From 85a3986cdce72f6165e761c838ef1ca2d4659178 Mon Sep 17 00:00:00 2001 From: matuskalas Date: Tue, 1 Nov 2016 03:36:54 +0100 Subject: [PATCH] History of releases: Added EDAM.obo, beta05 --- releases/EDAM.obo | 28382 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 28382 insertions(+) create mode 100644 releases/EDAM.obo diff --git a/releases/EDAM.obo b/releases/EDAM.obo new file mode 100644 index 0000000..4d8b5fb --- /dev/null +++ b/releases/EDAM.obo @@ -0,0 +1,28382 @@ +format-version: 1.2 +date: 13:05:2010 14:26 +data-version: Beta05 +! Use for mapping to "global" id space(s) e.g.: +! idspace: EDAM urn:lsid:ebi.ac.uk:edam: "EDAM terms" +! idspace: EDAM http://purl.org/edam/ "EDAM terms" +! NEXT term number is 2028 +subsetdef: EDAM_EXTRA "EDAM extra terms" +! xref: WHATIF: CorrectedPDBasXML +! xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB +! xref: Moby:GI_Gene +! xref: Moby_namespace:iHOPorganism +! xref: SO:0000348 + + + +! +! EDAM relations +! +[Typedef] +id: concerns +name: concerns +def: "Defines that a term ('Topic') concerns (covers) another term ('Entity', 'Database', 'Ontology' or 'Operation')." [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 ('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 ('Entity', 'Database', 'Ontology' 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 reading (inputting) another term ('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 writing (outputting) another term ('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 ('Entity' or 'Data') as having a conceptual part ('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 ('Tool', 'Database' or 'Ontology')." [EDAM:EBI] +comment: is_source_of +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +inverse_of: is_source_of + + +[Typedef] +id: has_syntax +name: has_syntax +def: "Defines a term ('Data') has a data format specification ('Data syntax')." [EDAM:EBI] +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +inverse_of: is_attribute_of + +[Typedef] +id: is_attribute_of +name: is_attribute_of +def: "Defines that a term ('Data') is an attribute of another term ('Entity')." [EDAM:EBI] +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 ('Entity', 'Database', 'Ontology' 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 ('Entity', 'Database', 'Ontology' or '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 ('Entity' or 'Data') is a conceptual part of some other term ('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 ('Tool', 'Database' or 'Ontology') is a source of another term ('Data')." [EDAM:EBI] +comment: has_source +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +inverse_of: has_source + +[Typedef] +id: is_syntax_of +name: is_syntax_of +def: "Defines that a term ('Data syntax') is a data format specification for another term ('Data')." [EDAM:EBI] +is_anti_symmetric: true +is_cyclic: false +is_transitive: true +inverse_of: has_attribute + + + + +! +! Top-level +! +[Term] +id: EDAM:0000002 +name: 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_identifier EDAM:0000842 ! Identifier +! relationship: has_attribute EDAM:0000006 ! Data + +[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 ! Entity +! relationship: concerns EDAM:0000004 ! Operation +! relationship: concerns EDAM:0000581 ! Database +! relationship: concerns EDAM:0000582 ! Ontology + +[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: Data resource +def: "A data resource or archive including databases, databanks and ontologies." [EDAM:EBI "EMBRACE definition"] +is_obsolete: true +consider: EDAM:0000581 ! Database +consider: EDAM:0000582 ! Ontology + +[Term] +id: EDAM:0000581 +name: Database +namespace: database +def: "A category (of content) of a relational or object-oriented database or flat-file databank." [EDAM:EBI "EMBRACE definition"] +comment: Terms in this branch are for database categories; individual databases are not listed. +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0000006 ! Data +! relationship: has_identifier EDAM:0001048 ! Database identifier + +[Term] +id: EDAM:0000582 +name: Ontology +namespace: ontology +def: "An ontology of biological or bioinformatics terms and relations, a controlled vocabulary, structured glossary etc." [EDAM:EBI "EMBRACE definition"] +! relationship: is_concern_of EDAM:0000076 ! Undefined +! relationship: is_source_of EDAM:0000966 ! Ontology term +! relationship: is_source_of EDAM:0001730 ! Ontology relation +! relationship: has_identifier EDAM:0000842 ! Identifier + +[Term] +id: EDAM:0000006 +name: Data +namespace: data +def: "A semantic description of a data entity (datum) commonly used in bioinformatics." [EDAM:EBI "EMBRACE definition"] +! relationship: is_attribute_of EDAM:0000002 ! Entity +! relationship: is_input_of EDAM:0000004 ! Operation +! relationship: is_output_of EDAM:0000004 ! Operation +! relationship: has_source EDAM:0000581 ! Database +! relationship: has_identifier EDAM:0000842 ! Identifier + +[Term] +id: EDAM:0001915 +name: Data syntax +namespace: syntax +def: "A reference (typically a URL) of a data format specification." [EDAM:EBI "EMBRACE definition"] +relationship: is_syntax_of EDAM:0000006 ! Data + + + +[Term] +id: EDAM:0000007 +name: Tool +def: "A bioinformatics package or tool, e.g. a standalone application or web service." [EDAM:EBI "EMBRACE definition"] +is_obsolete: true +consider: EDAM:0000958 ! Tool metadata + + + +! +! Entity +! +[Term] +id: EDAM:0000008 +name: Undefined +namespace: entity +def: "Debugging." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000002 ! Entity +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + + +[Term] +id: EDAM:0000009 +name: Discrete entity +namespace: entity +def: "Any biological thing with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000002 ! Entity +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000006 ! Data + +[Term] +id: EDAM:0000010 +name: Entity feature +namespace: entity +def: "A physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000002 ! Entity +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000006 ! Data + +[Term] +id: EDAM:0000011 +name: Entity collection +namespace: entity +def: "A collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000002 ! Entity +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000006 ! Data + +[Term] +id: EDAM:0000012 +name: Phenomena +namespace: entity +def: "A physical, observable biological occurence or event." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000002 ! Entity +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000006 ! Data + + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000982 ! Molecule identifier +relationship: has_attribute EDAM:0000883 ! Tertiary structure + + + + + + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000983 ! Atom identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0000015 +name: Small molecule +namespace: entity +def: "Any small molecule." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000013 ! Molecular entity +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001086 ! Chemical compound identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000982 ! Molecule identifier +relationship: has_attribute EDAM:0002044 ! Sequence data + +[Term] +id: EDAM:0000017 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000982 ! Molecule identifier +relationship: has_attribute EDAM:0000841 ! Undefined + + + + + +! +! Entity<-Discrete entity<-Molecular entity<-Atom +! + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000982 ! Molecule identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000992 ! Ligand identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000993 ! Drug identifier +relationship: has_attribute EDAM:0000841 ! Undefined + + + +! +! 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 and one of (typically) 20 common R-groups (side-chain)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000018 ! Biomonomer +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000994 ! Amino acid identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0000022 +name: Nucleotide +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000995 ! Nucleotide identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000996 ! Monosaccharide identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +! +! Entity<-Discrete entity<-Molecular entity<-Small molecule<-Ligand +! + +! +! Entity<-Discrete entity<-Molecular entity<-Small molecule<-Drug +! + + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer +! +[Term] +id: EDAM:0000024 +name: Nucleic acid +namespace: entity +def: "An organic polymer of nucleotide monomers in an unbranched chain, bound together by covalent bonds." [EDAM:EBI "EMBRACE definition"] +synonym: "Polynucleotide chain" EXACT [] +synonym: "Polynucleotide" EXACT [] +xref: SO:0000348 +is_a: EDAM:0000016 ! Biopolymer +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0001207 ! Nucleotide sequence +relationship: has_attribute EDAM:0001459 ! Nucleic acid tertiary structure + +[Term] +id: EDAM:0000025 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000988 ! Polypeptide identifier +relationship: has_attribute EDAM:0001208 ! Protein sequence +relationship: has_attribute EDAM:0001460 ! Protein tertiary structure + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + + +! +! 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"] +synonym: "Polynucleotide chain" EXACT [] +is_a: EDAM:0000024 ! Nucleic acid +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0001207 ! Nucleotide sequence + +[Term] +id: EDAM:0000028 +name: DNA +namespace: entity +def: "A deoxyribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] +xref: SO:0000352 +is_a: EDAM:0000024 ! Nucleic acid +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0001212 ! DNA sequence +relationship: has_attribute EDAM:0001464 ! DNA tertiary structure + +[Term] +id: EDAM:0000029 +name: RNA +namespace: entity +def: "A ribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] +xref: SO:0000356 +is_a: EDAM:0000024 ! Nucleic acid +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0001213 ! RNA sequence +relationship: has_attribute EDAM:0001465 ! RNA tertiary structure + + + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-Oligonucleotide +! + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0002010 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0001212 ! DNA sequence +relationship: has_attribute EDAM:0001464 ! DNA tertiary structure + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element +! +[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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0000841 ! Undefined + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0000034 +name: Insertion sequence +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0000841 ! Undefined + + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element<-Plasmid +! + + + + + + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-RNA +! +[Term] +id: EDAM:0000035 +name: tRNA +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier +relationship: has_attribute EDAM:0001213 ! RNA sequence + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000982 ! Molecule identifier +relationship: has_attribute EDAM:0001208 ! Protein sequence + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000989 ! Protein identifier +relationship: has_attribute EDAM:0001460 ! Protein tertiary structure + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000989 ! Protein identifier +relationship: has_attribute EDAM:0001460 ! Protein tertiary structure + +[Term] +id: EDAM:0000039 +name: Enzyme +namespace: entity +def: "Enzyme." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000037 ! Protein +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001010 ! Enzyme identifier +relationship: has_attribute EDAM:0001460 ! Protein tertiary structure + +[Term] +id: EDAM:0000040 +name: Transmembrane protein +namespace: entity +def: "A transmembrane protein molecule." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000037 ! Protein +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000989 ! Protein identifier +relationship: has_attribute EDAM:0001460 ! Protein tertiary structure + +[Term] +id: EDAM:0000041 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000989 ! Protein identifier +relationship: has_attribute EDAM:0001460 ! Protein tertiary structure + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Uncomplexed protein +! + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001010 ! Enzyme identifier +relationship: has_attribute EDAM:0001460 ! Protein tertiary structure + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Transmembrane protein +! + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Transcription factor +! + + + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polysaccharide +! + + + + + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000982 ! Molecule identifier +relationship: has_attribute EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_identifier EDAM:0000989 ! Protein identifier +relationship: has_attribute EDAM:0001460 ! Protein tertiary structure + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + + +[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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + + +[Term] +id: EDAM:0000047 +name: Protein complex +namespace: entity +def: "A protein comprising two or more polypeptide chain subunits in a stable association." [EDAM:EBI "EMBRACE definition"] +is_obsolete: true +consider: EDAM:0000044 ! Protein-protein complex + + +! +! Entity<-Discrete entity<-Molecular entity<-Molecular complex<-RNA/DNA hybrid +! + +! +! Entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-protein complex +! + +! +! Entity<-Discrete entity<-Molecular entity<-Molecular complex<-Protein-ligand complex +! + +! +! 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"] +xref: SO:0000340 +is_a: EDAM:0000046 ! Protein-nucleic acid complex +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide +! + + + + + +! +! Entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polysaccharide +! + + + + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0001854 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + + + + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001025 ! Gene identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + + + +[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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0000054 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0000056 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +! +! Entity<-Entity feature<-Nucleic acid feature<-Codon +! + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001025 ! Gene identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +! +! Entity<-Entity feature<-Nucleic acid feature<-Operon +! + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0000059 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +! +! Entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element<-Gene-regulatory element +! + + + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001742 ! PDB residue number +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0001751 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0001468 ! Protein domain tertiary structure + + +! +! Entity<-Entity feature<-Protein feature<-Protein residue +! + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0001753 +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0001754 +name: Protein residue group (discontinuous) +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000841 ! Undefined +relationship: has_attribute EDAM:0000841 ! Undefined + + +! +! Entity<-Entity feature<-Protein feature<-Protein domain +! + + + + + + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000841 ! Undefined + + + + +! +! Entity<-Entity collection<-Genome +! + +! +! Entity<-Entity collection<-Proteome +! + +! +! Entity<-Entity collection<-Nucleosome +! + +! +! 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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001044 ! Kingdom name +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001870 ! Genus name +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001045 ! Species name +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +id: EDAM:0000072 +name: Strain +namespace: entity +def: "A strain or prokaryotic organisms." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000069 ! Taxonomic rank +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001046 ! Strain name +relationship: has_attribute EDAM:0000841 ! Undefined + + +! +! Entity<-Phenomena +! + +[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 ! Phenomena +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0001082 ! Biological pathway identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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 ! Phenomena +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000841 ! Undefined + +[Term] +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 ! Phenomena +relationship: is_concern_of EDAM:0000076 ! Undefined +relationship: has_identifier EDAM:0000842 ! Identifier +relationship: has_attribute EDAM:0000841 ! Undefined + + + + + + + +! +! 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:0000077 +name: Nucleic acid analysis +namespace: topic +def: "Nucleic acid data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000078 +name: Protein analysis +namespace: topic +def: "Protein data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000079 +name: Metabolite analysis +namespace: topic +def: "Metabolite data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000080 +name: Sequence analysis +namespace: topic +def: "Analyse molecular sequences." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000081 +name: Structure analysis +namespace: topic +def: "Analyse molecular structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000082 +name: Structure prediction +namespace: topic +def: "Predict molecular structure." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000083 +name: Alignment +namespace: topic +def: "Generation or analysis of alignments 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 + +[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. +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000085 +name: Functional genomics +namespace: topic +def: "Study gene or protein functions and their interactions." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[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 + +[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 + +[Term] +id: EDAM:0000088 +name: Literature and documentation +namespace: topic +def: "Study biomedical and informatic literature, bibliographic data and documentation." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000089 +name: Ontologies +namespace: topic +def: "Study biomedical ontologies, controlled vocabularies, glossaries etc." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000090 +name: Database search and retrieval +namespace: topic +def: "Search or query a biological database and retrieve entries or other information." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000091 +name: Database and file management +namespace: topic +def: "Manage a biological database or file, for example indexing, annotation, reformatting etc." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000092 +name: Visualisation and rendering +namespace: topic +def: "Render (display or print) molecular sequences, structures or other biomolecular data." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000003 ! Topic +relationship: concerns EDAM:0000008 ! Undefined + + + + + + + + + +! +! Topic<-Nucleic acid analysis +! +[Term] +id: EDAM:0000093 +name: Genomics +namespace: topic +def: "Study whole genomes of organisms." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000077 ! Nucleic acid analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000094 +name: Nucleic acid physicochemical properties +namespace: topic +def: "Determine, predict or analyse the physicochemical properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000077 ! Nucleic acid analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000095 +name: Nucleic acid features +namespace: topic +def: "Identify, predict or analyse features of nucleic acid sequences and structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000077 ! Nucleic acid analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000096 +name: Nucleic acid sequence analysis +namespace: topic +def: "Nucleic acid sequence data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000077 ! Nucleic acid analysis +is_a: EDAM:0000080 ! Sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000097 +name: Nucleic acid structure analysis +namespace: topic +def: "Nucleic acid structural data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000077 ! Nucleic acid analysis +is_a: EDAM:0000081 ! Structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000098 +name: DNA analysis +namespace: topic +def: "DNA data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000077 ! Nucleic acid analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000099 +name: RNA analysis +namespace: topic +def: "RNA data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000077 ! Nucleic acid analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000100 +name: Nucleic acid restriction +namespace: topic +def: "Data and analysis concerning restriction enzymes, for example, predict, analyse or process restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000077 ! Nucleic acid analysis +relationship: concerns EDAM:0000008 ! Undefined + + + +! +! Topic<-Nucleic acid analysis<-Genomics +! +[Term] +id: EDAM:0000101 +name: Comparative genomics +namespace: topic +def: "Compare the structure or function of multiple genomes." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000093 ! Genomics +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000102 +name: Sequencing +namespace: topic +def: "Determine complete nucleotide sequences from sequencing project data." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000093 ! Genomics +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000103 +name: Genetic mapping +namespace: topic +def: "Identify or map genetic markers in DNA sequences, for example to determine a genetic (linkage) map for a chromosome, or analyse known genetic maps." [EDAM:EBI "EMBRACE definition"] +synonym: "Genetic linkage" EXACT [] +synonym: "Linkage mapping" EXACT [] +is_a: EDAM:0000093 ! Genomics +relationship: concerns EDAM:0000008 ! Undefined + + + + + +! +! Topic<-Nucleic acid analysis<-Nucleic acid physicochemical properties +! + +[Term] +id: EDAM:0000104 +name: Nucleic acid denaturation +namespace: topic +def: "Analyse DNA or DNA/RNA denaturation (melting) including thermal and conformational properties." [EDAM:EBI "EMBRACE definition"] +synonym: "DNA melting" EXACT [] +is_a: EDAM:0000094 ! Nucleic acid physicochemical properties +relationship: concerns EDAM:0000008 ! Undefined + + + + +! +! Topic<-Nucleic acid analysis<-Nucleic acid features +! +[Term] +id: EDAM:0000105 +name: Nucleic acid sequence features +namespace: topic +def: "Identify, predict or analyse features in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000095 ! Nucleic acid features +is_a: EDAM:0000160 ! Sequence features +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000106 +name: Nucleic acid structural features +namespace: topic +def: "Identify, predict or analyse nucleic acid structural features." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000077 ! Nucleic acid analysis +is_a: EDAM:0000170 ! Structural features +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis +! +[Term] +id: EDAM:0000107 +name: Codon usage +namespace: topic +def: "Anaylse codon usage data in nucleotide sequence(s)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000096 ! Nucleic acid sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000108 +name: Transcription and translation +namespace: topic +def: "Handle transcription and translation of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +comment: For example, translate a nucleotide sequence or back translate a protein sequence, construct mRNA sequences from genomic sequences etc. +is_a: EDAM:0000096 ! Nucleic acid sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + +[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. +synonym: "Gene prediction" EXACT [] +is_a: EDAM:0000096 ! Nucleic acid sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + + + + +! +! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis<-Codon usage +! + +! +! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis<-Transcription and translation +! + + +! +! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis<-Gene finding +! +[Term] +id: EDAM:0000110 +name: Transcription regulatory sequence analysis +namespace: topic +def: "Identify, predict or analyse transcription regulatory motifs, patterns, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"] +comment: This includes promoters, enhancers, silencers and boundary elements / insulators. Transcription regulatory regions bind regulatory proteins such as transcription factors. +is_a: EDAM:0000109 ! Gene finding +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis<-Gene finding<-Transcription regulatory sequence analysis +! + +[Term] +id: EDAM:0000111 +name: Promoters +namespace: topic +def: "Analyse, compare, classify or model promoters in DNA sequences." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000110 ! Transcription regulatory sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + + + + + + + + + +! +! Topic<-Nucleic acid analysis<-Nucleic acid structure analysis +! +[Term] +id: EDAM:0000112 +name: Nucleic acid folding +namespace: topic +def: "Model, predict and analyse RNA/DNA folding." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000097 ! Nucleic acid structure analysis +relationship: concerns EDAM:0000008 ! Undefined + + + +! +! Topic<-Nucleic acid analysis<-DNA analysis +! + +! +! Topic<-Nucleic acid analysis<-RNA analysis +! + +[Term] +id: EDAM:0000113 +name: Functional RNA analysis +namespace: topic +def: "Analyse functional or non-coding RNA." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000099 ! RNA analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000114 +name: RNA splicing +namespace: topic +def: "Analyse RNA splicing, identify splice sites, calculate splicing alternatives etc." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000099 ! RNA analysis +is_a: EDAM:0000197 ! Gene expression +is_a: EDAM:0000096 ! Nucleic acid sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + + + +! +! Topic<-Nucleic acid analysis<-RNA analysis<-Functional RNA analysis +! + +[Term] +id: EDAM:0000115 +name: tRNA analysis +namespace: topic +def: "Transfer RNA (tRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000113 ! Functional RNA analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000116 +name: rRNA analysis +namespace: topic +def: "Ribosomal RNA (rRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000113 ! Functional RNA analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000117 +name: microRNA analysis +namespace: topic +def: "MicroRNA (miRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. +is_a: EDAM:0000113 ! Functional RNA analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000118 +name: siRNA analysis +namespace: topic +def: "Small interfering (silencing) RNA (siRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000113 ! Functional RNA analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000119 +name: piRNA analysis +namespace: topic +def: "Piwi-interacting RNA (piRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000113 ! Functional RNA analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000120 +name: snoRNA analysis +namespace: topic +def: "Small nucleolar RNA (snoRNAs) data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000113 ! Functional RNA analysis +relationship: concerns EDAM:0000008 ! Undefined + + + +! +! Topic<-Nucleic acid analysis<-Nucleic acid restriction +! + + + + + + + + + + +! +! Topic<-Protein analysis +! +[Term] +id: EDAM:0000121 +name: Proteomics +namespace: topic +def: "Study 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). +synonym: "Protein expression" EXACT [] +is_a: EDAM:0000078 ! Protein analysis +is_a: EDAM:0000085 ! Functional genomics +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000122 +name: Structural genomics +namespace: topic +def: "Determine the three dimensional structure for all 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). +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + + +[Term] +id: EDAM:0000123 +name: Protein physicochemical properties +namespace: topic +def: "Determine, predict or analyse the physicochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000124 +name: Protein features +namespace: topic +def: "Predict, identify or analyse features of protein sequences and structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000125 +name: Protein sequence analysis +namespace: topic +def: "Protein sequence data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +is_a: EDAM:0000080 ! Sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000126 +name: Protein structure analysis +namespace: topic +def: "Protein structural data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +is_a: EDAM:0000081 ! Structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0001775 +name: Protein function analysis +namespace: topic +def: "Protein functional data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000127 +name: Protein domains +namespace: topic +def: "Protein structural domain data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000128 +name: Protein interactions +namespace: topic +def: "Analyse protein-protein, protein-DNA/RNA and protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000129 +name: Protein classification +namespace: topic +def: "Protein sequence or structure classification." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000130 +name: Protein folding, stability and design +namespace: topic +def: "Analyse or predict sequence-structure-function relationships, protein folding, the effect of mutation, protein design etc." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000131 +name: Transmembrane protein analysis +namespace: topic +def: "Data and analysis on transmembrane proteins / regions." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000132 +name: Enzymes +namespace: topic +def: "Enzymes and the kinetics of enzyme-catalysed reactions." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +! +! Topic<-Protein analysis<-Proteomics +! +[Term] +id: EDAM:0000133 +name: Two-dimensional gel electrophoresis +namespace: topic +def: "Handle two-dimensional gel electrophoresis data." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000121 ! Proteomics +relationship: concerns EDAM:0000008 ! Undefined + + +[Term] +id: EDAM:0000134 +name: Mass spectrometry +namespace: topic +def: "Handle mass spectrometry and related data." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000121 ! Proteomics +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000135 +name: Protein microarrays +namespace: topic +def: "Protein microarray data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000121 ! Proteomics +is_a: EDAM:0000200 ! Microarrays +is_a: EDAM:0000197 ! Gene expression +relationship: concerns EDAM:0000008 ! Undefined + +! +! Topic<-Protein analysis<-Structural genomics +! +[Term] +id: EDAM:0000136 +name: X-ray crystallographic data analysis +namespace: topic +def: "Assign, validate or refine a protein structure from X-ray crystallography data." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000122 ! Structural genomics +is_a: EDAM:0000126 ! Protein structure analysis +relationship: concerns EDAM:0000008 ! Undefined + + + +! +! Topic<-Protein analysis<-Protein physicochemical properties +! +[Term] +id: EDAM:0000137 +name: Protein hydropathy +namespace: topic +def: "Analyse the hydrophobic, hydrophilic and charge properties of a protein sequence or structure." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000123 ! Protein physicochemical properties +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Protein analysis<-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"] +is_a: EDAM:0000124 ! Protein features +is_a: EDAM:0000160 ! Sequence features +is_a: EDAM:0000125 ! Protein sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000139 +name: Protein structural features +namespace: topic +def: "Predict, identify or analyse protein structural features." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000124 ! Protein features +is_a: EDAM:0000170 ! Structural features +is_a: EDAM:0000126 ! Protein structure analysis +relationship: concerns EDAM:0000008 ! Undefined + + + +! +! Topic<-Protein analysis<-Protein sequence analysis +! +[Term] +id: EDAM:0000140 +name: Protein targeting +namespace: topic +def: "Predict or analyse protein targeting (signal peptides) and protein subcellular localization or export." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000125 ! Protein sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000141 +name: Proteolysis and peptide mass +namespace: topic +def: "Proteolytic or mass calculations on a protein sequence and related analyses." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000125 ! Protein sequence analysis +is_a: EDAM:0000134 ! Mass spectrometry +relationship: concerns EDAM:0000008 ! Undefined + + +[Term] +id: EDAM:0000142 +name: Protein post-translation modification +namespace: topic +def: "Data and analysis concerning protein post-translation modification." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000125 ! Protein sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Protein analysis<-Protein structure analysis +! +[Term] +id: EDAM:0002124 +name: Protein secondary structure analysis +namespace: topic +def: "Protein secondary structural data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +is_a: EDAM:0000081 ! Structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0002125 +name: Protein tertiary structure analysis +namespace: topic +def: "Protein tertiary structural data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000078 ! Protein analysis +is_a: EDAM:0000081 ! Structure analysis +relationship: concerns EDAM:0000008 ! Undefined + + +[Term] +id: EDAM:0000143 +name: Protein structure comparison +namespace: topic +def: "Compare two or more protein structures." [EDAM:EBI "EMBRACE definition"] +comment: For example to identify structural neighbors, find structural similarities or define a structural core. +is_a: EDAM:0000126 ! Protein structure analysis +is_a: EDAM:0001770 ! Structure comparison +relationship: concerns EDAM:0000008 ! Undefined + + +[Term] +id: EDAM:0000144 +name: Protein residue interactions +namespace: topic +def: "Data and analysis on inter-atomic or inter-residue interactions in protein structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000126 ! Protein structure analysis +relationship: concerns EDAM:0000008 ! Undefined + + +[Term] +id: EDAM:0000145 +name: Protein flexibility and motion +namespace: topic +def: "Study flexibility and motion in protein structure." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000126 ! Protein structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000146 +name: Protein surface analysis +namespace: topic +def: "Analyse or visualise the surface (shape, hydropathy, electrostatic patches etc) of a protein structure, including biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000126 ! Protein structure analysis +relationship: concerns EDAM:0000008 ! Undefined + + + +! +! Topic<-Protein analysis<-Protein domains +! + + + + +! +! Topic<-Protein analysis<-Protein interactions +! +[Term] +id: EDAM:0000147 +name: Protein-protein interactions +namespace: topic +def: "Study protein-protein interactions." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000128 ! Protein interactions +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000148 +name: Protein-ligand interactions +namespace: topic +def: "Study protein-ligand (small molecule) interactions." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000128 ! Protein interactions +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000149 +name: Protein-nucleic acid interactions +namespace: topic +def: "Study protein-DNA/RNA interactions." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000128 ! Protein interactions +relationship: concerns EDAM:0000008 ! Undefined + + + + + +! +! Topic<-Protein analysis<-Protein classification +! + + +! +! Topic<-Protein analysis<-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"] +is_a: EDAM:0000130 ! Protein folding, stability and design +relationship: concerns EDAM:0000008 ! Undefined + + + + + +! +! Topic<-Protein analysis<-Transmembrane protein analysis +! +[Term] +id: EDAM:0000151 +name: G protein-coupled receptor (GPCR) analysis +namespace: topic +def: "Study G-protein coupled receptors (GPCRs)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000131 ! Transmembrane protein analysis +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Protein analysis<-Enzymes +! + + + +! +! Topic<-Metabolite analysis +! +[Term] +id: EDAM:0000152 +name: Carbohydrates analysis +namespace: topic +def: "Carbohydrate data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000079 ! Metabolite analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000153 +name: Lipid analysis +namespace: topic +def: "Lipid data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000079 ! Metabolite analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000154 +name: Small molecules analysis +namespace: topic +def: "Small molecules data and analysis." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000079 ! Metabolite analysis +relationship: concerns EDAM:0000008 ! Undefined + + + + + + +! +! Topic<-Sequence analysis +! +[Term] +id: EDAM:0000155 +name: Sequence retrieval +namespace: topic +def: "Search or query a database and retrieve molecular sequences and associated data." [EDAM:EBI "EMBRACE definition"] +comment: This refers to direct retrieval methods (e.g. the dbfetch program) which do not perform sequence similarity calculations. +is_a: EDAM:0000080 ! Sequence analysis +is_a: EDAM:0000090 ! Database search and retrieval +relationship: concerns EDAM:0000008 ! Undefined + +[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"] +is_a: EDAM:0000080 ! Sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + +[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:0000008 ! Undefined + + +[Term] +id: EDAM:0000158 +name: Sequence motifs +namespace: topic +def: "Discover, identify or analyse conserved patterns (motifs) in molecular sequences." [EDAM:EBI "EMBRACE definition"] +synonym: "Motifs" EXACT [] +is_a: EDAM:0000080 ! Sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000159 +name: Sequence comparison +namespace: topic +def: "Compare 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:0000008 ! Undefined + +[Term] +id: EDAM:0000160 +name: Sequence features +namespace: topic +def: "Identify, predict, handle or analyse the features or feature tables of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000080 ! Sequence analysis +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Sequence analysis<-Sequence retrieval +! + + +! +! Topic<-Sequence analysis<-Sequence editing +! + + + +! +! Topic<-Sequence analysis<-Sequence composition +! + +! +! Topic<-Sequence analysis<-Sequence motifs +! +[Term] +id: EDAM:0000161 +name: Protein sequence motifs +namespace: topic +def: "Discover, identify or analyse motifs or conserved patterns in protein sequences." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000158 ! Sequence motifs +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000162 +name: Nucleic acid sequence motifs +namespace: topic +def: "Discover, identify or analyse motifs or conserved patterns in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000158 ! Sequence motifs +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Sequence analysis<-Sequence comparison +! +[Term] +id: EDAM:0000163 +name: Sequence similarity search +namespace: topic +def: "Search for and retrieve molecular sequences that are similar to a query." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000159 ! Sequence comparison +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000164 +name: Sequence clustering +namespace: topic +def: "Compare and cluster multiple sequences on the basis of similarity, process or analyse sequence clusters." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000159 ! Sequence comparison +relationship: concerns EDAM:0000008 ! Undefined + +! +! Topic<-Sequence analysis<-Sequence features +! + + + + + +! +! Topic<-Structure analysis +! +[Term] +id: EDAM:0000165 +name: Structure retrieval +namespace: topic +def: "Search or query a database and retrieve molecular structures." [EDAM:EBI "EMBRACE definition"] +comment: This refers to direct retrieval methods which do not perform calculations on the structure. +is_a: EDAM:0000081 ! Structure analysis +is_a: EDAM:0000090 ! Database search and retrieval +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000166 +name: Structural motifs +namespace: topic +def: "Discover, identify or analyse common 3D motifs in molecular structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000081 ! Structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000167 +name: Structural profiles +namespace: topic +def: "Generate, manipulate, analyse or use some type of structural (3D) profile or template (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000081 ! Structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0001770 +name: Structure comparison +namespace: topic +def: "Compare two or more molecular structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000081 ! Structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000170 +name: Structural features +namespace: topic +def: "Handle, predict or analyse structural features of molecules(s)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000081 ! Structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +! +! Topic<-Structure analysis<-Structure retrieval +! + +! +! Topic<-Structure analysis<-Structural motifs +! + + +! +! Topic<-Structure analysis<-Structural profiles +! + + +! +! Topic<-Structure analysis<-Structure comparison +! +[Term] +id: EDAM:0000168 +name: Secondary structure comparison +namespace: topic +def: "Compare two or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001770 ! Structure comparison +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000169 +name: Tertiary structure comparison +namespace: topic +def: "Compare two or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001770 ! Structure comparison +relationship: concerns EDAM:0000008 ! Undefined + + + +! +! Topic<-Structure analysis<-Structure comparison<-Secondary structure comparison +! + +! +! Topic<-Structure analysis<-Structure comparison<-Tertiary structure comparison +! + +! +! Topic<-Structure analysis<-Structural features +! + + +! +! Topic<-Structure prediction +! + +[Term] +id: EDAM:0000171 +name: Tertiary structure prediction +namespace: topic +def: "Predict protein or nucleic acid tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000082 ! Structure prediction +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000172 +name: Protein structure prediction +namespace: topic +def: "Predict secondary or tertiary structure or other structural features of protein sequences." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000082 ! Structure prediction +is_a: EDAM:0000078 ! Protein analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000173 +name: Nucleic acid structure prediction +namespace: topic +def: "Predict secondary or tertiary structure of nucleic acids." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000082 ! Structure prediction +is_a: EDAM:0000077 ! Nucleic acid analysis +relationship: concerns EDAM:0000008 ! Undefined + + + + + +! +! Topic<-Structure prediction<-Tertiary structure prediction +! + +[Term] +id: EDAM:0000174 +name: Ab initio structure prediction +namespace: topic +def: "Predict three-dimensional structure of a molecular sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [EDAM:EBI "EMBRACE definition"] +synonym: "de novo protein structure prediction" EXACT [] +is_a: EDAM:0000171 ! Tertiary structure prediction +is_a: EDAM:0002125 ! Protein tertiary structure analysis +relationship: concerns EDAM:0000008 ! Undefined + + +[Term] +id: EDAM:0000175 +name: Molecular modelling +namespace: topic +def: "Build or assess a three-dimensional molecular model using known sequence and structural data." [EDAM:EBI "EMBRACE definition"] +comment: Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. +synonym: "Comparative modelling" EXACT [] +is_a: EDAM:0000171 ! Tertiary structure prediction +is_a: EDAM:0002125 ! Protein tertiary structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000176 +name: Molecular dynamics +namespace: topic +def: "Simulate protein conformation using molecular dynamics." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000171 ! Tertiary structure prediction +is_a: EDAM:0002125 ! Protein tertiary structure analysis +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Structure prediction<-Tertiary structure prediction<-Ab initio structure prediction +! + +! +! Topic<-Structure prediction<-Tertiary structure prediction<-Molecular modelling +! +[Term] +id: EDAM:0000177 +name: Protein docking +namespace: topic +def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000175 ! Molecular modelling +is_a: EDAM:0000179 ! Protein tertiary structure prediction +relationship: concerns EDAM:0000008 ! Undefined + + + +! +! Topic<-Structure prediction<-Tertiary structure prediction<-Molecular dynamics +! + +! +! Topic<-Structure prediction<-Tertiary structure prediction<-Protein docking +! + + +! +! Topic<-Structure prediction<-Protein structure prediction +! + +[Term] +id: EDAM:0000178 +name: Protein secondary structure prediction +namespace: topic +def: "Predict secondary or supersecondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000172 ! Protein structure prediction +is_a: EDAM:0002124 ! Protein secondary structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000179 +name: Protein tertiary structure prediction +namespace: topic +def: "Predict tertiary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000172 ! Protein structure prediction +is_a: EDAM:0000171 ! Tertiary structure prediction +is_a: EDAM:0002125 ! Protein tertiary structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000180 +name: Protein fold recognition +namespace: topic +def: "Recognize (predict and assign) known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000172 ! Protein structure prediction +is_a: EDAM:0000129 ! Protein classification +is_a: EDAM:0002125 ! Protein tertiary structure analysis +relationship: concerns EDAM:0000008 ! Undefined + +! +! Topic<-Structure prediction<-Nucleic acid structure prediction +! +[Term] +id: EDAM:0000181 +name: RNA structure prediction +namespace: topic +def: "Predict or design secondary or tertiary structure of RNA." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000173 ! Nucleic acid structure prediction +is_a: EDAM:0000099 ! RNA analysis +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Structure prediction<-Molecular modelling +! + + + + + + +! +! Topic<-Alignment +! +[Term] +id: EDAM:0000182 +name: Sequence alignment +namespace: topic +def: "Alignment of molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000083 ! Alignment +is_a: EDAM:0000159 ! Sequence comparison +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000183 +name: Structure alignment +namespace: topic +def: "Alignment (superimposition) of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000083 ! Alignment +is_a: EDAM:0000169 ! Tertiary structure comparison +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000184 +name: Sequence-structure alignment +namespace: topic +def: "Alignment of molecular sequence to structure or to structural (3D) profiles or templates (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000083 ! Alignment +is_a: EDAM:0000159 ! Sequence comparison +relationship: concerns EDAM:0000008 ! Undefined + + + + + +! +! Topic<-Alignment<-Sequence alignment +! +[Term] +id: EDAM:0000185 +name: Pairwise sequence alignment +namespace: topic +def: "Alignment of multiple molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000182 ! Sequence alignment +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000186 +name: Multiple sequence alignment +namespace: topic +def: "Alignment of two molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000182 ! Sequence alignment +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000187 +name: Sequence alignment analysis +namespace: topic +def: "Handle, analyse or compare alignments of molecular sequences or sequence profiles (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000182 ! Sequence alignment +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000188 +name: Sequence profiles +namespace: topic +def: "Generate, manipulate, analyse or use some type of sequence profile (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] +comment: Profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. +is_a: EDAM:0000182 ! Sequence alignment +relationship: concerns EDAM:0000008 ! Undefined + +[Term] +id: EDAM:0000189 +name: Structure-based sequence alignment +namespace: topic +def: "Alignment of molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0000182 ! Sequence alignment +relationship: concerns EDAM:0000008 ! Undefined + + +! +! Topic<-Alignment