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