @@ name: Sequence trace image namespace: data def: "Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases)." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002969 ! Sequence image or plot +is_a: EDAM:0002969 ! Sequence image [Term] id: EDAM:0002969 -name: Sequence image or plot +name: Sequence image namespace: data def: "Image of a molecular sequence, possibly with sequence features or properties shown." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002968 ! Image or plot +is_a: EDAM:0002968 ! Image is_a: EDAM:0002955 ! Sequence report [Term] id: EDAM:0001712 -name: Small molecule structure image +name: Structure image (small molecule) namespace: data def: "An image of the structure of a small chemical compound." [EDAM:EBI "EMBRACE definition"] comment: The molecular identifier and formula are typically included. subset: data synonym: "Chemical structure image" EXACT [] +synonym: "Small molecule structure image" EXACT [] is_a: EDAM:0001710 ! Structure image -is_a: EDAM:0000962 ! Small molecule report +is_a: EDAM:0000962 ! Small molecule annotation + [Term] id: EDAM:0002992 name: Protein structure image namespace: data -def: "An image of a protein structure." [EDAM:EBI "EMBRACE definition"] +def: "An image of protein structure." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "Structure image (protein)" EXACT [] +is_a: EDAM:0001710 ! Structure image +is_a: EDAM:0003153 ! Protein image + + +[Term] +id: EDAM:0003154 +name: Protein alignment +namespace: data +def: "An alignment of protein sequences and/or structures." [EDAM:EBI "EMBRACE definition"] +subset: data +is_a: EDAM:0000896 ! Protein report +is_a: EDAM:0001916 ! Alignment + +[Term] +id: EDAM:0003153 +name: Protein image +namespace: data +def: "An image of a protein." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001710 ! Structure image -is_a: EDAM:0001537 ! Protein structure report +is_a: EDAM:0000896 ! Protein report + [Term] id: EDAM:0001713 @@ -17438,17 +17246,20 @@ name: Fate map namespace: data def: " A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002968 ! Image or plot +is_a: EDAM:0002724 ! Embryo annotation [Term] id: EDAM:0002967 -name: Microarray image or plot +name: Microarray image namespace: data -def: "An image (array spots) from a microarray experiment." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0001635 +def: "An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0001635 ! Gene expression image +synonym: "Gene expression image" EXACT [] is_a: EDAM:0002603 ! Microarray data +is_a: EDAM:0002968 ! Image +relationship: has_topic EDAM:0000197 ! Gene expression resources [Term] id: EDAM:0001714 @@ -17456,8 +17267,8 @@ name: Microarray spots image namespace: data def: "An image of spots from a microarray experiment." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002967 ! Microarray image or plot - +is_a: EDAM:0002967 ! Microarray image +is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0002162 @@ -17487,12 +17298,22 @@ is_a: EDAM:0002307 ! Virus annotation [Term] id: EDAM:0000582 -alt_id: EDAM:0002221 name: Ontology namespace: data +alt_id: EDAM:0000829 +alt_id: EDAM:0000830 +alt_id: EDAM:0000834 +alt_id: EDAM:0000836 +alt_id: EDAM:0000837 +alt_id: EDAM:0000838 +alt_id: EDAM:0000839 +alt_id: EDAM:0000840 +alt_id: EDAM:0002221 def: "An ontology of biological or bioinformatics terms and relations, a controlled vocabulary, structured glossary etc." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002353 ! Ontological data +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000089 ! Ontologies + [Term] id: EDAM:0002858 @@ -17501,7 +17322,9 @@ namespace: data def: "A concept from a biological ontology." [EDAM:EBI "EMBRACE definition"] comment: This includes any fields from the term definition such as term name, definition, comments and so on. subset: data -is_a: EDAM:0002353 ! Ontological data +is_a: EDAM:0003031 ! Core data +relationship: has_topic EDAM:0000089 ! Ontologies + [Term] id: EDAM:0000966 @@ -17518,7 +17341,9 @@ name: Ontology concept metadata namespace: data def: "Data concerning or derived from a concept from a biological ontology." [EDAM:EBI "EMBRACE definition"] subset: data -is_a: EDAM:0002353 ! Ontological data +is_a: EDAM:0002337 ! Metadata +relationship: has_topic EDAM:0000089 ! Ontologies + [Term] id: EDAM:0001715 @@ -17719,7 +17544,6 @@ namespace: data def: "A single thing." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -! is_a: EDAM:0002176 ! Cardinality [Term] @@ -17729,7 +17553,6 @@ namespace: data def: "One or more things." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -! is_a: EDAM:0002176 ! Cardinality [Term] @@ -17739,7 +17562,6 @@ namespace: data def: "Exactly two things." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -! is_a: EDAM:0002176 ! Cardinality [Term] @@ -17749,7 +17571,6 @@ namespace: data def: "Two or more things." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true -! is_a: EDAM:0002176 ! Cardinality ! Identifier @@ -17757,9 +17578,9 @@ is_obsolete: true [Term] id: EDAM:0000973 name: Undefined -namespace: data +namespace: identifier def: "Debugging." [EDAM:EBI "EMBRACE definition"] -subset: data +subset: identifier is_obsolete: true @@ -17822,7 +17643,7 @@ consider: EDAM:0000842 ! Identifier id: EDAM:0000981 name: Phenomenon identifier namespace: identifier -def: "Name or other identifier of a physical, observable biological occurence or event." [EDAM:EBI "EMBRACE definition"] +def: "Name or other identifier of a physical, observable biological occurrence or event." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0000842 ! Identifier @@ -17832,6 +17653,7 @@ consider: EDAM:0000842 ! Identifier id: EDAM:0002091 name: Accession namespace: identifier +alt_id: EDAM:0002862 def: "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000842 ! Identifier @@ -17840,8 +17662,10 @@ is_a: EDAM:0000842 ! Identifier id: EDAM:0002099 name: Name namespace: identifier +alt_id: EDAM:0002863 def: "A name of a thing, which need not necessarily uniquely identify it." [EDAM:EBI "EMBRACE definition"] subset: identifier +synonym: "Symbolic name" EXACT [] is_a: EDAM:0000842 ! Identifier [Term] @@ -17849,7 +17673,7 @@ id: EDAM:0000976 name: Identifier (typed) namespace: identifier def: "An identifier that identifies a particular type of data." [EDAM:EBI "EMBRACE definition"] -comment: This branch provides an alternative organisation of the terms nested under 'Accession' and 'Name'. All terms under here are already included under 'Accession' or 'Name'. +comment: This term exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the terms nested under 'Accession' and 'Name'. All terms under here are already included under 'Accession' or 'Name'. subset: identifier is_a: EDAM:0000842 ! Identifier @@ -17871,7 +17695,6 @@ namespace: identifier def: "An identifier of a bioinformatics tool, e.g. an application or web service." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) -! is_a: EDAM:0000958 ! Tool metadata [Term] id: EDAM:0001190 @@ -17934,7 +17757,6 @@ namespace: identifier def: "An identifier of a submitted job." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) -! is_a: EDAM:0000959 ! Job metadata [Term] id: EDAM:0001676 @@ -17952,7 +17774,6 @@ namespace: identifier def: "An identifier of a software end-user (typically a person)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) -! is_a: EDAM:0000960 ! User metadata [Term] @@ -18047,7 +17868,8 @@ def: "Identifier of a genetic code in the NCBI list of genetic codes." [EDAM:EBI subset: identifier regex: "[1-9][0-9]?" ! example: 16 -is_a: EDAM:0001598 ! Genetic code +is_a: EDAM:0000976 ! Identifier (typed) +is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0000982 @@ -18056,17 +17878,51 @@ namespace: identifier def: "Name or other identifier of a molecule." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0002528 ! Molecular data +relationship: is_identifier_of EDAM:0002529 ! Molecule report [Term] id: EDAM:0001015 name: Sequence feature ID namespace: identifier -def: "Name or other identifier of a molecular sequence feature." [EDAM:EBI "EMBRACE definition"] +def: "A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002091 ! Accession +is_a: EDAM:0003034 ! Sequence feature identifier + +[Term] +id: EDAM:0003107 +name: Sequence feature name +namespace: identifier +def: "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." [EDAM:EBI "EMBRACE definition"] +subset: identifier +is_a: EDAM:0002099 ! Name +is_a: EDAM:0003034 ! Sequence feature identifier + + + + +[Term] +id: EDAM:0003034 +name: Sequence feature identifier +namespace: identifier +def: "Name or other identifier of molecular sequence feature(s)." [EDAM:EBI "EMBRACE definition"] +subset: identifier is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0001270 ! Feature table +is_a: EDAM:0002914 ! Sequence feature metadata +relationship: is_identifier_of EDAM:0001255 ! Sequence features + +[Term] +id: EDAM:0001023 +name: EMBOSS Uniform Feature Object +namespace: data +def: "The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "UFO" EXACT [] +is_a: EDAM:0003034 ! Sequence feature identifier +is_a: EDAM:0002099 ! Name + + + [Term] id: EDAM:0001893 @@ -18321,6 +18177,7 @@ namespace: identifier def: "An identifier of molecular sequence(s) or entries from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) +is_a: EDAM:0000855 ! Sequence metadata relationship: is_identifier_of EDAM:0002044 ! Sequence @@ -18383,6 +18240,17 @@ is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000872 ! Phylogenetic tree + +[Term] +id: EDAM:0003036 +name: Matrix identifier +namespace: identifier +def: "An identifier of an array of numerical values, such as a comparison matrix." [EDAM:EBI "EMBRACE definition"] +subset: identifier +is_a: EDAM:0000976 ! Identifier (typed) +relationship: is_identifier_of EDAM:0002082 ! Matrix + + [Term] id: EDAM:0001069 name: Comparison matrix identifier @@ -18390,20 +18258,43 @@ namespace: identifier def: "An identifier of a comparison matrix." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Substitution matrix identifier" EXACT [] -is_a: EDAM:0000976 ! Identifier (typed) +is_a: EDAM:0003036 ! Matrix identifier relationship: is_identifier_of EDAM:0000874 ! Comparison matrix + [Term] -id: EDAM:0001070 -name: Structure ID +id: EDAM:0003035 +name: Structure identifier namespace: identifier def: "An identifier of a molecular tertiary structure, typically an entry from a structure database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) -is_a: EDAM:0002091 ! Accession +is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0000883 ! Structure [Term] +id: EDAM:0001070 +name: Structure ID +namespace: identifier +def: "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." [EDAM:EBI "EMBRACE definition"] +subset: identifier +is_a: EDAM:0003035 ! Structure identifier +is_a: EDAM:0002091 ! Accession + + +[Term] +id: EDAM:0001759 +name: PDB model number +namespace: identifier +def: "Identifier of a model structure from a PDB file." [EDAM:EBI "EMBRACE definition"] +subset: identifier +synonym: "Model number" EXACT [] +xref: WHATIF: model_number +is_a: EDAM:0003035 ! Structure identifier +! pdbx_PDB_model_num in PDBML + + +[Term] id: EDAM:0001071 name: Structural (3D) profile ID namespace: identifier @@ -18430,7 +18321,7 @@ name: Amino acid index ID namespace: identifier def: "Identifier of an index of amino acid physicochemical and biochemical property data." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0000976 ! Identifier (typed) +is_a: EDAM:0003036 ! Matrix identifier is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0001501 ! Amino acid index @@ -18443,7 +18334,7 @@ def: "Identifier of a report of molecular interactions from a database (typicall subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0002599 ! Molecular interaction data +relationship: is_identifier_of EDAM:0002599 ! Molecular interaction [Term] id: EDAM:0001075 @@ -18453,7 +18344,7 @@ def: "Identifier of a protein family." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Protein secondary database record identifier" EXACT [] is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000907 ! Protein family annotation +relationship: is_identifier_of EDAM:0000907 ! Protein family [Term] id: EDAM:0002910 @@ -18503,7 +18394,6 @@ subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0000989 ! Protein identifier relationship: is_identifier_of EDAM:0001315 ! Gene features (TFBS) -relationship: is_identifier_of EDAM:0002147 ! Protein report (transcription factor) [Term] id: EDAM:0002911 @@ -18532,21 +18422,20 @@ def: "Identifier of an entry from a database of electron microscopy data." [EDAM subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000941 ! Experiment annotation (electron microscopy model) +relationship: is_identifier_of EDAM:0000941 ! Electron microscopy model [Term] id: EDAM:0001080 -alt_id: EDAM:0002708 -name: Gene annotation (expression) ID +name: Gene expression report ID namespace: identifier +alt_id: EDAM:0002708 def: "Accession of a report of gene expression (e.g. a gene expression profile) from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Gene expression profile identifier" EXACT [] is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000929 ! Gene annotation (expression) -relationship: is_identifier_of EDAM:0000928 ! Gene expression profile +relationship: is_identifier_of EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0001081 @@ -18605,7 +18494,7 @@ def: "Identifier of a biological reaction from a database." [EDAM:EBI "EMBRACE d subset: identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0000976 ! Identifier (typed) -relationship: is_identifier_of EDAM:0000908 ! Reaction annotation +relationship: is_identifier_of EDAM:0002978 ! Reaction data [Term] @@ -18616,11 +18505,11 @@ def: "Identifier of a biological or biomedical workflow, typically from a databa subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0002971 ! Workflow data +relationship: is_identifier_of EDAM:0002972 ! Workflow [Term] id: EDAM:0001084 -name: Data definition identifier +name: Data resource definition identifier namespace: identifier def: "Identifier of a data type definition from some provider." [EDAM:EBI "EMBRACE definition"] subset: identifier @@ -18662,10 +18551,9 @@ def: "Identifier of an entry from a database of chemicals." [EDAM:EBI "EMBRACE d subset: identifier synonym: "Small molecule identifier" EXACT [] synonym: "Chemical compound identifier" EXACT [] -is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0000962 ! Small molecule report -relationship: is_identifier_of EDAM:0001712 ! Small molecule structure image +relationship: is_identifier_of EDAM:0000962 ! Small molecule annotation +relationship: is_identifier_of EDAM:0001712 ! Structure image (small molecule) relationship: is_identifier_of EDAM:0000846 ! Chemical formula [Term] @@ -18759,7 +18647,7 @@ is_a: EDAM:0002091 ! Accession id: EDAM:0002587 name: Blot ID namespace: identifier -def: "Unique identifier of a blot from a Nothern Blot." [EDAM:EBI "EMBRACE definition"] +def: "Unique identifier of a blot from a Northern Blot." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0000976 ! Identifier (typed) @@ -19346,7 +19234,7 @@ relationship: is_identifier_of EDAM:0001354 ! Sequence profile id: EDAM:0002660 name: BioNumbers ID namespace: identifier -def: "Identifier of a entry from the BioNumbers database of key numbers and associated data in molecular biology." [EDAM:EBI "EMBRACE definition"] +def: "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002091 ! Accession @@ -19396,7 +19284,7 @@ namespace: identifier def: "Name or other identifier of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0002525 ! Nucleic acid data +relationship: is_identifier_of EDAM:0002084 ! Nucleic acid report [Term] @@ -19440,13 +19328,13 @@ namespace: identifier def: "Identifier of a protein." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0002524 ! Protein data +relationship: is_identifier_of EDAM:0000896 ! Protein report [Term] id: EDAM:0002907 name: Protein accession namespace: identifier -def: "Accession of a protein despoited in a database." [EDAM:EBI "EMBRACE definition"] +def: "Accession of a protein deposited in a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000989 ! Protein identifier is_a: EDAM:0002901 ! Molecule accession @@ -19567,7 +19455,7 @@ def: "Identifier of an amino acid." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Residue identifier" EXACT [] is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0002016 ! Amino acid data +relationship: is_identifier_of EDAM:0002016 ! Amino acid property [Term] @@ -19772,7 +19660,7 @@ is_a: EDAM:0000990 ! Compound name id: EDAM:0001000 name: Chemical name (brand) namespace: identifier -def: "Brandname of a chemical compound." [EDAM:EBI "EMBRACE definition"] +def: "Brand name of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Brand chemical name" EXACT [] is_a: EDAM:0000990 ! Compound name @@ -19875,6 +19763,36 @@ regex: "DAP[0-9]+" is_a: EDAM:0002895 ! Drug accession [Term] +id: EDAM:0003102 +name: CAS number +namespace: identifier +def: "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." [EDAM:EBI "EMBRACE definition"] +subset: identifier +synonym: "CAS registry number" EXACT [] +is_a: EDAM:0002895 ! Drug accession + +[Term] +id: EDAM:0003103 +name: ATC code +namespace: identifier +def: "Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC)." [EDAM:EBI "EMBRACE definition"] +subset: identifier +is_a: EDAM:0002895 ! Drug accession + +[Term] +id: EDAM:0003104 +name: UNII +namespace: identifier +def: "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." [EDAM:EBI "EMBRACE definition"] +subset: identifier +synonym: "Unique Ingredient Identifier" EXACT [] +is_a: EDAM:0001086 ! Compound identifier + + + + + +[Term] id: EDAM:0002578 name: ArachnoServer ID namespace: identifier @@ -19916,6 +19834,18 @@ def: "Three letter amino acid identifier, e.g. GLY." [EDAM:EBI "EMBRACE definiti subset: identifier is_a: EDAM:0001006 ! Amino acid name + +[Term] +id: EDAM:0001758 +name: PDB residue name +namespace: identifier +def: "Three-letter amino acid residue names as used in PDB files." [EDAM:EBI "EMBRACE definition"] +subset: format +xref: WHATIF: type +is_a: EDAM:0002564 ! Amino acid name (three letter) + + + [Term] id: EDAM:0002565 name: Amino acid name (full name) @@ -19999,7 +19929,7 @@ def: "Name of a chromosome." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002119 ! Nucleic acid identifier is_a: EDAM:0000984 ! Molecule name -relationship: is_identifier_of EDAM:0000919 ! Gene annotation (chromosome) +relationship: is_identifier_of EDAM:0000919 ! Nucleic acid features (chromosome) [Term] id: EDAM:0002208 @@ -20081,7 +20011,6 @@ def: "Name of a protein." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000989 ! Protein identifier is_a: EDAM:0000984 ! Molecule name -relationship: is_identifier_of EDAM:0002524 ! Protein data [Term] id: EDAM:0001010 @@ -20090,7 +20019,7 @@ namespace: identifier def: "Name or other identifier of an enzyme or record from a database of enzymes." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000989 ! Protein identifier -relationship: is_identifier_of EDAM:0001509 ! Protein report (enzyme) +relationship: is_identifier_of EDAM:0001509 ! Enzyme property [Term] @@ -20122,6 +20051,17 @@ is_a: EDAM:0002907 ! Protein accession [Term] +id: EDAM:0003029 +name: Protein ID (EMBL/GenBank/DDBJ) +namespace: identifier +def: "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators." [EDAM:EBI "EMBRACE definition"] +comment: This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. +subset: identifier +is_a: EDAM:0002907 ! Protein accession + + + +[Term] id: EDAM:0002398 name: Protein ID (Ensembl) namespace: identifier @@ -20339,7 +20279,7 @@ namespace: identifier def: "Name of a restriction enzyme." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001012 ! Enzyme name -relationship: is_identifier_of EDAM:0001517 ! Protein report (restriction enzyme) +relationship: is_identifier_of EDAM:0001517 ! Restriction enzyme property [Term] id: EDAM:0001018 @@ -20379,7 +20319,7 @@ is_obsolete: true consider: EDAM:0001276 ! Nucleic acid features -! Don't know whether the loci identifiers listered here are 'ordered' or not. +! Don't know whether the loci identifiers listed here are 'ordered' or not. [Term] id: EDAM:0002009 @@ -20553,7 +20493,7 @@ is_a: EDAM:0001893 ! Locus ID id: EDAM:0001026 name: Gene symbol namespace: identifier -def: "The short name of a gene; a single word that does not contain whitespace characters. It is typically derived from the gene name." [EDAM:EBI "EMBRACE definition"] +def: "The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:Global_GeneSymbol xref: Moby_namespace:Global_GeneCommonName @@ -20563,7 +20503,7 @@ is_a: EDAM:0002299 ! Gene name id: EDAM:0002299 name: Gene name namespace: identifier -def: "The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain whitespace characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol." [EDAM:EBI "EMBRACE definition"] +def: "The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001025 ! Gene identifier is_a: EDAM:0002099 ! Name @@ -20578,7 +20518,7 @@ subset: identifier synonym: "Gene code" EXACT [] synonym: "Gene accession" EXACT [] is_a: EDAM:0001025 ! Gene identifier -is_a: EDAM:0002091 ! Accession +is_a: EDAM:0001893 ! Locus ID [Term] @@ -20938,7 +20878,7 @@ synonym: "Entrez gene ID" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID is_a: EDAM:0002295 ! Gene ID - +is_a: EDAM:0001098 ! RefSeq accession [Term] id: EDAM:0001031 @@ -21168,7 +21108,8 @@ namespace: identifier def: "Gene identifier from Glossina morsitans GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans -is_a: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true +consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] @@ -21178,7 +21119,8 @@ namespace: identifier def: "Gene identifier from Leishmania major GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor -is_a: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true +consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] @@ -21188,7 +21130,8 @@ namespace: identifier def: "Gene identifier from Plasmodium falciparum GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum -is_a: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true +consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] @@ -21198,7 +21141,8 @@ namespace: identifier def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe -is_a: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true +consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] @@ -21208,7 +21152,8 @@ namespace: identifier def: "Gene identifier from Trypanosoma brucei GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei -is_a: EDAM:0001035 ! Gene ID (GeneDB) +is_obsolete: true +consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] id: EDAM:0001887 @@ -21218,7 +21163,8 @@ def: "Identifier for genetic elements in MIPS Maize database." [EDAM:EBI "EMBRAC subset: identifier synonym: "MIPS genetic element identifier (Maize)" EXACT [] xref: Moby_namespace:MIPS_GE_Maize -is_a: EDAM:0002285 ! Gene ID (MIPS) +is_obsolete: true +consider: EDAM:0002285 ! Gene ID (MIPS) [Term] @@ -21229,7 +21175,8 @@ def: "Identifier for genetic elements in MIPS Medicago database." [EDAM:EBI "EMB subset: identifier synonym: "MIPS genetic element identifier (Medicago)" EXACT [] xref: Moby_namespace:MIPS_GE_Medicago -is_a: EDAM:0002285 ! Gene ID (MIPS) +is_obsolete: true +consider: EDAM:0002285 ! Gene ID (MIPS) [Term] id: EDAM:0002751 @@ -21564,7 +21511,8 @@ name: Genus name (virus) namespace: identifier def: "The name of a genus of viruses." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001870 ! Genus name +is_obsolete: true +consider: EDAM:0001870 ! Genus name [Term] id: EDAM:0002734 @@ -21572,7 +21520,8 @@ name: Family name (virus) namespace: identifier def: "The name of a family of viruses." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0002732 ! Family name +is_obsolete: true +consider: EDAM:0002732 ! Family name [Term] @@ -21631,7 +21580,8 @@ name: Sequence database name namespace: identifier def: "The name of a molecular sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001056 ! Database name +is_obsolete: true +consider: EDAM:0001056 ! Database name [Term] id: EDAM:0002735 @@ -21639,7 +21589,8 @@ name: Database name (SwissRegulon) namespace: identifier def: "The name of a SwissRegulon database." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001056 ! Database name +is_obsolete: true +consider: EDAM:0001056 ! Database name [Term] @@ -21648,7 +21599,8 @@ name: Database name (CMD) namespace: identifier def: "The name of a subdivision of the Collagen Mutation Database (CMD) database." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001056 ! Database name +is_obsolete: true +consider: EDAM:0001056 ! Database name [Term] @@ -21657,7 +21609,8 @@ name: Database name (Osteogenesis) namespace: identifier def: "The name of a subdivision of the Osteogenesis database." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001056 ! Database name +is_obsolete: true +consider: EDAM:0001056 ! Database name [Term] id: EDAM:0001058 @@ -21726,6 +21679,8 @@ subset: identifier synonym: "Sequence accession number" EXACT [] is_a: EDAM:0001063 ! Sequence identifier is_a: EDAM:0002091 ! Accession +is_a: EDAM:0002914 ! Sequence feature metadata + [Term] id: EDAM:0002154 @@ -21736,6 +21691,19 @@ subset: identifier is_a: EDAM:0001063 ! Sequence identifier is_a: EDAM:0002099 ! Name + +[Term] +id: EDAM:0001095 +name: EMBOSS Uniform Sequence Address +namespace: identifier +def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"] +subset: data +synonym: "USA" EXACT [] +is_a: EDAM:0001063 ! Sequence identifier +is_a: EDAM:0002099 ! Name + + + [Term] id: EDAM:0002291 name: UniProt ID @@ -21781,41 +21749,51 @@ relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0002290 -name: EMBL identifier +name: EMBL accession namespace: identifier -def: "An identifier of an entry from the EMBL sequence database." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0001107 +def: "An accession number of an entry from the EMBL sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier +synonym: "EMBL accession number" EXACT [] +synonym: "EMBL identifier" EXACT [] synonym: "EMBL ID" EXACT [] is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ ID [Term] id: EDAM:0002292 -name: GenBank identifier +name: GenBank accession namespace: identifier -def: "An identifier of an entry from the GenBank sequence database." [EDAM:EBI "EMBRACE definition"] +alt_id: EDAM:0001108 +def: "Accession number of an entry from the GenBank sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ ID +synonym: "GenBank accession number" EXACT [] +synonym: "GenBank identifier" EXACT [] synonym: "GenBank ID" EXACT [] [Term] id: EDAM:0002916 -name: DDBJ identifier +name: DDBJ accession namespace: identifier +alt_id: EDAM:0001109 def: "An identifier of an entry from the DDBJ sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ ID +synonym: "DDBJ accession number" EXACT [] +synonym: "DDBJ identifier" EXACT [] synonym: "DDBJ ID" EXACT [] + [Term] id: EDAM:0001855 name: Clone ID namespace: identifier def: "An identifier of a clone (cloned molecular sequence) from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001097 ! Sequence accession (nucleic acid) -relationship: is_identifier_of EDAM:0002703 ! Gene annotation (clone or EST) +is_a: EDAM:0002769 ! Transcript ID + [Term] id: EDAM:0002386 @@ -21873,7 +21851,7 @@ name: RefSeq accession namespace: identifier def: "Accession number of a RefSeq database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier -regex: "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_[0-9]+" +regex: "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+" is_a: EDAM:0002362 ! Sequence accession (hybrid) synonym: "RefSeq ID" EXACT [] @@ -22001,13 +21979,13 @@ name: EST accession namespace: identifier def: "Identifier of an EST sequence." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001097 ! Sequence accession (nucleic acid) +is_a: EDAM:0001855 ! Clone ID [Term] id: EDAM:0001103 name: EMBL/GenBank/DDBJ ID namespace: identifier -def: "Identifier of an entry from the EMBL/GenBank/DDBJ databases." [EDAM:EBI "EMBRACE definition"] +def: "Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001097 ! Sequence accession (nucleic acid) @@ -22066,7 +22044,7 @@ id: EDAM:0002730 name: COGEME unisequence ID namespace: identifier def: "Identifier of a unisequence from the COGEME database." [EDAM:EBI "EMBRACE definition"] -comment: A unisequence is a single sequence assembled from ESTs. +comment: A unisequence is a single sequence assembled from ESTs. subset: identifier is_a: EDAM:0002728 ! EST accession @@ -22080,38 +22058,13 @@ is_a: EDAM:0002728 ! EST accession [Term] -id: EDAM:0001107 -name: EMBL accession number -namespace: identifier -def: "Accession number of an EMBL sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002290 ! EMBL identifier - -[Term] -id: EDAM:0001108 -name: GenBank accession -namespace: identifier -def: "Accession number of a GenBank sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002292 ! GenBank identifier - - -[Term] -id: EDAM:0001109 -name: DDBJ accession -namespace: identifier -def: "Accession number of a DDBJ sequence database entry." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_a: EDAM:0002916 ! DDBJ identifier - -[Term] id: EDAM:0001105 name: dbEST accession namespace: identifier def: "Identifier of a dbEST database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "dbEST ID" EXACT [] -is_a: EDAM:0001108 ! GenBank accession +is_a: EDAM:0002292 ! GenBank accession is_a: EDAM:0002728 ! EST accession [Term] @@ -22132,6 +22085,7 @@ namespace: identifier def: "A unique identifier of a cDNA molecule catalogued in the RefSeq database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001855 ! Clone ID +is_a: EDAM:0001098 ! RefSeq accession [Term] id: EDAM:0001110 @@ -22752,7 +22706,7 @@ namespace: identifier def: "Accession number of an entry from the GEO database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "o^GDS[0-9]+" -is_a: EDAM:0001080 ! Gene annotation (expression) ID +is_a: EDAM:0001080 ! Gene expression report ID [Term] id: EDAM:0001148 @@ -22760,7 +22714,7 @@ name: GermOnline ID namespace: identifier def: "Identifier of an entry from the GermOnline database." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001080 ! Gene annotation (expression) ID +is_a: EDAM:0001080 ! Gene expression report ID [Term] @@ -22769,7 +22723,7 @@ name: EMAGE ID namespace: identifier def: "Identifier of an entry from the EMAGE database." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001080 ! Gene annotation (expression) ID +is_a: EDAM:0001080 ! Gene expression report ID [Term] id: EDAM:0002709 @@ -22777,7 +22731,7 @@ name: CleanEx entry name namespace: identifier def: "An identifier of a gene expression profile from the CleanEx database." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001080 ! Gene annotation (expression) ID +is_a: EDAM:0001080 ! Gene expression report ID [Term] id: EDAM:0001150 @@ -23031,7 +22985,7 @@ is_a: EDAM:0002365 ! Pathway or network accession id: EDAM:0002670 name: Pathway ID (DQCS) namespace: identifier -def: "Identifier of a signalling pathway from the Database of Quantitative Cellular Signaling (DQCS)." [EDAM:EBI "EMBRACE definition"] +def: "Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002365 ! Pathway or network accession @@ -23052,7 +23006,7 @@ def: "Unique identifier of a MIRIAM data resource." [EDAM:EBI "EMBRACE definitio comment: This is the identifier used internally by MIRIAM for a data type. For example 'MIR:00100005'. subset: identifier regex: "MIR:[0-9]{8}" -is_a: EDAM:0002902 ! Data definition accession +is_a: EDAM:0002902 ! Data resource definition accession relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype [Term] @@ -23061,27 +23015,26 @@ name: MIRIAM data type name namespace: identifier def: "The name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0002253 ! Data definition name -is_a: EDAM:0002099 ! Name +is_a: EDAM:0002253 ! Data resource definition name relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype [Term] id: EDAM:0002253 -name: Data definition name +name: Data resource definition name namespace: identifier def: "The name of a data type." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001084 ! Data definition identifier +is_a: EDAM:0001084 ! Data resource definition identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002902 -name: Data definition accession +name: Data resource definition accession namespace: identifier def: "Accession of a data definition (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier -is_a: EDAM:0001084 ! Data definition identifier +is_a: EDAM:0001084 ! Data resource definition identifier is_a: EDAM:0002091 ! Accession @@ -23092,7 +23045,7 @@ namespace: identifier def: "The URI (URL or URN) of a data entity from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] comment: A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. For example: urn:miriam:pubmed:16333295 is the MIRIAM URI of the publication about MIRIAM, whereas 'urn:miriam:obo.go:GO%3A0045202' refers to GO. subset: identifier -is_a: EDAM:0002902 ! Data definition accession +is_a: EDAM:0002902 ! Data resource definition accession is_a: EDAM:0001047 ! URI relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype @@ -23123,7 +23076,7 @@ def: "Identifier of a biological reaction from the BioCyc reactions database." [ subset: identifier is_a: EDAM:0002108 ! Reaction ID is_a: EDAM:0002104 ! BioCyc ID -relationship: in_topic EDAM:0000613 ! Peptides and amino acids +relationship: has_topic EDAM:0000613 ! Peptides and amino acids [Term] @@ -23182,30 +23135,12 @@ def: "Unique identifier of a Taverna workflow." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001083 ! Workflow ID -[Term] -id: EDAM:0001168 -name: Workflow URL -namespace: identifier -def: "URL of a workflow." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001052 ! URL - - -[Term] -id: EDAM:0001169 -name: Taverna workflow URL -namespace: identifier -def: "URL of a Taverna workflow." [EDAM:EBI "EMBRACE definition"] -subset: identifier -is_obsolete: true -consider: EDAM:0001052 ! URL [Term] id: EDAM:0001170 name: Biological model name namespace: identifier -def: "Name of a biological / mathematical model." [EDAM:EBI "EMBRACE definition"] +def: "Name of a biological (mathematical) model." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001085 ! Biological model identifier is_a: EDAM:0002099 ! Name @@ -23228,17 +23163,6 @@ subset: identifier regex: "[0-9]+" is_a: EDAM:0002891 ! Biological model accession -[Term] -id: EDAM:0001759 -name: PDB model number -namespace: identifier -def: "Identifier of a model structure from a PDB file." [EDAM:EBI "EMBRACE definition"] -subset: identifier -synonym: "Model number" EXACT [] -xref: WHATIF: model_number -is_a: EDAM:0001170 ! Biological model name -relationship: is_identifier_of EDAM:0000883 ! Structure -! pdbx_PDB_model_num in PDBML [Term] id: EDAM:0002339 @@ -23402,7 +23326,7 @@ namespace: identifier def: "The name of a term for a biological process from the GO ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true -consider: EDAM:00002339 ! Ontology term name +consider: EDAM:0002339 ! Ontology term name [Term] id: EDAM:0003027 @@ -23411,7 +23335,7 @@ namespace: identifier def: "The name of a term for a molecular function from the GO ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true -consider: EDAM:00002339 ! Ontology term name +consider: EDAM:0002339 ! Ontology term name [Term] id: EDAM:0002584 @@ -23436,7 +23360,6 @@ subset: identifier synonym: "PMID" EXACT [] regex: "[1-9][0-9]{0,8}" ! regex: "^[0-9]+" - is_a: EDAM:0001088 ! Article ID [Term] @@ -23489,7 +23412,7 @@ is_a: EDAM:0002373 ! Spot ID id: EDAM:0002588 name: BlotBase blot ID namespace: identifier -def: "Unique identifier of a blot from a Nothern Blot from the BlotBase database." [EDAM:EBI "EMBRACE definition"] +def: "Unique identifier of a blot from a Northern Blot from the BlotBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002587 ! Blot ID @@ -23581,8 +23504,8 @@ is_obsolete: true id: EDAM:0002350 name: Format (typed) namespace: format -def: "A format for a particular datatype." [EDAM:EBI "EMBRACE definition"] -comment: This branch provides an alternative organisation of the terms nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All terms under here are already included under those branches. +def: "A broad class of format distinguished by the scientific nature of the data that is identified." [EDAM:EBI "EMBRACE definition"] +comment: This term exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The term branch under 'Format (typed)' provides an alternative organisation of the terms nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All terms under here are already included under those branches. subset: format is_a: EDAM:0001915 ! Format @@ -23649,7 +23572,7 @@ namespace: format def: "Format of sequence variation annotation." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000918 ! Sequence variation annotation +relationship: is_format_of EDAM:0000918 ! Nucleic acid features (variation) [Term] @@ -23678,9 +23601,8 @@ name: URI format namespace: format def: "Typical textual representation of a URI." [EDAM:EBI "EMBRACE definition"] subset: format -is_a: EDAM:0002330 ! Text -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001047 ! URI +is_obsolete: true +consider: EDAM:0001047 ! URI [Term] id: EDAM:0001918 @@ -23688,8 +23610,8 @@ name: Atomic data format namespace: format def: "Data format for an individual atom." [EDAM:EBI "EMBRACE definition"] subset: format -is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001755 ! Protein atom +is_obsolete: true +consider: EDAM:0001475 ! PDB database entry format [Term] id: EDAM:0001919 @@ -23722,7 +23644,7 @@ relationship: is_format_of EDAM:0000863 ! Sequence alignment id: EDAM:0002920 name: Alignment format (pair only) namespace: format -def: "Data format for molecular sequence alignment information that can hold pairwise sequence alignment(s)." [EDAM:EBI "EMBRACE definition"] +def: "Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001921 ! Alignment format relationship: is_format_of EDAM:0001381 ! Sequence alignment (pair) @@ -23768,7 +23690,8 @@ name: Amino acid identifier format namespace: format def: "Text format (representation) of amino acid residues." [EDAM:EBI "EMBRACE definition"] subset: format -is_a: EDAM:0002350 ! Format (typed) +is_obsolete: true +consider: EDAM:0000994 ! Amino acid identifier [Term] id: EDAM:0002017 @@ -23776,7 +23699,7 @@ name: Amino acid index format namespace: format def: "Data format for an amino acid index." [EDAM:EBI "EMBRACE definition"] subset: format -is_a: EDAM:0002350 ! Format (typed) +is_a: EDAM:0003033 ! Matrix format relationship: is_format_of EDAM:0001501 ! Amino acid index [Term] @@ -23815,7 +23738,7 @@ def: "Format of a report on a chemical compound." [EDAM:EBI "EMBRACE definition" subset: format synonym: "Chemical compound annotation format" EXACT [] is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000962 ! Small molecule report +relationship: is_format_of EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002031 @@ -23854,8 +23777,46 @@ is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000871 ! Phylogenetic character data [Term] +id: EDAM:0003097 +name: Protein domain classification format +namespace: format +def: "Format of data concerning the classification of the sequences and/or structures of protein structural domain(s)." [EDAM:EBI "EMBRACE definition"] +subset: format +is_a: EDAM:0002350 ! Format (typed) +relationship: is_format_of EDAM:0000900 ! Protein domain classification + + +[Term] +id: EDAM:0003098 +name: Raw SCOP domain classification format +namespace: data +def: "Format of raw SCOP domain classification data files." [EDAM:EBI "EMBRACE definition"] +comment: These are the parsable data files provided by SCOP. +subset: format +is_a: EDAM:0003097 ! Protein domain classification format + +[Term] +id: EDAM:0003099 +name: Raw CATH domain classification format +namespace: data +def: "Format of raw CATH domain classification data files." [EDAM:EBI "EMBRACE definition"] +comment: These are the parsable data files provided by CATH. +subset: format +is_a: EDAM:0003097 ! Protein domain classification format + +[Term] +id: EDAM:0003100 +name: CATH domain report format +namespace: data +def: "Format of summary of domain classification information for a CATH domain." [EDAM:EBI "EMBRACE definition"] +comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. +subset: data +is_a: EDAM:0003097 ! Protein domain classification format + + +[Term] id: EDAM:0002045 -name: Experiment annotation (electron microscopy model) format +name: Electron microscopy model format namespace: format def: "Annotation format for electron microscopy models." [EDAM:EBI "EMBRACE definition"] subset: format @@ -23865,12 +23826,12 @@ consider: EDAM:0002350 ! Format (typed) [Term] id: EDAM:0002049 -name: Phylogenetic report (tree distances) format +name: Phylogenetic tree report (tree distances) format namespace: format def: "Format for phylogenetic tree distance data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001442 ! Phylogenetic report (tree distances) +relationship: is_format_of EDAM:0001442 ! Phylogenetic tree report (tree distances) [Term] id: EDAM:0002051 @@ -23879,7 +23840,7 @@ namespace: format def: "Format for sequence polymorphism data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0002885 ! Polymorphism annotation +relationship: is_format_of EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0002052 @@ -23888,7 +23849,7 @@ namespace: format def: "Format for reports on a protein family." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000907 ! Protein family annotation +relationship: is_format_of EDAM:0000907 ! Protein family [Term] id: EDAM:0002054 @@ -23897,7 +23858,7 @@ namespace: format def: "Format for protein interaction data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000906 ! Protein interaction report +relationship: is_format_of EDAM:0000906 ! Protein report (interaction) [Term] @@ -23920,12 +23881,12 @@ relationship: is_format_of EDAM:0000931 ! Experiment annotation (microarray) [Term] id: EDAM:0002058 -name: Gene annotation (expression) format +name: Gene expression report format namespace: format def: "Format for a report on gene expression." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002031 ! Gene annotation format -relationship: is_format_of EDAM:0000929 ! Gene annotation (expression) +relationship: is_format_of EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0002059 @@ -23965,12 +23926,21 @@ is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000896 ! Protein report [Term] +id: EDAM:0003033 +name: Matrix format +namespace: format +def: "Format of a matrix (array) of numerical values." [EDAM:EBI "EMBRACE definition"] +subset: format +is_a: EDAM:0002350 ! Format (typed) +relationship: is_format_of EDAM:0002082 ! Matrix + +[Term] id: EDAM:0002064 name: 3D-1D scoring matrix format namespace: format def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [EDAM:EBI "EMBRACE definition"] subset: format -is_a: EDAM:0002350 ! Format (typed) +is_a: EDAM:0003033 ! Matrix format relationship: is_format_of EDAM:0001499 ! 3D-1D scoring matrix [Term] @@ -23980,7 +23950,7 @@ namespace: format def: "Format of a report on the quality of a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0001539 ! Protein structure report (quality evaluation) +relationship: is_format_of EDAM:0001539 ! Protein structural quality report [Term] @@ -24089,7 +24059,7 @@ namespace: format def: "Format used for report on coding regions in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002031 ! Gene annotation format -relationship: is_format_of EDAM:0001313 ! Gene features (coding region) +relationship: is_format_of EDAM:0001313 ! Nucleic acid features (coding sequence) [Term] id: EDAM:0002170 @@ -24126,7 +24096,6 @@ def: "Format of a report on protein features (domain composition)." [EDAM:EBI "E subset: format is_obsolete: true consider: EDAM:0002350 ! Format (typed) -relationship: is_format_of EDAM:0000901 ! Protein features (domains) [Term] id: EDAM:0002571 @@ -24181,8 +24150,8 @@ name: PDB atom record format namespace: format def: "Format of an ATOM record (describing data for an individual atom) from a PDB file." [EDAM:EBI "EMBRACE definition"] subset: format -is_a: EDAM:0001918 ! Atomic data format -is_a: EDAM:0002330 ! Text +is_obsolete: true +consider: EDAM:0001476 ! PDB format [Term] id: EDAM:0002551 @@ -24290,8 +24259,6 @@ def: "GFF feature file format with sequence in the header." [EDAM:EBI "EMBRACE d subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0001974 ! GFF2 -! is_obsolete: true -! consider: EDAM:0001974 ! GFF [Term] @@ -24302,8 +24269,6 @@ def: "GFF3 feature file format with sequence." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0001975 ! GFF2 -! is_obsolete: true -! consider: EDAM:0001975 ! GFF3 [Term] @@ -24891,7 +24856,7 @@ def: "BAM format, the binary, BGZF-formatted compressed version of SAM format fo subset: format spec: http://samtools.sourceforge.net/SAM-1.3.pdf is_a: EDAM:0002057 ! Sequence trace format -is_a: EDAM:0002920 ! Alignment format (pair only) +is_a: EDAM:0001921 ! Alignment format is_a: EDAM:0002333 ! Binary [Term] @@ -24955,7 +24920,7 @@ namespace: format def: "Format for a sequence feature table." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001920 ! Sequence feature annotation format -relationship: is_format_of EDAM:0001270 ! Feature table +relationship: is_format_of EDAM:0001255 ! Sequence features [Term] id: EDAM:0001979 @@ -25239,7 +25204,7 @@ consider: EDAM:0001973 ! nexusnon id: EDAM:0001996 name: pair namespace: format -def: "EMBOSS simple pairwise alignment format." [EDAM:EBI "EMBRACE definition"] +def: "EMBOSS simple sequence pair alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) @@ -25311,7 +25276,7 @@ is_a: EDAM:0002330 ! Text id: EDAM:0002003 name: srspair namespace: format -def: "Simple pairwise sequence (alignment) format for SRS." [EDAM:EBI "EMBRACE definition"] +def: "Simple sequence pair (alignment) format for SRS." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002920 ! Alignment format (pair only) is_a: EDAM:0002330 ! Text @@ -25568,7 +25533,7 @@ def: "The format of an entry from the INOH signal transduction pathways database subset: format is_obsolete: true consider: EDAM:0002331 ! HTML -!is_a: EDAM:0002013 ! Biological pathway or network format + [Term] @@ -25667,15 +25632,6 @@ subset: format is_a: EDAM:0002014 ! Sequence-profile alignment format is_a: EDAM:0002330 ! Text -[Term] -id: EDAM:0001758 -name: PDB residue name format -namespace: format -def: "Format of amino acid residue names as used in PDB files." [EDAM:EBI "EMBRACE definition"] -subset: format -xref: WHATIF: type -is_a: EDAM:0002562 ! Amino acid identifier format -is_a: EDAM:0002330 ! Text [Term] @@ -25837,7 +25793,7 @@ is_a: EDAM:0002330 ! Text id: EDAM:0001808 name: GeneIlluminator gene report format namespace: format -def: "Report format for biological functions associated with a gene name and its alternative names (synomyms, homonyms), as generated by the GeneIlluminater service." [EDAM:EBI "EMBRACE definition"] +def: "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service." [EDAM:EBI "EMBRACE definition"] comment: This includes a gene name and abbreviation of the name which may be in a namespace indicating the gene status and relevant organisation. subset: format xref: Moby:GI_Gene @@ -26136,22 +26092,22 @@ relationship: is_format_of EDAM:0001427 ! Phylogenetic discrete data [Term] id: EDAM:0002039 -name: Phylogenetic report (cliques) format +name: Phylogenetic tree report (cliques) format namespace: format def: "Format of phylogenetic cliques data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002036 ! Phylogenetic character data format -relationship: is_format_of EDAM:0001428 ! Phylogenetic report (cliques) +relationship: is_format_of EDAM:0001428 ! Phylogenetic tree report (cliques) [Term] id: EDAM:0002040 -name: Phylogenetic report (invariants) format +name: Phylogenetic tree report (invariants) format namespace: format def: "Format of phylogenetic invariants data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002036 ! Phylogenetic character data format -relationship: is_format_of EDAM:0001429 ! Phylogenetic report (invariants) +relationship: is_format_of EDAM:0001429 ! Phylogenetic tree report (invariants) [Term] id: EDAM:0001430 @@ -26195,7 +26151,7 @@ name: phylip cliques namespace: format def: "Format of PHYLIP cliques data." [EDAM:EBI "EMBRACE definition"] subset: format -is_a: EDAM:0002039 ! Phylogenetic report (cliques) format +is_a: EDAM:0002039 ! Phylogenetic tree report (cliques) format is_a: EDAM:0002330 ! Text @@ -26214,7 +26170,7 @@ name: phylip tree distance namespace: format def: "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." [EDAM:EBI "EMBRACE definition"] subset: format -is_a: EDAM:0002049 ! Phylogenetic report (tree distances) format +is_a: EDAM:0002049 ! Phylogenetic tree report (tree distances) format is_a: EDAM:0002330 ! Text [Term] @@ -26470,8 +26426,9 @@ namespace: format def: "Format of Affymetrix data file of information about (raw) expression levels of the individual probes." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Affymetrix probe raw data format" EXACT [] -is_a: EDAM:0002058 ! Gene annotation (expression) format +is_a: EDAM:0002058 ! Gene expression report format is_a: EDAM:0002330 ! Text +relationship: is_format_of EDAM:0003110 ! Raw microarray data [Term] @@ -26481,8 +26438,9 @@ namespace: format def: "Format of Affymetrix data file of information about (normalised) expression levels of the individual probes." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Affymetrix probe normalised data format" EXACT [] -is_a: EDAM:0002058 ! Gene annotation (expression) format +is_a: EDAM:0002058 ! Gene expression report format is_a: EDAM:0002330 ! Text +relationship: is_format_of EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0001637 @@ -26491,9 +26449,9 @@ namespace: format def: "Format of Affymetrix data file of raw image data." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Affymetrix image data file format" EXACT [] -is_a: EDAM:0002058 ! Gene annotation (expression) format +is_a: EDAM:0002058 ! Gene expression report format is_a: EDAM:0002330 ! Text - +relationship: is_format_of EDAM:0001714 ! Microarray spots image [Term] id: EDAM:0001623 @@ -27012,13 +26970,13 @@ consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002175 -alt_id: EDAM:0002918 name: Gene cluster format namespace: format +alt_id: EDAM:0002918 def: "Format used for clusters of genes." [EDAM:EBI "EMBRACE definition"] subset: format -is_a: EDAM:0002172 ! Sequence cluster format (nucleic acid) -relationship: is_format_of EDAM:0002198 ! Gene cluster +is_obsolete: true +consider: EDAM:0002172 ! Sequence cluster format (nucleic acid) [Term] @@ -27038,7 +26996,7 @@ namespace: format def: "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002330 ! Text -is_a: EDAM:0002175 ! Gene cluster format +is_a: EDAM:0002172 ! Sequence cluster format (nucleic acid) [Term] id: EDAM:0002196 @@ -27193,20 +27151,20 @@ is_a: EDAM:0002330 ! Text id: EDAM:0003008 name: MAF namespace: format -def: "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track." [EDAM:EBI "EMBRACE definition"] -comment: This should not be confused with MIRA Assembly Format or Mutation Annotation Format. +def: "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth." [EDAM:EBI "EMBRACE definition"] +comment: Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. subset: format spec: http://genome.ucsc.edu/FAQ/FAQformat#format5 -is_a: EDAM:0001921 ! Alignment format +is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002919 ! Sequence annotation track format -is_a: EDAM:0002330 ! Text + [Term] id: EDAM:0003009 name: 2bit namespace: format -def: "2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nuleotides and lower-case 'masking'." [EDAM:EBI "EMBRACE definition"] +def: "2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://jcomeau.freeshell.org/www/genome/2bitformat.html http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD is_a: EDAM:0002571 ! Raw sequence format @@ -27230,7 +27188,6 @@ def: "EMBOSS alphabet for molecular sequence with possible unknown positions but subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text -! relationship: is_attribute_of EDAM:0000016 ! Biopolymer [Term] id: EDAM:0002095 @@ -27240,7 +27197,6 @@ def: "EMBOSS alphabet for a molecular sequence with possible unknown positions b subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text -! relationship: is_attribute_of EDAM:0000016 ! Biopolymer [Term] id: EDAM:0002096 @@ -27250,7 +27206,6 @@ def: "EMBOSS alphabet for a molecular sequence with possible unknown positions b subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text -! relationship: is_attribute_of EDAM:0000016 ! Biopolymer [Term] id: EDAM:0002566 @@ -27260,7 +27215,6 @@ def: "EMBOSS alphabet for a molecular sequence without any unknown positions or subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text -! relationship: is_attribute_of EDAM:0000016 ! Biopolymer [Term] id: EDAM:0002097 @@ -27270,7 +27224,6 @@ def: "EMBOSS alphabet for a molecular sequence with possible unknown positions a subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text -! relationship: is_attribute_of EDAM:0000016 ! Biopolymer [Term] id: EDAM:0001207 @@ -27281,7 +27234,6 @@ comment: Non-sequence characters may be used for example for gaps. subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text -! relationship: is_attribute_of EDAM:0000024 ! Nucleic acid [Term] id: EDAM:0001208 @@ -27293,7 +27245,6 @@ subset: format synonym: "Amino acid sequence" EXACT [] is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text -! relationship: is_attribute_of EDAM:0000025 ! Polypeptide [Term] @@ -27304,7 +27255,6 @@ def: "EMBOSS alphabet for a molecular sequence with possible unknown positions b subset: format is_a: EDAM:0002094 ! pure is_a: EDAM:0002096 ! unambiguous -! relationship: is_attribute_of EDAM:0000016 ! Biopolymer [Term] id: EDAM:0002567 @@ -27314,7 +27264,6 @@ def: "EMBOSS alphabet for a molecular sequence without unknown positions, ambigu subset: format is_a: EDAM:0002094 ! pure is_a: EDAM:0002566 ! completely unambiguous -! relationship: is_attribute_of EDAM:0000016 ! Biopolymer [Term] @@ -27334,7 +27283,6 @@ def: "EMBOSS alphabet for a nucleotide sequence with possible ambiguity and unkn subset: format is_a: EDAM:0002094 ! pure is_a: EDAM:0001207 ! nucleotide -! relationship: is_attribute_of EDAM:0000028 ! DNA [Term] id: EDAM:0001211 @@ -27344,7 +27292,6 @@ def: "EMBOSS alphabet for a nucleotide sequence (characters ACGTU only) with pos subset: format is_a: EDAM:0001207 ! nucleotide is_a: EDAM:0001206 ! unambiguous pure -! relationship: is_attribute_of EDAM:0000028 ! DNA [Term] @@ -27355,7 +27302,6 @@ def: "EMBOSS alphabet for a nucleotide sequence (characters ACGTU only) without subset: format is_a: EDAM:0001207 ! nucleotide is_a: EDAM:0002567 ! completely unambiguous pure -! relationship: is_attribute_of EDAM:0000028 ! DNA [Term] @@ -27365,7 +27311,6 @@ namespace: format def: "EMBOSS alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001207 ! nucleotide -! relationship: is_attribute_of EDAM:0000028 ! DNA [Term] id: EDAM:0001213 @@ -27374,7 +27319,6 @@ namespace: format def: "EMBOSS alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001207 ! nucleotide -! relationship: is_attribute_of EDAM:0000028 ! DNA [Term] id: EDAM:0001214 @@ -27384,7 +27328,6 @@ def: "EMBOSS alphabet for a DNA sequence (characters ACGT only) with possible un subset: format is_a: EDAM:0001206 ! unambiguous pure is_a: EDAM:0001212 ! dna -! relationship: is_attribute_of EDAM:0000028 ! DNA [Term] id: EDAM:0002569 @@ -27394,7 +27337,6 @@ def: "EMBOSS alphabet for a DNA sequence (characters ACGT only) without unknown subset: format is_a: EDAM:0002567 ! completely unambiguous pure is_a: EDAM:0001212 ! dna -! relationship: is_attribute_of EDAM:0000028 ! DNA [Term] id: EDAM:0001215 @@ -27404,7 +27346,6 @@ def: "EMBOSS alphabet for a DNA sequence with possible ambiguity and unknown pos subset: format is_a: EDAM:0001210 ! pure nucleotide is_a: EDAM:0001212 ! dna -! relationship: is_attribute_of EDAM:0000028 ! DNA [Term] id: EDAM:0001216 @@ -27414,7 +27355,6 @@ def: "EMBOSS alphabet for an RNA sequence (characters ACGU only) with possible u subset: format is_a: EDAM:0001206 ! unambiguous pure is_a: EDAM:0001213 ! rna -! relationship: is_attribute_of EDAM:0000029 ! RNA [Term] id: EDAM:0002570 @@ -27424,7 +27364,6 @@ def: "EMBOSS alphabet for an RNA sequence (characters ACGU only) without unknown subset: format is_a: EDAM:0002567 ! completely unambiguous pure is_a: EDAM:0001213 ! rna -! relationship: is_attribute_of EDAM:0000029 ! RNA [Term] id: EDAM:0001217 @@ -27434,7 +27373,6 @@ def: "EMBOSS alphabet for an RNA sequence with possible ambiguity and unknown po subset: format is_a: EDAM:0001210 ! pure nucleotide is_a: EDAM:0001213 ! rna -! relationship: is_attribute_of EDAM:0000029 ! RNA [Term] id: EDAM:0001218 @@ -27444,7 +27382,6 @@ def: "EMBOSS alphabet for any protein sequence with possible unknown positions b subset: format is_a: EDAM:0001206 ! unambiguous pure is_a: EDAM:0001208 ! protein -! relationship: is_attribute_of EDAM:0000037 ! Protein [Term] id: EDAM:0002607 @@ -27454,7 +27391,6 @@ def: "EMBOSS alphabet for any protein sequence without unknown positions, ambigu subset: format is_a: EDAM:0002567 ! completely unambiguous pure is_a: EDAM:0001208 ! protein -! relationship: is_attribute_of EDAM:0000037 ! Protein [Term] id: EDAM:0001219 @@ -27464,7 +27400,6 @@ def: "EMBOSS alphabet for any protein sequence with possible ambiguity and unkno subset: format is_a: EDAM:0002094 ! pure is_a: EDAM:0001208 ! protein -! relationship: is_attribute_of EDAM:0000037 ! Protein [Term] id: EDAM:0003011 @@ -27555,7 +27490,7 @@ is_a: EDAM:0002333 ! Binary id: EDAM:0003018 name: ZTR namespace: format -def: "ZTR format for storing chromotogram data from DNA sequencing instruments." [http://staden.sourceforge.net/manual/formats_unix_12.html EDAM:EBI "EMBRACE definition"] +def: "ZTR format for storing chromatogram data from DNA sequencing instruments." [http://staden.sourceforge.net/manual/formats_unix_12.html EDAM:EBI "EMBRACE definition"] subset: format spec: http://staden.sourceforge.net/manual/formats_unix_12.html is_a: EDAM:0002057 ! Sequence trace format