From dc88320177b30bec2b516d71163a3a7784f2a2e4 Mon Sep 17 00:00:00 2001 From: matuskalas Date: Tue, 1 Nov 2016 03:39:40 +0100 Subject: [PATCH] History of releases: beta11 --- releases/EDAM.obo | 3490 +++++++++++++++++++++++++++-------------------------- 1 file changed, 1810 insertions(+), 1680 deletions(-) diff --git a/releases/EDAM.obo b/releases/EDAM.obo index c93ca76..8258670 100644 --- a/releases/EDAM.obo +++ b/releases/EDAM.obo @@ -1,9 +1,9 @@ format-version: 1.2 date: 01:12:2010 12:25 -data-version: Beta10 +data-version: Beta11 ! Use for mapping to "global" id space(s) e.g.: ! idspace: EDAM http://purl.org/edam/ "EDAM terms" -! NEXT term number is 0002604 +! NEXT term number is 0002608 ! xref: WHATIF: CorrectedPDBasXML ! xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB ! xref: Moby:GI_Gene @@ -11,6 +11,8 @@ data-version: Beta10 ! xref: SO:0000348 ! xref: BioCatalogue:Protein Multiple Alignment +! + ! @@ -19,149 +21,149 @@ data-version: Beta10 [Typedef] id: concerns name: concerns -def: "Defines that a term ('Topic') concerns (covers) another term ('Biological entity', 'Data resource' or 'Operation')." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: is_concern_of - -[Typedef] -id: has_attribute -name: has_attribute -def: "Defines a term ('Biological entity') has (or can have) an attribute ('Data')." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: is_attribute_of - -[Typedef] -id: has_identifier -name: has_identifier -def: "Defines a term ('Biological entity', 'Data resource' or 'Data') has (or can have) an identifier ('Identifier')." [EDAM:EBI] +def: "Defines that a term ('Topic') concerns (covers) another term ('Data', 'Resource' or 'Operation')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -inverse_of: is_identifier_of +! inverse_of: is_concern_of + +! [Typedef] +! id: has_attribute +! name: has_attribute +! def: "Defines a term ('Biological entity') has (or can have) an attribute ('Data')." [EDAM:EBI] +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: is_attribute_of + +! [Typedef] +! id: has_identifier +! name: has_identifier +! def: "Defines a term ('Biological entity', 'Resource' or 'Data') has (or can have) an identifier ('Identifier')." [EDAM:EBI] +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: is_identifier_of [Typedef] id: has_input name: has_input -def: "Defines a term ('Operation') as reading (inputting) another term ('Data')." [EDAM:EBI] +def: "Defines a term ('Operation') as necessarily consuming another term ('Data') as input." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -inverse_of: is_input_of +! 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 ('Biological entity' or 'Data') as having a conceptual part ('Biological entity' or 'Data')." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: is_part_of - -[Typedef] -id: has_source -name: has_source -def: "Defines a term ('Data') has a source ('Tool', 'Data resource')." [EDAM:EBI] -comment: is_source_of -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: is_source_of - - -[Typedef] -id: has_format -name: has_format -def: "Defines a term ('Data') has a data format specification ('Data format')." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: is_format_of - -[Typedef] -id: is_attribute_of -name: is_attribute_of -def: "Defines that a term ('Data') is an attribute of another term ('Biological entity')." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: has_attribute - -[Typedef] -id: is_concern_of -name: is_concern_of -def: "Defines a term ('Biological entity', 'Data resource' or 'Operation') as a concern of another term ('Topic')." [EDAM:EBI] +def: "Defines a term ('Operation') as necessarily producing another term ('Data') as output." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -inverse_of: concerns +! inverse_of: is_output_of + +! [Typedef] +! id: has_part +! name: has_part +! def: "Defines a term ('Biological entity' or 'Data') as having a conceptual part ('Biological entity' or 'Data')." [EDAM:EBI] +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: is_part_of + +! [Typedef] +! id: has_source +! name: has_source +! def: "Defines a term ('Data') has a source ('Operation', 'Resource')." [EDAM:EBI] +! comment: is_source_of +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: is_source_of + + +! [Typedef] +! id: has_format +! name: has_format +! def: "Defines a term ('Data') has a data format specification ('Format')." [EDAM:EBI] +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: is_format_of + +! [Typedef] +! id: is_attribute_of +! name: is_attribute_of +! def: "Defines that a term ('Data') is an attribute of another term ('Biological entity')." [EDAM:EBI] +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: has_attribute + +! [Typedef] +! id: is_concern_of +! name: is_concern_of +! def: "Defines a term ('Biological entity', 'Resource' or 'Operation') as a concern of another term ('Topic')." [EDAM:EBI] +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: concerns [Typedef] id: is_identifier_of name: is_identifier_of -def: "Defines that a term ('Identifier') is an identifier of another term ('Biological entity', 'Data resource' 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] +def: "Defines that a term ('Identifier') is an identifier of another term ('Resource' or 'Data')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -inverse_of: has_output - -[Typedef] -id: is_part_of -name: is_part_of -def: "Defines that a term ('Biological entity' or 'Data') is a conceptual part of some other term ('Biological entity' or 'Data')." [EDAM:EBI] -is_anti_symmetric: true -is_cyclic: false -is_transitive: true -inverse_of: has_part +! inverse_of: has_identifier + +! [Typedef] +! id: is_input_of +! name: is_input_of +! def: "Defines a term ('Data') as an input of another term ('Operation')." [EDAM:EBI] +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: has_input + +! [Typedef] +! id: is_output_of +! name: is_output_of +! def: "Defines a term ('Data') as an output of another term ('Operation')." [EDAM:EBI] +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: has_output + +! [Typedef] +! id: is_part_of +! name: is_part_of +! def: "Defines that a term ('Biological entity' or 'Data') is a conceptual part of some other term ('Biological entity' or 'Data')." [EDAM:EBI] +! is_anti_symmetric: true +! is_cyclic: false +! is_transitive: true +! inverse_of: has_part [Typedef] id: is_source_of name: is_source_of -def: "Defines a term ('Tool', 'Data resource') is a source of another term ('Data')." [EDAM:EBI] +def: "Defines a term ('Resource') 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 +! inverse_of: has_source [Typedef] id: is_format_of name: is_format_of -def: "Defines that a term ('Data format') is a data format specification for another term ('Data')." [EDAM:EBI] +def: "Defines that a term ('Format') is a data format specification for another term ('Data')." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true -inverse_of: has_format +! inverse_of: has_format @@ -176,6 +178,7 @@ namespace: entity def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things or an observable phenonema or occurence." [EDAM:EBI "EMBRACE definition"] ! relationship: is_concern_of EDAM:0000003 ! Topic ! relationship: has_attribute EDAM:0000006 ! Data +is_obsolete: true [Term] id: EDAM:0000003 @@ -184,7 +187,7 @@ namespace: topic def: "A general field of bioinformatics study, data, processing and analysis or technology." [EDAM:EBI "EMBRACE definition"] ! relationship: concerns EDAM:0000002 ! Biological entity ! relationship: concerns EDAM:0000004 ! Operation -! relationship: concerns EDAM:0000005 ! Data resource +! relationship: concerns EDAM:0000005 ! Resource ! relationship: concerns EDAM:0000582 ! Ontology [Term] @@ -198,7 +201,7 @@ def: "A specific, singular function or process performed by a tool, for example [Term] id: EDAM:0000005 -name: Data resource +name: Resource namespace: resource def: "A category of content of a data resource including databases, ontologies and servers." [EDAM:EBI "EMBRACE definition"] @@ -217,7 +220,7 @@ def: "A semantic description of a data entity (datum) commonly used in bioinform [Term] id: EDAM:0001915 -name: Data format +name: Format namespace: format def: "A reference (typically a URL) of a data format specification." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} @@ -229,13 +232,13 @@ comment: See OBO file for URL of format specification. {url=} ! ! Biological entity ! -[Term] -id: EDAM:0000008 -name: Undefined -namespace: entity -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000002 ! Biological entity -relationship: has_attribute EDAM:0000841 ! Undefined +! [Term] +! id: EDAM:0000008 +! name: Undefined +! namespace: entity +! def: "Debugging." [EDAM:EBI "EMBRACE definition"] +! is_a: EDAM:0000002 ! Biological entity +! relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -243,15 +246,17 @@ id: EDAM:0002199 name: Physical entity namespace: entity def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000002 ! Biological entity +! is_a: EDAM:0000002 ! Biological entity +is_obsolete: true [Term] id: EDAM:0000012 name: Phenomenon namespace: entity def: "An observable biological occurence or event with a physical basis." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000002 ! Biological entity -relationship: has_attribute EDAM:0000006 ! Data +! is_a: EDAM:0000002 ! Biological entity +! relationship: has_attribute EDAM:0000006 ! Data +is_obsolete: true ! @@ -262,24 +267,27 @@ id: EDAM:0000009 name: Discrete entity namespace: entity def: "Any biological thing with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0002199 ! Physical entity -relationship: has_attribute EDAM:0000006 ! Data +! is_a: EDAM:0002199 ! Physical entity +! relationship: has_attribute EDAM:0000006 ! Data +is_obsolete: true [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:0002199 ! Physical entity -relationship: has_attribute EDAM:0000006 ! Data +! is_a: EDAM:0002199 ! Physical entity +! relationship: has_attribute EDAM:0000006 ! Data +is_obsolete: true [Term] id: EDAM:0000011 name: Entity collection namespace: entity def: "A collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0002199 ! Physical entity -relationship: has_attribute EDAM:0000006 ! Data +! is_a: EDAM:0002199 ! Physical entity +! relationship: has_attribute EDAM:0000006 ! Data +is_obsolete: true @@ -292,8 +300,9 @@ id: EDAM:0000013 name: Molecular entity namespace: entity def: "Any atom, molecule or molecular complex with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000009 ! Discrete entity -relationship: has_attribute EDAM:0000883 ! Tertiary structure +! is_a: EDAM:0000009 ! Discrete entity +! relationship: has_attribute EDAM:0000883 ! Tertiary structure +is_obsolete: true @@ -310,24 +319,27 @@ id: EDAM:0000014 name: Atom namespace: entity def: "The basic unit of matter consisting of negatively charged electrons bound by electromagnetic force to a nucleus of protons and neutrons." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000013 ! Molecular entity -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000013 ! Molecular entity +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0000015 name: Small molecule namespace: entity def: "Any small molecule." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000013 ! Molecular entity -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000013 ! Molecular entity +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0002044 ! Sequence data +! is_a: EDAM:0000013 ! Molecular entity +! relationship: has_attribute EDAM:0002044 ! Sequence data +is_obsolete: true [Term] id: EDAM:0000017 @@ -335,8 +347,9 @@ name: Molecular complex namespace: entity def: "Two or more whole molecules in association with one another." [EDAM:EBI "EMBRACE definition"] synonym: "Molecular assembly" EXACT [] -is_a: EDAM:0000013 ! Molecular entity -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000013 ! Molecular entity +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true @@ -355,32 +368,36 @@ id: EDAM:0000018 name: Biomonomer namespace: entity def: "A small organic molecule that can chemically bond to other monomers to form a biopolymer." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000015 ! Small molecule -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000015 ! Small molecule +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000015 ! Small molecule +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000015 ! Small molecule +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0002577 name: Toxin namespace: entity def: "A poisonous substance produced by living cells or organisms." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000015 ! Small molecule -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000015 ! Small molecule +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! @@ -391,8 +408,9 @@ id: EDAM:0000021 name: Amino acid namespace: entity def: "The building block of proteins, an alpha amino acid consists of a carbon atom (C-alpha) attached to a hydrogen atom, an amino group, a carboxylate group and one of (typically) 20 common R-groups (side-chain)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000018 ! Biomonomer -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000018 ! Biomonomer +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0000022 @@ -401,16 +419,18 @@ namespace: entity def: "The building block of nucleic acids, a nucleotide consists of a nucleobase (nitrogenous base, either a purine or pyrimidine), a five-carbon sugar (either ribose or 2'-deoxyribose), and one to three phosphate groups." [EDAM:EBI "EMBRACE definition"] synonym: "Base" EXACT [] xref: SO:0001236 -is_a: EDAM:0000018 ! Biomonomer -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000018 ! Biomonomer +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000018 ! Biomonomer +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! ! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Small molecule<-Ligand @@ -432,9 +452,10 @@ def: "An organic polymer of nucleotide monomers in an unbranched chain, bound to synonym: "Polynucleotide chain" EXACT [] synonym: "Polynucleotide" EXACT [] xref: SO:0000348 -is_a: EDAM:0000016 ! Biopolymer -relationship: has_attribute EDAM:0001207 ! Nucleotide sequence -relationship: has_attribute EDAM:0001459 ! Nucleic acid tertiary structure +! is_a: EDAM:0000016 ! Biopolymer +! relationship: has_attribute EDAM:0001207 ! Nucleotide sequence +! relationship: has_attribute EDAM:0001459 ! Nucleic acid tertiary structure +is_obsolete: true [Term] id: EDAM:0000025 @@ -442,18 +463,20 @@ name: Polypeptide namespace: entity def: "An organic polymer of alpha amino acid residues in an unbranched chain, bound together by peptide bonds." [EDAM:EBI "EMBRACE definition"] synonym: "Polypeptide chain" EXACT [] -is_a: EDAM:0000016 ! Biopolymer -relationship: has_attribute EDAM:0001208 ! Protein sequence -relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! is_a: EDAM:0000016 ! Biopolymer +! relationship: has_attribute EDAM:0001208 ! Protein sequence +! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +is_obsolete: true [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 +! is_a: EDAM:0000016 ! Biopolymer -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! @@ -464,8 +487,9 @@ id: EDAM:0000027 name: Oligonucleotide namespace: entity def: "An organic polymer of nucleotide monomers in a short (typically less than 30 subunits) unbranched chain, bound together by covalent bonds." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000024 ! Nucleic acid -relationship: has_attribute EDAM:0001207 ! Nucleotide sequence +! is_a: EDAM:0000024 ! Nucleic acid +! relationship: has_attribute EDAM:0001207 ! Nucleotide sequence +is_obsolete: true [Term] id: EDAM:0000028 @@ -473,9 +497,10 @@ name: DNA namespace: entity def: "A deoxyribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] xref: SO:0000352 -is_a: EDAM:0000024 ! Nucleic acid -relationship: has_attribute EDAM:0001212 ! DNA sequence -relationship: has_attribute EDAM:0001464 ! DNA tertiary structure +! is_a: EDAM:0000024 ! Nucleic acid +! relationship: has_attribute EDAM:0001212 ! DNA sequence +! relationship: has_attribute EDAM:0001464 ! DNA tertiary structure +is_obsolete: true [Term] id: EDAM:0000029 @@ -483,9 +508,10 @@ name: RNA namespace: entity def: "A ribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] xref: SO:0000356 -is_a: EDAM:0000024 ! Nucleic acid -relationship: has_attribute EDAM:0001213 ! RNA sequence -relationship: has_attribute EDAM:0001465 ! RNA tertiary structure +! is_a: EDAM:0000024 ! Nucleic acid +! relationship: has_attribute EDAM:0001213 ! RNA sequence +! relationship: has_attribute EDAM:0001465 ! RNA tertiary structure +is_obsolete: true @@ -502,8 +528,9 @@ id: EDAM:0000030 name: Mobile genetic element namespace: entity def: "A DNA molecule that can move around within a genome." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000028 ! DNA -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000028 ! DNA +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0002010 @@ -511,9 +538,10 @@ name: cDNA namespace: entity def: "A deoxyribonucleic acid molecule synthesises by reverse transcriptase from an RNA template." [EDAM:EBI "EMBRACE definition"] xref: SO:0000756 -is_a: EDAM:0000028 ! DNA -relationship: has_attribute EDAM:0001212 ! DNA sequence -relationship: has_attribute EDAM:0001464 ! DNA tertiary structure +! is_a: EDAM:0000028 ! DNA +! relationship: has_attribute EDAM:0001212 ! DNA sequence +! relationship: has_attribute EDAM:0001464 ! DNA tertiary structure +is_obsolete: true ! ! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Nucleic acid<-DNA<-Mobile genetic element @@ -523,16 +551,18 @@ id: EDAM:0000031 name: Transposon namespace: entity def: "A DNA sequence that can undergo transposition or move to different positions in the genome of a single cell." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000030 ! Mobile genetic element -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000030 ! Mobile genetic element +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000030 ! Mobile genetic element +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! @@ -543,8 +573,9 @@ id: EDAM:0000033 name: Retrotransposon namespace: entity def: "A DNA element that can amplify itself in a genome, by copying itself to RNA then back to DNA using a reverse transcriptase." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000031 ! Transposon -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000031 ! Transposon +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0000034 @@ -553,8 +584,9 @@ namespace: entity def: "A DNA sequence that is smaller than most other transposable elements and which codes only for proteins involved in transposition." [EDAM:EBI "EMBRACE definition"] synonym: "Insertion sequence element" EXACT [] synonym: "IS element" EXACT [] -is_a: EDAM:0000031 ! Transposon -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000031 ! Transposon +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! @@ -576,8 +608,9 @@ namespace: entity def: "Transfer RNA (tRNA) is a small ribonucleic acid molecule that binds a specific amino acid." [EDAM:EBI "EMBRACE definition"] comment: The amino acid is transferred to a nascent polypeptide chain during protein synthesis at the ribosome. synonym: "Transfer RNA" EXACT [] -is_a: EDAM:0000029 ! RNA -relationship: has_attribute EDAM:0001213 ! RNA sequence +! is_a: EDAM:0000029 ! RNA +! relationship: has_attribute EDAM:0001213 ! RNA sequence +is_obsolete: true ! ! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide @@ -587,16 +620,18 @@ id: EDAM:0000036 name: Peptide namespace: entity def: "An organic polymer of alpha amino acid residues in a short unbranched chain. Peptides typically have fewer than 50 subunits and can be made synthetically." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000025 ! Polypeptide -relationship: has_attribute EDAM:0001208 ! Protein sequence +! is_a: EDAM:0000025 ! Polypeptide +! relationship: has_attribute EDAM:0001208 ! Protein sequence +is_obsolete: true [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: has_attribute EDAM:0001460 ! Protein tertiary structure +! is_a: EDAM:0000025 ! Polypeptide +! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +is_obsolete: true ! @@ -608,24 +643,27 @@ id: EDAM:0000038 name: Uncomplexed protein namespace: entity def: "A single polypeptide chain in a stable conformation." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000037 ! Protein -relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! is_a: EDAM:0000037 ! Protein +! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +is_obsolete: true [Term] id: EDAM:0000039 name: Enzyme namespace: entity def: "Enzyme." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000037 ! Protein -relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! is_a: EDAM:0000037 ! Protein +! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +is_obsolete: true [Term] id: EDAM:0000040 name: Transmembrane protein namespace: entity def: "A transmembrane protein molecule." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000037 ! Protein -relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! is_a: EDAM:0000037 ! Protein +! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +is_obsolete: true [Term] id: EDAM:0000041 @@ -633,8 +671,9 @@ name: Transcription factor namespace: entity def: "A protein that, upon binding a cis-regulatory DNA element, regulates (enhances or represses) transcription." [EDAM:EBI "EMBRACE definition"] synonym: "Sequence-specific DNA binding factor" EXACT [] -is_a: EDAM:0000037 ! Protein -relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! is_a: EDAM:0000037 ! Protein +! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +is_obsolete: true ! ! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Uncomplexed protein @@ -649,8 +688,9 @@ id: EDAM:0000042 name: Restriction enzyme namespace: entity def: "An enzyme that cuts DNA at specific nucleotide subsequence(s) (restriction sites)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000039 ! Enzyme -relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! is_a: EDAM:0000039 ! Enzyme +! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +is_obsolete: true ! ! Biological entity<-Physical entity<-Discrete entity<-Molecular entity<-Biopolymer<-Polypeptide<-Protein<-Transmembrane protein @@ -679,9 +719,10 @@ id: EDAM:0000043 name: RNA/DNA hybrid namespace: entity def: "A hybrid (complementary base-paired) molecule of DNA and RNA." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000017 ! Molecular complex -relationship: has_attribute EDAM:0000841 ! Undefined -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000017 ! Molecular complex +! relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0000044 @@ -689,19 +730,19 @@ name: Protein-protein complex namespace: entity def: "A protein comprising two or more polypeptide chain subunits in a stable association." [EDAM:EBI "EMBRACE definition"] synonym: "Protein complex" EXACT [] -is_a: EDAM:0000017 ! Molecular complex -is_a: EDAM:0000037 ! Protein - -relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +! is_a: EDAM:0000017 ! Molecular complex +! is_a: EDAM:0000037 ! Protein +! relationship: has_attribute EDAM:0001460 ! Protein tertiary structure +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000017 ! Molecular complex +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] @@ -709,9 +750,9 @@ id: EDAM:0000046 name: Protein-nucleic acid complex namespace: entity def: "A protein-DNA/RNA complex." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000017 ! Molecular complex - -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000017 ! Molecular complex +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] @@ -720,7 +761,7 @@ 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 +! consider: EDAM:0000044 ! Protein-protein complex ! @@ -744,9 +785,10 @@ 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 +! is_a: EDAM:0000046 ! Protein-nucleic acid complex -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! @@ -773,27 +815,30 @@ 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 +! is_a: EDAM:0000010 ! Entity feature -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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 +! is_a: EDAM:0000010 ! Entity feature -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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 +! is_a: EDAM:0000010 ! Entity feature -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0001854 @@ -801,9 +846,10 @@ 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 +! is_a: EDAM:0000010 ! Entity feature -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true @@ -817,9 +863,10 @@ 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 +! is_a: EDAM:0001749 ! Atom group -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! ! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature @@ -829,26 +876,29 @@ 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 +! is_a: EDAM:0000048 ! Nucleic acid feature -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000048 ! Nucleic acid feature +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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 +! is_a: EDAM:0000048 ! Nucleic acid feature -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true @@ -858,9 +908,10 @@ 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 +! is_a: EDAM:0000048 ! Nucleic acid feature -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0000054 @@ -868,18 +919,20 @@ 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 +! is_a: EDAM:0000048 ! Nucleic acid feature -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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 +! is_a: EDAM:0000048 ! Nucleic acid feature -relationship: has_attribute EDAM:0000841 ! Undefined +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0000056 @@ -887,18 +940,18 @@ name: Scaffold / matrix attachment site namespace: entity def: "Regions of DNA sequence in eukaryotic chromosomes where the nuclear matrix attaches." [EDAM:EBI "EMBRACE definition"] synonym: "Matrix attachment region" EXACT [] -is_a: EDAM:0000048 ! Nucleic acid feature - -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000048 ! Nucleic acid feature +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000048 ! Nucleic acid feature +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! ! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Codon @@ -912,8 +965,9 @@ id: EDAM:0001909 name: Allele namespace: entity def: "An alternative form of a gene that can exist at a single locus." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000051 ! Gene -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000051 ! Gene +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! ! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Operon @@ -928,9 +982,9 @@ name: Gene cis-regulatory element namespace: entity def: "A DNA element that can bind a transcription factor to regulate (enhance or repress) the expression (transcription) of genes located on the same strand." [EDAM:EBI "EMBRACE definition"] synonym: "Cis-element" EXACT [] -is_a: EDAM:0000054 ! Transcription regulatory element - -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000054 ! Transcription regulatory element +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0000059 @@ -938,9 +992,9 @@ name: Gene trans-regulatory element namespace: entity def: "A DNA element that encodes a transcription factor which regulates gene(s) distant from the gene from which they were transcribed." [EDAM:EBI "EMBRACE definition"] synonym: "Trans-element" EXACT [] -is_a: EDAM:0000054 ! Transcription regulatory element - -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000054 ! Transcription regulatory element +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! @@ -951,36 +1005,36 @@ id: EDAM:0000060 name: Promoter namespace: entity def: "The DNA element where transcription is initiated." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000058 ! Gene cis-regulatory element - -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000058 ! Gene cis-regulatory element +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000058 ! Gene cis-regulatory element +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000058 ! Gene cis-regulatory element +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000058 ! Gene cis-regulatory element +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! ! Biological entity<-Physical entity<-Entity feature<-Nucleic acid feature<-Transcription regulatory element<-Gene-regulatory element @@ -998,8 +1052,9 @@ name: Protein residue namespace: entity def: "A single amino acid position in a protein, bound to one (C or N-terminal positions) or two other residues by covalent (peptide) bonds." [EDAM:EBI "EMBRACE definition"] synonym: "Residue" EXACT [] -is_a: EDAM:0000049 ! Protein feature -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000049 ! Protein feature +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0001751 @@ -1007,18 +1062,18 @@ name: Protein residue group namespace: entity def: "A group of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue group" EXACT [] -is_a: EDAM:0000049 ! Protein feature - -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000049 ! Protein feature +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0001468 ! Protein domain tertiary structure +! is_a: EDAM:0000049 ! Protein feature +! relationship: has_attribute EDAM:0001468 ! Protein domain tertiary structure +is_obsolete: true ! @@ -1034,9 +1089,9 @@ name: Protein residue pair namespace: entity def: "A pair of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue pair" EXACT [] -is_a: EDAM:0001751 ! Protein residue group - -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0001751 ! Protein residue group +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0001753 @@ -1044,9 +1099,9 @@ name: Protein residue group (continuous) namespace: entity def: "A group of continuous (adjacent) amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue group (continuous)" EXACT [] -is_a: EDAM:0001751 ! Protein residue group - -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0001751 ! Protein residue group +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [Term] id: EDAM:0001754 @@ -1055,9 +1110,9 @@ namespace: entity def: "A group of discontinuous amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] comment: One or more residues in the group are discontinuous (non-adjacent). synonym: "Residue group (discontinuous)" EXACT [] -is_a: EDAM:0001751 ! Protein residue group - -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0001751 ! Protein residue group +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! @@ -1077,32 +1132,36 @@ id: EDAM:0000066 name: Genome namespace: entity def: "An organisms total complement of DNA or RNA (some viruses) and therefore its hereditary information. A genome includes genes and non-coding regions." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000011 ! Entity collection -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000011 ! Entity collection +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000011 ! Entity collection +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000011 ! Entity collection +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000011 ! Entity collection +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true @@ -1127,32 +1186,36 @@ id: EDAM:0000070 name: Kingdom namespace: entity def: "A kingdom or organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000069 ! Taxonomic rank -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000069 ! Taxonomic rank +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000069 ! Taxonomic rank +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000069 ! Taxonomic rank +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000069 ! Taxonomic rank +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true ! @@ -1164,24 +1227,27 @@ id: EDAM:0000073 name: Metabolic pathway namespace: entity def: "A group of related chemical (enzyme catalysed) reactions occuring within a cell." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000012 ! Phenomenon -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000012 ! Phenomenon +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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 ! Phenomenon -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000012 ! Phenomenon +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true [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 ! Phenomenon -relationship: has_attribute EDAM:0000841 ! Undefined +! is_a: EDAM:0000012 ! Phenomenon +! relationship: has_attribute EDAM:0000841 ! Undefined +is_obsolete: true @@ -1192,13 +1258,13 @@ 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: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 @@ -1223,7 +1289,7 @@ name: Metabolites namespace: topic def: "Study metabolites." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000080 @@ -1265,7 +1331,7 @@ name: Alignment namespace: topic def: "Study the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000084 @@ -1302,7 +1368,7 @@ synonym: "Protein expression" EXACT [] xref: BioCatalogue:Proteomics is_a: EDAM:0000003 ! Topic ! is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] @@ -1324,7 +1390,7 @@ namespace: topic def: "Study gene or protein functions and their interactions." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Functional Genomics is_a: EDAM:0000093 ! Genomics -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000122 @@ -1348,7 +1414,7 @@ name: Model organisms namespace: topic def: "Study a model organism." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000087 @@ -1356,7 +1422,7 @@ 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 +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000088 @@ -1376,7 +1442,7 @@ namespace: topic def: "Study concerning biomedical ontologies, controlled vocabularies, glossaries and so on." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Ontology is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] @@ -1427,7 +1493,7 @@ synonym: "Cheminformatics" EXACT [] synonym: "Chemical informatics" EXACT [] xref: BioCatalogue:Chemoinformatics is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0002259 @@ -1436,7 +1502,7 @@ namespace: topic def: "Holistic analysis of biological systems, the modelling of systems and interactions therein." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Systems Biology is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0002269 @@ -1447,7 +1513,7 @@ synonym: "Biometry" EXACT [] synonym: "Biometrics" EXACT [] xref: BioCatalogue:Biostatistics is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined @@ -1504,7 +1570,7 @@ name: DNA namespace: topic def: "Study DNA." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000077 ! Nucleic acids -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000099 @@ -1571,7 +1637,7 @@ consider: EDAM:0000097 ! Nucleic acid structure analysis ! is_a: EDAM:0000095 ! Nucleic acid features ! is_a: EDAM:0000170 ! Structural features and motifs ! is_a: EDAM:0000097 ! Nucleic acid structure analysis -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined ! @@ -1725,7 +1791,7 @@ name: rRNA namespace: topic def: "Study of ribosomal RNA (rRNA)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000113 ! Functional RNA -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000117 @@ -1751,7 +1817,7 @@ name: piRNA namespace: topic def: "Study of piwi-interacting RNA (piRNA)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000113 ! Functional RNA -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000120 @@ -1759,7 +1825,7 @@ name: snoRNA namespace: topic def: "Study of small nucleolar RNA (snoRNAs)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000113 ! Functional RNA -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined @@ -1881,7 +1947,7 @@ name: Lipoproteins namespace: topic def: "Study lipoproteins." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000132 @@ -2018,7 +2084,7 @@ name: Protein residue interactions namespace: topic def: "Study inter-atomic or inter-residue interactions in protein structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002124 ! Protein secondary structure analysis -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined relationship: concerns EDAM:0000248 ! Residue interaction calculation relationship: concerns EDAM:0001850 ! Protein cysteine and disulfide bond assignment relationship: concerns EDAM:0000272 ! Prediction of protein residue distances, contacts and interactions @@ -2141,7 +2207,7 @@ relationship: concerns EDAM:0000473 ! GPCR analysis id: EDAM:0002278 name: Transmembrane protein prediction namespace: topic -def: "Predict transmembrane domains and topolgy in protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Predict transmembrane domains and topology in protein sequences." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000131 ! Transmembrane proteins consider: EDAM:0000178 ! Protein secondary structure prediction @@ -2164,7 +2230,7 @@ name: Carbohydrates namespace: topic def: "Study carbohydrates." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000079 ! Metabolites -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000153 @@ -2172,7 +2238,7 @@ name: Lipids namespace: topic def: "Study lipids." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000079 ! Metabolites -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000154 @@ -2487,7 +2553,7 @@ def: "Search for and retrieve molecular structures that are similar to a structu comment: The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. is_a: EDAM:0001770 ! Structure comparison is_a: EDAM:0000090 ! Search and retrieval -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined ! @@ -2524,7 +2590,7 @@ namespace: topic def: "Predict secondary or tertiary structure or other structural features of protein sequences." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Protein Structure Prediction is_a: EDAM:0000082 ! Structure prediction -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] @@ -2558,7 +2624,7 @@ namespace: topic def: "Study concering the construction or analysis of models of a molecules properties or behaviour. " [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000082 ! Structure prediction is_a: EDAM:0000082 ! -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] @@ -2581,7 +2647,7 @@ namespace: topic def: "Study concerning the simulation of molecular (typically protein) conformation using a computational model of physicalal forces and computer simulation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002275 ! Molecular modelling is_a: EDAM:0000179 ! Protein tertiary structure prediction -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined ! @@ -2642,7 +2708,7 @@ name: Protein fold recognition namespace: topic def: "Study concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000179 ! Protein tertiary structure prediction -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined ! ! Topic<-Structure prediction<-Nucleic acid structure prediction @@ -2696,7 +2762,7 @@ synonym: "Sequence profile alignment" EXACT [] is_a: EDAM:0000083 ! Alignment is_a: EDAM:0000159 ! Sequence comparison is_a: EDAM:0000188 ! Sequence profiles and HMMs -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000183 @@ -2777,7 +2843,7 @@ name: Structure alignment analysis namespace: topic def: "Handle or analyse alignments of molecular structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000183 ! Structure alignment -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] @@ -2856,7 +2922,7 @@ name: Phylogenetic clocks, dating and stratigraphy namespace: topic def: "Estimate or use molecular clock and stratigraphic (age) data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000084 ! Phylogenetics -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000194 @@ -2919,7 +2985,7 @@ name: Two-dimensional gel electrophoresis namespace: topic def: "Study concerning two-dimensional gel electrophoresis data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000121 ! Proteomics -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] @@ -2928,7 +2994,7 @@ name: Mass spectrometry namespace: topic def: "Study concerning mass spectrometry and related data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000121 ! Proteomics -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000135 @@ -2937,7 +3003,7 @@ namespace: topic def: "Study concerning protein microarray data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000121 ! Proteomics is_a: EDAM:0000200 ! Microarrays -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined ! ! Topic<-Genomics @@ -2949,7 +3015,7 @@ namespace: topic def: "Study (typically compare) the structure or function of multiple genomes." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Comparative Genomics is_a: EDAM:0000093 ! Genomics -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000102 @@ -3029,7 +3095,7 @@ name: Pharmacology namespace: topic def: "Study concerning drugs." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined @@ -3108,7 +3174,7 @@ def: "Handle or analyse raw data from X-ray crystallography or nuclear magnetic is_a: EDAM:0000122 ! Structural genomics is_a: EDAM:0000126 ! Protein structure analysis is_a: EDAM:0002275 ! Molecular modelling -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined @@ -3152,7 +3218,7 @@ name: Pharmacogenomics namespace: topic def: "Study the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000202 ! Pharmacology -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000209 @@ -3161,7 +3227,7 @@ namespace: topic def: "Study concerning the design of drugs or potential drug compounds." [EDAM:EBI "EMBRACE definition"] comment: This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse druG 3D conformations, identify drug targets with structural docking etc. is_a: EDAM:0000202 ! Pharmacology -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined @@ -3183,7 +3249,7 @@ name: Model organisms (fish) namespace: topic def: "Study fish model organisms." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000086 ! Model organisms -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000211 @@ -3191,7 +3257,7 @@ name: Model organisms (fly) namespace: topic def: "Study fly model organisms." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000086 ! Model organisms -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000212 @@ -3199,7 +3265,7 @@ name: Model organisms (microbes) namespace: topic def: "Study microbial model organism." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000086 ! Model organisms -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000213 @@ -3207,7 +3273,7 @@ name: Model organisms (mouse and rat) namespace: topic def: "Study mice and rat model organisms." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000086 ! Model organisms -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000214 @@ -3215,7 +3281,7 @@ name: Model organisms (plants) namespace: topic def: "Study plants model organisms." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000086 ! Model organisms -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000215 @@ -3223,7 +3289,7 @@ name: Model organisms (worm) namespace: topic def: "Study of worm model organisms." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000086 ! Model organisms -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000216 @@ -3231,7 +3297,7 @@ name: Model organisms (yeast) namespace: topic def: "Study yeast model organisms." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000086 ! Model organisms -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined @@ -3269,7 +3335,7 @@ xref: BioCatalogue:Document Similarity xref: BioCatalogue:Document Clustering xref: BioCatalogue:Named Entity Recognition is_a: EDAM:0000088 ! Literature and documentation -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined @@ -3421,7 +3487,7 @@ namespace: topic def: "Construct a biological model." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Model Creation is_a: EDAM:0002268 ! Biological model analysis -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined [Term] @@ -3432,7 +3498,7 @@ def: "Handle or analyse a biological model." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Model Analysis xref: BioCatalogue:Model Execution is_a: EDAM:0002259 ! Systems biology and modelling -relationship: concerns EDAM:0000008 ! Undefined +! relationship: concerns EDAM:0000008 ! Undefined @@ -3440,14 +3506,14 @@ relationship: concerns EDAM:0000008 ! Undefined ! ! Operation ! -[Term] -id: EDAM:0000223 -name: Undefined -namespace: operation -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! [Term] +! id: EDAM:0000223 +! name: Undefined +! namespace: operation +! def: "Debugging." [EDAM:EBI "EMBRACE definition"] +! is_a: EDAM:0000004 ! Operation +! ! relationship: has_input EDAM:0000841 ! Undefined +! ! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3456,8 +3522,8 @@ name: Processing namespace: operation def: "Process (read and / or write) data of a specific type." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002423 @@ -3465,8 +3531,8 @@ name: Prediction, detection and recognition namespace: operation def: "Predict, recognise, detect or identify some properties of a biomolecule." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002424 @@ -3474,8 +3540,8 @@ name: Comparison and alignment namespace: operation def: "Compare two or more things to find similarities or identify equivalent components, typically equivalent subunits of a macromolecular sequence or structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002425 @@ -3483,8 +3549,8 @@ name: Optimisation and refinement namespace: operation def: "Refine or optimise some data model." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002426 @@ -3492,8 +3558,8 @@ name: Modelling and simulation namespace: operation def: "Model or simulate some biological entity or system." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002427 @@ -3510,8 +3576,8 @@ name: Validation and standardisation namespace: operation def: "Validate or standardise some data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3520,8 +3586,8 @@ name: Mapping and assembly namespace: operation def: "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3530,8 +3596,8 @@ name: Design namespace: operation def: "Design a biological entity (typically a molecular sequence or structure) with specific properties." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3552,8 +3618,8 @@ namespace: operation def: "Search or query a data resource and retrieve entries and / or annotation." [EDAM:EBI "EMBRACE definition"] synonym: "Database retrieval" EXACT [] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -3565,8 +3631,8 @@ name: Nucleic acid data processing namespace: operation def: "Process (read and / or write) nucleic acid sequence or structural data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3575,8 +3641,8 @@ name: Protein data processing namespace: operation def: "Process (read and / or write) protein sequence or structural data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -3597,7 +3663,7 @@ namespace: operation def: "Process (read and / or write) an index of (typically a file of) biological data." [EDAM:EBI "EMBRACE definition"] synonym: "Database index processing" EXACT [] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000955 ! Data index [Term] @@ -3606,8 +3672,8 @@ name: Structural data processing namespace: operation def: "Process (read and / or write) molecular structural data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002484 @@ -3615,8 +3681,8 @@ name: Structure processing namespace: operation def: "Process (read and / or write) one or more molecular structures (secondary or tertiary)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002504 ! Structural data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3628,8 +3694,8 @@ is_obsolete: true consider: EDAM:0002480 ! Tertiary structure analysis ! is_a: EDAM:0002484 ! Structure processing ! relationship: is_concern_of EDAM:0000081 ! Structure analysis -! relationship: has_input EDAM:0000841 ! Undefined -! relationship: has_output EDAM:0000841 ! Undefined +! ! relationship: has_input EDAM:0000841 ! Undefined +! ! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3638,8 +3704,8 @@ name: Sequence analysis namespace: operation def: "Analyse one or more molecular sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002408 @@ -3656,8 +3722,8 @@ name: Sequence motif processing namespace: operation def: "Process (read and / or write) molecular sequence motifs." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002503 ! Sequence data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -3676,8 +3742,8 @@ name: Physicochemical property data processing namespace: operation def: "Process (read and / or write) data on the physicochemical property of a molecule." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3689,8 +3755,8 @@ is_obsolete: true consider: EDAM:0002481 ! Tertiary structure analysis (nucleic acid) ! is_a: EDAM:0002431 ! Structure analysis ! relationship: is_concern_of EDAM:0000097 ! Nucleic acid structure analysis -! relationship: has_input EDAM:0000841 ! Undefined -! relationship: has_output EDAM:0000841 ! Undefined +! ! relationship: has_input EDAM:0000841 ! Undefined +! ! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3703,8 +3769,8 @@ consider: EDAM:0002406 ! Tertiary structure analysis (protein) ! is_a: EDAM:0002431 ! Structure analysis ! relationship: is_concern_of EDAM:0000126 ! Protein structure analysis -! relationship: has_input EDAM:0000841 ! Undefined -! relationship: has_output EDAM:0000841 ! Undefined +! ! relationship: has_input EDAM:0000841 ! Undefined +! ! relationship: has_output EDAM:0000841 ! Undefined @@ -3715,7 +3781,7 @@ name: Protein function data processing namespace: operation def: "Process (read and / or write) protein functional data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001776 ! Protein function annotation @@ -3727,7 +3793,7 @@ name: Sequence alignment analysis namespace: operation def: "Analyse a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002463 ! Sequence alignment processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000867 ! Sequence alignment metadata @@ -3738,7 +3804,7 @@ namespace: operation def: "Analyse a protein sequence alignment." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000867 ! Sequence alignment metadata [Term] @@ -3748,7 +3814,7 @@ namespace: operation def: "Analyse a protein sequence alignment." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000867 ! Sequence alignment metadata @@ -3760,8 +3826,8 @@ name: Protein secondary structure analysis namespace: operation def: "Analyse protein secondary structure data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002444 ! Secondary structure processing (protein) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -3773,7 +3839,7 @@ namespace: operation def: "Process (read and / or write) data on transmembrane proteins and domains / regions." [EDAM:EBI "EMBRACE definition"] comment: Use this (or child) term for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001456 ! Membrane protein annotation (secondary structure) @@ -3795,7 +3861,7 @@ namespace: operation def: "Predict tertiary structure of a molecular (biopolymer) sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002423 ! Prediction, detection and recognition is_a: EDAM:0002465 ! Tertiary structure processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure @@ -3806,8 +3872,8 @@ name: Protein interaction data processing namespace: operation def: "Process (read and / or write) protein interaction data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3826,7 +3892,7 @@ name: DNA mapping namespace: operation def: "Generate a DNA map of some type." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002521 ! DNA map data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001274 ! Map [Term] @@ -3839,7 +3905,7 @@ synonym: "Genetic map generation" EXACT [] synonym: "Linkage mapping" EXACT [] is_a: EDAM:0002520 ! DNA mapping is_a: EDAM:0000283 ! Linkage analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001278 ! Genetic map @@ -3851,8 +3917,8 @@ def: "Analyse genetic linkage." [EDAM:EBI "EMBRACE definition"] comment: For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. ! is_a: EDAM:0002429 ! Mapping and assembly is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3861,7 +3927,7 @@ name: Codon usage data processing namespace: operation def: "Process (read and / or write) codon usage data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000914 ! Codon usage data [Term] @@ -3870,8 +3936,8 @@ name: Sequence data processing namespace: operation def: "Process (read and / or write) molecular sequence data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -3891,7 +3957,7 @@ def: "Align molecular sequences." [EDAM:EBI "EMBRACE definition"] synonym: "Sequence alignment generation" EXACT [] is_a: EDAM:0002463 ! Sequence alignment processing is_a: EDAM:0002451 ! Sequence comparison -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000863 ! Sequence alignment [Term] @@ -3900,7 +3966,7 @@ name: Hybrid sequence alignment namespace: operation def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000292 ! Sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000863 ! Sequence alignment [Term] @@ -3909,7 +3975,7 @@ name: Structure-based sequence alignment namespace: operation def: "Align molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000292 ! Sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000863 ! Sequence alignment @@ -3921,7 +3987,7 @@ namespace: operation def: "Analyse a molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002424 ! Comparison and alignment is_a: EDAM:0002465 ! Tertiary structure processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000886 ! Tertiary structure alignment @@ -3933,7 +3999,7 @@ namespace: operation def: "Compare two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002424 ! Comparison and alignment is_a: EDAM:0002465 ! Tertiary structure processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000886 ! Undefined @@ -3944,7 +4010,7 @@ namespace: operation def: "Align (superimpose) molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002424 ! Comparison and alignment is_a: EDAM:0002483 ! Tertiary structure comparison -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000886 ! Tertiary structure alignment @@ -3954,8 +4020,8 @@ name: Sequence profile processing namespace: operation def: "Process (read and / or write) some type of sequence profile." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002503 ! Sequence data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -3985,7 +4051,7 @@ synonym: "Protein fold prediction" EXACT [] is_a: EDAM:0002479 ! Sequence analysis (protein) is_a: EDAM:0000474 ! Tertiary structure prediction (protein) is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000901 ! Protein features (domain composition) @@ -3995,8 +4061,8 @@ name: Demonstration namespace: operation def: "An operation performing purely illustrative (pedagogical) purposes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -4005,7 +4071,7 @@ name: Text processing namespace: operation def: "Process (read and / or write) text." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000972 ! Text mining report [Term] @@ -4015,7 +4081,7 @@ namespace: operation def: "Process and analyse the biomedical and informatics literature to extract information from it." [EDAM:EBI "EMBRACE definition"] synonym: "Text data mining" EXACT [] is_a: EDAM:0002505 ! Text processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000972 ! Text mining report @@ -4026,8 +4092,8 @@ namespace: operation def: "Design oligonucleotide primers or probes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) is_a: EDAM:0002430 ! Design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -4039,7 +4105,7 @@ def: "Assemble fragments of a DNA sequence to reconstruct the original sequence. comment: Typically, contigs (for example ESTs and genomic DNA fragments) are aligned and merged, depending on the detected fragment overlaps. Annotation of the assembled sequence might be generated. is_a: EDAM:0002429 ! Mapping and assembly is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000925 ! Sequence assembly @@ -4049,8 +4115,8 @@ name: Microarray data processing namespace: operation def: "Process (read and / or write) microarray data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -4059,8 +4125,8 @@ name: Microarray data analysis namespace: operation def: "Analyse microarray data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002432 ! Microarray data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000311 @@ -4070,8 +4136,8 @@ def: "Standardize or normalize microarray data." [EDAM:EBI "EMBRACE definition"] comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. is_a: EDAM:0002500 ! Microarray data analysis is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -4081,8 +4147,8 @@ name: Gene expression data processing namespace: operation def: "Process (read and / or write) gene expression and regulation data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -4094,8 +4160,8 @@ namespace: operation def: "Identify and select targets for protein structural determination." [EDAM:EBI "EMBRACE definition"] comment: Methods will typically navigate a graph of protein families of known structure. is_a: EDAM:0002406 ! Tertiary structure analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002406 @@ -4104,8 +4170,8 @@ namespace: operation def: "Analyse protein tertiary structural data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002480 ! Tertiary structure analysis is_a: EDAM:0002459 ! Tertiary structure processing (protein) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002481 @@ -4114,8 +4180,8 @@ namespace: operation def: "Analyse nucleic acid tertiary structural data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002480 ! Tertiary structure analysis is_a: EDAM:0002519 ! Tertiary structure processing (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -4126,7 +4192,7 @@ name: Phylogenetic tree analysis namespace: operation def: "Analyse a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002443 ! Phylogenetic tree processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001438 ! Phylogenetic tree metadata @@ -4136,8 +4202,8 @@ name: Pathway or network processing namespace: operation def: "Generate, analyse or handle a biological pathway or network." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002420 ! Processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -4146,8 +4212,8 @@ name: Pathway or network analysis namespace: operation def: "Analyse a biological pathway or network." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002438 ! Pathway or network processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -4159,7 +4225,7 @@ namespace: operation def: "Analyse (typically by modelling) protein folding." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002502 ! Protein data processing is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000903 ! Protein folding model @@ -4173,7 +4239,7 @@ comment: Methods might predict silent or pathological mutations. is_a: EDAM:0002406 ! Tertiary structure analysis (protein) is_a: EDAM:0002426 ! Modelling and simulation is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000904 ! Protein mutation model @@ -4201,8 +4267,8 @@ def: "Process (read and / or write) a data file (or equivalent entity). Processi synonym: "Report handling" EXACT [] synonym: "File handling" EXACT [] is_a: EDAM:0002505 ! Text processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -4212,8 +4278,8 @@ namespace: operation def: "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." [EDAM:EBI "EMBRACE definition"] synonym: "Visualisation" EXACT [] is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -4228,8 +4294,8 @@ namespace: operation def: "Perform basic (non-analytical) operations on (a report or file of( sequences (which might include features), such as file creation or concatenation, removal or ordering of sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002446 ! Sequence processing is_a: EDAM:0002409 ! Report processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002122 @@ -4238,8 +4304,8 @@ namespace: operation def: "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002409 ! Report processing is_a: EDAM:0002463 ! Sequence alignment processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002234 @@ -4248,8 +4314,8 @@ namespace: operation def: "Perform basic operations on a file of molecular tertiary structural data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002409 ! Report processing is_a: EDAM:0002465 ! Tertiary structure processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -4258,8 +4324,8 @@ name: Listfile processing namespace: operation def: "Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002409 ! Report processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0001812 @@ -4269,8 +4335,8 @@ def: "Retrieve, prepare or load a user-specified data file so that it is availab xref: WHATIF:UploadPDB is_a: EDAM:0002409 ! Report processing is_a: EDAM:0000224 ! Search and retrieval -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000335 @@ -4278,8 +4344,8 @@ name: Report reformatting namespace: operation def: "Reformat a file of data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002409 ! Report processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -4289,8 +4355,8 @@ namespace: operation def: "Test and validate the format and content of a data file." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002409 ! Report processing is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -4306,16 +4372,16 @@ namespace: operation def: "Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000224 ! Search and retrieval is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined id: EDAM:0002422 name: Data and annotation retrieval namespace: operation -def: "Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching suppplied keywords." [EDAM:EBI "EMBRACE definition"] +def: "Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000224 ! Search and retrieval -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -4352,7 +4418,7 @@ name: Database cross-reference retrieval namespace: operation def: "Search database to retrieve all relevant cross-references for a particular entity or entry." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000954 ! Data cross-reference [Term] @@ -4363,7 +4429,7 @@ def: "Query a sequence data resource (typically a database) and retrieve sequenc comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. is_a: EDAM:0002422 ! Data and annotation retrieval is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record [Term] @@ -4376,7 +4442,7 @@ xref: WHATIF:DownloadPDB xref: WHATIF:EchoPDB is_a: EDAM:0002422 ! Data and annotation retrieval is_a: EDAM:0002465 ! Tertiary structure processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure [Term] @@ -4388,7 +4454,7 @@ comment: This includes direct retrieval methods that retrieve a profile by, e.g. synonym: "Sequence profile retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval is_a: EDAM:0002413 ! Sequence profile processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record [Term] @@ -4398,7 +4464,7 @@ namespace: operation def: "Retrieve a codon usage table and / or associated annotation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002422 ! Data and annotation retrieval is_a: EDAM:0002433 ! Codon usage table processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record [Term] @@ -4408,7 +4474,7 @@ namespace: operation def: "Query a biological pathways database and retrieve annotation on one or more pathways." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002422 ! Data and annotation retrieval is_a: EDAM:0002438 ! Pathway or network processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000946 ! Pathway or network annotation [Term] @@ -4417,7 +4483,7 @@ name: Identifier retrieval namespace: operation def: "Query a database and retrieve one or more data identifiers." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000842 ! Identifier @@ -4430,7 +4496,7 @@ namespace: operation def: "Query an ontology and retrieve terms or relations." [EDAM:EBI "EMBRACE definition"] synonym: "Ontology retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000966 ! Ontology term @@ -4441,7 +4507,7 @@ namespace: operation def: "Retrieve a phylogenetic tree from a data resource." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002422 ! Data and annotation retrieval is_a: EDAM:0002443 ! Phylogenetic tree processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001438 ! Phylogenetic tree metadata [Term] @@ -4451,7 +4517,7 @@ namespace: operation def: "Display basic information about a sequence alignment." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002463 ! Sequence alignment processing is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000867 ! Sequence alignment metadata @@ -4463,7 +4529,7 @@ namespace: operation def: "Retrieve information on a specific genotype or phenotype." [EDAM:EBI "EMBRACE definition"] synonym: "Genotype / phenotype information retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000920 ! Genotype / phenotype annotation [Term] @@ -4473,7 +4539,7 @@ namespace: operation def: "Retrieve information on a specific gene." [EDAM:EBI "EMBRACE definition"] synonym: "Gene information retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000916 ! Gene annotation [Term] @@ -4483,7 +4549,7 @@ namespace: operation def: "Retrieve information on an RNA family." [EDAM:EBI "EMBRACE definition"] synonym: "RNA family information retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002354 ! RNA family annotation [Term] @@ -4493,7 +4559,7 @@ namespace: operation def: "Retrieve information on a protein family." [EDAM:EBI "EMBRACE definition"] synonym: "Protein family information retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000907 ! Protein family annotation [Term] @@ -4503,7 +4569,7 @@ namespace: operation def: "Retrieve information on a protein interaction." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002422 ! Data and annotation retrieval is_a: EDAM:0002405 ! Protein interaction data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000906 ! Protein interaction annotation @@ -4517,7 +4583,7 @@ def: "Retrieve information on a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Protein information retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000896 ! Protein annotation [Term] @@ -4527,7 +4593,7 @@ namespace: operation def: "Retrieve information on restriction enzymes or restriction enzyme sites." [EDAM:EBI "EMBRACE definition"] synonym: "Restriction enzyme information retrieval" EXACT [] is_a: EDAM:0002467 ! Protein annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001517 ! Restriction enzyme annotation @@ -4538,7 +4604,7 @@ namespace: operation def: "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." [EDAM:EBI "EMBRACE definition"] synonym: "Tool information retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000958 ! Tool metadata [Term] @@ -4548,7 +4614,7 @@ namespace: operation def: "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." [EDAM:EBI "EMBRACE definition"] synonym: "Database information retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000957 ! Database metadata [Term] @@ -4558,7 +4624,7 @@ namespace: operation def: "Search and retrieve documentation on a bioinformatics ontology." [EDAM:EBI "EMBRACE definition"] synonym: "Ontology information retrieval" EXACT [] is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002223 ! Ontology metadata @@ -4574,7 +4640,7 @@ name: Sequence retrieval (by code) namespace: operation def: "Query a database and retrieve sequences with a given entry code or accession number." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001813 ! Sequence retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record [Term] @@ -4583,7 +4649,7 @@ name: Sequence retrieval (by keyword) namespace: operation def: "Query a database and retrieve sequences containing a given keyword." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001813 ! Sequence retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record @@ -4615,7 +4681,7 @@ name: Literature search namespace: operation def: "Query the biomedical and informatics literature." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002421 ! Database search -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000970 ! Citation @@ -4626,8 +4692,8 @@ namespace: operation def: "Search a sequence database by sequence comparison and retrieve similar sequences." [EDAM:EBI "EMBRACE definition"] comment: This excludes direct retrieval methods (e.g. the dbfetch program). is_a: EDAM:0002421 ! Database search -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000339 @@ -4635,7 +4701,7 @@ name: Structure database search namespace: operation def: "Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002421 ! Database search -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000885 ! Tertiary structure database hits [Term] @@ -4646,7 +4712,7 @@ def: "Search a secondary protein database (of classification information) to ass comment: Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). synonym: "Protein sequence classification" EXACT [] is_a: EDAM:0002421 ! Database search -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000858 ! Secondary database hits [Term] @@ -4655,7 +4721,7 @@ name: Motif database search namespace: operation def: "Screen a sequence against a motif or pattern database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002421 ! Database search -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001298 ! Sequence motif report [Term] @@ -4666,7 +4732,7 @@ def: "Search a database of sequence profiles with a query sequence." [EDAM:EBI " synonym: "Sequence profile database search" EXACT [] is_a: EDAM:0002421 ! Database search is_a: EDAM:0000300 ! Sequence-profile alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000869 ! Sequence-profile alignment relationship: has_output EDAM:0001298 ! Sequence motif report @@ -4689,7 +4755,7 @@ def: "Search a sequence database and retrieve sequences that are similar to a qu synonym: "Sequence similarity search" EXACT [] is_a: EDAM:0000338 ! Sequence database search is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000857 ! Sequence database hits @@ -4700,7 +4766,7 @@ namespace: operation def: "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000338 ! Sequence database search is_a: EDAM:0000239 ! Sequence motif recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record @@ -4710,7 +4776,7 @@ name: Sequence database search (by amino acid composition) namespace: operation def: "Search a sequence database and retrieve sequences of a given amino acid composition." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000338 ! Sequence database search -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record [Term] @@ -4719,7 +4785,7 @@ name: Sequence database search (by physicochemical property) namespace: operation def: "Search a sequence database and retrieve sequences with a specified physicochemical property." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000338 ! Sequence database search -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record @@ -4736,7 +4802,7 @@ comment: Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAS synonym: "Sequence similarity search (word-based methods)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000288 ! Sequence word comparison -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000857 ! Sequence database hits [Term] @@ -4748,7 +4814,7 @@ comment: This includes tools based on PSI-BLAST. synonym: "Sequence similarity search (profile-based methods)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000300 ! Sequence-profile alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000857 ! Sequence database hits [Term] @@ -4760,7 +4826,7 @@ comment: This includes tools based on the Smith-Waterman algorithm or FASTA. synonym: "Sequence similarity search (local alignment-based methods) " EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000493 ! Pairwise sequence alignment (local) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000857 ! Sequence database hits [Term] @@ -4772,7 +4838,7 @@ comment: This includes tools based on the Needleman and Wunsch algorithm. synonym: "Sequence similarity search (global alignment-based methods)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000494 ! Pairwise sequence alignment (global) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000857 ! Sequence database hits [Term] @@ -4783,7 +4849,7 @@ def: "Search a DNA database (for example a database of conserved sequence tags) comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. synonym: "Sequence similarity search (primer sequences)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000857 ! Sequence database hits @@ -4812,7 +4878,7 @@ def: "Search sequence(s) or a sequence database for sequences which match a set synonym: "Protein fingerprinting" EXACT [] synonym: "Peptide mass fingerprinting" EXACT [] is_a: EDAM:0000349 ! Sequence database search (by physicochemical property) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record @@ -4822,7 +4888,7 @@ name: Sequence database search (by isoelectric point) namespace: operation def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000349 ! Sequence database search (by physicochemical property) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000849 ! Sequence record @@ -4836,7 +4902,7 @@ name: Tertiary structure retrieval (by code) namespace: operation def: "Query a tertiary structure database and retrieve entries with a given entry code or accession number." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001814 ! Tertiary structure retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure [Term] @@ -4845,7 +4911,7 @@ name: Tertiary structure retrieval (by keyword) namespace: operation def: "Query a tertiary structure database and retrieve entries containing a given keyword." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001814 ! Tertiary structure retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure [Term] @@ -4855,7 +4921,7 @@ namespace: operation def: "Query a tertiary structure database and retrieve water molecules." [EDAM:EBI "EMBRACE definition"] xref: WHATIF:MovedWaterPDB is_a: EDAM:0001814 ! Tertiary structure retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure @@ -4870,7 +4936,7 @@ namespace: operation def: "Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence." [EDAM:EBI "EMBRACE definition"] synonym: "Tertiary structure retrieval by sequence" EXACT [] is_a: EDAM:0000339 ! Structure database search -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure [Term] @@ -4881,7 +4947,7 @@ def: "Search a tertiary structure database and retrieve structures that are simi synonym: "Tertiary structure retrieval by structure" EXACT [] synonym: "Structural similarity search" EXACT [] is_a: EDAM:0000339 ! Structure database search -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure @@ -4935,10 +5001,10 @@ id: EDAM:0000226 name: Annotation namespace: operation def: "Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] -comment: Use this terms for tools which allow for manual annotations, not for automated methods such as prediciton algorithms. +comment: Use this terms for tools which allow for manual annotations, not for automated methods such as prediction algorithms. is_a: EDAM:0000004 ! Operation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0001774 @@ -4960,7 +5026,7 @@ name: Sequence annotation namespace: operation def: "Annotate a molecular sequence with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000226 ! Annotation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation [Term] @@ -4969,8 +5035,8 @@ name: Genome annotation namespace: operation def: "Annotate a genome sequence with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000361 ! Sequence annotation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -4980,8 +5046,8 @@ namespace: operation def: "Annotate a DNA map of some type with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000226 ! Annotation is_a: EDAM:0002521 ! DNA map data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -4995,7 +5061,7 @@ namespace: operation def: "Generate an index of (typically a file of) biological data." [EDAM:EBI "EMBRACE definition"] synonym: "Database indexing" EXACT [] is_a: EDAM:0002412 ! Data index processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000955 ! Data index [Term] @@ -5005,7 +5071,7 @@ namespace: operation def: "Analyse an index of biological data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002412 ! Data index processing synonym: "Database index analysis" EXACT [] -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000956 ! Data index metadata @@ -5044,8 +5110,8 @@ namespace: operation def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002479 @@ -5054,8 +5120,8 @@ namespace: operation def: "Analyse a protein sequence (using methods that might be applicable to protein sequences)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -5064,8 +5130,8 @@ name: Sequence processing namespace: operation def: "Process (read and / or write) one or more molecular sequences and associated annotation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002503 ! Sequence data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002447 @@ -5075,8 +5141,8 @@ def: "Process (read and / or write) a protein sequence (using methods that are o is_obsolete: true consider: EDAM:0002446 ! Sequence processing ! is_a: EDAM:0002446 ! Sequence processing -! relationship: has_input EDAM:0000841 ! Undefined -! relationship: has_output EDAM:0000841 ! Undefined +! ! relationship: has_input EDAM:0000841 ! Undefined +! ! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002448 @@ -5086,8 +5152,8 @@ def: "Process (read and / or write) a nucleotide sequence (using methods that ar is_obsolete: true consider: EDAM:0002446 ! Sequence processing ! is_a: EDAM:0002446 ! Sequence processing -! relationship: has_input EDAM:0000841 ! Undefined -! relationship: has_output EDAM:0000841 ! Undefined +! ! relationship: has_input EDAM:0000841 ! Undefined +! ! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002449 @@ -5097,8 +5163,8 @@ def: "Process (read and / or write) a sequence (using methods that might be appl is_obsolete: true consider: EDAM:0002446 ! Sequence processing ! is_a: EDAM:0002446 ! Sequence processing -! relationship: has_input EDAM:0000841 ! Undefined -! relationship: has_output EDAM:0000841 ! Undefined +! ! relationship: has_input EDAM:0000841 ! Undefined +! ! relationship: has_output EDAM:0000841 ! Undefined @@ -5119,7 +5185,7 @@ name: Sequence generation namespace: operation def: "Generate a molecular sequence by some means." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002121 ! Sequence report processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5129,7 +5195,7 @@ namespace: operation def: "Generate a nucleic acid sequence by some means." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000230 ! Sequence generation is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5139,7 +5205,7 @@ namespace: operation def: "Generate a protein sequence by some means." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000230 ! Sequence generation is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data @@ -5151,7 +5217,7 @@ name: Sequence editing namespace: operation def: "Edit or change a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002121 ! Sequence report processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5161,7 +5227,7 @@ namespace: operation def: "Edit or change a nucleic acid sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000231 ! Sequence editing is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5171,7 +5237,7 @@ namespace: operation def: "Edit or change a protein sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000231 ! Sequence editing is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data @@ -5182,7 +5248,7 @@ namespace: operation def: "Merge two or more (typically overlapping) molecular sequences." [EDAM:EBI "EMBRACE definition"] synonym: "Sequence splicing" EXACT [] is_a: EDAM:0002121 ! Sequence report processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5191,7 +5257,7 @@ name: Sequence conversion namespace: operation def: "Convert a molecular sequence from one type to another." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002121 ! Sequence report processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5200,7 +5266,7 @@ name: Sequence submission namespace: operation def: "Submit a molecular sequence to a database." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000848 ! Undefined [Term] @@ -5209,7 +5275,7 @@ name: Sequence complexity calculation namespace: operation def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002403 ! Sequence analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001259 ! Sequence complexity [Term] @@ -5218,7 +5284,7 @@ name: Sequence ambiguity calculation namespace: operation def: "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002403 ! Sequence analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001260 ! Sequence ambiguity [Term] @@ -5229,7 +5295,7 @@ def: "Build clusters of similar sequences, typically using scores from pair-wise synonym: "Sequence cluster generation" EXACT [] is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002452 ! Sequence cluster processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001235 ! Sequence cluster @@ -5240,7 +5306,7 @@ name: Sequence composition calculation namespace: operation def: "Calculate character or word composition or frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002403 ! Sequence analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001261 ! Sequence composition [Term] @@ -5250,7 +5316,7 @@ namespace: operation def: "Find or analyse repeat sequences in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] comment: Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. is_a: EDAM:0002403 ! Sequence analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001299 ! Repeat sequence report @@ -5260,8 +5326,8 @@ name: Sequence redundancy removal namespace: operation def: "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002451 ! Sequence comparison -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -5271,8 +5337,8 @@ namespace: operation def: "Compare two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002446 ! Sequence processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002508 @@ -5281,8 +5347,8 @@ namespace: operation def: "Compare two or more nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002509 @@ -5291,8 +5357,8 @@ namespace: operation def: "Compare two or more protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002479 ! Sequence analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -5302,7 +5368,7 @@ name: Sequence word comparison namespace: operation def: "Find exact character or word matches between molecular sequences without full sequence alignment." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002451 ! Sequence comparison -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000861 ! Sequence word alignment [Term] @@ -5312,7 +5378,7 @@ namespace: operation def: "Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences." [EDAM:EBI "EMBRACE definition"] synonym: "Phylogenetic distance matrix generation" EXACT [] is_a: EDAM:0002451 ! Sequence comparison -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000870 ! Sequence distance matrix @@ -5323,8 +5389,8 @@ namespace: operation def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002508 ! Sequence comparison (nucleic acid) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -5336,7 +5402,7 @@ namespace: operation def: "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001235 ! Sequence cluster @@ -5363,8 +5429,8 @@ def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [ED comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. is_a: EDAM:0002508 ! Sequence comparison (nucleic acid) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -5375,8 +5441,8 @@ namespace: operation def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000281 @@ -5387,8 +5453,8 @@ comment: A genetic marker is any DNA sequence of known chromosomal location that is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) is_a: EDAM:0002429 ! Mapping and assembly is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -5405,7 +5471,7 @@ name: Nucleic acid sequence reverse and complement namespace: operation def: "Generate the reverse and / or complement of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002513 ! Sequence generation (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5414,7 +5480,7 @@ name: Random sequence generation namespace: operation def: "Generate a random sequence, for example, with a specific character composition." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000230 ! Sequence generation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5423,7 +5489,7 @@ name: Nucleic acid sequence restriction digest namespace: operation def: "Generate digest fragments for a nucleotide sequence containing restriction sites." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002513 ! Sequence generation (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001239 ! Restriction digest [Term] @@ -5432,7 +5498,7 @@ name: Protein sequence cleavage namespace: operation def: "Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002514 ! Sequence generation (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001238 ! Proteolytic digest @@ -5446,7 +5512,7 @@ name: Sequence mutation and randomization namespace: operation def: "Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000231 ! Sequence editing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5456,7 +5522,7 @@ namespace: operation def: "Mask characters in a molecular sequence (replacing those characters with a mask character)." [EDAM:EBI "EMBRACE definition"] comment: For example, SNPs or repeats in a DNA sequence might be masked. is_a: EDAM:0000231 ! Sequence editing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5465,7 +5531,7 @@ name: Sequence cutting namespace: operation def: "Cut (remove) characters or a region from a molecular sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000231 ! Sequence editing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data @@ -5475,7 +5541,7 @@ name: Restriction site creation namespace: operation def: "Create (or remove) restriction sites in sequences, for example using silent mutations." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002511 ! Sequence editing (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data @@ -5496,7 +5562,7 @@ name: DNA translation namespace: operation def: "Translate a DNA sequence into protein." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000233 ! Sequence conversion -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5505,7 +5571,7 @@ name: DNA transcription namespace: operation def: "Transcribe a nucleotide sequence into mRNA sequence(s)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000233 ! Sequence conversion -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data [Term] @@ -5514,7 +5580,7 @@ name: DNA back-translation namespace: operation def: "Back-translate a protein sequence into DNA." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000233 ! Sequence conversion -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002044 ! Sequence data @@ -5582,7 +5648,7 @@ namespace: operation def: "Calculate base frequency or word composition of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000236 ! Sequence composition calculation is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001261 ! Sequence composition [Term] @@ -5592,7 +5658,7 @@ namespace: operation def: "Calculate amino acid frequency or word composition of a protein sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000236 ! Sequence composition calculation is_a: EDAM:0002479 ! Sequence analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001261 ! Sequence composition @@ -5606,7 +5672,7 @@ namespace: operation def: "Calculate a density plot (of base composition) for a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000377 ! Sequence composition calculation (nucleic acid) is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001261 ! Sequence composition @@ -5621,7 +5687,7 @@ namespace: operation def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000237 ! Repeat sequence analysis is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001299 ! Repeat sequence report [Term] @@ -5630,7 +5696,7 @@ name: Repeat sequence organisation analysis namespace: operation def: "Analyse repeat sequence organization such as periodicity." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000237 ! Repeat sequence analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001299 ! Repeat sequence report [Term] @@ -5660,7 +5726,7 @@ namespace: operation def: "Draw a dotplot of sequence similarities identified from word-matching or character comparison." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000288 ! Sequence word comparison is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000862 ! Dotplot @@ -5698,8 +5764,8 @@ comment: For example cross-species comparison of transcription factor binding si is_a: EDAM:0000241 ! Transcription regulatory sequence analysis is_a: EDAM:0002424 ! Comparison and alignment is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -5719,7 +5785,7 @@ comment: Motifs and patterns might be conserved or over-represented (occur with synonym: "Motif discovery" EXACT [] is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002404 ! Sequence motif processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001298 ! Sequence motif report [Term] @@ -5731,7 +5797,7 @@ synonym: "Sequence motif detection" EXACT [] is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002404 ! Sequence motif processing is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001298 ! Sequence motif report [Term] @@ -5742,8 +5808,8 @@ def: "Find motifs shared by molecular sequences and identify similar sequences o is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002404 ! Sequence motif processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -5761,7 +5827,7 @@ namespace: operation def: "Find (scan for) known motifs, patterns and regular expressions in nucleotide sequence(s)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000239 ! Sequence motif recognition is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001298 ! Sequence motif report [Term] @@ -5771,7 +5837,7 @@ namespace: operation def: "Find (scan for) known motifs, patterns and regular expressions in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000239 ! Sequence motif recognition is_a: EDAM:0002479 ! Sequence analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001298 ! Sequence motif report ! @@ -5791,8 +5857,8 @@ name: Physicochemical property data processing (small molecule) namespace: operation def: "Calculate or extract a physicochemical property of a small molecule." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002417 ! Physicochemical property data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000250 @@ -5802,7 +5868,7 @@ def: "Calculate or extract a physicochemical property of protein sequence(s)." [ is_a: EDAM:0002417 ! Physicochemical property data processing is_a: EDAM:0002479 ! Sequence analysis (protein) is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000897 ! Protein physicochemical property @@ -5814,7 +5880,7 @@ def: "Calculate or extract a physicochemical property of nucleotide sequence(s). is_a: EDAM:0002417 ! Physicochemical property data processing is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000912 ! Nucleic acid physicochemical property @@ -5835,7 +5901,7 @@ name: Enzyme kinetics calculation namespace: operation def: "Calculate Km, Vmax and derived data for an enzyme reaction." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000250 ! Physicochemical property data processing (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002024 ! Enzyme kinetics report [Term] @@ -5845,7 +5911,7 @@ namespace: operation def: "Calculate, compare or process molecular weight data of a protein sequence or fragments." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000250 ! Physicochemical property data processing (protein) is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000897 ! Protein physicochemical property [Term] @@ -5855,7 +5921,7 @@ namespace: operation def: "Predict extinction coefficients or optical density of a protein sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000250 ! Physicochemical property data processing (protein) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000897 ! Protein physicochemical property [Term] @@ -5864,7 +5930,7 @@ name: Protein pH-dependent property calculation namespace: operation def: "Calculate pH-dependent properties from pKa calculations of a protein sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000250 ! Physicochemical property data processing (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000897 ! Protein physicochemical property @@ -5875,7 +5941,7 @@ namespace: operation def: "Hydropathy calculation on a protein sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002574 ! Protein hydropathy calculation is_a: EDAM:0000250 ! Physicochemical property data processing (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000897 ! Protein physicochemical property [Term] @@ -5888,7 +5954,7 @@ is_a: EDAM:0002414 ! Protein function data processing is_a: EDAM:0000250 ! Physicochemical property data processing (protein) is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001534 ! Peptide immunogenicity report @@ -5922,7 +5988,7 @@ namespace: operation def: "Plot a protein titration curve." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000400 ! Protein pH-dependent property calculation is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001527 ! Protein titration curve @@ -5932,7 +5998,7 @@ name: Protein isoelectric point calculation namespace: operation def: "Calculate isoelectric point of a protein sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000400 ! Protein pH-dependent property calculation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001528 ! Protein isoelectric point @@ -5942,7 +6008,7 @@ name: Protein hydrogen exchange rate calculation namespace: operation def: "Estimate hydrogen exchange rate of a protein sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000400 ! Protein pH-dependent property calculation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001530 ! Protein hydrogen exchange rate @@ -5957,7 +6023,7 @@ namespace: operation def: "Calculate hydrophobic or hydrophilic / charged regions of a protein sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001522 ! Protein sequence hydropathy plot relationship: has_output EDAM:0001523 ! Protein charge plot @@ -5968,7 +6034,7 @@ name: Protein aliphatic index calculation namespace: operation def: "Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001521 ! Protein aliphatic index [Term] @@ -5979,7 +6045,7 @@ def: "Calculate the hydrophobic moment of a peptide sequence and recognize amphi comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001520 ! Peptide hydrophobic moment [Term] @@ -5989,7 +6055,7 @@ namespace: operation def: "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001526 ! Protein globularity data [Term] @@ -5999,7 +6065,7 @@ namespace: operation def: "Predict the solubility or atomic solvation energy of a protein sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001524 ! Protein solubility data [Term] @@ -6009,7 +6075,7 @@ namespace: operation def: "Predict crystallizability of a protein sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001525 ! Protein crystallizability data @@ -6028,7 +6094,7 @@ name: Nucleic acid melting temperature calculation namespace: operation def: "Calculate DNA or DNA/RNA melting temperature, enthalpy and entropy." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000261 ! Physicochemical property data processing (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000912 ! Nucleic acid physicochemical property [Term] @@ -6039,7 +6105,7 @@ def: "Calculate and plot a DNA or DNA/RNA melting profile." [EDAM:EBI "EMBRACE d comment: A melting profile is used to visualise and analyse partly melted DNA conformations. is_a: EDAM:0000261 ! Physicochemical property data processing (nucleic acid) is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001583 ! Nucleic acid melting profile @@ -6054,7 +6120,7 @@ name: Nucleic acid structural property calculation namespace: operation def: "Calculate or extract a property of nucleic acid structure such as conformational parameters or properties." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002481 ! Tertiary structure analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000912 ! Nucleic acid physicochemical property @@ -6101,7 +6167,7 @@ def: "Predict RNA secondary structure (for example knots, pseudoknots, alternati comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). is_a: EDAM:0002439 ! Secondary structure processing (RNA) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000880 ! RNA secondary structure [Term] @@ -6111,7 +6177,7 @@ namespace: operation def: "Predict RNA tertiary structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002440 ! Tertiary structure processing (RNA) is_a: EDAM:0000475 ! Tertiary structure prediction (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001465 ! RNA tertiary structure @@ -6121,7 +6187,7 @@ name: DNA tertiary structure prediction namespace: operation def: "Predict DNA tertiary structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000475 ! Tertiary structure prediction (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001465 ! RNA tertiary structure @@ -6134,7 +6200,7 @@ namespace: operation def: "Analyse or model RNA/DNA folding." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002426 ! Modelling and simulation is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001596 ! Nucleic acid folding model @@ -6154,7 +6220,7 @@ def: "Calculate curvature and flexibility / stiffness of a nuclotide sequence." comment: This includes properties such as. is_a: EDAM:0000262 ! Nucleic acid structural property calculation is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000912 ! Nucleic acid physicochemical property @@ -6180,7 +6246,7 @@ name: Nucleic acid folding energy calculation namespace: operation def: "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000279 ! Nucleic acid folding analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001596 ! Nucleic acid folding model @@ -6194,8 +6260,8 @@ name: Quadruplex structure prediction namespace: operation def: "Predict quadruplex (4 stranded) structures in DNA." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002442 ! DNA tertiary structure prediction -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -6211,7 +6277,7 @@ def: "Predict general functional properties of a protein." [EDAM:EBI "EMBRACE de comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. is_a: EDAM:0002414 ! Protein function data processing is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001776 ! Protein function annotation @@ -6223,7 +6289,7 @@ namespace: operation def: "Compare the general functional properties of two or more proteins." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002414 ! Protein function data processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001776 ! Protein function annotation @@ -6243,8 +6309,8 @@ name: MHC peptide immunogenicity prediction namespace: operation def: "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000252 ! Peptide immunogenicity prediction -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -6259,7 +6325,7 @@ namespace: operation def: "Predict, recognise and identify features in molecular sequences such as key functional sites or regions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6281,7 +6347,7 @@ namespace: operation def: "Extract a sequence feature table from a sequence database entry." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002453 ! Sequence feature table processing is_a: EDAM:0002422 ! Data and annotation retrieval -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001270 ! Sequence feature table @@ -6291,8 +6357,8 @@ name: Sequence feature table query namespace: operation def: "Query the features (in a feature table) of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002453 ! Sequence feature table processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000256 @@ -6301,7 +6367,7 @@ namespace: operation def: "Compare the feature tables of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002453 ! Sequence feature table processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001256 ! Sequence feature comparison report @@ -6318,7 +6384,7 @@ def: "Predict, recognise and identify features in protein sequences such as func comment: Methods might use protein sequence alignments, linear motifs and patterns. is_a: EDAM:0000253 ! Sequence feature detection is_a: EDAM:0002479 ! Sequence analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation [Term] @@ -6329,7 +6395,7 @@ def: "Predict, recognise and identify features in nucleotide sequences such as f comment: Methods might use protein sequence alignments, linear motifs and patterns. is_a: EDAM:0000253 ! Sequence feature detection is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6344,7 +6410,7 @@ def: "Predict antigenic determinant sites (epitopes) in protein sequences." [EDA comment: Epitope mapping is commonly done during vaccine design. is_a: EDAM:0000414 ! Sequence feature detection (protein) is_a: EDAM:0002429 ! Mapping and assembly -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation [Term] @@ -6354,7 +6420,7 @@ namespace: operation def: "Predict post-translation modification sites in protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. is_a: EDAM:0000414 ! Sequence feature detection (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6367,7 +6433,7 @@ comment: The prediction might include subcellular localization (nuclear, cytopla synonym: "Protein targeting prediction" EXACT [] is_a: EDAM:0002479 ! Sequence analysis (protein) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation [Term] @@ -6378,7 +6444,7 @@ def: "Detect or predict signal peptides and signal peptide cleavage sites in pro comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. is_a: EDAM:0000414 ! Sequence feature detection (protein) is_a: EDAM:0002489 ! Protein subcellular localization prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation [Term] @@ -6388,7 +6454,7 @@ namespace: operation def: "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000414 ! Sequence feature detection (protein) is_a: EDAM:0002575 ! Ligand-binding and active site prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6399,7 +6465,7 @@ namespace: operation def: "Predict RNA and DNA-binding binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000414 ! Sequence feature detection (protein) is_a: EDAM:0000389 ! Protein-nucleic acid binding site analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation [Term] @@ -6409,7 +6475,7 @@ namespace: operation def: "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000414 ! Sequence feature detection (protein) is_a: EDAM:0002415 ! Protein folding analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6419,7 +6485,7 @@ name: Protein cleavage site prediction namespace: operation def: "Dectect or predict cleavage sites (enzymatic or chemical) in protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000414 ! Sequence feature detection (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6433,7 +6499,7 @@ name: MHC Class I epitope mapping namespace: operation def: "Predict epitopes that bind to MHC class I molecules." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000416 ! Epitope mapping -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6443,7 +6509,7 @@ name: MHC Class II epitope mapping namespace: operation def: "Predict epitopes that bind to MHC class II molecules." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000416 ! Epitope mapping -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6460,8 +6526,8 @@ name: Protein signal peptide detection (eukaryotes) namespace: operation def: "Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000418 ! Protein signal peptide detection -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -6470,8 +6536,8 @@ name: Protein signal peptide detection (bacteria) namespace: operation def: "Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000418 ! Protein signal peptide detection -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -6503,7 +6569,7 @@ namespace: operation def: "Detect, predict and identify genes or components of genes in DNA sequences." [EDAM:EBI "EMBRACE definition"] synonym: "Gene finding" EXACT [] is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001300 ! Gene features @@ -6514,7 +6580,7 @@ name: Whole gene prediction namespace: operation def: "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002454 ! Gene and gene component prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001300 ! Gene features @@ -6525,7 +6591,7 @@ namespace: operation def: "Detect, predict and identify genetic elements such as 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. is_a: EDAM:0002454 ! Gene and gene component prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001300 ! Gene features @@ -6535,7 +6601,7 @@ name: Transposon prediction namespace: operation def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001301 ! Nucleic acid features (transposons) [Term] @@ -6544,7 +6610,7 @@ name: PolyA signal detection namespace: operation def: "Detect polyA signals in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001302 ! Nucleic acid features (PolyA signal) [Term] @@ -6554,7 +6620,7 @@ namespace: operation def: "Detect quadruplex-forming motifs in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: Quadruplex structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation [Term] @@ -6564,7 +6630,7 @@ namespace: operation def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences." [EDAM:EBI "EMBRACE definition"] comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001304 ! Nucleic acid features (CpG island and isochore) [Term] @@ -6573,7 +6639,7 @@ name: Restriction site recognition namespace: operation def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001305 ! Nucleic acid features (restriction sites) @@ -6585,7 +6651,7 @@ namespace: operation def: "Identify, predict or analyse splice sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might require a pre-mRNA or genomic DNA sequence. is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001307 ! Nucleic acid features (splice sites) @@ -6603,7 +6669,7 @@ name: Nucleosome formation or exclusion sequence prediction namespace: operation def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000415 ! Sequence feature detection (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001306 ! Nucleic acid features (nucleosome exclusion sequences) @@ -6617,7 +6683,7 @@ name: Integrated gene prediction namespace: operation def: "Predict whole gene structure using a combination of multiple methods to achieve better predictions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000425 ! Whole gene prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6627,7 +6693,7 @@ name: Operon prediction namespace: operation def: "Find operons (operators, promoters and genes) in bacteria genes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000425 ! Whole gene prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001311 ! Gene features (operon) [Term] @@ -6636,8 +6702,8 @@ name: tRNA gene prediction namespace: operation def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000425 ! Whole gene prediction -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! @@ -6649,7 +6715,7 @@ name: Coding region prediction namespace: operation def: "Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000426 ! Gene component prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001313 ! Gene features (coding region) @@ -6660,7 +6726,7 @@ namespace: operation def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. is_a: EDAM:0000426 ! Gene component prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001314 ! Gene features (SECIS element) @@ -6672,7 +6738,7 @@ def: "Identify or predict transcription regulatory motifs, patterns, elements or comment: This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. is_a: EDAM:0000426 ! Gene component prediction is_a: EDAM:0000241 ! Transcription regulatory sequence analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6685,7 +6751,7 @@ name: Translation initiation site prediction namespace: operation def: "Predict translation initiation sites, possibly by searching a database of sites." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000436 ! Coding region prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6703,7 +6769,7 @@ namespace: operation def: "Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. is_a: EDAM:0000438 ! Transcription regulatory element prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001312 ! Gene features (promoter) [Term] @@ -6713,7 +6779,7 @@ namespace: operation def: "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. is_a: EDAM:0000438 ! Transcription regulatory element prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6724,7 +6790,7 @@ namespace: operation def: "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." [EDAM:EBI "EMBRACE definition"] comment: Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. is_a: EDAM:0000438 ! Transcription regulatory element prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6737,7 +6803,7 @@ comment: Trans-regulatory elements regulate genes distant from the gene from whi synonym: "Functional RNA identification" EXACT [] is_a: EDAM:0000438 ! Transcription regulatory element prediction is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001255 ! Sequence feature annotation @@ -6749,7 +6815,7 @@ namespace: operation def: "Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. is_a: EDAM:0000438 ! Transcription regulatory element prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001308 ! Nucleic acid features (matrix/scaffold attachment sites) @@ -6762,7 +6828,7 @@ name: Transcription factor binding site prediction namespace: operation def: "Identify or predict transcription factor binding sites in DNA sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000440 ! Promoter prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001315 ! Gene features (TFBS) @@ -6773,7 +6839,7 @@ namespace: operation def: "Identify or predict exonic splicing enhancers (ESE) in exons." [EDAM:EBI "EMBRACE definition"] comment: An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. is_a: EDAM:0000440 ! Promoter prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001309 ! Nucleic acid features (exonic splicing enhancer) @@ -6796,8 +6862,8 @@ name: siRNA duplex prediction namespace: operation def: "Identify or predict siRNA duplexes in RNA." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -6807,8 +6873,8 @@ namespace: operation def: "Design an siRNA sequence and assess binding specificity, for example for a functional assay." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) is_a: EDAM:0002430 ! Design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -6817,7 +6883,7 @@ name: microRNA detection namespace: operation def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001310 ! Nucleic acid features (microRNA) @@ -6855,7 +6921,7 @@ def: "Compare two molecular sequence alignments." [EDAM:EBI "EMBRACE definition" comment: See also 'Sequence profile alignment'. is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000867 ! Sequence alignment metadata [Term] @@ -6864,7 +6930,7 @@ name: Sequence alignment conversion namespace: operation def: "Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002122 ! Sequence alignment report processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000863 ! Sequence alignment @@ -6878,7 +6944,7 @@ def: "Evaluate molecular sequence alignment accuracy." [EDAM:EBI "EMBRACE defini comment: Evaluation might be purely sequence-based or use structural information. is_a: EDAM:0002428 ! Validation and standardisation is_a: EDAM:0000258 ! Sequence alignment analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001414 ! Sequence alignment metadata (quality report) [Term] @@ -6888,7 +6954,7 @@ namespace: operation def: "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. is_a: EDAM:0000258 ! Sequence alignment analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001415 ! Sequence alignment metadata (conservation report) [Term] @@ -6898,7 +6964,7 @@ namespace: operation def: "Analyse correlations between sites in a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. is_a: EDAM:0000258 ! Sequence alignment analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001416 ! Sequence alignment metadata (correlation report) [Term] @@ -6909,7 +6975,7 @@ def: "Detects chimeric sequences (chimeras) from a sequence alignment." [EDAM:EB comment: A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000867 ! Sequence alignment metadata [Term] @@ -6920,7 +6986,7 @@ def: "Detect recombination (hotspots and coldspots) and identify recombination b comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000867 ! Sequence alignment metadata [Term] @@ -6931,7 +6997,7 @@ def: "Identify insertion, deletion and duplication events from a sequence alignm comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000867 ! Sequence alignment metadata @@ -6995,7 +7061,7 @@ namespace: operation def: "Calculate and plot a DNA or DNA/RNA stitch profile." [EDAM:EBI "EMBRACE definition"] comment: A stich profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. is_a: EDAM:0000456 ! Nucleic acid melting profile plotting -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001587 ! Nucleic acid stitch profile [Term] @@ -7004,7 +7070,7 @@ name: Nucleic acid melting curve plotting namespace: operation def: "Calculate and plot a DNA or DNA/RNA melting curve." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000456 ! Nucleic acid melting profile plotting -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001583 ! Nucleic acid melting profile [Term] @@ -7013,7 +7079,7 @@ name: Nucleic acid probability profile plotting namespace: operation def: "Calculate and plot a DNA or DNA/RNA probability profile." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000456 ! Nucleic acid melting profile plotting -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001583 ! Nucleic acid melting profile [Term] @@ -7022,7 +7088,7 @@ name: Nucleic acid temperature profile plotting namespace: operation def: "Calculate and plot a DNA or DNA/RNA temperature profile." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000456 ! Nucleic acid melting profile plotting -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001583 ! Nucleic acid melting profile @@ -7061,7 +7127,7 @@ name: Protein secondary structure assignment namespace: operation def: "Assign secondary structure from protein coordinate or experimental data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002444 ! Secondary structure processing (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000876 ! Protein secondary structure @@ -7074,7 +7140,7 @@ comment: Methods might use amino acid composition, local sequence information, m is_a: EDAM:0002444 ! Secondary structure processing (protein) is_a: EDAM:0002479 ! Sequence analysis (protein) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000876 ! Protein secondary structure [Term] @@ -7084,8 +7150,8 @@ namespace: operation def: "Predict super-secondary structure of protein sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! ! Operation<-Protein secondary structure analysis<-Protein secondary structure assignment @@ -7096,7 +7162,7 @@ name: Protein secondary structure assignment (from coordinate data) namespace: operation def: "Assign secondary structure from protein coordinate data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000319 ! Protein secondary structure assignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000876 ! Protein secondary structure [Term] @@ -7105,7 +7171,7 @@ name: Protein secondary structure assignment (from CD data) namespace: operation def: "Assign secondary structure from circular dichroism (CD) spectroscopic data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000319 ! Protein secondary structure assignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000876 ! Protein secondary structure @@ -7135,7 +7201,7 @@ name: Protein secondary structure prediction (integrated) namespace: operation def: "Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000876 ! Protein secondary structure [Term] @@ -7144,7 +7210,7 @@ name: Protein secondary structure prediction (helices) namespace: operation def: "Predict helical secondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000876 ! Protein secondary structure @@ -7154,7 +7220,7 @@ name: Protein secondary structure prediction (turns) namespace: operation def: "Predict turn structure (for example beta hairpin turns) of protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000876 ! Protein secondary structure [Term] @@ -7163,7 +7229,7 @@ name: Protein secondary structure prediction (coils) namespace: operation def: "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000876 ! Protein secondary structure [Term] @@ -7172,7 +7238,7 @@ name: Protein secondary structure prediction (disulfide bonds) namespace: operation def: "Predict cysteine bonding state and disulfide bond partners in protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000876 ! Protein secondary structure @@ -7200,7 +7266,7 @@ namespace: operation def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000270 ! Transmembrane protein data processing is_a: EDAM:0000267 ! Protein secondary structure prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001456 ! Membrane protein annotation (secondary structure) @@ -7212,8 +7278,8 @@ namespace: operation def: "Classify G-protein coupled receptors (GPCRs) into families and subfamilies." [EDAM:EBI "EMBRACE definition"] synonym: "G protein-coupled receptor (GPCR) classification" EXACT [] is_a: EDAM:0000473 ! GPCR analysis -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -7223,8 +7289,8 @@ namespace: operation def: "Predict G-protein coupled receptor (GPCR) coupling selectivity." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000473 ! GPCR analysis is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000473 @@ -7233,8 +7299,8 @@ namespace: operation def: "Analyse G-protein coupled receptor proteins (GPCRs)." [EDAM:EBI "EMBRACE definition"] synonym: "G protein-coupled receptor (GPCR) analysis" EXACT [] is_a: EDAM:0000270 ! Transmembrane protein data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! @@ -7248,8 +7314,8 @@ def: "Predict G protein-coupled receptors (GPCR)." [EDAM:EBI "EMBRACE definition synonym: "G protein-coupled receptor (GPCR) prediction" EXACT [] is_a: EDAM:0000269 ! Transmembrane protein prediction is_a: EDAM:0000473 ! GPCR analysis -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -7270,7 +7336,7 @@ synonym: "Protein structure prediction" EXACT [] is_a: EDAM:0000271 ! Tertiary structure prediction is_a: EDAM:0002459 ! Tertiary structure processing (protein) is_a: EDAM:0002479 ! Sequence analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure @@ -7283,7 +7349,7 @@ comment: Methods might identify thermodynamically stable or evolutionarily conse is_a: EDAM:0000271 ! Tertiary structure prediction is_a: EDAM:0002519 ! Tertiary structure processing (nucleic acid) is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure @@ -7296,7 +7362,7 @@ name: Ab initio structure prediction namespace: operation def: "Predict tertiary structure of protein sequence(s) without homologues of known structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000474 ! Tertiary structure prediction (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure [Term] @@ -7311,7 +7377,7 @@ synonym: "Protein structure comparative modelling" EXACT [] is_a: EDAM:0000474 ! Tertiary structure prediction (protein) is_a: EDAM:0002424 ! Comparison and alignment is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure [Term] @@ -7322,7 +7388,7 @@ def: "Model the structure of a protein in complex with a small molecule or anoth comment: This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. is_a: EDAM:0002459 ! Tertiary structure processing (protein) is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001460 ! Protein tertiary structure @@ -7336,7 +7402,7 @@ comment: Methods usually involve multiple sequence alignment analysis. is_a: EDAM:0000474 ! Tertiary structure prediction (protein) is_a: EDAM:0002479 ! Sequence analysis (protein) is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001540 ! Protein residue interaction @@ -7348,7 +7414,7 @@ def: "Align molecular sequence to structure in 3D space (threading)." [EDAM:EBI comment: Use this term for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. synonym: "Sequence-structure alignment" EXACT [] is_a: EDAM:0000303 ! Protein fold recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000893 ! Sequence-structure alignment @@ -7369,7 +7435,7 @@ namespace: operation def: "Model protein backbone conformation." [EDAM:EBI "EMBRACE definition"] comment: Methods might require a preliminary C(alpha) trace. is_a: EDAM:0000477 ! Protein modelling -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure [Term] @@ -7379,7 +7445,7 @@ namespace: operation def: "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc." [EDAM:EBI "EMBRACE definition"] comment: Methods might use a residue rotamer library. is_a: EDAM:0000477 ! Protein modelling -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure [Term] @@ -7388,7 +7454,7 @@ name: Protein modelling (loops) namespace: operation def: "Model loop conformation in protein structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000477 ! Protein modelling -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure @@ -7412,8 +7478,8 @@ xref: WHATIF:ShowLikelyRotamers700 xref: WHATIF:ShowLikelyRotamers800 xref: WHATIF:ShowLikelyRotamers900 is_a: EDAM:0000480 ! Protein modelling (side chains) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -7428,7 +7494,7 @@ def: "Model protein-ligand (for example protein-peptide) binding using comparati comment: Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. synonym: "Virtual ligand screening" EXACT [] is_a: EDAM:0000478 ! Protein docking -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000883 ! Tertiary structure @@ -7454,8 +7520,8 @@ is_a: EDAM:0000278 ! RNA secondary structure prediction is_a: EDAM:0002441 ! RNA tertiary structure prediction is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) is_a: EDAM:0002430 ! Design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -7469,8 +7535,8 @@ name: Protein-protein interaction experimental data analysis namespace: operation def: "Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002405 ! Protein interaction data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002492 @@ -7479,7 +7545,7 @@ namespace: operation def: "Predict the interactions of proteins with other molecules." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002405 ! Protein interaction data processing is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001565 ! Protein-protein interaction [Term] @@ -7488,7 +7554,7 @@ name: Protein-protein interaction prediction namespace: operation def: "Identify or predict protein-protein interactions, interfaces, binding sites etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002492 ! Protein interaction prediction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001565 ! Protein-protein interaction [Term] @@ -7498,7 +7564,7 @@ namespace: operation def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002464 ! Protein-protein interaction prediction is_a: EDAM:0002479 ! Sequence analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001565 ! Protein-protein interaction [Term] @@ -7508,7 +7574,7 @@ namespace: operation def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002464 ! Protein-protein interaction prediction is_a: EDAM:0002459 ! Tertiary structure processing (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001565 ! Protein-protein interaction @@ -7518,8 +7584,8 @@ name: Protein-protein interaction network processing namespace: operation def: "Process (read and / or write) a network of protein interactions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002405 ! Protein interaction data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -7532,8 +7598,8 @@ def: "Predict and design zinc finger protein domains for DNA/RNA binding (for ex is_a: EDAM:0002492 ! Protein interaction prediction is_a: EDAM:0000389 ! Protein-nucleic acid binding site analysis is_a: EDAM:0002430 ! Design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! @@ -7545,8 +7611,8 @@ name: Protein-protein interaction network analysis namespace: operation def: "Analyse a network of protein interactions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002445 ! Protein-protein interaction network processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000277 @@ -7555,8 +7621,8 @@ namespace: operation def: "Compare two or more networks of protein interactions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002445 ! Protein-protein interaction network processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -7600,7 +7666,7 @@ namespace: operation def: "Find single nucleotide polymorphisms (SNPs) between sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated nonsynonymous SNPs etc. is_a: EDAM:0000281 ! Genetic marker identification -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000918 ! Sequence variation annotation @@ -7617,7 +7683,7 @@ namespace: operation def: "Map genetic markers using radiation hybrid scores, using provided radiation hybrid (RH) scores for one or more markers." [EDAM:EBI "EMBRACE definition"] comment: Markers might be mapped relative to each other or to a framework map. For example, Expressed Sequence Tags (ESTs) might be positioned relative to microsatellites. is_a: EDAM:0000282 ! Genetic mapping -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001278 ! Genetic map [Term] @@ -7642,8 +7708,8 @@ namespace: operation def: "Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated." [EDAM:EBI "EMBRACE definition"] comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). is_a: EDAM:0000283 ! Linkage analysis -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -7653,7 +7719,7 @@ namespace: operation def: "Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [EDAM:EBI "EMBRACE definition"] comment: Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. is_a: EDAM:0000283 ! Linkage analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001634 ! Genetic linkage annotation (linkage disequilibrium) @@ -7668,7 +7734,7 @@ name: Codon usage data analysis namespace: operation def: "Analyse codon usage data, typically from processing molecular sequences or codon usage tables." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002493 ! Codon usage data processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000914 ! Codon usage data @@ -7696,7 +7762,7 @@ def: "Identify and plot third base position variability in a nucleotide sequence is_a: EDAM:0000286 ! Codon usage data analysis is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001263 ! Base position variability [Term] @@ -7707,7 +7773,7 @@ def: "Predict genetic code from analysis of codon usage data." [EDAM:EBI "EMBRAC is_a: EDAM:0000286 ! Codon usage data analysis is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001598 ! Genetic code @@ -7732,7 +7798,7 @@ name: Codon usage table generation namespace: operation def: "Calculate codon usage statistics and create a codon usage table." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002433 ! Codon usage table processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001597 ! Codon usage table [Term] @@ -7742,8 +7808,8 @@ namespace: operation def: "Compare two or more codon usage tables." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002433 ! Codon usage table processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -7786,7 +7852,7 @@ namespace: operation def: "Align exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. is_a: EDAM:0000292 ! Sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001381 ! Sequence alignment (pairwise) [Term] @@ -7796,7 +7862,7 @@ namespace: operation def: "Align two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. is_a: EDAM:0000292 ! Sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001382 ! Sequence alignment (multiple) [Term] @@ -7820,7 +7886,7 @@ namespace: operation def: "Locally align exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Local alignment methods identify regions of local similarity. is_a: EDAM:0000491 ! Pairwise sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001381 ! Sequence alignment (pairwise) [Term] @@ -7830,7 +7896,7 @@ namespace: operation def: "Globally align exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Global alignment methods identify similarity across the entire length of the sequences. is_a: EDAM:0000491 ! Pairwise sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001381 ! Sequence alignment (pairwise) ! @@ -7843,7 +7909,7 @@ namespace: operation def: "Locally align two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Local alignment methods identify regions of local similarity. is_a: EDAM:0000492 ! Multiple sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001382 ! Sequence alignment (multiple) [Term] @@ -7853,7 +7919,7 @@ namespace: operation def: "Globally align two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Global alignment methods identify similarity across the entire length of the sequences. is_a: EDAM:0000492 ! Multiple sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001382 ! Sequence alignment (multiple) [Term] @@ -7862,7 +7928,7 @@ name: Multiple sequence alignment (constrained) namespace: operation def: "Align two or more molecular sequences with user-defined constraints." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000492 ! Multiple sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001382 ! Sequence alignment (multiple) [Term] @@ -7871,7 +7937,7 @@ name: Multiple sequence alignment (consensus) namespace: operation def: "Align two or more molecular sequences using multiple methods to achieve higher quality." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000492 ! Multiple sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001382 ! Sequence alignment (multiple) [Term] @@ -7881,7 +7947,7 @@ namespace: operation def: "Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree." [EDAM:EBI "EMBRACE definition"] comment: This is supposed to give a more biologically meaningful alignment than standard alignments. is_a: EDAM:0000492 ! Multiple sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001382 ! Sequence alignment (multiple) @@ -7903,7 +7969,7 @@ namespace: operation def: "Align molecular secondary structure (represented as a 1D string)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002482 ! Secondary structure processing is_a: EDAM:0000294 ! Structure-based sequence alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000863 ! Sequence alignment @@ -7918,7 +7984,7 @@ namespace: operation def: "Align protein secondary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000500 ! Secondary structure alignment is_a: EDAM:0002488 ! Secondary structure comparison (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000878 ! Secondary structure alignment (protein) [Term] @@ -7928,7 +7994,7 @@ namespace: operation def: "Align RNA secondary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002439 ! Secondary structure processing (RNA) is_a: EDAM:0000500 ! Secondary structure alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000881 ! Secondary structure alignment (RNA) ! @@ -7941,7 +8007,7 @@ name: Pairwise tertiary structure alignment namespace: operation def: "Align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000295 ! Tertiary structure alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001479 ! Tertiary structure alignment (pairwise) [Term] @@ -7951,7 +8017,7 @@ namespace: operation def: "Align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: This includes methods that use an existing alignment. is_a: EDAM:0000295 ! Tertiary structure alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001480 ! Tertiary structure alignment (multiple) @@ -7962,8 +8028,8 @@ name: Secondary structure comparison (protein) namespace: operation def: "Compare protein secondary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002444 ! Secondary structure processing (protein) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -7974,7 +8040,7 @@ def: "Compare protein tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Methods might identify structural neighbors, find structural similarities or define a structural core. is_a: EDAM:0002459 ! Tertiary structure processing (protein) is_a: EDAM:0002483 ! Tertiary structure comparison -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001481 ! Tertiary structure alignment (protein) @@ -7985,8 +8051,8 @@ namespace: operation def: "Compare nucleic acid tertiary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002483 ! Tertiary structure comparison is_a: EDAM:0002519 ! Tertiary structure processing (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -7999,7 +8065,7 @@ namespace: operation def: "Align protein tertiary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000295 ! Tertiary structure alignment is_a: EDAM:0002487 ! Tertiary structure comparison (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001481 ! Tertiary structure alignment (protein) [Term] @@ -8010,7 +8076,7 @@ def: "Align RNA tertiary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000295 ! Tertiary structure alignment is_a: EDAM:0002440 ! Tertiary structure processing (RNA) is_a: EDAM:0002518 ! Tertiary structure comparison (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001493 ! Tertiary structure alignment (RNA) @@ -8024,7 +8090,7 @@ namespace: operation def: "Locally align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Local alignment methods identify regions of local similarity, common substructures etc. is_a: EDAM:0000503 ! Pairwise tertiary structure alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001479 ! Tertiary structure alignment (pairwise) [Term] @@ -8034,7 +8100,7 @@ namespace: operation def: "Globally align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Global alignment methods identify similarity across the entire structures. is_a: EDAM:0000503 ! Pairwise tertiary structure alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001479 ! Tertiary structure alignment (pairwise) @@ -8051,7 +8117,7 @@ namespace: operation def: "Locally align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Local alignment methods identify regions of local similarity, common substructures etc. is_a: EDAM:0000504 ! Multiple tertiary structure alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001480 ! Tertiary structure alignment (multiple) [Term] @@ -8061,7 +8127,7 @@ namespace: operation def: "Globally align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Global alignment methods identify similarity across the entire structures. is_a: EDAM:0000504 ! Multiple tertiary structure alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001480 ! Tertiary structure alignment (multiple) @@ -8097,7 +8163,7 @@ def: "Generate some type of sequence profile (for example a hidden Markov model) synonym: "Sequence profile generation" EXACT [] is_a: EDAM:0002413 ! Sequence profile processing is_a: EDAM:0002463 ! Sequence alignment processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001354 ! Sequence profile [Term] @@ -8109,7 +8175,7 @@ comment: See also 'Sequence alignment comparison'. synonym: "Sequence profile alignment" EXACT [] is_a: EDAM:0002413 ! Sequence profile processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000868 ! Sequence profile alignment @@ -8121,7 +8187,7 @@ def: "Align molecular sequence(s) to sequence profile(s) (representing a sequenc comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. is_a: EDAM:0002413 ! Sequence profile processing is_a: EDAM:0002451 ! Sequence comparison -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000869 ! Sequence-profile alignment @@ -8143,7 +8209,7 @@ namespace: operation def: "Align exactly two molecular profiles." [EDAM:EBI "EMBRACE definition"] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. is_a: EDAM:0000298 ! Sequence profile alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000868 ! Sequence profile alignment @@ -8153,7 +8219,7 @@ name: Sequence profile alignment (multiple) namespace: operation def: "Align two or more molecular profiles." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000298 ! Sequence profile alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000868 ! Sequence profile alignment @@ -8174,7 +8240,7 @@ def: "Generate some type of structural (3D) profile or template from a structure synonym: "Structural profile generation" EXACT [] is_a: EDAM:0002411 ! Structural (3D) profile processing is_a: EDAM:0002465 ! Tertiary structure processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000889 ! Structural (3D) profile [Term] @@ -8185,7 +8251,7 @@ def: "Align structural (3D) profiles or templates (representing structures or st synonym: "Structural profile alignment" EXACT [] is_a: EDAM:0002411 ! Structural (3D) profile processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000890 ! Structural (3D) profile alignment @@ -8207,7 +8273,7 @@ namespace: operation def: "Align exactly two molecular Structural (3D) profiles." [EDAM:EBI "EMBRACE definition"] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. is_a: EDAM:0000299 ! Structural (3D) profile alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000890 ! Structural (3D) profile alignment @@ -8217,7 +8283,7 @@ name: Structural (3D) profile alignment (multiple) namespace: operation def: "Align two or more molecular 3D profiles." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000299 ! Structural (3D) profile alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000890 ! Structural (3D) profile alignment @@ -8235,7 +8301,7 @@ def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) ( comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. is_a: EDAM:0000303 ! Protein fold recognition is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000891 ! Sequence-3D profile alignment @@ -8266,8 +8332,8 @@ namespace: operation def: "Design oligonucleotide primers for PCR and DNA amplification etc." [EDAM:EBI "EMBRACE definition"] comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. is_a: EDAM:0002419 ! Primer and probe design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -8276,8 +8342,8 @@ name: Microarray probe design namespace: operation def: "Design and optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002419 ! Primer and probe design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000307 @@ -8285,7 +8351,7 @@ name: Virtual PCR namespace: operation def: "Perform in-silico (virtual) PCR." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000923 ! PCR assay data @@ -8299,8 +8365,8 @@ name: PCR primer design (for large scale sequencing) namespace: operation def: "Design primers for large scale sequencing." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000308 ! PCR primer design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -8309,8 +8375,8 @@ name: PCR primer design (for genotyping polymorphisms) namespace: operation def: "Design primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000308 ! PCR primer design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000519 @@ -8318,8 +8384,8 @@ name: PCR primer design (for gene transcription profiling) namespace: operation def: "Design primers for gene transcription profiling." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000308 ! PCR primer design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000520 @@ -8327,8 +8393,8 @@ name: PCR primer design (for conserved primers) namespace: operation def: "Design primers that are conserved across multiple genomes or species." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000308 ! PCR primer design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000521 @@ -8336,8 +8402,8 @@ name: PCR primer design (based on gene structure) namespace: operation def: "Design primers based on gene structure, promoters, exon-exon junctions etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000308 ! PCR primer design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000522 @@ -8345,8 +8411,8 @@ name: PCR primer design (for methylation PCRs) namespace: operation def: "Design primers for methylation PCRs." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000308 ! PCR primer design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -8371,7 +8437,7 @@ namespace: operation def: "Sequence assembly by combining fragments using an existing backbone sequence." [EDAM:EBI "EMBRACE definition"] comment: The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. is_a: EDAM:0000310 ! Sequence assembly -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000925 ! Sequence assembly [Term] @@ -8381,7 +8447,7 @@ namespace: operation def: "Sequence assembly by combining fragments into a new, previously unknown sequence." [EDAM:EBI "EMBRACE definition"] comment: De-novo assemblers are much slower and more memory intensive than mapping assemblers. is_a: EDAM:0000310 ! Sequence assembly -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000925 ! Sequence assembly [Term] @@ -8390,7 +8456,7 @@ name: Sequence assembly (genome assembly) namespace: operation def: "Sequence assembly capable on a very large scale such as assembly of whole genomes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000310 ! Sequence assembly -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000925 ! Sequence assembly [Term] @@ -8400,7 +8466,7 @@ namespace: operation def: "Sequence assembly for EST sequences (transcribed mRNA)." [EDAM:EBI "EMBRACE definition"] comment: Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. is_a: EDAM:0000310 ! Sequence assembly -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000925 ! Sequence assembly @@ -8431,8 +8497,8 @@ namespace: operation def: "Process (read and / or write) a gene expression profile." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002495 ! Gene expression data processing is_a: EDAM:0002432 ! Microarray data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -8447,8 +8513,8 @@ name: Sequencing-based expression profile data processing namespace: operation def: "Process (read and / or write) SAGE, MPSS or SBS experimental data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002495 ! Gene expression data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002498 @@ -8456,8 +8522,8 @@ name: Sequencing-based expression profile data analysis namespace: operation def: "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000312 ! Sequencing-based expression profile data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002496 @@ -8465,8 +8531,8 @@ name: Gene regulatory network processing namespace: operation def: "Process (read and / or write) a network of gene regulation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002438 ! Pathway or network processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0001781 @@ -8475,8 +8541,8 @@ namespace: operation def: "Analyse a network of gene regulation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002496 ! Gene regulatory network processing is_a: EDAM:0002497 ! Pathway or network analysis -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002437 @@ -8485,8 +8551,8 @@ namespace: operation def: "Predict a network of gene regulation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002496 ! Gene regulatory network processing is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -8506,7 +8572,7 @@ namespace: operation def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000915 ! RNA splice model [Term] @@ -8516,7 +8582,7 @@ namespace: operation def: "Characterize or model alternative splicing events from analysis of sequence data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000915 ! RNA splice model @@ -8532,8 +8598,8 @@ name: Gene expression profile clustering namespace: operation def: "Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000315 ! Gene expression profile comparison -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000314 @@ -8541,7 +8607,7 @@ name: Gene expression profile generation namespace: operation def: "Generate a gene expression profile or pattern, for example from microarray data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002435 ! Gene expression profile processing -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000928 ! Gene expression profile [Term] @@ -8551,8 +8617,8 @@ namespace: operation def: "Compare gene expression profiles or patterns." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002435 ! Gene expression profile processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002436 @@ -8572,8 +8638,8 @@ def: "Analyse a gene expression profile, typically to interpret it in functional synonym: "Functional profiling" EXACT [] is_a: EDAM:0002435 ! Gene expression profile processing is_a: EDAM:0002500 ! Microarray data analysis -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000533 @@ -8582,8 +8648,8 @@ namespace: operation def: "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000532 ! Gene expression profile analysis is_a: EDAM:0002497 ! Pathway or network analysis -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -8600,7 +8666,7 @@ def: "Make tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data." [E comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. synonym: "Tag to gene assignment" EXACT [] is_a: EDAM:0002498 ! Sequencing-based expression profile data analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000936 ! Tag to gene assignment [Term] @@ -8651,7 +8717,7 @@ def: "Generate a heat map of gene expression from microarray data." [EDAM:EBI "E comment: Heat maps show how expression of mRNA by a set of genes was influenced by experimental conditions. is_a: EDAM:0000314 ! Gene expression profile generation is_a: EDAM:0000571 ! Microarray data rendering -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001636 ! Heat map @@ -8693,8 +8759,8 @@ namespace: operation def: "Process (read and / or write) a protein tertiary structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002465 ! Tertiary structure processing is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000243 @@ -8703,7 +8769,7 @@ namespace: operation def: "Calculate or extract a property of protein structure." [EDAM:EBI "EMBRACE definition"] comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. is_a: EDAM:0002406 ! Tertiary structure analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001537 ! Protein structure annotation @@ -8714,7 +8780,7 @@ namespace: operation def: "Analyse flexibility and motion in protein structure." [EDAM:EBI "EMBRACE definition"] comment: Use this term for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. is_a: EDAM:0002406 ! Tertiary structure analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001541 ! Protein structure annotation (flexibility or motion) @@ -8727,7 +8793,7 @@ comment: This includes conserved substructures and conserved geometry, such as s synonym: "Protein structural feature identification" EXACT [] is_a: EDAM:0002406 ! Tertiary structure analysis (protein) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000899 ! Protein structure annotation (3D motif) @@ -8738,7 +8804,7 @@ namespace: operation def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002406 ! Tertiary structure analysis (protein) is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000901 ! Protein features (domain composition) [Term] @@ -8747,8 +8813,8 @@ name: Protein architecture analysis namespace: operation def: "Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002406 ! Tertiary structure analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -8760,8 +8826,8 @@ is_a: EDAM:0000247 ! Protein architecture analysis is_a: EDAM:0002487 ! Tertiary structure comparison (protein) is_a: EDAM:0002488 ! Secondary structure comparison (protein) is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002475 @@ -8770,8 +8836,8 @@ namespace: operation def: "Identify the architecture of a protein structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000247 ! Protein architecture analysis is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -8788,7 +8854,7 @@ xref: WHATIF: SymShellTwoXML xref: WHATIF: SymShellFiveXML xref: WHATIF: SymShellTenXML is_a: EDAM:0000243 ! Protein structural property calculation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001540 ! Protein residue interaction @@ -8798,8 +8864,8 @@ name: Torsion angle calculation namespace: operation def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000243 ! Protein structural property calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -8808,7 +8874,7 @@ name: Protein tertiary structure assignment namespace: operation def: "Assign a protein tertiary structure (3D coordinates) from raw experimental data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002459 ! Tertiary structure processing (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001460 ! Protein tertiary structure [Term] @@ -8822,7 +8888,7 @@ xref: WHATIF: UseFileDB is_a: EDAM:0002406 ! Tertiary structure analysis (protein) is_a: EDAM:0002426 ! Modelling and simulation is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001539 ! Protein structure annotation (quality evaluation) @@ -8836,7 +8902,7 @@ xref: WHATIF: CorrectedPDBasXML is_a: EDAM:0000474 ! Tertiary structure prediction (protein) is_a: EDAM:0002426 ! Modelling and simulation is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001460 ! Protein tertiary structure [Term] @@ -8846,7 +8912,7 @@ namespace: operation def: "Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002406 ! Tertiary structure analysis (protein) is_a: EDAM:0002479 ! Sequence analysis (protein) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000870 ! Sequence distance matrix @@ -8864,8 +8930,8 @@ name: Protein hydropathy calculation namespace: operation def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000383 @@ -8874,7 +8940,7 @@ namespace: operation def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002574 ! Protein hydropathy calculation is_a: EDAM:0000243 ! Protein structural property calculation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001537 ! Protein structure annotation @@ -8884,7 +8950,7 @@ name: Protein solvent accessibility calculation namespace: operation def: "Calculate solvent accessible or buried surface areas in protein structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000243 ! Protein structural property calculation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001542 ! Protein solvent accessibility [Term] @@ -8893,8 +8959,8 @@ name: Protein cysteine and disulfide bond assignment namespace: operation def: "Assign cysteine bonding state and disulfide bond partners in protein structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000319 ! Protein secondary structure assignment -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! ! Operation<-Tertiary structure analysis (protein)<-Protein structural property calculation<-Protein hydropathy calculation (from structure) @@ -8905,7 +8971,7 @@ name: Protein hydropathy cluster calculation namespace: operation def: "Identify clusters of hydrophobic or charged residues in a protein structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000383 ! Protein hydropathy calculation (from structure) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001537 ! Protein structure annotation [Term] @@ -8914,7 +8980,7 @@ name: Protein dipole moment calculation namespace: operation def: "Calculate whether a protein structure has an unusually large net charge (dipole moment)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000383 ! Protein hydropathy calculation (from structure) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001545 ! Protein dipole moment @@ -8929,7 +8995,7 @@ name: Protein surface and interior calculation namespace: operation def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000384 ! Protein solvent accessibility calculation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001543 ! Protein surface @@ -8945,8 +9011,8 @@ comment: A dot has three coordinates (x,y,z) and (typically) a colour. xref: WHATIF:GetSurfaceDots is_a: EDAM:0000387 ! Protein surface and interior calculation is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -8956,8 +9022,8 @@ namespace: operation def: "Calculate the solvent accessibility for each atom in a structure." [EDAM:WHATIF "EMBRACE definition"] comment: Waters are not considered. is_a: EDAM:0000387 ! Protein surface and interior calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -8969,8 +9035,8 @@ comment: Waters are not considered. xref: WHATIF:AtomAccessibilitySolvent xref: WHATIF:AtomAccessibilitySolventPlus is_a: EDAM:0002460 ! Protein atom surface calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -8982,8 +9048,8 @@ comment: Waters are not considered. xref: WHATIF:AtomAccessibilityMolecular xref: WHATIF:AtomAccessibilityMolecularPlus is_a: EDAM:0002460 ! Protein atom surface calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -8992,8 +9058,8 @@ name: Protein residue surface calculation namespace: operation def: "Calculate the solvent accessibility for each residue in a structure." [EDAM:WHATIF "EMBRACE definition"] is_a: EDAM:0000387 ! Protein surface and interior calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9004,8 +9070,8 @@ def: "Calculate the solvent accessibility ('accessible surface') for each residu comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). xref: WHATIF:ResidueAccessibilitySolvent is_a: EDAM:0002461 ! Protein residue surface calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9016,8 +9082,8 @@ def: "Calculate the solvent accessibility ('vacuum accessible surface') for each comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). xref: WHATIF:ResidueAccessibilityVacuum is_a: EDAM:0002461 ! Protein residue surface calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9028,8 +9094,8 @@ def: "Calculate the solvent accessibility ('accessible molecular surface') for e comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). xref: WHATIF:ResidueAccessibilityMolecular is_a: EDAM:0002461 ! Protein residue surface calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9041,8 +9107,8 @@ def: "Calculate the solvent accessibility ('vacuum molecular surface') for each comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). xref: WHATIF:ResidueAccessibilityVacuumMolecular is_a: EDAM:0002461 ! Protein residue surface calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9051,8 +9117,8 @@ name: Protein surface calculation namespace: operation def: "Calculate the solvent accessibility of a structure as a whole." [EDAM:WHATIF "EMBRACE definition"] is_a: EDAM:0000387 ! Protein surface and interior calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9062,8 +9128,8 @@ namespace: operation def: "Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole." [EDAM:WHATIF "EMBRACE definition"] xref: WHATIF:TotAccessibilityMolecular is_a: EDAM:0002462 ! Protein surface calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9073,8 +9139,8 @@ namespace: operation def: "Calculate the solvent accessibility ('accessible surface') for a structure as a whole." [EDAM:WHATIF "EMBRACE definition"] xref: WHATIF:TotAccessibilitySolvent is_a: EDAM:0002462 ! Protein surface calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9089,8 +9155,8 @@ def: "Detect cysteine bridges (from coordinate data) in a protein structure." [E xref: WHATIF:ShowCysteineBridge is_a: EDAM:0001850 ! Protein cysteine and disulfide bond assignment is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9102,8 +9168,8 @@ comment: A free cysteine is neither involved in a cysteine bridge, nor functions xref: WHATIF:ShowCysteineFree is_a: EDAM:0001850 ! Protein cysteine and disulfide bond assignment is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9114,8 +9180,8 @@ def: "Detect cysteines that are bound to metal in a protein structure." [EDAM:WH xref: WHATIF:ShowCysteineMetal is_a: EDAM:0001850 ! Protein cysteine and disulfide bond assignment is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! @@ -9136,8 +9202,8 @@ name: Ligand-binding and active site prediction namespace: operation def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000388 @@ -9146,8 +9212,8 @@ namespace: operation def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000245 ! Protein structural motif recognition is_a: EDAM:0002575 ! Ligand-binding and active site prediction -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000389 @@ -9156,8 +9222,8 @@ namespace: operation def: "Detect, predict or analyse RNA or DNA-binding sites in protein structure, for example conserved protein motifs with a gene regulatory function." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000245 ! Protein structural motif recognition is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9170,7 +9236,7 @@ name: Protein peeling namespace: operation def: "Decompose a structure into compact or globular fragments (protein peeling)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000246 ! Protein domain recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000901 ! Protein features (domain composition) @@ -9193,8 +9259,8 @@ def: "Calculate contacts between an amino acid (side chain and / or main chain a is_obsolete: true consider: EDAM:0000248 ! Residue interaction calculation ! is_a: EDAM:0000248 ! Residue interaction calculation -! relationship: has_input EDAM:0000841 ! Undefined -! relationship: has_output EDAM:0000841 ! Undefined +! ! relationship: has_input EDAM:0000841 ! Undefined +! ! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000391 @@ -9203,7 +9269,7 @@ namespace: operation def: "Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000248 ! Residue interaction calculation is_a: EDAM:0000243 ! Protein structural property calculation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001546 ! Protein distance matrix @@ -9219,8 +9285,8 @@ xref: WHATIF:ShowHydrogenBonds xref: WHATIF:ShowHydrogenBonds xref: WHATIF:HasHydrogenBonds is_a: EDAM:0000248 ! Residue interaction calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Protein hydrogen bonds +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Protein hydrogen bonds [Term] @@ -9230,8 +9296,8 @@ namespace: operation def: "Identify potential hydrogen bonds between amino acid residues." [EDAM:WHATIF "EMBRACE definition"] is_a: EDAM:0000394 ! Hydrogen bond calculation is_a: EDAM:0002490 ! Residue-residue contact calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Protein hydrogen bonds +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Protein hydrogen bonds @@ -9247,8 +9313,8 @@ xref: WHATIF:HasSaltBridgePlus xref: WHATIF:ShowSaltBridges xref: WHATIF:ShowSaltBridgesH is_a: EDAM:0002490 ! Residue-residue contact calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0001846 @@ -9259,8 +9325,8 @@ comment: A HET group usually corresponds to ligands, lipids, but might also (not xref: WHATIF: HETGroupNames is_a: EDAM:0001838 ! Residue-ligand contact calculation is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9274,7 +9340,7 @@ name: Protein contact map calculation namespace: operation def: "Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002490 ! Residue-residue contact calculation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001547 ! Protein contact map [Term] @@ -9284,7 +9350,7 @@ namespace: operation def: "Calculate clusters of contacting residues in protein structures." [EDAM:EBI "EMBRACE definition"] comment: Cluster of contacting residues might be key structural residues. is_a: EDAM:0000248 ! Residue interaction calculation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001548 ! Protein residue cluster ! Undefined check against other cluster analysis of structure (charged groups) @@ -9297,8 +9363,8 @@ xref: WHATIF:HasNucleicContacts xref: WHATIF:ShowProteiNucleicContacts is_a: EDAM:0000248 ! Residue interaction calculation is_a: EDAM:0000389 ! Protein-nucleic acid binding site analysis -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0001834 @@ -9309,8 +9375,8 @@ xref: WHATIF:HasMetalContacts xref: WHATIF:HasMetalContactsPlus is_a: EDAM:0000248 ! Residue interaction calculation is_a: EDAM:0000388 ! Ligand-binding and active site prediction (from structure) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9321,8 +9387,8 @@ def: "Calculate ion contacts in a structure (all ions for all side chain atoms). xref: WHATIF:HasNegativeIonContacts xref: WHATIF:HasNegativeIonContactsPlus is_a: EDAM:0000248 ! Residue interaction calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9333,8 +9399,8 @@ def: "Calculate the number of symmetry contacts made by residues in a protein st comment: A symmetry contact is a contact between two atoms in different asymmetric unit. xref: WHATIF:SymmetryContact is_a: EDAM:0002490 ! Residue-residue contact calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0001838 @@ -9346,8 +9412,8 @@ xref: WHATIF:ShowDrugContacts xref: WHATIF:ShowDrugContactsShort is_a: EDAM:0000248 ! Residue interaction calculation is_a: EDAM:0000388 ! Ligand-binding and active site prediction (from structure) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002490 @@ -9355,8 +9421,8 @@ name: Residue-residue contact calculation namespace: operation def: "Calculate contacts between residues in a protein structure." [EDAM:WHATIF "EMBRACE definition"] is_a: EDAM:0000248 ! Residue interaction calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9391,7 +9457,7 @@ namespace: operation def: "Calculate a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000249 ! Torsion angle calculation is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001544 ! Ramachandran plot [Term] @@ -9401,7 +9467,7 @@ namespace: operation def: "Analyse a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000249 ! Torsion angle calculation relationship: has_input EDAM:0001544 ! Ramachandran plot -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0001825 @@ -9410,8 +9476,8 @@ namespace: operation def: "Calculate for each residue in a protein structure all its backbone torsion angles." [EDAM:WHATIF "EMBRACE definition"] xref: WHATIF:ResidueTorsionsBB is_a: EDAM:0000249 ! Torsion angle calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9421,8 +9487,8 @@ namespace: operation def: "Calculate for each residue in a protein structure all its torsion angles." [EDAM:WHATIF "EMBRACE definition"] xref: WHATIF:ResidueTorsions is_a: EDAM:0000249 ! Torsion angle calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9432,8 +9498,8 @@ namespace: operation def: "Calculate for each cysteine (bridge) all its torsion angles." [EDAM:WHATIF "EMBRACE definition"] xref: WHATIF:CysteineTorsions is_a: EDAM:0000249 ! Torsion angle calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9444,8 +9510,8 @@ def: "For each amino acid in a protein structure calculate the backbone angle ta comment: Tau is the backbone angle N-Calpha-C (angle over the C-alpha). xref: WHATIF:ShowTauAngle is_a: EDAM:0000249 ! Torsion angle calculation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9486,7 +9552,7 @@ namespace: operation def: "Calculate non-canonical atomic interactions in protein structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000248 ! Residue interaction calculation is_a: EDAM:0000321 ! Protein tertiary structure evaluation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001550 ! Protein non-canonical atomic interactions [Term] @@ -9497,8 +9563,8 @@ def: "Identify poor quality amino acid positions in protein structures." [EDAM:W comment: The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). xref: WHATIF: UseResidueDB is_a: EDAM:0000321 ! Protein tertiary structure evaluation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0001843 @@ -9507,8 +9573,8 @@ namespace: operation def: "Identify poorly packed residues in protein structures." [EDAM:WHATIF "EMBRACE definition"] xref: WHATIF: PackingQuality is_a: EDAM:0000321 ! Protein tertiary structure evaluation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0001844 @@ -9518,8 +9584,8 @@ def: "Identify for each residue in a protein structure any improper dihedral ang xref: WHATIF: ImproperQualitySum xref: WHATIF: ImproperQualityMax is_a: EDAM:0000321 ! Protein tertiary structure evaluation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! ! Operation<-Tertiary structure analysis (protein)<-Protein tertiary structure evaluation<-Residue interaction calculation (non-canonical) @@ -9533,8 +9599,8 @@ xref: WHATIF:ShowBumps is_a: EDAM:0000395 ! Residue interaction calculation (non-canonical) is_a: EDAM:0000321 ! Protein tertiary structure evaluation is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! ! Operation<-Tertiary structure analysis (protein)<-Protein tertiary structure refinement @@ -9568,7 +9634,7 @@ namespace: operation def: "Identify a plausible model of DNA substitution that explains a DNA sequence alignment." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001439 ! Phylogenetic tree metadata (DNA substitution model) @@ -9579,8 +9645,8 @@ namespace: operation def: "Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive)." [EDAM:EBI "EMBRACE definition"] comment: Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. is_a: EDAM:0000324 ! Phylogenetic tree analysis -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9599,7 +9665,7 @@ comment: Phylogenetic trees are usually constructed from a set of sequences from synonym: "Phylogenetic tree generation" EXACT [] is_a: EDAM:0002443 ! Phylogenetic tree processing is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree [Term] @@ -9610,7 +9676,7 @@ def: "Compare two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] comment: For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. is_a: EDAM:0000324 ! Phylogenetic tree analysis is_a: EDAM:0002424 ! Comparison and alignment -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001438 ! Phylogenetic tree metadata [Term] @@ -9630,7 +9696,7 @@ namespace: operation def: "Analyse the shape (topology) of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] synonym: "Phylogenetic tree topology analysis" EXACT [] is_a: EDAM:0000324 ! Phylogenetic tree analysis -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001440 ! Phylogenetic tree metadata (shape data) [Term] @@ -9640,7 +9706,7 @@ namespace: operation def: "Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000324 ! Phylogenetic tree analysis is_a: EDAM:0002428 ! Validation and standardisation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001441 ! Phylogenetic tree metadata (confidence data) @@ -9651,8 +9717,8 @@ namespace: operation def: "Predict families of genes and gene function based on their position in a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000324 ! Phylogenetic tree analysis is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9668,7 +9734,7 @@ name: Phylogenetic tree construction (data centric) namespace: operation def: "Construct a phylogenetic tree from a specific type of data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000323 ! Phylogenetic tree construction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree [Term] @@ -9677,7 +9743,7 @@ name: Phylogenetic tree construction (method centric) namespace: operation def: "Construct a phylogenetic tree using a specific method." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000323 ! Phylogenetic tree construction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree @@ -9693,7 +9759,7 @@ namespace: operation def: "Phylogenetic tree construction from molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree @@ -9703,7 +9769,7 @@ name: Phylogenetic tree construction (from continuous quantitative characters) namespace: operation def: "Phylogenetic tree construction from continuous quantitative character data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree @@ -9714,7 +9780,7 @@ namespace: operation def: "Phylogenetic tree construction from gene frequency data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree @@ -9724,7 +9790,7 @@ name: Phylogenetic tree construction (from polymorphism data) namespace: operation def: "Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree @@ -9738,7 +9804,7 @@ name: Phylogenetic species tree construction namespace: operation def: "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000540 ! Phylogenetic tree construction (from molecular sequences) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree @@ -9749,8 +9815,8 @@ namespace: operation def: "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing)." [EDAM:EBI "EMBRACE definition"] comment: A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. is_a: EDAM:0000540 ! Phylogenetic tree construction (from molecular sequences) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9764,7 +9830,7 @@ namespace: operation def: "Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment." [EDAM:EBI "EMBRACE definition"] comment: This includes evolutionary parsimony (invariants) methods. is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree [Term] @@ -9774,7 +9840,7 @@ namespace: operation def: "Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances." [EDAM:EBI "EMBRACE definition"] comment: This includes neighbor joining (NJ) clustering method. is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree [Term] @@ -9784,7 +9850,7 @@ namespace: operation def: "Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution." [EDAM:EBI "EMBRACE definition"] comment: Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree [Term] @@ -9793,7 +9859,7 @@ name: Phylogenetic tree construction (quartet methods) namespace: operation def: "Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree [Term] @@ -9802,7 +9868,7 @@ name: Phylogenetic tree construction (AI methods) namespace: operation def: "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree @@ -9821,7 +9887,7 @@ def: "Compare two or more phylogenetic trees to produce a consensus tree." [EDAM comment: Methods typically test for topological similarity between trees using for example a congruence index. is_a: EDAM:0000325 ! Phylogenetic tree comparison is_a: EDAM:0000323 ! Phylogenetic tree construction -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0002247 ! Phylogenetic consensus tree @@ -9832,7 +9898,7 @@ namespace: operation def: "Compare two or more phylogenetic trees to detect subtrees or supertrees." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000325 ! Phylogenetic tree comparison is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000872 ! Phylogenetic tree @@ -9842,7 +9908,7 @@ name: Phylogenetic tree distances calculation namespace: operation def: "Compare two or more phylogenetic trees to calculate distances between trees." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000325 ! Phylogenetic tree comparison -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001442 ! Phylogenetic tree metadata (distance data) @@ -9856,7 +9922,7 @@ namespace: operation def: "Annotate a phylogenetic tree with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000326 ! Phylogenetic tree editing is_a: EDAM:0000226 ! Annotation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0001438 ! Phylogenetic tree metadata @@ -9877,7 +9943,7 @@ namespace: operation def: "Simulate the folding of a protein." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002415 ! Protein folding analysis is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000903 ! Protein folding model @@ -9888,7 +9954,7 @@ namespace: operation def: "Predict the folding pathway(s) or non-native structural intermediates of a protein." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002415 ! Protein folding analysis is_a: EDAM:0002423 ! Prediction, detection and recognition -relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined relationship: has_output EDAM:0000903 ! Protein folding model @@ -9917,8 +9983,8 @@ def: "Calculate for each position in a protein structure the chance that a proli xref: WHATIF:ProlineMutationValue is_a: EDAM:0000331 ! Protein mutation modelling is_a: EDAM:0002426 ! Modelling and simulation -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -9927,8 +9993,8 @@ name: Protein SNP mapping namespace: operation def: "Map single nucleotide polymorphisms (SNPs) on protein structure(s)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000331 ! Protein mutation modelling -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9939,8 +10005,8 @@ namespace: operation def: "Design peptide ligands that elicit an immunological response." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002479 ! Sequence analysis (protein) is_a: EDAM:0002430 ! Design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000560 @@ -9949,8 +10015,8 @@ namespace: operation def: "Design DNA to elicit (via DNA vaccination) an immunological response." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002478 ! Sequence analysis (nucleic acid) is_a: EDAM:0002430 ! Design -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -9995,8 +10061,8 @@ def: "Reformat a file of tertiary structure data." [EDAM:WHATIF "EMBRACE definit xref: WHATIF: PDBasXML is_a: EDAM:0000335 ! Report reformatting is_a: EDAM:0002234 ! Tertiary structure report processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! ! Operation<-Report validation @@ -10014,8 +10080,8 @@ namespace: operation def: "Visualise, format or render a molecular sequence, possibly with sequence features or properties shown." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002446 ! Sequence processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002515 @@ -10025,8 +10091,8 @@ def: "Visualise, format or render a nucleic acid sequence." [EDAM:EBI "EMBRACE d is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0000564 ! Sequence rendering is_a: EDAM:0002501 ! Nucleic acid data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002516 @@ -10036,8 +10102,8 @@ def: "Visualise, format or render a protein sequence." [EDAM:EBI "EMBRACE defini is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0000564 ! Sequence rendering is_a: EDAM:0002502 ! Protein data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -10048,8 +10114,8 @@ namespace: operation def: "Visualise, format or print a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002463 ! Sequence alignment processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002452 @@ -10057,8 +10123,8 @@ name: Sequence cluster processing namespace: operation def: "Process (read and / or write) a sequence cluster." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002503 ! Sequence data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000566 @@ -10067,8 +10133,8 @@ namespace: operation def: "Visualise, format or render sequence clusters." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002452 ! Sequence cluster processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000567 @@ -10077,8 +10143,8 @@ namespace: operation def: "Visualise or plot a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002443 ! Phylogenetic tree processing is_a: EDAM:0000337 ! Plotting and rendering -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -10088,8 +10154,8 @@ namespace: operation def: "Visualise RNA secondary structure, knots, pseudoknots etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002439 ! Secondary structure processing (RNA) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000569 @@ -10098,8 +10164,8 @@ namespace: operation def: "Render and visualise protein secondary structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002444 ! Secondary structure processing (protein) -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] @@ -10108,8 +10174,8 @@ name: Helical wheel rendering namespace: operation def: "Render a helical wheel representation of protein secondary structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000569 ! Protein secondary structure rendering -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002486 @@ -10117,8 +10183,8 @@ name: Toplogy diagram rendering namespace: operation def: "Render a topology diagram of protein secondary structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000569 ! Protein secondary structure rendering -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0002241 @@ -10127,8 +10193,8 @@ namespace: operation def: "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000569 ! Protein secondary structure rendering is_a: EDAM:0000270 ! Transmembrane protein data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -10160,8 +10226,8 @@ namespace: operation def: "Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002465 ! Tertiary structure processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000571 @@ -10170,8 +10236,8 @@ namespace: operation def: "Visualise microarray data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002432 ! Microarray data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000572 @@ -10180,8 +10246,8 @@ namespace: operation def: "Identify and analyse networks of protein interactions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002445 ! Protein-protein interaction network processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined ! @@ -10194,8 +10260,8 @@ namespace: operation def: "Render and visualise a DNA map." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002515 ! Sequence rendering (nucleic acid) is_a: EDAM:0002521 ! DNA map data processing -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000574 @@ -10236,8 +10302,8 @@ name: DNA circular map rendering namespace: operation def: "Draw a circular maps of DNA, for example a plasmid map." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000573 ! DNA map rendering -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000579 @@ -10245,8 +10311,8 @@ name: Operon rendering namespace: operation def: "Visualise operon structure etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000573 ! DNA map rendering -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined [Term] id: EDAM:0000575 @@ -10255,8 +10321,8 @@ namespace: operation def: "Visualise restriction maps in DNA sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000573 ! DNA map rendering is_a: EDAM:0000431 ! Restriction site recognition -relationship: has_input EDAM:0000841 ! Undefined -relationship: has_output EDAM:0000841 ! Undefined +! relationship: has_input EDAM:0000841 ! Undefined +! relationship: has_output EDAM:0000841 ! Undefined @@ -10284,7 +10350,7 @@ relationship: has_output EDAM:0000841 ! Undefined ! -! Data resource +! Resource ! [Term] @@ -10292,7 +10358,7 @@ id: EDAM:0002231 name: Phenotype and disease namespace: resource def: "An information resource for biological genotypes, phenotypes and/or diseases." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data [Term] @@ -10300,7 +10366,7 @@ id: EDAM:0002230 name: Classification and nomenclature namespace: resource def: "An information resource for biological classification and nomenclature." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data [Term] @@ -10308,7 +10374,7 @@ id: EDAM:0002229 name: Cell biology and culture namespace: resource def: "An information resource for cellular biology and cell culture." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data [Term] @@ -10316,7 +10382,7 @@ id: EDAM:0002228 name: Sequence-related namespace: resource def: "An information resource for molecular sequence and related data such as alignments and motifs." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data [Term] @@ -10324,7 +10390,7 @@ id: EDAM:0002227 name: Genetics namespace: resource def: "An information resource for genetics." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data [Term] @@ -10333,16 +10399,16 @@ name: Ontology namespace: resource def: "An ontology of biological or bioinformatics terms and relations, a controlled vocabulary or structured glossary, or other resource in this area." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002230 ! Classification and nomenclature resource -relationship: is_source_of EDAM:0000841 ! Undefined +! relationship: is_source_of EDAM:0000841 ! Undefined -[Term] -id: EDAM:0000580 -name: Undefined -namespace: resource -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource -relationship: is_source_of EDAM:0000841 ! Undefined +! [Term] +! id: EDAM:0000580 +! name: Undefined +! namespace: resource +! def: "Debugging." [EDAM:EBI "EMBRACE definition"] +! is_a: EDAM:0000005 ! Resource +! relationship: is_source_of EDAM:0000841 ! Undefined [Term] @@ -10368,7 +10434,7 @@ id: EDAM:0002226 name: Structural biology namespace: resource def: "An information resource on biological molecular structures." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data [Term] @@ -10376,7 +10442,7 @@ id: EDAM:0002225 name: Protein namespace: resource def: "A database of information on proteins, peptides or amino acids." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data [Term] @@ -10523,7 +10589,7 @@ id: EDAM:0000602 name: Pathways and networks namespace: resource def: "A database of biological pathways or networks." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000946 ! Pathway or network annotation [Term] @@ -10550,7 +10616,7 @@ id: EDAM:0000605 name: Informatics namespace: resource def: "A database concerning biological data management and modelling, including datatypes, workflows and models." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data [Term] @@ -10558,7 +10624,7 @@ id: EDAM:0000606 name: Literature namespace: resource def: "A biological or biomedical literature database." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000970 ! Citation relationship: is_source_of EDAM:0000971 ! Article @@ -10567,7 +10633,7 @@ id: EDAM:0000607 name: Biological resource namespace: resource def: "A database of biological resources for use in the lab." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data @@ -10592,7 +10658,7 @@ id: EDAM:0000610 name: Ecology namespace: resource def: "A database of ecological data." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data [Term] @@ -10667,7 +10733,7 @@ id: EDAM:0000621 name: Organism-specific namespace: resource def: "A database on a specific organism (e.g. a model organism) or group of organisms, either describing the organism(s) itself or data associated with it." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000005 ! Data resource +is_a: EDAM:0000005 ! Resource relationship: is_source_of EDAM:0000006 ! Data @@ -10794,7 +10860,7 @@ relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Sequence +! Resource<-Sequence ! [Term] id: EDAM:0000639 @@ -10873,7 +10939,7 @@ is_a: EDAM:0000584 ! Sequence relationship: is_source_of EDAM:0000849 ! Sequence record ! -! Data resource<-Sequence<-Protein sequence +! Resource<-Sequence<-Protein sequence ! @@ -10882,7 +10948,7 @@ relationship: is_source_of EDAM:0000849 ! Sequence record ! -! Data resource<-Sequence<-Nucleotide sequence +! Resource<-Sequence<-Nucleotide sequence ! [Term] @@ -10921,7 +10987,7 @@ relationship: is_source_of EDAM:0001207 ! Nucleotide sequence ! -! Data resource<-Sequence<-Nucleotide sequence<-RNA sequence +! Resource<-Sequence<-Nucleotide sequence<-RNA sequence ! [Term] @@ -10935,7 +11001,7 @@ relationship: is_source_of EDAM:0001213 ! RNA sequence ! -! Data resource<-Sequence<-Nucleotide sequence<-RNA sequence<-Functional RNA sequence +! Resource<-Sequence<-Nucleotide sequence<-RNA sequence<-Functional RNA sequence ! [Term] id: EDAM:0000660 @@ -10985,7 +11051,7 @@ relationship: is_source_of EDAM:0001213 ! RNA sequence ! -! Data resource<-Sequence<-Nucleotide sequence<-RNA sequence<-Functional RNA sequence<-snRNA sequence +! Resource<-Sequence<-Nucleotide sequence<-RNA sequence<-Functional RNA sequence<-snRNA sequence ! [Term] @@ -11000,7 +11066,7 @@ relationship: is_source_of EDAM:0001213 ! RNA sequence ! -! Data resource<-Sequence<-Nucleotide sequence<-DNA sequence +! Resource<-Sequence<-Nucleotide sequence<-DNA sequence ! [Term] @@ -11014,7 +11080,7 @@ relationship: is_source_of EDAM:0001212 ! DNA sequence ! -! Data resource<-Sequence<-Nucleotide sequence<-mRNA, EST or cDNA +! Resource<-Sequence<-Nucleotide sequence<-mRNA, EST or cDNA ! @@ -11022,22 +11088,22 @@ relationship: is_source_of EDAM:0001212 ! DNA sequence ! -! Data resource<-Sequence<-Repeat sequence +! Resource<-Sequence<-Repeat sequence ! ! -! Data resource<-Sequence<-Low complexity sequence +! Resource<-Sequence<-Low complexity sequence ! ! -! Data resource<-Sequence<-Polymorphism +! Resource<-Sequence<-Polymorphism ! ! -! Data resource<-Sequence<-Genome +! Resource<-Sequence<-Genome ! [Term] @@ -11072,7 +11138,7 @@ relationship: is_source_of EDAM:0002044 ! Sequence data ! -! Data resource<-Sequence<-Genome<-Eukaryote genome +! Resource<-Sequence<-Genome<-Eukaryote genome ! [Term] id: EDAM:0000675 @@ -11123,12 +11189,12 @@ relationship: is_source_of EDAM:0002044 ! Sequence data ! -! Data resource<-Sequence<-Genome<-Eukaryote genome<-Unicellular eukaryote genome +! Resource<-Sequence<-Genome<-Eukaryote genome<-Unicellular eukaryote genome ! ! -! Data resource<-Sequence<-Genome<-Eukaryote genome<-Fungal genome +! Resource<-Sequence<-Genome<-Eukaryote genome<-Fungal genome ! [Term] @@ -11141,16 +11207,16 @@ relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data ! -! Data resource<-Sequence<-Genome<-Eukaryote genome<-Fungal genome<-Yeast genome +! Resource<-Sequence<-Genome<-Eukaryote genome<-Fungal genome<-Yeast genome ! ! -! Data resource<-Sequence<-Genome<-Eukaryote genome<-Plant genome +! Resource<-Sequence<-Genome<-Eukaryote genome<-Plant genome ! ! -! Data resource<-Sequence<-Genome<-Eukaryote genome<-Invertebrate genome +! Resource<-Sequence<-Genome<-Eukaryote genome<-Invertebrate genome ! @@ -11158,7 +11224,7 @@ relationship: is_source_of EDAM:0002044 ! Sequence data ! -! Data resource<-Sequence<-Genome<-Eukaryote genome<-Vertebrate genome +! Resource<-Sequence<-Genome<-Eukaryote genome<-Vertebrate genome ! [Term] @@ -11175,19 +11241,19 @@ relationship: is_source_of EDAM:0002044 ! Sequence data ! -! Data resource<-Sequence<-Genome<-Prokaryote genome +! Resource<-Sequence<-Genome<-Prokaryote genome ! ! -! Data resource<-Sequence<-Genome<-Viral genome +! Resource<-Sequence<-Genome<-Viral genome ! ! -! Data resource<-Sequence<-Proteome +! Resource<-Sequence<-Proteome ! [Term] id: EDAM:0000691 @@ -11208,7 +11274,7 @@ relationship: is_source_of EDAM:0000849 ! Sequence record relationship: is_source_of EDAM:0002044 ! Sequence data ! -! Data resource<-Structure +! Resource<-Structure ! [Term] id: EDAM:0000693 @@ -11246,7 +11312,7 @@ relationship: is_source_of EDAM:0000962 ! Small molecule annotation ! -! Data resource<-Structure<-Tertiary structure +! Resource<-Structure<-Tertiary structure ! [Term] id: EDAM:0000698 @@ -11268,7 +11334,7 @@ relationship: is_source_of EDAM:0001459 ! Nucleic acid tertiary structure ! -! Data resource<-Structure<-Tertiary structure<-Protein structure +! Resource<-Structure<-Tertiary structure<-Protein structure ! [Term] @@ -11285,7 +11351,7 @@ relationship: is_source_of EDAM:0001468 ! Protein domain tertiary structure ! -! Data resource<-Structure<-Tertiary structure<-Protein structure<-Protein domain structure +! Resource<-Structure<-Tertiary structure<-Protein structure<-Protein domain structure ! [Term] id: EDAM:0000703 @@ -11300,7 +11366,7 @@ relationship: is_source_of EDAM:0001468 ! Protein domain tertiary structure ! -! Data resource<-Structure<-Tertiary structure<-Nucleic acid structure +! Resource<-Structure<-Tertiary structure<-Nucleic acid structure ! [Term] @@ -11317,18 +11383,18 @@ relationship: is_source_of EDAM:0001465 ! RNA tertiary structure ! -! Data resource<-Structure<-Protein secondary structure and alignment +! Resource<-Structure<-Protein secondary structure and alignment ! ! -! Data resource<-Structure<-Carbohydrate structure +! Resource<-Structure<-Carbohydrate structure ! ! -! Data resource<-Structure<-Chemical and small molecule +! Resource<-Structure<-Chemical and small molecule ! [Term] id: EDAM:0000620 @@ -11352,12 +11418,12 @@ relationship: is_source_of EDAM:0000964 ! Scent annotation ! -! Data resource<-General protein +! Resource<-General protein ! ! -! Data resource<-Protein interaction +! Resource<-Protein interaction ! [Term] id: EDAM:0000717 @@ -11387,49 +11453,49 @@ relationship: is_source_of EDAM:0001565 ! Protein-protein interaction ! -! Data resource<-Protein interaction<-Protein-ligand interaction +! Resource<-Protein interaction<-Protein-ligand interaction ! ! -! Data resource<-Protein interaction<-Protein-nucleic acid interaction +! Resource<-Protein interaction<-Protein-nucleic acid interaction ! ! -! Data resource<-Protein interaction<-Protein-protein interaction +! Resource<-Protein interaction<-Protein-protein interaction ! ! -! Data resource<-Protein localization +! Resource<-Protein localization ! ! -! Data resource<-Protein structural motif +! Resource<-Protein structural motif ! ! -! Data resource<-Protein structure annotation +! Resource<-Protein structure annotation ! ! -! Data resource<-Proteome annotation +! Resource<-Proteome annotation ! ! -! Data resource<-Molecular motions +! Resource<-Molecular motions ! ! -! Data resource<-NMR +! Resource<-NMR ! ! -! Data resource<-Sequence classification +! Resource<-Sequence classification ! [Term] id: EDAM:0000722 @@ -11442,7 +11508,7 @@ relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Protein classification +! Resource<-Protein classification ! [Term] @@ -11470,7 +11536,7 @@ relationship: is_source_of EDAM:0001235 ! Sequence cluster ! -! Data resource<-Protein classification<-Protein families +! Resource<-Protein classification<-Protein families ! @@ -11480,7 +11546,7 @@ relationship: is_source_of EDAM:0001235 ! Sequence cluster ! -! Data resource<-Protein classification<-Protein structure classification +! Resource<-Protein classification<-Protein structure classification ! [Term] id: EDAM:0000736 @@ -11496,7 +11562,7 @@ relationship: is_source_of EDAM:0000901 ! Protein features (domain composition) ! -! Data resource<-Protein classification<-Protein structure classification<-Protein domain classification +! Resource<-Protein classification<-Protein structure classification<-Protein domain classification ! @@ -11504,7 +11570,7 @@ relationship: is_source_of EDAM:0000901 ! Protein features (domain composition) ! -! Data resource<-Sequence alignment +! Resource<-Sequence alignment ! [Term] id: EDAM:0000740 @@ -11524,12 +11590,12 @@ relationship: is_source_of EDAM:0000863 ! Sequence alignment ! -! Data resource<-Structure alignment +! Resource<-Structure alignment ! ! -! Data resource<-Sequence motif or profile +! Resource<-Sequence motif or profile ! [Term] @@ -11561,18 +11627,18 @@ relationship: is_source_of EDAM:0001354 ! Sequence profile ! -! Data resource<-Sequence motif or profile<-Nucleotide sequence motif or profile +! Resource<-Sequence motif or profile<-Nucleotide sequence motif or profile ! ! -! Data resource<-Sequence motif or profile<-Protein sequence motif or profile +! Resource<-Sequence motif or profile<-Protein sequence motif or profile ! ! -! Data resource<-Sequence motif or profile<-Sequence profile library +! Resource<-Sequence motif or profile<-Sequence profile library ! [Term] id: EDAM:0000746 @@ -11584,7 +11650,7 @@ relationship: is_source_of EDAM:0001364 ! Hidden Markov model ! -! Data resource<-Sequence motif or profile<-Sequence profile library<-HMM sequence profile library +! Resource<-Sequence motif or profile<-Sequence profile library<-HMM sequence profile library ! [Term] id: EDAM:0001763 @@ -11595,7 +11661,7 @@ is_a: EDAM:0000744 ! HMM sequence profile library relationship: is_source_of EDAM:0001364 ! Hidden Markov model ! -! Data resource<-Functional sites +! Resource<-Functional sites ! [Term] id: EDAM:0000747 @@ -11614,7 +11680,7 @@ is_a: EDAM:0000600 ! Functional sites relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Functional sites<-Nucleic acid functional sites +! Resource<-Functional sites<-Nucleic acid functional sites ! [Term] @@ -11640,7 +11706,7 @@ relationship: is_source_of EDAM:0001307 ! Nucleic acid features (splice sites) ! -! Data resource<-Functional sites<-Protein functional sites +! Resource<-Functional sites<-Protein functional sites ! [Term] id: EDAM:0000751 @@ -11652,12 +11718,12 @@ relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-General protein modifications +! Resource<-General protein modifications ! ! -! Data resource<-Pathways and networks +! Resource<-Pathways and networks ! [Term] id: EDAM:0000753 @@ -11687,18 +11753,18 @@ consider: EDAM:0000602 ! Pathways and networks ! -! Data resource<-Pathways and networks<-Metabolic pathways +! Resource<-Pathways and networks<-Metabolic pathways ! ! -! Data resource<-Pathways and networks<-Signalling pathways +! Resource<-Pathways and networks<-Signalling pathways ! ! -! Data resource<-Proteomics +! Resource<-Proteomics ! [Term] id: EDAM:0000764 @@ -11735,32 +11801,32 @@ relationship: is_source_of EDAM:0000945 ! Peptide identification ! -! Data resource<-Proteomics<-General proteomics +! Resource<-Proteomics<-General proteomics ! ! -! Data resource<-Proteomics<-Two-dimensional gel electrophoresis +! Resource<-Proteomics<-Two-dimensional gel electrophoresis ! ! -! Data resource<-Proteomics<-Mass spectromery +! Resource<-Proteomics<-Mass spectromery ! ! -! Data resource<-Proteomics<-Peptide identification +! Resource<-Proteomics<-Peptide identification ! ! -! Data resource<-General peptides +! Resource<-General peptides ! ! -! Data resource<-Informatics +! Resource<-Informatics ! [Term] id: EDAM:0000769 @@ -11788,29 +11854,29 @@ relationship: is_source_of EDAM:0000950 ! Biological model annotation ! -! Data resource<-Informatics<-Workflow +! Resource<-Informatics<-Workflow ! ! -! Data resource<-Informatics<-Data type, object or resource +! Resource<-Informatics<-Data type, object or resource ! ! -! Data resource<-Informatics<-Biological models +! Resource<-Informatics<-Biological models ! ! -! Data resource<-Literature +! Resource<-Literature ! ! -! Data resource<-Biological resource +! Resource<-Biological resource ! [Term] id: EDAM:0000632 @@ -11828,46 +11894,46 @@ relationship: is_source_of EDAM:0000922 ! Nucleic acid features (primers) ! -! Data resource<-Cell culture +! Resource<-Cell culture ! ! -! Data resource<-Cell cycle +! Resource<-Cell cycle ! ! -! Data resource<-Ecology +! Resource<-Ecology ! ! -! Data resource<-Electron microscopy +! Resource<-Electron microscopy ! ! -! Data resource<-Embryology and development +! Resource<-Embryology and development ! ! -! Data resource<-Amino acid +! Resource<-Amino acid ! ! -! Data resource<-Nucleic acid physicochemical property +! Resource<-Nucleic acid physicochemical property ! ! -! Data resource<-Protein physicochemical property +! Resource<-Protein physicochemical property ! ! -! Data resource<-Organelle +! Resource<-Organelle ! [Term] @@ -11880,21 +11946,21 @@ relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Ribosome +! Resource<-Ribosome ! ! -! Data resource<-Scents +! Resource<-Scents ! ! -! Data resource<-Biochemical nomenclature +! Resource<-Biochemical nomenclature ! ! -! Data resource<-Organism-specific +! Resource<-Organism-specific ! [Term] @@ -11938,7 +12004,7 @@ is_a: EDAM:0000621 ! Organism-specific relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Organism-specific<-Plant +! Resource<-Organism-specific<-Plant ! [Term] id: EDAM:0000784 @@ -11958,12 +12024,12 @@ relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Organism-specific<-Plant<-General plant +! Resource<-Organism-specific<-Plant<-General plant ! ! -! Data resource<-Organism-specific<-Plant<-Plant-specific +! Resource<-Organism-specific<-Plant<-Plant-specific ! [Term] id: EDAM:0000786 @@ -11986,17 +12052,17 @@ relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Organism-specific<-Plant<-Plant-specific<-Arabidopsis +! Resource<-Organism-specific<-Plant<-Plant-specific<-Arabidopsis ! ! -! Data resource<-Organism-specific<-Plant<-Plant-specific<-Rice +! Resource<-Organism-specific<-Plant<-Plant-specific<-Rice ! ! -! Data resource<-Organism-specific<-Viral +! Resource<-Organism-specific<-Viral ! [Term] id: EDAM:0000790 @@ -12015,7 +12081,7 @@ is_a: EDAM:0000781 ! Viral relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Organism-specific<-Fungal +! Resource<-Organism-specific<-Fungal ! [Term] id: EDAM:0000792 @@ -12035,17 +12101,17 @@ relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Organism-specific<-Pathogen +! Resource<-Organism-specific<-Pathogen ! ! -! Data resource<-Organism-specific<-Bacteria +! Resource<-Organism-specific<-Bacteria ! ! -! Data resource<-Genomics +! Resource<-Genomics ! [Term] id: EDAM:0000794 @@ -12088,21 +12154,21 @@ is_a: EDAM:0000622 ! Genomics relationship: is_source_of EDAM:0000006 ! Data ! -! Data resource<-Genomics<-General genomics +! Resource<-Genomics<-General genomics ! ! -! Data resource<-Genome annotation +! Resource<-Genome annotation ! ! -! Data resource<-Genetic map or linkage +! Resource<-Genetic map or linkage ! [Term] id: EDAM:0000800 @@ -12116,23 +12182,23 @@ relationship: is_source_of EDAM:0001278 ! Genetic map ! -! Data resource<-Genetic map or linkage<-Genome map +! Resource<-Genetic map or linkage<-Genome map ! ! -! Data resource<-Comparative genomics +! Resource<-Comparative genomics ! ! -! Data resource<-Mobile genetic elements +! Resource<-Mobile genetic elements ! ! -! Data resource<-Specific genes +! Resource<-Specific genes ! [Term] id: EDAM:0000801 @@ -12146,7 +12212,7 @@ relationship: is_source_of EDAM:0000916 ! Gene annotation ! -! Data resource<-Specific genes<-Human genes +! Resource<-Specific genes<-Human genes ! [Term] @@ -12171,7 +12237,7 @@ relationship: is_source_of EDAM:0000916 ! Gene annotation ! -! Data resource<-Specific genes<-Human genes<-Human genes, mutation and disease +! Resource<-Specific genes<-Human genes<-Human genes, mutation and disease ! [Term] @@ -12184,11 +12250,11 @@ relationship: is_source_of EDAM:0000916 ! Gene annotation ! -! Data resource<-Chromosome +! Resource<-Chromosome ! ! -! Data resource<-Genotype / phenotype +! Resource<-Genotype / phenotype ! @@ -12197,21 +12263,21 @@ relationship: is_source_of EDAM:0000916 ! Gene annotation ! -! Data resource<-DNA methylation +! Resource<-DNA methylation ! ! -! Data resource<-DNA replication +! Resource<-DNA replication ! ! -! Data resource<-Gene structure +! Resource<-Gene structure ! ! -! Data resource<-Gene regulation +! Resource<-Gene regulation ! [Term] id: EDAM:0000811 @@ -12226,33 +12292,33 @@ relationship: is_source_of EDAM:0001315 ! Gene features (TFBS) ! -! Data resource<-Gene regulation<-Transcription factor and binding site +! Resource<-Gene regulation<-Transcription factor and binding site ! ! -! Data resource<-Gene expression and microarray +! Resource<-Gene expression and microarray ! ! -! Data resource<-Molecular probes or primers +! Resource<-Molecular probes or primers ! ! -! Data resource<-Immunological +! Resource<-Immunological ! ! -! Data resource<-Disease +! Resource<-Disease ! ! -! Data resource<-Specific protein +! Resource<-Specific protein ! [Term] @@ -12281,26 +12347,26 @@ relationship: is_source_of EDAM:0001509 ! Enzyme annotation ! -! Data resource<-Specific protein<-Disease-associated protein +! Resource<-Specific protein<-Disease-associated protein ! ! -! Data resource<-Specific protein<-Membrane protein +! Resource<-Specific protein<-Membrane protein ! ! -! Data resource<-Specific protein<-Enzyme +! Resource<-Specific protein<-Enzyme ! ! -! Data resource<-Phylogenetic +! Resource<-Phylogenetic ! ! -! Data resource<-Taxonomic +! Resource<-Taxonomic ! @@ -12444,12 +12510,12 @@ consider: EDAM:0000582 ! Ontology ! ! Data ! -[Term] -id: EDAM:0000841 -name: Undefined -namespace: data -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000006 ! Data +! [Term] +! id: EDAM:0000841 +! name: Undefined +! namespace: data +! def: "Debugging." [EDAM:EBI "EMBRACE definition"] +! is_a: EDAM:0000006 ! Data @@ -12479,9 +12545,9 @@ namespace: data def: "Something that identifies (typically uniquely) something such as an entity, database, ontology, datatype." [EDAM:EBI "EMBRACE definition"] comment: This term is used for datatypes with the sole purpose of identification. It is not used for datatypes which contain other fields not related to identification. See OBO file for regular expression. {regexp=} is_a: EDAM:0000006 ! Data -relationship: is_identifier_of EDAM:0000002 ! Biological entity -relationship: is_identifier_of EDAM:0000005 ! Data resource -relationship: is_identifier_of EDAM:0000582 ! Ontology +! relationship: is_identifier_of EDAM:0000002 ! Biological entity +relationship: is_identifier_of EDAM:0000005 ! Resource +! relationship: is_identifier_of EDAM:0000582 ! Ontology relationship: is_identifier_of EDAM:0000006 ! Data @@ -12502,7 +12568,7 @@ namespace: data def: "A data resource or archive including relational, object-oriented and other databases, flat-file databanks and ontologies." [EDAM:EBI "EMBRACE definition"] comment: This term is required for completeness and should not be subclassed (have child terms): EDAM does not include individual databases. is_obsolete: true -consider: EDAM:0000005 ! Data resource +consider: EDAM:0000005 ! Resource @@ -13264,7 +13330,7 @@ xref: SO:0001248 is_a: EDAM:0002044 ! Sequence data - +! @@ -13606,14 +13672,14 @@ is_a: EDAM:0000959 ! Job metadata ! ! Data<-Identifier ! -[Term] -id: EDAM:0000973 -name: Undefined -namespace: data -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -comment: See OBO file for regular expression. {regexp=} -is_obsolete: true -consider: EDAM:0000841 ! Undefined +! [Term] +! id: EDAM:0000973 +! name: Undefined +! namespace: data +! def: "Debugging." [EDAM:EBI "EMBRACE definition"] +! comment: See OBO file for regular expression. {regexp=} +! is_obsolete: true +! consider: EDAM:0000841 ! Undefined [Term] id: EDAM:0000974 @@ -13641,7 +13707,7 @@ namespace: data def: "An identifier of a bioinformatics tool, e.g. an application or web service." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -13698,7 +13764,7 @@ namespace: data def: "A name of a thing, which need not necessarily uniquely identify it." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000842 ! Identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002100 @@ -13707,7 +13773,7 @@ namespace: data def: "The type of a thing, which is usually an enumerated string (a string with one of a limited set of values)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000842 ! Identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -13726,7 +13792,7 @@ namespace: data def: "An identifier for data objects of different type (typically served from a single database)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000842 ! Identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -13736,7 +13802,7 @@ namespace: data def: "An identifier of a catalogue of biological resources." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000842 ! Identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -13753,7 +13819,7 @@ namespace: data def: "Name or other identifier of a molecule." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000013 ! Molecular entity +! relationship: is_identifier_of EDAM:0000013 ! Molecular entity [Term] id: EDAM:0001015 @@ -13762,7 +13828,7 @@ namespace: data def: "Name or other identifier of a molecular sequence feature." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000010 ! Entity feature +! relationship: is_identifier_of EDAM:0000010 ! Entity feature [Term] id: EDAM:0001893 @@ -13782,7 +13848,7 @@ namespace: data def: "An identifier of a build of a particular genome." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000066 ! Genome +! relationship: is_identifier_of EDAM:0000066 ! Genome [Term] id: EDAM:0001025 @@ -13792,7 +13858,7 @@ def: "An identifier of a gene, such as a name/symbol or a unique identifier of a comment: See OBO file for regular expression. {regexp=} xref: Moby:GeneAccessionList is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0002127 @@ -13810,7 +13876,7 @@ namespace: data def: "Identifier of a protein structural domain." [EDAM:EBI "EMBRACE definition"] comment: This is typically a character or string concatenated with a PDB identifier and a chain identifier. See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000065 ! Protein domain +! relationship: is_identifier_of EDAM:0000065 ! Protein domain [Term] @@ -13820,7 +13886,7 @@ namespace: data def: "The name of a protein fold." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000065 ! Protein domain +! relationship: is_identifier_of EDAM:0000065 ! Protein domain [Term] @@ -13830,7 +13896,7 @@ namespace: data def: "A unique identifier of a (group of) organisms." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001047 @@ -13839,7 +13905,7 @@ namespace: data def: "A string of characters that name or otherwise identify a resource on the Internet." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -13849,7 +13915,7 @@ namespace: data def: "An identifier of a biological or bioinformatics database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001049 @@ -13859,7 +13925,7 @@ def: "The name of a directory." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002099 ! Name is_a: EDAM:0000583 ! Directory metadata -relationship: is_identifier_of EDAM:0000223 ! Undefined +! relationship: is_identifier_of EDAM:0000223 ! Undefined [Term] id: EDAM:0001050 @@ -13868,7 +13934,7 @@ namespace: data def: "The name (or part of a name) of a file (of any type)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001051 @@ -13928,7 +13994,7 @@ namespace: data def: "An identifier of an entry from a database of molecular sequence variation." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -14152,7 +14218,7 @@ namespace: data def: "Identifier of a biological reaction from a database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -14171,7 +14237,7 @@ namespace: data def: "Identifier of a data type definition from some provider." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002219 @@ -14180,7 +14246,7 @@ namespace: data def: "The name of a field in a database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -14203,7 +14269,7 @@ synonym: "Chemical compound identifier" EXACT [] is_a: EDAM:0000976 ! Datatype identifier is_a: EDAM:0000982 ! Molecule identifier relationship: is_identifier_of EDAM:0000962 ! Small molecule annotation -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14246,7 +14312,7 @@ namespace: data def: "Unique identifier of a spot from a two-dimensional (protein) gel." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002587 @@ -14255,7 +14321,7 @@ namespace: data def: "Unique identifier of a blot from a Nothern Blot." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -14266,7 +14332,7 @@ namespace: data def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -14315,7 +14381,7 @@ def: "Identifier of an object from one of the BioCyc databases." [EDAM:EBI "EMBR comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002109 ! Hybrid data identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001154 @@ -14344,7 +14410,7 @@ def: "A unique identifier of an item from the CABRI database." [EDAM:EBI "EMBRAC comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002109 ! Hybrid data identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000072 ! Strain +! relationship: is_identifier_of EDAM:0000072 ! Strain [Term] id: EDAM:0002387 @@ -14414,7 +14480,7 @@ namespace: data def: "The name of a catalogue of biological resources from the CABRI database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002596 ! Catalogue identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -14425,7 +14491,7 @@ namespace: data def: "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002131 @@ -14434,7 +14500,7 @@ namespace: data def: "Name of a computer operating system such as Linux, PC or Mac." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002132 @@ -14444,7 +14510,7 @@ def: "A type of point or block mutation, including insertion, deletion, change, comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002538 ! Mutation identifier is_a: EDAM:0002100 ! Type -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -14455,7 +14521,7 @@ namespace: data def: "An identifier of a mutation." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000976 ! Datatype identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -14465,7 +14531,7 @@ namespace: data def: "A unique identifier of a specific mutation catalogued in a database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002538 ! Mutation identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002133 @@ -14474,7 +14540,7 @@ namespace: data def: "A logical operator such as OR, AND, XOR, and NOT." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -14484,7 +14550,7 @@ namespace: data def: "A type of protein family signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002100 ! Type -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -14519,7 +14585,7 @@ namespace: data def: "Identifier (e.g. character symbol) of a specific atom." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0000014 ! Atom +! relationship: is_identifier_of EDAM:0000014 ! Atom [Term] @@ -14530,7 +14596,7 @@ def: "Name of a specific molecule." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000982 ! Molecule identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000013 ! Molecular entity +! relationship: is_identifier_of EDAM:0000013 ! Molecular entity [Term] id: EDAM:0000985 @@ -14540,7 +14606,7 @@ def: "The type a molecule." [EDAM:EBI "EMBRACE definition"] comment: For example, 'Protein', 'DNA', 'RNA' etc. See OBO file for regular expression. {regexp=} is_a: EDAM:0000982 ! Molecule identifier is_a: EDAM:0002100 ! Type -relationship: is_identifier_of EDAM:0000013 ! Molecular entity +! relationship: is_identifier_of EDAM:0000013 ! Molecular entity [Term] id: EDAM:0000986 @@ -14559,7 +14625,7 @@ namespace: data def: "Name or other identifier of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0000024 ! Nucleic acid +! relationship: is_identifier_of EDAM:0000024 ! Nucleic acid [Term] id: EDAM:0000988 @@ -14568,7 +14634,7 @@ namespace: data def: "Name or other identifier of a polypeptide chain." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0000025 ! Polypeptide +! relationship: is_identifier_of EDAM:0000025 ! Polypeptide [Term] id: EDAM:0000989 @@ -14577,7 +14643,7 @@ namespace: data def: "Name or other identifier of a protein." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000982 ! Molecule identifier -relationship: is_identifier_of EDAM:0000037 ! Protein +! relationship: is_identifier_of EDAM:0000037 ! Protein @@ -14595,7 +14661,7 @@ xref: WHATIF: alternate_atom xref: WHATIF: PDBx_auth_atom_id xref: WHATIF: PDBx_type_symbol is_a: EDAM:0000983 ! Atom identifier -relationship: is_identifier_of EDAM:0000014 ! Atom +! relationship: is_identifier_of EDAM:0000014 ! Atom ! pdbx_PDB_atom_name in PDBML @@ -14607,7 +14673,7 @@ def: "Name of an atom." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000983 ! Atom identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000014 ! Atom +! relationship: is_identifier_of EDAM:0000014 ! Atom ! @@ -14630,7 +14696,7 @@ def: "Unique name of a chemical compound." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001086 ! Compound identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14641,7 +14707,7 @@ namespace: data def: "Unique registry number of a chemical compound." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14652,7 +14718,7 @@ namespace: data def: "Code word for a ligand, for example from a PDB file." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0000019 ! Ligand +! relationship: is_identifier_of EDAM:0000019 ! Ligand ! relationship: is_identifier_of EDAM:0001704 ! MSDchem ligand dictionary entry format ! relationship: is_identifier_of EDAM:0001705 ! HET group dictionary entry format @@ -14663,7 +14729,7 @@ namespace: data def: "Unique identifier of a drug." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0000020 ! Drug +! relationship: is_identifier_of EDAM:0000020 ! Drug [Term] id: EDAM:0002576 @@ -14672,7 +14738,7 @@ namespace: data def: "Unique identifier of a toxin." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0002577 ! Toxin +! relationship: is_identifier_of EDAM:0002577 ! Toxin [Term] @@ -14683,7 +14749,7 @@ def: "Name or other identifier of an amino acid." [EDAM:EBI "EMBRACE definition" comment: See OBO file for regular expression. {regexp=} synonym: "Residue identifier" EXACT [] is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0000021 ! Amino acid annotation +! relationship: is_identifier_of EDAM:0000021 ! Amino acid annotation [Term] id: EDAM:0000995 @@ -14692,7 +14758,7 @@ namespace: data def: "Name or other identifier of a nucleotide." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0000022 ! Nucleotide +! relationship: is_identifier_of EDAM:0000022 ! Nucleotide [Term] id: EDAM:0000996 @@ -14701,10 +14767,10 @@ namespace: data def: "Name or other identifier of a monosaccharide." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001086 ! Compound identifier -relationship: is_identifier_of EDAM:0000023 ! Monosaccharide +! relationship: is_identifier_of EDAM:0000023 ! Monosaccharide [Term] -id: EDAM:0000990 +id: EDAM:0002605 name: Compound ID (KEGG) namespace: data def: "Unique name of a chemical compound." [EDAM:EBI "EMBRACE definition"] @@ -14713,7 +14779,7 @@ synonym: "KEGG compound ID" EXACT [] synonym: "KEGG compound identifier" EXACT [] is_a: EDAM:0001086 ! Compound identifier is_a: EDAM:0001154 ! KEGG object identifier -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule [Term] @@ -14724,7 +14790,7 @@ def: "Unique identifier of a monomer from the BindingDB database." [EDAM:EBI "EM comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001086 ! Compound identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule [Term] @@ -14781,7 +14847,7 @@ def: "Unique name from Chemical Entities of Biological Interest (ChEBI) of a che comment: This is the recommended chemical name for use for example in database annotation. See OBO file for regular expression. {regexp=} synonym: "ChEBI chemical name" EXACT [] is_a: EDAM:0000990 ! Chemical name -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14793,7 +14859,7 @@ def: "IUPAC recommended name of a chemical compound." [EDAM:EBI "EMBRACE definit comment: See OBO file for regular expression. {regexp=} synonym: "IUPAC chemical name" EXACT [] is_a: EDAM:0000990 ! Chemical name -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14805,7 +14871,7 @@ def: "International Non-proprietary Name (INN or 'generic name') of a chemical c comment: See OBO file for regular expression. {regexp=} synonym: "INN chemical name" EXACT [] is_a: EDAM:0000990 ! Chemical name -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14817,7 +14883,7 @@ def: "Brandname of a chemical compound." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} synonym: "Brand chemical name" EXACT [] is_a: EDAM:0000990 ! Chemical name -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14829,7 +14895,7 @@ def: "Synonymous name of a chemical compound." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} synonym: "Synonymous chemical name" EXACT [] is_a: EDAM:0000990 ! Chemical name -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14844,7 +14910,7 @@ def: "CAS registry number of a chemical compound." [EDAM:EBI "EMBRACE definition comment: See OBO file for regular expression. {regexp=} synonym: "CAS chemical registry number" EXACT [] is_a: EDAM:0000991 ! Chemical registry number -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14856,7 +14922,7 @@ def: "Beilstein registry number of a chemical compound." [EDAM:EBI "EMBRACE defi comment: See OBO file for regular expression. {regexp=} synonym: "Beilstein chemical registry number" EXACT [] is_a: EDAM:0000991 ! Chemical registry number -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14868,7 +14934,7 @@ def: "Gmelin registry number of a chemical compound." [EDAM:EBI "EMBRACE definit comment: See OBO file for regular expression. {regexp=} synonym: "Gmelin chemical registry number" EXACT [] is_a: EDAM:0000991 ! Chemical registry number -relationship: is_identifier_of EDAM:0000015 ! Small molecule +! relationship: is_identifier_of EDAM:0000015 ! Small molecule relationship: is_identifier_of EDAM:0001712 ! Chemical structure image relationship: is_identifier_of EDAM:0000846 ! Chemical formula @@ -14887,7 +14953,7 @@ comment: See OBO file for regular expression. {regexp=} synonym: "Short ligand name" EXACT [] is_a: EDAM:0000992 ! Ligand identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000019 ! Ligand +! relationship: is_identifier_of EDAM:0000019 ! Ligand @@ -14903,7 +14969,7 @@ def: "Unique identifier of a drug from the DrugBank database." [EDAM:EBI "EMBRAC comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000993 ! Drug identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000020 ! Drug +! relationship: is_identifier_of EDAM:0000020 ! Drug ! ! Data<-Identifier<-Molecule identifier<-Compound identifier<-Toxin identifier @@ -14916,7 +14982,7 @@ def: "Unique identifier of a toxin from the ArachnoServer database." [EDAM:EBI " comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002576 ! Toxin identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0002577 ! Toxin +! relationship: is_identifier_of EDAM:0002577 ! Toxin ! @@ -14948,7 +15014,7 @@ def: "String of one or more ASCII characters representing a nucleotide." [EDAM:E comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000995 ! Nucleotide identifier is_a: EDAM:0000984 ! Molecule name -relationship: is_identifier_of EDAM:0000022 ! Nucleotide +! relationship: is_identifier_of EDAM:0000022 ! Nucleotide ! ! Data<-Identifier<-Molecule identifier<-Compound identifier<-Monosaccharide identifier @@ -14967,7 +15033,7 @@ def: "Name of a chromosome." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002119 ! Nucleic acid identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0001851 ! Chromosome +! relationship: is_identifier_of EDAM:0001851 ! Chromosome [Term] id: EDAM:0002208 @@ -14976,7 +15042,7 @@ namespace: data def: "A unique identifier of a plasmid in a database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002119 ! Nucleic acid identifier -relationship: is_identifier_of EDAM:0000032 ! Plasmid +! relationship: is_identifier_of EDAM:0000032 ! Plasmid @@ -14996,7 +15062,7 @@ synonym: "Chain identifier" EXACT [] synonym: "PDB strand id" EXACT [] xref: WHATIF: chain is_a: EDAM:0000988 ! Polypeptide identifier -relationship: is_identifier_of EDAM:0000025 ! Polypeptide +! relationship: is_identifier_of EDAM:0000025 ! Polypeptide ! pdbx_PDB_strand_id in PDBML @@ -15025,7 +15091,7 @@ def: "Name of a protein." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000989 ! Protein identifier is_a: EDAM:0000984 ! Molecule name -relationship: is_identifier_of EDAM:0000037 ! Protein +! relationship: is_identifier_of EDAM:0000037 ! Protein [Term] id: EDAM:0001010 @@ -15034,7 +15100,7 @@ namespace: data def: "Name or other identifier of an enzyme or record from a database of enzymes." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000989 ! Protein identifier -relationship: is_identifier_of EDAM:0000039 ! Enzyme +! relationship: is_identifier_of EDAM:0000039 ! Enzyme relationship: is_identifier_of EDAM:0001509 ! Enzyme annotation @@ -15047,7 +15113,7 @@ comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000989 ! Protein identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0002113 ! WormBase identifier -relationship: is_identifier_of EDAM:0000037 ! Protein +! relationship: is_identifier_of EDAM:0000037 ! Protein @@ -15059,7 +15125,7 @@ def: "Unique identifier for a protein from the Ensembl database." [EDAM:EBI "EMB comment: See OBO file for regular expression. {regexp=} synonym: "Ensembl protein ID" EXACT [] is_a: EDAM:0000989 ! Protein identifier -relationship: is_identifier_of EDAM:0000037 ! Protein +! relationship: is_identifier_of EDAM:0000037 ! Protein ! @@ -15079,7 +15145,7 @@ comment: See OBO file for regular expression. {regexp=} synonym: "Enzyme ID" EXACT [] is_a: EDAM:0001010 ! Enzyme identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000039 ! Enzyme +! relationship: is_identifier_of EDAM:0000039 ! Enzyme [Term] @@ -15090,7 +15156,7 @@ def: "Name of an enzyme." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001010 ! Enzyme identifier is_a: EDAM:0001009 ! Protein name -relationship: is_identifier_of EDAM:0000039 ! Enzyme +! relationship: is_identifier_of EDAM:0000039 ! Enzyme ! ! Data<-Identifier<-Molecule identifier<-Protein identifier<-Enzyme identifier<-Enzyme accession @@ -15105,7 +15171,7 @@ synonym: "Enzyme Commission number" EXACT [] xref: Moby:EC_Number xref: Moby:Annotated_EC_Number is_a: EDAM:0002091 ! Enzyme accession -relationship: is_identifier_of EDAM:0000039 ! Enzyme +! relationship: is_identifier_of EDAM:0000039 ! Enzyme relationship: is_identifier_of EDAM:0001509 ! Enzyme annotation [Term] @@ -15117,7 +15183,7 @@ comment: See OBO file for regular expression. {regexp=} synonym: "BioCyc enzyme ID" EXACT [] is_a: EDAM:0002104 ! BioCyc identifier is_a: EDAM:0002091 ! Enzyme accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -15127,7 +15193,7 @@ namespace: data def: "Identifier of an enzyme from the REBASE enzymes database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002091 ! Enzyme accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! @@ -15145,7 +15211,7 @@ namespace: data def: "Name of a restriction enzyme." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001012 ! Enzyme name -relationship: is_identifier_of EDAM:0000042 ! Restriction enzyme +! relationship: is_identifier_of EDAM:0000042 ! Restriction enzyme @@ -15162,7 +15228,7 @@ namespace: data def: "Name or other identifier of an nucleic acid feature." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_obsolete: true -consider: EDAM:0000841 ! Identifier +! consider: EDAM:0000841 ! Identifier [Term] id: EDAM:0001019 @@ -15171,7 +15237,7 @@ namespace: data def: "Name or other identifier of a protein feature." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_obsolete: true -consider: EDAM:0000841 ! Identifier +! consider: EDAM:0000841 ! Identifier [Term] id: EDAM:0001020 @@ -15181,7 +15247,7 @@ def: "Typically one of the EMBL or SwissProt sequence feature keys." [EDAM:EBI " comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. See OBO file for regular expression. {regexp=} synonym: "Sequence feature type" EXACT [] is_a: EDAM:0001015 ! Sequence feature identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001021 @@ -15190,7 +15256,7 @@ namespace: data def: "Typically one of the EMBL or SwissProt feature qualifiers." [EDAM:EBI "EMBRACE definition"] comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location. See OBO file for regular expression. {regexp=} is_a: EDAM:0001015 ! Sequence feature identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001022 @@ -15200,7 +15266,7 @@ def: "Typically an EMBL or SwissProt feature label." [EDAM:EBI "EMBRACE definiti comment: A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. See OBO file for regular expression. {regexp=} synonym: "Sequence feature name" EXACT [] is_a: EDAM:0001015 ! Sequence feature identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -15400,7 +15466,7 @@ synonym: "Gene symbol" EXACT [] xref: Moby_namespace:Global_GeneSymbol xref: Moby_namespace:Global_GeneCommonName is_a: EDAM:0001025 ! Gene identifier -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0002299 @@ -15409,7 +15475,7 @@ namespace: data def: "The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain whitespace characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001025 ! Gene identifier -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] @@ -15422,7 +15488,7 @@ synonym: "Gene code" EXACT [] synonym: "Gene accession" EXACT [] is_a: EDAM:0001025 ! Gene identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] @@ -15434,8 +15500,8 @@ comment: See OBO file for regular expression. {regexp=} xref: Moby_namespace:iHOPsymbol is_a: EDAM:0001025 ! Gene identifier is_a: EDAM:0000989 ! Protein identifier -relationship: is_identifier_of EDAM:0000051 ! Gene -relationship: is_identifier_of EDAM:0000037 ! Protein +! relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000037 ! Protein ! Suspect this identifiers more than just genes [Term] @@ -15495,7 +15561,7 @@ namespace: data def: "The name of an open reading frame attributed by a sequencing project." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002299 ! Gene name -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene ! GeneFarm gene ID is also given @@ -15507,7 +15573,7 @@ def: "Name of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE definition" comment: See OBO file for regular expression. {regexp=} xref: Moby_namespace:GENEFARM_GeneName is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] @@ -15518,7 +15584,7 @@ def: "The name of an Antirrhinum Gene from the DragonDB database." [EDAM:EBI "EM comment: See OBO file for regular expression. {regexp=} xref: Moby_namespace:DragonDB_Gene is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] @@ -15529,7 +15595,7 @@ def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbrev comment: See OBO file for regular expression. {regexp=} xref: Moby_namespace:ArabidopsisGeneSymbol is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001783 @@ -15539,7 +15605,7 @@ def: "Name of a gene from Aspergillus Genome Database." [EDAM:EBI "EMBRACE defin comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001784 @@ -15549,7 +15615,7 @@ def: "Name of a gene from Candida Genome Database." [EDAM:EBI "EMBRACE definitio comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001785 @@ -15559,7 +15625,7 @@ def: "Name of a gene from dictyBase database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001786 @@ -15570,17 +15636,17 @@ comment: See OBO file for regular expression. {regexp=} synonym: "EcoGene primary gene name" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] -comment: See OBO file for regular expression. {regexp=} id: EDAM:0001787 name: Gene name (MaizeGDB) namespace: data def: "Name of a gene from MaizeGDB (maize genes) database." [EDAM:EBI "EMBRACE definition"] +comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001788 @@ -15590,7 +15656,7 @@ def: "Name of a gene from Saccharomyces Genome Database." [EDAM:EBI "EMBRACE def comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001789 @@ -15600,7 +15666,7 @@ def: "Name of a gene from Tetrahymena Genome Database." [EDAM:EBI "EMBRACE defin comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001790 @@ -15610,7 +15676,7 @@ def: "Symbol of a gene from E.coli Genetic Stock Center." [EDAM:EBI "EMBRACE def comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001791 @@ -15628,7 +15694,7 @@ synonym: "HUGO gene name" EXACT [] synonym: "HGNC gene name" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001792 @@ -15638,7 +15704,7 @@ def: "Symbol of a gene from the Mouse Genome Database." [EDAM:EBI "EMBRACE defin comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001793 @@ -15648,7 +15714,7 @@ def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [EDAM:EB comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0002103 @@ -15669,7 +15735,7 @@ def: "Name of an entry (gene) from the AceView genes database." [EDAM:EBI "EMBRA comment: See OBO file for regular expression. {regexp=} synonym: "AceView gene name" EXACT [] is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002300 @@ -15679,7 +15745,7 @@ def: "Name of an entry (gene) from the NCBI genes database." [EDAM:EBI "EMBRACE comment: See OBO file for regular expression. {regexp=} synonym: "NCBI gene name" EXACT [] is_a: EDAM:0001026 ! Gene symbol -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! @@ -15721,7 +15787,7 @@ def: "The blattner identifier for a gene." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} xref: Moby_namespace:Blattner_number is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -15787,7 +15853,7 @@ def: "Identifier of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE defin comment: See OBO file for regular expression. {regexp=} xref: Moby_namespace:GENEFARM_GeneID is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001907 @@ -15797,7 +15863,7 @@ def: "Identifier of a gene from the KOME database." [EDAM:EBI "EMBRACE definitio comment: See OBO file for regular expression. {regexp=} xref: Moby_namespace:GeneId is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001794 @@ -15807,7 +15873,7 @@ def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [EDAM:EBI comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001795 @@ -15818,7 +15884,7 @@ comment: See OBO file for regular expression. {regexp=} synonym: "EcoGene Accession" EXACT [] synonym: "EcoGene ID" EXACT [] is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0002297 @@ -15830,7 +15896,7 @@ synonym: "E. coli K-12 gene identifier" EXACT [] synonym: "ECK accession" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK is_a: EDAM:0001795 ! Gene ID (EcoGene) -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene @@ -15843,7 +15909,7 @@ comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] @@ -15855,7 +15921,7 @@ comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001803 @@ -15866,7 +15932,7 @@ comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001804 @@ -15876,7 +15942,7 @@ def: "Gene identifier from Sol Genomics Network." [EDAM:EBI "EMBRACE definition" comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001805 @@ -15888,7 +15954,7 @@ xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase is_a: EDAM:0002295 ! Gene ID is_a: EDAM:0002113 ! WormBase identifier -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001035 @@ -15909,7 +15975,7 @@ def: "Identifier for genetic elements in MIPS database." [EDAM:EBI "EMBRACE defi comment: See OBO file for regular expression. {regexp=} synonym: "MIPS genetic element identifier" EXACT [] is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -15920,7 +15986,7 @@ def: "Identifier for a gene approved by the HUGO Gene Nomenclature Committee." [ comment: See OBO file for regular expression. {regexp=} synonym: "HGNC ID" EXACT [] is_a: EDAM:0002295 ! Gene ID -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -15935,7 +16001,7 @@ def: "Gene identifier from Glossina morsitans GeneDB database." [EDAM:EBI "EMBRA comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans is_a: EDAM:0001035 ! Gene ID (GeneDB) -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001798 @@ -15945,7 +16011,7 @@ def: "Gene identifier from Leishmania major GeneDB database." [EDAM:EBI "EMBRACE comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor is_a: EDAM:0001035 ! Gene ID (GeneDB) -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001799 @@ -15955,7 +16021,7 @@ def: "Gene identifier from Plasmodium falciparum GeneDB database." [EDAM:EBI "EM comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum is_a: EDAM:0001035 ! Gene ID (GeneDB) -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001800 @@ -15965,7 +16031,7 @@ def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [EDAM:EBI comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe is_a: EDAM:0001035 ! Gene ID (GeneDB) -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene [Term] id: EDAM:0001801 @@ -15975,7 +16041,7 @@ def: "Gene identifier from Trypanosoma brucei GeneDB database." [EDAM:EBI "EMBRA comment: See OBO file for regular expression. {regexp=} xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei is_a: EDAM:0001035 ! Gene ID (GeneDB) -relationship: is_identifier_of EDAM:0000051 ! Gene +! relationship: is_identifier_of EDAM:0000051 ! Gene @@ -15991,7 +16057,7 @@ comment: See OBO file for regular expression. {regexp=} synonym: "MIPS genetic element identifier (Maize)" EXACT [] xref: Moby_namespace:MIPS_GE_Maize is_a: EDAM:0002285 ! Gene ID (MIPS) -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001888 @@ -16002,7 +16068,7 @@ comment: See OBO file for regular expression. {regexp=} synonym: "MIPS genetic element identifier (Medicago)" EXACT [] xref: Moby_namespace:MIPS_GE_Medicago is_a: EDAM:0002285 ! Gene ID (MIPS) -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -16041,7 +16107,7 @@ namespace: data def: "Identifier of a protein domain (or other node) from the SCOP database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001038 ! Protein domain identifier -relationship: is_identifier_of EDAM:0000065 ! Protein domain +! relationship: is_identifier_of EDAM:0000065 ! Protein domain [Term] id: EDAM:0001040 @@ -16051,7 +16117,7 @@ def: "Identifier of a protein domain from CATH." [EDAM:EBI "EMBRACE definition"] comment: For example '1nr3A00'. See OBO file for regular expression. {regexp=} synonym: "CATH domain identifier" EXACT [] is_a: EDAM:0001038 ! Protein domain identifier -relationship: is_identifier_of EDAM:0000065 ! Protein domain +! relationship: is_identifier_of EDAM:0000065 ! Protein domain ! ! Data<-Identifier<-Protein domain identifier<-SCOP domain identifier @@ -16119,7 +16185,7 @@ xref: Moby:BriefTaxonConcept xref: Moby:PotentialTaxon is_a: EDAM:0001869 ! Organism identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001872 @@ -16135,7 +16201,7 @@ xref: Moby:TaxonTCS xref: Moby:TaxonScientificName xref: Moby:iANT_organism-xml is_a: EDAM:0001869 ! Organism identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001874 @@ -16145,7 +16211,7 @@ def: "Common name for an organism as used in the GenBank database." [EDAM:EBI "E comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001869 ! Organism identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -16157,7 +16223,7 @@ comment: See OBO file for regular expression. {regexp=} xref: Moby_namespace:iHOPorganism is_a: EDAM:0001869 ! Organism identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002102 @@ -16167,7 +16233,7 @@ def: "A three-letter code used in the KEGG databases to uniquely identify organi comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001869 ! Organism identifier is_a: EDAM:0001154 ! KEGG object identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002593 @@ -16177,7 +16243,7 @@ def: "A unique identifier for an organism used in the BRENDA database." [EDAM:EB comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001869 ! Organism identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -16194,7 +16260,7 @@ namespace: data def: "The name of a taxon from the NCBI taxonomy database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001868 ! Taxon -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -16205,7 +16271,7 @@ def: "The name of a taxon using the controlled vocabulary of the UniGene databas comment: See OBO file for regular expression. {regexp=} synonym: "UniGene organism abbreviation" EXACT [] is_a: EDAM:0001868 ! Taxon -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002595 @@ -16214,7 +16280,7 @@ namespace: data def: "The name of a taxon using the controlled vocabulary of the UTRdb database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001868 ! Taxon -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -16226,7 +16292,7 @@ namespace: data def: "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001868 ! Taxon -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001870 @@ -16235,7 +16301,7 @@ namespace: data def: "The name of a genus of organism." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001868 ! Taxon -relationship: is_identifier_of EDAM:0001871 ! Genus +! relationship: is_identifier_of EDAM:0001871 ! Genus [Term] id: EDAM:0001045 @@ -16245,7 +16311,7 @@ def: "The name of a species (typically a taxonomic group) of organism." [EDAM:EB comment: See OBO file for regular expression. {regexp=} synonym: "Organism species" EXACT [] is_a: EDAM:0001868 ! Taxon -relationship: is_identifier_of EDAM:0000071 ! Species +! relationship: is_identifier_of EDAM:0000071 ! Species @@ -16263,7 +16329,7 @@ namespace: data def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002316 ! Cell line name -relationship: is_identifier_of EDAM:0000072 ! Strain +! relationship: is_identifier_of EDAM:0000072 ! Strain [Term] id: EDAM:0002318 @@ -16272,7 +16338,7 @@ namespace: data def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002316 ! Cell line name -relationship: is_identifier_of EDAM:0000072 ! Strain +! relationship: is_identifier_of EDAM:0000072 ! Strain [Term] id: EDAM:0002319 @@ -16281,7 +16347,7 @@ namespace: data def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002316 ! Cell line name -relationship: is_identifier_of EDAM:0000072 ! Strain +! relationship: is_identifier_of EDAM:0000072 ! Strain [Term] id: EDAM:0002320 @@ -16290,7 +16356,7 @@ namespace: data def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002316 ! Cell line name -relationship: is_identifier_of EDAM:0000072 ! Strain +! relationship: is_identifier_of EDAM:0000072 ! Strain ! @@ -16305,7 +16371,7 @@ comment: See OBO file for regular expression. {regexp=} xref: Moby:URL xref: Moby:Link is_a: EDAM:0001047 ! URI -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001053 @@ -16314,7 +16380,7 @@ namespace: data def: "A Uniform Resource Name (URN)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001047 ! URI -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -16344,7 +16410,7 @@ def: "A Life Science Identifier (LSID) - a unique identifier of some data." [EDA comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:::[:] See OBO file for regular expression. {regexp=} synonym: "Life Science Identifier" EXACT [] is_a: EDAM:0001053 ! URN -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! ! Data<-Identifier<-URI<-MIRIAM URI @@ -16363,7 +16429,7 @@ def: "The name of a biological or bioinformatics database." [EDAM:EBI "EMBRACE d comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001048 ! Database identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002149 @@ -16373,7 +16439,7 @@ def: "The name of a category of biological or bioinformatics database." [EDAM:EB comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001048 ! Database identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! ! Data<-Identifier<-Database identifier<-Database name @@ -16385,7 +16451,7 @@ namespace: data def: "The name of a molecular sequence database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001056 ! Database name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -16405,7 +16471,7 @@ namespace: data def: "The name of a file (of any type) with restricted possible values." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001050 ! File name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001059 @@ -16414,7 +16480,7 @@ namespace: data def: "The extension of a file name." [EDAM:EBI "EMBRACE definition"] comment: A file extension is the characters appearing after the final '.' in the file name. See OBO file for regular expression. {regexp=} is_a: EDAM:0001050 ! File name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001060 @@ -16423,7 +16489,7 @@ namespace: data def: "The base name of a file." [EDAM:EBI "EMBRACE definition"] comment: A file base name is the file name stripped of its directory specification and extension. See OBO file for regular expression. {regexp=} is_a: EDAM:0001050 ! File name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -17195,7 +17261,7 @@ is_a: EDAM:0001208 ! Protein sequence ! relationship: is_attribute_of EDAM:0000037 ! Protein [Term] -id: EDAM:0002570 +id: EDAM:0002607 name: Completely unambiguous pure protein sequence namespace: data def: "Any protein sequence without unknown positions, ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] @@ -17365,7 +17431,7 @@ def: "Identifier of an entry from the ELMdb database of protein functional sites comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001114 ! Sequence motif identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001117 @@ -17616,7 +17682,7 @@ is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0002354 ! RNA family annotation [Term] -id: EDAM:0002357 +id: EDAM:0002606 name: RFAM name namespace: data def: "Name (not necessarily stable) an entry (RNA family) from the RFAM database." [EDAM:EBI "EMBRACE definition"] @@ -17770,7 +17836,7 @@ def: "Identifier of an entry from the TRANSFAC database." [EDAM:EBI "EMBRACE def comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001077 ! Transcription factor identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! @@ -17795,7 +17861,7 @@ def: "PRIDE experiment accession number." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001078 ! Microarray experiment annotation identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -17826,7 +17892,7 @@ def: "Accession number of an entry from the GEO database." [EDAM:EBI "EMBRACE de comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001080 ! Gene expression annotation identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001148 @@ -17835,7 +17901,7 @@ namespace: data def: "Identifier of an entry from the GermOnline database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001080 ! Gene expression annotation identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001149 @@ -17845,7 +17911,7 @@ def: "Identifier of an entry from the EMAGE database." [EDAM:EBI "EMBRACE defini comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001080 ! Gene expression annotation identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! @@ -18101,7 +18167,7 @@ def: "The name of a data type." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001084 ! Data definition identifier is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] @@ -18128,7 +18194,7 @@ namespace: data def: "The primary name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] comment: The primary name of a MIRIAM data type is taken from a controlled vocabulary. For example, a protein entity has the data type 'UniProt', an enzyme has the type 'Enzyme Nomenclature' etc. See OBO file for regular expression. {regexp=} is_a: EDAM:0001163 ! MIRIAM data type name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -18139,7 +18205,7 @@ namespace: data def: "A synonymous name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] comment: A synonymous name for a MIRIAM data type taken from a controlled vocabulary. See OBO file for regular expression. {regexp=} is_a: EDAM:0001163 ! MIRIAM data type name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! @@ -18159,7 +18225,7 @@ def: "Identifier of a biological reaction from the BioCyc reactions database." [ comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002108 ! Reaction identifier is_a: EDAM:0002104 ! BioCyc identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002309 @@ -18168,7 +18234,7 @@ namespace: data def: "Identifier of a biological reaction from the SABIO-RK reactions database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002108 ! Reaction identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! ! Data<-Identifier<-Workflow identifier @@ -18414,7 +18480,7 @@ namespace: data def: "A protein family signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. See OBO file for regular expression. {regexp=} is_a: EDAM:0002357 ! Protein signature type -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001373 @@ -18423,7 +18489,7 @@ namespace: data def: "A protein domain signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries. See OBO file for regular expression. {regexp=} is_a: EDAM:0002357 ! Protein signature type -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001374 @@ -18432,7 +18498,7 @@ namespace: data def: "A protein region signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein region signature defines a region which cannot be described as a protein family or domain signature. See OBO file for regular expression. {regexp=} is_a: EDAM:0002357 ! Protein signature type -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001375 @@ -18441,7 +18507,7 @@ namespace: data def: "A protein repeat signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. See OBO file for regular expression. {regexp=} is_a: EDAM:0002357 ! Protein signature type -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001376 @@ -18450,7 +18516,7 @@ namespace: data def: "A protein site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein site signature is a classifier for a specific site in a protein. See OBO file for regular expression. {regexp=} is_a: EDAM:0002357 ! Protein signature type -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! ! Data<-Identifier<-Protein signature type<-Protein site signature @@ -18462,7 +18528,7 @@ namespace: data def: "A protein conserved site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. See OBO file for regular expression. {regexp=} is_a: EDAM:0001376 ! Protein site signature -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001378 @@ -18471,7 +18537,7 @@ namespace: data def: "A protein active site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. See OBO file for regular expression. {regexp=} is_a: EDAM:0001376 ! Protein site signature -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001379 @@ -18480,7 +18546,7 @@ namespace: data def: "A protein binding site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. See OBO file for regular expression. {regexp=} is_a: EDAM:0001376 ! Protein site signature -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001380 @@ -18489,7 +18555,7 @@ namespace: data def: "A protein post-translational modification signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. See OBO file for regular expression. {regexp=} is_a: EDAM:0001376 ! Protein site signature -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -18540,7 +18606,7 @@ namespace: data def: "Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002373 ! Spot identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0002375 @@ -18549,7 +18615,7 @@ namespace: data def: "Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002373 ! Spot identifier -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -18564,7 +18630,7 @@ def: "Unique identifier of a blot from a Nothern Blot from the BlotBase database comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002587 ! Blot identifier is_a: EDAM:0002091 ! Accession -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! @@ -18577,7 +18643,7 @@ namespace: data def: "The name of a strain of an organism variant, typically a plant, virus or bacterium." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002379 ! Strain identifier -relationship: is_identifier_of EDAM:0000072 ! Strain +! relationship: is_identifier_of EDAM:0000072 ! Strain @@ -18592,7 +18658,7 @@ namespace: data def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001046 ! Strain name -relationship: is_identifier_of EDAM:0000072 ! Strain +! relationship: is_identifier_of EDAM:0000072 ! Strain @@ -18655,7 +18721,7 @@ namespace: data def: "Name of an OBO file format such as OBO-XML, plain and so on." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0002129 ! File format name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -18672,7 +18738,7 @@ comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0000977 ! Tool identifier is_a: EDAM:0000958 ! Tool metadata is_a: EDAM:0002099 ! Name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined @@ -18686,7 +18752,7 @@ namespace: data def: "The unique name of a signature (sequence classifier) method." [EDAM:EBI "EMBRACE definition"] comment: Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. See OBO file for regular expression. {regexp=} is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001192 @@ -18696,7 +18762,7 @@ def: "The name of a BLAST tool." [EDAM:EBI "EMBRACE definition"] comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. See OBO file for regular expression. {regexp=} synonym: "BLAST name" EXACT [] is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001193 @@ -18705,7 +18771,7 @@ namespace: data def: "The name of a FASTA tool." [EDAM:EBI "EMBRACE definition"] comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. See OBO file for regular expression. {regexp=} is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001194 @@ -18714,7 +18780,7 @@ namespace: data def: "The name of an EMBOSS application." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined [Term] id: EDAM:0001195 @@ -18723,7 +18789,7 @@ namespace: data def: "The name of an EMBASSY package." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for regular expression. {regexp=} is_a: EDAM:0001190 ! Tool name -relationship: is_identifier_of EDAM:0000008 ! Undefined +! relationship: is_identifier_of EDAM:0000008 ! Undefined ! @@ -19101,7 +19167,7 @@ namespace: data def: "A sequence record in FASTA format." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001929 ! fasta sequence format +consider: EDAM:0001929 ! FASTA sequence format [Term] @@ -19127,7 +19193,7 @@ namespace: data def: "An entry from DDBJ." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001936 ! genbank sequence format +consider: EDAM:0001936 ! GenBank sequence format [Term] @@ -19137,7 +19203,7 @@ namespace: data def: "An entry from EMBL." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001936 ! genbank sequence format +consider: EDAM:0001936 ! GenBank sequence format @@ -19148,7 +19214,7 @@ namespace: data def: "An entry from GenBank." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001936 ! genbank sequence format +consider: EDAM:0001936 ! GenBank sequence format @@ -19171,7 +19237,7 @@ namespace: data def: "An entry from dbEST." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000849 ! Sequence record -consider: EDAM:0001936 ! genbank sequence format +consider: EDAM:0001936 ! GenBank sequence format @@ -19852,7 +19918,7 @@ name: DAS sequence feature annotation namespace: data def: "Annotation of a molecular sequence in DAS format." [EDAM:EBI "EMBRACE definition"] is_obsolete: true -consider: EDAM:0001978 ! dasgff feature +consider: EDAM:0001978 ! DASGFF feature @@ -23493,7 +23559,7 @@ is_a: EDAM:0002028 ! Experimental data id: EDAM:0000924 name: Sequence trace namespace: data -def: "A molecular sequence and associated metadata (quality scores) from a sequencing machine." [EDAM:EBI "EMBRACE definition"] +def: "A molecular sequence with associated sequencing metadata (e.g. base-call quality scores or raw sequencing data)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002028 ! Experimental data is_a: EDAM:0000849 ! Sequence record @@ -25956,16 +26022,16 @@ is_a: EDAM:0002176 ! Cardinality ! -! Data format +! Format ! -[Term] -id: EDAM:0002351 -name: Undefined -namespace: format -def: "Debugging." [EDAM:EBI "EMBRACE definition"] -comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0001915 ! Data format -relationship: is_format_of EDAM:0000841 ! Undefined +! [Term] +! id: EDAM:0002351 +! name: Undefined +! namespace: format +! def: "Debugging." [EDAM:EBI "EMBRACE definition"] +! comment: See OBO file for URL of format specification. {url=} +! is_a: EDAM:0001915 ! Format +! ! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002350 @@ -25973,8 +26039,8 @@ name: Datatype format namespace: format def: "A format for a particular datatype." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0001915 ! Data format -relationship: is_format_of EDAM:0000841 ! Undefined +is_a: EDAM:0001915 ! Format +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002330 @@ -25982,8 +26048,8 @@ name: Text format namespace: format def: "Text format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0001915 ! Data format -relationship: is_format_of EDAM:0000841 ! Undefined +is_a: EDAM:0001915 ! Format +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002331 @@ -25991,8 +26057,8 @@ name: HTML format namespace: format def: "HTML format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0001915 ! Data format -relationship: is_format_of EDAM:0000841 ! Undefined +is_a: EDAM:0001915 ! Format +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002332 @@ -26000,8 +26066,8 @@ name: XML format namespace: format def: "XML format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0001915 ! Data format -relationship: is_format_of EDAM:0000841 ! Undefined +is_a: EDAM:0001915 ! Format +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002333 @@ -26009,18 +26075,19 @@ name: Binary format namespace: format def: "Binary format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0001915 ! Data format -relationship: is_format_of EDAM:0000841 ! Undefined +is_a: EDAM:0001915 ! Format +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002352 -name: BioXSD format +name: BioXSD synonym: "BioXSD XML format" EXACT [] namespace: format -def: "BioXSD XML format" [EDAM:EBI "EMBRACE definition"] -comment: See OBO file for URL of format specification. {url=} +def: "BioXSD XML format of some of basic bioinformatics data types (sequences, sequence records, annotated sequences, sequence alignments, references to resources, and more)." [EDAM:EBI "EMBRACE definition"] +spec_url: http://bioxsd.org +comment: See OBO file for URL of format specification. {spec_url=} is_a: EDAM:0002332 ! XML format -relationship: is_format_of EDAM:0000841 ! Undefined +! ! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002376 @@ -26029,22 +26096,22 @@ namespace: format def: "Serialisation of RDF into an XML format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002332 ! XML format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined ! -! Data format<-Datatype format +! Format<-Datatype format ! [Term] id: EDAM:0002334 name: URI format namespace: format -def: "Typical textual representation of a URI" [EDAM:EBI "EMBRACE definition"] +def: "Typical textual representation of a URI." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002330 ! Text format is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0001918 @@ -26053,7 +26120,7 @@ namespace: format def: "Data format for an individual atom." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0001919 @@ -26062,7 +26129,7 @@ namespace: format def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] @@ -26072,7 +26139,7 @@ namespace: format def: "Data format for molecular sequence feature information." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0001921 @@ -26081,7 +26148,7 @@ namespace: format def: "Data format for molecular sequence alignment information." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] @@ -26091,7 +26158,7 @@ namespace: format def: "Data format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002033 @@ -26100,7 +26167,7 @@ namespace: format def: "Data format for a molecular tertiary structure." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002034 @@ -26109,7 +26176,7 @@ namespace: format def: "Data format for a biological model." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002014 @@ -26118,7 +26185,7 @@ namespace: format def: "Data format for a sequence-profile alignment." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] @@ -26129,7 +26196,7 @@ def: "Text format (representation) of amino acid residues." [EDAM:EBI "EMBRACE d comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format is_a: EDAM:0002330 ! Text format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002017 @@ -26138,7 +26205,7 @@ namespace: format def: "Data format for an amino acid index." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002020 @@ -26148,7 +26215,7 @@ def: "Data format for a full-text scientific article." [EDAM:EBI "EMBRACE defini synonym: "Literature format" EXACT [] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002021 @@ -26157,7 +26224,7 @@ namespace: format def: "Data format for an abstract (report) from text mining." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002027 @@ -26166,7 +26233,7 @@ namespace: format def: "Data format for reports on enzyme kinetics." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002030 @@ -26177,7 +26244,7 @@ synonym: "Chemical compound annotation format" EXACT [] synonym: "Small molecule annotation format" EXACT [] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002031 @@ -26186,7 +26253,7 @@ namespace: format def: "Format of a report on a particular locus, gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002032 @@ -26195,7 +26262,7 @@ namespace: format def: "Format of a workflow." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002035 @@ -26205,7 +26272,7 @@ def: "Text format of a chemical formula." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format is_a: EDAM:0002330 ! Text format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002036 @@ -26214,7 +26281,7 @@ namespace: format def: "Format of raw (unplotted) phylogenetic data." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002045 @@ -26223,7 +26290,7 @@ namespace: format def: "Annotation format for electron microscopy models." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002049 @@ -26232,7 +26299,7 @@ namespace: format def: "Format for phylogenetic tree distance data." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002051 @@ -26241,7 +26308,7 @@ namespace: format def: "Format for sequence polymorphism data." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002052 @@ -26250,7 +26317,7 @@ namespace: format def: "Format for reports on a protein family." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002054 @@ -26259,7 +26326,7 @@ namespace: format def: "Format for protein interaction data." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002055 @@ -26268,7 +26335,7 @@ namespace: format def: "Format for sequence assembly data." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002056 @@ -26277,7 +26344,7 @@ namespace: format def: "Format for microarray experimental data." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002058 @@ -26286,7 +26353,7 @@ namespace: format def: "Format for a report on gene expression." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002059 @@ -26295,7 +26362,7 @@ namespace: format def: "Format of a report on genotype / phenotype information." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002060 @@ -26304,7 +26371,7 @@ namespace: format def: "Format of a map of (typically one) molecular sequence annotated with features." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002061 @@ -26313,7 +26380,7 @@ namespace: format def: "Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002062 @@ -26322,7 +26389,7 @@ namespace: format def: "Format of a report of general information about a specific protein." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002064 @@ -26331,7 +26398,7 @@ namespace: format def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] @@ -26341,7 +26408,7 @@ namespace: format def: "Format of a report on the quality of a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] @@ -26351,7 +26418,7 @@ namespace: format def: "Format of a report on sequence hits and associated data from searching a sequence database." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] @@ -26361,7 +26428,7 @@ namespace: format def: "Format of a matrix of genetic distances between molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002068 @@ -26370,7 +26437,7 @@ namespace: format def: "Format of a sequence motif." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002069 @@ -26380,7 +26447,7 @@ def: "Format of a sequence profile." [EDAM:EBI "EMBRACE definition"] synonym: "Sequence profile format" EXACT [] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002074 @@ -26389,7 +26456,7 @@ namespace: format def: "Data format of a dirichlet distribution." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002075 @@ -26398,7 +26465,7 @@ namespace: format def: "Data format for the emission and transition counts of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] @@ -26408,7 +26475,7 @@ namespace: format def: "Format for secondary structure (predicted or real) of a protein molecule." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002076 @@ -26417,7 +26484,7 @@ namespace: format def: "Format for secondary structure (predicted or real) of an RNA molecule." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002078 @@ -26426,7 +26493,7 @@ namespace: format def: "Format used to specify range(s) of sequence positions." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002155 @@ -26435,7 +26502,7 @@ namespace: format def: "Format used for map of repeats in molecular (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002158 @@ -26444,7 +26511,7 @@ namespace: format def: "Format used for report on restriction enzyme recognition sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002159 @@ -26453,7 +26520,7 @@ namespace: format def: "Format used for report on coding regions in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002170 @@ -26462,7 +26529,7 @@ namespace: format def: "Format used for clusters of molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002195 @@ -26471,7 +26538,7 @@ namespace: format def: "Format used for ontologies." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002210 @@ -26480,7 +26547,7 @@ namespace: format def: "Format of a report on organism strain data / cell line." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] @@ -26490,7 +26557,7 @@ namespace: format def: "Format of a report on protein features (domain composition)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] @@ -26500,11 +26567,11 @@ namespace: format def: "Format of a raw molecular sequence (i.e. the alphabet used)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined ! -! Data format<-Atomic data format +! Format<-Atomic data format ! [Term] @@ -26518,7 +26585,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence record format +! Format<-Sequence record format ! [Term] id: EDAM:0002551 @@ -26528,17 +26595,17 @@ def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definitio comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0001919 ! Sequence record format is_a: EDAM:0002330 ! Text format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002552 -name: Sequence record format (xml) +name: Sequence record format (XML) namespace: format def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0001919 ! Sequence record format is_a: EDAM:0002332 ! XML format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002203 @@ -26568,7 +26635,7 @@ is_a: EDAM:0001919 ! Sequence record format ! -! Data format<-Sequence record format<-Sequence record format (text) +! Format<-Sequence record format<-Sequence record format (text) ! @@ -26629,22 +26696,22 @@ is_a: EDAM:0002551 ! Sequence record format (text) [Term] id: EDAM:0001938 -name: gff2-seq +name: GFF2-seq namespace: format def: "GFF feature file format with sequence in the header." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0001974 ! gff2 +is_a: EDAM:0001974 ! GFF2 [Term] id: EDAM:0001939 -name: gff3-seq +name: GFF3-seq namespace: format def: "GFF3 feature file format with sequence." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002551 ! Sequence record format (text) -is_a: EDAM:0001975 ! gff2 +is_a: EDAM:0001975 ! GFF2 [Term] @@ -26812,11 +26879,12 @@ is_a: EDAM:0002551 ! Sequence record format (text) [Term] id: EDAM:0001961 -name: stockholm +name: Stockholm format namespace: format -def: "Stockholm (pfam) sequence format." [EDAM:EBI "EMBRACE definition"] -comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002551 ! Sequence record format (text) +def: "Stockholm multiple sequence alignement format (used by Pfam and Rfam)." [EDAM:EBI "EMBRACE definition"] +spec_url: http://en.wikipedia.org/wiki/Stockholm_format +is_a: EDAM:0002330 ! Text format +relationship: is_format_of EDAM:0001382 ! Sequence alignment (multiple) [Term] @@ -26893,7 +26961,7 @@ is_a: EDAM:0002554 ! Alignment format (text) ! -! Data format<-Sequence record format<-Sequence record format (xml) +! Format<-Sequence record format<-Sequence record format (XML) ! [Term] @@ -26903,7 +26971,7 @@ namespace: format def: "DAS sequence (XML) format (any type)." [EDAM:EBI "EMBRACE definition"] synonym: "das sequence format" EXACT [] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002552 ! Sequence record format (xml) +is_a: EDAM:0002552 ! Sequence record format (XML) [Term] id: EDAM:0001968 @@ -26911,7 +26979,7 @@ name: dasdna namespace: format def: "DAS sequence (XML) format (nucleotide-only)." [EDAM:EBI "EMBRACE definition"] comment: The use of this format is deprecated. See OBO file for URL of format specification. {url=} -is_a: EDAM:0002552 ! Sequence record format (xml) +is_a: EDAM:0002552 ! Sequence record format (XML) @@ -26919,54 +26987,54 @@ is_a: EDAM:0002552 ! Sequence record format (xml) ! -! Data format<-Sequence record format<-Sequence record lite format +! Format<-Sequence record format<-Sequence record lite format ! [Term] id: EDAM:0002546 -name: fasta-like +name: FASTA-like format namespace: format def: "A format resembling FASTA format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the many non-standard fasta-like formats. See OBO file for URL of format specification. {url=} +comment: This term may be used for the many non-standard FASTA-like formats. See OBO file for URL of format specification. {url=} is_a: EDAM:0002203 ! Sequence record lite format ! -! Data format<-Sequence record format<-Sequence record lite format<-fasta-like +! Format<-Sequence record format<-Sequence record lite format<-FASTA-like ! [Term] id: EDAM:0002200 -name: fasta-like (text) +name: FASTA-like format (text) namespace: format def: "A text format resembling FASTA format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the many non-standard fasta-like formats. See OBO file for URL of format specification. {url=} -is_a: EDAM:0002546 ! fasta-like +comment: This term may be used for the many non-standard FASTA-like formats. See OBO file for URL of format specification. {url=} +is_a: EDAM:0002546 ! FASTA-like is_a: EDAM:0002330 ! Text format [Term] id: EDAM:0002310 -name: fasta-html +name: FASTA-HTML namespace: format def: "FASTA format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002546 ! fasta-like +is_a: EDAM:0002546 ! FASTA-like is_a: EDAM:0002331 ! HTML format ! -! Data format<-Sequence record format<-Sequence record lite format<-fasta-like<-fasta-like (text) +! Format<-Sequence record format<-Sequence record lite format<-FASTA-like<-FASTA-like (text) ! [Term] id: EDAM:0001929 -name: fasta +name: FASTA format namespace: format def: "FASTA format including NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] synonym: "FASTA" EXACT [] -synonym: "fasta sequence format" EXACT [] +synonym: "FASTA sequence format" EXACT [] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002200 ! fasta-like (text) +is_a: EDAM:0002200 ! FASTA-like (text) is_a: EDAM:0002554 ! Alignment format (text) [Term] @@ -26975,41 +27043,41 @@ name: dbid namespace: format def: "Fasta format variant with database name before ID." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002200 ! fasta-like (text) +is_a: EDAM:0002200 ! FASTA-like (text) [Term] id: EDAM:0001940 -name: gifasta +name: giFASTA format namespace: format def: "FASTA sequence format including NCBI-style GIs." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002200 ! fasta-like (text) +is_a: EDAM:0002200 ! FASTA-like (text) [Term] id: EDAM:0001954 -name: pearson +name: Pearson format namespace: format -def: "Plain old fasta sequence format (unspecified format for IDs)." [EDAM:EBI "EMBRACE definition"] +def: "Plain old FASTA sequence format (unspecified format for IDs)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002200 ! fasta-like (text) +is_a: EDAM:0002200 ! FASTA-like (text) [Term] id: EDAM:0001972 -name: ncbi +name: NCBI format namespace: format -def: "NCBI fasta sequence format with NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] +def: "NCBI FASTA sequence format with NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] comment: There are several variants of this. See OBO file for URL of format specification. {url=} -is_a: EDAM:0002200 ! fasta-like (text) +is_a: EDAM:0002200 ! FASTA-like (text) ! -! Data format<-Sequence record format<-Sequence record full format +! Format<-Sequence record format<-Sequence record full format ! [Term] id: EDAM:0002543 -name: embl-like +name: EMBL-like format namespace: format def: "A format resembling EMBL entry (plain text) format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the many non-standard EMBL-like formats. See OBO file for URL of format specification. {url=} @@ -27018,15 +27086,15 @@ is_a: EDAM:0002202 ! Sequence record full format [Term] id: EDAM:0002559 -name: genbank-like +name: GenBank-like format namespace: format def: "A format resembling GenBank entry (plain text) format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the non-standard genbank-like formats. See OBO file for URL of format specification. {url=} +comment: This term may be used for the non-standard GenBank-like formats. See OBO file for URL of format specification. {url=} is_a: EDAM:0002202 ! Sequence record full format [Term] id: EDAM:0002547 -name: uniprotkb-like +name: uniprotkb-like format namespace: format def: "A sequence format resembling uniprotkb entry format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} @@ -27050,49 +27118,49 @@ is_a: EDAM:0002202 ! Sequence record full format ! -! Data format<-Sequence record format<-Sequence record full format<-embl-like +! Format<-Sequence record format<-Sequence record full format<-EMBL-like ! [Term] id: EDAM:0002181 -name: embl-like (text) +name: EMBL-like format (text) namespace: format def: "A text format resembling EMBL entry format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the many non-standard EMBL-like text formats. See OBO file for URL of format specification. {url=} -is_a: EDAM:0002543 ! embl-like +is_a: EDAM:0002543 ! EMBL-like is_a: EDAM:0002330 ! Text format [Term] id: EDAM:0002558 -name: embl-like (xml) +name: EMBL-like format (XML) namespace: format def: "An XML format resembling EMBL entry format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the any non-standard EMBL-like XML formats. See OBO file for URL of format specification. {url=} -is_a: EDAM:0002543 ! embl-like +is_a: EDAM:0002543 ! EMBL-like is_a: EDAM:0002332 ! XML format [Term] id: EDAM:0002311 -name: embl-html +name: EMBL-HTML namespace: format def: "EMBL entry format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002543 ! embl-like +is_a: EDAM:0002543 ! EMBL-like is_a: EDAM:0002331 ! HTML format ! -! Data format<-Sequence record format<-Sequence record full format<-embl-like<-embl-like (text) +! Format<-Sequence record format<-Sequence record full format<-EMBL-like<-EMBL-like (text) ! [Term] id: EDAM:0001927 -name: embl +name: EMBL format namespace: format def: "EMBL entry format." [EDAM:EBI "EMBRACE definition"] -synonym: "embl sequence format" EXACT [] +synonym: "EMBL sequence format" EXACT [] synonym: "EMBL" EXACT [] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002181 ! embl-like (text) +is_a: EDAM:0002181 ! EMBL-like (text) is_a: EDAM:0002206 ! Sequence feature table format (text) [Term] @@ -27101,31 +27169,31 @@ name: geneseq namespace: format def: "Geneseq sequence format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002181 ! embl-like (text) +is_a: EDAM:0002181 ! EMBL-like (text) ! -! Data format<-Sequence record format<-Sequence record full format<-embl-like<-embl-like (xml) +! Format<-Sequence record format<-Sequence record full format<-EMBL-like<-EMBL-like (XML) ! [Term] id: EDAM:0002204 -name: embl (xml) +name: EMBL format (XML) namespace: format def: "An XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] comment: This is a placeholder for other more specific terms. It should not normally be used for annotation. See OBO file for URL of format specification. {url=} -is_a: EDAM:0002558 ! embl-like (xml) +is_a: EDAM:0002558 ! EMBL-like (XML) ! -! Data format<-Sequence record format<-Sequence record full format<-embl-like<-embl-like (xml)<-embl (xml) +! Format<-Sequence record format<-Sequence record full format<-EMBL-like<-EMBL-like (XML)<-EMBL (XML) ! [Term] id: EDAM:0002183 -name: emblxml +name: EMBLXML namespace: format def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002204 ! embl (xml) +is_a: EDAM:0002204 ! EMBL (XML) [Term] @@ -27134,7 +27202,7 @@ name: cdsxml namespace: format def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002204 ! embl (xml) +is_a: EDAM:0002204 ! EMBL (XML) [Term] id: EDAM:0002185 @@ -27142,42 +27210,42 @@ name: insdxml namespace: format def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002204 ! embl (xml) +is_a: EDAM:0002204 ! EMBL (XML) ! -! Data format<-Sequence record format<-Sequence record full format<-genbank-like +! Format<-Sequence record format<-Sequence record full format<-GenBank-like ! [Term] id: EDAM:0002205 -name: genbank-like (text) +name: GenBank-like format (text) namespace: format def: "A text format resembling GenBank entry (plain text) format." [EDAM:EBI "EMBRACE definition"] -comment: This term may be used for the non-standard genbank-like text formats. See OBO file for URL of format specification. {url=} -is_a: EDAM:0002559 ! genbank-like +comment: This term may be used for the non-standard GenBank-like text formats. See OBO file for URL of format specification. {url=} +is_a: EDAM:0002559 ! GenBank-like is_a: EDAM:0002330 ! Text format [Term] id: EDAM:0002532 -name: genbank-html +name: GenBank-HTML namespace: format def: "Genbank entry format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002559 ! genbank-like +is_a: EDAM:0002559 ! GenBank-like is_a: EDAM:0002331 ! HTML format ! -! Data format<-Sequence record format<-Sequence record full format<-genbank-like<-genbank-like (text) +! Format<-Sequence record format<-Sequence record full format<-GenBank-like<-GenBank-like (text) ! [Term] id: EDAM:0001936 -name: genbank +name: GenBank format namespace: format def: "Genbank entry format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002205 ! genbank-like (text) +is_a: EDAM:0002205 ! GenBank-like (text) is_a: EDAM:0002206 ! Sequence feature table format (text) @@ -27187,19 +27255,19 @@ name: genpept namespace: format def: "Genpept protein entry format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002205 ! genbank-like (text) +is_a: EDAM:0002205 ! GenBank-like (text) ! -! Data format<-Sequence record format<-Sequence record full format<-uniprotkb-like +! Format<-Sequence record format<-Sequence record full format<-uniprotkb-like ! [Term] id: EDAM:0002187 -name: uniprotkb-like (text) +name: uniprotkb-like format (text) namespace: format def: "A text sequence format resembling uniprotkb entry format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} @@ -27208,23 +27276,23 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence record format<-Sequence record full format<-uniprotkb-like<-uniprotkb-like (text) +! Format<-Sequence record format<-Sequence record full format<-uniprotkb-like<-uniprotkb-like (text) ! [Term] id: EDAM:0001963 -name: swiss +name: Swiss-Prot format namespace: format -def: "Swissprot entry sequence format." [EDAM:EBI "EMBRACE definition"] +def: "Swiss-Prot entry sequence format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002187 ! uniprotkb-like (text) is_a: EDAM:0002206 ! Sequence feature table format (text) [Term] id: EDAM:0002188 -name: uniprot +name: UniProt format namespace: format -def: "Uniprot entry sequence format." [EDAM:EBI "EMBRACE definition"] +def: "UniProt entry sequence format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002187 ! uniprotkb-like (text) @@ -27239,11 +27307,11 @@ is_a: EDAM:0002187 ! uniprotkb-like (text) ! -! Data format<-Sequence record format<-Sequence trace format +! Format<-Sequence record format<-Sequence trace format ! [Term] id: EDAM:0001628 -name: abi +name: ABI namespace: format def: "Format of raw sequence data from an ABI sequencing machine." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} @@ -27262,81 +27330,92 @@ is_a: EDAM:0002330 ! Text format [Term] id: EDAM:0002545 -name: fastq-like +name: FASTQ-like format namespace: format def: "A format resembling FASTQ short read format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for non-standard FASTQ short read-like formats. See OBO file for URL of format specification. {url=} is_a: EDAM:0002057 ! Sequence trace format +relationship: is_format_of EDAM:0000924 ! Sequence trace [Term] id: EDAM:0002572 -name: bam +name: BAM namespace: format -def: "Binary version of the sam format for nucleotide sequence data, quality of each base, and (optionally) information about the alignment of the reads to a reference genome." [EDAM:EBI "EMBRACE definition"] +def: "BAM format, the binary, BGZF-formatted compressed version of the SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [EDAM:EBI "EMBRACE definition"] +spec_url: http://samtools.sourceforge.net/SAM-1.3.pdf is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0001921 ! Alignment format is_a: EDAM:0002333 ! Binary format +relationship: is_format_of EDAM:0001383 ! Sequence alignment (nucleic acid) +relationship: is_format_of EDAM:0001381 ! Sequence alignment (pairwise) +! relationship: is_format_of EDAM:0000855 ! Sequence metadata +! relationship: is_format_of EDAM:0000924 ! Sequence trace [Term] id: EDAM:0002573 -name: sam +name: SAM namespace: format -def: "Format for nucleotide sequence data, quality of each base, and (optionally) information about the alignment of the reads to a reference genome." [EDAM:EBI "EMBRACE definition"] -comment: The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. See OBO file for URL of format specification. {url=} +def: "Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [EDAM:EBI "EMBRACE definition"] +spec_url: http://samtools.sourceforge.net/SAM-1.3.pdf +comment: The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. See OBO file for URL of format specification. {spec_url=} is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0001921 ! Alignment format is_a: EDAM:0002330 ! Text format +relationship: is_format_of EDAM:0001383 ! Sequence alignment (nucleic acid) +relationship: is_format_of EDAM:0001381 ! Sequence alignment (pairwise) +! relationship: is_format_of EDAM:0000855 ! Sequence metadata +! relationship: is_format_of EDAM:0000924 ! Sequence trace ! -! Data format<-Sequence record format<-Sequence trace format<-fastq-like +! Format<-Sequence record format<-Sequence trace format<-FASTQ-like ! [Term] id: EDAM:0002182 -name: fastq-like (text) +name: FASTQ-like format (text) namespace: format def: "A text format resembling FASTQ short read format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for non-standard FASTQ short read-like formats. See OBO file for URL of format specification. {url=} -is_a: EDAM:0002545 ! fastq-like +is_a: EDAM:0002545 ! FASTQ-like is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence record format<-Sequence trace format<-fastq-like<-fastq-like (text) +! Format<-Sequence record format<-Sequence trace format<-FASTQ-like<-FASTQ-like (text) ! [Term] id: EDAM:0001930 -name: fastq +name: FASTQ namespace: format def: "FASTQ short read format ignoring quality scores." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002182 ! fastq-like (text) +is_a: EDAM:0002182 ! FASTQ-like (text) [Term] id: EDAM:0001931 -name: fastq-illumina +name: FASTQ-illumina namespace: format def: "FASTQ Illumina 1.3 short read format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002182 ! fastq-like (text) +is_a: EDAM:0002182 ! FASTQ-like (text) [Term] id: EDAM:0001932 -name: fastq-sanger +name: FASTQ-sanger namespace: format def: "FASTQ short read format with phred quality." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002182 ! fastq-like (text) +is_a: EDAM:0002182 ! FASTQ-like (text) [Term] id: EDAM:0001933 -name: fastq-solexa +name: FASTQ-solexa namespace: format def: "FASTQ Solexa/Illumina 1.0 short read format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002182 ! fastq-like (text) +is_a: EDAM:0002182 ! FASTQ-like (text) @@ -27346,7 +27425,7 @@ is_a: EDAM:0002182 ! fastq-like (text) ! -! Data format<-Sequence feature annotation format +! Format<-Sequence feature annotation format ! @@ -27370,7 +27449,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence feature annotation format<-Sequence feature table format +! Format<-Sequence feature annotation format<-Sequence feature table format ! [Term] id: EDAM:0002206 @@ -27383,7 +27462,7 @@ is_a: EDAM:0002330 ! Text format [Term] id: EDAM:0002553 -name: Sequence feature table format (xml) +name: Sequence feature table format (XML) namespace: format def: "XML format for a sequence feature table." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} @@ -27395,12 +27474,12 @@ is_a: EDAM:0002332 ! XML format ! -! Data format<-Sequence feature annotation format<-Sequence feature table format<-Sequence feature table format (text) +! Format<-Sequence feature annotation format<-Sequence feature table format<-Sequence feature table format (text) ! [Term] id: EDAM:0002305 -name: gff +name: GFF namespace: format def: "GFF feature format (of indeterminate version)." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} @@ -27427,65 +27506,65 @@ consider: EDAM:0001963 ! swiss [Term] id: EDAM:0001980 -name: embl feature +name: EMBL feature namespace: format def: "EMBL feature format." [EDAM:EBI "EMBRACE definition"] is_obsolete: true -consider: EDAM:0001927 ! embl +consider: EDAM:0001927 ! EMBL [Term] id: EDAM:0001981 -name: genbank feature +name: GenBank feature namespace: format def: "Genbank feature format." [EDAM:EBI "EMBRACE definition"] is_obsolete: true -consider: EDAM:0001936 ! genbank +consider: EDAM:0001936 ! GenBank ! -! Data format<-Sequence feature annotation format<-Sequence feature table format (text)<-Sequence feature table format (text)<-gff feature +! Format<-Sequence feature annotation format<-Sequence feature table format (text)<-Sequence feature table format (text)<-GFF feature ! [Term] id: EDAM:0001974 -name: gff2 +name: GFF2 namespace: format def: "GFF version 1 or 2 feature format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002305 ! gff feature +is_a: EDAM:0002305 ! GFF feature [Term] id: EDAM:0001975 -name: gff3 +name: GFF3 namespace: format def: "GFF version 3 feature format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002305 ! gff feature +is_a: EDAM:0002305 ! GFF feature [Term] id: EDAM:0002306 -name: gtf +name: GTF namespace: format def: "GFF feature format with extra tags." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002305 ! gff feature +is_a: EDAM:0002305 ! GFF feature ! -! Data format<-Sequence feature annotation format<-Sequence feature table format (xml) +! Format<-Sequence feature annotation format<-Sequence feature table format (XML) ! [Term] id: EDAM:0001978 -name: dasgff +name: DASGFF namespace: format def: "DAS GFF (XML) feature format." [EDAM:EBI "EMBRACE definition"] -synonym: "dasgff feature" EXACT [] +synonym: "DASGFF feature" EXACT [] synonym: "das feature" EXACT [] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002553 ! Sequence feature table format (xml) +is_a: EDAM:0002553 ! Sequence feature table format (XML) ! -! Data format<-Alignment format +! Format<-Alignment format ! [Term] id: EDAM:0002554 @@ -27495,25 +27574,25 @@ def: "Text format for molecular sequence alignment information." [EDAM:EBI "EMBR comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0001921 ! Alignment format is_a: EDAM:0002330 ! Text format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002555 -name: Alignment format (xml) +name: Alignment format (XML) namespace: format def: "XML format for molecular sequence alignment information." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0001921 ! Alignment format is_a: EDAM:0002332 ! XML format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined ! -! Data format<-Alignment format<-Alignment format (text) +! Format<-Alignment format<-Alignment format (text) ! [Term] id: EDAM:0001982 @@ -27535,12 +27614,12 @@ is_a: EDAM:0002554 ! Alignment format (text) [Term] id: EDAM:0001984 -name: fasta-aln +name: FASTA-aln namespace: format def: "Fasta format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002554 ! Alignment format (text) -is_a: EDAM:0002200 ! fasta-like (text) +is_a: EDAM:0002200 ! FASTA-like (text) @@ -27771,7 +27850,7 @@ is_a: EDAM:0002554 ! Alignment format (text) ! -! Data format<-Phylogenetic tree format +! Format<-Phylogenetic tree format ! [Term] id: EDAM:0002556 @@ -27781,21 +27860,21 @@ def: "Text format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002006 ! Phylogenetic tree format is_a: EDAM:0002330 ! Text format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002557 -name: Phylogenetic tree format (xml) +name: Phylogenetic tree format (XML) namespace: format def: "XML format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002006 ! Phylogenetic tree format is_a: EDAM:0002332 ! XML format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined ! -! Data format<-Phylogenetic tree format<-Phylogenetic tree format (text) +! Format<-Phylogenetic tree format<-Phylogenetic tree format (text) ! [Term] @@ -27872,7 +27951,7 @@ is_a: EDAM:0002556 ! Phylogenetic tree format (text) ! -! Data format<-Tertiary structure format +! Format<-Tertiary structure format ! [Term] id: EDAM:0001475 @@ -27884,11 +27963,11 @@ comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002033 ! Tertiary structure format ! -! Data format<-Tertiary structure format<-PDB database entry format +! Format<-Tertiary structure format<-PDB database entry format ! [Term] id: EDAM:0001476 -name: pdb +name: PDB format namespace: format def: "Entry format of PDB database in PDB format, or any report in the same format." [EDAM:EBI "EMBRACE definition"] synonym: "PDB" EXACT [] @@ -27912,7 +27991,7 @@ is_a: EDAM:0002330 ! Text format [Term] id: EDAM:0001478 -name: pdbml +name: PDBML namespace: format def: "Entry format of PDB database in PDBML (XML) format, or any report in the same format." [EDAM:EBI "EMBRACE definition"] synonym: "PDBML" EXACT [] @@ -27923,7 +28002,7 @@ is_a: EDAM:0002332 ! XML format ! -! Data format<-Biological model format +! Format<-Biological model format ! [Term] id: EDAM:0002013 @@ -27936,7 +28015,7 @@ is_a: EDAM:0002034 ! Biological model format [Term] id: EDAM:0002585 -name: sbml +name: SBML namespace: format def: "XML format for models of biological processes such as metabolism, cell signaling and so on." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} @@ -27959,7 +28038,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-Biological model format<-Biological pathway or network format +! Format<-Biological model format<-Biological pathway or network format ! [Term] id: EDAM:0001647 @@ -28064,7 +28143,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-Sequence-profile alignment format +! Format<-Sequence-profile alignment format ! [Term] id: EDAM:0002015 @@ -28085,7 +28164,7 @@ is_a: EDAM:0002014 ! Sequence-profile alignment format is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence-profile alignment format<-Sequence-profile alignment (HMM) format +! Format<-Sequence-profile alignment format<-Sequence-profile alignment (HMM) format ! [Term] @@ -28108,7 +28187,7 @@ is_a: EDAM:0002015 ! Sequence-profile alignment (HMM) format is_a: EDAM:0002330 ! Text format ! -! Data format<-Amino acid identifier format +! Format<-Amino acid identifier format ! [Term] id: EDAM:0002563 @@ -28117,7 +28196,7 @@ namespace: format def: "Single letter amino acid identifier format, e.g. G." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002562 ! Amino acid identifier format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002564 @@ -28126,7 +28205,7 @@ namespace: format def: "Three letter amino acid identifier format, e.g. GLY." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002562 ! Amino acid identifier format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined [Term] id: EDAM:0002565 @@ -28135,11 +28214,11 @@ namespace: format def: "Full name amino acid identifier format, e.g. Glycine." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002562 ! Amino acid identifier format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined ! -! Data format<-Amino acid identifier format<-Amino acid identifier format (three letter) +! Format<-Amino acid identifier format<-Amino acid identifier format (three letter) ! [Term] id: EDAM:0001758 @@ -28149,12 +28228,12 @@ def: "Format of amino acid residue names as used in PDB files." [EDAM:EBI "EMBRA xref: WHATIF: type comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002564 ! Amino acid identifier format (three letter) -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined ! -! Data format<-Amino acid index format +! Format<-Amino acid index format ! [Term] id: EDAM:0001504 @@ -28167,7 +28246,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Article format +! Format<-Article format ! [Term] id: EDAM:0001739 @@ -28188,7 +28267,7 @@ is_a: EDAM:0002020 ! Article format is_a: EDAM:0002330 ! Text format ! -! Data format<-Text mining report format +! Format<-Text mining report format ! [Term] id: EDAM:0001740 @@ -28211,7 +28290,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Enzyme kinetics report format +! Format<-Enzyme kinetics report format ! [Term] id: EDAM:0001582 @@ -28225,7 +28304,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Small molecule annotation format +! Format<-Small molecule annotation format ! [Term] id: EDAM:0001697 @@ -28327,7 +28406,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Gene annotation format +! Format<-Gene annotation format ! [Term] id: EDAM:0001808 @@ -28562,7 +28641,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-Workflow format +! Format<-Workflow format ! [Term] id: EDAM:0001665 @@ -28575,7 +28654,7 @@ is_a: EDAM:0002332 ! XML format ! -! Data format<-Chemical formula format +! Format<-Chemical formula format ! [Term] id: EDAM:0001196 @@ -28628,7 +28707,7 @@ is_a: EDAM:0001196 ! Chemical formula (SMILES) format ! -! Data format<-Phylogenetic raw data format +! Format<-Phylogenetic raw data format ! [Term] id: EDAM:0002037 @@ -28674,7 +28753,7 @@ is_a: EDAM:0002036 ! Phylogenetic raw data format ! -! Data format<-Phylogenetic raw data format<-Phylogenetic continuous quantitative character format +! Format<-Phylogenetic raw data format<-Phylogenetic continuous quantitative character format ! [Term] id: EDAM:0001430 @@ -28695,7 +28774,7 @@ is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format is_a: EDAM:0002330 ! Text format ! -! Data format<-Phylogenetic raw data format<-Phylogenetic property values format +! Format<-Phylogenetic raw data format<-Phylogenetic property values format ! [Term] @@ -28709,7 +28788,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Phylogenetic raw data format<-Phylogenetic discrete states format +! Format<-Phylogenetic raw data format<-Phylogenetic discrete states format ! [Term] id: EDAM:0001433 @@ -28721,7 +28800,7 @@ is_a: EDAM:0002038 ! Phylogenetic discrete states format is_a: EDAM:0002330 ! Text format ! -! Data format<-Phylogenetic raw data format<-Phylogenetic cliques format +! Format<-Phylogenetic raw data format<-Phylogenetic cliques format ! [Term] id: EDAM:0001434 @@ -28734,13 +28813,13 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Phylogenetic raw data format<-Phylogenetic invariants format +! Format<-Phylogenetic raw data format<-Phylogenetic invariants format ! ! -! Data format<-Experiment annotation (electron microscopy model) format +! Format<-Experiment annotation (electron microscopy model) format ! [Term] id: EDAM:0001645 @@ -28753,7 +28832,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-Phylogenetic tree metadata (distance data) format +! Format<-Phylogenetic tree metadata (distance data) format ! [Term] id: EDAM:0001445 @@ -28766,7 +28845,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Polymorphism report format +! Format<-Polymorphism report format ! [Term] id: EDAM:0001620 @@ -28779,7 +28858,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-Protein family report format +! Format<-Protein family report format ! [Term] id: EDAM:0001570 @@ -28914,7 +28993,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-Protein interaction format +! Format<-Protein interaction format ! [Term] id: EDAM:0001568 @@ -28967,7 +29046,7 @@ is_a: EDAM:0002332 ! XML format ! -! Data format<-Sequence assembly format +! Format<-Sequence assembly format ! [Term] id: EDAM:0002561 @@ -28976,20 +29055,26 @@ namespace: format def: "Text format for sequence assembly data." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002350 ! Datatype format -relationship: is_format_of EDAM:0000841 ! Undefined +! relationship: is_format_of EDAM:0000841 ! Undefined ! -! Data format<-Sequence assembly format (text) +! Format<-Sequence assembly format (text) ! [Term] id: EDAM:0001630 -name: caf +name: CAF namespace: format -def: "Sequence assembly project file in Common Assembly Format (CAF) format." [EDAM:EBI "EMBRACE definition"] -comment: See OBO file for URL of format specification. {url=} +def: "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." [EDAM:EBI "EMBRACE definition"] +spec_url: http://www.sanger.ac.uk/resources/software/caf/ +is_a: EDAM:0002330 ! Text format is_a: EDAM:0002561 ! Sequence assembly format (text) +! relationship: is_format_of EDAM:0001383 ! Sequence alignment (nucleic acid) +! relationship: is_format_of EDAM:0002333 ! Sequence alignment (pairwise) +! relationship: is_format_of EDAM:0000855 ! Sequence metadata +! relationship: is_format_of EDAM:0000924 ! Sequence trace +relationship: is_format_of EDAM:0000925 ! Sequence assembly [Term] id: EDAM:0001631 @@ -29001,24 +29086,26 @@ is_a: EDAM:0002561 ! Sequence assembly format (text) [Term] id: EDAM:0001632 -name: scf +name: SCF namespace: format -def: "Sequence assembly project file SCF format." [EDAM:EBI "EMBRACE definition"] -comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002561 ! Sequence assembly format (text) +def: "Staden Chromatogram Files format (SCF) of base-called sequence, qualities, and other metadata." [EDAM:EBI "EMBRACE definition"] +spec_url: http://staden.sourceforge.net/manual/formats_unix_2.html +is_a: EDAM:0002330 ! Text format +relationship: is_format_of EDAM:0000924 ! Sequence trace [Term] id: EDAM:0001633 -name: phd +name: PHD namespace: format -def: "Sequence assembly project file PHD format." [EDAM:EBI "EMBRACE definition"] -comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002561 ! Sequence assembly format (text) +def: "PHD sequence trace format (to store serialised chromatogram data)." [EDAM:EBI "EMBRACE definition"] +spec_url: http://www.bioperl.org/wiki/PHD_sequence_format +is_a: EDAM:0002330 ! Text format +relationship: is_format_of EDAM:0000924 ! Sequence trace ! -! Data format<-Microarray experiment data format +! Format<-Microarray experiment data format ! [Term] id: EDAM:0001640 @@ -29045,7 +29132,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Gene expression annotation format +! Format<-Gene expression annotation format ! [Term] @@ -29094,7 +29181,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Genotype / phenotype annotation format +! Format<-Genotype / phenotype annotation format ! [Term] id: EDAM:0001623 @@ -29136,7 +29223,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-Map format +! Format<-Map format ! [Term] id: EDAM:0001861 @@ -29150,7 +29237,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Nucleic acid features (primers) format +! Format<-Nucleic acid features (primers) format ! [Term] id: EDAM:0001627 @@ -29163,7 +29250,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Protein annotation format +! Format<-Protein annotation format ! [Term] id: EDAM:0002063 @@ -29175,7 +29262,7 @@ is_a: EDAM:0002062 ! Protein annotation format ! -! Data format<-Protein annotation format<-Enzyme annotation format +! Format<-Protein annotation format<-Enzyme annotation format ! [Term] id: EDAM:0001511 @@ -29256,7 +29343,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-3D-1D scoring matrix format +! Format<-3D-1D scoring matrix format ! [Term] id: EDAM:0001500 @@ -29269,7 +29356,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Protein structure annotation (quality evaluation) format +! Format<-Protein structure annotation (quality evaluation) format ! [Term] id: EDAM:0001551 @@ -29292,7 +29379,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence database hits format +! Format<-Sequence database hits format ! [Term] id: EDAM:0001332 @@ -29353,7 +29440,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence distance matrix format +! Format<-Sequence distance matrix format ! [Term] id: EDAM:0001423 @@ -29367,7 +29454,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence motif format +! Format<-Sequence motif format ! [Term] id: EDAM:0001360 @@ -29399,7 +29486,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence profile format +! Format<-Sequence profile format ! [Term] id: EDAM:0002072 @@ -29433,7 +29520,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence profile format<-Hidden Markov model format +! Format<-Sequence profile format<-Hidden Markov model format ! [Term] id: EDAM:0001369 @@ -29456,7 +29543,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Dirichlet distribution format +! Format<-Dirichlet distribution format ! [Term] id: EDAM:0001349 @@ -29477,7 +29564,7 @@ is_a: EDAM:0002074 ! Dirichlet distribution format is_a: EDAM:0002330 ! Text format ! -! Data format<-HMM emission and transition counts format +! Format<-HMM emission and transition counts format ! [Term] id: EDAM:0001351 @@ -29490,7 +29577,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Protein secondary structure format +! Format<-Protein secondary structure format ! [Term] id: EDAM:0001454 @@ -29515,7 +29602,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-RNA secondary structure format +! Format<-RNA secondary structure format ! [Term] id: EDAM:0001457 @@ -29537,7 +29624,7 @@ is_a: EDAM:0002076 ! RNA secondary structure format is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence range format +! Format<-Sequence range format ! [Term] id: EDAM:0001248 @@ -29550,7 +29637,7 @@ is_a: EDAM:0002078 ! Sequence range format is_a: EDAM:0002330 ! Text format ! -! Data format<-Repeat sequence map format +! Format<-Repeat sequence map format ! [Term] id: EDAM:0001295 @@ -29580,7 +29667,7 @@ is_a: EDAM:0002155 ! Repeat sequence map format is_a: EDAM:0002330 ! Text format ! -! Data format<-Nucleic acid features (restriction sites) format +! Format<-Nucleic acid features (restriction sites) format ! [Term] id: EDAM:0001318 @@ -29613,7 +29700,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Gene features (coding region) format +! Format<-Gene features (coding region) format ! [Term] id: EDAM:0001316 @@ -29626,7 +29713,7 @@ is_a: EDAM:0002330 ! Text format ! -! Data format<-Sequence cluster format +! Format<-Sequence cluster format ! [Term] id: EDAM:0002171 @@ -29646,7 +29733,7 @@ is_a: EDAM:0002170 ! Sequence cluster format ! -! Data format<-Sequence cluster format<-Sequence cluster format (protein) +! Format<-Sequence cluster format<-Sequence cluster format (protein) ! [Term] id: EDAM:0001247 @@ -29663,7 +29750,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-Sequence cluster format<-Sequence cluster format (nucleic acid) +! Format<-Sequence cluster format<-Sequence cluster format (nucleic acid) ! [Term] id: EDAM:0002175 @@ -29676,7 +29763,7 @@ is_a: EDAM:0002172 ! Sequence cluster format (nucleic acid) ! -! Data format<-Sequence cluster format<-Sequence cluster format (nucleic acid)<-Gene cluster format +! Format<-Sequence cluster format<-Sequence cluster format (nucleic acid)<-Gene cluster format ! [Term] id: EDAM:0001228 @@ -29697,7 +29784,7 @@ comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002330 ! Text format ! -! Data format<-Ontology format +! Format<-Ontology format ! [Term] @@ -29709,32 +29796,26 @@ comment: See OBO file for URL of format specification. {url=} is_a: EDAM:0002195 ! Ontology format [Term] -id: EDAM:0002197 -name: owl +id: EDAM:0002549 +name: OBO namespace: format -def: "OWL ontology format." [EDAM:EBI "EMBRACE definition"] +def: "OBO ontology text format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002195 ! Ontology format +is_a: EDAM:0002196 ! OBO format is_a: EDAM:0002330 ! Text format - - -! -! Data format<-Ontology format<-OBO format -! - [Term] -id: EDAM:0002549 -name: obo +id: EDAM:0002197 +name: OWL namespace: format -def: "OBO ontology text format." [EDAM:EBI "EMBRACE definition"] +def: "OWL ontology format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} -is_a: EDAM:0002196 ! OBO format +is_a: EDAM:0002195 ! Ontology format is_a: EDAM:0002330 ! Text format [Term] id: EDAM:0002550 -name: obo-xml +name: OBO-XML namespace: format def: "OBO ontology XML format." [EDAM:EBI "EMBRACE definition"] comment: See OBO file for URL of format specification. {url=} @@ -29744,7 +29825,7 @@ is_a: EDAM:0002332 ! XML format ! -! Data format<-Strain data format +! Format<-Strain data format ! [Term] @@ -29758,7 +29839,7 @@ consider: EDAM:0002331 ! HTML format ! -! Data format<-Protein features (domain composition) format +! Format<-Protein features (domain composition) format ! [Term] id: EDAM:0001760 @@ -29795,3 +29876,52 @@ is_obsolete: true consider: EDAM:0002331 ! HTML format ! is_a: EDAM:0002542 ! Protein features (domain composition) format ! relationship: is_format_of EDAM:0000841 ! Undefined + + + + + +! +! +! + + + +! +! +! +! +! +! +! +! +! +! + + + + + +[Term] +id: EDAM:0003000 +name: AB1 +namespace: format +def: "AB1 binary format of raw DNA data taken from a scientific instrument and output from Applied Biosystems' Sequencing Analysis Software. Contains an electropherogram and the DNA base sequence." [http://www.fileinfo.com/extension/ab1] +is_a: EDAM:0002333 ! Binary format +relationship: is_format_of EDAM:0000924 ! Sequence trace + + +[Term] +id: EDAM:0003001 +name: ACE +namespace: format +def: "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." [EDAM:EBI "EMBRACE definition"] +spec_url: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt +is_a: EDAM:0002330 ! Text format +! relationship: is_format_of EDAM:0001383 ! Sequence alignment (nucleic acid) +! relationship: is_format_of EDAM:0002333 ! Sequence alignment (pairwise) +! relationship: is_format_of EDAM:0000855 ! Sequence metadata +! relationship: is_format_of EDAM:0000924 ! Sequence trace +relationship: is_format_of EDAM:0000925 ! Sequence assembly + +