From 1c215d6c1dd7d826cbf83e4b47516f76b2e1ebd7 Mon Sep 17 00:00:00 2001 From: matuskalas Date: Tue, 1 Nov 2016 03:39:22 +0100 Subject: [PATCH] History of releases: beta10 --- releases/EDAM.obo | 21564 ++++++++++++++++++++++++++-------------------------- 1 file changed, 10644 insertions(+), 10920 deletions(-) diff --git a/releases/EDAM.obo b/releases/EDAM.obo index 0a6e748..c93ca76 100644 --- a/releases/EDAM.obo +++ b/releases/EDAM.obo @@ -1,10 +1,9 @@ format-version: 1.2 -date: 07:10:2010 13:29 -data-version: Beta09 +date: 01:12:2010 12:25 +data-version: Beta10 ! Use for mapping to "global" id space(s) e.g.: -! idspace: EDAM urn:lsid:ebi.ac.uk:edam: "EDAM terms" ! idspace: EDAM http://purl.org/edam/ "EDAM terms" -! NEXT term number is 2330 +! NEXT term number is 0002604 ! xref: WHATIF: CorrectedPDBasXML ! xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB ! xref: Moby:GI_Gene @@ -89,7 +88,7 @@ def: "Defines a term ('Data') has a data format specification ('Data format')." is_anti_symmetric: true is_cyclic: false is_transitive: true -inverse_of: is_attribute_of +inverse_of: is_format_of [Typedef] id: is_attribute_of @@ -162,7 +161,7 @@ def: "Defines that a term ('Data format') is a data format specification for ano is_anti_symmetric: true is_cyclic: false is_transitive: true -inverse_of: has_attribute +inverse_of: has_format @@ -176,7 +175,6 @@ name: Biological entity namespace: entity def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things or an observable phenonema or occurence." [EDAM:EBI "EMBRACE definition"] ! relationship: is_concern_of EDAM:0000003 ! Topic -! relationship: has_identifier EDAM:0000842 ! Identifier ! relationship: has_attribute EDAM:0000006 ! Data [Term] @@ -216,16 +214,13 @@ name: Data namespace: data def: "A semantic description of a data entity (datum) commonly used in bioinformatics." [EDAM:EBI "EMBRACE definition"] ! relationship: is_attribute_of EDAM:0000002 ! Biological entity -! relationship: is_input_of EDAM:0000004 ! Operation -! relationship: is_output_of EDAM:0000004 ! Operation -! relationship: has_source EDAM:0000005 ! Data resource -! relationship: has_identifier EDAM:0000842 ! Identifier [Term] id: EDAM:0001915 name: Data format namespace: format def: "A reference (typically a URL) of a data format specification." [EDAM:EBI "EMBRACE definition"] +comment: See OBO file for URL of format specification. {url=} ! relationship: is_format_of EDAM:0000006 ! Data @@ -240,8 +235,6 @@ name: Undefined namespace: entity def: "Debugging." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000002 ! Biological entity -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined relationship: has_attribute EDAM:0000841 ! Undefined @@ -254,12 +247,10 @@ is_a: EDAM:0000002 ! Biological entity [Term] id: EDAM:0000012 -name: Phenomena +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: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000006 ! Data @@ -272,8 +263,6 @@ 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: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000006 ! Data [Term] @@ -282,8 +271,6 @@ 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: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000006 ! Data [Term] @@ -292,8 +279,6 @@ name: Entity collection namespace: entity def: "A collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002199 ! Physical entity -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000006 ! Data @@ -308,8 +293,6 @@ name: Molecular entity namespace: entity def: "Any atom, molecule or molecular complex with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000009 ! Discrete entity -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000982 ! Molecule identifier relationship: has_attribute EDAM:0000883 ! Tertiary structure @@ -328,8 +311,6 @@ name: Atom namespace: entity def: "The basic unit of matter consisting of negatively charged electrons bound by electromagnetic force to a nucleus of protons and neutrons." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000013 ! Molecular entity -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000983 ! Atom identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -338,8 +319,6 @@ name: Small molecule namespace: entity def: "Any small molecule." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000013 ! Molecular entity -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001086 ! Chemical compound identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -348,8 +327,6 @@ name: Biopolymer namespace: entity def: "A single organic macromolecule made up of monomeric units." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000013 ! Molecular entity -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000982 ! Molecule identifier relationship: has_attribute EDAM:0002044 ! Sequence data [Term] @@ -359,8 +336,6 @@ namespace: entity def: "Two or more whole molecules in association with one another." [EDAM:EBI "EMBRACE definition"] synonym: "Molecular assembly" EXACT [] is_a: EDAM:0000013 ! Molecular entity -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000982 ! Molecule identifier relationship: has_attribute EDAM:0000841 ! Undefined @@ -381,8 +356,6 @@ name: Biomonomer namespace: entity def: "A small organic molecule that can chemically bond to other monomers to form a biopolymer." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000015 ! Small molecule -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000982 ! Molecule identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -391,8 +364,6 @@ name: Ligand namespace: entity def: "A molecule that can bind and form a complex with a biopolymer, typically a protein." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000015 ! Small molecule -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000992 ! Ligand identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -401,10 +372,15 @@ name: Drug namespace: entity def: "A substance that changes the normal functioning of an organism." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000015 ! Small molecule -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000993 ! Drug identifier relationship: has_attribute EDAM:0000841 ! Undefined +[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 ! @@ -416,8 +392,6 @@ 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: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000994 ! Amino acid identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -428,8 +402,6 @@ def: "The building block of nucleic acids, a nucleotide consists of a nucleobase synonym: "Base" EXACT [] xref: SO:0001236 is_a: EDAM:0000018 ! Biomonomer -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000995 ! Nucleotide identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -438,8 +410,6 @@ name: Monosaccharide namespace: entity def: "The building block of polysaccharides, a monosaccharide is an aldehyde or ketone with hydroxyl groups." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000018 ! Biomonomer -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000996 ! Monosaccharide identifier relationship: has_attribute EDAM:0000841 ! Undefined ! @@ -463,8 +433,6 @@ synonym: "Polynucleotide chain" EXACT [] synonym: "Polynucleotide" EXACT [] xref: SO:0000348 is_a: EDAM:0000016 ! Biopolymer -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0001207 ! Nucleotide sequence relationship: has_attribute EDAM:0001459 ! Nucleic acid tertiary structure @@ -475,8 +443,6 @@ namespace: entity def: "An organic polymer of alpha amino acid residues in an unbranched chain, bound together by peptide bonds." [EDAM:EBI "EMBRACE definition"] synonym: "Polypeptide chain" EXACT [] is_a: EDAM:0000016 ! Biopolymer -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000988 ! Polypeptide identifier relationship: has_attribute EDAM:0001208 ! Protein sequence relationship: has_attribute EDAM:0001460 ! Protein tertiary structure @@ -486,8 +452,7 @@ name: Polysaccharide namespace: entity def: "An organic polymer of either mono- or di-saccharide subunits in an unbranched chain, bound together by glycosidic bonds." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000016 ! Biopolymer -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined @@ -500,8 +465,6 @@ 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: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0001207 ! Nucleotide sequence [Term] @@ -511,8 +474,6 @@ namespace: entity def: "A deoxyribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] xref: SO:0000352 is_a: EDAM:0000024 ! Nucleic acid -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0001212 ! DNA sequence relationship: has_attribute EDAM:0001464 ! DNA tertiary structure @@ -523,8 +484,6 @@ namespace: entity def: "A ribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] xref: SO:0000356 is_a: EDAM:0000024 ! Nucleic acid -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0001213 ! RNA sequence relationship: has_attribute EDAM:0001465 ! RNA tertiary structure @@ -544,8 +503,6 @@ name: Mobile genetic element namespace: entity def: "A DNA molecule that can move around within a genome." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000028 ! DNA -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -555,8 +512,6 @@ namespace: entity def: "A deoxyribonucleic acid molecule synthesises by reverse transcriptase from an RNA template." [EDAM:EBI "EMBRACE definition"] xref: SO:0000756 is_a: EDAM:0000028 ! DNA -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0001212 ! DNA sequence relationship: has_attribute EDAM:0001464 ! DNA tertiary structure @@ -569,8 +524,6 @@ name: Transposon namespace: entity def: "A DNA sequence that can undergo transposition or move to different positions in the genome of a single cell." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000030 ! Mobile genetic element -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -579,8 +532,6 @@ name: Plasmid namespace: entity def: "A DNA molecule existing outside a chromosome and capable of independent replication." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000030 ! Mobile genetic element -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0000841 ! Undefined @@ -593,8 +544,6 @@ name: Retrotransposon namespace: entity def: "A DNA element that can amplify itself in a genome, by copying itself to RNA then back to DNA using a reverse transcriptase." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000031 ! Transposon -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -605,8 +554,6 @@ def: "A DNA sequence that is smaller than most other transposable elements and w synonym: "Insertion sequence element" EXACT [] synonym: "IS element" EXACT [] is_a: EDAM:0000031 ! Transposon -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0000841 ! Undefined @@ -630,8 +577,6 @@ def: "Transfer RNA (tRNA) is a small ribonucleic acid molecule that binds a spec comment: The amino acid is transferred to a nascent polypeptide chain during protein synthesis at the ribosome. synonym: "Transfer RNA" EXACT [] is_a: EDAM:0000029 ! RNA -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0002119 ! Nucleic acid identifier relationship: has_attribute EDAM:0001213 ! RNA sequence ! @@ -643,8 +588,6 @@ name: Peptide namespace: entity def: "An organic polymer of alpha amino acid residues in a short unbranched chain. Peptides typically have fewer than 50 subunits and can be made synthetically." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000025 ! Polypeptide -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000982 ! Molecule identifier relationship: has_attribute EDAM:0001208 ! Protein sequence [Term] @@ -653,8 +596,6 @@ name: Protein namespace: entity def: "One or more polypeptide chains in a stable conformation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000025 ! Polypeptide -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000989 ! Protein identifier relationship: has_attribute EDAM:0001460 ! Protein tertiary structure @@ -668,8 +609,6 @@ name: Uncomplexed protein namespace: entity def: "A single polypeptide chain in a stable conformation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000037 ! Protein -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000989 ! Protein identifier relationship: has_attribute EDAM:0001460 ! Protein tertiary structure [Term] @@ -678,8 +617,6 @@ name: Enzyme namespace: entity def: "Enzyme." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000037 ! Protein -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001010 ! Enzyme identifier relationship: has_attribute EDAM:0001460 ! Protein tertiary structure [Term] @@ -688,8 +625,6 @@ name: Transmembrane protein namespace: entity def: "A transmembrane protein molecule." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000037 ! Protein -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000989 ! Protein identifier relationship: has_attribute EDAM:0001460 ! Protein tertiary structure [Term] @@ -699,8 +634,6 @@ namespace: entity def: "A protein that, upon binding a cis-regulatory DNA element, regulates (enhances or represses) transcription." [EDAM:EBI "EMBRACE definition"] synonym: "Sequence-specific DNA binding factor" EXACT [] is_a: EDAM:0000037 ! Protein -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000989 ! Protein identifier relationship: has_attribute EDAM:0001460 ! Protein tertiary structure ! @@ -717,8 +650,6 @@ name: Restriction enzyme namespace: entity def: "An enzyme that cuts DNA at specific nucleotide subsequence(s) (restriction sites)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000039 ! Enzyme -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001010 ! Enzyme identifier relationship: has_attribute EDAM:0001460 ! Protein tertiary structure ! @@ -749,8 +680,6 @@ name: RNA/DNA hybrid namespace: entity def: "A hybrid (complementary base-paired) molecule of DNA and RNA." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000017 ! Molecular complex -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000982 ! Molecule identifier relationship: has_attribute EDAM:0000841 ! Undefined relationship: has_attribute EDAM:0000841 ! Undefined @@ -762,9 +691,7 @@ def: "A protein comprising two or more polypeptide chain subunits in a stable as synonym: "Protein complex" EXACT [] is_a: EDAM:0000017 ! Molecular complex is_a: EDAM:0000037 ! Protein -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined -relationship: has_identifier EDAM:0000989 ! Protein identifier + relationship: has_attribute EDAM:0001460 ! Protein tertiary structure [Term] @@ -773,8 +700,7 @@ name: Protein-ligand complex namespace: entity def: "A protein-ligand (small molecule) complex." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000017 ! Molecular complex -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined @@ -784,8 +710,7 @@ name: Protein-nucleic acid complex namespace: entity def: "A protein-DNA/RNA complex." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000017 ! Molecular complex -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined @@ -820,8 +745,7 @@ namespace: entity def: "A nucleic acid molecule which control its own replication via the action of proteins at replication start sites." [EDAM:EBI "EMBRACE definition"] xref: SO:0000340 is_a: EDAM:0000046 ! Protein-nucleic acid complex -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined @@ -850,8 +774,7 @@ name: Atom group namespace: entity def: "A group of two or more atoms from a molecular structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000010 ! Entity feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -860,8 +783,7 @@ name: Nucleic acid feature namespace: entity def: "A feature of a nucleic acid molecule that can be mapped to a specific region(s) in its molecular sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000010 ! Entity feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -870,8 +792,7 @@ name: Protein feature namespace: entity def: "A feature of a protein molecule that can be mapped to a specific region(s) in its molecular sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000010 ! Entity feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -881,8 +802,7 @@ namespace: entity def: "A region of a molecular surface involved in interactions with other molecules." [EDAM:EBI "EMBRACE definition"] xref: SO:0000409 is_a: EDAM:0000010 ! Entity feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined @@ -898,8 +818,7 @@ name: Atom pair namespace: entity def: "A pair (exactly 2) atoms from a molecular structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0001749 ! Atom group -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined ! @@ -911,8 +830,7 @@ name: Codon namespace: entity def: "Three nucleotides encoding typically a single, specific amino acid." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000048 ! Nucleic acid feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -921,8 +839,6 @@ name: Gene namespace: entity def: "The hereditary unit, corresponding to the genomic sequence(s) encoding one or more functional products." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000048 ! Nucleic acid feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001025 ! Gene identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -931,8 +847,7 @@ name: Operon namespace: entity def: "A functional unit of DNA including an operator, a common promoter, and one or more structural genes under common control." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000048 ! Nucleic acid feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined @@ -944,8 +859,7 @@ namespace: entity def: "The portion of a gene's DNA or RNA that is composed of exons and encodes a protein product." [EDAM:EBI "EMBRACE definition"] synonym: "Coding region" EXACT [] is_a: EDAM:0000048 ! Nucleic acid feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -955,8 +869,7 @@ namespace: entity def: "A region of DNA involved in transcription regulation." [EDAM:EBI "EMBRACE definition"] synonym: "Gene regulatory element" EXACT [] is_a: EDAM:0000048 ! Nucleic acid feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -965,8 +878,7 @@ name: Restriction site namespace: entity def: "A restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000048 ! Nucleic acid feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -976,8 +888,7 @@ namespace: entity def: "Regions of DNA sequence in eukaryotic chromosomes where the nuclear matrix attaches." [EDAM:EBI "EMBRACE definition"] synonym: "Matrix attachment region" EXACT [] is_a: EDAM:0000048 ! Nucleic acid feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -986,8 +897,7 @@ name: Splice site namespace: entity def: "A site in a transcribed RNA sequence at which RNA splicing occurs (introns are removed and exons are joined)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000048 ! Nucleic acid feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined ! @@ -1003,8 +913,6 @@ name: Allele namespace: entity def: "An alternative form of a gene that can exist at a single locus." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000051 ! Gene -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001025 ! Gene identifier relationship: has_attribute EDAM:0000841 ! Undefined ! @@ -1021,8 +929,7 @@ namespace: entity def: "A DNA element that can bind a transcription factor to regulate (enhance or repress) the expression (transcription) of genes located on the same strand." [EDAM:EBI "EMBRACE definition"] synonym: "Cis-element" EXACT [] is_a: EDAM:0000054 ! Transcription regulatory element -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1032,8 +939,7 @@ namespace: entity def: "A DNA element that encodes a transcription factor which regulates gene(s) distant from the gene from which they were transcribed." [EDAM:EBI "EMBRACE definition"] synonym: "Trans-element" EXACT [] is_a: EDAM:0000054 ! Transcription regulatory element -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined @@ -1046,8 +952,7 @@ name: Promoter namespace: entity def: "The DNA element where transcription is initiated." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000058 ! Gene cis-regulatory element -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1056,8 +961,7 @@ name: Enhancer namespace: entity def: "An element that can bind a transcription factor to enhance transcription." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000058 ! Gene cis-regulatory element -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1066,8 +970,7 @@ name: Silencer namespace: entity def: "An element that can bind a transcription factor to repress transcription." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000058 ! Gene cis-regulatory element -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1076,8 +979,7 @@ name: Response element namespace: entity def: "An element within or near the promoter that can bind certain transcription factors, for example a hormone receptor complex." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000058 ! Gene cis-regulatory element -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined ! @@ -1097,8 +999,6 @@ namespace: entity def: "A single amino acid position in a protein, bound to one (C or N-terminal positions) or two other residues by covalent (peptide) bonds." [EDAM:EBI "EMBRACE definition"] synonym: "Residue" EXACT [] is_a: EDAM:0000049 ! Protein feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001742 ! PDB residue number relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1108,8 +1008,7 @@ namespace: entity def: "A group of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue group" EXACT [] is_a: EDAM:0000049 ! Protein feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1118,8 +1017,7 @@ name: Protein domain namespace: entity def: "A region of a protein (typically a region of a single polypeptide chain) forming a distinct, compact conformation. Domains show some independence in terms of evolution, folding, structure or function and (typically) reoccur in other proteins." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000049 ! Protein feature -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0001468 ! Protein domain tertiary structure @@ -1137,8 +1035,7 @@ namespace: entity def: "A pair of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue pair" EXACT [] is_a: EDAM:0001751 ! Protein residue group -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1148,8 +1045,7 @@ namespace: entity def: "A group of continuous (adjacent) amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue group (continuous)" EXACT [] is_a: EDAM:0001751 ! Protein residue group -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1160,8 +1056,7 @@ def: "A group of discontinuous amino acid positions in a protein." [EDAM:EBI "EM comment: One or more residues in the group are discontinuous (non-adjacent). synonym: "Residue group (discontinuous)" EXACT [] is_a: EDAM:0001751 ! Protein residue group -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000841 ! Undefined + relationship: has_attribute EDAM:0000841 ! Undefined @@ -1183,8 +1078,6 @@ name: Genome namespace: entity def: "An organisms total complement of DNA or RNA (some viruses) and therefore its hereditary information. A genome includes genes and non-coding regions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000011 ! Entity collection -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1193,8 +1086,6 @@ name: Proteome namespace: entity def: "An organisms total complement of expressed proteins. More specifically, those proteins expressed in a cell, tissue or the whole organism under defined conditions at a specific time." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000011 ! Entity collection -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1203,8 +1094,6 @@ name: Nucleosome namespace: entity def: "The repeating structural unit of eukaryotic chromatin, which is folded successively into chromosomes." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000011 ! Entity collection -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1213,8 +1102,6 @@ name: Taxonomic rank namespace: entity def: "One of the major taxonomic ranks of life." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000011 ! Entity collection -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier relationship: has_attribute EDAM:0000841 ! Undefined @@ -1241,8 +1128,6 @@ name: Kingdom namespace: entity def: "A kingdom or organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000069 ! Taxonomic rank -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001044 ! Kingdom name relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1251,8 +1136,6 @@ name: Genus namespace: entity def: "A genus of organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000069 ! Taxonomic rank -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001870 ! Genus name relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1261,8 +1144,6 @@ name: Species namespace: entity def: "A species or organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000069 ! Taxonomic rank -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001045 ! Species name relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1271,13 +1152,11 @@ name: Strain namespace: entity def: "A strain or prokaryotic organisms." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000069 ! Taxonomic rank -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001046 ! Strain name relationship: has_attribute EDAM:0000841 ! Undefined ! -! Biological entity<-Phenomena +! Biological entity<-Phenomenon ! [Term] @@ -1285,9 +1164,7 @@ id: EDAM:0000073 name: Metabolic pathway namespace: entity def: "A group of related chemical (enzyme catalysed) reactions occuring within a cell." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000012 ! Phenomena -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0001082 ! Biological pathway identifier +is_a: EDAM:0000012 ! Phenomenon relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1295,9 +1172,7 @@ id: EDAM:0000074 name: Mutation namespace: entity def: "A change to the nucleotide sequence of an organism's genome." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000012 ! Phenomena -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier +is_a: EDAM:0000012 ! Phenomenon relationship: has_attribute EDAM:0000841 ! Undefined [Term] @@ -1305,9 +1180,7 @@ id: EDAM:0000075 name: Single-nucleotide polymorphism namespace: entity def: "A single nucleotide variation in the genome of members of a species, or between paired chromosomes of an individual." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000012 ! Phenomena -relationship: is_concern_of EDAM:0000076 ! Undefined -relationship: has_identifier EDAM:0000842 ! Identifier +is_a: EDAM:0000012 ! Phenomenon relationship: has_attribute EDAM:0000841 ! Undefined @@ -1331,23 +1204,24 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000077 name: Nucleic acids namespace: topic -def: "Nucleic acid data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study nucleic acids." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002501 ! Nucleic acid data processing [Term] id: EDAM:0000078 name: Proteins namespace: topic -def: "Protein data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study proteins." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002502 ! Protein data processing + [Term] id: EDAM:0000079 name: Metabolites namespace: topic -def: "Metabolite data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study metabolites." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic relationship: concerns EDAM:0000008 ! Undefined @@ -1355,32 +1229,41 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000080 name: Sequence analysis namespace: topic -def: "Analyse molecular sequences." [EDAM:EBI "EMBRACE definition"] +def: "Handle or analyse molecular sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic xref: BioCatalogue:Sequence Analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002403 ! Sequence analysis +relationship: concerns EDAM:0002503 ! Sequence data processing +relationship: concerns EDAM:0000323 ! Phylogenetic tree construction [Term] id: EDAM:0000081 name: Structure analysis namespace: topic -def: "Analyse molecular structures." [EDAM:EBI "EMBRACE definition"] +def: "Handle or analyse molecular structures (secondary or tertiary)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002504 ! Structural data processing +relationship: concerns EDAM:0002484 ! Structure processing + [Term] id: EDAM:0000082 name: Structure prediction namespace: topic -def: "Predict molecular structure." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the prediction of molecular structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002476 ! Molecular dynamics simulation +relationship: concerns EDAM:0000271 ! Tertiary structure prediction + + + + [Term] id: EDAM:0000083 name: Alignment namespace: topic -def: "Generate or analyse alignments of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"] +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 @@ -1393,16 +1276,21 @@ comment: Phylogenetics involves phylogenetic tree construction, manipulation, vi xref: BioCatalogue:Phylogeny xref: BioCatalogue:Statistical Robustness is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000289 ! Sequence distance matrix generation +relationship: concerns EDAM:0002443 ! Phylogenetic tree processing +relationship: concerns EDAM:0000499 ! Multiple sequence alignment (phylogenetic tree-based) +relationship: concerns EDAM:0000550 ! Phylogenetic model selection + [Term] id: EDAM:0000200 name: Microarrays namespace: topic -def: "Process, analyse, interpret and visualise microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning microarrays, for example, process microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Microarrays is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002432 ! Microarray data processing +relationship: concerns EDAM:0000309 ! Microarray probe design [Term] id: EDAM:0000121 @@ -1424,7 +1312,9 @@ namespace: topic def: "Study whole genomes of organisms." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Genomics is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002472 ! Gene annotation retrieval +relationship: concerns EDAM:0002473 ! Genotype / phenotype annotation retrieval + [Term] @@ -1445,7 +1335,11 @@ comment: Structural genomics uses experimental data (for example from X-ray crys xref: BioCatalogue:Structural Genomics is_a: EDAM:0000093 ! Genomics ! is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000318 ! Structural genomics target selection +relationship: concerns EDAM:0000319 ! Protein secondary structure assignment +relationship: concerns EDAM:0000320 ! Protein tertiary structure assignment +relationship: concerns EDAM:0000321 ! Protein tertiary structure evaluation +relationship: concerns EDAM:0000322 ! Protein tertiary structure refinement [Term] @@ -1468,53 +1362,53 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000088 name: Literature and documentation namespace: topic -def: "Biomedical and informatic literature, bibliographic data and documentation." [EDAM:EBI "EMBRACE definition"] +def: "Study the biomedical and informatic literature, bibliographic data and documentation." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000515 ! Tool annotation retrieval +relationship: concerns EDAM:0000516 ! Database annotation retrieval +relationship: concerns EDAM:0002222 ! Ontology annotation retrieval +relationship: concerns EDAM:0002246 ! Demonstration [Term] id: EDAM:0000089 name: Ontologies namespace: topic -def: "Biomedical ontologies, controlled vocabularies, glossaries etc." [EDAM:EBI "EMBRACE definition"] +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 + [Term] id: EDAM:0000090 -name: Database search and retrieval +name: Search and retrieval namespace: topic -def: "Search or query a biological database or ontology and retrieve entries or other information." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Data Retrieval xref: BioCatalogue:Identifier Retrieval xref: BioCatalogue:Image Retrieval is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000224 ! Search and retrieval -[Term] -id: EDAM:0000219 -name: Annotation -namespace: topic -def: "Annotate biological database or ontology entities." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined [Term] id: EDAM:0000091 name: Database and file management namespace: topic -def: "Manage a biological database or file, for example submissions, indexing, reformatting etc." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the basic handling or manipulation of files, reports or databases of biological data." [EDAM:EBI "EMBRACE definition"] +comment: This includes areas such as data indexing, editing, reformatting, conversion, transformation, validation, debugging, database submission and so on. is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002409 ! Report processing +relationship: concerns EDAM:0001780 ! Sequence submission + [Term] id: EDAM:0000092 -name: Visualisation and rendering +name: Plotting, rendering and visualisation namespace: topic -def: "Render (display or print) molecular sequences, structures or other biomolecular data." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the rendering of molecular sequences, structures or other biomolecular data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000337 ! Plotting and rendering [Term] id: EDAM:0002282 @@ -1522,13 +1416,13 @@ name: Datatypes, workflows and data handling namespace: topic def: "Handling of biological data in a generic sense, including datatypes, data identifiers, data management, workflows etc." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000003 ! Topic -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000605 ! Informatics [Term] id: EDAM:0002258 name: Chemoinformatics namespace: topic -def: "Computing of data-centric problems in chemistry." [EDAM:EBI "EMBRACE definition"] +def: "Compute data-centric problems in chemistry." [EDAM:EBI "EMBRACE definition"] synonym: "Cheminformatics" EXACT [] synonym: "Chemical informatics" EXACT [] xref: BioCatalogue:Chemoinformatics @@ -1539,7 +1433,7 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0002259 name: Systems biology and modelling namespace: topic -def: "Holistic analysis of biological systems and modelling of the systems and interactions therein." [EDAM:EBI "EMBRACE definition"] +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 @@ -1565,44 +1459,50 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000094 name: Nucleic acid physicochemistry namespace: topic -def: "Determine, predict or analyse the physicochemical properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"] +def: "Study the physicochemical properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000077 ! Nucleic acids -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000261 ! Physicochemical property data processing (nucleic acid) [Term] id: EDAM:0000095 name: Nucleic acid features namespace: topic -def: "Identify, predict or analyse features of nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study the positional features of nucleic acids." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000160 ! Sequence features is_a: EDAM:0000096 ! Nucleic acid sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000415 ! Sequence feature detection (nucleic acid) [Term] id: EDAM:0000096 name: Nucleic acid sequence analysis namespace: topic -def: "Nucleic acid sequence data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Handle or analyse nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Nucleotide Sequence Analysis is_a: EDAM:0000077 ! Nucleic acids is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002478 ! Sequence analysis (nucleic acid) +relationship: concerns EDAM:0000461 ! Nucleic acid curvature calculation +relationship: concerns EDAM:0002513 ! Sequence generation (nucleic acid) +relationship: concerns EDAM:0002515 ! Sequence rendering (nucleic acid) [Term] id: EDAM:0000097 name: Nucleic acid structure analysis namespace: topic -def: "Identify, predict, analyse or handle nucleic acid structure or structural features." [EDAM:EBI "EMBRACE definition"] +def: "Handle or analyse nucleic acid structures or structural features." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000077 ! Nucleic acids is_a: EDAM:0000081 ! Structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000262 ! Nucleic acid structural property calculation +relationship: concerns EDAM:0002439 ! Secondary structure processing (RNA) +relationship: concerns EDAM:0002519 ! Tertiary structure processing (nucleic acid) + [Term] id: EDAM:0000098 name: DNA namespace: topic -def: "DNA data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study DNA." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000077 ! Nucleic acids relationship: concerns EDAM:0000008 ! Undefined @@ -1610,19 +1510,22 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000099 name: RNA namespace: topic -def: "RNA data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study RNA." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000077 ! Nucleic acids -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002439 ! Secondary structure processing (RNA) +relationship: concerns EDAM:0002440 ! Tertiary structure processing (RNA) [Term] id: EDAM:0000100 name: Nucleic acid restriction namespace: topic -def: "Study restriction enzymes and their cleavage sites, for example, identify restriction sites in DNA sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning restriction enzymes and their cleavage sites." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000096 ! Nucleic acid sequence analysis is_a: EDAM:0000132 ! Enzymes -relationship: concerns EDAM:0000008 ! Undefined - +relationship: concerns EDAM:0000280 ! Restriction enzyme annotation retrieval +relationship: concerns EDAM:0000365 ! Nucleic acid sequence restriction digest +relationship: concerns EDAM:0000370 ! Restriction site creation +relationship: concerns EDAM:0000431 ! Restriction site recognition @@ -1637,10 +1540,11 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000104 name: Nucleic acid denaturation namespace: topic -def: "Analyse DNA or DNA/RNA denaturation (melting) including thermal and conformational properties." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning DNA or DNA/RNA denaturation (melting) including thermal and conformational properties." [EDAM:EBI "EMBRACE definition"] synonym: "DNA melting" EXACT [] is_a: EDAM:0000094 ! Nucleic acid physicochemistry -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000455 ! Nucleic acid melting temperature calculation +relationship: concerns EDAM:0000456 ! Nucleic acid melting profile plotting @@ -1652,7 +1556,7 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000105 name: Nucleic acid sequence features namespace: topic -def: "Identify, predict or analyse features in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study positional features in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000095 ! Nucleic acid features @@ -1661,7 +1565,7 @@ consider: EDAM:0000095 ! Nucleic acid features id: EDAM:0000106 name: Nucleic acid structural features namespace: topic -def: "Identify, predict or analyse nucleic acid structural features." [EDAM:EBI "EMBRACE definition"] +def: "Study positional features in nucleic acid structural features." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000097 ! Nucleic acid structure analysis ! is_a: EDAM:0000095 ! Nucleic acid features @@ -1677,19 +1581,24 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000107 name: Codon usage namespace: topic -def: "Anaylse codon usage data in nucleotide sequence(s)." [EDAM:EBI "EMBRACE definition"] +def: "Study codon usage in nucleotide sequence(s)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000096 ! Nucleic acid sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002493 ! Codon usage data processing + [Term] id: EDAM:0000108 name: Transcription and translation namespace: topic -def: "Handle transcription and translation of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] -comment: For example, translate a nucleotide sequence or back translate a protein sequence, construct mRNA sequences from genomic sequences etc. +def: "Study or handle the transcription and translation of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000096 ! Nucleic acid sequence analysis is_a: EDAM:0000197 ! Gene expression -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000371 ! DNA translation +relationship: concerns EDAM:0000372 ! DNA transcription +relationship: concerns EDAM:0000439 ! Translation initiation site prediction +relationship: concerns EDAM:0002510 ! DNA back-translation + + [Term] id: EDAM:0000109 @@ -1700,7 +1609,10 @@ comment: Methods for gene prediction might be ab initio, based on phylogenetic c synonym: "Gene prediction" EXACT [] xref: BioCatalogue:Gene Prediction is_a: EDAM:0000096 ! Nucleic acid sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000287 ! Base position variability plotting +relationship: concerns EDAM:0002454 ! Gene and gene component prediction +relationship: concerns EDAM:0000521 ! PCR primer design (based on gene structure) +relationship: concerns EDAM:0000579 ! Operon rendering @@ -1719,28 +1631,29 @@ relationship: concerns EDAM:0000008 ! Undefined ! [Term] id: EDAM:0000110 -name: Transcription regulators +name: Transcription regulation namespace: topic -def: "Identify, predict or analyse transcription regulatory motifs, patterns, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"] -comment: This includes promoters, enhancers, silencers and boundary elements / insulators. Transcription regulatory regions bind regulatory proteins such as transcription factors. +def: "The study of transcription regulation including transcription factors and regulatory motifs, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"] +comment: This includes promoters, enhancers, silencers and boundary elements / insulators. xref: BioCatalogue:Transcription Factors is_a: EDAM:0000197 ! Gene expression is_a: EDAM:0000109 ! Gene finding -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000241 ! Transcription regulatory sequence analysis + ! -! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Gene finding<-Transcription regulators +! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Gene finding<-Transcription regulation ! [Term] id: EDAM:0000111 name: Promoters namespace: topic -def: "Analyse, compare, classify or model promoters in DNA sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study promoters in DNA sequences." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Promoter Prediction -is_a: EDAM:0000110 ! Transcription regulators -relationship: concerns EDAM:0000008 ! Undefined +is_a: EDAM:0000110 ! Transcription regulation +relationship: concerns EDAM:0000440 ! Promoter prediction @@ -1757,9 +1670,9 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000112 name: Nucleic acid folding namespace: topic -def: "Model, predict and analyse RNA/DNA folding." [EDAM:EBI "EMBRACE definition"] +def: "Study the folding of nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000097 ! Nucleic acid structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000279 ! Nucleic acid folding analysis @@ -1775,19 +1688,22 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000113 name: Functional RNA namespace: topic -def: "Analyse functional or non-coding RNA." [EDAM:EBI "EMBRACE definition"] +def: "Study functional or non-coding RNA." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000099 ! RNA -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000443 ! Transcription regulatory element prediction (trans) [Term] id: EDAM:0000114 name: RNA splicing namespace: topic -def: "Analyse RNA splicing, identify splice sites, calculate splicing alternatives etc." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning RNA splicing; splice sites, splicing alternatives and so on." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000099 ! RNA is_a: EDAM:0000197 ! Gene expression is_a: EDAM:0000096 ! Nucleic acid sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000264 ! Splice transcript prediction +relationship: concerns EDAM:0000433 ! Splice site prediction +relationship: concerns EDAM:0000446 ! Exonic splicing enhancer prediction +relationship: concerns EDAM:0002499 ! Splicing modelling @@ -1799,15 +1715,15 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000115 name: tRNA namespace: topic -def: "Transfer RNA (tRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study of transfer RNA (tRNA)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000113 ! Functional RNA -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000464 ! tRNA gene prediction [Term] id: EDAM:0000116 name: rRNA namespace: topic -def: "Ribosomal RNA (rRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study of ribosomal RNA (rRNA)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000113 ! Functional RNA relationship: concerns EDAM:0000008 ! Undefined @@ -1815,24 +1731,25 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000117 name: microRNA namespace: topic -def: "MicroRNA (miRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study of microRNA (miRNA)." [EDAM:EBI "EMBRACE definition"] comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. is_a: EDAM:0000113 ! Functional RNA -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000463 ! microRNA detection [Term] id: EDAM:0000118 name: siRNA namespace: topic -def: "Small interfering (silencing) RNA (siRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study of small interfering (silencing) RNA (siRNA)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000113 ! Functional RNA -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000465 ! siRNA assay design +relationship: concerns EDAM:0002008 ! siRNA duplex prediction [Term] id: EDAM:0000119 name: piRNA namespace: topic -def: "Piwi-interacting RNA (piRNA) data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study of piwi-interacting RNA (piRNA)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000113 ! Functional RNA relationship: concerns EDAM:0000008 ! Undefined @@ -1840,7 +1757,7 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000120 name: snoRNA namespace: topic -def: "Small nucleolar RNA (snoRNAs) data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study of small nucleolar RNA (snoRNAs)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000113 ! Functional RNA relationship: concerns EDAM:0000008 ! Undefined @@ -1867,55 +1784,60 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000123 name: Protein physicochemistry namespace: topic -def: "Determine, predict or analyse the physicochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"] +def: "Study the physicochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000250 ! Physicochemical property data processing (protein) +relationship: concerns EDAM:0000355 ! Sequence database search (by molecular weight) +relationship: concerns EDAM:0000356 ! Sequence database search (by isoelectric point) +relationship: concerns EDAM:0000243 ! Protein structural property calculation [Term] id: EDAM:0000124 name: Protein features namespace: topic -def: "Predict, identify or analyse features of protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study the positional features of protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000160 ! Sequence features is_a: EDAM:0000125 ! Protein sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000414 ! Sequence feature detection (protein) [Term] id: EDAM:0000125 name: Protein sequence analysis namespace: topic -def: "Protein sequence data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Handle or analyse protein sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000078 ! Proteins is_a: EDAM:0000080 ! Sequence analysis xref: BioCatalogue:Protein Sequence Analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002479 ! Sequence analysis (protein) +relationship: concerns EDAM:0002514 ! Sequence generation (protein) [Term] id: EDAM:0000126 name: Protein structure analysis namespace: topic -def: "Protein structural data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Handle or analyse protein structural data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000078 ! Proteins is_a: EDAM:0000081 ! Structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000243 ! Protein structural property calculation [Term] id: EDAM:0001775 name: Protein function namespace: topic -def: "Protein functional data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study protein function." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Function Prediction is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002414 ! Protein function data processing [Term] id: EDAM:0000127 name: Protein domains namespace: topic -def: "Protein structural domain data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study protein structural domains." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Domains is_a: EDAM:0002125 ! Protein tertiary structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000246 ! Protein domain recognition + [Term] id: EDAM:0000128 @@ -1925,37 +1847,39 @@ def: "Study protein-protein, protein-DNA/RNA and protein-ligand interactions." [ xref: BioCatalogue:Protein Interaction is_a: EDAM:0000078 ! Proteins is_a: EDAM:0000085 ! Functional genomics -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002405 ! Protein interaction data processing [Term] id: EDAM:0000129 name: Protein classification namespace: topic -def: "Protein sequence or structure classification." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the classification of proteins (from sequence or structural data)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000340 ! Protein secondary database search +relationship: concerns EDAM:0002470 ! Protein family annotation retrieval [Term] id: EDAM:0000130 name: Protein folding, stability and design namespace: topic -def: "Analyse or predict sequence-structure-function relationships, protein folding, the effect of mutation and the implications for protein design." [EDAM:EBI "EMBRACE definition"] +def: "The study of protein folding and protein sequence-structure-function relationships, for example the effect of mutation and the implications for protein design." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000331 ! Protein mutation modelling +relationship: concerns EDAM:0002415 ! Protein folding analysis [Term] id: EDAM:0000131 name: Transmembrane proteins namespace: topic -def: "Handle or analyse transmembrane proteins / regions." [EDAM:EBI "EMBRACE definition"] +def: "Study transmembrane proteins / regions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000270 ! Transmembrane protein data processing [Term] id: EDAM:0002232 name: Lipoproteins namespace: topic -def: "Handle or analyse lipoproteins." [EDAM:EBI "EMBRACE definition"] +def: "Study lipoproteins." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000078 ! Proteins relationship: concerns EDAM:0000008 ! Undefined @@ -1963,9 +1887,9 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000132 name: Enzymes namespace: topic -def: "Enzymes and the kinetics of enzyme-catalysed reactions." [EDAM:EBI "EMBRACE definition"] +def: "Study enzymes and the kinetics of enzyme-catalysed reactions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000078 ! Proteins -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000334 ! Enzyme kinetics calculation @@ -1980,9 +1904,11 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000137 name: Protein hydropathy namespace: topic -def: "Analyse the hydrophobic, hydrophilic and charge properties of a protein sequence or structure." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the hydrophobic, hydrophilic and charge properties of a protein." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000123 ! Protein physicochemistry -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002574 ! Protein hydropathy calculation +relationship: concerns EDAM:0000384 ! Protein solvent accessibility calculation +relationship: concerns EDAM:0000400 ! Protein pH-dependent property calculation ! @@ -2017,27 +1943,31 @@ consider: EDAM:0000166 ! Protein structural motifs id: EDAM:0000140 name: Protein targeting namespace: topic -def: "Predict or analyse protein targeting (signal peptides) and protein subcellular localization or export." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning protein targeting (signal peptides) and protein subcellular localization or export." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000125 ! Protein sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000418 ! Protein signal peptide detection +relationship: concerns EDAM:0002489 ! Protein subcellular localization prediction [Term] id: EDAM:0000141 name: Proteolysis and peptide mass namespace: topic -def: "Proteolytic or mass calculations on a protein sequence and related analyses." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning proteolytic or mass calculations on a protein." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000125 ! Protein sequence analysis is_a: EDAM:0000134 ! Mass spectrometry -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000355 ! Sequence database search (by molecular weight) +relationship: concerns EDAM:0000366 ! Protein sequence cleavage +relationship: concerns EDAM:0000398 ! Protein molecular weight calculation +relationship: concerns EDAM:0000422 ! Protein cleavage site prediction [Term] id: EDAM:0000142 name: Protein post-translation modification namespace: topic -def: "Data and analysis concerning protein post-translation modification." [EDAM:EBI "EMBRACE definition"] +def: "Study of protein post-translation modification." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000125 ! Protein sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000417 ! Protein post-translation modification prediction ! @@ -2047,47 +1977,51 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0002124 name: Protein secondary structure analysis namespace: topic -def: "Protein secondary structural data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Handle and analyse protein secondary structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000126 ! Protein structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002444 ! Secondary structure processing (protein) [Term] id: EDAM:0002125 name: Protein tertiary structure analysis namespace: topic -def: "Protein tertiary structural data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Handle or analyse protein tertiary structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000126 ! Protein structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002459 ! Tertiary structure processing (protein) [Term] id: EDAM:0000143 name: Protein structure comparison namespace: topic -def: "Compare two or more protein structures." [EDAM:EBI "EMBRACE definition"] -comment: Use this term for methods that are exclusively for protein structure. Methods might identify structural neighbors, find structural similarities or define a structural core. -is_a: EDAM:0002125 ! Protein tertiary structure analysis -is_a: EDAM:0001770 ! Structure comparison -relationship: concerns EDAM:0000008 ! Undefined +def: "Study concerning the comparison of two or more protein structures." [EDAM:EBI "EMBRACE definition"] +comment: Use this term for methods that are exclusively for protein structure. +is_obsolete: true +consider: EDAM:0002125 ! Protein tertiary structure analysis +consider: EDAM:0001770 ! Structure comparison + [Term] id: EDAM:0002280 name: Nucleic acid structure comparison namespace: topic -def: "Compare two or more nucleic acid (typically RNA) secondary or tertiary structures." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that are exclusively for nucleic acid structures. -is_a: EDAM:0000097 ! Nucleic acid structure analysis -is_a: EDAM:0001770 ! Structure comparison -relationship: concerns EDAM:0000008 ! Undefined +is_obsolete: true +consider: EDAM:0000097 ! Nucleic acid structure analysis +consider: EDAM:0001770 ! Structure comparison [Term] id: EDAM:0000144 name: Protein residue interactions namespace: topic -def: "Analyse inter-atomic or inter-residue interactions in protein structures." [EDAM:EBI "EMBRACE definition"] +def: "Study inter-atomic or inter-residue interactions in protein structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002124 ! Protein secondary structure analysis relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000248 ! Residue interaction calculation +relationship: concerns EDAM:0001850 ! Protein cysteine and disulfide bond assignment +relationship: concerns EDAM:0000272 ! Prediction of protein residue distances, contacts and interactions [Term] @@ -2097,20 +2031,23 @@ namespace: topic def: "Study flexibility and motion in protein structure." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002125 ! Protein tertiary structure analysis is_a: EDAM:0000176 ! Molecular dynamics -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000244 ! Protein flexibility and motion analysis [Term] id: EDAM:0000146 name: Protein surfaces namespace: topic -def: "Caclulate, analyse or visualise the surface (shape, hydropathy, electrostatic patches etc) of a protein structure, including biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"] +def: "Study the surface of a protein structure, including biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"] +comment: This includes the analysis of shape, hydropathy, electrostatic patches and so on. is_a: EDAM:0002125 ! Protein tertiary structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000387 ! Protein surface and interior calculation ! ! Topic<-Proteins<-Protein function ! + + [Term] id: EDAM:0002276 name: Protein function prediction @@ -2118,7 +2055,7 @@ namespace: topic def: "Predict general functional properties of a protein." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Function Prediction is_a: EDAM:0001775 ! Protein function -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0001777 ! Protein function prediction ! ! Topic<-Proteins<-Protein domains @@ -2136,7 +2073,11 @@ name: Protein-protein interactions namespace: topic def: "Study protein-protein interactions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000128 ! Protein interactions -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000273 ! Protein-protein interaction experimental data analysis +relationship: concerns EDAM:0002464 ! Protein-protein interaction prediction +relationship: concerns EDAM:0002445 ! Protein-protein interaction network processing + + [Term] id: EDAM:0000148 @@ -2145,7 +2086,8 @@ namespace: topic def: "Study protein-ligand (small molecule) interactions." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Ligand Interaction is_a: EDAM:0000128 ! Protein interactions -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002575 ! Ligand-binding and active site prediction +relationship: concerns EDAM:0000482 ! Protein-ligand docking [Term] id: EDAM:0000149 @@ -2153,7 +2095,7 @@ name: Protein-nucleic acid interactions namespace: topic def: "Study protein-DNA/RNA interactions." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000128 ! Protein interactions -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000389 ! Protein-nucleic acid binding site analysis @@ -2168,13 +2110,16 @@ relationship: concerns EDAM:0000008 ! Undefined ! Topic<-Proteins<-Protein folding, stability and design ! + [Term] id: EDAM:0000150 name: Protein rational design namespace: topic def: "Design proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000130 ! Protein folding, stability and design -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000333 ! Protein-nucleic acid binding site design +relationship: concerns EDAM:0000559 ! Peptide immunogen design +relationship: concerns EDAM:0000560 ! DNA vaccine design @@ -2187,18 +2132,20 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000151 name: G protein-coupled receptors (GPCR) namespace: topic -def: "Study G-protein coupled receptors (GPCRs)." [EDAM:EBI "EMBRACE definition"] +def: "Study G-protein coupled receptors (GPCRs)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000131 ! Transmembrane proteins -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000473 ! GPCR analysis + [Term] id: EDAM:0002278 name: Transmembrane protein prediction namespace: topic -def: "Predict transmembrane domains and topolgy in protein sequences." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000131 ! Transmembrane proteins -is_a: EDAM:0000178 ! Protein secondary structure prediction -relationship: concerns EDAM:0000008 ! Undefined +def: "Predict transmembrane domains and topolgy in protein sequences." [EDAM:EBI "EMBRACE definition"] +is_obsolete: true +consider: EDAM:0000131 ! Transmembrane proteins +consider: EDAM:0000178 ! Protein secondary structure prediction + @@ -2215,7 +2162,7 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000152 name: Carbohydrates namespace: topic -def: "Carbohydrate data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study carbohydrates." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000079 ! Metabolites relationship: concerns EDAM:0000008 ! Undefined @@ -2223,7 +2170,7 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000153 name: Lipids namespace: topic -def: "Lipid data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study lipids." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000079 ! Metabolites relationship: concerns EDAM:0000008 ! Undefined @@ -2231,9 +2178,9 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000154 name: Small molecules namespace: topic -def: "Small molecule data and analysis." [EDAM:EBI "EMBRACE definition"] +def: "Study small molecules of biological significance." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000079 ! Metabolites -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002123 ! Physicochemical property data processing (small molecule) @@ -2243,23 +2190,27 @@ relationship: concerns EDAM:0000008 ! Undefined ! ! Topic<-Sequence analysis ! + [Term] id: EDAM:0000155 name: Sequence search and retrieval namespace: topic def: "Search or query a database and retrieve molecular sequences and associated data." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Sequence Retrieval -is_a: EDAM:0000080 ! Sequence analysis -is_a: EDAM:0000090 ! Database search and retrieval -relationship: concerns EDAM:0000008 ! Undefined +is_obsolete: true +consider: EDAM:0000090 ! Search and retrieval +! is_a: EDAM:0000080 ! Sequence analysis + [Term] id: EDAM:0000156 name: Sequence editing namespace: topic def: "Create, edit, change or convert a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +is_obsolete: true +consider: EDAM:0000080 ! Sequence analysis +consider: EDAM:0000091 ! Database and file management + [Term] id: EDAM:0000157 @@ -2267,46 +2218,56 @@ name: Sequence composition namespace: topic def: "Analyse the basic composition of a molecular sequence, for example character or word frequency, ambiguity, complexity or repeats." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000236 ! Sequence composition calculation +relationship: concerns EDAM:0000235 ! Sequence ambiguity calculation +relationship: concerns EDAM:0000348 ! Sequence database search (by amino acid composition) +relationship: concerns EDAM:0000430 ! CpG island and isochores detection [Term] id: EDAM:0000158 name: Sequence motifs namespace: topic -def: "Discover, identify or analyse conserved patterns (motifs) in molecular sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning conserved patterns (motifs) in molecular sequences." [EDAM:EBI "EMBRACE definition"] synonym: "Motifs" EXACT [] is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002404 ! Sequence motif processing +relationship: concerns EDAM:0000341 ! Motif database search +relationship: concerns EDAM:0000347 ! Sequence database search (by motif or pattern) + + + [Term] id: EDAM:0000188 name: Sequence profiles and HMMs namespace: topic -def: "Generate, manipulate, analyse or use some type of sequence profile (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] -comment: Profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. +def: "Study concerning sequence profiles (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] +comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. is_a: EDAM:0000080 ! Sequence analysis is_a: EDAM:0000182 ! Sequence alignment -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002413 ! Sequence profile processing [Term] id: EDAM:0000159 name: Sequence comparison namespace: topic -def: "Compare two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the comparison of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000338 ! Sequence database search +relationship: concerns EDAM:0000359 ! Structure database search (by sequence) +relationship: concerns EDAM:0002451 ! Sequence comparison [Term] id: EDAM:0000160 name: Sequence features namespace: topic -def: "Identify, predict, handle or analyse the features or feature tables of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] +def: "Study the positional features of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000080 ! Sequence analysis -relationship: concerns EDAM:0000008 ! Undefined - +relationship: concerns EDAM:0002453 ! Sequence feature table processing +relationship: concerns EDAM:0000253 ! Sequence feature detection ! ! Topic<-Sequence analysis<-Sequence search and retrieval @@ -2326,18 +2287,18 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0002262 name: Repeat sequences namespace: topic -def: "Analyse the repetitive nature of a molecular sequence." [EDAM:EBI "EMBRACE definition"] +def: "Study the repetitive nature of molecular sequences." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Repeats is_a: EDAM:0000157 ! Sequence composition -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000237 ! Repeat sequence analysis [Term] id: EDAM:0002263 name: Sequence complexity namespace: topic -def: "Analyse the complexity of a molecular sequence." [EDAM:EBI "EMBRACE definition"] +def: "Study the complexity of molecular sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000157 ! Sequence composition -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000234 ! Sequence complexity calculation @@ -2348,18 +2309,19 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000161 name: Protein sequence motifs namespace: topic -def: "Discover, identify or analyse motifs or conserved patterns in protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning conserved patterns (motifs) in protein sequences." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Motifs is_a: EDAM:0000158 ! Sequence motifs -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000382 ! Sequence motif recognition (protein) + [Term] id: EDAM:0000162 name: Nucleic acid sequence motifs namespace: topic -def: "Discover, identify or analyse motifs or conserved patterns in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning conserved patterns (motifs) in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000158 ! Sequence motifs -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000381 ! Sequence motif recognition (nucleic acid) ! @@ -2370,6 +2332,8 @@ relationship: concerns EDAM:0000008 ! Undefined ! ! Topic<-Sequence analysis<-Sequence comparison ! + + [Term] id: EDAM:0000163 name: Sequence similarity search @@ -2377,8 +2341,10 @@ namespace: topic def: "Search for and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence)." [EDAM:EBI "EMBRACE definition"] comment: The query is a sequence-based entity such as another sequence, a motif or profile. is_a: EDAM:0000159 ! Sequence comparison -is_a: EDAM:0000155 ! Sequence search and retrieval -relationship: concerns EDAM:0000008 ! Undefined +is_a: EDAM:0000090 ! Search and retrieval +relationship: concerns EDAM:0000338 ! Sequence database search + + [Term] id: EDAM:0000164 @@ -2386,7 +2352,11 @@ name: Sequence clustering namespace: topic def: "Compare and cluster multiple sequences on the basis of similarity, process or analyse sequence clusters." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000159 ! Sequence comparison -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002452 ! Sequence cluster processing +relationship: concerns EDAM:0000290 ! Sequence redundancy removal +relationship: concerns EDAM:0002233 ! Representative sequence identification + + [Term] id: EDAM:0002260 @@ -2395,9 +2365,11 @@ namespace: topic def: "Compare two or more protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that are exclusively for protein sequences. xref: BioCatalogue:Protein Sequence Similarity -is_a: EDAM:0000159 ! Sequence comparison -is_a: EDAM:0000125 ! Protein sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +is_obsolete: true +consider: EDAM:0000159 ! Sequence comparison +consider: EDAM:0000125 ! Protein sequence analysis + + [Term] id: EDAM:0002261 @@ -2406,9 +2378,11 @@ namespace: topic def: "Compare two or more nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that are exclusively for nucleotide sequences. xref: BioCatalogue:Nucleotide Sequence Similarity -is_a: EDAM:0000159 ! Sequence comparison -is_a: EDAM:0000096 ! Nucleic acid sequence analysis -relationship: concerns EDAM:0000008 ! Undefined +is_obsolete: true +consider: EDAM:0000159 ! Sequence comparison +consider: EDAM:0000096 ! Nucleic acid sequence analysis + + ! ! Topic<-Sequence analysis<-Sequence features @@ -2421,46 +2395,51 @@ relationship: concerns EDAM:0000008 ! Undefined ! ! Topic<-Structure analysis ! + [Term] id: EDAM:0000165 name: Structure search and retrieval namespace: topic def: "Search or query a database and retrieve molecular structures." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Structure Retrieval -is_a: EDAM:0000081 ! Structure analysis -is_a: EDAM:0000090 ! Database search and retrieval -relationship: concerns EDAM:0000008 ! Undefined +is_obsolete: true +consider: EDAM:0000081 ! Structure analysis +consider: EDAM:0000090 ! Search and retrieval + [Term] id: EDAM:0000166 name: Protein structural motifs namespace: topic -def: "Discover, identify, predict or analyse structural features or common 3D motifs of protein structures." [EDAM:EBI "EMBRACE definition"] +def: "Study structural features or common 3D motifs of protein structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002125 ! Protein tertiary structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000245 ! Protein structural motif recognition [Term] id: EDAM:0000167 -name: Structural profiles +name: Structural (3D) profiles namespace: topic def: "Generate, manipulate, analyse or use some type of structural (3D) profile or template (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +synonym: "Structural profiles" EXACT [] is_a: EDAM:0000081 ! Structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002411 ! Structural (3D) profile processing +relationship: concerns EDAM:0002239 ! 3D-1D scoring matrix generation + [Term] id: EDAM:0001770 name: Structure comparison namespace: topic -def: "Compare two or more molecular structures." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the comparison of two or more molecular structures." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000081 ! Structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000360 ! Structure database search (by structure) [Term] id: EDAM:0000170 name: Structural features and motifs namespace: topic -def: "Discover, identify, predict or analyse structural features and common motifs of molecular structures." [EDAM:EBI "EMBRACE definition"] +def: "Study structural features and common motifs of molecular structures." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000166 ! Protein structural motifs @@ -2471,30 +2450,34 @@ consider: EDAM:0000166 ! Protein structural motifs ! -! Topic<-Structure analysis<-Structural profiles +! Topic<-Structure analysis<-Structural (3D) profiles ! ! ! Topic<-Structure analysis<-Structure comparison ! + [Term] id: EDAM:0000168 name: Secondary structure comparison namespace: topic -def: "Compare two or more protein secondary structures." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000143 ! Protein structure comparison +def: "Study concerning the comparison of two or more protein secondary structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001770 ! Structure comparison is_a: EDAM:0002124 ! Protein secondary structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002488 ! Secondary structure comparison (protein) + [Term] id: EDAM:0000169 name: Tertiary structure comparison namespace: topic -def: "Compare two or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] -is_a: EDAM:0000143 ! Protein structure comparison +def: "Study concerning the comparison of two or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] +is_a: EDAM:0001770 ! Structure comparison is_a: EDAM:0002125 ! Protein tertiary structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002483 ! Tertiary structure comparison + + [Term] id: EDAM:0002271 @@ -2503,7 +2486,7 @@ namespace: topic def: "Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure)." [EDAM:EBI "EMBRACE definition"] 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:0000165 ! Structure search and retrieval +is_a: EDAM:0000090 ! Search and retrieval relationship: concerns EDAM:0000008 ! Undefined @@ -2524,6 +2507,7 @@ relationship: concerns EDAM:0000008 ! Undefined ! Topic<-Structure prediction ! + [Term] id: EDAM:0000171 name: Tertiary structure prediction @@ -2532,6 +2516,7 @@ def: "Predict protein or nucleic acid tertiary (3D) structure." [EDAM:EBI "EMBRA is_obsolete: true consider: EDAM:0000082 ! Structure prediction + [Term] id: EDAM:0000172 name: Protein structure prediction @@ -2541,6 +2526,7 @@ xref: BioCatalogue:Protein Structure Prediction is_a: EDAM:0000082 ! Structure prediction relationship: concerns EDAM:0000008 ! Undefined + [Term] id: EDAM:0000173 name: Nucleic acid structure prediction @@ -2551,7 +2537,9 @@ xref: BioCatalogue:Nucleotide Secondary Structure xref: BioCatalogue:Nucleotide Tertiary Structure is_a: EDAM:0000082 ! Structure prediction is_a: EDAM:0000097 ! Nucleic acid structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000278 ! RNA secondary structure prediction +relationship: concerns EDAM:0000429 ! Quadruplex formation site detection +relationship: concerns EDAM:0000475 ! Tertiary structure prediction (nucleic acid) [Term] @@ -2561,13 +2549,13 @@ namespace: topic def: "Predict three-dimensional structure of a protein sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [EDAM:EBI "EMBRACE definition"] synonym: "de novo protein structure prediction" EXACT [] is_a: EDAM:0000179 ! Protein tertiary structure prediction -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000476 ! Ab initio structure prediction [Term] id: EDAM:0002275 name: Molecular modelling namespace: topic -def: "Build or assess a model of a molecules properties or behaviour using computational methods. " [EDAM:EBI "EMBRACE definition"] +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 @@ -2577,18 +2565,20 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000175 name: Homology modelling namespace: topic -def: "Build or assess a three-dimensional protein model using known sequence and structural data." [EDAM:EBI "EMBRACE definition"] -comment: Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. +def: "Study concerning the modelling of the three-dimensional structure of a protein using known sequence and structural data." [EDAM:EBI "EMBRACE definition"] synonym: "Comparative modelling" EXACT [] is_a: EDAM:0000179 ! Protein tertiary structure prediction is_a: EDAM:0002275 ! Molecular modelling -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000302 ! Protein threading +relationship: concerns EDAM:0000477 ! Protein modelling +relationship: concerns EDAM:0000321 ! Protein tertiary structure evaluation +relationship: concerns EDAM:0000322 ! Protein tertiary structure refinement [Term] id: EDAM:0000176 name: Molecular dynamics namespace: topic -def: "Simulate molecular (typically protein) conformation using a computational model of physicalal forces and computer simulation." [EDAM:EBI "EMBRACE definition"] +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 @@ -2605,9 +2595,9 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000177 name: Protein docking namespace: topic -def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the modelling of the structure of a protein in complex with a small molecule or another macromolecule." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0002275 ! Molecular modelling -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000478 ! Protein docking @@ -2628,27 +2618,29 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000178 name: Protein secondary structure prediction namespace: topic -def: "Predict secondary or supersecondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the prediction of secondary or supersecondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Protein Secondary Structure is_a: EDAM:0000172 ! Protein structure prediction is_a: EDAM:0002124 ! Protein secondary structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000267 ! Protein secondary structure prediction [Term] id: EDAM:0000179 name: Protein tertiary structure prediction namespace: topic -def: "Predict tertiary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the prediction of tertiary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Protein Tertiary Structure is_a: EDAM:0000172 ! Protein structure prediction is_a: EDAM:0002125 ! Protein tertiary structure analysis -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000474 ! Tertiary structure prediction (protein) +relationship: concerns EDAM:0000321 ! Protein tertiary structure evaluation + [Term] id: EDAM:0000180 name: Protein fold recognition namespace: topic -def: "Recognize (predict and assign) known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] +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 @@ -2678,22 +2670,29 @@ is_a: EDAM:0000099 ! RNA ! ! Topic<-Alignment ! + [Term] id: EDAM:0000182 name: Sequence alignment namespace: topic -def: "Generate or analyse alignments of molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the alignment (equivalence between sites) of molecular sequences." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Protein Sequence Alignment xref: BioCatalogue:Nucleotide Sequence Alignment is_a: EDAM:0000083 ! Alignment is_a: EDAM:0000159 ! Sequence comparison -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002463 ! Sequence alignment processing +relationship: concerns EDAM:0000352 ! Sequence database search (by sequence using local alignment-based methods) +relationship: concerns EDAM:0000353 ! Sequence database search (by sequence using global alignment-based methods) + + + [Term] id: EDAM:0002283 name: Sequence profile alignment namespace: topic -def: "Generate or analyse alignments involving ." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the alignment (equivalence between sites) of sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] +synonym: "Sequence profile alignment" EXACT [] is_a: EDAM:0000083 ! Alignment is_a: EDAM:0000159 ! Sequence comparison is_a: EDAM:0000188 ! Sequence profiles and HMMs @@ -2703,28 +2702,33 @@ relationship: concerns EDAM:0000008 ! Undefined id: EDAM:0000183 name: Structure alignment namespace: topic -def: "Generate or analyse alignments (superimpositions) of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the alignment (superimposition) of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +synonym: "Structure alignment generation" EXACT [] is_a: EDAM:0000083 ! Alignment is_a: EDAM:0000169 ! Tertiary structure comparison -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0000295 ! Tertiary structure alignment +relationship: concerns EDAM:0000299 ! Structural (3D) profile alignment + [Term] id: EDAM:0000184 name: Sequence-structure alignment namespace: topic -def: "Generate or analyse alignments of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] +synonym: "Sequence-structure alignment generation" EXACT [] synonym: "Threading" EXACT [] is_a: EDAM:0000083 ! Alignment is_a: EDAM:0000175 ! Homology modelling -relationship: concerns EDAM:0000008 ! Undefined - - +relationship: concerns EDAM:0000302 ! Protein threading +relationship: concerns EDAM:0000303 ! Protein fold recognition +relationship: concerns EDAM:0000301 ! Sequence-3D profile alignment ! ! Topic<-Alignment<-Sequence alignment ! + [Term] id: EDAM:0000185 name: Pairwise sequence alignment @@ -2732,8 +2736,9 @@ namespace: topic def: "Align exactly two molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Protein Pairwise Alignment xref: BioCatalogue:Nucleotide Pairwise Alignment -is_a: EDAM:0000182 ! Sequence alignment -relationship: concerns EDAM:0000008 ! Undefined +is_obsolete: true +consider: EDAM:0000182 ! Sequence alignment + [Term] id: EDAM:0000186 @@ -2742,25 +2747,26 @@ namespace: topic def: "Align two or more molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] xref: BioCatalogue:Protein Multiple Alignment xref: BioCatalogue:Nucleotide Multiple Alignment -is_a: EDAM:0000182 ! Sequence alignment -relationship: concerns EDAM:0000008 ! Undefined +is_obsolete: true +consider: EDAM:0000182 ! Sequence alignment + [Term] id: EDAM:0000187 name: Sequence alignment analysis namespace: topic -def: "Handle, analyse or compare alignments of molecular sequences or sequence profiles (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] +def: "Handle or analyse alignments of molecular sequences or sequence profiles (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000182 ! Sequence alignment -relationship: concerns EDAM:0000008 ! Undefined +relationship: concerns EDAM:0002463 ! Sequence alignment processing [Term] id: EDAM:0000189 name: Structure-based sequence alignment namespace: topic -def: "Align molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"] +def: "Study concerning the alignment of molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000182 ! Sequence alignment -relationship: concerns EDAM:0000008 ! Undefined - +relationship: concerns EDAM:0000294 ! Structure-based sequence alignment +relationship: concerns EDAM:0000500 ! Secondary structure alignment ! ! Topic<-Alignment