diff --git a/releases/EDAM.obo b/releases/EDAM.obo index 8258670..a1f742c 100644 --- a/releases/EDAM.obo +++ b/releases/EDAM.obo @@ -1,230 +1,122 @@ format-version: 1.2 -date: 01:12:2010 12:25 -data-version: Beta11 -! Use for mapping to "global" id space(s) e.g.: +date: 17:06:2011 10:32 +data-version: Beta12 +subsetdef: topic "Topic" +subsetdef: data "Data" +subsetdef: format "Format" +subsetdef: identifier "Identifier" +subsetdef: operation "Operation" +! Use for mapping to "global" id space(s) e.g.: ! idspace: EDAM http://purl.org/edam/ "EDAM terms" -! NEXT term number is 0002608 +! NEXT term number is 0003029 ! xref: WHATIF: CorrectedPDBasXML -! xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB -! xref: Moby:GI_Gene -! xref: Moby_namespace:iHOPorganism +! xref:http://www.geneontology.org/doc/GO.xrf_abbs: FB +! xref:Moby:GI_Gene ! xref: Moby_namespace:iHOPorganism ! xref: SO:0000348 ! xref: BioCatalogue:Protein Multiple Alignment - -! - +! xref: GO:0006464 ! protein modification process +! regex: Regular expression for validating a "data<-identifier" instance. +! spec: URL of format specification for a "format" term +! seealso: Ontology term ID of term in external ontology for fine-grained annotation +! {cardinality=1, minCardinality=1, maxCardinality=1} ! -! EDAM relations +! Relations ! [Typedef] -id: concerns -name: concerns -def: "Defines that a term ('Topic') concerns (covers) another term ('Data', 'Resource' or 'Operation')." [EDAM:EBI] +id: in_topic +name: in_topic +def: "'Data' or 'Operation' is within the scope of a 'Topic'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -! inverse_of: is_concern_of - -! [Typedef] -! id: has_attribute -! name: has_attribute -! 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 -! inverse_of: is_attribute_of - -! [Typedef] -! id: has_identifier -! name: has_identifier -! def: "Defines a term ('Biological entity', 'Resource' or 'Data') has (or can have) an identifier ('Identifier')." [EDAM:EBI] -! is_anti_symmetric: true -! is_cyclic: false -! is_transitive: true -! inverse_of: is_identifier_of [Typedef] id: has_input name: has_input -def: "Defines a term ('Operation') as necessarily consuming another term ('Data') as input." [EDAM:EBI] +def: "An 'Operation' consumes a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -! inverse_of: is_input_of [Typedef] id: has_output name: has_output -def: "Defines a term ('Operation') as necessarily producing another term ('Data') as output." [EDAM:EBI] +def: "An 'Operation' produces a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -! inverse_of: is_output_of - -! [Typedef] -! id: has_part -! name: has_part -! 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 -! inverse_of: is_part_of - -! [Typedef] -! id: has_source -! name: has_source -! def: "Defines a term ('Data') has a source ('Operation', 'Resource')." [EDAM:EBI] -! comment: is_source_of -! is_anti_symmetric: true -! is_cyclic: false -! is_transitive: true -! inverse_of: is_source_of - - -! [Typedef] -! id: has_format -! name: has_format -! def: "Defines a term ('Data') has a data format specification ('Format')." [EDAM:EBI] -! is_anti_symmetric: true -! is_cyclic: false -! is_transitive: true -! inverse_of: is_format_of - -! [Typedef] -! id: is_attribute_of -! name: is_attribute_of -! 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 -! inverse_of: has_attribute - -! [Typedef] -! id: is_concern_of -! name: is_concern_of -! def: "Defines a term ('Biological entity', 'Resource' or 'Operation') as a concern of another term ('Topic')." [EDAM:EBI] -! is_anti_symmetric: true -! is_cyclic: false -! is_transitive: true -! inverse_of: concerns [Typedef] -id: is_identifier_of -name: is_identifier_of -def: "Defines that a term ('Identifier') is an identifier of another term ('Resource' or 'Data')." [EDAM:EBI] +id: is_format_of +name: is_format_of +def: "A data 'Format' is a format of a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -! inverse_of: has_identifier - -! [Typedef] -! id: is_input_of -! name: is_input_of -! def: "Defines a term ('Data') as an input of another term ('Operation')." [EDAM:EBI] -! is_anti_symmetric: true -! is_cyclic: false -! is_transitive: true -! inverse_of: has_input - -! [Typedef] -! id: is_output_of -! name: is_output_of -! def: "Defines a term ('Data') as an output of another term ('Operation')." [EDAM:EBI] -! is_anti_symmetric: true -! is_cyclic: false -! is_transitive: true -! inverse_of: has_output - -! [Typedef] -! id: is_part_of -! name: is_part_of -! 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 -! inverse_of: has_part [Typedef] -id: is_source_of -name: is_source_of -def: "Defines a term ('Resource') is a source of another term ('Data')." [EDAM:EBI] -comment: has_source +id: is_identifier_of +name: is_identifier_of +def: "A data 'Identifier' is an identifier of a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -! inverse_of: has_source -[Typedef] -id: is_format_of -name: is_format_of -def: "Defines that a term ('Format') is a data format specification for another term ('Data')." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -! inverse_of: has_format ! -! Top-level +! Top-level terms (sub-ontologies) ! -[Term] -id: EDAM:0000002 -name: Biological entity -namespace: entity -def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things or an observable phenonema or occurence." [EDAM:EBI "EMBRACE definition"] -! relationship: is_concern_of EDAM:0000003 ! Topic -! relationship: has_attribute EDAM:0000006 ! Data -is_obsolete: true [Term] 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 ! Biological entity -! relationship: concerns EDAM:0000004 ! Operation -! relationship: concerns EDAM:0000005 ! Resource -! relationship: concerns EDAM:0000582 ! Ontology +def: "A general bioinformatics subject or category, such as a field of study, data, processing, analysis or technology." [EDAM:EBI "EMBRACE definition"] +subset: topic [Term] id: EDAM:0000004 name: Operation namespace: operation -def: "A specific, singular function or process performed by a tool, for example a WS operation. What is done, but not (typically) how or in what context." [EDAM:EBI "EMBRACE definition"] -! relationship: is_concern_of EDAM:0000003 ! Topic -! relationship: has_input EDAM:0000006 ! Data -! relationship: has_output EDAM:0000006 ! Data - -[Term] -id: EDAM:0000005 -name: Resource -namespace: resource -def: "A category of content of a data resource including databases, ontologies and servers." [EDAM:EBI "EMBRACE definition"] - - - - - - +def: "A function or process performed by a tool; what is done, but not (typically) how or in what context." [EDAM:EBI "EMBRACE definition"] +subset: operation [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 ! Biological entity +def: "A type of data in common use in bioinformatics." [EDAM:EBI "EMBRACE definition"] +subset: data [Term] id: EDAM:0001915 name: Format namespace: format -def: "A reference (typically a URL) of a data format specification." [EDAM:EBI "EMBRACE definition"] -comment: See OBO file for URL of format specification. {url=} -! relationship: is_format_of EDAM:0000006 ! Data +def: "A specific layout for encoding a specific type of data in a computer file or memory." [EDAM:EBI "EMBRACE definition"] +subset: format + +[Term] +id: EDAM:0000842 +name: Identifier +namespace: identifier +def: "A label that identifies (typically uniquely) something such as data, a resource or a biological entity." [EDAM:EBI "EMBRACE definition"] +comment: This term is used for datatypes with the sole purpose of identification. It is not used for datatypes which contain other fields not related to identification. +subset: identifier + + +[Term] +id: EDAM:0000002 +name: Biological entity +namespace: entity +def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things or an observable phenonema or occurence." [EDAM:EBI "EMBRACE definition"] +! relationship: has_attribute EDAM:0000006 ! Data +is_obsolete: true + @@ -232,21 +124,19 @@ comment: See OBO file for URL of format specification. {url=} ! ! Biological entity ! -! [Term] -! id: EDAM:0000008 -! name: Undefined -! namespace: entity -! def: "Debugging." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000002 ! Biological entity -! relationship: has_attribute EDAM:0000841 ! Undefined +[Term] +id: EDAM:0000008 +name: Undefined +namespace: entity +def: "Debugging." [EDAM:EBI "EMBRACE definition"] +is_obsolete: true [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 is_obsolete: true [Term] @@ -254,20 +144,14 @@ id: EDAM:0000012 name: Phenomenon namespace: entity def: "An observable biological occurence or event with a physical basis." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000002 ! Biological entity ! relationship: has_attribute EDAM:0000006 ! Data is_obsolete: true - -! -! 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:0002199 ! Physical entity ! relationship: has_attribute EDAM:0000006 ! Data is_obsolete: true @@ -276,7 +160,6 @@ id: EDAM:0000010 name: Entity feature namespace: entity def: "A physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0002199 ! Physical entity ! relationship: has_attribute EDAM:0000006 ! Data is_obsolete: true @@ -285,42 +168,22 @@ id: EDAM:0000011 name: Entity collection namespace: entity def: "A collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0002199 ! Physical entity ! relationship: has_attribute EDAM:0000006 ! Data is_obsolete: true - - -! -! Biological entity<-Physical entity<-Discrete entity -! - [Term] id: EDAM:0000013 name: Molecular entity namespace: entity def: "Any atom, molecule or molecular complex with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000009 ! Discrete entity -! relationship: has_attribute EDAM:0000883 ! Tertiary structure +! relationship: has_attribute EDAM:0000883 ! Structure is_obsolete: true - - - - - - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity -! - [Term] id: EDAM:0000014 name: Atom namespace: entity def: "The basic unit of matter consisting of negatively charged electrons bound by electromagnetic force to a nucleus of protons and neutrons." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000013 ! Molecular entity -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -328,8 +191,6 @@ id: EDAM:0000015 name: Small molecule namespace: entity def: "Any small molecule." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000013 ! Molecular entity -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -337,8 +198,7 @@ id: EDAM:0000016 name: Biopolymer namespace: entity def: "A single organic macromolecule made up of monomeric units." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000013 ! Molecular entity -! relationship: has_attribute EDAM:0002044 ! Sequence data +! relationship: has_attribute EDAM:0002044 ! Sequence is_obsolete: true [Term] @@ -347,29 +207,13 @@ name: Molecular complex namespace: entity def: "Two or more whole molecules in association with one another." [EDAM:EBI "EMBRACE definition"] synonym: "Molecular assembly" EXACT [] -! is_a: EDAM:0000013 ! Molecular entity -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - - - - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Atom -! - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Small molecule -! - [Term] id: EDAM:0000018 name: Biomonomer namespace: entity def: "A small organic molecule that can chemically bond to other monomers to form a biopolymer." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000015 ! Small molecule -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -377,8 +221,6 @@ id: EDAM:0000019 name: Ligand namespace: entity def: "A molecule that can bind and form a complex with a biopolymer, typically a protein." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000015 ! Small molecule -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -386,8 +228,6 @@ id: EDAM:0000020 name: Drug namespace: entity def: "A substance that changes the normal functioning of an organism." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000015 ! Small molecule -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -395,21 +235,13 @@ id: EDAM:0002577 name: Toxin namespace: entity def: "A poisonous substance produced by living cells or organisms." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000015 ! Small molecule -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Small molecule<-Biomonomer -! [Term] id: EDAM:0000021 name: Amino acid namespace: entity def: "The building block of proteins, an alpha amino acid consists of a carbon atom (C-alpha) attached to a hydrogen atom, an amino group, a carboxylate group and one of (typically) 20 common R-groups (side-chain)." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000018 ! Biomonomer -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -419,8 +251,6 @@ namespace: entity def: "The building block of nucleic acids, a nucleotide consists of a nucleobase (nitrogenous base, either a purine or pyrimidine), a five-carbon sugar (either ribose or 2'-deoxyribose), and one to three phosphate groups." [EDAM:EBI "EMBRACE definition"] synonym: "Base" EXACT [] xref: SO:0001236 -! is_a: EDAM:0000018 ! Biomonomer -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -428,22 +258,8 @@ id: EDAM:0000023 name: Monosaccharide namespace: entity def: "The building block of polysaccharides, a monosaccharide is an aldehyde or ketone with hydroxyl groups." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000018 ! Biomonomer -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Small molecule<-Ligand -! - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Small molecule<-Drug -! - - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer -! [Term] id: EDAM:0000024 name: Nucleic acid @@ -452,9 +268,8 @@ def: "An organic polymer of nucleotide monomers in an unbranched chain, bound to synonym: "Polynucleotide chain" EXACT [] synonym: "Polynucleotide" EXACT [] xref: SO:0000348 -! is_a: EDAM:0000016 ! Biopolymer ! relationship: has_attribute EDAM:0001207 ! Nucleotide sequence -! relationship: has_attribute EDAM:0001459 ! Nucleic acid tertiary structure +! relationship: has_attribute EDAM:0001459 ! Nucleic acid structure is_obsolete: true [Term] @@ -463,9 +278,8 @@ name: Polypeptide namespace: entity def: "An organic polymer of alpha amino acid residues in an unbranched chain, bound together by peptide bonds." [EDAM:EBI "EMBRACE definition"] synonym: "Polypeptide chain" EXACT [] -! is_a: EDAM:0000016 ! Biopolymer ! relationship: has_attribute EDAM:0001208 ! Protein sequence -! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] @@ -473,21 +287,13 @@ id: EDAM:0000026 name: Polysaccharide namespace: entity def: "An organic polymer of either mono- or di-saccharide subunits in an unbranched chain, bound together by glycosidic bonds." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000016 ! Biopolymer - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid -! [Term] id: EDAM:0000027 name: Oligonucleotide namespace: entity def: "An organic polymer of nucleotide monomers in a short (typically less than 30 subunits) unbranched chain, bound together by covalent bonds." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000024 ! Nucleic acid ! relationship: has_attribute EDAM:0001207 ! Nucleotide sequence is_obsolete: true @@ -497,9 +303,8 @@ name: DNA namespace: entity def: "A deoxyribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] xref: SO:0000352 -! is_a: EDAM:0000024 ! Nucleic acid ! relationship: has_attribute EDAM:0001212 ! DNA sequence -! relationship: has_attribute EDAM:0001464 ! DNA tertiary structure +! relationship: has_attribute EDAM:0001464 ! DNA structure is_obsolete: true [Term] @@ -508,28 +313,15 @@ name: RNA namespace: entity def: "A ribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] xref: SO:0000356 -! is_a: EDAM:0000024 ! Nucleic acid ! relationship: has_attribute EDAM:0001213 ! RNA sequence -! relationship: has_attribute EDAM:0001465 ! RNA tertiary structure +! relationship: has_attribute EDAM:0001465 ! RNA structure is_obsolete: true - - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-Oligonucleotide -! - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA -! - [Term] id: EDAM:0000030 name: Mobile genetic element namespace: entity def: "A DNA molecule that can move around within a genome." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000028 ! DNA -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -538,21 +330,15 @@ name: cDNA namespace: entity def: "A deoxyribonucleic acid molecule synthesises by reverse transcriptase from an RNA template." [EDAM:EBI "EMBRACE definition"] xref: SO:0000756 -! is_a: EDAM:0000028 ! DNA ! relationship: has_attribute EDAM:0001212 ! DNA sequence -! relationship: has_attribute EDAM:0001464 ! DNA tertiary structure +! relationship: has_attribute EDAM:0001464 ! DNA structure is_obsolete: true -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element -! [Term] id: EDAM:0000031 name: Transposon namespace: entity def: "A DNA sequence that can undergo transposition or move to different positions in the genome of a single cell." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000030 ! Mobile genetic element -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -560,21 +346,13 @@ id: EDAM:0000032 name: Plasmid namespace: entity def: "A DNA molecule existing outside a chromosome and capable of independent replication." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000030 ! Mobile genetic element -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element<-Transposon -! [Term] id: EDAM:0000033 name: Retrotransposon namespace: entity def: "A DNA element that can amplify itself in a genome, by copying itself to RNA then back to DNA using a reverse transcriptase." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000031 ! Transposon -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -584,23 +362,8 @@ namespace: entity def: "A DNA sequence that is smaller than most other transposable elements and which codes only for proteins involved in transposition." [EDAM:EBI "EMBRACE definition"] synonym: "Insertion sequence element" EXACT [] synonym: "IS element" EXACT [] -! is_a: EDAM:0000031 ! Transposon -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element<-Plasmid -! - - - - - - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-RNA -! [Term] id: EDAM:0000035 name: tRNA @@ -608,19 +371,14 @@ namespace: entity def: "Transfer RNA (tRNA) is a small ribonucleic acid molecule that binds a specific amino acid." [EDAM:EBI "EMBRACE definition"] comment: The amino acid is transferred to a nascent polypeptide chain during protein synthesis at the ribosome. synonym: "Transfer RNA" EXACT [] -! is_a: EDAM:0000029 ! RNA ! relationship: has_attribute EDAM:0001213 ! RNA sequence is_obsolete: true -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide -! [Term] id: EDAM:0000036 name: Peptide namespace: entity def: "An organic polymer of alpha amino acid residues in a short unbranched chain. Peptides typically have fewer than 50 subunits and can be made synthetically." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000025 ! Polypeptide ! relationship: has_attribute EDAM:0001208 ! Protein sequence is_obsolete: true @@ -629,22 +387,15 @@ id: EDAM:0000037 name: Protein namespace: entity def: "One or more polypeptide chains in a stable conformation." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000025 ! Polypeptide -! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein -! - [Term] id: EDAM:0000038 name: Uncomplexed protein namespace: entity def: "A single polypeptide chain in a stable conformation." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000037 ! Protein -! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] @@ -652,8 +403,7 @@ id: EDAM:0000039 name: Enzyme namespace: entity def: "Enzyme." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000037 ! Protein -! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] @@ -661,8 +411,7 @@ id: EDAM:0000040 name: Transmembrane protein namespace: entity def: "A transmembrane protein molecule." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000037 ! Protein -! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] @@ -671,57 +420,22 @@ name: Transcription factor namespace: entity def: "A protein that, upon binding a cis-regulatory DNA element, regulates (enhances or represses) transcription." [EDAM:EBI "EMBRACE definition"] synonym: "Sequence-specific DNA binding factor" EXACT [] -! is_a: EDAM:0000037 ! Protein -! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Uncomplexed protein -! - - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Enzyme -! [Term] id: EDAM:0000042 name: Restriction enzyme namespace: entity def: "An enzyme that cuts DNA at specific nucleotide subsequence(s) (restriction sites)." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000039 ! Enzyme -! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Transmembrane protein -! - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Transcription factor -! - - - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polysaccharide -! - - - - - - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex -! [Term] id: EDAM:0000043 name: RNA/DNA hybrid namespace: entity def: "A hybrid (complementary base-paired) molecule of DNA and RNA." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000017 ! Molecular complex -! relationship: has_attribute EDAM:0000841 ! Undefined -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -729,10 +443,8 @@ id: EDAM:0000044 name: Protein-protein complex namespace: entity def: "A protein comprising two or more polypeptide chain subunits in a stable association." [EDAM:EBI "EMBRACE definition"] -synonym: "Protein complex" EXACT [] -! is_a: EDAM:0000017 ! Molecular complex -! is_a: EDAM:0000037 ! Protein -! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! synonym: "Protein complex" EXACT [] +! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] @@ -740,21 +452,15 @@ id: EDAM:0000045 name: Protein-ligand complex namespace: entity def: "A protein-ligand (small molecule) complex." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000017 ! Molecular complex -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - [Term] id: EDAM:0000046 name: Protein-nucleic acid complex namespace: entity def: "A protein-DNA/RNA complex." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000017 ! Molecular complex -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - [Term] id: EDAM:0000047 name: Protein complex @@ -763,61 +469,19 @@ def: "A protein comprising two or more polypeptide chain subunits in a stable as is_obsolete: true ! consider: EDAM:0000044 ! Protein-protein complex - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex<-RNA/DNA hybrid -! - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-protein complex -! - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-ligand complex -! - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-nucleic acid complex -! [Term] id: EDAM:0001851 name: Chromosome namespace: entity -def: "A nucleic acid molecule which control its own replication via the action of proteins at replication start sites." [EDAM:EBI "EMBRACE definition"] +def: "A nucleic acid molecule which controls its own replication via the action of proteins at replication start sites." [EDAM:EBI "EMBRACE definition"] xref: SO:0000340 -! is_a: EDAM:0000046 ! Protein-nucleic acid complex - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide -! - - - - - -! -! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polysaccharide -! - - - - - -! -! Biological entity<-Physical entity<-Entity feature -! [Term] id: EDAM:0001749 name: Atom group namespace: entity def: "A group of two or more atoms from a molecular structure." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000010 ! Entity feature - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -825,9 +489,6 @@ id: EDAM:0000048 name: Nucleic acid feature namespace: entity def: "A feature of a nucleic acid molecule that can be mapped to a specific region(s) in its molecular sequence." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000010 ! Entity feature - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -835,9 +496,6 @@ id: EDAM:0000049 name: Protein feature namespace: entity def: "A feature of a protein molecule that can be mapped to a specific region(s) in its molecular sequence." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000010 ! Entity feature - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -846,39 +504,20 @@ name: Binding site namespace: entity def: "A region of a molecular surface involved in interactions with other molecules." [EDAM:EBI "EMBRACE definition"] xref: SO:0000409 -! is_a: EDAM:0000010 ! Entity feature - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - - - - -! -! Biological entity<-Physical entity<-Entity feature<-Atom group -! [Term] id: EDAM:0001750 name: Atom pair namespace: entity def: "A pair (exactly 2) atoms from a molecular structure." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0001749 ! Atom group - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true -! -! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature -! [Term] id: EDAM:0000050 name: Codon namespace: entity def: "Three nucleotides encoding typically a single, specific amino acid." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000048 ! Nucleic acid feature - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -886,8 +525,6 @@ id: EDAM:0000051 name: Gene namespace: entity def: "The hereditary unit, corresponding to the genomic sequence(s) encoding one or more functional products." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000048 ! Nucleic acid feature -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -895,22 +532,14 @@ id: EDAM:0000052 name: Operon namespace: entity def: "A functional unit of DNA including an operator, a common promoter, and one or more structural genes under common control." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000048 ! Nucleic acid feature - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - - [Term] id: EDAM:0000053 name: Protein-coding region namespace: entity def: "The portion of a gene's DNA or RNA that is composed of exons and encodes a protein product." [EDAM:EBI "EMBRACE definition"] synonym: "Coding region" EXACT [] -! is_a: EDAM:0000048 ! Nucleic acid feature - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -919,9 +548,6 @@ name: Transcription regulatory element namespace: entity def: "A region of DNA involved in transcription regulation." [EDAM:EBI "EMBRACE definition"] synonym: "Gene regulatory element" EXACT [] -! is_a: EDAM:0000048 ! Nucleic acid feature - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -929,9 +555,6 @@ id: EDAM:0000055 name: Restriction site namespace: entity def: "A restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000048 ! Nucleic acid feature - -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -940,8 +563,6 @@ name: Scaffold / matrix attachment site namespace: entity def: "Regions of DNA sequence in eukaryotic chromosomes where the nuclear matrix attaches." [EDAM:EBI "EMBRACE definition"] synonym: "Matrix attachment region" EXACT [] -! is_a: EDAM:0000048 ! Nucleic acid feature -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -949,41 +570,21 @@ id: EDAM:0000057 name: Splice site namespace: entity def: "A site in a transcribed RNA sequence at which RNA splicing occurs (introns are removed and exons are joined)." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000048 ! Nucleic acid feature -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true -! -! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Codon -! - -! -! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Gene -! [Term] id: EDAM:0001909 name: Allele namespace: entity def: "An alternative form of a gene that can exist at a single locus." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000051 ! Gene -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true -! -! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Operon -! - -! -! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element -! [Term] id: EDAM:0000058 name: Gene cis-regulatory element namespace: entity def: "A DNA element that can bind a transcription factor to regulate (enhance or repress) the expression (transcription) of genes located on the same strand." [EDAM:EBI "EMBRACE definition"] synonym: "Cis-element" EXACT [] -! is_a: EDAM:0000054 ! Transcription regulatory element -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -992,21 +593,13 @@ name: Gene trans-regulatory element namespace: entity def: "A DNA element that encodes a transcription factor which regulates gene(s) distant from the gene from which they were transcribed." [EDAM:EBI "EMBRACE definition"] synonym: "Trans-element" EXACT [] -! is_a: EDAM:0000054 ! Transcription regulatory element -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - -! -! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element<-Gene cis-regulatory element -! [Term] id: EDAM:0000060 name: Promoter namespace: entity def: "The DNA element where transcription is initiated." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000058 ! Gene cis-regulatory element -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1014,8 +607,6 @@ id: EDAM:0000061 name: Enhancer namespace: entity def: "An element that can bind a transcription factor to enhance transcription." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000058 ! Gene cis-regulatory element -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1023,8 +614,6 @@ id: EDAM:0000062 name: Silencer namespace: entity def: "An element that can bind a transcription factor to repress transcription." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000058 ! Gene cis-regulatory element -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1032,28 +621,14 @@ id: EDAM:0000063 name: Response element namespace: entity def: "An element within or near the promoter that can bind certain transcription factors, for example a hormone receptor complex." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000058 ! Gene cis-regulatory element -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true -! -! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element<-Gene-regulatory element -! - - - - -! -! Biological entity<-Physical entity<-Entity feature<-Protein feature -! [Term] id: EDAM:0000064 name: Protein residue namespace: entity def: "A single amino acid position in a protein, bound to one (C or N-terminal positions) or two other residues by covalent (peptide) bonds." [EDAM:EBI "EMBRACE definition"] synonym: "Residue" EXACT [] -! is_a: EDAM:0000049 ! Protein feature -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1062,8 +637,6 @@ name: Protein residue group namespace: entity def: "A group of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue group" EXACT [] -! is_a: EDAM:0000049 ! Protein feature -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1071,26 +644,15 @@ id: EDAM:0000065 name: Protein domain namespace: entity def: "A region of a protein (typically a region of a single polypeptide chain) forming a distinct, compact conformation. Domains show some independence in terms of evolution, folding, structure or function and (typically) reoccur in other proteins." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000049 ! Protein feature -! relationship: has_attribute EDAM:0001468 ! Protein domain tertiary structure +! relationship: has_attribute EDAM:0001468 ! Protein domain is_obsolete: true - -! -! Biological entity<-Physical entity<-Entity feature<-Protein feature<-Protein residue -! - -! -! Biological entity<-Physical entity<-Entity feature<-Protein feature<-Protein residue group -! [Term] id: EDAM:0001752 name: Protein residue pair namespace: entity def: "A pair of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue pair" EXACT [] -! is_a: EDAM:0001751 ! Protein residue group -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1099,8 +661,6 @@ name: Protein residue group (continuous) namespace: entity def: "A group of continuous (adjacent) amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue group (continuous)" EXACT [] -! is_a: EDAM:0001751 ! Protein residue group -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1110,30 +670,13 @@ namespace: entity def: "A group of discontinuous amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] comment: One or more residues in the group are discontinuous (non-adjacent). synonym: "Residue group (discontinuous)" EXACT [] -! is_a: EDAM:0001751 ! Protein residue group -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - -! -! Biological entity<-Physical entity<-Entity feature<-Protein feature<-Protein domain -! - - - - - - -! -! Biological entity<-Physical entity<-Entity collection -! [Term] id: EDAM:0000066 name: Genome namespace: entity def: "An organisms total complement of DNA or RNA (some viruses) and therefore its hereditary information. A genome includes genes and non-coding regions." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000011 ! Entity collection -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1141,8 +684,6 @@ id: EDAM:0000067 name: Proteome namespace: entity def: "An organisms total complement of expressed proteins. More specifically, those proteins expressed in a cell, tissue or the whole organism under defined conditions at a specific time." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000011 ! Entity collection -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1150,8 +691,6 @@ id: EDAM:0000068 name: Nucleosome namespace: entity def: "The repeating structural unit of eukaryotic chromatin, which is folded successively into chromosomes." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000011 ! Entity collection -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1159,35 +698,13 @@ id: EDAM:0000069 name: Taxonomic rank namespace: entity def: "One of the major taxonomic ranks of life." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000011 ! Entity collection -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - - - -! -! Biological entity<-Physical entity<-Entity collection<-Genome -! - -! -! Biological entity<-Physical entity<-Entity collection<-Proteome -! - -! -! Biological entity<-Physical entity<-Entity collection<-Nucleosome -! - -! -! Biological entity<-Physical entity<-Entity collection<-Taxonomic rank -! [Term] id: EDAM:0000070 name: Kingdom namespace: entity def: "A kingdom or organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000069 ! Taxonomic rank -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1195,8 +712,6 @@ id: EDAM:0001871 name: Genus namespace: entity def: "A genus of organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000069 ! Taxonomic rank -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1204,8 +719,6 @@ id: EDAM:0000071 name: Species namespace: entity def: "A species or organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000069 ! Taxonomic rank -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1213,22 +726,13 @@ id: EDAM:0000072 name: Strain namespace: entity def: "A strain or prokaryotic organisms." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000069 ! Taxonomic rank -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - -! -! Biological entity<-Phenomenon -! - [Term] id: EDAM:0000073 name: Metabolic pathway namespace: entity def: "A group of related chemical (enzyme catalysed) reactions occuring within a cell." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000012 ! Phenomenon -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1236,8 +740,6 @@ id: EDAM:0000074 name: Mutation namespace: entity def: "A change to the nucleotide sequence of an organism's genome." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000012 ! Phenomenon -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true [Term] @@ -1245,1075 +747,803 @@ id: EDAM:0000075 name: Single-nucleotide polymorphism namespace: entity def: "A single nucleotide variation in the genome of members of a species, or between paired chromosomes of an individual." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000012 ! Phenomenon -! relationship: has_attribute EDAM:0000841 ! Undefined is_obsolete: true - - ! ! Topic ! -! [Term] -! id: EDAM:0000076 -! name: Undefined -! namespace: topic -! def: "Debugging." [EDAM:EBI "EMBRACE definition"] -! is_a: EDAM:0000003 ! Topic -! ! relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000076 +name: Undefined +namespace: topic +def: "Debugging." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true + +[Term] +id: EDAM:0002807 +name: Tool topic +namespace: topic +def: "A topic concerning primarily bioinformatics tools, typically the broad function or purpose of a software tool." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000003 ! Topic + +[Term] +id: EDAM:0002808 +name: Data topic +namespace: topic +def: "A topic concerning primarily bioinformatics data, typically the broad category of content of a data resource." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000003 ! Topic + +[Term] +id: EDAM:0002809 +name: Study topic +namespace: topic +def: "A topic concerning primarily a general area of bioinformatics study that is not better modelled in as a tool or data topic, typically the broad category of content of bioinformatics journals or conference proceedings." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000003 ! Topic [Term] id: EDAM:0000077 name: Nucleic acids namespace: topic -def: "Study nucleic acids." [EDAM:EBI "EMBRACE definition"] +def: "The study of nucleic acids." [EDAM:EBI "EMBRACE definition"] +subset: topic is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0002501 ! Nucleic acid data processing + +[Term] +id: EDAM:0002839 +name: Molecules +namespace: topic +def: "The study of specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true [Term] id: EDAM:0000078 name: Proteins namespace: topic -def: "Study proteins." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0002502 ! Protein data processing - +def: "The study of proteins." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000586 ! Proteins [Term] id: EDAM:0000079 name: Metabolites namespace: topic -def: "Study metabolites." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of the reactants or products of metabolism, typically small molecules such as including vitamins, polyols, nucleotides and amino acids." [EDAM:EBI "EMBRACE definition"] +comment: This concept excludes macromolecules such as proteins and nucleic acids. +subset: topic +is_a: EDAM:0000154 ! Small molecules [Term] id: EDAM:0000080 -name: Sequence analysis +alt_id: EDAM:0002228 +alt_id: EDAM:0000584 +name: Sequence namespace: topic -def: "Handle or analyse molecular sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic +def: "The study of molecular sequences (mononmer composition of polymers) and related data such as alignments and motifs." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Sequence Analysis -relationship: concerns EDAM:0002403 ! Sequence analysis -relationship: concerns EDAM:0002503 ! Sequence data processing -relationship: concerns EDAM:0000323 ! Phylogenetic tree construction +is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0000081 -name: Structure analysis +alt_id: EDAM:0002827 +alt_id: EDAM:0000585 +name: Structure namespace: topic -def: "Handle or analyse molecular structures (secondary or tertiary)." [EDAM:EBI "EMBRACE definition"] +def: "The study of molecular secondary or tertiary (3D) structures and related data such as alignments and structural motifs." [EDAM:EBI "EMBRACE definition"] +subset: topic +synonym: "Structure analysis" EXACT [] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0002504 ! Structural data processing -relationship: concerns EDAM:0002484 ! Structure processing - [Term] id: EDAM:0000082 name: Structure prediction namespace: topic -def: "Study concerning the prediction of molecular structure." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0002476 ! Molecular dynamics simulation -relationship: concerns EDAM:0000271 ! Tertiary structure prediction - - - +def: "Study concerning the prediction of molecular (secondary or tertiary) structure." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000081 ! Structure [Term] id: EDAM:0000083 name: Alignment namespace: topic -def: "Study the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic -! relationship: concerns EDAM:0000008 ! Undefined +def: "Study concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000182 ! Sequence alignment +consider: EDAM:0000183 ! Structure alignment +consider: EDAM:0000184 ! Threading [Term] id: EDAM:0000084 name: Phylogenetics namespace: topic -def: "Study evolutionary relationships amongst organisms and the genetic basis of heredity and variation." [EDAM:EBI "EMBRACE definition"] -comment: Phylogenetics involves phylogenetic tree construction, manipulation, visualisation and analysis. +def: "The study of evolutionary relationships amongst organisms." [EDAM:EBI "EMBRACE definition"] +comment: Phylogenetics involves phylogenetic tree construction, typically from molecular sequence or morphological data. It can be used to analyse the genetic basis of heredity and variation, gene transfer, mode of selection / evolution etc. +subset: topic xref: BioCatalogue:Phylogeny xref: BioCatalogue:Statistical Robustness is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000289 ! Sequence distance matrix generation -relationship: concerns EDAM:0002443 ! Phylogenetic tree processing -relationship: concerns EDAM:0000499 ! Multiple sequence alignment (phylogenetic tree-based) -relationship: concerns EDAM:0000550 ! Phylogenetic model selection - [Term] id: EDAM:0000200 name: Microarrays namespace: topic -def: "Study concerning microarrays, for example, process microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"] +def: "The study of microarrays, for example, to process microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Microarrays is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0002432 ! Microarray data processing -relationship: concerns EDAM:0000309 ! Microarray probe design [Term] id: EDAM:0000121 +alt_id: EDAM:0000764 name: Proteomics namespace: topic -def: "Study whole proteomes of organisms." [EDAM:EBI "EMBRACE definition"] +def: "The study of experimental methods for studying the whole proteomes of organisms." [EDAM:EBI "EMBRACE definition"] comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues). +subset: topic synonym: "Protein expression" EXACT [] xref: BioCatalogue:Proteomics is_a: EDAM:0000003 ! Topic -! is_a: EDAM:0000078 ! Proteins -! relationship: concerns EDAM:0000008 ! Undefined - - -[Term] -id: EDAM:0000093 -name: Genomics -namespace: topic -def: "Study whole genomes of organisms." [EDAM:EBI "EMBRACE definition"] -xref: BioCatalogue:Genomics -is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0002472 ! Gene annotation retrieval -relationship: concerns EDAM:0002473 ! Genotype / phenotype annotation retrieval - [Term] id: EDAM:0000085 name: Functional genomics namespace: topic -def: "Study gene or protein functions and their interactions." [EDAM:EBI "EMBRACE definition"] -xref: BioCatalogue:Functional Genomics -is_a: EDAM:0000093 ! Genomics -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of gene or protein functions and their interactions." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000622 ! Genomics [Term] id: EDAM:0000122 name: Structural genomics namespace: topic def: "Determine or study the three dimensional structure for all (available) proteins in a given organism." [EDAM:EBI "EMBRACE definition"] -comment: Structural genomics uses experimental data (for example from X-ray crystallography or NMR spectroscopy) and computational methods (for example molecular modelling). -xref: BioCatalogue:Structural Genomics -is_a: EDAM:0000093 ! Genomics -! is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000318 ! Structural genomics target selection -relationship: concerns EDAM:0000319 ! Protein secondary structure assignment -relationship: concerns EDAM:0000320 ! Protein tertiary structure assignment -relationship: concerns EDAM:0000321 ! Protein tertiary structure evaluation -relationship: concerns EDAM:0000322 ! Protein tertiary structure refinement - +subset: topic +is_obsolete: true +consider: EDAM:0002226 ! Structure determination [Term] id: EDAM:0000086 name: Model organisms namespace: topic -def: "Study a model organism." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of a model organism." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000621 ! Organism [Term] id: EDAM:0000087 name: Health and disease namespace: topic -def: "Study health and disease, particularly in humans." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of health and disease, particularly in humans." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000634 ! Disease +consider: EDAM:0000803 ! Human disease [Term] id: EDAM:0000088 name: Literature and documentation namespace: topic -def: "Study the biomedical and informatic literature, bibliographic data and documentation." [EDAM:EBI "EMBRACE definition"] +def: "The study of the bioinformatics literature, bibliographic data and documentation." [EDAM:EBI "EMBRACE definition"] +subset: topic +xref: BioCatalogue: Document Discovery +xref: BioCatalogue: Literature retrieval is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000515 ! Tool annotation retrieval -relationship: concerns EDAM:0000516 ! Database annotation retrieval -relationship: concerns EDAM:0002222 ! Ontology annotation retrieval -relationship: concerns EDAM:0002246 ! Demonstration [Term] id: EDAM:0000089 name: Ontologies namespace: topic -def: "Study concerning biomedical ontologies, controlled vocabularies, glossaries and so on." [EDAM:EBI "EMBRACE definition"] +def: "The study of ontologies of biological or bioinformatics concepts (terms and relations), controlled vocabularies, structured glossary or other related resource." [EDAM:EBI "EMBRACE definition"] +comment: This includes the annotation of entities (typically biological database entries) with terms from a controlled vocabulary. +subset: topic +synonym: "Ontology" EXACT [] xref: BioCatalogue:Ontology -is_a: EDAM:0000003 ! Topic -! relationship: concerns EDAM:0000008 ! Undefined - +xref: BioCatalogue:Ontology Lookup +is_a: EDAM:0002829 ! Ontologies and nomenclature [Term] id: EDAM:0000090 -name: Search and retrieval +name: Data retrieval namespace: topic def: "Study concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Data Retrieval xref: BioCatalogue:Identifier Retrieval xref: BioCatalogue:Image Retrieval -is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000224 ! Search and retrieval - +is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0000091 -name: Database and file management +name: Data handling namespace: topic -def: "Study concerning the basic handling or manipulation of files, reports or databases of biological data." [EDAM:EBI "EMBRACE definition"] -comment: This includes areas such as data indexing, editing, reformatting, conversion, transformation, validation, debugging, database submission and so on. +def: "The study of the generic management of biological data including basic handling of files and databases, datatypes and workflows." [EDAM:EBI "EMBRACE definition"] +subset: topic +synonym: "Data types, processing and visualisation" EXACT [] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0002409 ! Report processing -relationship: concerns EDAM:0001780 ! Sequence submission - [Term] id: EDAM:0000092 -name: Plotting, rendering and visualisation +name: Data rendering and visualisation namespace: topic -def: "Study concerning the rendering of molecular sequences, structures or other biomolecular data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000337 ! Plotting and rendering +def: "The plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0002282 name: Datatypes, workflows and data handling namespace: topic -def: "Handling of biological data in a generic sense, including datatypes, data identifiers, data management, workflows etc." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000605 ! Informatics +def: "The study of handling biological data in a generic sense, including datatypes, data identifiers, data management, workflows etc." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000769 ! Workflows +consider: EDAM:0000770 ! Data types and objects [Term] id: EDAM:0002258 name: Chemoinformatics namespace: topic -def: "Compute data-centric problems in chemistry." [EDAM:EBI "EMBRACE definition"] +def: "The application of information technology to chemistry." [EDAM:EBI "EMBRACE definition"] +subset: topic synonym: "Cheminformatics" EXACT [] synonym: "Chemical informatics" EXACT [] +synonym: "Computational chemistry" EXACT [] xref: BioCatalogue:Chemoinformatics -is_a: EDAM:0000003 ! Topic -! relationship: concerns EDAM:0000008 ! Undefined - -[Term] -id: EDAM:0002259 -name: Systems biology and modelling -namespace: topic -def: "Holistic analysis of biological systems, the modelling of systems and interactions therein." [EDAM:EBI "EMBRACE definition"] -xref: BioCatalogue:Systems Biology -is_a: EDAM:0000003 ! Topic -! relationship: concerns EDAM:0000008 ! Undefined +is_a: EDAM:0002841 ! Informatics [Term] id: EDAM:0002269 -name: Biostatistics +name: Biostatistics namespace: topic -def: "Apply statistical methods to biological problems." [EDAM:EBI "EMBRACE definition"] +def: "The application of statistical methods to biological problems." [EDAM:EBI "EMBRACE definition"] +subset: topic synonym: "Biometry" EXACT [] synonym: "Biometrics" EXACT [] xref: BioCatalogue:Biostatistics -is_a: EDAM:0000003 ! Topic -! relationship: concerns EDAM:0000008 ! Undefined - - - +is_obsolete: true +consider: EDAM:0000091 ! Data handling -! -! Topic<-Nucleic acids -! [Term] id: EDAM:0000094 name: Nucleic acid physicochemistry namespace: topic -def: "Study the physicochemical properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"] +def: "The study of the physical or chemical properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"] +subset: topic is_a: EDAM:0000077 ! Nucleic acids -relationship: concerns EDAM:0000261 ! Physicochemical property data processing (nucleic acid) [Term] id: EDAM:0000095 name: Nucleic acid features namespace: topic -def: "Study the positional features of nucleic acids." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000160 ! Sequence features -is_a: EDAM:0000096 ! Nucleic acid sequence analysis -relationship: concerns EDAM:0000415 ! Sequence feature detection (nucleic acid) - - -[Term] -id: EDAM:0000096 -name: Nucleic acid sequence analysis -namespace: topic -def: "Handle or analyse nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] -xref: BioCatalogue:Nucleotide Sequence Analysis -is_a: EDAM:0000077 ! Nucleic acids -is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: concerns EDAM:0000461 ! Nucleic acid curvature calculation -relationship: concerns EDAM:0002513 ! Sequence generation (nucleic acid) -relationship: concerns EDAM:0002515 ! Sequence rendering (nucleic acid) +def: "The study of the positional features of nucleic acids." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000747 ! Nucleic acid functional sites [Term] id: EDAM:0000097 -name: Nucleic acid structure analysis +alt_id: EDAM:0002833 +name: Nucleic acid structure namespace: topic -def: "Handle or analyse nucleic acid structures or structural features." [EDAM:EBI "EMBRACE definition"] +def: "The study of nucleic acid (secondary or tertiary) structural data such as whole structures, structural features and associated annotation." [EDAM:EBI "EMBRACE definition"] +subset: topic is_a: EDAM:0000077 ! Nucleic acids -is_a: EDAM:0000081 ! Structure analysis -relationship: concerns EDAM:0000262 ! Nucleic acid structural property calculation -relationship: concerns EDAM:0002439 ! Secondary structure processing (RNA) -relationship: concerns EDAM:0002519 ! Tertiary structure processing (nucleic acid) - +is_a: EDAM:0000081 ! Structure [Term] id: EDAM:0000098 name: DNA namespace: topic -def: "Study DNA." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000077 ! Nucleic acids -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of DNA." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000654 ! DNA [Term] id: EDAM:0000099 name: RNA namespace: topic -def: "Study RNA." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000077 ! Nucleic acids -relationship: concerns EDAM:0002439 ! Secondary structure processing (RNA) -relationship: concerns EDAM:0002440 ! Tertiary structure processing (RNA) +def: "The study of RNA." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM: EDAM:0000653 ! RNA [Term] id: EDAM:0000100 name: Nucleic acid restriction namespace: topic -def: "Study concerning restriction enzymes and their cleavage sites." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000096 ! Nucleic acid sequence analysis -is_a: EDAM:0000132 ! Enzymes -relationship: concerns EDAM:0000280 ! Restriction enzyme annotation retrieval -relationship: concerns EDAM:0000365 ! Nucleic acid sequence restriction digest -relationship: concerns EDAM:0000370 ! Restriction site creation -relationship: concerns EDAM:0000431 ! Restriction site recognition - - - - - - -! -! Topic<-Nucleic acids<-Nucleic acid physicochemistry -! +def: "The study of restriction enzymes and their cleavage sites." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000640 ! Nucleic acid sequences +is_a: EDAM:0000821 ! Enzymes [Term] id: EDAM:0000104 name: Nucleic acid denaturation namespace: topic -def: "Study concerning DNA or DNA/RNA denaturation (melting) including thermal and conformational properties." [EDAM:EBI "EMBRACE definition"] +def: "The study of DNA or DNA/RNA denaturation (melting) including thermal and conformational properties." [EDAM:EBI "EMBRACE definition"] +subset: topic synonym: "DNA melting" EXACT [] is_a: EDAM:0000094 ! Nucleic acid physicochemistry -relationship: concerns EDAM:0000455 ! Nucleic acid melting temperature calculation -relationship: concerns EDAM:0000456 ! Nucleic acid melting profile plotting - - - -! -! Topic<-Nucleic acids<-Nucleic acid features -! [Term] id: EDAM:0000105 name: Nucleic acid sequence features namespace: topic -def: "Study positional features in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] +def: "The study of positional features in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] +subset: topic is_obsolete: true -consider: EDAM:0000095 ! Nucleic acid features - +consider: EDAM:0000747 ! Nucleic acid functional sites [Term] id: EDAM:0000106 name: Nucleic acid structural features namespace: topic -def: "Study positional features in nucleic acid structural features." [EDAM:EBI "EMBRACE definition"] +def: "The study of positional features in nucleic acid structures." [EDAM:EBI "EMBRACE definition"] +subset: topic is_obsolete: true -consider: EDAM:0000097 ! Nucleic acid structure analysis -! is_a: EDAM:0000095 ! Nucleic acid features -! is_a: EDAM:0000170 ! Structural features and motifs -! is_a: EDAM:0000097 ! Nucleic acid structure analysis -! relationship: concerns EDAM:0000008 ! Undefined - +consider: EDAM:0000097 ! Nucleic acid structure -! -! Topic<-Nucleic acids<-Nucleic acid sequence analysis -! [Term] id: EDAM:0000107 name: Codon usage namespace: topic -def: "Study codon usage in nucleotide sequence(s)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000096 ! Nucleic acid sequence analysis -relationship: concerns EDAM:0002493 ! Codon usage data processing - - -[Term] -id: EDAM:0000108 -name: Transcription and translation -namespace: topic -def: "Study or handle the transcription and translation of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000096 ! Nucleic acid sequence analysis -is_a: EDAM:0000197 ! Gene expression -relationship: concerns EDAM:0000371 ! DNA translation -relationship: concerns EDAM:0000372 ! DNA transcription -relationship: concerns EDAM:0000439 ! Translation initiation site prediction -relationship: concerns EDAM:0002510 ! DNA back-translation - - +def: "The study of codon usage in nucleotide sequence(s)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000640 ! Nucleic acid sequences [Term] id: EDAM:0000109 name: Gene finding namespace: topic -def: "Identify, predict, model or analyse genes or gene structure (promoters, coding regions, splice sites, etc) in DNA sequences." [EDAM:EBI "EMBRACE definition"] -comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. +def: "Study that aims to identify, predict, model or analyse genes or gene structure in DNA sequences." [EDAM:EBI "EMBRACE definition"] +comment: This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. +subset: topic synonym: "Gene prediction" EXACT [] xref: BioCatalogue:Gene Prediction -is_a: EDAM:0000096 ! Nucleic acid sequence analysis -relationship: concerns EDAM:0000287 ! Base position variability plotting -relationship: concerns EDAM:0002454 ! Gene and gene component prediction -relationship: concerns EDAM:0000521 ! PCR primer design (based on gene structure) -relationship: concerns EDAM:0000579 ! Operon rendering - - - - -! -! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Codon usage -! - -! -! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Transcription and translation -! - +is_a: EDAM:0002816 ! Genes -! -! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Gene finding -! [Term] id: EDAM:0000110 -name: Transcription regulation +name: Transcription namespace: topic -def: "The study of transcription regulation including transcription factors and regulatory motifs, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"] -comment: This includes promoters, enhancers, silencers and boundary elements / insulators. +def: "The study of the transcription of DNA into mRNA and transcription regulation including transcription factors and regulatory motifs, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"] +comment: This includes promoters, enhancers, silencers and boundary elements / insulators. +subset: topic xref: BioCatalogue:Transcription Factors -is_a: EDAM:0000197 ! Gene expression -is_a: EDAM:0000109 ! Gene finding -relationship: concerns EDAM:0000241 ! Transcription regulatory sequence analysis +is_a: EDAM:0000197 ! Gene expression and regulation - - -! -! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Gene finding<-Transcription regulation -! +[Term] +id: EDAM:0000108 +name: Translation +namespace: topic +def: "The study of the translation of mRNA into protein." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000197 ! Gene expression and regulation [Term] id: EDAM:0000111 name: Promoters namespace: topic -def: "Study promoters in DNA sequences." [EDAM:EBI "EMBRACE definition"] +def: "The study of promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene)." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Promoter Prediction -is_a: EDAM:0000110 ! Transcription regulation -relationship: concerns EDAM:0000440 ! Promoter prediction - +is_a: EDAM:0000110 ! Transcription - - - - - - - -! -! Topic<-Nucleic acids<-Nucleic acid structure analysis -! [Term] id: EDAM:0000112 name: Nucleic acid folding namespace: topic -def: "Study the folding of nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000097 ! Nucleic acid structure analysis -relationship: concerns EDAM:0000279 ! Nucleic acid folding analysis - - - -! -! Topic<-Nucleic acids<-DNA -! - -! -! Topic<-Nucleic acids<-RNA -! +def: "The study of the folding (in 3D space) of nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0000113 name: Functional RNA namespace: topic -def: "Study functional or non-coding RNA." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000099 ! RNA -relationship: concerns EDAM:0000443 ! Transcription regulatory element prediction (trans) +def: "The study of functional or non-coding RNA." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000659 ! Functional RNA [Term] id: EDAM:0000114 name: RNA splicing namespace: topic -def: "Study concerning RNA splicing; splice sites, splicing alternatives and so on." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000099 ! RNA -is_a: EDAM:0000197 ! Gene expression -is_a: EDAM:0000096 ! Nucleic acid sequence analysis -relationship: concerns EDAM:0000264 ! Splice transcript prediction -relationship: concerns EDAM:0000433 ! Splice site prediction -relationship: concerns EDAM:0000446 ! Exonic splicing enhancer prediction -relationship: concerns EDAM:0002499 ! Splicing modelling - - - -! -! Topic<-Nucleic acids<-RNA<-Functional RNA -! +def: "The study of RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [EDAM:EBI "EMBRACE definition"] +comment: This includes splice sites, splicing patterns and alternatives, etc. +subset: topic +is_a: EDAM:0000653 ! RNA +is_a: EDAM:0000197 ! Gene expression and regulation +is_a: EDAM:0000630 ! Gene structure [Term] id: EDAM:0000115 name: tRNA namespace: topic -def: "Study of transfer RNA (tRNA)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000113 ! Functional RNA -relationship: concerns EDAM:0000464 ! tRNA gene prediction +def: "The study of transfer RNA (tRNA)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000663 ! tRNA [Term] id: EDAM:0000116 name: rRNA namespace: topic -def: "Study of ribosomal RNA (rRNA)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000113 ! Functional RNA -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of ribosomal RNA (rRNA)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000660 ! rRNA [Term] id: EDAM:0000117 name: microRNA namespace: topic -def: "Study of microRNA (miRNA)." [EDAM:EBI "EMBRACE definition"] +def: "The study of microRNA (miRNA)." [EDAM:EBI "EMBRACE definition"] comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. -is_a: EDAM:0000113 ! Functional RNA -relationship: concerns EDAM:0000463 ! microRNA detection +subset: topic +is_obsolete: true +consider: EDAM:0000661 ! miRNA [Term] id: EDAM:0000118 name: siRNA namespace: topic -def: "Study of small interfering (silencing) RNA (siRNA)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000113 ! Functional RNA -relationship: concerns EDAM:0000465 ! siRNA assay design -relationship: concerns EDAM:0002008 ! siRNA duplex prediction +def: "The study of small interfering (silencing) RNA (siRNA)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000662 ! siRNA [Term] id: EDAM:0000119 name: piRNA namespace: topic -def: "Study of piwi-interacting RNA (piRNA)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000113 ! Functional RNA -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of piwi-interacting RNA (piRNA)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000659 ! Functional RNA sequence [Term] id: EDAM:0000120 name: snoRNA namespace: topic -def: "Study of small nucleolar RNA (snoRNAs)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000113 ! Functional RNA -! relationship: concerns EDAM:0000008 ! Undefined - - - -! -! Topic<-Nucleic acids<-Nucleic acid restriction -! - - - - - - - - - - -! -! Topic<-Proteins -! +def: "The study of small nucleolar RNA (snoRNAs)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000665 ! snoRNA [Term] id: EDAM:0000123 name: Protein physicochemistry namespace: topic -def: "Study the physicochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000250 ! Physicochemical property data processing (protein) -relationship: concerns EDAM:0000355 ! Sequence database search (by molecular weight) -relationship: concerns EDAM:0000356 ! Sequence database search (by isoelectric point) -relationship: concerns EDAM:0000243 ! Protein structural property calculation +def: "The study of the physical and biochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000586 ! Proteins [Term] id: EDAM:0000124 name: Protein features namespace: topic -def: "Study the positional features of protein sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000160 ! Sequence features -is_a: EDAM:0000125 ! Protein sequence analysis -relationship: concerns EDAM:0000414 ! Sequence feature detection (protein) - -[Term] -id: EDAM:0000125 -name: Protein sequence analysis -namespace: topic -def: "Handle or analyse protein sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000078 ! Proteins -is_a: EDAM:0000080 ! Sequence analysis -xref: BioCatalogue:Protein Sequence Analysis -relationship: concerns EDAM:0002479 ! Sequence analysis (protein) -relationship: concerns EDAM:0002514 ! Sequence generation (protein) - -[Term] -id: EDAM:0000126 -name: Protein structure analysis -namespace: topic -def: "Handle or analyse protein structural data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000078 ! Proteins -is_a: EDAM:0000081 ! Structure analysis -relationship: concerns EDAM:0000243 ! Protein structural property calculation +def: "The study of the positional features of protein sequences." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000748 ! Protein functional sites [Term] id: EDAM:0001775 name: Protein function namespace: topic -def: "Study protein function." [EDAM:EBI "EMBRACE definition"] +def: "The study of protein function." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Function Prediction -is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0002414 ! Protein function data processing +is_a: EDAM:0000586 ! Proteins [Term] id: EDAM:0000127 name: Protein domains namespace: topic -def: "Study protein structural domains." [EDAM:EBI "EMBRACE definition"] -xref: BioCatalogue:Domains -is_a: EDAM:0002125 ! Protein tertiary structure analysis -relationship: concerns EDAM:0000246 ! Protein domain recognition - +def: "The study of protein structural domains." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000736 ! Protein domains [Term] id: EDAM:0000128 name: Protein interactions namespace: topic -def: "Study protein-protein, protein-DNA/RNA and protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] +def: "The study of protein-protein, protein-DNA/RNA and protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Protein Interaction -is_a: EDAM:0000078 ! Proteins -is_a: EDAM:0000085 ! Functional genomics -relationship: concerns EDAM:0002405 ! Protein interaction data processing +is_a: EDAM:0000586 ! Proteins [Term] id: EDAM:0000129 name: Protein classification namespace: topic -def: "Study concerning the classification of proteins (from sequence or structural data)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000340 ! Protein secondary database search -relationship: concerns EDAM:0002470 ! Protein family annotation retrieval +def: "The study of the classification of proteins (from sequence or structural data)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000595 ! Protein classification [Term] id: EDAM:0000130 name: Protein folding, stability and design namespace: topic -def: "The study of protein folding and protein sequence-structure-function relationships, for example the effect of mutation and the implications for protein design." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000331 ! Protein mutation modelling -relationship: concerns EDAM:0002415 ! Protein folding analysis +def: "The study of protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation and the implications for protein design." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000586 ! Proteins [Term] id: EDAM:0000131 name: Transmembrane proteins namespace: topic -def: "Study transmembrane proteins / regions." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000270 ! Transmembrane protein data processing +def: "The study of a protein or region of a protein that spans a membrane." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000820 ! Membrane protein [Term] id: EDAM:0002232 name: Lipoproteins namespace: topic -def: "Study lipoproteins." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000078 ! Proteins -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of lipoproteins (protein-lipid assemblies)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000635 ! Specific protein [Term] id: EDAM:0000132 name: Enzymes namespace: topic -def: "Study enzymes and the kinetics of enzyme-catalysed reactions." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000334 ! Enzyme kinetics calculation - - - - - - +def: "The study of proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000821 ! Enzymes -! -! Topic<-Proteins<-Protein physicochemistry -! [Term] id: EDAM:0000137 name: Protein hydropathy namespace: topic -def: "Study concerning the hydrophobic, hydrophilic and charge properties of a protein." [EDAM:EBI "EMBRACE definition"] +def: "The study of the hydrophobic, hydrophilic and charge properties of a protein." [EDAM:EBI "EMBRACE definition"] +subset: topic is_a: EDAM:0000123 ! Protein physicochemistry -relationship: concerns EDAM:0002574 ! Protein hydropathy calculation -relationship: concerns EDAM:0000384 ! Protein solvent accessibility calculation -relationship: concerns EDAM:0000400 ! Protein pH-dependent property calculation - -! -! Topic<-Proteins<-Protein features -! [Term] id: EDAM:0000138 name: Protein sequence features namespace: topic def: "Predict, identify or analyse features in protein sequences." [EDAM:EBI "EMBRACE definition"] +subset: topic is_obsolete: true -consider: EDAM:0000124 ! Protein features - - - - +consider: EDAM:0000748 ! Protein functional sites [Term] id: EDAM:0000139 name: Protein structural features namespace: topic def: "Predict, identify or analyse protein structural features." [EDAM:EBI "EMBRACE definition"] +subset: topic is_obsolete: true consider: EDAM:0000166 ! Protein structural motifs - - -! -! Topic<-Proteins<-Protein sequence analysis -! [Term] id: EDAM:0000140 -name: Protein targeting -namespace: topic -def: "Study concerning protein targeting (signal peptides) and protein subcellular localization or export." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000125 ! Protein sequence analysis -relationship: concerns EDAM:0000418 ! Protein signal peptide detection -relationship: concerns EDAM:0002489 ! Protein subcellular localization prediction - -[Term] -id: EDAM:0000141 -name: Proteolysis and peptide mass +name: Protein targeting and localization namespace: topic -def: "Study concerning proteolytic or mass calculations on a protein." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000125 ! Protein sequence analysis -is_a: EDAM:0000134 ! Mass spectrometry -relationship: concerns EDAM:0000355 ! Sequence database search (by molecular weight) -relationship: concerns EDAM:0000366 ! Protein sequence cleavage -relationship: concerns EDAM:0000398 ! Protein molecular weight calculation -relationship: concerns EDAM:0000422 ! Protein cleavage site prediction +def: "The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000586 ! Proteins - -[Term] -id: EDAM:0000142 -name: Protein post-translation modification -namespace: topic -def: "Study of protein post-translation modification." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000125 ! Protein sequence analysis -relationship: concerns EDAM:0000417 ! Protein post-translation modification prediction - - -! -! Topic<-Proteins<-Protein structure analysis -! [Term] id: EDAM:0002124 name: Protein secondary structure analysis namespace: topic def: "Handle and analyse protein secondary structure." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000126 ! Protein structure analysis -relationship: concerns EDAM:0002444 ! Secondary structure processing (protein) - -[Term] -id: EDAM:0002125 -name: Protein tertiary structure analysis -namespace: topic -def: "Handle or analyse protein tertiary structures." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000126 ! Protein structure analysis -relationship: concerns EDAM:0002459 ! Tertiary structure processing (protein) - +subset: topic +is_obsolete: true +consider: EDAM:0000694 ! Protein secondary structure [Term] id: EDAM:0000143 name: Protein structure comparison namespace: topic def: "Study concerning the comparison of two or more protein structures." [EDAM:EBI "EMBRACE definition"] -comment: Use this term for methods that are exclusively for protein structure. +comment: Use this term for methods that are exclusively for protein structure. +subset: topic is_obsolete: true -consider: EDAM:0002125 ! Protein tertiary structure analysis +consider: EDAM:0000698 ! Protein tertiary structure consider: EDAM:0001770 ! Structure comparison - [Term] id: EDAM:0002280 name: Nucleic acid structure comparison namespace: topic -def: "Study concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [EDAM:EBI "EMBRACE definition"] +def: "The study of the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that are exclusively for nucleic acid structures. +subset: topic is_obsolete: true -consider: EDAM:0000097 ! Nucleic acid structure analysis +consider: EDAM:0000097 ! Nucleic acid structure consider: EDAM:0001770 ! Structure comparison - [Term] id: EDAM:0000144 name: Protein residue interactions namespace: topic -def: "Study inter-atomic or inter-residue interactions in protein structures." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0002124 ! Protein secondary structure analysis -! relationship: concerns EDAM:0000008 ! Undefined -relationship: concerns EDAM:0000248 ! Residue interaction calculation -relationship: concerns EDAM:0001850 ! Protein cysteine and disulfide bond assignment -relationship: concerns EDAM:0000272 ! Prediction of protein residue distances, contacts and interactions - +def: "The study of inter-atomic or inter-residue interactions in protein (3D) structures." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000694 ! Protein secondary structure [Term] id: EDAM:0000145 -name: Protein flexibility and motion +name: Molecular flexibility and motion namespace: topic -def: "Study flexibility and motion in protein structure." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0002125 ! Protein tertiary structure analysis +def: "The study of flexibility and motion in protein and other molecular structures." [EDAM:EBI "EMBRACE definition"] +subset: topic is_a: EDAM:0000176 ! Molecular dynamics -relationship: concerns EDAM:0000244 ! Protein flexibility and motion analysis [Term] id: EDAM:0000146 name: Protein surfaces namespace: topic -def: "Study the surface of a protein structure, including biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"] -comment: This includes the analysis of shape, hydropathy, electrostatic patches and so on. -is_a: EDAM:0002125 ! Protein tertiary structure analysis -relationship: concerns EDAM:0000387 ! Protein surface and interior calculation - - -! -! Topic<-Proteins<-Protein function -! - +def: "The study of the surface of a protein structure, including biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"] +comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. +subset: topic +is_a: EDAM:0000698 ! Protein tertiary structure [Term] id: EDAM:0002276 name: Protein function prediction namespace: topic -def: "Predict general functional properties of a protein." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the prediction of functional properties of a protein." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Function Prediction is_a: EDAM:0001775 ! Protein function -relationship: concerns EDAM:0001777 ! Protein function prediction - -! -! Topic<-Proteins<-Protein domains -! - - - -! -! Topic<-Proteins<-Protein interactions -! [Term] id: EDAM:0000147 name: Protein-protein interactions namespace: topic -def: "Study protein-protein interactions." [EDAM:EBI "EMBRACE definition"] +def: "The study of protein-protein interactions, protein complexes, protein functional coupling etc." [EDAM:EBI "EMBRACE definition"] +subset: topic is_a: EDAM:0000128 ! Protein interactions -relationship: concerns EDAM:0000273 ! Protein-protein interaction experimental data analysis -relationship: concerns EDAM:0002464 ! Protein-protein interaction prediction -relationship: concerns EDAM:0002445 ! Protein-protein interaction network processing - - [Term] id: EDAM:0000148 name: Protein-ligand interactions namespace: topic -def: "Study protein-ligand (small molecule) interactions." [EDAM:EBI "EMBRACE definition"] +def: "The study of protein-ligand (small molecule) interactions." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Ligand Interaction is_a: EDAM:0000128 ! Protein interactions -relationship: concerns EDAM:0002575 ! Ligand-binding and active site prediction -relationship: concerns EDAM:0000482 ! Protein-ligand docking [Term] id: EDAM:0000149 name: Protein-nucleic acid interactions namespace: topic -def: "Study protein-DNA/RNA interactions." [EDAM:EBI "EMBRACE definition"] +def: "The study of protein-DNA/RNA interactions." [EDAM:EBI "EMBRACE definition"] +subset: topic is_a: EDAM:0000128 ! Protein interactions -relationship: concerns EDAM:0000389 ! Protein-nucleic acid binding site analysis - - - - - -! -! Topic<-Proteins<-Protein classification -! - - -! -! Topic<-Proteins<-Protein folding, stability and design -! - [Term] id: EDAM:0000150 name: Protein rational design namespace: topic -def: "Design proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [EDAM:EBI "EMBRACE definition"] +def: "The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [EDAM:EBI "EMBRACE definition"] +subset: topic is_a: EDAM:0000130 ! Protein folding, stability and design -relationship: concerns EDAM:0000333 ! Protein-nucleic acid binding site design -relationship: concerns EDAM:0000559 ! Peptide immunogen design -relationship: concerns EDAM:0000560 ! DNA vaccine design - - - - -! -! Topic<-Proteins<-Transmembrane proteins -! [Term] id: EDAM:0000151 name: G protein-coupled receptors (GPCR) namespace: topic -def: "Study G-protein coupled receptors (GPCRs)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000131 ! Transmembrane proteins -relationship: concerns EDAM:0000473 ! GPCR analysis - +def: "The study of G-protein coupled receptors (GPCRs)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_obsolete: true +consider: EDAM:0000820 ! Membrane protein [Term] id: EDAM:0002278 name: Transmembrane protein prediction namespace: topic def: "Predict transmembrane domains and topology in protein sequences." [EDAM:EBI "EMBRACE definition"] +subset: topic is_obsolete: true -consider: EDAM:0000131 ! Transmembrane proteins -consider: EDAM:0000178 ! Protein secondary structure prediction - - - - -! -! Topic<-Proteins<-Enzymes -! - +consider: EDAM:0000820 ! Membrane proteins +consider: EDAM:0000178 ! Protein secondary structure prediction - -! -! Topic<-Metabolites -! [Term] id: EDAM:0000152 +alt_id: EDAM:0000695 name: Carbohydrates namespace: topic -def: "Study carbohydrates." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000079 ! Metabolites -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of carbohydrates, typically including structural information." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000081 ! Structure [Term] id: EDAM:0000153 +alt_id: EDAM:0002624 name: Lipids namespace: topic -def: "Study lipids." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000079 ! Metabolites -! relationship: concerns EDAM:0000008 ! Undefined +def: "The study of lipids and their structures." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000081 ! Structure [Term] id: EDAM:0000154 +alt_id: EDAM:0000696 name: Small molecules namespace: topic -def: "Study small molecules of biological significance." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000079 ! Metabolites -relationship: concerns EDAM:0002123 ! Physicochemical property data processing (small molecule) - - - - - - -! -! Topic<-Sequence analysis -! +def: "The study of small molecules of biological significance." [EDAM:EBI "EMBRACE definition"] +comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. +subset: topic +is_a: EDAM:0000081 ! Structure [Term] id: EDAM:0000155 name: Sequence search and retrieval namespace: topic def: "Search or query a database and retrieve molecular sequences and associated data." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Sequence Retrieval is_obsolete: true -consider: EDAM:0000090 ! Search and retrieval -! is_a: EDAM:0000080 ! Sequence analysis - +consider: EDAM:0000090 ! Data retrieval [Term] id: EDAM:0000156 name: Sequence editing namespace: topic def: "Create, edit, change or convert a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] +subset: topic is_obsolete: true -consider: EDAM:0000080 ! Sequence analysis -consider: EDAM:0000091 ! Database and file management - +consider: EDAM:0000080 ! Sequence +consider: EDAM:0000091 ! Data handling [Term] id: EDAM:0000157 name: Sequence composition namespace: topic -def: "Analyse the basic composition of a molecular sequence, for example character or word frequency, ambiguity, complexity or repeats." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0000236 ! Sequence composition calculation -relationship: concerns EDAM:0000235 ! Sequence ambiguity calculation -relationship: concerns EDAM:0000348 ! Sequence database search (by amino acid composition) -relationship: concerns EDAM:0000430 ! CpG island and isochores detection - +def: "Analyse the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000080 ! Sequence [Term] id: EDAM:0000158 name: Sequence motifs namespace: topic -def: "Study concerning conserved patterns (motifs) in molecular sequences." [EDAM:EBI "EMBRACE definition"] +def: "The study of conserved patterns (motifs) in molecular sequences." [EDAM:EBI "EMBRACE definition"] +subset: topic synonym: "Motifs" EXACT [] -is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0002404 ! Sequence motif processing -relationship: concerns EDAM:0000341 ! Motif database search -relationship: concerns EDAM:0000347 ! Sequence database search (by motif or pattern) - - - +is_a: EDAM:0000080 ! Sequence [Term] id: EDAM:0000188 name: Sequence profiles and HMMs namespace: topic -def: "Study concerning sequence profiles (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] +def: "The study of sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. -is_a: EDAM:0000080 ! Sequence analysis +subset: topic +is_a: EDAM:0000080 ! Sequence is_a: EDAM:0000182 ! Sequence alignment -relationship: concerns EDAM:0002413 ! Sequence profile processing - [Term] id: EDAM:0000159 @@ -2321,108 +1551,56 @@ name: Sequence comparison namespace: topic def: "Study concerning the comparison of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. -is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0000338 ! Sequence database search -relationship: concerns EDAM:0000359 ! Structure database search (by sequence) -relationship: concerns EDAM:0002451 ! Sequence comparison +subset: topic +is_a: EDAM:0000080 ! Sequence [Term] id: EDAM:0000160 name: Sequence features namespace: topic -def: "Study the positional features of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0002453 ! Sequence feature table processing -relationship: concerns EDAM:0000253 ! Sequence feature detection - -! -! Topic<-Sequence analysis<-Sequence search and retrieval -! - - -! -! Topic<-Sequence analysis<-Sequence editing -! - - - -! -! Topic<-Sequence analysis<-Sequence composition -! -[Term] -id: EDAM:0002262 -name: Repeat sequences -namespace: topic -def: "Study the repetitive nature of molecular sequences." [EDAM:EBI "EMBRACE definition"] -xref: BioCatalogue:Repeats -is_a: EDAM:0000157 ! Sequence composition -relationship: concerns EDAM:0000237 ! Repeat sequence analysis - -[Term] -id: EDAM:0002263 -name: Sequence complexity -namespace: topic -def: "Study the complexity of molecular sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000157 ! Sequence composition -relationship: concerns EDAM:0000234 ! Sequence complexity calculation +def: "The study of the positional features of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] +subset: topic +is_a: EDAM:0000080 ! Sequence - - -! -! Topic<-Sequence analysis<-Sequence motifs -! [Term] id: EDAM:0000161 name: Protein sequence motifs namespace: topic -def: "Study concerning conserved patterns (motifs) in protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "The study of conserved patterns (motifs) in protein sequences." [EDAM:EBI "EMBRACE definition"] +subset: topic xref: BioCatalogue:Motifs -is_a: EDAM:0000158 ! Sequence motifs -relationship: concerns EDAM:0000382 ! Sequence motif recognition (protein) - +is_obsolete: true +consider: EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0000162 name: Nucleic acid sequence motifs namespace: topic -def: "Study concerning conserved patterns (motifs) in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000158 ! Sequence motifs -relationship: concerns EDAM:0000381 ! Sequence motif recognition (nucleic acid) - - -! -! Topic<-Sequence analysis