From 02e6abbf4fe5fc7f33b2e918a10149b04d7726ae Mon Sep 17 00:00:00 2001 From: matuskalas Date: Tue, 1 Nov 2016 03:38:00 +0100 Subject: [PATCH] History of releases: beta07 --- releases/EDAM.obo | 3282 +++++++++++++++++++++++++++++------------------------ 1 file changed, 1811 insertions(+), 1471 deletions(-) diff --git a/releases/EDAM.obo b/releases/EDAM.obo index 4d8b5fb..afc72d6 100644 --- a/releases/EDAM.obo +++ b/releases/EDAM.obo @@ -1,6 +1,6 @@ format-version: 1.2 -date: 13:05:2010 14:26 -data-version: Beta05 +date: 28:05:2010 15:40 +data-version: Beta07 ! Use for mapping to "global" id space(s) e.g.: ! idspace: EDAM urn:lsid:ebi.ac.uk:edam: "EDAM terms" ! idspace: EDAM http://purl.org/edam/ "EDAM terms" @@ -20,7 +20,7 @@ subsetdef: EDAM_EXTRA "EDAM extra terms" [Typedef] id: concerns name: concerns -def: "Defines that a term ('Topic') concerns (covers) another term ('Entity', 'Database', 'Ontology' or 'Operation')." [EDAM:EBI] +def: "Defines that a term ('Topic') concerns (covers) another term ('Biological entity', 'Data resource' or 'Operation')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -29,7 +29,7 @@ inverse_of: is_concern_of [Typedef] id: has_attribute name: has_attribute -def: "Defines a term ('Entity') has (or can have) an attribute ('Data')." [EDAM:EBI] +def: "Defines a term ('Biological entity') has (or can have) an attribute ('Data')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -38,7 +38,7 @@ inverse_of: is_attribute_of [Typedef] id: has_identifier name: has_identifier -def: "Defines a term ('Entity', 'Database', 'Ontology' or 'Data') has (or can have) an identifier ('Identifier')." [EDAM:EBI] +def: "Defines a term ('Biological entity', 'Data resource' or 'Data') has (or can have) an identifier ('Identifier')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -65,7 +65,7 @@ inverse_of: is_output_of [Typedef] id: has_part name: has_part -def: "Defines a term ('Entity' or 'Data') as having a conceptual part ('Entity' or 'Data')." [EDAM:EBI] +def: "Defines a term ('Biological entity' or 'Data') as having a conceptual part ('Biological entity' or 'Data')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -74,7 +74,7 @@ inverse_of: is_part_of [Typedef] id: has_source name: has_source -def: "Defines a term ('Data') has a source ('Tool', 'Database' or 'Ontology')." [EDAM:EBI] +def: "Defines a term ('Data') has a source ('Tool', 'Data resource')." [EDAM:EBI] comment: is_source_of is_anti_symmetric: true is_cyclic: false @@ -83,9 +83,9 @@ inverse_of: is_source_of [Typedef] -id: has_syntax -name: has_syntax -def: "Defines a term ('Data') has a data format specification ('Data syntax')." [EDAM:EBI] +id: has_format +name: has_format +def: "Defines a term ('Data') has a data format specification ('Data format')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -94,7 +94,7 @@ inverse_of: is_attribute_of [Typedef] id: is_attribute_of name: is_attribute_of -def: "Defines that a term ('Data') is an attribute of another term ('Entity')." [EDAM:EBI] +def: "Defines that a term ('Data') is an attribute of another term ('Biological entity')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -103,7 +103,7 @@ inverse_of: has_attribute [Typedef] id: is_concern_of name: is_concern_of -def: "Defines a term ('Entity', 'Database', 'Ontology' or 'Operation') as a concern of another term ('Topic')." [EDAM:EBI] +def: "Defines a term ('Biological entity', 'Data resource' or 'Operation') as a concern of another term ('Topic')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -112,7 +112,7 @@ inverse_of: concerns [Typedef] id: is_identifier_of name: is_identifier_of -def: "Defines that a term ('Identifier') is an identifier of another term ('Entity', 'Database', 'Ontology' or 'Data')." [EDAM:EBI] +def: "Defines that a term ('Identifier') is an identifier of another term ('Biological entity', 'Data resource' or 'Data')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -139,7 +139,7 @@ inverse_of: has_output [Typedef] id: is_part_of name: is_part_of -def: "Defines that a term ('Entity' or 'Data') is a conceptual part of some other term ('Entity' or 'Data')." [EDAM:EBI] +def: "Defines that a term ('Biological entity' or 'Data') is a conceptual part of some other term ('Biological entity' or 'Data')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -148,7 +148,7 @@ inverse_of: has_part [Typedef] id: is_source_of name: is_source_of -def: "Defines a term ('Tool', 'Database' or 'Ontology') is a source of another term ('Data')." [EDAM:EBI] +def: "Defines a term ('Tool', 'Data resource') is a source of another term ('Data')." [EDAM:EBI] comment: has_source is_anti_symmetric: true is_cyclic: false @@ -156,9 +156,9 @@ is_transitive: true inverse_of: has_source [Typedef] -id: is_syntax_of -name: is_syntax_of -def: "Defines that a term ('Data syntax') is a data format specification for another term ('Data')." [EDAM:EBI] +id: is_format_of +name: is_format_of +def: "Defines that a term ('Data format') is a data format specification for another term ('Data')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true @@ -172,7 +172,7 @@ inverse_of: has_attribute ! [Term] id: EDAM:0000002 -name: Entity +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: is_concern_of EDAM:0000003 ! Topic @@ -184,9 +184,9 @@ id: EDAM:0000003 name: Topic namespace: topic def: "A general field of bioinformatics study, data, processing and analysis or technology." [EDAM:EBI "EMBRACE definition"] -! relationship: concerns EDAM:0000002 ! Entity +! relationship: concerns EDAM:0000002 ! Biological entity ! relationship: concerns EDAM:0000004 ! Operation -! relationship: concerns EDAM:0000581 ! Database +! relationship: concerns EDAM:0000005 ! Data resource ! relationship: concerns EDAM:0000582 ! Ontology [Term] @@ -201,80 +201,76 @@ def: "A specific, singular function or process performed by a tool, for example [Term] id: EDAM:0000005 name: Data resource -def: "A data resource or archive including databases, databanks and ontologies." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000581 ! Database -consider: EDAM:0000582 ! Ontology +def: "A category of content of a data resource including databases, ontologies and servers." [EDAM:EBI "EMBRACE definition"] + + + + -[Term] -id: EDAM:0000581 -name: Database -namespace: database -def: "A category (of content) of a relational or object-oriented database or flat-file databank." [EDAM:EBI "EMBRACE definition"] -comment: Terms in this branch are for database categories; individual databases are not listed. -! relationship: is_concern_of EDAM:0000076 ! Undefined -! relationship: is_source_of EDAM:0000006 ! Data -! relationship: has_identifier EDAM:0001048 ! Database identifier -[Term] -id: EDAM:0000582 -name: Ontology -namespace: ontology -def: "An ontology of biological or bioinformatics terms and relations, a controlled vocabulary, structured glossary etc." [EDAM:EBI "EMBRACE definition"] -! relationship: is_concern_of EDAM:0000076 ! Undefined -! relationship: is_source_of EDAM:0000966 ! Ontology term -! relationship: is_source_of EDAM:0001730 ! Ontology relation -! relationship: has_identifier EDAM:0000842 ! Identifier [Term] id: EDAM:0000006 name: Data namespace: data def: "A semantic description of a data entity (datum) commonly used in bioinformatics." [EDAM:EBI "EMBRACE definition"] -! relationship: is_attribute_of EDAM:0000002 ! Entity +! relationship: is_attribute_of EDAM:0000002 ! Biological entity ! relationship: is_input_of EDAM:0000004 ! Operation ! relationship: is_output_of EDAM:0000004 ! Operation -! relationship: has_source EDAM:0000581 ! Database +! relationship: has_source EDAM:0000005 ! Data resource ! relationship: has_identifier EDAM:0000842 ! Identifier [Term] id: EDAM:0001915 -name: Data syntax -namespace: syntax +name: Data format +namespace: format def: "A reference (typically a URL) of a data format specification." [EDAM:EBI "EMBRACE definition"] -relationship: is_syntax_of EDAM:0000006 ! Data - +! relationship: is_format_of EDAM:0000006 ! Data -[Term] -id: EDAM:0000007 -name: Tool -def: "A bioinformatics package or tool, e.g. a standalone application or web service." [EDAM:EBI "EMBRACE definition"] -is_obsolete: true -consider: EDAM:0000958 ! Tool metadata - ! -! Entity +! Biological entity ! [Term] id: EDAM:0000008 name: Undefined namespace: entity def: "Debugging." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000002 ! Entity +is_a: EDAM:0000002 ! Biological entity relationship: is_concern_of EDAM:0000076 ! Undefined relationship: has_identifier EDAM:0000841 ! Undefined relationship: has_attribute EDAM:0000841 ! Undefined [Term] +id: EDAM:0002199 +name: Physical entity +namespace: entity +def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000002 ! Biological entity + +[Term] +id: EDAM:0000012 +name: Phenomena +namespace: entity +def: "An observable biological occurence or event with a physical basis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000002 ! Biological entity +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000006 ! Data + + +! +! Biological entity<-Physical entity +! +[Term] id: EDAM:0000009 name: Discrete entity namespace: entity def: "Any biological thing with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000002 ! Entity +is_a: EDAM:0002199 ! Physical entity relationship: is_concern_of EDAM:0000076 ! Undefined relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000006 ! Data @@ -284,7 +280,7 @@ id: EDAM:0000010 name: Entity feature namespace: entity def: "A physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000002 ! Entity +is_a: EDAM:0002199 ! Physical entity relationship: is_concern_of EDAM:0000076 ! Undefined relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000006 ! Data @@ -294,17 +290,7 @@ id: EDAM:0000011 name: Entity collection namespace: entity def: "A collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000002 ! Entity -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier -relationship: has_attribute EDAM:0000006 ! Data - -[Term] -id: EDAM:0000012 -name: Phenomena -namespace: entity -def: "A physical, observable biological occurence or event." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000002 ! Entity +is_a: EDAM:0002199 ! Physical entity relationship: is_concern_of EDAM:0000076 ! Undefined relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000006 ! Data @@ -312,7 +298,7 @@ relationship: has_attribute EDAM:0000006 ! Data ! -! Entity<-Discrete entity +! Biological entity<-Physical entity<-Discrete entity ! [Term] @@ -332,7 +318,7 @@ relationship: has_attribute EDAM:0000883 ! Tertiary structure ! -! Entity<-Discrete entity<-Molecular entity +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity ! [Term] @@ -381,11 +367,11 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Discrete entity<-Molecular entity<-Atom +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Atom ! ! -! Entity<-Discrete entity<-Molecular entity<-Small molecule +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Small molecule ! [Term] @@ -421,7 +407,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Discrete entity<-Molecular entity<-Small molecule<-Biomonomer +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Small molecule<-Biomonomer ! [Term] id: EDAM:0000021 @@ -456,16 +442,16 @@ relationship: has_identifier EDAM:0000996 ! Monosaccharide identifier relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Discrete entity<-Molecular entity<-Small molecule<-Ligand +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Small molecule<-Ligand ! ! -! Entity<-Discrete entity<-Molecular entity<-Small molecule<-Drug +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Small molecule<-Drug ! ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer ! [Term] id: EDAM:0000024 @@ -505,7 +491,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid ! [Term] id: EDAM:0000027 @@ -545,11 +531,11 @@ relationship: has_attribute EDAM:0001465 ! RNA tertiary structure ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-Oligonucleotide +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-Oligonucleotide ! ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA ! [Term] @@ -575,7 +561,7 @@ relationship: has_attribute EDAM:0001212 ! DNA sequence relationship: has_attribute EDAM:0001464 ! DNA tertiary structure ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element ! [Term] id: EDAM:0000031 @@ -599,7 +585,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element<-Transposon +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element<-Transposon ! [Term] id: EDAM:0000033 @@ -625,7 +611,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element<-Plasmid +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element<-Plasmid ! @@ -634,7 +620,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-RNA +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-RNA ! [Term] id: EDAM:0000035 @@ -649,7 +635,7 @@ relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0001213 ! RNA sequence ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide ! [Term] id: EDAM:0000036 @@ -673,7 +659,7 @@ relationship: has_attribute EDAM:0001460 ! Protein tertiary structure ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein ! [Term] @@ -718,12 +704,12 @@ relationship: has_identifier EDAM:0000989 ! Protein identifier relationship: has_attribute EDAM:0001460 ! Protein tertiary structure ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Uncomplexed protein +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Uncomplexed protein ! ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Enzyme +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Enzyme ! [Term] id: EDAM:0000042 @@ -736,17 +722,17 @@ relationship: has_identifier EDAM:0001010 ! Enzyme identifier relationship: has_attribute EDAM:0001460 ! Protein tertiary structure ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Transmembrane protein +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Transmembrane protein ! ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Transcription factor +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Transcription factor ! ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polysaccharide +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polysaccharide ! @@ -755,7 +741,7 @@ relationship: has_attribute EDAM:0001460 ! Protein tertiary structure ! -! Entity<-Discrete entity<-Molecular entity<-Molecular complex +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex ! [Term] id: EDAM:0000043 @@ -813,19 +799,19 @@ consider: EDAM:0000044 ! Protein-protein complex ! -! Entity<-Discrete entity<-Molecular entity<-Molecular complex<-RNA/DNA hybrid +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex<-RNA/DNA hybrid ! ! -! Entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-protein complex +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-protein complex ! ! -! Entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-ligand complex +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-ligand complex ! ! -! Entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-nucleic acid complex +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-nucleic acid complex ! [Term] id: EDAM:0001851 @@ -840,7 +826,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide ! @@ -848,7 +834,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polysaccharide +! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polysaccharide ! @@ -856,7 +842,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity feature +! Biological entity<-Physical entity<-Entity feature ! [Term] id: EDAM:0001749 @@ -904,7 +890,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity feature<-Atom group +! Biological entity<-Physical entity<-Entity feature<-Atom group ! [Term] id: EDAM:0001750 @@ -917,7 +903,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity feature<-Nucleic acid feature +! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature ! [Term] id: EDAM:0000050 @@ -1005,11 +991,11 @@ relationship: has_identifier EDAM:0000841 ! Undefined relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity feature<-Nucleic acid feature<-Codon +! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Codon ! ! -! Entity<-Entity feature<-Nucleic acid feature<-Gene +! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Gene ! [Term] id: EDAM:0001909 @@ -1022,11 +1008,11 @@ relationship: has_identifier EDAM:0001025 ! Gene identifier relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity feature<-Nucleic acid feature<-Operon +! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Operon ! ! -! Entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element +! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element ! [Term] id: EDAM:0000058 @@ -1052,7 +1038,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element<-Gene cis-regulatory element +! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element<-Gene cis-regulatory element ! [Term] id: EDAM:0000060 @@ -1095,14 +1081,14 @@ relationship: has_identifier EDAM:0000841 ! Undefined relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element<-Gene-regulatory element +! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element<-Gene-regulatory element ! ! -! Entity<-Entity feature<-Protein feature +! Biological entity<-Physical entity<-Entity feature<-Protein feature ! [Term] id: EDAM:0000064 @@ -1138,11 +1124,11 @@ relationship: has_attribute EDAM:0001468 ! Protein domain tertiary structure ! -! Entity<-Entity feature<-Protein feature<-Protein residue +! Biological entity<-Physical entity<-Entity feature<-Protein feature<-Protein residue ! ! -! Entity<-Entity feature<-Protein feature<-Protein residue group +! Biological entity<-Physical entity<-Entity feature<-Protein feature<-Protein residue group ! [Term] id: EDAM:0001752 @@ -1180,7 +1166,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity feature<-Protein feature<-Protein domain +! Biological entity<-Physical entity<-Entity feature<-Protein feature<-Protein domain ! @@ -1189,7 +1175,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity collection +! Biological entity<-Physical entity<-Entity collection ! [Term] id: EDAM:0000066 @@ -1235,19 +1221,19 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Entity collection<-Genome +! Biological entity<-Physical entity<-Entity collection<-Genome ! ! -! Entity<-Entity collection<-Proteome +! Biological entity<-Physical entity<-Entity collection<-Proteome ! ! -! Entity<-Entity collection<-Nucleosome +! Biological entity<-Physical entity<-Entity collection<-Nucleosome ! ! -! Entity<-Entity collection<-Taxonomic rank +! Biological entity<-Physical entity<-Entity collection<-Taxonomic rank ! [Term] id: EDAM:0000070 @@ -1291,7 +1277,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined ! -! Entity<-Phenomena +! Biological entity<-Phenomena ! [Term] @@ -4891,7 +4877,7 @@ comment: Use this terms for tools which allow for manual annotations. For automa is_a: EDAM:0000226 ! Annotation relationship: is_concern_of EDAM:0000221 ! Sequence annotation relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0001255 ! Sequence feature annotation +relationship: has_output EDAM:0001255 ! Sequence features [Term] id: EDAM:0000362 @@ -5272,7 +5258,7 @@ relationship: has_output EDAM:0001543 ! Protein surface ! [Term] id: EDAM:0001816 -name: "Surface rendering" +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. @@ -8572,24 +8558,24 @@ relationship: has_output EDAM:0000841 ! Undefined ! -! Database +! Data resource ! [Term] id: EDAM:0000580 name: Undefined -namespace: database +namespace: resource def: "Debugging." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000841 ! Undefined relationship: has_identifier EDAM:0000841 ! Undefined [Term] id: EDAM:0000584 -name: Sequence database -namespace: database +name: Sequence data resource +namespace: resource def: "A database of molecular sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -8598,100 +8584,100 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000585 -name: Structure database -namespace: database +name: Structure data resource +namespace: resource def: "A database of molecular secondary or tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000586 -name: General protein database -namespace: database +name: General protein data resource +namespace: resource def: "A database of protein information in general." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000896 ! Protein annotation relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000587 -name: Protein interaction database -namespace: database +name: Protein interaction data resource +namespace: resource def: "A database of protein interactions." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_source_of EDAM:0000906 ! Protein interaction relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000588 -name: Protein localization database -namespace: database +name: Protein localization data resource +namespace: resource def: "A database concerning protein localization." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000589 -name: Protein structural motif database -namespace: database +name: Protein structural motif data resource +namespace: resource def: "A database of protein structural motifs." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000899 ! Protein 3D structural motif annotation relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000590 -name: Protein structure annotation database -namespace: database +name: Protein structure annotation data resource +namespace: resource def: "A database of protein structure annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001537 ! Protein structure annotation relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000591 -name: Proteome annotation database -namespace: database +name: Proteome annotation data resource +namespace: resource def: "A database of annotation for an entire proteome." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000592 -name: Molecular motions database -namespace: database +name: Molecular motions data resource +namespace: resource def: "A database of molecular motions." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000593 -name: NMR database -namespace: database +name: NMR data resource +namespace: resource def: "A database of raw NMR data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000594 -name: Sequence classification database -namespace: database +name: Sequence classification data resource +namespace: resource def: "A database of molecular sequence classifications or clusters." [EDAM:EBI "EMBRACE definition"] comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001235 ! Sequence cluster relationship: has_identifier EDAM:0001056 ! Database name @@ -8699,10 +8685,10 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000595 -name: Protein classification database -namespace: database +name: Protein classification data resource +namespace: resource def: "A database of protein sequence or structural classifications." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name @@ -8710,30 +8696,30 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000596 -name: Sequence alignment database -namespace: database +name: Sequence alignment data resource +namespace: resource def: "A database of molecular sequence alignments." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000863 ! Sequence alignment relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000597 -name: Structure alignment database -namespace: database +name: Structure alignment data resource +namespace: resource def: "A database of molecular tertiary (3D) structure alignments." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000886 ! Tertiary structure alignment relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000598 -name: Sequence motif or profile database -namespace: database +name: Sequence motif or profile data resource +namespace: resource def: "A database of sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001353 ! Sequence motif relationship: is_source_of EDAM:0001354 ! Sequence profile @@ -8741,20 +8727,20 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000599 -name: Structural profile database -namespace: database +name: Structural profile data resource +namespace: resource def: "A database 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_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000889 ! Structural (3D) profile relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000600 -name: Functional sites database -namespace: database +name: Functional sites data resource +namespace: resource def: "A database of functional sites in molecular sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name @@ -8762,20 +8748,20 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000601 -name: General protein modifications database -namespace: database +name: General protein modifications data resource +namespace: resource def: "A database on protein modification, e.g. post-translational modifications." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000602 -name: Biological pathways database -namespace: database +name: Biological pathways data resource +namespace: resource def: "A database of biological pathways." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000946 ! Biological pathway relationship: is_source_of EDAM:0000947 ! Biological pathway map @@ -8783,20 +8769,20 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000603 -name: Proteomics database -namespace: database +name: Proteomics data resource +namespace: resource def: "A proteomics database." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000604 -name: General peptides database -namespace: database +name: General peptides data resource +namespace: resource def: "A general database about peptides." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000895 ! Peptide relationship: has_identifier EDAM:0001056 ! Database name @@ -8806,20 +8792,20 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000605 -name: Informatics database -namespace: database +name: Informatics data resource +namespace: resource def: "A database concerning biological data management and modelling, including datatypes, workflows and models." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000606 -name: Literature database -namespace: database +name: Literature data resource +namespace: resource def: "A biological or biomedical literature database." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000970 ! Citation relationship: is_source_of EDAM:0000971 ! Article @@ -8827,50 +8813,50 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000607 -name: Biological resource database -namespace: database +name: Biological resource data resource +namespace: resource def: "A database of biological resources for use in the lab." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000608 -name: Cell culture database -namespace: database +name: Cell culture data resource +namespace: resource def: "A database of general cell culture or data on a specific cell lines." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000609 -name: Cell cycle database -namespace: database +name: Cell cycle data resource +namespace: resource def: "A database on the cell cycle including key genes and proteins." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000610 -name: Ecological database -namespace: database +name: Ecological data resource +namespace: resource def: "A database of ecological data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000611 -name: Electron microscopy database -namespace: database +name: Electron microscopy data resource +namespace: resource def: "A database of electron microscopy data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000940 ! Electron microscopy volume map relationship: is_source_of EDAM:0000941 ! Electron microscopy model annotation @@ -8878,80 +8864,80 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000612 -name: Embryology and development database -namespace: database +name: Embryology and development data resource +namespace: resource def: "A database on embryology and cell and tissue development." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000613 -name: Amino acid database -namespace: database +name: Amino acid data resource +namespace: resource def: "A database of amino acid physicochemical and biochemical property data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0002016 ! Amino acid data relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000614 -name: Nucleic acid physicochemical property database -namespace: database +name: Nucleic acid physicochemical property data resource +namespace: resource def: "A database of nucleic acid physicochemical and biochemical property data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000615 -name: Protein physicochemical property database -namespace: database +name: Protein physicochemical property data resource +namespace: resource def: "A database of protein physicochemical and biochemical property data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000616 -name: Organelle database -namespace: database +name: Organelle data resource +namespace: resource def: "A database on a specific organelle, or organelles in general." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000617 -name: Ribosome database -namespace: database +name: Ribosome data resource +namespace: resource def: "A database on ribosome-specific data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000618 -name: Scents database -namespace: database +name: Scents data resource +namespace: resource def: "A database about scents." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000964 ! Scent annotation relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000619 -name: Biochemical nomenclature database -namespace: database +name: Biochemical nomenclature data resource +namespace: resource def: "A database of biochemical nomenclature, symbols or terminology." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name @@ -8960,10 +8946,10 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000621 -name: Organism-specific database -namespace: database +name: Organism-specific data resource +namespace: resource def: "A database on 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"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name @@ -8971,10 +8957,10 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000622 -name: Genomics database -namespace: database +name: Genomics data resource +namespace: resource def: "A database in the broad field of genomics." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name @@ -8982,30 +8968,30 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000623 -name: Genes database -namespace: database +name: Genes data resource +namespace: resource def: "A database on a particular gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000916 ! Gene annotation relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000624 -name: Chromosome database -namespace: database +name: Chromosome data resource +namespace: resource def: "A database on chromosomes." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000919 ! Chromosome annotation relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000625 -name: Genotype / phenotype database -namespace: database +name: Genotype / phenotype data resource +namespace: resource def: "A database on genotypes and / or phenotypes especially concerning diseases, mutations and variations." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001081 ! Genotype / phenotype report identifier @@ -9013,30 +8999,30 @@ relationship: has_identifier EDAM:0001081 ! Genotype / phenotype report identifi [Term] id: EDAM:0000627 -name: DNA methylation database -namespace: database +name: DNA methylation data resource +namespace: resource def: "A database on DNA methylation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000628 -name: DNA replication database -namespace: database +name: DNA replication data resource +namespace: resource def: "A database on DNA replication." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000629 -name: Gene expression and microarray database -namespace: database +name: Gene expression and microarray data resource +namespace: resource def: "A database of gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000931 ! Microarray experimental data relationship: is_source_of EDAM:0000928 ! Gene expression profile @@ -9045,30 +9031,30 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000630 -name: Gene structure database -namespace: database +name: Gene structure data resource +namespace: resource def: "A database on gene structure, including introns, exons and splice sites, splicing pattern, gene fusion etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000631 -name: Gene regulation database -namespace: database +name: Gene regulation data resource +namespace: resource def: "A database of gene regulation including regulatory networks, regulatory sequences etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000632 -name: Molecular probes or primers database -namespace: database +name: Molecular probes or primers data resource +namespace: resource def: "A database of molecular probes or primers." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000932 ! Microarray probe data relationship: is_source_of EDAM:0000922 ! Primer report @@ -9076,40 +9062,40 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000633 -name: Immunological database -namespace: database +name: Immunological data resource +namespace: resource def: "A database concerning immunology in general, including immune processes, immunity related proteins and peptide ligands etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000634 -name: Disease database -namespace: database +name: Disease data resource +namespace: resource def: "A database of disease." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001622 ! Disease relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000635 -name: Specific protein database -namespace: database +name: Specific protein data resource +namespace: resource def: "A database on a particular protein or group of proteins." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000636 -name: Phylogenetic database -namespace: database +name: Phylogenetic data resource +namespace: resource def: "A database on phylogeny; phylogenetic trees, gene transfer, mode of selection / evolution etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000872 ! Phylogenetic tree relationship: has_identifier EDAM:0001056 ! Database name @@ -9117,10 +9103,10 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000637 -name: Taxonomic database -namespace: database +name: Taxonomic data resource +namespace: resource def: "A database on taxonomy and identification." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000581 ! Database +is_a: EDAM:0000005 ! Data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name @@ -9128,14 +9114,14 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Sequence database +! Data resource<-Sequence data resource ! [Term] id: EDAM:0000639 name: Protein sequence database -namespace: database +namespace: resource def: "A database of one or more protein sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000584 ! Sequence database +is_a: EDAM:0000584 ! Sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001208 ! Protein sequence @@ -9144,10 +9130,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000640 -name: Nucleotide sequence database -namespace: database +name: Nucleotide sequence data resource +namespace: resource def: "A database of one or more nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000584 ! Sequence database +is_a: EDAM:0000584 ! Sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001207 ! Nucleotide sequence @@ -9156,10 +9142,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000641 -name: Repeat sequence database -namespace: database +name: Repeat sequence data resource +namespace: resource def: "A database of repeat sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000584 ! Sequence database +is_a: EDAM:0000584 ! Sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9168,10 +9154,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000642 -name: Low complexity sequence database -namespace: database +name: Low complexity sequence data resource +namespace: resource def: "A database of low complexity sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000584 ! Sequence database +is_a: EDAM:0000584 ! Sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9180,10 +9166,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000626 -name: Polymorphism database -namespace: database +name: Polymorphism data resource +namespace: resource def: "A database on gene polymorphism, polymorphic sequences etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000584 ! Sequence database +is_a: EDAM:0000584 ! Sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000918 ! Sequence variation specification relationship: has_identifier EDAM:0001056 ! Database name @@ -9191,11 +9177,11 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000643 -name: Genome database -namespace: database +name: Genome data resource +namespace: resource def: "Information on a specific genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000584 ! Sequence database -is_a: EDAM:0000622 ! Genomics database +is_a: EDAM:0000584 ! Sequence data resource +is_a: EDAM:0000622 ! Genomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9206,11 +9192,11 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000644 -name: Proteome database -namespace: database +name: Proteome data resource +namespace: resource def: "Information on a specific proteome including protein sequences and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000584 ! Sequence database -is_a: EDAM:0000603 ! Proteomics database +is_a: EDAM:0000584 ! Sequence data resource +is_a: EDAM:0000603 ! Proteomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9220,10 +9206,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000646 -name: BLAST database -namespace: database +name: BLAST data resource +namespace: resource def: "A BLAST-format database of sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000584 ! Sequence database +is_a: EDAM:0000584 ! Sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: has_identifier EDAM:0001056 ! Database name @@ -9231,7 +9217,7 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address relationship: has_identifier EDAM:0001111 ! EMBOSS listfile ! -! Database<-Sequence database<-Protein sequence database +! Data resource<-Sequence data resource<-Protein sequence data resource ! @@ -9240,15 +9226,15 @@ relationship: has_identifier EDAM:0001111 ! EMBOSS listfile ! -! Database<-Sequence database<-Nucleotide sequence database +! Data resource<-Sequence data resource<-Nucleotide sequence data resource ! [Term] id: EDAM:0000653 -name: RNA sequence database -namespace: database +name: RNA sequence data resource +namespace: resource def: "A database of one or more RNA sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000640 ! Nucleotide sequence database +is_a: EDAM:0000640 ! Nucleotide sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001213 ! RNA sequence @@ -9257,11 +9243,11 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000654 -name: DNA sequence database -namespace: database +name: DNA sequence data resource +namespace: resource def: "A database of one or more DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: The DNA sequences might be coding or non-coding sequences. -is_a: EDAM:0000640 ! Nucleotide sequence database +is_a: EDAM:0000640 ! Nucleotide sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001212 ! DNA sequence @@ -9270,12 +9256,12 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000655 -name: mRNA, EST or cDNA database -namespace: database +name: mRNA, EST or cDNA data resource +namespace: resource def: "A database of mRNA, EST or cDNA sequences." [EDAM:EBI "EMBRACE definition"] -synonym: "Transcriptome database" EXACT [] -is_a: EDAM:0000640 ! Nucleotide sequence database -is_a: EDAM:0000629 ! Gene expression and microarray database +synonym: "Transcriptome data resource" EXACT [] +is_a: EDAM:0000640 ! Nucleotide sequence data resource +is_a: EDAM:0000629 ! Gene expression and microarray data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001207 ! Nucleotide sequence @@ -9288,15 +9274,15 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Nucleotide sequence database<-RNA sequence database +! Data resource<-Sequence data resource<-Nucleotide sequence data resource<-RNA sequence data resource ! [Term] id: EDAM:0000659 -name: Functional RNA sequence database -namespace: database +name: Functional RNA sequence data resource +namespace: resource def: "A database of one or more functional RNA sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000653 ! RNA sequence database +is_a: EDAM:0000653 ! RNA sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001213 ! RNA sequence @@ -9305,14 +9291,14 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Nucleotide sequence database<-RNA sequence database<-Functional RNA sequence database +! Data resource<-Sequence data resource<-Nucleotide sequence data resource<-RNA sequence data resource<-Functional RNA sequence data resource ! [Term] id: EDAM:0000660 -name: rRNA sequence database -namespace: database +name: rRNA sequence data resource +namespace: resource def: "A database of one or more ribosomal RNA (rRNA) sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000659 ! Functional RNA sequence database +is_a: EDAM:0000659 ! Functional RNA sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001213 ! RNA sequence @@ -9321,10 +9307,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000661 -name: miRNA sequence database -namespace: database +name: miRNA sequence data resource +namespace: resource def: "A database of one or more microRNA (miRNA) sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000659 ! Functional RNA sequence database +is_a: EDAM:0000659 ! Functional RNA sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001213 ! RNA sequence @@ -9333,10 +9319,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000662 -name: siRNA sequence database -namespace: database +name: siRNA sequence data resource +namespace: resource def: "A database of one or more small interfering RNA (siRNA) sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000659 ! Functional RNA sequence database +is_a: EDAM:0000659 ! Functional RNA sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001213 ! RNA sequence @@ -9346,10 +9332,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000663 -name: tRNA sequence database -namespace: database +name: tRNA sequence data resource +namespace: resource def: "A database of one or more transfer RNA (tRNA) sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000659 ! Functional RNA sequence database +is_a: EDAM:0000659 ! Functional RNA sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001213 ! RNA sequence @@ -9358,10 +9344,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000664 -name: snRNA sequence database -namespace: database +name: snRNA sequence data resource +namespace: resource def: "A database of one or more small nuclear RNA (snRNA) sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000659 ! Functional RNA sequence database +is_a: EDAM:0000659 ! Functional RNA sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001213 ! RNA sequence @@ -9370,15 +9356,15 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Nucleotide sequence database<-RNA sequence database<-Functional RNA sequence database<-snRNA sequence database +! Data resource<-Sequence data resource<-Nucleotide sequence data resource<-RNA sequence data resource<-Functional RNA sequence data resource<-snRNA sequence data resource ! [Term] id: EDAM:0000665 -name: snoRNA sequence database -namespace: database +name: snoRNA sequence data resource +namespace: resource def: "A database of one or more small nucleolar RNA (snoRNA) sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000664 ! snRNA sequence database +is_a: EDAM:0000664 ! snRNA sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001213 ! RNA sequence @@ -9388,15 +9374,15 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Nucleotide sequence database<-DNA sequence database +! Data resource<-Sequence data resource<-Nucleotide sequence data resource<-DNA sequence data resource ! [Term] id: EDAM:0000666 -name: rDNA sequence database -namespace: database +name: rDNA sequence data resource +namespace: resource def: "A database of one or more ribosomal DNA (rDNA) sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000654 ! DNA sequence database +is_a: EDAM:0000654 ! DNA sequence data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0001212 ! DNA sequence @@ -9405,7 +9391,7 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Nucleotide sequence database<-mRNA, EST or cDNA database +! Data resource<-Sequence data resource<-Nucleotide sequence data resource<-mRNA, EST or cDNA data resource ! @@ -9413,30 +9399,30 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Repeat sequence database +! Data resource<-Sequence data resource<-Repeat sequence data resource ! ! -! Database<-Sequence database<-Low complexity sequence database +! Data resource<-Sequence data resource<-Low complexity sequence data resource ! ! -! Database<-Sequence database<-Polymorphism database +! Data resource<-Sequence data resource<-Polymorphism data resource ! ! -! Database<-Sequence database<-Genome database +! Data resource<-Sequence data resource<-Genome data resource ! [Term] id: EDAM:0000669 -name: Eukaryote genome database -namespace: database +name: Eukaryote genome data resource +namespace: resource def: "Information on a specific eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000643 ! Genome database +is_a: EDAM:0000643 ! Genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9445,10 +9431,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000670 -name: Prokaryote genome database -namespace: database +name: Prokaryote genome data resource +namespace: resource def: "Information on a specific prokaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000643 ! Genome database +is_a: EDAM:0000643 ! Genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9457,10 +9443,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000671 -name: Viral genome database -namespace: database +name: Viral genome data resource +namespace: resource def: "Information on a specific viral genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000643 ! Genome database +is_a: EDAM:0000643 ! Genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9472,14 +9458,14 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Genome database<-Eukaryote genome database +! Data resource<-Sequence data resource<-Genome data resource<-Eukaryote genome data resource ! [Term] id: EDAM:0000675 -name: Unicellular eukaryote genome database -namespace: database +name: Unicellular eukaryote genome data resource +namespace: resource def: "Information on a specific unicellular eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000669 ! Eukaryote genome database +is_a: EDAM:0000669 ! Eukaryote genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9488,10 +9474,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000676 -name: Fungal genome database -namespace: database +name: Fungal genome data resource +namespace: resource def: "Information on a specific fungal genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000669 ! Eukaryote genome database +is_a: EDAM:0000669 ! Eukaryote genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9500,10 +9486,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000677 -name: Plant genome database -namespace: database +name: Plant genome data resource +namespace: resource def: "Information on a specific plant genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000669 ! Eukaryote genome database +is_a: EDAM:0000669 ! Eukaryote genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9512,10 +9498,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000678 -name: Invertebrate genome database -namespace: database +name: Invertebrate genome data resource +namespace: resource def: "Information on a specific invertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000669 ! Eukaryote genome database +is_a: EDAM:0000669 ! Eukaryote genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9524,10 +9510,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000679 -name: Vertebrate genome database -namespace: database +name: Vertebrate genome data resource +namespace: resource def: "Information on a specific vertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000669 ! Eukaryote genome database +is_a: EDAM:0000669 ! Eukaryote genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9538,20 +9524,20 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Genome database<-Eukaryote genome database<-Unicellular eukaryote genome database +! Data resource<-Sequence data resource<-Genome data resource<-Eukaryote genome data resource<-Unicellular eukaryote genome data resource ! ! -! Database<-Sequence database<-Genome database<-Eukaryote genome database<-Fungal genome database +! Data resource<-Sequence data resource<-Genome data resource<-Eukaryote genome data resource<-Fungal genome data resource ! [Term] id: EDAM:0000682 -name: Yeast genome database -namespace: database +name: Yeast genome data resource +namespace: resource def: "Information on a specific yeast genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000676 ! Fungal genome database +is_a: EDAM:0000676 ! Fungal genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9559,16 +9545,16 @@ relationship: has_identifier EDAM:0001057 ! Sequence database name relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Genome database<-Eukaryote genome database<-Fungal genome database<-Yeast genome database +! Data resource<-Sequence data resource<-Genome data resource<-Eukaryote genome data resource<-Fungal genome data resource<-Yeast genome data resource ! ! -! Database<-Sequence database<-Genome database<-Eukaryote genome database<-Plant genome database +! Data resource<-Sequence data resource<-Genome data resource<-Eukaryote genome data resource<-Plant genome data resource ! ! -! Database<-Sequence database<-Genome database<-Eukaryote genome database<-Invertebrate genome database +! Data resource<-Sequence data resource<-Genome data resource<-Eukaryote genome data resource<-Invertebrate genome data resource ! @@ -9576,15 +9562,15 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Genome database<-Eukaryote genome database<-Vertebrate genome database +! Data resource<-Sequence data resource<-Genome data resource<-Eukaryote genome data resource<-Vertebrate genome data resource ! [Term] id: EDAM:0000687 -name: Human genome database -namespace: database +name: Human genome data resource +namespace: resource def: "Information on the human genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000679 ! Vertebrate genome database +is_a: EDAM:0000679 ! Vertebrate genome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9596,26 +9582,26 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Sequence database<-Genome database<-Prokaryote genome database +! Data resource<-Sequence data resource<-Genome data resource<-Prokaryote genome data resource ! ! -! Database<-Sequence database<-Genome database<-Viral genome database +! Data resource<-Sequence data resource<-Genome data resource<-Viral genome data resource ! ! -! Database<-Sequence database<-Proteome database +! Data resource<-Sequence data resource<-Proteome data resource ! [Term] id: EDAM:0000691 -name: Prokaryote proteome database -namespace: database +name: Prokaryote proteome data resource +namespace: resource def: "Information on a specific prokaryote proteome including molecular sequences and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000644 ! Proteome database +is_a: EDAM:0000644 ! Proteome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9624,10 +9610,10 @@ relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address [Term] id: EDAM:0000692 -name: Human proteome database -namespace: database +name: Human proteome data resource +namespace: resource def: "Information on the human proteome including molecular sequences and annotation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000644 ! Proteome database +is_a: EDAM:0000644 ! Proteome data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data @@ -9635,45 +9621,45 @@ relationship: has_identifier EDAM:0001057 ! Sequence database name relationship: has_identifier EDAM:0001095 ! EMBOSS Uniform Sequence Address ! -! Database<-Structure database +! Data resource<-Structure data resource ! [Term] id: EDAM:0000693 -name: Tertiary structure database -namespace: database +name: Tertiary structure data resource +namespace: resource def: "A database of molecular tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000585 ! Structure database +is_a: EDAM:0000585 ! Structure data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000883 ! Tertiary structure relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000694 -name: Protein secondary structure and alignment database -namespace: database +name: Protein secondary structure and alignment data resource +namespace: resource def: "A database of protein secondary structure or secondary structure alignments." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000585 ! Structure database +is_a: EDAM:0000585 ! Structure data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000876 ! Protein secondary structure relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000695 -name: Carbohydrate structure database -namespace: database +name: Carbohydrate structure data resource +namespace: resource def: "A database of carbohydrate structure." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000585 ! Structure database +is_a: EDAM:0000585 ! Structure data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001462 ! Carbohydrate structure relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000696 -name: Chemical and small molecule database -namespace: database +name: Chemical and small molecule data resource +namespace: resource def: "A database of chemical and other small molecular structures." [EDAM:EBI "EMBRACE definition"] comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, polysaccharides and oligonucleotides. -is_a: EDAM:0000585 ! Structure database +is_a: EDAM:0000585 ! Structure data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001463 ! Chemical or small molecule structure relationship: is_source_of EDAM:0000962 ! Chemical compound @@ -9681,14 +9667,14 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Structure database<-Tertiary structure database +! Data resource<-Structure data resource<-Tertiary structure data resource ! [Term] id: EDAM:0000698 -name: Protein structure database -namespace: database +name: Protein structure data resource +namespace: resource def: "A database of protein tertiary structure." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000693 ! Tertiary structure database +is_a: EDAM:0000693 ! Tertiary structure data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000883 ! Tertiary structure relationship: is_source_of EDAM:0001460 ! Protein tertiary structure @@ -9696,10 +9682,10 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000699 -name: Nucleic acid structure database -namespace: database +name: Nucleic acid structure data resource +namespace: resource def: "A database of nucleic acid tertiary structure." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000693 ! Tertiary structure database +is_a: EDAM:0000693 ! Tertiary structure data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000883 ! Tertiary structure relationship: is_source_of EDAM:0001459 ! Nucleic acid tertiary structure @@ -9707,16 +9693,16 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Structure database<-Tertiary structure database<-Protein structure database +! Data resource<-Structure data resource<-Tertiary structure data resource<-Protein structure data resource ! [Term] id: EDAM:0000700 -name: Protein domain structure database -namespace: database +name: Protein domain structure data resource +namespace: resource def: "A database or other collection of tertiary structures of protein domains." [EDAM:EBI "EMBRACE definition"] synonym: "Domain structure library" EXACT [] -is_a: EDAM:0000698 ! Protein structure database +is_a: EDAM:0000698 ! Protein structure data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000883 ! Tertiary structure relationship: is_source_of EDAM:0001468 ! Protein domain tertiary structure @@ -9726,15 +9712,15 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Structure database<-Tertiary structure database<-Protein structure database<-Protein domain structure database +! Data resource<-Structure data resource<-Tertiary structure data resource<-Protein structure data resource<-Protein domain structure data resource ! [Term] id: EDAM:0000703 -name: CATH domain structure database -namespace: database +name: CATH domain structure data resource +namespace: resource def: "A collection of tertiary structures of protein domains defined in CATH." [EDAM:EBI "EMBRACE definition"] synonym: "CATH structure library" EXACT [] -is_a: EDAM:0000698 ! Protein structure database +is_a: EDAM:0000698 ! Protein structure data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000883 ! Tertiary structure relationship: is_source_of EDAM:0001468 ! Protein domain tertiary structure @@ -9743,16 +9729,16 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Structure database<-Tertiary structure database<-Nucleic acid structure database +! Data resource<-Structure data resource<-Tertiary structure data resource<-Nucleic acid structure data resource ! [Term] id: EDAM:0000697 -name: RNA structure and alignment database -namespace: database +name: RNA structure and alignment data resource +namespace: resource def: "A database of RNA secondary or tertiary structure and alignments." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000585 ! Nucleic acid structure database -is_a: EDAM:0000597 ! Structure alignment database +is_a: EDAM:0000585 ! Nucleic acid structure data resource +is_a: EDAM:0000597 ! Structure alignment data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000880 ! RNA secondary structure relationship: is_source_of EDAM:0001465 ! RNA tertiary structure @@ -9762,25 +9748,25 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Structure database<-Protein secondary structure and alignment database +! Data resource<-Structure data resource<-Protein secondary structure and alignment data resource ! ! -! Database<-Structure database<-Carbohydrate structure database +! Data resource<-Structure data resource<-Carbohydrate structure data resource ! ! -! Database<-Structure database<-Chemical and small molecule database +! Data resource<-Structure data resource<-Chemical and small molecule data resource ! [Term] id: EDAM:0000620 -name: Drug and drug design database -namespace: database +name: Drug and drug design data resource +namespace: resource def: "A database concerning drugs, drug targets, interactions, binding affinities, drug response, drug effects etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000696 ! Chemical and small molecule database +is_a: EDAM:0000696 ! Chemical and small molecule data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001696 ! Drug relationship: has_identifier EDAM:0001056 ! Database name @@ -9791,39 +9777,39 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-General protein database +! Data resource<-General protein data resource ! ! -! Database<-Protein interaction database +! Data resource<-Protein interaction data resource ! [Term] id: EDAM:0000717 -name: Protein-ligand interaction database -namespace: database +name: Protein-ligand interaction data resource +namespace: resource def: "A database of protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000587 ! Protein interaction database +is_a: EDAM:0000587 ! Protein interaction data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001566 ! Protein-ligand interaction relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000718 -name: Protein-nucleic acid interaction database -namespace: database +name: Protein-nucleic acid interaction data resource +namespace: resource def: "A database of protein-nucleic acid interactions." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000587 ! Protein interaction database +is_a: EDAM:0000587 ! Protein interaction data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001567 ! Protein-nucleic acid interaction relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000719 -name: Protein-protein interaction database -namespace: database +name: Protein-protein interaction data resource +namespace: resource def: "A database of protein-protein interactions; protein complexes, protein functional coupling etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000587 ! Protein interaction database +is_a: EDAM:0000587 ! Protein interaction data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001565 ! Protein-protein interaction relationship: has_identifier EDAM:0001056 ! Database name @@ -9832,56 +9818,56 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Protein interaction database<-Protein-ligand interaction database +! Data resource<-Protein interaction data resource<-Protein-ligand interaction data resource ! ! -! Database<-Protein interaction database<-Protein-nucleic acid interaction database +! Data resource<-Protein interaction data resource<-Protein-nucleic acid interaction data resource ! ! -! Database<-Protein interaction database<-Protein-protein interaction database +! Data resource<-Protein interaction data resource<-Protein-protein interaction data resource ! ! -! Database<-Protein localization database +! Data resource<-Protein localization data resource ! ! -! Database<-Protein structural motif database +! Data resource<-Protein structural motif data resource ! ! -! Database<-Protein structure annotation database +! Data resource<-Protein structure annotation data resource ! ! -! Database<-Proteome annotation database +! Data resource<-Proteome annotation data resource ! ! -! Database<-Molecular motions database +! Data resource<-Molecular motions data resource ! ! -! Database<-NMR database +! Data resource<-NMR data resource ! ! -! Database<-Sequence classification database +! Data resource<-Sequence classification data resource ! [Term] id: EDAM:0000722 -name: Nucleic acid sequence classification database -namespace: database +name: Nucleic acid sequence classification data resource +namespace: resource def: "A database of nucleic acid sequence classifications." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000594 ! Sequence classification database +is_a: EDAM:0000594 ! Sequence classification data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name @@ -9889,30 +9875,30 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Protein classification database +! Data resource<-Protein classification data resource ! [Term] id: EDAM:0000723 -name: Protein structure classification database -namespace: database +name: Protein structure classification data resource +namespace: resource def: "A database of protein structural classifications." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000595 ! Protein classification database +is_a: EDAM:0000595 ! Protein classification data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000724 -name: Protein families database -namespace: database +name: Protein families data resource +namespace: resource def: "A database of protein sequences that are classified into groups or families." [EDAM:EBI "EMBRACE definition"] comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. -synonym: "Protein sequence classification database" EXACT [] -synonym: "Protein secondary database" EXACT [] -is_a: EDAM:0000595 ! Protein classification database -is_a: EDAM:0000594 ! Sequence classification database -is_a: EDAM:0000598 ! Sequence motif or profile database +synonym: "Protein sequence classification data resource" EXACT [] +synonym: "Protein secondary data resource" EXACT [] +is_a: EDAM:0000595 ! Protein classification data resource +is_a: EDAM:0000594 ! Sequence classification data resource +is_a: EDAM:0000598 ! Sequence motif or profile data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000907 ! Protein family relationship: is_source_of EDAM:0001235 ! Sequence cluster @@ -9921,7 +9907,7 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Protein classification database<-Protein families database +! Data resource<-Protein classification data resource<-Protein families data resource ! @@ -9931,14 +9917,14 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Protein classification database<-Protein structure classification database +! Data resource<-Protein classification data resource<-Protein structure classification data resource ! [Term] id: EDAM:0000736 -name: Protein domain classification database -namespace: database +name: Protein domain classification data resource +namespace: resource def: "A database of protein structural domain classifications." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000723 ! Protein structure classification database +is_a: EDAM:0000723 ! Protein structure classification data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000900 ! Protein domain classification relationship: is_source_of EDAM:0000901 ! Protein domain composition report @@ -9949,7 +9935,7 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Protein classification database<-Protein structure classification database<-Protein domain classification database +! Data resource<-Protein classification data resource<-Protein structure classification data resource<-Protein domain classification data resource ! @@ -9957,44 +9943,44 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Sequence alignment database +! Data resource<-Sequence alignment data resource ! [Term] id: EDAM:0000740 -name: Nucleotide sequence alignment database -namespace: database +name: Nucleotide sequence alignment data resource +namespace: resource def: "A database of nucleotide sequence alignments." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000596 ! Sequence alignment database +is_a: EDAM:0000596 ! Sequence alignment data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001383 ! Nucleotide sequence alignment relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000741 -name: Protein sequence alignment database -namespace: database +name: Protein sequence alignment data resource +namespace: resource def: "A database of protein sequence alignments." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000596 ! Sequence alignment database +is_a: EDAM:0000596 ! Sequence alignment data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001384 ! Protein sequence alignment relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Structure alignment database +! Data resource<-Structure alignment data resource ! ! -! Database<-Sequence motif or profile database +! Data resource<-Sequence motif or profile data resource ! [Term] id: EDAM:0000742 -name: Nucleotide sequence motif or profile database -namespace: database +name: Nucleotide sequence motif or profile data resource +namespace: resource def: "A database of nucleotide sequence motifs, or sequence profiles derived from an nucleic acid sequence alignment." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000598 ! Sequence motif or profile database +is_a: EDAM:0000598 ! Sequence motif or profile data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001353 ! Sequence motif relationship: is_source_of EDAM:0001354 ! Sequence profile @@ -10002,10 +9988,10 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000743 -name: Protein sequence motif or profile database -namespace: database +name: Protein sequence motif or profile data resource +namespace: resource def: "A database of protein sequence motifs, or sequence profiles derived from an protein sequence alignment." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000598 ! Sequence motif or profile database +is_a: EDAM:0000598 ! Sequence motif or profile data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001353 ! Sequence motif relationship: is_source_of EDAM:0001354 ! Sequence profile @@ -10014,9 +10000,9 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000744 name: Sequence profile library -namespace: database +namespace: resource def: "A library of sequence profiles (each profile representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000598 ! Sequence motif or profile database +is_a: EDAM:0000598 ! Sequence motif or profile data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001354 ! Sequence profile relationship: has_identifier EDAM:0001056 ! Database name @@ -10024,23 +10010,23 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Sequence motif or profile database<-Nucleotide sequence motif or profile database +! Data resource<-Sequence motif or profile data resource<-Nucleotide sequence motif or profile data resource ! ! -! Database<-Sequence motif or profile database<-Protein sequence motif or profile database +! Data resource<-Sequence motif or profile data resource<-Protein sequence motif or profile data resource ! ! -! Database<-Sequence motif or profile database<-Sequence profile library +! Data resource<-Sequence motif or profile data resource<-Sequence profile library ! [Term] id: EDAM:0000746 name: HMM sequence profile library -namespace: database +namespace: resource def: "A library of hidden Markov models (each model representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000744 ! Sequence profile library relationship: is_concern_of EDAM:0000076 ! Undefined @@ -10049,12 +10035,12 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Sequence motif or profile database<-Sequence profile library<-HMM sequence profile library +! Data resource<-Sequence motif or profile data resource<-Sequence profile library<-HMM sequence profile library ! [Term] id: EDAM:0001763 name: CATH HMM library -namespace: database +namespace: resource def: "A library of hidden Markov models for CATH domain." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000744 ! HMM sequence profile library relationship: is_concern_of EDAM:0000076 ! Undefined @@ -10062,40 +10048,40 @@ relationship: is_source_of EDAM:0001364 ! Hidden Markov model relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Functional sites database +! Data resource<-Functional sites data resource ! [Term] id: EDAM:0000747 -name: Nucleic acid functional sites database -namespace: database +name: Nucleic acid functional sites data resource +namespace: resource def: "A database of functional sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000600 ! Functional sites database +is_a: EDAM:0000600 ! Functional sites data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000748 -name: Protein functional sites database -namespace: database +name: Protein functional sites data resource +namespace: resource def: "A database of functional sites in protein sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000600 ! Functional sites database +is_a: EDAM:0000600 ! Functional sites data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Functional sites database<-Nucleic acid functional sites database +! Data resource<-Functional sites data resource<-Nucleic acid functional sites data resource ! [Term] id: EDAM:0000749 -name: Transcription regulatory sites database -namespace: database +name: Transcription regulatory sites data resource +namespace: resource def: "A database of transcription regulatory sites database in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes promoters, transcription factor binding sites etc. -is_a: EDAM:0000747 ! Nucleic acid functional sites database -is_a: EDAM:0000631 ! Gene regulation database +is_a: EDAM:0000747 ! Nucleic acid functional sites data resource +is_a: EDAM:0000631 ! Gene regulation data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name @@ -10103,10 +10089,10 @@ relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000750 -name: Splice sites database -namespace: database +name: Splice sites data resource +namespace: resource def: "A database of splice sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000747 ! Nucleic acid functional sites database +is_a: EDAM:0000747 ! Nucleic acid functional sites data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001307 ! Splice site report relationship: has_identifier EDAM:0001056 ! Database name @@ -10115,54 +10101,54 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Functional sites database<-Protein functional sites database +! Data resource<-Functional sites data resource<-Protein functional sites data resource ! [Term] id: EDAM:0000751 -name: Phosphorylation sites database -namespace: database +name: Phosphorylation sites data resource +namespace: resource def: "A database of phosphorylation sites in protein sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000748 ! Protein functional sites database +is_a: EDAM:0000748 ! Protein functional sites data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-General protein modifications database +! Data resource<-General protein modifications data resource ! ! -! Database<-Biological pathways database +! Data resource<-Biological pathways data resource ! [Term] id: EDAM:0000753 -name: Metabolic pathways database -namespace: database +name: Metabolic pathways data resource +namespace: resource def: "A database of metabolic pathways." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000602 ! Biological pathways database +is_a: EDAM:0000602 ! Biological pathways data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000946 ! Biological pathway relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000754 -name: Signalling pathways database -namespace: database +name: Signalling pathways data resource +namespace: resource def: "A database of signalling pathways." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000602 ! Biological pathways database +is_a: EDAM:0000602 ! Biological pathways data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000946 ! Biological pathway relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000755 -name: KEGG PATHWAY database -namespace: database +name: KEGG PATHWAY data resource +namespace: resource 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. -is_a: EDAM:0000602 ! Biological pathways database +is_a: EDAM:0000602 ! Biological pathways data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000946 ! Biological pathway ! relationship: is_source_of EDAM:0001647 ! KEGG PATHWAY entry format @@ -10171,55 +10157,55 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Biological pathways database<-Metabolic pathways database +! Data resource<-Biological pathways data resource<-Metabolic pathways data resource ! ! -! Database<-Biological pathways database<-Signalling pathways database +! Data resource<-Biological pathways data resource<-Signalling pathways data resource ! ! -! Database<-Proteomics database +! Data resource<-Proteomics data resource ! [Term] id: EDAM:0000764 -name: General proteomics database -namespace: database +name: General proteomics data resource +namespace: resource def: "A general database on proteomics." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000603 ! Proteomics database +is_a: EDAM:0000603 ! Proteomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000765 -name: Two-dimensional gel electrophoresis database -namespace: database +name: Two-dimensional gel electrophoresis data resource +namespace: resource def: "A database of two-dimensional gel electrophoresis image and related data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000603 ! Proteomics database +is_a: EDAM:0000603 ! Proteomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000942 ! Two-dimensional gel electrophoresis image relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000766 -name: Mass spectromery database -namespace: database +name: Mass spectromery data resource +namespace: resource def: "A database of mass spectromery data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000603 ! Proteomics database +is_a: EDAM:0000603 ! Proteomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000943 ! Mass spectrometry spectra relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000767 -name: Peptide identification database -namespace: database +name: Peptide identification data resource +namespace: resource def: "A database of peptide (e.g. digest product) identifications from mass spectrometry and peptide chip data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000603 ! Proteomics database +is_a: EDAM:0000603 ! Proteomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000944 ! Peptide mass fingerprint relationship: is_source_of EDAM:0000945 ! Peptide identification @@ -10227,263 +10213,263 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Proteomics database<-General proteomics database +! Data resource<-Proteomics data resource<-General proteomics data resource ! ! -! Database<-Proteomics database<-Two-dimensional gel electrophoresis database +! Data resource<-Proteomics data resource<-Two-dimensional gel electrophoresis data resource ! ! -! Database<-Proteomics database<-Mass spectromery database +! Data resource<-Proteomics data resource<-Mass spectromery data resource ! ! -! Database<-Proteomics database<-Peptide identification database +! Data resource<-Proteomics data resource<-Peptide identification data resource ! ! -! Database<-General peptides database +! Data resource<-General peptides data resource ! ! -! Database<-Informatics database +! Data resource<-Informatics data resource ! [Term] id: EDAM:0000769 -name: Workflow database -namespace: database +name: Workflow data resource +namespace: resource def: "A biological or biomedical workflow database." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000605 ! Informatics database +is_a: EDAM:0000605 ! Informatics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000949 ! Workflow relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000770 -name: Data type, object or resource database -namespace: database +name: Data type, object or resource data resource +namespace: resource def: "A database of data resources such as data types or objects." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000605 ! Informatics database +is_a: EDAM:0000605 ! Informatics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000006 ! Data relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000771 -name: Biological models database -namespace: database +name: Biological models data resource +namespace: resource def: "A database of mathematical or other biological models." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000605 ! Informatics database +is_a: EDAM:0000605 ! Informatics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000950 ! Biological model relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Informatics database<-Workflow database +! Data resource<-Informatics data resource<-Workflow data resource ! ! -! Database<-Informatics database<-Data type, object or resource database +! Data resource<-Informatics data resource<-Data type, object or resource data resource ! ! -! Database<-Informatics database<-Biological models database +! Data resource<-Informatics data resource<-Biological models data resource ! ! -! Database<-Literature database +! Data resource<-Literature data resource ! ! -! Database<-Biological resource database +! Data resource<-Biological resource data resource ! ! -! Database<-Cell culture database +! Data resource<-Cell culture data resource ! ! -! Database<-Cell cycle database +! Data resource<-Cell cycle data resource ! ! -! Database<-Ecological database +! Data resource<-Ecological data resource ! ! -! Database<-Electron microscopy database +! Data resource<-Electron microscopy data resource ! ! -! Database<-Embryology and development database +! Data resource<-Embryology and development data resource ! ! -! Database<-Amino acid database +! Data resource<-Amino acid data resource ! ! -! Database<-Nucleic acid physicochemical property database +! Data resource<-Nucleic acid physicochemical property data resource ! ! -! Database<-Protein physicochemical property database +! Data resource<-Protein physicochemical property data resource ! ! -! Database<-Organelle database +! Data resource<-Organelle data resource ! [Term] id: EDAM:0000779 -name: Mitochondrial genes and proteins database -namespace: database +name: Mitochondrial genes and proteins data resource +namespace: resource def: "A database on mitochondrial genes and proteins." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000616 ! Organelle database +is_a: EDAM:0000616 ! Organelle data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Ribosome database +! Data resource<-Ribosome data resource ! ! -! Database<-Scents database +! Data resource<-Scents data resource ! ! -! Database<-Biochemical nomenclature database +! Data resource<-Biochemical nomenclature data resource ! ! -! Database<-Organism-specific database +! Data resource<-Organism-specific data resource ! [Term] id: EDAM:0000780 -name: Plant database -namespace: database +name: Plant data resource +namespace: resource def: "A database of plants or data concerning plants." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000621 ! Organism-specific database +is_a: EDAM:0000621 ! Organism-specific data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000781 -name: Viral database -namespace: database +name: Viral data resource +namespace: resource def: "A database of viruses or data concerning viruses." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000621 ! Organism-specific database +is_a: EDAM:0000621 ! Organism-specific data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000782 -name: Fungal database -namespace: database +name: Fungal data resource +namespace: resource def: "A database of fungis and molds or data concerning fungis and molds." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000621 ! Organism-specific database +is_a: EDAM:0000621 ! Organism-specific data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000783 -name: Pathogen database -namespace: database +name: Pathogen data resource +namespace: resource def: "A database of pathogens or data concerning pathogens." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000621 ! Organism-specific database +is_a: EDAM:0000621 ! Organism-specific data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0001811 -name: Bacteria database -namespace: database +name: Bacteria data resource +namespace: resource def: "A database concerning specific bacteria." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000621 ! Organism-specific database +is_a: EDAM:0000621 ! Organism-specific data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Organism-specific database<-Plant database +! Data resource<-Organism-specific data resource<-Plant data resource ! [Term] id: EDAM:0000784 -name: General plant database -namespace: database +name: General plant data resource +namespace: resource def: "A general database about plants." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000780 ! Plant database +is_a: EDAM:0000780 ! Plant data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000785 -name: Plant-specific database -namespace: database +name: Plant-specific data resource +namespace: resource def: "A database for a specific plant or groups of plants." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000780 ! Plant database +is_a: EDAM:0000780 ! Plant data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Organism-specific database<-Plant database<-General plant database +! Data resource<-Organism-specific data resource<-Plant data resource<-General plant data resource ! ! -! Database<-Organism-specific database<-Plant database<-Plant-specific database +! Data resource<-Organism-specific data resource<-Plant data resource<-Plant-specific data resource ! [Term] id: EDAM:0000786 -name: Arabidopsis database -namespace: database +name: Arabidopsis data resource +namespace: resource def: "A database of Arabidopsis-specific data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000785 ! Plant-specific database +is_a: EDAM:0000785 ! Plant-specific data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000787 -name: Rice database -namespace: database +name: Rice data resource +namespace: resource def: "A database of rice-specific data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000785 ! Plant-specific database +is_a: EDAM:0000785 ! Plant-specific data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name @@ -10493,148 +10479,148 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Organism-specific database<-Plant database<-Plant-specific database<-Arabidopsis database +! Data resource<-Organism-specific data resource<-Plant data resource<-Plant-specific data resource<-Arabidopsis data resource ! ! -! Database<-Organism-specific database<-Plant database<-Plant-specific database<-Rice database +! Data resource<-Organism-specific data resource<-Plant data resource<-Plant-specific data resource<-Rice data resource ! ! -! Database<-Organism-specific database<-Viral database +! Data resource<-Organism-specific data resource<-Viral data resource ! [Term] id: EDAM:0000790 -name: General virus database -namespace: database +name: General virus data resource +namespace: resource def: "A general database about viruses." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000781 ! Viral database +is_a: EDAM:0000781 ! Viral data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000791 -name: Virus-specific database -namespace: database +name: Virus-specific data resource +namespace: resource def: "A database of data specific to a virus or group of viruses; sequence and structural data, interactions of viral proteins etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000781 ! Viral database +is_a: EDAM:0000781 ! Viral data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Organism-specific database<-Fungal database +! Data resource<-Organism-specific data resource<-Fungal data resource ! [Term] id: EDAM:0000792 -name: General fungal database -namespace: database +name: General fungal data resource +namespace: resource def: "A general database about viruses." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000782 ! Fungal database +is_a: EDAM:0000782 ! Fungal data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000793 -name: Fungi-specific database -namespace: database +name: Fungi-specific data resource +namespace: resource def: "A database of data specific to a fungus or group of fungi." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000782 ! Fungal database +is_a: EDAM:0000782 ! Fungal data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Organism-specific database<-Pathogen database +! Data resource<-Organism-specific data resource<-Pathogen data resource ! ! -! Database<-Organism-specific database<-Bacteria database +! Data resource<-Organism-specific data resource<-Bacteria data resource ! ! -! Database<-Genomics database +! Data resource<-Genomics data resource ! [Term] id: EDAM:0000794 -name: General genomics database -namespace: database +name: General genomics data resource +namespace: resource def: "A database of general genome information, such as meta-information on genomes, gene names etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000622 ! Genomics database +is_a: EDAM:0000622 ! Genomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000795 -name: Genome annotation database -namespace: database +name: Genome annotation data resource +namespace: resource def: "Annotation on a specific genome sequence." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000622 ! Genomics database +is_a: EDAM:0000622 ! Genomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000796 -name: Genetic map or linkage database -namespace: database +name: Genetic map or linkage data resource +namespace: resource def: "A database on genetic (linkage) maps, synteny, genetic markers etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000622 ! Genomics database +is_a: EDAM:0000622 ! Genomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001278 ! Genetic map relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000797 -name: Comparative genomics database -namespace: database +name: Comparative genomics data resource +namespace: resource def: "A database of data for comparative genomic analysis." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000622 ! Genomics database +is_a: EDAM:0000622 ! Genomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000798 -name: Mobile genetic elements database -namespace: database +name: Mobile genetic elements data resource +namespace: resource def: "A database on mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000622 ! Genomics database +is_a: EDAM:0000622 ! Genomics data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Genomics database<-General genomics database +! Data resource<-Genomics data resource<-General genomics data resource ! ! -! Database<-Genome annotation database +! Data resource<-Genome annotation data resource ! ! -! Database<-Genetic map or linkage database +! Data resource<-Genetic map or linkage data resource ! [Term] id: EDAM:0000800 -name: Genome map database -namespace: database +name: Genome map data resource +namespace: resource def: "A database containing a map of an entire genome." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000796 ! Genetic map or linkage database +is_a: EDAM:0000796 ! Genetic map or linkage data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001278 ! Genetic map relationship: has_identifier EDAM:0000841 ! Undefined @@ -10642,30 +10628,30 @@ relationship: has_identifier EDAM:0000841 ! Undefined ! -! Database<-Genetic map or linkage database<-Genome map database +! Data resource<-Genetic map or linkage data resource<-Genome map data resource ! ! -! Database<-Comparative genomics database +! Data resource<-Comparative genomics data resource ! ! -! Database<-Mobile genetic elements database +! Data resource<-Mobile genetic elements data resource ! ! -! Database<-Genes database +! Data resource<-Genes data resource ! [Term] id: EDAM:0000801 -name: Human genes database -namespace: database +name: Human genes data resource +namespace: resource def: "A database of human genes." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000623 ! Genes database +is_a: EDAM:0000623 ! Genes data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000916 ! Gene annotation relationship: has_identifier EDAM:0001056 ! Database name @@ -10674,27 +10660,27 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Genes database<-Human genes database +! Data resource<-Genes data resource<-Human genes data resource ! [Term] id: EDAM:0000803 -name: Human genes, mutation and disease database -namespace: database +name: Human genes, mutation and disease data resource +namespace: resource def: "A database of human genes and mutations implicated in disease." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000801 ! Human genes database +is_a: EDAM:0000801 ! Human genes data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000916 ! Gene annotation relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000804 -name: Immunological genes or proteins database -namespace: database +name: Immunological genes or proteins data resource +namespace: resource def: "A database of human immunological genes or proteins." [EDAM:EBI "EMBRACE definition"] comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system. -is_a: EDAM:0000801 ! Human genes database -is_a: EDAM:0000635 ! Specific protein database +is_a: EDAM:0000801 ! Human genes data resource +is_a: EDAM:0000635 ! Specific protein data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000916 ! Gene annotation relationship: has_identifier EDAM:0001056 ! Database name @@ -10703,26 +10689,26 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Genes database<-Human genes database<-Human genes, mutation and disease database +! Data resource<-Genes data resource<-Human genes data resource<-Human genes, mutation and disease data resource ! [Term] id: EDAM:0000805 -name: Cancer gene database -namespace: database +name: Cancer gene data resource +namespace: resource def: "A database of genes implicated in cancer." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000803 ! Human genes, mutation and disease database +is_a: EDAM:0000803 ! Human genes, mutation and disease data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000916 ! Gene annotation relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Chromosome database +! Data resource<-Chromosome data resource ! ! -! Database<-Genotype / phenotype database +! Data resource<-Genotype / phenotype data resource ! @@ -10731,118 +10717,118 @@ relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-DNA methylation database +! Data resource<-DNA methylation data resource ! ! -! Database<-DNA replication database +! Data resource<-DNA replication data resource ! ! -! Database<-Gene structure database +! Data resource<-Gene structure data resource ! ! -! Database<-Gene regulation database +! Data resource<-Gene regulation data resource ! [Term] id: EDAM:0000811 -name: Transcription factor and binding site database -namespace: database +name: Transcription factor and binding site data resource +namespace: resource def: "A database on transcription factors and transcription factor binding sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes sequence and structural information, binding profiles etc. -is_a: EDAM:0000631 ! Gene regulation database -is_a: EDAM:0000749 ! Transcription regulatory sites database -is_a: EDAM:0000635 ! Specific protein database +is_a: EDAM:0000631 ! Gene regulation data resource +is_a: EDAM:0000749 ! Transcription regulatory sites data resource +is_a: EDAM:0000635 ! Specific protein data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001315 ! Transcription factor binding site report relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Gene regulation database<-Transcription factor and binding site database +! Data resource<-Gene regulation data resource<-Transcription factor and binding site data resource ! ! -! Database<-Gene expression and microarray database +! Data resource<-Gene expression and microarray data resource ! ! -! Database<-Molecular probes or primers database +! Data resource<-Molecular probes or primers data resource ! ! -! Database<-Immunological database +! Data resource<-Immunological data resource ! ! -! Database<-Disease database +! Data resource<-Disease data resource ! ! -! Database<-Specific protein database +! Data resource<-Specific protein data resource ! [Term] id: EDAM:0000819 -name: Disease-associated protein database -namespace: database +name: Disease-associated protein data resource +namespace: resource def: "A database on disease-associated proteins." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000635 ! Specific protein database +is_a: EDAM:0000635 ! Specific protein data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000820 -name: Membrane protein database -namespace: database +name: Membrane protein data resource +namespace: resource def: "A database on membrane proteins." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000635 ! Specific protein database +is_a: EDAM:0000635 ! Specific protein data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0000843 ! Database entry relationship: has_identifier EDAM:0001056 ! Database name [Term] id: EDAM:0000821 -name: Enzyme database -namespace: database +name: Enzyme data resource +namespace: resource def: "A database of enzymes, enzyme nomenclature etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000635 ! Specific protein database +is_a: EDAM:0000635 ! Specific protein data resource relationship: is_concern_of EDAM:0000076 ! Undefined relationship: is_source_of EDAM:0001509 ! Enzyme annotation relationship: has_identifier EDAM:0001056 ! Database name ! -! Database<-Specific protein database<-Disease-associated protein database +! Data resource<-Specific protein data resource<-Disease-associated protein data resource ! ! -! Database<-Specific protein database<-Membrane protein database +! Data resource<-Specific protein data resource<-Membrane protein data resource ! ! -! Database<-Specific protein database<-Enzyme database +! Data resource<-Specific protein data resource<-Enzyme data resource ! ! -! Database<-Phylogenetic database +! Data resource<-Phylogenetic data resource ! ! -! Database<-Taxonomic database +! Data resource<-Taxonomic data resource ! @@ -10861,70 +10847,84 @@ id: EDAM:0001884 name: UniProt keywords namespace: ontology def: "A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0002007 ! UniProt keyword -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0002007 ! UniProt keyword +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000829 name: BioPax ontology namespace: ontology def: "BioPax ontology of biological pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001715 ! BioPax term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001715 ! BioPax term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000830 name: Gene Ontology namespace: ontology def: "The Gene Ontology (GO) is a controlled vocabulary for gene and gene product attributes in any organism." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001716 ! GO term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001716 ! GO term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000831 name: MeSH vocabulary namespace: ontology def: "Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001717 ! MeSH term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001717 ! MeSH term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000832 name: HGNC vocabulary namespace: ontology def: "Controlled vocabulary for gene symbols and names from HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001718 ! HGNC term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001718 ! HGNC term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000834 name: Plant Ontology namespace: ontology 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"] -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001720 ! Plant Ontology term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001720 ! Plant Ontology term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000835 name: UMLS vocabulary namespace: ontology def: "Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001721 ! UMLS term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001721 ! UMLS term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000836 @@ -10932,20 +10932,24 @@ name: FMA ontology namespace: ontology 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. -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001722 ! FMA term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001722 ! FMA term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000837 name: EMAP ontology namespace: ontology 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"] -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001723 ! EMAP term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001723 ! EMAP term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000838 @@ -10953,20 +10957,24 @@ name: ChEBI ontology namespace: ontology 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. -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001724 ! ChEBI term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001724 ! ChEBI term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000839 name: MGED ontology namespace: ontology def: "Terms for the standardized description of a microarray experiment." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001725 ! MGED term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001725 ! MGED term +! relationship: has_identifier EDAM:0001051 ! Ontology name [Term] id: EDAM:0000840 @@ -10974,10 +10982,12 @@ name: myGrid ontology namespace: ontology 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. -is_a: EDAM:0000582 ! Ontology -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: is_source_of EDAM:0001726 ! myGrid term -relationship: has_identifier EDAM:0001051 ! Ontology name +is_obsolete: true +consider: EDAM:0000582 ! Ontology +! is_a: EDAM:0000582 ! Ontology +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0001726 ! myGrid term +! relationship: has_identifier EDAM:0001051 ! Ontology name @@ -11005,14 +11015,55 @@ namespace: data def: "Something that identifies (typically uniquely) an entity, databasem, ontology or datatype." [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. is_a: EDAM:0000006 ! Data -relationship: is_identifier_of EDAM:0000002 ! Entity -relationship: is_identifier_of EDAM:0000581 ! Database +relationship: is_identifier_of EDAM:0000002 ! Biological entity +relationship: is_identifier_of EDAM:0000005 ! Data resource relationship: is_identifier_of EDAM:0000582 ! Ontology relationship: is_identifier_of EDAM:0000006 ! Data relationship: is_input_of EDAM:0000004 ! Operation relationship: is_output_of EDAM:0000004 ! Operation relationship: has_source EDAM:0000580 ! Undefined +[Term] +id: EDAM:0000581 +name: Database +namespace: resource +def: "A data resource or archive including relational, object-oriented and other databases, flat-file databanks and ontologies." [EDAM:EBI "EMBRACE definition"] +comment: This term is required for completeness and should not be subclassed (have child terms): EDAM does not include individual databases. +is_a: EDAM:0000006 ! Data +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0001048 ! Database identifier + +[Term] +id: EDAM:0000582 +name: Ontology +namespace: ontology +def: "An ontology of biological or bioinformatics terms and relations, a controlled vocabulary, structured glossary etc." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000006 ! Data +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0001048 ! Database identifier +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0000966 ! Ontology term +! relationship: is_source_of EDAM:0001730 ! Ontology relation +! relationship: has_identifier EDAM:0000842 ! Identifier + + +[Term] +id: EDAM:0000007 +name: Tool +def: "A bioinformatics package or tool, e.g. a standalone application or web service." [EDAM:EBI "EMBRACE definition"] +comment: This term is required for completeness and should not be subclassed (have child terms): EDAM does not include individual tools. +is_a: EDAM:0000006 ! Data +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0000977 ! Tool identifier [Term] id: EDAM:0000843 @@ -11086,7 +11137,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined id: EDAM:0002044 name: Sequence data namespace: data -def: "One or more unaligned molecular sequences, possibly with annotation." [EDAM:EBI "EMBRACE definition"] +def: "Sequence-associated data, typically one or more molecular sequences (or sequence identifiers) and associated annotation. The sequences might be aligned or unaligned. The annotation might include positional features (such as a feature table) or non-positional properties." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined @@ -11099,9 +11150,10 @@ relationship: has_identifier EDAM:0001063 ! Sequence identifier id: EDAM:0000855 name: Sequence annotation namespace: data -def: "A report of general information, properties or features of one or more molecular sequences." [EDAM:EBI "EMBRACE definition"] +def: "A report of general information, non-positional properties or positional features of one or more molecular sequences." [EDAM:EBI "EMBRACE definition"] synonym: "Sequence-derived report" EXACT [] is_a: EDAM:0002048 ! Annotation +is_a: EDAM:0002044 ! Sequence data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined @@ -11172,7 +11224,7 @@ is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000598 ! Sequence motif or profile database +relationship: has_source EDAM:0000598 ! Sequence motif or profile data resource relationship: has_identifier EDAM:0001065 ! Sequence signature identifier @@ -11223,6 +11275,7 @@ namespace: data def: "Annotation on a molecular alignment of some type, including alignment-derived data and metadata." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. is_a: EDAM:0002048 ! Annotation +is_a: EDAM:0002044 ! Sequence data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined @@ -11325,7 +11378,7 @@ is_a: EDAM:0000950 ! Biological model relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000636 ! Phylogenetic database +relationship: has_source EDAM:0000636 ! Phylogenetic data resource relationship: has_identifier EDAM:0001068 ! Phylogenetic tree identifier @@ -11444,7 +11497,7 @@ is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000599 ! Structural profile database +relationship: has_source EDAM:0000599 ! Structural profile data resource relationship: has_identifier EDAM:0001071 ! Structural profile identifier @@ -11475,7 +11528,7 @@ is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000613 ! Amino acid database +relationship: has_source EDAM:0000613 ! Amino acid data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -11488,7 +11541,7 @@ is_a: EDAM:0000962 ! Chemical compound relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000604 ! General peptides database +relationship: has_source EDAM:0000604 ! General peptides data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -11504,7 +11557,7 @@ relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined relationship: has_identifier EDAM:0000841 ! Undefined -relationship: has_source EDAM:0000586 ! General protein database +relationship: has_source EDAM:0000586 ! General protein data resource @@ -11593,7 +11646,7 @@ is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000587 ! Protein interaction database +relationship: has_source EDAM:0000587 ! Protein interaction data resource relationship: has_identifier EDAM:0001074 ! Protein interaction identifier @@ -11606,7 +11659,7 @@ is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000724 ! Protein families database +relationship: has_source EDAM:0000724 ! Protein families data resource relationship: has_identifier EDAM:0001075 ! Protein family identifier [Term] @@ -11732,8 +11785,8 @@ is_a: EDAM:0002048 ! Annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000623 ! Genes database -relationship: has_source EDAM:0000643 ! Genome database +relationship: has_source EDAM:0000623 ! Genes data resource +relationship: has_source EDAM:0000643 ! Genome data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -11744,7 +11797,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined id: EDAM:0000918 name: Sequence variation specification namespace: data -def: "Report on a polymorphism in a molecular sequence such as single base nucleotide subsitutions and short deletion and insertion polymorphisms." [EDAM:EBI "EMBRACE definition"] +def: "Report on a mutation in a molecular sequence such as single base nucleotide subsitutions, deletions and insertions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined @@ -11763,7 +11816,7 @@ is_a: EDAM:0002084 ! Nucleic acid annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000624 ! Chromosome database +relationship: has_source EDAM:0000624 ! Chromosome data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -11863,7 +11916,7 @@ is_a: EDAM:0002048 ! Annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000611 ! Electron microscopy database +relationship: has_source EDAM:0000611 ! Electron microscopy data resource relationship: has_identifier EDAM:0001079 ! Electron microscopy model identifier @@ -11880,7 +11933,7 @@ is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000769 ! Workflow database +relationship: has_source EDAM:0000769 ! Workflow data resource relationship: has_identifier EDAM:0001083 ! Workflow identifier @@ -11894,7 +11947,7 @@ relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined -relationship: has_source EDAM:0000771 ! Biological models database +relationship: has_source EDAM:0000771 ! Biological models data resource relationship: has_identifier EDAM:0001085 ! Biological model identifier @@ -12018,7 +12071,7 @@ is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000696 ! Chemical and small molecule database +relationship: has_source EDAM:0000696 ! Chemical and small molecule data resource relationship: has_identifier EDAM:0001086 ! Chemical compound identifier ! relationship: is_source_of EDAM:0001247 ! Chemical formula @@ -12029,7 +12082,7 @@ relationship: has_identifier EDAM:0001086 ! Chemical compound identifier id: EDAM:0000963 name: Organism strain data namespace: data -def: "Strain data file, including the name of a sequence read and the strain name of the organism the read comes from, as for example used by the MIRA program." [EDAM:EBI "EMBRACE definition"] +def: "Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined @@ -12049,7 +12102,7 @@ is_a: EDAM:0002048 ! Annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000618 ! Scents database +relationship: has_source EDAM:0000618 ! Scents data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -12108,7 +12161,7 @@ is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000606 ! Literature database +relationship: has_source EDAM:0000606 ! Literature data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -12122,7 +12175,7 @@ is_a: EDAM:0000006 ! Data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000606 ! Literature database +relationship: has_source EDAM:0000606 ! Literature data resource relationship: has_identifier EDAM:0001088 ! Article identifier [Term] @@ -12255,7 +12308,7 @@ name: Tool identifier namespace: data def: "An identifier of a bioinformatics tool, e.g. an application or web service." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000842 ! Identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +relationship: is_identifier_of EDAM:0000007 ! Tool relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined @@ -12785,11 +12838,22 @@ name: Data definition identifier namespace: data def: "Identifier of a data type definition from some provider." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000842 ! Identifier -relationship: is_identifier_of EDAM:0000949 ! Workflow +relationship: is_identifier_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined +[Term] +id: EDAM:0002219 +name: Database field name +namespace: data +def: "The name of a field in a database." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000842 ! Identifier +is_a: EDAM:0002099 ! Name +relationship: is_identifier_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined [Term] @@ -12919,6 +12983,17 @@ relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined [Term] +id: EDAM:0002209 +name: Mutation ID +namespace: data +def: "A unique identifier of a specific mutation catalogued in a database." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000842 ! Identifier +relationship: is_identifier_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined + +[Term] id: EDAM:0002133 name: Logical operator namespace: data @@ -13396,6 +13471,18 @@ relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined +[Term] +id: EDAM:0002208 +name: Plasmid identifier +namespace: data +def: "A unique identifier of a plasmid in a database." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002119 ! Nucleic acid identifier +relationship: is_identifier_of EDAM:0000032 ! Plasmid +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined + + ! ! Data<-Identifier<-Molecule identifier<-Polypeptide identifier @@ -13574,6 +13661,7 @@ name: Sequence feature key namespace: data def: "One of the EMBL or SwissProt sequence feature keys." [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. +synonym: "Sequence feature type" EXACT [] is_a: EDAM:0001015 ! Sequence feature identifier relationship: is_identifier_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined @@ -13605,6 +13693,8 @@ relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined + + [Term] id: EDAM:0001023 name: EMBOSS Uniform Feature Object @@ -14722,7 +14812,7 @@ relationship: has_source EDAM:0000580 ! Undefined [Term] id: EDAM:0002149 -name: Database category +name: Database category name namespace: data def: "The name of a category of biological or bioinformatics database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001048 ! Database identifier @@ -14741,7 +14831,7 @@ name: Sequence database name namespace: data def: "The name of a molecular sequence database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001056 ! Database name -relationship: is_identifier_of EDAM:0000584 ! Sequence database +relationship: is_identifier_of EDAM:0000581 ! Database relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined @@ -15163,6 +15253,16 @@ relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined +[Term] +id: EDAM:0002220 +name: SYSTERS cluster ID +namespace: data +def: "Unique identifier of a sequence cluster from the SYSTERS database." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001112 ! Sequence cluster identifier +! relationship: is_identifier_of EDAM:0001228 ! UniGene entry +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined @@ -16092,9 +16192,11 @@ relationship: has_source EDAM:0000580 ! Undefined [Term] id: EDAM:0001179 -name: NCBI taxonomy term identifier +name: NCBI taxonomy ID namespace: data -def: "An identifier of an entry from the NCBI taxonomy database." [EDAM:EBI "EMBRACE definition"] +def: "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." [EDAM:EBI "EMBRACE definition"] +synonym: "NCBI taxonomy term identifier" EXACT [] +synonym: "NCBI tax ID" EXACT [] is_a: EDAM:0001087 ! Ontology term identifier relationship: is_identifier_of EDAM:0001719 ! NCBI taxonomy vocabulary term relationship: is_input_of EDAM:0000223 ! Undefined @@ -16299,7 +16401,7 @@ def: "The name of a computer package, application, method or function." [EDAM:EB is_a: EDAM:0000977 ! Tool identifier is_a: EDAM:0000958 ! Tool metadata is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +relationship: is_identifier_of EDAM:0000007 ! Tool relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined @@ -16316,7 +16418,7 @@ namespace: data def: "The unique name of a signature (sequence classifier) method." [EDAM:EBI "EMBRACE definition"] comment: Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +relationship: is_identifier_of EDAM:0000007 ! Tool relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined @@ -16329,7 +16431,7 @@ def: "The name of a BLAST tool." [EDAM:EBI "EMBRACE definition"] comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. synonym: "BLAST name" EXACT [] is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +relationship: is_identifier_of EDAM:0000007 ! Tool relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined @@ -16341,7 +16443,7 @@ namespace: data def: "The name of a FASTA tool." [EDAM:EBI "EMBRACE definition"] comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +relationship: is_identifier_of EDAM:0000007 ! Tool relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined @@ -16352,7 +16454,7 @@ name: EMBOSS application name namespace: data def: "The name of an EMBOSS application." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +relationship: is_identifier_of EDAM:0000007 ! Tool relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined @@ -16363,7 +16465,7 @@ name: EMBASSY package name namespace: data def: "The name of an EMBASSY package." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +relationship: is_identifier_of EDAM:0000007 ! Tool relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined @@ -16647,7 +16749,7 @@ relationship: has_identifier EDAM:0001061 ! QSAR descriptor name id: EDAM:0000848 name: Sequence namespace: data -def: "A raw molecular sequence which might include ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] +def: "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] comment: Non-sequence characters may be used for example for gaps and translation stop. is_a: EDAM:0002044 ! Sequence data relationship: is_attribute_of EDAM:0000008 ! Undefined @@ -16656,12 +16758,26 @@ relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined relationship: has_identifier EDAM:0001063 ! Sequence identifier + +[Term] +id: EDAM:0002201 +name: Sequence record full +namespace: data +def: "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] +xref: SO:2000061 +is_a: EDAM:0000849 ! Sequence record +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000584 ! Sequence database +relationship: has_identifier EDAM:0001063 ! Sequence identifier + + [Term] id: EDAM:0000849 name: Sequence record namespace: data -def: "A molecular sequence and associated metadata (possibly including a feature table), typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] -xref: SO:2000061 +def: "A molecular sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002044 ! Sequence data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined @@ -16674,7 +16790,7 @@ relationship: has_identifier EDAM:0001063 ! Sequence identifier id: EDAM:0000850 name: Sequence set namespace: data -def: "Any collection of multiple molecular sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [EDAM:EBI "EMBRACE definition"] +def: "A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for arbitrary sequence sets and associated data arising from processing. is_a: EDAM:0002044 ! Sequence data relationship: is_attribute_of EDAM:0000008 ! Undefined @@ -17000,7 +17116,7 @@ consider: EDAM:0002043 ! Sequence record lite id: EDAM:0002043 name: Sequence record lite namespace: data -def: "A molecular sequence and minimal associated metadata, typically an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] +def: "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000849 ! Sequence record relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined @@ -17490,7 +17606,7 @@ consider: EDAM:0000855 ! Sequence annotation id: EDAM:0001254 name: Sequence property namespace: data -def: "A report on general properties (non-positional) of molecular sequence(s) derived from sequence data." [EDAM:EBI "EMBRACE definition"] +def: "Annotation of non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." [EDAM:EBI "EMBRACE definition"] synonym: "Sequence properties report" EXACT [] is_a: EDAM:0000855 ! Sequence annotation relationship: is_attribute_of EDAM:0000008 ! Undefined @@ -17501,9 +17617,9 @@ relationship: has_identifier EDAM:0000841 ! Undefined [Term] id: EDAM:0001255 -name: Sequence feature annotation +name: Sequence features namespace: data -def: "Annotation of features of molecular sequence(s) that can be mapped to position(s) in the sequence." [EDAM:EBI "EMBRACE definition"] +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"] is_a: EDAM:0000855 ! Sequence annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined @@ -17529,7 +17645,7 @@ is_a: EDAM:0001274 ! Map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -17544,7 +17660,7 @@ is_a: EDAM:0001274 ! Map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -17559,7 +17675,7 @@ is_a: EDAM:0001274 ! Map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -17573,7 +17689,7 @@ is_a: EDAM:0001274 ! Map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -17589,7 +17705,7 @@ is_a: EDAM:0001278 ! Genetic map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -17602,7 +17718,7 @@ is_a: EDAM:0001278 ! Genetic map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined ! @@ -17619,7 +17735,7 @@ is_a: EDAM:0001274 ! Map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -17637,7 +17753,7 @@ is_a: EDAM:0001279 ! Sequence map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined ! @@ -17652,7 +17768,7 @@ is_a: EDAM:0001280 ! DNA physical map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -17664,7 +17780,7 @@ is_a: EDAM:0001280 ! DNA physical map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -17676,7 +17792,7 @@ is_a: EDAM:0001280 ! DNA physical map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -17688,7 +17804,7 @@ is_a: EDAM:0001280 ! DNA physical map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined ! @@ -17960,8 +18076,8 @@ consider: EDAM:0001978 ! dasgff feature format id: EDAM:0001270 name: Sequence feature table namespace: data -def: "Annotation of molecular sequence features, organized in a feature table in any known sequence feature table format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001255 ! Sequence feature annotation +def: "Annotation of positional sequence features, organized into a standard feature table." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001255 ! Sequence features relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined @@ -17973,9 +18089,9 @@ relationship: has_identifier EDAM:0001023 ! EMBOSS Uniform Feature Object id: EDAM:0001271 name: Sequence feature report namespace: data -def: "Sequence feature annotation not in standard feature table format, including the location or matches of motifs and patterns in a sequence." [EDAM:EBI "EMBRACE definition"] +def: "Annotation of positional sequence features not in standard feature table format, such as matches (hits) to motifs and patterns." [EDAM:EBI "EMBRACE definition"] comment: Is a source of sequence feature table information although internal conversion would be required. -is_a: EDAM:0001255 ! Sequence feature annotation +is_a: EDAM:0001255 ! Sequence features relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined @@ -18005,7 +18121,7 @@ name: Protein sequence feature table namespace: data def: "Protein sequence feature annotation in any known sequence feature table format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001270 ! Sequence feature table -relationship: has_source EDAM:0000584 ! Sequence database +relationship: has_source EDAM:0000584 ! Sequence data resource relationship: has_identifier EDAM:0001023 ! EMBOSS Uniform Feature Object @@ -18015,7 +18131,7 @@ name: Nucleotide sequence feature table namespace: data def: "Nucleotide sequence feature annotation in any known sequence feature table format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001270 ! Sequence feature table -relationship: has_source EDAM:0000584 ! Sequence database +relationship: has_source EDAM:0000584 ! Sequence data resource relationship: has_identifier EDAM:0001023 ! EMBOSS Uniform Feature Object @@ -18161,7 +18277,7 @@ is_a: EDAM:0000965 ! Image relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000800 ! Genome map database +relationship: has_source EDAM:0000800 ! Genome map data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -19159,7 +19275,7 @@ is_a: EDAM:0002082 ! Matrix relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000598 ! Sequence motif or profile database +relationship: has_source EDAM:0000598 ! Sequence motif or profile data resource relationship: has_identifier EDAM:0001115 ! Sequence profile identifier @@ -19175,7 +19291,7 @@ is_a: EDAM:0002082 ! Matrix relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000598 ! Sequence motif or profile database +relationship: has_source EDAM:0000598 ! Sequence motif or profile data resource relationship: has_identifier EDAM:0001115 ! Sequence profile identifier @@ -19190,7 +19306,7 @@ is_a: EDAM:0002082 ! Matrix relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000598 ! Sequence motif or profile database +relationship: has_source EDAM:0000598 ! Sequence motif or profile data resource relationship: has_identifier EDAM:0001115 ! Sequence profile identifier @@ -19204,7 +19320,7 @@ is_a: EDAM:0001354 ! Sequence profile relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000598 ! Sequence motif or profile database +relationship: has_source EDAM:0000598 ! Sequence motif or profile data resource relationship: has_identifier EDAM:0001115 ! Sequence profile identifier [Term] @@ -19454,6 +19570,7 @@ name: Sequence alignment namespace: data def: "Alignment of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001916 ! Alignment +is_a: EDAM:0002044 ! Sequence data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined @@ -19494,7 +19611,7 @@ is_a: EDAM:0001916 ! Alignment relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000694 ! Protein secondary structure and alignment database +relationship: has_source EDAM:0000694 ! Protein secondary structure and alignment data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -20617,7 +20734,7 @@ is_a: EDAM:0002053 ! Structure relationship: is_attribute_of EDAM:0000013 ! Molecular entity relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000693 ! Tertiary structure database +relationship: has_source EDAM:0000693 ! Tertiary structure data resource relationship: has_identifier EDAM:0001070 ! Tertiary structure identifier @@ -20737,7 +20854,7 @@ is_a: EDAM:0002081 ! Secondary structure relationship: is_attribute_of EDAM:0000025 ! Polypeptide relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000694 ! Protein secondary structure and alignment database +relationship: has_source EDAM:0000694 ! Protein secondary structure and alignment data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -20751,7 +20868,7 @@ is_a: EDAM:0002081 ! Secondary structure relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000697 ! RNA structure and alignment database +relationship: has_source EDAM:0000697 ! RNA structure and alignment data resource relationship: has_identifier EDAM:0000841 ! Undefined ! @@ -20811,7 +20928,7 @@ relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined relationship: has_identifier EDAM:0000841 ! Undefined -relationship: has_syntax EDAM:0001747 ! PDB atom record format +relationship: has_format EDAM:0001747 ! PDB atom record format [Term] @@ -21175,7 +21292,7 @@ is_a: EDAM:0000962 ! Chemical compound relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000613 ! Amino acid database +relationship: has_source EDAM:0000613 ! Amino acid data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -21187,7 +21304,7 @@ is_a: EDAM:0002016 ! Amino acid data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000613 ! Amino acid database +relationship: has_source EDAM:0000613 ! Amino acid data resource relationship: has_identifier EDAM:0001073 ! Amino acid index identifier [Term] @@ -21199,7 +21316,7 @@ is_a: EDAM:0002016 ! Amino acid data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000613 ! Amino acid database +relationship: has_source EDAM:0000613 ! Amino acid data resource relationship: has_identifier EDAM:0001010 ! Undefined ! @@ -21214,7 +21331,7 @@ is_a: EDAM:0001501 ! Amino acid index relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000613 ! Amino acid database +relationship: has_source EDAM:0000613 ! Amino acid data resource relationship: has_identifier EDAM:0001073 ! Amino acid index identifier @@ -21227,7 +21344,7 @@ is_a: EDAM:0001501 ! Amino acid index relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000613 ! Amino acid database +relationship: has_source EDAM:0000613 ! Amino acid data resource relationship: has_identifier EDAM:0001073 ! Amino acid index identifier [Term] @@ -21239,7 +21356,7 @@ is_a: EDAM:0001501 ! Amino acid index relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000613 ! Amino acid database +relationship: has_source EDAM:0000613 ! Amino acid data resource relationship: has_identifier EDAM:0001073 ! Amino acid index identifier @@ -21252,7 +21369,7 @@ is_a: EDAM:0001501 ! Amino acid index relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000613 ! Amino acid database +relationship: has_source EDAM:0000613 ! Amino acid data resource relationship: has_identifier EDAM:0001073 ! Amino acid index identifier [Term] @@ -21264,7 +21381,7 @@ is_a: EDAM:0001501 ! Amino acid index relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000613 ! Amino acid database +relationship: has_source EDAM:0000613 ! Amino acid data resource relationship: has_identifier EDAM:0001073 ! Amino acid index identifier @@ -21291,7 +21408,7 @@ is_a: EDAM:0000896 ! Protein annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000821 ! Enzyme database +relationship: has_source EDAM:0000821 ! Enzyme data resource relationship: has_identifier EDAM:0001010 ! Enzyme identifier [Term] @@ -21321,7 +21438,7 @@ is_a: EDAM:0001509 ! Enzyme annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000821 ! Enzyme database +relationship: has_source EDAM:0000821 ! Enzyme data resource relationship: has_identifier EDAM:0001011 ! Enzyme Commission number @@ -21339,7 +21456,7 @@ is_a: EDAM:0001510 ! Restriction enzyme report relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000821 ! Enzyme database +relationship: has_source EDAM:0000821 ! Enzyme data resource relationship: has_identifier EDAM:0001011 ! Enzyme Commission number [Term] @@ -21351,7 +21468,7 @@ is_a: EDAM:0001510 ! Restriction enzyme report relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000821 ! Enzyme database +relationship: has_source EDAM:0000821 ! Enzyme data resource relationship: has_identifier EDAM:0001011 ! Enzyme Commission number @@ -21700,7 +21817,7 @@ is_a: EDAM:0001537 ! Protein structure annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000589 ! Protein structural motif database +relationship: has_source EDAM:0000589 ! Protein structural motif data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -21926,7 +22043,7 @@ is_a: EDAM:0000906 ! Protein interaction relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000587 ! Protein interaction database +relationship: has_source EDAM:0000587 ! Protein interaction data resource relationship: has_identifier EDAM:0001074 ! Protein interaction identifier [Term] @@ -21938,7 +22055,7 @@ is_a: EDAM:0000906 ! Protein interaction relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000587 ! Protein interaction database +relationship: has_source EDAM:0000587 ! Protein interaction data resource relationship: has_identifier EDAM:0001074 ! Protein interaction identifier @@ -21951,7 +22068,7 @@ is_a: EDAM:0000906 ! Protein interaction relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000587 ! Protein interaction database +relationship: has_source EDAM:0000587 ! Protein interaction data resource relationship: has_identifier EDAM:0001074 ! Protein interaction identifier @@ -22373,7 +22490,7 @@ is_a: EDAM:0000916 ! Gene annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000629 ! Gene expression and microarray database +relationship: has_source EDAM:0000629 ! Gene expression and microarray data resource relationship: has_identifier EDAM:0001080 ! Gene expression report identifier [Term] @@ -22508,7 +22625,7 @@ is_a: EDAM:0000919 ! Chromosome annotation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000624 ! Chromosome database +relationship: has_source EDAM:0000624 ! Chromosome data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -22528,7 +22645,6 @@ relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined relationship: has_identifier EDAM:0000841 ! Undefined - [Term] id: EDAM:0001622 name: Disease @@ -22538,11 +22654,71 @@ is_a: EDAM:0000920 ! Genotype / phenotype report relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000634 ! Disease database +relationship: has_source EDAM:0000634 ! Disease data resource relationship: has_identifier EDAM:0001150 ! Disease identifier +[Term] +id: EDAM:0002212 +name: Mutation data +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"] +is_a: EDAM:0000920 ! Genotype / phenotype report +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0002213 +name: Mutation prevalence data +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"] +is_a: EDAM:0000920 ! Genotype / phenotype report +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0002214 +name: Mutation prognostic data +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"] +is_a: EDAM:0000920 ! Genotype / phenotype report +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0002215 +name: Mutant functional data +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"] +is_a: EDAM:0000920 ! Genotype / phenotype report +is_a: EDAM:0000904 ! Protein mutation model +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0002217 +name: Tumor data +namespace: data +def: "Data on a 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"] +is_a: EDAM:0000920 ! Genotype / phenotype report +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined ! ! Data<-Genotype / phenotype report<-Pharmacogenomic report @@ -22604,9 +22780,9 @@ relationship: has_identifier EDAM:0000841 ! Undefined [Term] id: EDAM:0000924 -name: Sequence read data +name: Sequence trace namespace: data -def: "Raw sequence and associated data from a sequencing machine." [EDAM:EBI "EMBRACE definition"] +def: "A molecular sequence and associated metadata (quality scores) from a sequencing machine." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002028 ! Experimental data is_a: EDAM:0000849 ! Sequence record relationship: is_attribute_of EDAM:0000008 ! Undefined @@ -22653,7 +22829,7 @@ is_a: EDAM:0002028 ! Experimental data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000766 ! Mass spectromery database +relationship: has_source EDAM:0000766 ! Mass spectromery data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -22681,7 +22857,7 @@ is_a: EDAM:0002028 ! Experimental data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000767 ! Peptide identification database +relationship: has_source EDAM:0000767 ! Peptide identification data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -22732,7 +22908,7 @@ is_a: EDAM:0002028 ! Experimental data relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000611 ! Electron microscopy database +relationship: has_source EDAM:0000611 ! Electron microscopy data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -22833,7 +23009,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined ! -! Data<-Experimental data<-Sequence read data +! Data<-Experimental data<-Sequence trace ! @@ -23027,7 +23203,7 @@ is_a: EDAM:0000950 ! Biological model relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Biological pathways database +relationship: has_source EDAM:0000602 ! Biological pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier [Term] @@ -23046,7 +23222,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined id: EDAM:0000904 name: Protein mutation model namespace: data -def: "Data on the effect of point mutation on protein folding, stability, structure and function." [EDAM:EBI "EMBRACE definition"] +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. is_a: EDAM:0000950 ! Biological model relationship: is_attribute_of EDAM:0000008 ! Undefined @@ -23178,7 +23354,7 @@ is_a: EDAM:0000965 ! Image relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Biological pathways database +relationship: has_source EDAM:0000602 ! Biological pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier @@ -23197,7 +23373,7 @@ is_a: EDAM:0000947 ! Biological pathway map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Metabolic pathways database +relationship: has_source EDAM:0000602 ! Metabolic pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier @@ -23211,7 +23387,7 @@ is_a: EDAM:0000947 ! Biological pathway map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Biological pathways database +relationship: has_source EDAM:0000602 ! Biological pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier @@ -23225,7 +23401,7 @@ is_a: EDAM:0000947 ! Biological pathway map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Biological pathways database +relationship: has_source EDAM:0000602 ! Biological pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier @@ -23238,7 +23414,7 @@ is_a: EDAM:0000947 ! Biological pathway map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Signalling pathways database +relationship: has_source EDAM:0000602 ! Signalling pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier @@ -23251,7 +23427,7 @@ is_a: EDAM:0000947 ! Biological pathway map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Biological pathways database +relationship: has_source EDAM:0000602 ! Biological pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier [Term] @@ -23263,7 +23439,7 @@ is_a: EDAM:0000947 ! Biological pathway map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Biological pathways database +relationship: has_source EDAM:0000602 ! Biological pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier [Term] @@ -23275,7 +23451,7 @@ is_a: EDAM:0000947 ! Biological pathway map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Biological pathways database +relationship: has_source EDAM:0000602 ! Biological pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier @@ -23288,7 +23464,7 @@ is_a: EDAM:0000947 ! Biological pathway map relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000602 ! Biological pathways database +relationship: has_source EDAM:0000602 ! Biological pathways data resource relationship: has_identifier EDAM:0001082 ! Biological pathway identifier @@ -23601,6 +23777,17 @@ relationship: is_output_of EDAM:0000223 ! Undefined relationship: has_source EDAM:0000580 ! Undefined relationship: has_identifier EDAM:0000841 ! Undefined +[Term] +id: EDAM:0002218 +name: Server metadata +namespace: data +def: "Basic information about one or servers on the web, such as an SRS server." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002018 ! Metadata +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined [Term] id: EDAM:0000959 @@ -23957,7 +24144,7 @@ is_a: EDAM:0002091 ! Accession relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000606 ! Literature database +relationship: has_source EDAM:0000606 ! Literature data resource relationship: has_identifier EDAM:0000841 ! Undefined @@ -24411,7 +24598,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined id: EDAM:0002012 name: Map position namespace: data -def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval." [EDAM:EBI "EMBRACE definition"] +def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval. This includes position in genomes based on a reference sequence." [EDAM:EBI "EMBRACE definition"] comment: 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. xref: Moby:GCP_MapPoint xref: Moby:GCP_MapPosition @@ -24431,11 +24618,25 @@ relationship: has_identifier EDAM:0000841 ! Undefined -! -! Data<-Parameter<-Sequence position specification<-Sequence position -! [Term] -id: EDAM:0001742 +id: EDAM:0002216 +name: Codon number +namespace: data +def: "The number of a codon, for instance, at which a mutation is located (1-393)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001014 ! Sequence position specification +relationship: is_attribute_of EDAM:0000008 ! Undefined +relationship: is_input_of EDAM:0000223 ! Undefined +relationship: is_output_of EDAM:0000223 ! Undefined +relationship: has_source EDAM:0000580 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined + + + +! +! Data<-Parameter<-Sequence position specification<-Sequence position +! +[Term] +id: EDAM:0001742 name: PDB residue number namespace: data def: "A residue identifier (a string) from a PDB file." [EDAM:EBI "EMBRACE definition"] @@ -25021,7 +25222,7 @@ is_a: EDAM:0000962 ! Chemical compound relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000696 ! Chemical and small molecule database +relationship: has_source EDAM:0000696 ! Chemical and small molecule data resource relationship: has_identifier EDAM:0001086 ! Chemical compound identifier @@ -25151,7 +25352,7 @@ is_a: EDAM:0000965 ! Image relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000696 ! Chemical and small molecule database +relationship: has_source EDAM:0000696 ! Chemical and small molecule data resource relationship: has_identifier EDAM:0000990 ! Chemical name relationship: has_identifier EDAM:0000991 ! Chemical registry number @@ -25225,7 +25426,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000829 ! BioPax ontology +! relationship: has_source EDAM:0000829 ! BioPax ontology relationship: has_identifier EDAM:0001175 ! BioPax term identifier [Term] @@ -25243,7 +25444,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000830 ! Gene Ontology +! relationship: has_source EDAM:0000830 ! Gene Ontology relationship: has_identifier EDAM:0001176 ! GO term identifier [Term] @@ -25255,7 +25456,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000831 ! MeSH vocabulary +! relationship: has_source EDAM:0000831 ! MeSH vocabulary relationship: has_identifier EDAM:0001177 ! MeSH term identifier [Term] @@ -25267,7 +25468,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000832 ! HGNC vocabulary +! relationship: has_source EDAM:0000832 ! HGNC vocabulary relationship: has_identifier EDAM:0001178 ! HGNC term identifier [Term] @@ -25291,7 +25492,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000834 ! Plant Ontology +! relationship: has_source EDAM:0000834 ! Plant Ontology relationship: has_identifier EDAM:0001180 ! Plant Ontology term identifier [Term] @@ -25303,7 +25504,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000835 ! UMLS vocabulary +! relationship: has_source EDAM:0000835 ! UMLS vocabulary relationship: has_identifier EDAM:0001181 ! UMLS term identifier [Term] @@ -25316,7 +25517,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000836 ! FMA ontology +! relationship: has_source EDAM:0000836 ! FMA ontology relationship: has_identifier EDAM:0001182 ! FMA term identifier [Term] @@ -25328,7 +25529,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000837 ! EMAP ontology +! relationship: has_source EDAM:0000837 ! EMAP ontology relationship: has_identifier EDAM:0001183 ! EMAP term identifier [Term] @@ -25340,7 +25541,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000838 ! ChEBI ontology +! relationship: has_source EDAM:0000838 ! ChEBI ontology relationship: has_identifier EDAM:0001184 ! ChEBI term identifier [Term] @@ -25352,7 +25553,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000839 ! MGED ontology +! relationship: has_source EDAM:0000839 ! MGED ontology relationship: has_identifier EDAM:0001185 ! MGED term identifier [Term] @@ -25365,7 +25566,7 @@ is_a: EDAM:0000966 ! Ontology term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000840 ! myGrid ontology +! relationship: has_source EDAM:0000840 ! myGrid ontology relationship: has_identifier EDAM:0001186 ! myGrid term identifier @@ -25383,7 +25584,7 @@ is_a: EDAM:0001716 ! GO term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000830 ! Gene Ontology +! relationship: has_source EDAM:0000830 ! Gene Ontology relationship: has_identifier EDAM:0001176 ! GO term identifier [Term] @@ -25396,7 +25597,7 @@ is_a: EDAM:0001716 ! GO term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000830 ! Gene Ontology +! relationship: has_source EDAM:0000830 ! Gene Ontology relationship: has_identifier EDAM:0001176 ! GO term identifier [Term] @@ -25409,7 +25610,7 @@ is_a: EDAM:0001716 ! GO term relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000830 ! Gene Ontology +! relationship: has_source EDAM:0000830 ! Gene Ontology relationship: has_identifier EDAM:0001176 ! GO term identifier @@ -25426,7 +25627,7 @@ is_a: EDAM:0000967 ! Ontology term component relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000582 ! Ontology +! relationship: has_source EDAM:0000582 ! Ontology relationship: has_identifier EDAM:0001087 ! Ontology term identifier [Term] @@ -25438,7 +25639,7 @@ is_a: EDAM:0000967 ! Ontology term component relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000582 ! Ontology +! relationship: has_source EDAM:0000582 ! Ontology relationship: has_identifier EDAM:0001087 ! Ontology term identifier [Term] @@ -25450,7 +25651,7 @@ is_a: EDAM:0000967 ! Ontology term component relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000582 ! Ontology +! relationship: has_source EDAM:0000582 ! Ontology relationship: has_identifier EDAM:0001087 ! Ontology term identifier [Term] @@ -25463,7 +25664,7 @@ is_a: EDAM:0002093 ! Database cross-reference relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000582 ! Ontology +! relationship: has_source EDAM:0000582 ! Ontology relationship: has_identifier EDAM:0001087 ! Ontology term identifier @@ -25512,7 +25713,7 @@ is_a: EDAM:0000970 ! Citation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000606 ! Literature database +relationship: has_source EDAM:0000606 ! Literature data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -25524,7 +25725,7 @@ is_a: EDAM:0000970 ! Citation relationship: is_attribute_of EDAM:0000008 ! Undefined relationship: is_input_of EDAM:0000223 ! Undefined relationship: is_output_of EDAM:0000223 ! Undefined -relationship: has_source EDAM:0000606 ! Literature database +relationship: has_source EDAM:0000606 ! Literature data resource relationship: has_identifier EDAM:0000841 ! Undefined [Term] @@ -25609,756 +25810,724 @@ relationship: has_source EDAM:0000580 ! Undefined relationship: has_identifier EDAM:0000841 ! Undefined ! -! Data syntax +! Data format ! [Term] id: EDAM:0001918 name: Atomic data format -namespace: syntax +namespace: format def: "Data format for an individual atom." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0001919 -name: Sequence format -namespace: syntax -def: "Data format for a molecular sequence information." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +name: Sequence record format +namespace: format +def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0001920 -name: Feature format -namespace: syntax +name: Sequence feature annotation format +namespace: format def: "Data format for molecular sequence feature information." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0001921 name: Alignment format -namespace: syntax +namespace: format def: "Data format for molecular sequence alignment information." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002006 name: Phylogenetic tree format -namespace: syntax +namespace: format def: "Data format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002033 name: Tertiary structure format -namespace: syntax +namespace: format def: "Data format for a molecular tertiary structure." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002034 name: Biological model format -namespace: syntax +namespace: format def: "Data format for a biological pathway." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002014 name: Sequence-profile alignment format -namespace: syntax +namespace: format def: "Data format for a sequence-profile alignment." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002017 name: Amino acid index format -namespace: syntax +namespace: format def: "Data format for an amino acid index." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002020 name: Article format -namespace: syntax +namespace: format def: "Data format for a full-text scientific article." [EDAM:EBI "EMBRACE definition"] synonym: "Literature format" EXACT [] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002021 name: Text mining report format -namespace: syntax +namespace: format def: "Data format for an abstract (report) from text mining." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002027 name: Enzyme kinetics report format -namespace: syntax +namespace: format def: "Data format for reports on enzyme kinetics." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002030 name: Chemical compound report format -namespace: syntax +namespace: format def: "Format of a report on a chemical compound." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002031 name: Gene annotation format -namespace: syntax +namespace: format def: "Format of a report on a particular locus, gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002032 name: Workflow format -namespace: syntax +namespace: format def: "Format of a workflow." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002035 name: Chemical formula format -namespace: syntax +namespace: format def: "Format of a chemical formula." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002036 name: Phylogenetic raw data format -namespace: syntax +namespace: format def: "Format of raw (unplotted) phylogenetic data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002045 name: Electron microscopy model annotation format -namespace: syntax +namespace: format def: "Annotation format for electron microscopy models." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002049 name: Phylogenetic tree distance data format -namespace: syntax +namespace: format def: "Format for phylogenetic tree distance data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002051 name: Polymorphism report format -namespace: syntax +namespace: format def: "Format for sequence polymorphism data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002052 name: Protein family report format -namespace: syntax +namespace: format def: "Format for reports on a protein family." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002054 name: Protein interaction format -namespace: syntax +namespace: format def: "Format for protein interaction data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002055 name: Sequence assembly format -namespace: syntax +namespace: format def: "Format for sequence assembly data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002056 name: Microarray experiment data format -namespace: syntax +namespace: format def: "Format for microarray experimental data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002058 name: Gene expression report format -namespace: syntax +namespace: format def: "Format for a report on gene expression." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002059 name: Genotype / phenotype report format -namespace: syntax +namespace: format def: "Format of a report on genotype / phenotype information." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002060 name: Map format -namespace: syntax +namespace: format def: "Format of a map of (typically one) molecular sequence annotated with features." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002061 name: Primer report format -namespace: syntax +namespace: format def: "Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002062 name: Protein annotation format -namespace: syntax +namespace: format def: "Format of a report of general information about a specific protein." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002064 name: 3D-1D scoring matrix format -namespace: syntax +namespace: format def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002065 name: Protein structure evaluation format -namespace: syntax +namespace: format def: "Format of a report on the quality of a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002066 name: Sequence database hits format -namespace: syntax +namespace: format def: "Format of a report on sequence hits and associated data from searching a sequence database." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002067 name: Sequence distance matrix format -namespace: syntax +namespace: format def: "Format of a matrix of genetic distances between molecular sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002068 name: Sequence motif format -namespace: syntax +namespace: format def: "Format of a sequence motif." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002069 name: Sequence profile format -namespace: syntax +namespace: format def: "Format of a sequence profile." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002074 name: Dirichlet distribution format -namespace: syntax +namespace: format def: "Data format of a dirichlet distribution." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002075 name: HMM emission and transition counts format -namespace: syntax +namespace: format def: "Data format for the emission and transition counts of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002077 name: Protein secondary structure format -namespace: syntax +namespace: format def: "Format for secondary structure (predicted or real) of a protein molecule." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002076 name: RNA secondary structure format -namespace: syntax +namespace: format def: "Format for secondary structure (predicted or real) of an RNA molecule." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002078 name: Sequence range format -namespace: syntax +namespace: format def: "Format used to specify range(s) of sequence positions." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002155 name: Repeat sequence map format -namespace: syntax +namespace: format def: "Format used for map of repeats in molecular (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002158 name: Restriction site report format -namespace: syntax +namespace: format def: "Format used for report on restriction enzyme recognition sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002159 name: Coding region report format -namespace: syntax +namespace: format def: "Format used for report on coding regions in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002170 name: Sequence cluster format -namespace: syntax +namespace: format def: "Format used for clusters of molecular sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0002195 name: Ontology format -namespace: syntax +namespace: format def: "Format used for ontologies." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format + +[Term] +id: EDAM:0002210 +name: Strain data format +namespace: format +def: "Format of a report on organism strain data." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001915 ! Data format + + + ! -! Data syntax<-Atomic data format +! Data format<-Atomic data format ! [Term] id: EDAM:0001747 name: PDB atom record format -namespace: syntax +namespace: format def: "Format of an ATOM record (describing data for an individual atom) from a PDB file." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001918 ! Atomic data format + ! -! Data syntax<-Sequence format +! Data format<-Sequence record format ! +[Term] +id: EDAM:0002203 +name: Sequence record lite format +namespace: format +def: "Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001919 ! Sequence record format + + +[Term] +id: EDAM:0002202 +name: Sequence record full format +namespace: format +def: "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001919 ! Sequence record format + [Term] id: EDAM:0002057 name: Sequence trace format -namespace: syntax +namespace: format def: "Format for sequence trace data (i.e. including base call information)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format + + + + [Term] id: EDAM:0001923 name: acedb sequence format -namespace: syntax +namespace: format def: "ACEDB sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001924 name: clustal sequence format -namespace: syntax +namespace: format def: "Clustalw output format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001925 name: codata sequence format -namespace: syntax +namespace: format def: "Codata entry format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format - -[Term] -id: EDAM:0001926 -name: dbid sequence format -namespace: syntax -def: "Fasta format variant with database name before ID." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format - -[Term] -id: EDAM:0002181 -name: embl-like sequence format -namespace: syntax -def: "A format resembling EMBL entry format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the many non-standard EMBL-like formats. -is_a: EDAM:0001919 ! Sequence format -! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number - -[Term] -id: EDAM:0002183 -name: emblxml sequence format -namespace: syntax -def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format -! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number - - -[Term] -id: EDAM:0002184 -name: cdsxml sequence format -namespace: syntax -def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format -! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number - -[Term] -id: EDAM:0002185 -name: insdxml sequence format -namespace: syntax -def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format -! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number - - +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001928 name: experiment sequence format -namespace: syntax +namespace: format def: "Staden experiment file format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format - -[Term] -id: EDAM:0001929 -name: fasta sequence format -namespace: syntax -def: "FASTA format including NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format - - -[Term] -id: EDAM:0002182 -name: fastq-like sequence format -namespace: syntax -def: "A format resembling FASTQ short read format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for non-standard FASTQ short read-like formats. -is_a: EDAM:0001919 ! Sequence format - +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001934 name: fitch sequence format -namespace: syntax +namespace: format def: "Fitch program format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001935 name: gcg sequence format -namespace: syntax +namespace: format def: "GCG sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format - -[Term] -id: EDAM:0001936 -name: genbank sequence format -namespace: syntax -def: "Genbank entry format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format -! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number - -[Term] -id: EDAM:0001937 -name: genpept sequence format -namespace: syntax -def: "Genpept protein entry format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001938 name: gff2 sequence format -namespace: syntax +namespace: format def: "GFF feature file format with sequence in the header." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001939 name: gff3 sequence format -namespace: syntax +namespace: format def: "GFF3 feature file format with sequence." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format -[Term] -id: EDAM:0001940 -name: gifasta sequence format -namespace: syntax -def: "FASTA sequence format including NCBI-style GIs." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format [Term] id: EDAM:0001941 name: hennig86 sequence format -namespace: syntax +namespace: format def: "Hennig86 output sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001942 name: ig sequence format -namespace: syntax +namespace: format def: "Intelligenetics sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001943 name: igstrict sequence format -namespace: syntax +namespace: format def: "Intelligenetics sequence format (strict version)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001944 name: jackknifer sequence format -namespace: syntax +namespace: format def: "Jackknifer interleaved and non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001945 name: mase sequence format -namespace: syntax +namespace: format def: "Mase program sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001946 name: mega sequence format -namespace: syntax +namespace: format def: "Mega interleaved and non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001947 name: msf sequence format -namespace: syntax +namespace: format def: "GCG MSF (multiple sequence file) file format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format - -[Term] -id: EDAM:0001948 -name: nbrf sequence format -namespace: syntax -def: "NBRF/PIR entry sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001949 name: nexus sequence format -namespace: syntax +namespace: format def: "Nexus/paup interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001950 name: pdb sequence format -namespace: syntax +namespace: format def: "PDB protein databank sequence format (ATOM lines)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001951 name: pdbnuc sequence format -namespace: syntax +namespace: format def: "PDB protein databank nucleotide sequence format (ATOM lines)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001952 name: pdbnucseq sequence format -namespace: syntax +namespace: format def: "PDB protein databank nucleotide sequence format (SEQRES lines)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001953 name: pdbseq sequence format -namespace: syntax +namespace: format def: "PDB protein databank sequence format (SEQRES lines)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format -[Term] -id: EDAM:0001954 -name: pearson sequence format -namespace: syntax -def: "Plain old fasta sequence format (unspecified format for IDs)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format [Term] id: EDAM:0001955 name: phylip sequence format -namespace: syntax +namespace: format def: "Phylip interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001956 name: phylipnon sequence format -namespace: syntax +namespace: format def: "Phylip non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001957 name: raw sequence format -namespace: syntax +namespace: format def: "Raw sequence format with no non-sequence characters." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001958 name: refseqp sequence format -namespace: syntax +namespace: format def: "Refseq protein entry sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format ! relationship: has_source EDAM:0000645 ! RefSeq database [Term] id: EDAM:0001959 name: selex sequence format -namespace: syntax +namespace: format def: "Selex sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001960 name: staden sequence format -namespace: syntax +namespace: format def: "Old staden package sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001961 name: stockholm sequence format -namespace: syntax +namespace: format def: "Stockholm (pfam) sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001962 name: strider sequence format -namespace: syntax +namespace: format def: "DNA strider output sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format - -[Term] -id: EDAM:0002187 -name: uniprotkb-like sequence format -namespace: syntax -def: "A sequence format resembling uniprotkb entry format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format - - +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001964 name: text sequence format -namespace: syntax +namespace: format def: "Plain text sequence format (essentially unformatted)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001965 name: treecon sequence format -namespace: syntax +namespace: format def: "Treecon output sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001966 name: asn1 sequence format -namespace: syntax +namespace: format def: "NCBI ASN.1 sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001967 name: das sequence format -namespace: syntax +namespace: format def: "DASSEQUENCE DAS sequence format (any type)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001968 name: dasdna sequence format -namespace: syntax +namespace: format def: "DASDNA DAS sequence format (nucleotide-only)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001969 name: debug sequence format -namespace: syntax +namespace: format def: "EMBOSS debugging trace sequence format of full internal data content." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001970 name: jackknifernon sequence format -namespace: syntax +namespace: format def: "Jackknifer output sequence non-interleaved format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0001971 name: meganon sequence format -namespace: syntax +namespace: format def: "Mega non-interleaved output sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format + -[Term] -id: EDAM:0001972 -name: ncbi sequence format -namespace: syntax -def: "NCBI fasta sequence format with NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format [Term] id: EDAM:0001973 name: nexusnon sequence format -namespace: syntax +namespace: format def: "Nexus/paup non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001919 ! Sequence format +is_a: EDAM:0001919 ! Sequence record format + + ! -! Data syntax<-Sequence format<-Sequence trace format +! Data format<-Sequence record format<-Sequence record lite format ! [Term] -id: EDAM:0001628 -name: ABI sequence trace format -namespace: syntax -def: "Format of raw sequence data from an ABI sequencing machine." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0002057 ! Sequence trace format +id: EDAM:0002200 +name: fasta-like sequence format +namespace: format +def: "A format resembling FASTA format." [EDAM:EBI "EMBRACE definition"] +comment: This term may be used for the many non-standard fasta-like formats. +is_a: EDAM:0002203 ! Sequence record lite format + + + + +! +! Data format<-Sequence record format<-Sequence record full format +! [Term] -id: EDAM:0001629 -name: MIRA sequence trace format -namespace: syntax -def: "Format of MIRA sequence trace information file." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0002057 ! Sequence trace format +id: EDAM:0002181 +name: embl-like sequence format +namespace: format +def: "A format resembling EMBL entry (plain text) format." [EDAM:EBI "EMBRACE definition"] +comment: This term may be used for the many non-standard EMBL-like formats. +is_a: EDAM:0002202 ! Sequence record full format +! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number + +[Term] +id: EDAM:0002204 +name: embl xml sequence format +namespace: format +def: "An XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] +comment: This is a placeholder for other more specific terms. It should not normally be used for annotation. +is_a: EDAM:0002202 ! Sequence record full format +! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number + + +[Term] +id: EDAM:0002205 +name: genbank-like sequence format +namespace: format +def: "A format resembling GenBank entry (plain text) format." [EDAM:EBI "EMBRACE definition"] +comment: This term may be used for the non-standard genbank-like formats. +is_a: EDAM:0002202 ! Sequence record full format +! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number + +[Term] +id: EDAM:0001948 +name: nbrf sequence format +namespace: format +def: "NBRF/PIR entry sequence format." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002202 ! Sequence record full format + +[Term] +id: EDAM:0002187 +name: uniprotkb-like sequence format +namespace: format +def: "A sequence format resembling uniprotkb entry format." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002202 ! Sequence record full format + ! -! Data syntax<-Sequence format<-embl-like sequence format +! Data format<-Sequence record format<-Sequence record full format<-embl-like sequence format ! [Term] id: EDAM:0001927 name: embl sequence format -namespace: syntax +namespace: format def: "EMBL entry format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002181 ! embl-like sequence format ! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number @@ -26367,51 +26536,194 @@ is_a: EDAM:0002181 ! embl-like sequence format [Term] id: EDAM:0002186 name: geneseq sequence format -namespace: syntax +namespace: format def: "Geneseq sequence format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002181 ! embl-like sequence format ! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number + + ! -! Data syntax<-Sequence format<-fastq-like sequence format +! Data format<-Sequence record format<-Sequence record full format<-embl xml sequence format +! +[Term] +id: EDAM:0002183 +name: emblxml sequence format +namespace: format +def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002204 ! embl xml sequence format +! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number + + +[Term] +id: EDAM:0002184 +name: cdsxml sequence format +namespace: format +def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002204 ! embl xml sequence format +! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number + +[Term] +id: EDAM:0002185 +name: insdxml sequence format +namespace: format +def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002204 ! embl xml sequence format +! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number + + + +! +! Data format<-Sequence record format<-Sequence record full format<-genbank-like sequence format +! +[Term] +id: EDAM:0001936 +name: genbank sequence format +namespace: format +def: "Genbank entry format." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002205 ! genbank-like sequence format +! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number + +[Term] +id: EDAM:0001937 +name: genpept sequence format +namespace: format +def: "Genpept protein entry format." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002205 ! genbank-like sequence format + + + +! +! Data format<-Sequence record format<-Sequence record full format<-uniprotkb-like sequence format +! + + + +! +! Data format<-Sequence record format<-Sequence trace format +! +[Term] +id: EDAM:0001628 +name: ABI sequence trace format +namespace: format +def: "Format of raw sequence data from an ABI sequencing machine." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002057 ! Sequence trace format + + +[Term] +id: EDAM:0001629 +name: MIRA sequence trace format +namespace: format +def: "Format of MIRA sequence trace information file." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002057 ! Sequence trace format + + +[Term] +id: EDAM:0002182 +name: fastq-like sequence format +namespace: format +def: "A format resembling FASTQ short read format." [EDAM:EBI "EMBRACE definition"] +comment: This term may be used for non-standard FASTQ short read-like formats. +is_a: EDAM:0001919 ! Sequence record format + + + + + +! +! Data format<-Sequence record format<-Sequence trace format<-fastq-like sequence format ! [Term] id: EDAM:0001930 name: fastq sequence format -namespace: syntax +namespace: format def: "FASTQ short read format ignoring quality scores." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002182 ! fastq-like sequence format [Term] id: EDAM:0001931 name: fastq-illumina sequence format -namespace: syntax +namespace: format def: "FASTQ Illumina 1.3 short read format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002182 ! fastq-like sequence format [Term] id: EDAM:0001932 name: fastq-sanger sequence format -namespace: syntax +namespace: format def: "FASTQ short read format with phred quality." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002182 ! fastq-like sequence format [Term] id: EDAM:0001933 name: fastq-solexa sequence format -namespace: syntax +namespace: format def: "FASTQ Solexa/Illumina 1.0 short read format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002182 ! fastq-like sequence format + + + + + + + + + + + +! +! Data format<-Sequence record format<-fasta-like sequence format +! +[Term] +id: EDAM:0001929 +name: fasta sequence format +namespace: format +def: "FASTA format including NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002200 ! fasta-like sequence format + +[Term] +id: EDAM:0001926 +name: dbid sequence format +namespace: format +def: "Fasta format variant with database name before ID." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002200 ! fasta-like sequence format + +[Term] +id: EDAM:0001940 +name: gifasta sequence format +namespace: format +def: "FASTA sequence format including NCBI-style GIs." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002200 ! fasta-like sequence format + +[Term] +id: EDAM:0001954 +name: pearson sequence format +namespace: format +def: "Plain old fasta sequence format (unspecified format for IDs)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002200 ! fasta-like sequence format + +[Term] +id: EDAM:0001972 +name: ncbi sequence format +namespace: format +def: "NCBI fasta sequence format with NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] +comment: There are several variants of this. +is_a: EDAM:0002200 ! fasta-like sequence format + + + + + ! -! Data syntax<-Sequence format<-uniprotkb-like sequence format +! Data format<-Sequence record format<-uniprotkb-like sequence format ! [Term] id: EDAM:0001963 name: swiss sequence format -namespace: syntax +namespace: format def: "Swissprot entry sequence format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002187 ! uniprotkb-like sequence format ! relationship: has_source EDAM:0000651 ! UniProt database @@ -26422,246 +26734,262 @@ is_a: EDAM:0002187 ! uniprotkb-like sequence format [Term] id: EDAM:0002188 name: uniprot sequence format -namespace: syntax +namespace: format def: "Uniprot entry sequence format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002187 ! uniprotkb-like sequence format [Term] id: EDAM:0002189 name: ipi sequence format -namespace: syntax +namespace: format def: "ipi sequence format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002187 ! uniprotkb-like sequence format ! -! Data syntax<-Feature format +! Data format<-Sequence feature annotation format +! + + +[Term] +id: EDAM:0002206 +name: Sequence feature table format +namespace: format +def: "GFF version 1 or 2 feature format." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001920 ! Sequence feature annotation format + + +[Term] +id: EDAM:0001978 +name: dasgff feature format +namespace: format +def: "DAS GFF feature format." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001920 ! Sequence feature annotation format + +[Term] +id: EDAM:0001979 +name: debug feature format +namespace: format +def: "EMBOSS debugging trace feature format of full internal data content." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001920 ! Sequence feature annotation format + + + + +! +! Data format<-Sequence feature annotation format<-Sequence feature table format ! [Term] id: EDAM:0001974 name: gff2 feature format -namespace: syntax +namespace: format def: "GFF version 1 or 2 feature format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001920 ! Feature format +is_a: EDAM:0001920 ! Sequence feature annotation format [Term] id: EDAM:0001975 name: gff3 feature format -namespace: syntax +namespace: format def: "GFF version 3 feature format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001920 ! Feature format +is_a: EDAM:0001920 ! Sequence feature annotation format [Term] id: EDAM:0001976 name: pir feature format -namespace: syntax +namespace: format def: "PIR feature format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001920 ! Feature format +is_a: EDAM:0001920 ! Sequence feature annotation format [Term] id: EDAM:0001977 name: swiss feature format -namespace: syntax +namespace: format def: "SwissProt feature format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001920 ! Feature format - -[Term] -id: EDAM:0001978 -name: dasgff feature format -namespace: syntax -def: "DAS GFF feature format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001920 ! Feature format - -[Term] -id: EDAM:0001979 -name: debug feature format -namespace: syntax -def: "EMBOSS debugging trace feature format of full internal data content." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001920 ! Feature format +is_a: EDAM:0001920 ! Sequence feature annotation format [Term] id: EDAM:0001980 name: embl feature format -namespace: syntax +namespace: format def: "EMBL feature format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001920 ! Feature format +is_a: EDAM:0001920 ! Sequence feature annotation format [Term] id: EDAM:0001981 name: genbank feature format -namespace: syntax +namespace: format def: "Genbank feature format." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001920 ! Feature format +is_a: EDAM:0001920 ! Sequence feature annotation format ! -! Data syntax<-Alignment format +! Data format<-Alignment format ! [Term] id: EDAM:0001982 name: clustal alignment format -namespace: syntax +namespace: format def: "Clustalw format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001983 name: Debug alignment format -namespace: syntax +namespace: format def: "EMBOSS alignment format for debugging trace of full internal data content." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001984 name: fasta alignment format -namespace: syntax +namespace: format def: "Fasta format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001985 name: markx0 alignment format -namespace: syntax +namespace: format def: "Pearson MARKX0 alignment format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001986 name: markx1 alignment format -namespace: syntax +namespace: format def: "Pearson MARKX1 alignment format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001987 name: markx10 alignment format -namespace: syntax +namespace: format def: "Pearson MARKX10 alignment format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001988 name: markx2 alignment format -namespace: syntax +namespace: format def: "Pearson MARKX2 alignment format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001989 name: markx3 alignment format -namespace: syntax +namespace: format def: "Pearson MARKX3 alignment format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001990 name: match alignment format -namespace: syntax +namespace: format def: "Alignment format for start and end of matches between sequence pairs." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001991 name: mega alignment format -namespace: syntax +namespace: format def: "Mega format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001992 name: meganon alignment format -namespace: syntax +namespace: format def: "Mega non-interleaved format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001993 name: msf alignment format -namespace: syntax +namespace: format def: "MSF format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001994 name: nexus alignment format -namespace: syntax +namespace: format def: "Nexus/paup format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001995 name: nexusnon alignment format -namespace: syntax +namespace: format def: "Nexus/paup non-interleaved format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001996 name: pair alignment format -namespace: syntax +namespace: format def: "Simple pairwise alignment format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001997 name: phylip alignment format -namespace: syntax +namespace: format def: "Phylip format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001998 name: phylipnon alignment format -namespace: syntax +namespace: format def: "Phylip non-interleaved format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001999 name: score alignment format -namespace: syntax +namespace: format def: "Alignment format for score values for pairs of sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0002000 name: selex alignment format -namespace: syntax +namespace: format def: "SELEX format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0002001 name: simple alignment format -namespace: syntax +namespace: format def: "Simple multiple alignment format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0002002 name: srs alignment format -namespace: syntax +namespace: format def: "Simple multiple sequence (alignment) format for SRS." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0002003 name: srspair alignment format -namespace: syntax +namespace: format def: "Simple pairwise sequence (alignment) format for SRS." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0002004 name: tcoffee alignment format -namespace: syntax +namespace: format def: "TCOFFEE program alignment format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0002005 name: treecon alignment format -namespace: syntax +namespace: format def: "Treecon format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format @@ -26669,7 +26997,7 @@ is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001391 name: HMMER sequence alignment format -namespace: syntax +namespace: format def: "Multiple sequences aligned by HMMER package to an HMM, in FASTA-style format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format @@ -26677,7 +27005,7 @@ is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001392 name: DIALIGN sequence alignment format -namespace: syntax +namespace: format def: "Multiple sequences aligned by DIALIGN package." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001921 ! Alignment format @@ -26685,7 +27013,7 @@ is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001393 name: EMBASSY domain alignment file format -namespace: syntax +namespace: format def: "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family." [EDAM:EBI "EMBRACE definition"] comment: The format is clustal-like and includes annotation of domain family classification information. is_a: EDAM:0001921 ! Alignment format @@ -26693,26 +27021,26 @@ is_a: EDAM:0001921 ! Alignment format ! -! Data syntax<-Phylogenetic tree format +! Data format<-Phylogenetic tree format ! [Term] id: EDAM:0001435 name: PHYLIP phylogenetic tree format -namespace: syntax +namespace: format def: "Phylogenetic tree data format used by the PHYLIP program." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002006 ! Phylogenetic tree format [Term] id: EDAM:0001425 name: Phylip phylogenetic tree raw data format -namespace: syntax +namespace: format def: "Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002006 ! Phylogenetic tree format [Term] id: EDAM:0001424 name: Clustalw phylogenetic tree raw data format -namespace: syntax +namespace: format def: "Dendrogram (tree file) format generated by Clustalw." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002006 ! Phylogenetic tree format @@ -26720,7 +27048,7 @@ is_a: EDAM:0002006 ! Phylogenetic tree format [Term] id: EDAM:0001436 name: TreeBASE tree format -namespace: syntax +namespace: format def: "The format of an entry from the TreeBASE database of phylogenetic data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002006 ! Phylogenetic tree format ! relationship: has_source EDAM:0000827 ! TreeBASE database @@ -26729,7 +27057,7 @@ is_a: EDAM:0002006 ! Phylogenetic tree format [Term] id: EDAM:0001437 name: TreeFam tree format -namespace: syntax +namespace: format def: "The format of an entry from the TreeFam database of phylogenetic data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002006 ! Phylogenetic tree format ! relationship: has_source EDAM:0000828 ! TreeFam database @@ -26738,7 +27066,7 @@ is_a: EDAM:0002006 ! Phylogenetic tree format [Term] id: EDAM:0001910 name: Newick tree format -namespace: syntax +namespace: format def: "Phylogenetic tree Newick (text) format." [EDAM:EBI "EMBRACE definition"] xref: Moby:Newick_Text is_a: EDAM:0002006 ! Phylogenetic tree format @@ -26746,7 +27074,7 @@ is_a: EDAM:0002006 ! Phylogenetic tree format [Term] id: EDAM:0001911 name: TreeCon tree format -namespace: syntax +namespace: format def: "Phylogenetic tree TreeCon (text) format." [EDAM:EBI "EMBRACE definition"] xref: Moby:TreeCon is_a: EDAM:0002006 ! Phylogenetic tree format @@ -26754,19 +27082,19 @@ is_a: EDAM:0002006 ! Phylogenetic tree format [Term] id: EDAM:0001912 name: Nexus tree format -namespace: syntax +namespace: format def: "Phylogenetic tree Nexus (text) format." [EDAM:EBI "EMBRACE definition"] xref: Moby:Nexus_Text is_a: EDAM:0002006 ! Phylogenetic tree format ! -! Data syntax<-Tertiary structure format +! Data format<-Tertiary structure format ! [Term] id: EDAM:0001475 name: PDB database entry format -namespace: syntax +namespace: format def: "Format of an entry from the PDB database." [EDAM:EBI "EMBRACE definition"] synonym: "PDB entry" EXACT [] is_a: EDAM:0002033 ! Tertiary structure format @@ -26774,12 +27102,12 @@ is_a: EDAM:0002033 ! Tertiary structure format ! relationship: has_identifier EDAM:0001127 ! PDB identifier ! -! Data syntax<-Tertiary structure format<-PDB database entry format +! Data format<-Tertiary structure format<-PDB database entry format ! [Term] id: EDAM:0001476 name: PDB file format -namespace: syntax +namespace: format def: "An entry from the PDB database in PDB format, or any report in the same format." [EDAM:EBI "EMBRACE definition"] xref: Moby:PDB-formatted-text xref: Moby:PDB-Text @@ -26790,7 +27118,7 @@ is_a: EDAM:0001475 ! PDB database entry format [Term] id: EDAM:0001477 name: mmCIF file format -namespace: syntax +namespace: format def: "An entry from the PDB database in mmCIF format, or any report in the same format." [EDAM:EBI "EMBRACE definition"] xref: Moby:mmCIF-Text xref: Moby:mmCIF_Text @@ -26801,7 +27129,7 @@ is_a: EDAM:0001475 ! PDB database entry format [Term] id: EDAM:0001478 name: PDBML file format -namespace: syntax +namespace: format def: "An entry from the PDB database in PDBML (XML) format, or any report in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001475 ! PDB database entry format ! relationship: has_source EDAM:0000701 ! PDB database @@ -26810,12 +27138,12 @@ is_a: EDAM:0001475 ! PDB database entry format ! -! Data syntax<-Biological model format +! Data format<-Biological model format ! [Term] id: EDAM:0002013 name: Biological pathway format -namespace: syntax +namespace: format def: "Data format for a biological pathway." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002034 ! Biological model format @@ -26823,7 +27151,7 @@ is_a: EDAM:0002034 ! Biological model format [Term] id: EDAM:0001666 name: BioModel mathematical model format -namespace: syntax +namespace: format def: "Format of mathematical models from the BioModel database." [EDAM:EBI "EMBRACE definition"] comment: Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. is_a: EDAM:0002034 ! Biological model format @@ -26833,12 +27161,12 @@ is_a: EDAM:0002034 ! Biological model format ! -! Data syntax<-Biological model format<-Biological pathway format +! Data format<-Biological model format<-Biological pathway format ! [Term] id: EDAM:0001647 name: KEGG PATHWAY entry format -namespace: syntax +namespace: format def: "The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002013 ! Biological pathway format ! relationship: has_source EDAM:0000755 ! KEGG PATHWAY database @@ -26848,7 +27176,7 @@ is_a: EDAM:0002013 ! Biological pathway format [Term] id: EDAM:0001648 name: MetaCyc entry format -namespace: syntax +namespace: format def: "The format of an entry from the MetaCyc metabolic pathways database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002013 ! Biological pathway format ! relationship: has_source EDAM:0000761 ! MetaCyc database @@ -26858,7 +27186,7 @@ is_a: EDAM:0002013 ! Biological pathway format [Term] id: EDAM:0001649 name: HumanCyc entry format -namespace: syntax +namespace: format def: "The format of a report from the HumanCyc metabolic pathways database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002013 ! Biological pathway format ! relationship: has_source EDAM:0000762 ! HumanCyc database @@ -26868,7 +27196,7 @@ is_a: EDAM:0002013 ! Biological pathway format [Term] id: EDAM:0001650 name: INOH entry format -namespace: syntax +namespace: format def: "The format of an entry from the INOH signal transduction pathways database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002013 ! Biological pathway format ! relationship: has_source EDAM:0000763 ! INOH database @@ -26878,7 +27206,7 @@ is_a: EDAM:0002013 ! Biological pathway format [Term] id: EDAM:0001651 name: PATIKA entry format -namespace: syntax +namespace: format def: "The format of an entry from the PATIKA biological pathways database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002013 ! Biological pathway format ! relationship: has_source EDAM:0000756 ! PATIKA database @@ -26888,7 +27216,7 @@ is_a: EDAM:0002013 ! Biological pathway format [Term] id: EDAM:0001652 name: Reactome entry format -namespace: syntax +namespace: format def: "The format of an entry from the reactome biological pathways database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002013 ! Biological pathway format ! relationship: has_source EDAM:0000757 ! Reactome database @@ -26898,7 +27226,7 @@ is_a: EDAM:0002013 ! Biological pathway format [Term] id: EDAM:0001653 name: aMAZE entry format -namespace: syntax +namespace: format def: "The format of an entry from the aMAZE biological pathways and molecular interactions database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002013 ! Biological pathway format ! relationship: has_source EDAM:0000758 ! aMAZE database @@ -26908,7 +27236,7 @@ is_a: EDAM:0002013 ! Biological pathway format [Term] id: EDAM:0001654 name: CPDB entry format -namespace: syntax +namespace: format def: "The format of an entry from the CPDB database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002013 ! Biological pathway format ! relationship: has_source EDAM:0000759 ! CPDB database @@ -26918,7 +27246,7 @@ is_a: EDAM:0002013 ! Biological pathway format [Term] id: EDAM:0001655 name: Panther Pathways entry format -namespace: syntax +namespace: format def: "The format of an entry from the Panther Pathways database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002013 ! Biological pathway format ! relationship: has_source EDAM:0000760 ! Panther Pathways database @@ -26929,12 +27257,12 @@ is_a: EDAM:0002013 ! Biological pathway format ! -! Data syntax<-Sequence-profile alignment format +! Data format<-Sequence-profile alignment format ! [Term] id: EDAM:0002015 name: Sequence-hidden Markov model alignment format -namespace: syntax +namespace: format def: "Data format for a sequence-HMM profile alignment." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002014 ! Sequence-profile alignment format @@ -26942,19 +27270,19 @@ is_a: EDAM:0002014 ! Sequence-profile alignment format [Term] id: EDAM:0001419 name: Sequence-MEME profile alignment format -namespace: syntax +namespace: format def: "Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002014 ! Sequence-profile alignment format ! -! Data syntax<-Sequence-profile alignment format<-Sequence-hidden Markov model alignment format +! Data format<-Sequence-profile alignment format<-Sequence-hidden Markov model alignment format ! [Term] id: EDAM:0001421 name: HMMER alignment report format (sequences versus HMMs) -namespace: syntax +namespace: format def: "Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002015 ! Sequence-hidden Markov model alignment format @@ -26962,18 +27290,18 @@ is_a: EDAM:0002015 ! Sequence-hidden Markov model alignment format [Term] id: EDAM:0001422 name: HMMER alignment report format (HMM versus sequences) -namespace: syntax +namespace: format def: "Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002015 ! Sequence-hidden Markov model alignment format ! -! Data syntax<-Amino acid index format +! Data format<-Amino acid index format ! [Term] id: EDAM:0001504 name: AAindex entry format -namespace: syntax +namespace: format def: "Amino acid index format used by the AAindex database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002017 ! Amino acid index format ! relationship: has_source EDAM:0000778 ! AAindex database @@ -26981,12 +27309,12 @@ is_a: EDAM:0002017 ! Amino acid index format ! -! Data syntax<-Article format +! Data format<-Article format ! [Term] id: EDAM:0001739 name: PubMed Central article format -namespace: syntax +namespace: format def: "An article from the PubMed Central database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002020 ! Article format ! relationship: has_source EDAM:0000776 ! PubMed Central database @@ -26995,19 +27323,19 @@ is_a: EDAM:0002020 ! Article format [Term] id: EDAM:0002194 name: MedLine format -namespace: syntax +namespace: format def: "Abstract format used by MedLine database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002020 ! Article format ! relationship: has_source EDAM:0000776 ! PubMed Central database ! relationship: has_identifier EDAM:0001187 ! PubMed unique identifier ! -! Data syntax<-Text mining report format +! Data format<-Text mining report format ! [Term] id: EDAM:0001740 name: iHOP text mining abstract format -namespace: syntax +namespace: format def: "An iHOP abstract." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002021 ! Text mining report format @@ -27015,7 +27343,7 @@ is_a: EDAM:0002021 ! Text mining report format [Term] id: EDAM:0001741 name: Oscar3 text mining abstract format -namespace: syntax +namespace: format def: "Text mining abstract from the Oscar 3 application." [EDAM:EBI "EMBRACE definition"] comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology terms and chemical data from a document. is_a: EDAM:0002021 ! Text mining report format @@ -27023,12 +27351,12 @@ is_a: EDAM:0002021 ! Text mining report format ! -! Data syntax<-Enzyme kinetics report format +! Data format<-Enzyme kinetics report format ! [Term] id: EDAM:0001582 name: EMBOSS findkm enzyme kinetics report format -namespace: syntax +namespace: format def: "A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002027 ! Enzyme kinetics report format @@ -27036,12 +27364,12 @@ is_a: EDAM:0002027 ! Enzyme kinetics report format ! -! Data syntax<-Chemical compound report format +! Data format<-Chemical compound report format ! [Term] id: EDAM:0001697 name: KEGG LIGAND entry format -namespace: syntax +namespace: format def: "The format of an entry from the KEGG LIGAND chemical database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002030 ! Chemical compound report format ! relationship: has_source EDAM:0000706 ! KEGG LIGAND database @@ -27051,7 +27379,7 @@ is_a: EDAM:0002030 ! Chemical compound report format [Term] id: EDAM:0001698 name: KEGG COMPOUND entry format -namespace: syntax +namespace: format def: "The format of an entry from the KEGG COMPOUND database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002030 ! Chemical compound report format ! relationship: has_source EDAM:0000707 ! KEGG COMPOUND database @@ -27061,7 +27389,7 @@ is_a: EDAM:0002030 ! Chemical compound report format [Term] id: EDAM:0001699 name: KEGG PLANT entry format -namespace: syntax +namespace: format def: "The format of an entry from the KEGG PLANT database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002030 ! Chemical compound report format ! relationship: has_source EDAM:0000708 ! KEGG PLANT database @@ -27071,7 +27399,7 @@ is_a: EDAM:0002030 ! Chemical compound report format [Term] id: EDAM:0001700 name: KEGG GLYCAN entry format -namespace: syntax +namespace: format def: "The format of an entry from the KEGG GLYCAN database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002030 ! Chemical compound report format ! relationship: has_source EDAM:0000710 ! KEGG GLYCAN database @@ -27080,7 +27408,7 @@ is_a: EDAM:0002030 ! Chemical compound report format [Term] id: EDAM:0001706 name: KEGG DRUG entry format -namespace: syntax +namespace: format def: "The format of an entry from the KEGG DRUG database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002030 ! Chemical compound report format ! relationship: has_source EDAM:0000709 ! KEGG DRUG database @@ -27089,7 +27417,7 @@ is_a: EDAM:0002030 ! Chemical compound report format [Term] id: EDAM:0001701 name: PubChem entry format -namespace: syntax +namespace: format def: "The format of an entry from PubChem." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002030 ! Chemical compound report format ! relationship: has_source EDAM:0000712 ! PubChem database @@ -27099,7 +27427,7 @@ is_a: EDAM:0002030 ! Chemical compound report format [Term] id: EDAM:0001702 name: ChemSpider entry format -namespace: syntax +namespace: format def: "The format of an entry from a database of chemical structures and property predictions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002030 ! Chemical compound report format ! relationship: has_source EDAM:0000713 ! ChemSpider database @@ -27109,7 +27437,7 @@ is_a: EDAM:0002030 ! Chemical compound report format [Term] id: EDAM:0001703 name: ChEBI entry format -namespace: syntax +namespace: format def: "The format of an entry from Chemical Entities of Biological Interest (ChEBI)." [EDAM:EBI "EMBRACE definition"] comment: ChEBI includes an ontological classification defining relations between entities or classes of entities. is_a: EDAM:0002030 ! Chemical compound report format @@ -27120,7 +27448,7 @@ is_a: EDAM:0002030 ! Chemical compound report format [Term] id: EDAM:0001704 name: MSDchem ligand dictionary entry format -namespace: syntax +namespace: format def: "The format of an entry from the MSDchem ligand dictionary." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002030 ! Chemical compound report format ! relationship: has_source EDAM:0000715 ! MSDchem ligand dictionary database @@ -27130,7 +27458,7 @@ is_a: EDAM:0002030 ! Chemical compound report format [Term] id: EDAM:0001705 name: HET group dictionary entry format -namespace: syntax +namespace: format def: "The format of an entry from the HET group dictionary (HET groups from PDB files)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002030 ! Chemical compound report format ! relationship: has_source EDAM:0000716 ! HET group dictionary @@ -27138,12 +27466,12 @@ is_a: EDAM:0002030 ! Chemical compound report format ! -! Data syntax<-Gene annotation format +! Data format<-Gene annotation format ! [Term] id: EDAM:0001808 name: GeneIlluminator gene report format -namespace: syntax +namespace: format def: "A report on biological functions associated with a gene symbol and its alternative names (synomyms, homonyms), as generated by the GeneIlluminater service, or any file in the same format." [EDAM:EBI "EMBRACE definition"] comment: This includes a gene name and gene symbol (abbreviation of the name) which may be in a namespace indicating the gene status and relevant organisation. xref: Moby:GI_Gene @@ -27153,7 +27481,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001809 name: BacMap gene card format -namespace: syntax +namespace: format def: "An informative report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database." [EDAM:EBI "EMBRACE definition"] xref: Moby:BacMapGeneCard is_a: EDAM:0002031 ! Gene annotation format @@ -27162,7 +27490,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001810 name: ColiCard report format -namespace: syntax +namespace: format def: "A detailed report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [EDAM:EBI "EMBRACE definition"] xref: Moby:ColiCard is_a: EDAM:0002031 ! Gene annotation format @@ -27173,7 +27501,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001603 name: Ensembl gene report format -namespace: syntax +namespace: format def: "An entry from the Ensembl genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000680 ! Ensembl database @@ -27182,7 +27510,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001604 name: DictyBase gene report format -namespace: syntax +namespace: format def: "An entry from the DictyBase genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000681 ! DictyBase database @@ -27191,7 +27519,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001605 name: CGD gene report format -namespace: syntax +namespace: format def: "An entry from the Candida Genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000683 ! CGD database @@ -27201,7 +27529,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001606 name: DragonDB gene report format -namespace: syntax +namespace: format def: "An entry from the DragonDB genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000672 ! DragonDB database @@ -27209,7 +27537,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001607 name: EcoCyc gene report format -namespace: syntax +namespace: format def: "An entry from the EcoCyc genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000673 ! EcoCyc database @@ -27219,7 +27547,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001608 name: FlyBase gene report format -namespace: syntax +namespace: format def: "An entry from the FlyBase genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000685 ! FlyBase database @@ -27229,7 +27557,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001609 name: Gramene gene report format -namespace: syntax +namespace: format def: "An entry from the Gramene genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000808 ! Gramene database @@ -27239,7 +27567,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001610 name: KEGG GENES gene report format -namespace: syntax +namespace: format def: "An entry from the KEGG GENES genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000802 ! KEGG GENES database @@ -27248,7 +27576,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001611 name: MaizeGDB gene report format -namespace: syntax +namespace: format def: "An entry from the Maize genetics and genomics database (MaizeGDB) or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000788 ! MaizeGDB database @@ -27257,7 +27585,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001612 name: MGD gene report format -namespace: syntax +namespace: format def: "An entry from the Mouse Genome Database (MGD) or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000688 ! MGD database @@ -27267,7 +27595,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001613 name: RGD gene report format -namespace: syntax +namespace: format def: "An entry from the Rat Genome Database (RGD) or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000689 ! RGD database @@ -27277,7 +27605,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001614 name: SGD gene report format -namespace: syntax +namespace: format def: "An entry from the Saccharomyces Genome Database (SGD) or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000684 ! SGD database @@ -27287,7 +27615,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001615 name: GeneDB gene report format -namespace: syntax +namespace: format def: "An entry from the Sanger GeneDB genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000674 ! GeneDB database @@ -27299,7 +27627,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001616 name: TAIR gene report format -namespace: syntax +namespace: format def: "An entry from The Arabidopsis Information Resource (TAIR) genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000789 ! TAIR database @@ -27309,7 +27637,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001617 name: WormBase gene report format -namespace: syntax +namespace: format def: "An entry from the WormBase genomes database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000686 ! WormBase database @@ -27321,7 +27649,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001618 name: ZFIN gene report format -namespace: syntax +namespace: format def: "An entry from the Zebrafish Information Network (ZFIN) genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000690 ! ZFIN database @@ -27330,7 +27658,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001619 name: TIGR gene report format -namespace: syntax +namespace: format def: "An entry from the TIGR genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000799 ! TIGR database @@ -27339,7 +27667,7 @@ is_a: EDAM:0002031 ! Gene annotation format [Term] id: EDAM:0001782 name: NCBI gene report format -namespace: syntax +namespace: format def: "An entry (gene) from the NCBI database, or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002031 ! Gene annotation format ! relationship: has_source EDAM:0000799 ! RefSeq database @@ -27347,28 +27675,28 @@ is_a: EDAM:0002031 ! Gene annotation format ! -! Data syntax<-Workflow format +! Data format<-Workflow format ! [Term] id: EDAM:0001665 name: Taverna workflow format -namespace: syntax +namespace: format def: "Format of Taverna workflows." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002032 ! Workflow format -! relationship: has_source EDAM:0000769 ! Workflow database +! relationship: has_source EDAM:0000769 ! Workflow data resource ! relationship: has_identifier EDAM:0001167 ! Taverna workflow identifier ! -! Data syntax<-Chemical formula format +! Data format<-Chemical formula format ! [Term] id: EDAM:0001196 name: Chemical formula (SMILES) format -namespace: syntax +namespace: format def: "Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002035 ! Chemical formula format -! relationship: has_source EDAM:0000696 ! Chemical and small molecule database +! relationship: has_source EDAM:0000696 ! Chemical and small molecule data resource ! relationship: has_identifier EDAM:0000990 ! Chemical name ! relationship: has_identifier EDAM:0000991 ! Chemical registry number @@ -27376,10 +27704,10 @@ is_a: EDAM:0002035 ! Chemical formula format [Term] id: EDAM:0001197 name: Chemical formula (InChI) format -namespace: syntax +namespace: format def: "Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002035 ! Chemical formula format -! relationship: has_source EDAM:0000696 ! Chemical and small molecule database +! relationship: has_source EDAM:0000696 ! Chemical and small molecule data resource ! relationship: has_identifier EDAM:0000990 ! Chemical name ! relationship: has_identifier EDAM:0000991 ! Chemical registry number @@ -27387,22 +27715,22 @@ is_a: EDAM:0002035 ! Chemical formula format [Term] id: EDAM:0001198 name: Chemical formula (MF) format -namespace: syntax +namespace: format def: "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound." [EDAM:EBI "EMBRACE definition"] -comment: The general MF query syntax consists of a series of valid atomic symbols, with an optional number or range. +comment: The general MF query format consists of a series of valid atomic symbols, with an optional number or range. is_a: EDAM:0002035 ! Chemical formula format -! relationship: has_source EDAM:0000696 ! Chemical and small molecule database +! relationship: has_source EDAM:0000696 ! Chemical and small molecule data resource ! relationship: has_identifier EDAM:0000990 ! Chemical name ! relationship: has_identifier EDAM:0000991 ! Chemical registry number [Term] id: EDAM:0001199 name: Chemical InChIKey format -namespace: syntax +namespace: format def: "The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound." [EDAM:EBI "EMBRACE definition"] comment: An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. is_a: EDAM:0002035 ! Chemical formula format -! relationship: has_source EDAM:0000696 ! Chemical and small molecule database +! relationship: has_source EDAM:0000696 ! Chemical and small molecule data resource ! relationship: has_identifier EDAM:0000990 ! Chemical name ! relationship: has_identifier EDAM:0000991 ! Chemical registry number @@ -27414,10 +27742,10 @@ is_a: EDAM:0002035 ! Chemical formula format [Term] id: EDAM:0001200 name: Chemical formula (SMARTS) -namespace: syntax +namespace: format def: "Chemical structure specified in SMILES ARbitrary Target Specification (SMARTS), which is a subset of the SMILES line notation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001196 ! Chemical formula (SMILES) format -! relationship: has_source EDAM:0000696 ! Chemical and small molecule database +! relationship: has_source EDAM:0000696 ! Chemical and small molecule data resource ! relationship: has_identifier EDAM:0000990 ! Chemical name ! relationship: has_identifier EDAM:0000991 ! Chemical registry number @@ -27425,45 +27753,45 @@ is_a: EDAM:0001196 ! Chemical formula (SMILES) format ! -! Data syntax<-Phylogenetic raw data format +! Data format<-Phylogenetic raw data format ! [Term] id: EDAM:0002037 name: Phylogenetic continuous quantitative character format -namespace: syntax +namespace: format def: "Format of phylogenetic continuous quantitative character data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002036 ! Phylogenetic raw data format [Term] id: EDAM:0002038 name: Phylogenetic discrete states format -namespace: syntax +namespace: format def: "Format of phylogenetic discrete states data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002036 ! Phylogenetic raw data format [Term] id: EDAM:0002039 name: Phylogenetic cliques format -namespace: syntax +namespace: format def: "Format of phylogenetic cliques data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002036 ! Phylogenetic raw data format [Term] id: EDAM:0002040 name: Phylogenetic invariants format -namespace: syntax +namespace: format def: "Format of phylogenetic invariants data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002036 ! Phylogenetic raw data format ! -! Data syntax<-Phylogenetic raw data format<-Phylogenetic continuous quantitative character format +! Data format<-Phylogenetic raw data format<-Phylogenetic continuous quantitative character format ! [Term] id: EDAM:0001430 name: PHYLIP continuous quantitative characters format -namespace: syntax +namespace: format def: "A file containing continuous quantitative character data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format @@ -27471,7 +27799,7 @@ is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format [Term] id: EDAM:0001431 name: PHYLIP phylogenetic property values -namespace: syntax +namespace: format def: "A file of PHYLIP phylogenetic property data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format @@ -27480,48 +27808,48 @@ is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format [Term] id: EDAM:0001432 name: PHYLIP phylogenetic character frequencies -namespace: syntax +namespace: format def: "A file of PHYLIP phylogenetics character frequency data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format ! -! Data syntax<-Phylogenetic raw data format<-Phylogenetic discrete states format +! Data format<-Phylogenetic raw data format<-Phylogenetic discrete states format ! [Term] id: EDAM:0001433 name: PHYLIP discrete states format -namespace: syntax +namespace: format def: "A file of PHYLIP discrete states data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002038 ! Phylogenetic discrete states format ! -! Data syntax<-Phylogenetic raw data format<-Phylogenetic cliques format +! Data format<-Phylogenetic raw data format<-Phylogenetic cliques format ! [Term] id: EDAM:0001434 name: PHYLIP cliques file format -namespace: syntax +namespace: format def: "A file of PHYLIP cliques data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002039 ! Phylogenetic cliques format ! -! Data syntax<-Phylogenetic raw data format<-Phylogenetic invariants format +! Data format<-Phylogenetic raw data format<-Phylogenetic invariants format ! ! -! Data syntax<-Electron microscopy model annotation format +! Data format<-Electron microscopy model annotation format ! [Term] id: EDAM:0001645 name: EMDB entry format -namespace: syntax +namespace: format def: "Format of an entry from the Electron Microscopy DataBase (EMDB)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002045 ! Electron microscopy model annotation format ! relationship: has_source EDAM:0000777 ! The Electron Microscopy DataBase @@ -27529,23 +27857,23 @@ is_a: EDAM:0002045 ! Electron microscopy model annotation format ! -! Data syntax<-Phylogenetic tree distance data format +! Data format<-Phylogenetic tree distance data format ! [Term] id: EDAM:0001445 name: Phylip phylogenetic tree distance data format -namespace: syntax +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"] is_a: EDAM:0002049 ! Phylogenetic tree distance data format ! -! Data syntax<-Polymorphism report format +! Data format<-Polymorphism report format ! [Term] id: EDAM:0001620 name: dbSNP polymorphism report format -namespace: syntax +namespace: format def: "A record from dbSNP or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002051 ! Polymorphism report format ! relationship: has_source EDAM:0000810 ! dbSNP database @@ -27553,12 +27881,12 @@ is_a: EDAM:0002051 ! Polymorphism report format ! -! Data syntax<-Protein family report format +! Data format<-Protein family report format ! [Term] id: EDAM:0001570 name: InterPro entry format -namespace: syntax +namespace: format def: "An entry from the InterPro database of protein signatures (sequence classifiers) and classified sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. is_a: EDAM:0002052 ! Protein family report format @@ -27572,7 +27900,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001571 name: InterPro entry abstract format -namespace: syntax +namespace: format def: "A textual abstract of signatures in an InterPro entry and its protein matches." [EDAM:EBI "EMBRACE definition"] comment: References are included and a functional inference is made where possible. is_a: EDAM:0002052 ! Protein family report format @@ -27585,7 +27913,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001572 name: Gene3D entry format -namespace: syntax +namespace: format def: "An entry from the Gene3D protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000728 ! Gene3D database @@ -27595,7 +27923,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001573 name: PIRSF entry format -namespace: syntax +namespace: format def: "An entry from the PIRSF protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000729 ! PIRSF database @@ -27606,7 +27934,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001574 name: PRINTS entry format -namespace: syntax +namespace: format def: "An entry from the PRINTS protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000730 ! PRINTS database @@ -27618,7 +27946,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001575 name: Panther Families and HMMs entry format -namespace: syntax +namespace: format def: "An entry from the Panther library of protein families and subfamilies and associated data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000731 ! Panther Families and HMMs database @@ -27629,7 +27957,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001576 name: Pfam entry format -namespace: syntax +namespace: format def: "An entry from the Pfam protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000732 ! Pfam database @@ -27639,7 +27967,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001577 name: SMART entry format -namespace: syntax +namespace: format def: "An entry from the SMART protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000733 ! SMART database @@ -27651,7 +27979,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001578 name: Superfamily entry format -namespace: syntax +namespace: format def: "An entry from the Superfamily protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000734 ! Superfamily Database @@ -27661,7 +27989,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001579 name: TIGRFam entry format -namespace: syntax +namespace: format def: "An entry from the TIGRFam protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000735 ! TIGRFam database @@ -27672,7 +28000,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001580 name: ProDom entry format -namespace: syntax +namespace: format def: "An entry from the ProDom protein domain classification database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000725 ! ProDom database @@ -27682,7 +28010,7 @@ is_a: EDAM:0002052 ! Protein family report format [Term] id: EDAM:0001581 name: FSSP entry format -namespace: syntax +namespace: format def: "An entry from the FSSP database or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002052 ! Protein family report format ! relationship: has_source EDAM:0000737 ! FSSP database @@ -27691,12 +28019,12 @@ is_a: EDAM:0002052 ! Protein family report format ! -! Data syntax<-Protein interaction format +! Data format<-Protein interaction format ! [Term] id: EDAM:0001568 name: BIND entry format -namespace: syntax +namespace: format def: "An entry from the BIND database of protein interaction or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002054 ! Protein interaction format ! relationship: has_source EDAM:0000720 ! BIND database @@ -27706,7 +28034,7 @@ is_a: EDAM:0002054 ! Protein interaction format [Term] id: EDAM:0001569 name: IntAct entry format -namespace: syntax +namespace: format def: "An entry from the IntAct database of protein interaction or any file in the same format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002054 ! Protein interaction format ! relationship: has_source EDAM:0000721 ! IntAct database @@ -27717,12 +28045,12 @@ is_a: EDAM:0002054 ! Protein interaction format ! -! Data syntax<-Sequence assembly format +! Data format<-Sequence assembly format ! [Term] id: EDAM:0001630 name: Common Assembly Format (CAF) assembly project file format -namespace: syntax +namespace: format def: "Sequence assembly project file in Common Assembly Format (CAF) format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002055 ! Sequence assembly format @@ -27730,7 +28058,7 @@ is_a: EDAM:0002055 ! Sequence assembly format [Term] id: EDAM:0001631 name: EXP assembly project file -namespace: syntax +namespace: format def: "Sequence assembly project file in EXP format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002055 ! Sequence assembly format @@ -27738,7 +28066,7 @@ is_a: EDAM:0002055 ! Sequence assembly format [Term] id: EDAM:0001632 name: SCF assembly project file -namespace: syntax +namespace: format def: "Sequence assembly project file in SCF format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002055 ! Sequence assembly format @@ -27746,7 +28074,7 @@ is_a: EDAM:0002055 ! Sequence assembly format [Term] id: EDAM:0001633 name: PHD assembly project file -namespace: syntax +namespace: format def: "Sequence assembly project file in PHD format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002055 ! Sequence assembly format @@ -27754,12 +28082,12 @@ is_a: EDAM:0002055 ! Sequence assembly format ! -! Data syntax<-Microarray experiment data format +! Data format<-Microarray experiment data format ! [Term] id: EDAM:0001640 name: ArrayExpress entry format -namespace: syntax +namespace: format def: "Entry format for the ArrayExpress microarrays database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002056 ! Microarray experiment data format ! relationship: has_source EDAM:0000814 ! ArrayExpress database @@ -27769,7 +28097,7 @@ is_a: EDAM:0002056 ! Microarray experiment data format [Term] id: EDAM:0001641 name: EXP file format -namespace: syntax +namespace: format def: "Affymetrix data file of information about experimental conditions and protocols." [EDAM:EBI "EMBRACE definition"] synonym: "Affymetrix experimental conditions data file format" EXACT [] is_a: EDAM:0002056 ! Microarray experiment data format @@ -27780,13 +28108,13 @@ is_a: EDAM:0002056 ! Microarray experiment data format ! -! Data syntax<-Gene expression report format +! Data format<-Gene expression report format ! [Term] id: EDAM:0001638 name: CEL file format -namespace: syntax +namespace: format def: "Format of Affymetrix data file of information about (raw) expression levels of the individual probes." [EDAM:EBI "EMBRACE definition"] synonym: "Affymetrix probe raw data format" EXACT [] is_a: EDAM:0002058 ! Gene expression report format @@ -27795,7 +28123,7 @@ is_a: EDAM:0002058 ! Gene expression report format [Term] id: EDAM:0001644 name: CHP file format -namespace: syntax +namespace: format def: "Format of Affymetrix data file of information about (normalised) expression levels of the individual probes." [EDAM:EBI "EMBRACE definition"] synonym: "Affymetrix probe normalised data format" EXACT [] is_a: EDAM:0002058 ! Gene expression report format @@ -27803,19 +28131,19 @@ is_a: EDAM:0002058 ! Gene expression report format [Term] id: EDAM:0001637 name: DAT file format -namespace: syntax +namespace: format def: "Format of Affymetrix data file of raw image data." [EDAM:EBI "EMBRACE definition"] synonym: "Affymetrix image data file format" EXACT [] is_a: EDAM:0002058 ! Gene expression report format ! -! Data syntax<-Genotype / phenotype report format +! Data format<-Genotype / phenotype report format ! [Term] id: EDAM:0001623 name: OMIM entry format -namespace: syntax +namespace: format def: "Format of an entry from the OMIM database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002059 ! Genotype / phenotype report format ! relationship: has_source EDAM:0000807 ! OMIM database @@ -27824,7 +28152,7 @@ is_a: EDAM:0002059 ! Genotype / phenotype report format [Term] id: EDAM:0001624 name: HGVbase entry format -namespace: syntax +namespace: format def: "Format of a record from the HGVbase database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002059 ! Genotype / phenotype report format ! relationship: has_source EDAM:0000806 ! HGVbase database @@ -27833,7 +28161,7 @@ is_a: EDAM:0002059 ! Genotype / phenotype report format [Term] id: EDAM:0001625 name: HIVDB entry format -namespace: syntax +namespace: format def: "Format of a record from the HIVDB database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002059 ! Genotype / phenotype report format ! relationship: has_source EDAM:0000809 ! HIVDB database @@ -27842,7 +28170,7 @@ is_a: EDAM:0002059 ! Genotype / phenotype report format [Term] id: EDAM:0001626 name: KEGG DISEASE entry format -namespace: syntax +namespace: format def: "Format of an entry from the KEGG DISEASE database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002059 ! Genotype / phenotype report format ! relationship: has_source EDAM:0000818 ! KEGG DISEASE database @@ -27851,12 +28179,12 @@ is_a: EDAM:0002059 ! Genotype / phenotype report format ! -! Data syntax<-Map format +! Data format<-Map format ! [Term] id: EDAM:0001861 name: PlasMapper TextMap plasmid map format -namespace: syntax +namespace: format def: "Map of a plasmid (circular DNA) in PlasMapper TextMap format." [EDAM:EBI "EMBRACE definition"] xref: Moby:PlasMapperTextMap is_a: EDAM:0002060 ! Map format @@ -27864,34 +28192,34 @@ is_a: EDAM:0002060 ! Map format ! -! Data syntax<-Primer report format +! Data format<-Primer report format ! [Term] id: EDAM:0001627 name: Primer3 primer report format -namespace: syntax +namespace: format def: "Report on PCR primers and hybridization oligos generated by Whitehead primer3 program." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002061 ! Primer report format ! -! Data syntax<-Protein annotation format +! Data format<-Protein annotation format ! [Term] id: EDAM:0002063 name: Enzyme annotation format -namespace: syntax +namespace: format def: "Format of a report of general information about a specific enzyme." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002062 ! Protein annotation format ! -! Data syntax<-Protein annotation format<-Enzyme annotation format +! Data format<-Protein annotation format<-Enzyme annotation format ! [Term] id: EDAM:0001511 name: IntEnz enzyme report format -namespace: syntax +namespace: format def: "Format of an entry from IntEnz (The Integrated Relational Enzyme Database)." [EDAM:EBI "EMBRACE definition"] comment: IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. is_a: EDAM:0002063 ! Enzyme annotation format @@ -27901,7 +28229,7 @@ is_a: EDAM:0002063 ! Enzyme annotation format [Term] id: EDAM:0001512 name: BRENDA enzyme report format -namespace: syntax +namespace: format def: "Format of an entry from the BRENDA enzyme database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002063 ! Enzyme annotation format ! relationship: has_source EDAM:0000823 ! BRENDA database @@ -27910,7 +28238,7 @@ is_a: EDAM:0002063 ! Enzyme annotation format [Term] id: EDAM:0001513 name: KEGG REACTION enzyme report format -namespace: syntax +namespace: format def: "Format of an entry from the KEGG REACTION database of biochemical reactions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002063 ! Enzyme annotation format ! relationship: has_source EDAM:0000824 ! KEGG REACTION database @@ -27921,7 +28249,7 @@ is_a: EDAM:0002063 ! Enzyme annotation format [Term] id: EDAM:0001514 name: KEGG ENZYME enzyme report format -namespace: syntax +namespace: format def: "Format of an entry from the KEGG ENZYME database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002063 ! Enzyme annotation format ! relationship: has_source EDAM:0000825 ! KEGG ENZYME database @@ -27932,7 +28260,7 @@ is_a: EDAM:0002063 ! Enzyme annotation format [Term] id: EDAM:0001515 name: REBASE proto enzyme report format -namespace: syntax +namespace: format def: "Format of an entry from the proto section of the REBASE enzyme database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002063 ! Enzyme annotation format ! relationship: has_source EDAM:0000826 ! REBASE database @@ -27942,7 +28270,7 @@ is_a: EDAM:0002063 ! Enzyme annotation format [Term] id: EDAM:0001516 name: REBASE withrefm enzyme report format -namespace: syntax +namespace: format def: "Format of an entry from the withrefm section of the REBASE enzyme database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002063 ! Enzyme annotation format ! relationship: has_source EDAM:0000826 ! REBASE database @@ -27950,24 +28278,24 @@ is_a: EDAM:0002063 ! Enzyme annotation format ! -! Data syntax<-3D-1D scoring matrix format +! Data format<-3D-1D scoring matrix format ! [Term] id: EDAM:0001500 name: Domainatrix 3D-1D scoring matrix -namespace: syntax +namespace: format def: "Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002064 ! 3D-1D scoring matrix format ! -! Data syntax<-Protein structure evaluation format +! Data format<-Protein structure evaluation format ! [Term] id: EDAM:0001551 name: Pcons report format -namespace: syntax +namespace: format def: "Format of output of the Pcons Model Quality Assessment Program (MQAP)." [EDAM:EBI "EMBRACE definition"] comment: Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. is_a: EDAM:0002065 ! Protein structure evaluation format @@ -27976,19 +28304,19 @@ is_a: EDAM:0002065 ! Protein structure evaluation format [Term] id: EDAM:0001552 name: ProQ report format -namespace: syntax +namespace: format def: "Format of output of the ProQ protein model quality predictor." [EDAM:EBI "EMBRACE definition"] comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. is_a: EDAM:0002065 ! Protein structure evaluation format ! -! Data syntax<-Sequence database hits format +! Data format<-Sequence database hits format ! [Term] id: EDAM:0001332 name: FASTA search results format -namespace: syntax +namespace: format def: "Format of results of a sequence database search using FASTA." [EDAM:EBI "EMBRACE definition"] comment: This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) is_a: EDAM:0002066 ! Sequence database hits format @@ -27998,7 +28326,7 @@ is_a: EDAM:0002066 ! Sequence database hits format [Term] id: EDAM:0001333 name: BLAST search results format -namespace: syntax +namespace: format def: "Format of results of a sequence database search using some variant of BLAST." [EDAM:EBI "EMBRACE definition"] comment: This includes score data, alignment data and summary table. is_a: EDAM:0002066 ! Sequence database hits format @@ -28008,7 +28336,7 @@ is_a: EDAM:0002066 ! Sequence database hits format [Term] id: EDAM:0001334 name: MSPCrunch search results format -namespace: syntax +namespace: format def: "Format of results of a sequence database search using some variant of MSPCrunch." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002066 ! Sequence database hits format ! relationship: is_output_of EDAM:0000346 ! Sequence database search by sequence @@ -28017,7 +28345,7 @@ is_a: EDAM:0002066 ! Sequence database hits format [Term] id: EDAM:0001335 name: Smith Waterman search results format -namespace: syntax +namespace: format def: "Format of results of a sequence database search using some variant of Smith Waterman." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002066 ! Sequence database hits format ! relationship: is_output_of EDAM:0000346 ! Sequence database search by sequence @@ -28025,7 +28353,7 @@ is_a: EDAM:0002066 ! Sequence database hits format [Term] id: EDAM:0001336 name: EMBASSY domain hits format -namespace: syntax +namespace: format def: "Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information." [EDAM:EBI "EMBRACE definition"] comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. is_a: EDAM:0002066 ! Sequence database hits format @@ -28035,7 +28363,7 @@ is_a: EDAM:0002066 ! Sequence database hits format [Term] id: EDAM:0001337 name: EMBASSY ligand hits format -namespace: syntax +namespace: format def: "Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information." [EDAM:EBI "EMBRACE definition"] comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database. is_a: EDAM:0002066 ! Sequence database hits format @@ -28044,12 +28372,12 @@ is_a: EDAM:0002066 ! Sequence database hits format ! -! Data syntax<-Sequence distance matrix format +! Data format<-Sequence distance matrix format ! [Term] id: EDAM:0001423 name: PHYLIP phylogenetic distance matrix format -namespace: syntax +namespace: format def: "Format of PHYLIP phylogenetic distance matrix data." [EDAM:EBI "EMBRACE definition"] comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). is_a: EDAM:0002067 ! Sequence distance matrix format @@ -28058,12 +28386,12 @@ is_a: EDAM:0002067 ! Sequence distance matrix format ! -! Data syntax<-Sequence motif format +! Data format<-Sequence motif format ! [Term] id: EDAM:0001360 name: MEME sequence motif format -namespace: syntax +namespace: format def: "A motif in the format generated by the MEME program." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002068 ! Sequence motif format ! relationship: has_source EDAM:0000598 ! Sequence motif or profile database @@ -28072,7 +28400,7 @@ is_a: EDAM:0002068 ! Sequence motif format [Term] id: EDAM:0001356 name: Prosite pattern format -namespace: syntax +namespace: format def: "Format of a regular expression pattern from the Prosite database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002068 ! Sequence motif format ! relationship: has_source EDAM:0000745 ! Prosite database @@ -28082,28 +28410,28 @@ is_a: EDAM:0002068 ! Sequence motif format [Term] id: EDAM:0001357 name: EMBOSS sequence pattern -namespace: syntax +namespace: format def: "EMBOSS sequence pattern." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002068 ! Sequence motif format -! relationship: has_source EDAM:0000598 ! Sequence motif or profile database +! relationship: has_source EDAM:0000598 ! Sequence motif or profile data resource ! relationship: has_identifier EDAM:0001065 ! Sequence signature identifier ! -! Data syntax<-Sequence profile format +! Data format<-Sequence profile format ! [Term] id: EDAM:0002072 name: Hidden Markov model format -namespace: syntax +namespace: format def: "Format of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0001915 ! Data syntax +is_a: EDAM:0001915 ! Data format [Term] id: EDAM:0001367 name: JASPAR profile format -namespace: syntax +namespace: format def: "A profile (sequence classifier) in the format used in the JASPAR database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002069 ! Sequence profile format ! relationship: has_source EDAM:0000813 ! JASPAR database @@ -28113,7 +28441,7 @@ is_a: EDAM:0002069 ! Sequence profile format [Term] id: EDAM:0001366 name: Prosite profile format -namespace: syntax +namespace: format def: "Profile (sequence classifier) format used in the PROSITE database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002069 ! Sequence profile format ! relationship: has_source EDAM:0000745 ! Prosite database @@ -28123,35 +28451,35 @@ is_a: EDAM:0002069 ! Sequence profile format ! -! Data syntax<-Sequence profile format<-Hidden Markov model format +! Data format<-Sequence profile format<-Hidden Markov model format ! [Term] id: EDAM:0001369 name: MEME background Markov model format -namespace: syntax +namespace: format def: "Format of the model of random sequences used by MEME." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002072 ! Hidden Markov model format -! relationship: has_source EDAM:0000598 ! Sequence motif or profile database +! relationship: has_source EDAM:0000598 ! Sequence motif or profile data resource ! relationship: has_identifier EDAM:0001115 ! Sequence profile identifier [Term] id: EDAM:0001370 name: HMMER hidden Markov model format -namespace: syntax +namespace: format def: "Format of a hidden Markov model representation used by the HMMER package." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002072 ! Hidden Markov model format -! relationship: has_source EDAM:0000598 ! Sequence motif or profile database +! relationship: has_source EDAM:0000598 ! Sequence motif or profile data resource ! relationship: has_identifier EDAM:0001118 ! HMMER hidden Markov model identifier ! -! Data syntax<-Dirichlet distribution format +! Data format<-Dirichlet distribution format ! [Term] id: EDAM:0001349 name: HMMER Dirichlet prior record -namespace: syntax +namespace: format def: "Dirichlet distribution in HMMER format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002074 ! Dirichlet distribution format @@ -28159,30 +28487,30 @@ is_a: EDAM:0002074 ! Dirichlet distribution format [Term] id: EDAM:0001350 name: MEME Dirichlet prior record -namespace: syntax +namespace: format def: "Dirichlet distribution in MEME format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002074 ! Dirichlet distribution format ! -! Data syntax<-HMM emission and transition counts format +! Data format<-HMM emission and transition counts format ! [Term] id: EDAM:0001351 name: HMMER emission and transition count report -namespace: syntax +namespace: format def: "Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002075 ! HMM emission and transition counts format ! -! Data syntax<-Protein secondary structure format +! Data format<-Protein secondary structure format ! [Term] id: EDAM:0001454 name: DSSP entry format -namespace: syntax +namespace: format def: "Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins)." [EDAM:EBI "EMBRACE definition"] comment: The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. is_a: EDAM:0002077 ! Protein secondary structure format @@ -28193,7 +28521,7 @@ is_a: EDAM:0002077 ! Protein secondary structure format [Term] id: EDAM:0001455 name: HSSP entry format -namespace: syntax +namespace: format def: "An entry from the HSSP database (Homology-derived Secondary Structure in Proteins)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002077 ! Protein secondary structure format ! relationship: is_attribute_of EDAM:0000025 ! Polypeptide @@ -28202,41 +28530,41 @@ is_a: EDAM:0002077 ! Protein secondary structure format ! -! Data syntax<-RNA secondary structure format +! Data format<-RNA secondary structure format ! [Term] id: EDAM:0001457 name: Vienna RNA secondary structure report -namespace: syntax +namespace: format def: "Format of RNA secondary structure (in bracket notation) with free energy values, generated by the Vienna program." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002076 ! RNA secondary structure format [Term] id: EDAM:0001458 name: Vienna local RNA secondary structure report -namespace: syntax +namespace: format def: "Format of local RNA secondary structure components with free energy values, generated by the Vienna program." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002076 ! RNA secondary structure format ! -! Data syntax<-Sequence range format +! Data format<-Sequence range format ! [Term] id: EDAM:0001248 name: Sequence feature location format -namespace: syntax -def: "Format for sequence positions (feature location) as used in EMBL and SwissProt database." [EDAM:EBI "EMBRACE definition"] +namespace: format +def: "Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database." [EDAM:EBI "EMBRACE definition"] synonym: "Feature location" EXACT [] is_a: EDAM:0002078 ! Sequence range format ! -! Data syntax<-Repeat sequence map format +! Data format<-Repeat sequence map format ! [Term] id: EDAM:0001295 name: quicktandem repeat sequence map format -namespace: syntax +namespace: format def: "Report on tandem repeats in a nucleotide sequence in format generated by the Sanger Centre quicktandem program." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002155 ! Repeat sequence map format @@ -28244,7 +28572,7 @@ is_a: EDAM:0002155 ! Repeat sequence map format [Term] id: EDAM:0001296 name: Sanger inverted repeat sequence map format -namespace: syntax +namespace: format def: "Report on inverted repeats in a nucleotide sequence in format generated by the Sanger Centre inverted program." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002155 ! Repeat sequence map format @@ -28252,17 +28580,17 @@ is_a: EDAM:0002155 ! Repeat sequence map format [Term] id: EDAM:0001297 name: EMBOSS repeat sequence map format -namespace: syntax +namespace: format def: "Report on tandem repeats in a sequence in an EMBOSS report format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002155 ! Repeat sequence map format ! -! Data syntax<-Restriction site report format +! Data format<-Restriction site report format ! [Term] id: EDAM:0001318 name: EMBOSS restrict restriction site report format -namespace: syntax +namespace: format def: "Report format for restriction enzyme recognition sites used by EMBOSS restrict program." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002158 ! Restriction site report format @@ -28271,7 +28599,7 @@ is_a: EDAM:0002158 ! Restriction site report format [Term] id: EDAM:0001319 name: EMBOSS restover restriction site report format -namespace: syntax +namespace: format def: "Report format for restriction enzyme recognition sites used by EMBOSS restover program." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002158 ! Restriction site report format @@ -28280,49 +28608,49 @@ is_a: EDAM:0002158 ! Restriction site report format [Term] id: EDAM:0001320 name: REBASE restriction site report format -namespace: syntax +namespace: format def: "Report format for restriction enzyme recognition sites used by REBASE database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002158 ! Restriction site report format ! -! Data syntax<-Coding region report format +! Data format<-Coding region report format ! [Term] id: EDAM:0001316 name: EMBOSS est2genome coding region report format -namespace: syntax +namespace: format def: "Format of a report on exon-intron structure generated by EMBOSS est2genome." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002159 ! Coding region report format ! -! Data syntax<-Sequence cluster format +! Data format<-Sequence cluster format ! [Term] id: EDAM:0002171 name: Protein sequence cluster format -namespace: syntax +namespace: format def: "Format used for clusters of protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002170 ! Sequence cluster format [Term] id: EDAM:0002172 name: Nucleotide sequence cluster format -namespace: syntax +namespace: format def: "Format used for clusters of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002170 ! Sequence cluster format ! -! Data syntax<-Sequence cluster format<-Protein sequence cluster format +! Data format<-Sequence cluster format<-Protein sequence cluster format ! [Term] id: EDAM:0001247 name: COG sequence cluster format -namespace: syntax +namespace: format def: "Format of an entry from the COG database of clusters of (related) protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002171 ! Protein sequence cluster format @@ -28333,24 +28661,24 @@ is_a: EDAM:0002171 ! Protein sequence cluster format ! -! Data syntax<-Sequence cluster format<-Nucleotide sequence cluster format +! Data format<-Sequence cluster format<-Nucleotide sequence cluster format ! [Term] id: EDAM:0002175 name: Gene cluster format -namespace: syntax +namespace: format def: "Format used for clusters of genes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002172 ! Nucleotide sequence cluster format ! -! Data syntax<-Sequence cluster format<-Nucleotide sequence cluster format<-Gene cluster format +! Data format<-Sequence cluster format<-Nucleotide sequence cluster format<-Gene cluster format ! [Term] id: EDAM:0001228 name: UniGene entry format -namespace: syntax +namespace: format def: "Format of an entry from UniGene." [EDAM:EBI "EMBRACE definition"] comment: A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. is_a: EDAM:0002175 ! Gene cluster format @@ -28359,24 +28687,36 @@ is_a: EDAM:0002175 ! Gene cluster format [Term] id: EDAM:0001639 name: Affymetrix gene cluster format -namespace: syntax +namespace: format def: "Fromat of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002175 ! Gene cluster format ! -! Data syntax<-Ontology format +! Data format<-Ontology format ! [Term] id: EDAM:0002196 name: OBO format -namespace: syntax +namespace: format def: "OBO ontology format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002195 ! Ontology format [Term] id: EDAM:0002197 name: OWL format -namespace: syntax +namespace: format def: "OWL ontology format." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002195 ! Ontology format + + +! +! Data format<-Strain data format +! + +[Term] +id: EDAM:0002211 +name: CIP strain data format +namespace: format +def: "Format for a report of strain data as used for CIP database entries." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0002210 ! Strain data format \ No newline at end of file