format-version: 1.2 date: 15:01:2011 15:01 data-version: Beta13 subsetdef: topic "Topic" subsetdef: data "Data" subsetdef: format "Format" subsetdef: identifier "Identifier" subsetdef: operation "Operation" ! Use for mapping to "global" id space(s) e.g.: ! idspace: EDAM http://purl.org/edam/ "EDAM concepts" ! NEXT term number is 0003155 ! xref: WHATIF: CorrectedPDBasXML ! xref:http://www.geneontology.org/doc/GO.xrf_abbs: FB ! xref:Moby:GI_Gene ! xref: Moby_namespace:iHOPorganism ! xref: SO:0000348 ! xref: BioCatalogue:Protein Multiple Alignment ! xref: GO:0006464 ! protein modification process ! regex: Regular expression for validating a "data<-identifier" value. ! spec: URL of format specification for a "format" term ! seealso: Ontology concept ID of concept in external ontology for 'fine-grained' annotation ! {cardinality=1, minCardinality=1, maxCardinality=1} ! ! Relations ! [Typedef] id: has_topic name: has_topic def: "'Data' or 'Operation' is within the scope of a 'Topic'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: is_topic_of domain: EDAM:0000004 ! Operation domain: EDAM:0000006 ! Data range: EDAM:0000003 ! Topic ! Note: second 'domain' line is not visible in OBOEdit [Typedef] id: has_input name: has_input def: "An 'Operation' consumes a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: is_input_of domain: EDAM:0000004 ! Operation range: EDAM:0000006 ! Data [Typedef] id: has_output name: has_output def: "An 'Operation' produces a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: is_output_of domain: EDAM:0000004 ! Operation range: EDAM:0000006 ! Data [Typedef] id: has_format name: has_format def: "'Data' has a certain 'Format'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: is_format_of domain: EDAM:0000006 ! Data range: EDAM:0001915 ! Format [Typedef] id: has_identifier name: has_identifier def: "'Data' is identified by an 'Identifier'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: is_identifier_of domain: EDAM:0000006 ! Data range: EDAM:0000842 ! Identifier ! For annotating tools [Typedef] id: has_operation name: has_operation def: "A tool has an 'Operation'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true range: EDAM:0000004 ! Operation [Typedef] id: is_format_of name: is_format_of def: "A data 'Format' is a format of a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: has_format domain: EDAM:0001915 ! Format range: EDAM:0000006 ! Data [Typedef] id: is_identifier_of name: is_identifier_of def: "A data 'Identifier' is an identifier of a certain type of 'Data'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: has_identifier domain: EDAM:0000842 ! Identifier range: EDAM:0000006 ! Data [Typedef] id: is_topic_of name: is_topic_of def: "'Topic' is_topic_of 'Data' or 'Operation'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: has_topic domain: EDAM:0000003 ! Topic range: EDAM:0000003 ! Topic [Typedef] id: is_input_of name: is_input_of def: "'Data' is an input of an 'Operation'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: has_input domain: EDAM:0000006 ! Data range: EDAM:0000004 ! Operation [Typedef] id: is_output_of name: is_output_of def: "'Data' is an output of an 'Operation'." [EDAM:EBI] is_anti_symmetric: true is_cyclic: false is_transitive: true inverse_of: has_output domain: EDAM:0000006 ! Data range: EDAM:0000004 ! Operation [Typedef] id: regex name: regex is_metadata_tag: true [Typedef] id: spec name: spec is_metadata_tag: true [Typedef] id: seealso name: seealso is_metadata_tag: true ! ! Top-level terms (sub-ontologies) ! [Term] id: EDAM:0000003 name: Topic namespace: topic def: "A broad category within bioinformatics that covers one or (typically) a combination of fields of study, types of data, processing, analysis or technology." [EDAM:EBI "EMBRACE definition"] subset: topic [Term] id: EDAM:0000004 name: Operation namespace: operation def: "A function or process performed by a tool; what is done, but not (typically) how or in what context." [EDAM:EBI "EMBRACE definition"] subset: operation [Term] id: EDAM:0000006 name: Data namespace: data alt_id: EDAM:0003030 def: "A type of data in common use in bioinformatics." [EDAM:EBI "EMBRACE definition"] subset: data [Term] id: EDAM:0003031 name: Core data namespace: data def: "A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation." [EDAM:EBI "EMBRACE definition"] comment: Core data entities typically have a format and may be identified by an accession number. subset: data is_a: EDAM:0000006 ! Data [Term] id: EDAM:0001915 name: Format namespace: format def: "A specific layout for encoding a specific type of data in a computer file or memory." [EDAM:EBI "EMBRACE definition"] subset: format [Term] id: EDAM:0000842 name: Identifier namespace: identifier alt_id: EDAM:0002860 alt_id: EDAM:0002861 alt_id: EDAM:0002926 def: "A short numerical or textual label that identifies (typically uniquely) something such as data, a resource or a biological entity." [EDAM:EBI "EMBRACE definition"] comment: This term is used for datatypes with the sole purpose of identification. It is not used for datatypes which contain other fields not related to identification. Identifiers typically are enumerated string (a string with one of a limited set of values) or are strings that are conformant to a regular expression. An ID is not necessarily stable or persistent over time, for example between different versions of a database. subset: identifier is_a: EDAM:0000006 ! Data [Term] id: EDAM:0000002 name: Biological entity namespace: entity def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things or an observable phenomenon or occurrence." [EDAM:EBI "EMBRACE definition"] is_obsolete: true ! ! Biological entity ! [Term] id: EDAM:0000008 name: Undefined namespace: entity def: "Debugging." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0002199 name: Physical entity namespace: entity def: "Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000012 name: Phenomenon namespace: entity def: "An observable biological occurrence or event with a physical basis." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000009 name: Discrete entity namespace: entity def: "Any biological thing with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000010 name: Entity feature namespace: entity def: "A physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000011 name: Entity collection namespace: entity def: "A collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000013 name: Molecular entity namespace: entity def: "Any atom, molecule or molecular complex with a distinct, discrete physical existence." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0000883 ! Structure is_obsolete: true [Term] id: EDAM:0000014 name: Atom namespace: entity def: "The basic unit of matter consisting of negatively charged electrons bound by electromagnetic force to a nucleus of protons and neutrons." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000015 name: Small molecule namespace: entity def: "Any small molecule." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000016 name: Biopolymer namespace: entity def: "A single organic macromolecule made up of monomeric units." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0002044 ! Sequence is_obsolete: true [Term] id: EDAM:0000017 name: Molecular complex namespace: entity def: "Two or more whole molecules in association with one another." [EDAM:EBI "EMBRACE definition"] synonym: "Molecular assembly" EXACT [] is_obsolete: true [Term] id: EDAM:0000018 name: Biomonomer namespace: entity def: "A small organic molecule that can chemically bond to other monomers to form a biopolymer." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000019 name: Ligand namespace: entity def: "A molecule that can bind and form a complex with a biopolymer, typically a protein." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000020 name: Drug namespace: entity def: "A substance that changes the normal functioning of an organism." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0002577 name: Toxin namespace: entity def: "A poisonous substance produced by living cells or organisms." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000021 name: Amino acid namespace: entity def: "The building block of proteins, an alpha amino acid consists of a carbon atom (C-alpha) attached to a hydrogen atom, an amino group, a carboxylate group and one of (typically) 20 common R-groups (side-chain)." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000022 name: Nucleotide namespace: entity def: "The building block of nucleic acids, a nucleotide consists of a nucleobase (nitrogenous base, either a purine or pyrimidine), a five-carbon sugar (either ribose or 2'-deoxyribose), and one to three phosphate groups." [EDAM:EBI "EMBRACE definition"] synonym: "Base" EXACT [] xref: SO:0001236 is_obsolete: true [Term] id: EDAM:0000023 name: Monosaccharide namespace: entity def: "The building block of polysaccharides, a monosaccharide is an aldehyde or ketone with hydroxyl groups." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000024 name: Nucleic acid namespace: entity def: "An organic polymer of nucleotide monomers in an unbranched chain, bound together by covalent bonds." [EDAM:EBI "EMBRACE definition"] synonym: "Polynucleotide chain" EXACT [] synonym: "Polynucleotide" EXACT [] xref: SO:0000348 ! relationship: has_attribute EDAM:0001207 ! Nucleotide sequence ! relationship: has_attribute EDAM:0001459 ! Nucleic acid structure is_obsolete: true [Term] id: EDAM:0000025 name: Polypeptide namespace: entity def: "An organic polymer of alpha amino acid residues in an unbranched chain, bound together by peptide bonds." [EDAM:EBI "EMBRACE definition"] synonym: "Polypeptide chain" EXACT [] ! relationship: has_attribute EDAM:0001208 ! Protein sequence ! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] id: EDAM:0000026 name: Polysaccharide namespace: entity def: "An organic polymer of either mono- or di-saccharide subunits in an unbranched chain, bound together by glycosidic bonds." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000027 name: Oligonucleotide namespace: entity def: "An organic polymer of nucleotide monomers in a short (typically less than 30 subunits) unbranched chain, bound together by covalent bonds." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0001207 ! Nucleotide sequence is_obsolete: true [Term] id: EDAM:0000028 name: DNA namespace: entity def: "A deoxyribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] xref: SO:0000352 ! relationship: has_attribute EDAM:0001212 ! DNA sequence ! relationship: has_attribute EDAM:0001464 ! DNA structure is_obsolete: true [Term] id: EDAM:0000029 name: RNA namespace: entity def: "A ribonucleic acid molecule." [EDAM:EBI "EMBRACE definition"] xref: SO:0000356 ! relationship: has_attribute EDAM:0001213 ! RNA sequence ! relationship: has_attribute EDAM:0001465 ! RNA structure is_obsolete: true [Term] id: EDAM:0000030 name: Mobile genetic element namespace: entity def: "A DNA molecule that can move around within a genome." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0002010 name: cDNA namespace: entity def: "A deoxyribonucleic acid molecule synthesises by reverse transcriptase from an RNA template." [EDAM:EBI "EMBRACE definition"] xref: SO:0000756 ! relationship: has_attribute EDAM:0001212 ! DNA sequence ! relationship: has_attribute EDAM:0001464 ! DNA structure is_obsolete: true [Term] id: EDAM:0000031 name: Transposon namespace: entity def: "A DNA sequence that can undergo transposition or move to different positions in the genome of a single cell." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000032 name: Plasmid namespace: entity def: "A DNA molecule existing outside a chromosome and capable of independent replication." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000033 name: Retrotransposon namespace: entity def: "A DNA element that can amplify itself in a genome, by copying itself to RNA then back to DNA using a reverse transcriptase." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000034 name: Insertion sequence namespace: entity def: "A DNA sequence that is smaller than most other transposable elements and which codes only for proteins involved in transposition." [EDAM:EBI "EMBRACE definition"] synonym: "Insertion sequence element" EXACT [] synonym: "IS element" EXACT [] is_obsolete: true [Term] id: EDAM:0000035 name: tRNA namespace: entity def: "Transfer RNA (tRNA) is a small ribonucleic acid molecule that binds a specific amino acid." [EDAM:EBI "EMBRACE definition"] comment: The amino acid is transferred to a nascent polypeptide chain during protein synthesis at the ribosome. synonym: "Transfer RNA" EXACT [] ! relationship: has_attribute EDAM:0001213 ! RNA sequence is_obsolete: true [Term] id: EDAM:0000036 name: Peptide namespace: entity def: "An organic polymer of alpha amino acid residues in a short unbranched chain. Peptides typically have fewer than 50 subunits and can be made synthetically." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0001208 ! Protein sequence is_obsolete: true [Term] id: EDAM:0000037 name: Protein namespace: entity def: "One or more polypeptide chains in a stable conformation." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] id: EDAM:0000038 name: Uncomplexed protein namespace: entity def: "A single polypeptide chain in a stable conformation." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] id: EDAM:0000039 name: Enzyme namespace: entity def: "Enzyme." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] id: EDAM:0000040 name: Transmembrane protein namespace: entity def: "A transmembrane protein molecule." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] id: EDAM:0000041 name: Transcription factor namespace: entity def: "A protein that, upon binding a cis-regulatory DNA element, regulates (enhances or represses) transcription." [EDAM:EBI "EMBRACE definition"] synonym: "Sequence-specific DNA binding factor" EXACT [] ! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] id: EDAM:0000042 name: Restriction enzyme namespace: entity def: "An enzyme that cuts DNA at specific nucleotide subsequence(s) (restriction sites)." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] id: EDAM:0000043 name: RNA/DNA hybrid namespace: entity def: "A hybrid (complementary base-paired) molecule of DNA and RNA." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000044 name: Protein-protein complex namespace: entity def: "A protein comprising two or more polypeptide chain subunits in a stable association." [EDAM:EBI "EMBRACE definition"] ! synonym: "Protein complex" EXACT [] ! relationship: has_attribute EDAM:0001460 ! Protein structure is_obsolete: true [Term] id: EDAM:0000045 name: Protein-ligand complex namespace: entity def: "A protein-ligand (small molecule) complex." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000046 name: Protein-nucleic acid complex namespace: entity def: "A protein-DNA/RNA complex." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000047 name: Protein complex namespace: entity def: "A protein comprising two or more polypeptide chain subunits in a stable association." [EDAM:EBI "EMBRACE definition"] is_obsolete: true ! consider: EDAM:0000044 ! Protein-protein complex [Term] id: EDAM:0001851 name: Chromosome namespace: entity def: "A nucleic acid molecule which controls its own replication via the action of proteins at replication start sites." [EDAM:EBI "EMBRACE definition"] xref: SO:0000340 is_obsolete: true [Term] id: EDAM:0001749 name: Atom group namespace: entity def: "A group of two or more atoms from a molecular structure." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000048 name: Nucleic acid feature namespace: entity def: "A feature of a nucleic acid molecule that can be mapped to a specific region(s) in its molecular sequence." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000049 name: Protein feature namespace: entity def: "A feature of a protein molecule that can be mapped to a specific region(s) in its molecular sequence." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0001854 name: Binding site namespace: entity def: "A region of a molecular surface involved in interactions with other molecules." [EDAM:EBI "EMBRACE definition"] xref: SO:0000409 is_obsolete: true [Term] id: EDAM:0001750 name: Atom pair namespace: entity def: "A pair (exactly 2) atoms from a molecular structure." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000050 name: Codon namespace: entity def: "Three nucleotides encoding typically a single, specific amino acid." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000051 name: Gene namespace: entity def: "The hereditary unit, corresponding to the genomic sequence(s) encoding one or more functional products." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000052 name: Operon namespace: entity def: "A functional unit of DNA including an operator, a common promoter, and one or more structural genes under common control." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000053 name: Protein-coding region namespace: entity def: "The portion of a gene's DNA or RNA that is composed of exons and encodes a protein product." [EDAM:EBI "EMBRACE definition"] synonym: "Coding region" EXACT [] is_obsolete: true [Term] id: EDAM:0000054 name: Transcription regulatory element namespace: entity def: "A region of DNA involved in transcription regulation." [EDAM:EBI "EMBRACE definition"] synonym: "Gene regulatory element" EXACT [] is_obsolete: true [Term] id: EDAM:0000055 name: Restriction site namespace: entity def: "A restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000056 name: Scaffold / matrix attachment site namespace: entity def: "Regions of DNA sequence in eukaryotic chromosomes where the nuclear matrix attaches." [EDAM:EBI "EMBRACE definition"] synonym: "Matrix attachment region" EXACT [] is_obsolete: true [Term] id: EDAM:0000057 name: Splice site namespace: entity def: "A site in a transcribed RNA sequence at which RNA splicing occurs (introns are removed and exons are joined)." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0001909 name: Allele namespace: entity def: "An alternative form of a gene that can exist at a single locus." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000058 name: Gene cis-regulatory element namespace: entity def: "A DNA element that can bind a transcription factor to regulate (enhance or repress) the expression (transcription) of genes located on the same strand." [EDAM:EBI "EMBRACE definition"] synonym: "Cis-element" EXACT [] is_obsolete: true [Term] id: EDAM:0000059 name: Gene trans-regulatory element namespace: entity def: "A DNA element that encodes a transcription factor which regulates gene(s) distant from the gene from which they were transcribed." [EDAM:EBI "EMBRACE definition"] synonym: "Trans-element" EXACT [] is_obsolete: true [Term] id: EDAM:0000060 name: Promoter namespace: entity def: "The DNA element where transcription is initiated." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000061 name: Enhancer namespace: entity def: "An element that can bind a transcription factor to enhance transcription." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000062 name: Silencer namespace: entity def: "An element that can bind a transcription factor to repress transcription." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000063 name: Response element namespace: entity def: "An element within or near the promoter that can bind certain transcription factors, for example a hormone receptor complex." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000064 name: Protein residue namespace: entity def: "A single amino acid position in a protein, bound to one (C or N-terminal positions) or two other residues by covalent (peptide) bonds." [EDAM:EBI "EMBRACE definition"] synonym: "Residue" EXACT [] is_obsolete: true [Term] id: EDAM:0001751 name: Protein residue group namespace: entity def: "A group of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue group" EXACT [] is_obsolete: true [Term] id: EDAM:0000065 name: Protein domain namespace: entity def: "A region of a protein (typically a region of a single polypeptide chain) forming a distinct, compact conformation. Domains show some independence in terms of evolution, folding, structure or function and (typically) reoccur in other proteins." [EDAM:EBI "EMBRACE definition"] ! relationship: has_attribute EDAM:0001468 ! Protein domain is_obsolete: true [Term] id: EDAM:0001752 name: Protein residue pair namespace: entity def: "A pair of amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue pair" EXACT [] is_obsolete: true [Term] id: EDAM:0001753 name: Protein residue group (continuous) namespace: entity def: "A group of continuous (adjacent) amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] synonym: "Residue group (continuous)" EXACT [] is_obsolete: true [Term] id: EDAM:0001754 name: Protein residue group (discontinuous) namespace: entity def: "A group of discontinuous amino acid positions in a protein." [EDAM:EBI "EMBRACE definition"] comment: One or more residues in the group are discontinuous (non-adjacent). synonym: "Residue group (discontinuous)" EXACT [] is_obsolete: true [Term] id: EDAM:0000066 name: Genome namespace: entity def: "An organisms total complement of DNA or RNA (some viruses) and therefore its hereditary information. A genome includes genes and non-coding regions." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000067 name: Proteome namespace: entity def: "An organisms total complement of expressed proteins. More specifically, those proteins expressed in a cell, tissue or the whole organism under defined conditions at a specific time." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000068 name: Nucleosome namespace: entity def: "The repeating structural unit of eukaryotic chromatin, which is folded successively into chromosomes." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000069 name: Taxonomic rank namespace: entity def: "One of the major taxonomic ranks of life." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000070 name: Kingdom namespace: entity def: "A kingdom or organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0001871 name: Genus namespace: entity def: "A genus of organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000071 name: Species namespace: entity def: "A species or organisms (one of the major taxonomic ranks of life)." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000072 name: Strain namespace: entity def: "A strain or prokaryotic organisms." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000073 name: Metabolic pathway namespace: entity def: "A group of related chemical (enzyme catalysed) reactions occurring within a cell." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000074 name: Mutation namespace: entity def: "A change to the nucleotide sequence of an organism's genome." [EDAM:EBI "EMBRACE definition"] is_obsolete: true [Term] id: EDAM:0000075 name: Single-nucleotide polymorphism namespace: entity def: "A single nucleotide variation in the genome of members of a species, or between paired chromosomes of an individual." [EDAM:EBI "EMBRACE definition"] is_obsolete: true ! ! Topic ! [Term] id: EDAM:0000076 name: Undefined namespace: topic alt_id: EDAM:0000580 def: "Debugging." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true [Term] id: EDAM:0002807 name: Tool topic namespace: topic def: "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000003 ! Topic [Term] id: EDAM:0002809 name: Study topic namespace: topic def: "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000003 ! Topic [Term] id: EDAM:0003071 name: Biological data resources namespace: topic alt_id: EDAM:0002808 def: "A topic concerning primarily a specific type of bioinformatics data, typically the broad category of content of a digital archives of biological data, including databanks, databases proper, web portals and other data resources." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Biological databases" EXACT [] synonym: "Biological data resource" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0000077 name: Nucleic acid analysis namespace: topic alt_id: EDAM:0003046 def: "Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Nucleic acids" EXACT [] synonym: "Nucleic acid informatics" EXACT [] synonym: "Nucleic acid bioinformatics" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002839 name: Molecules namespace: topic def: "Resources concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true [Term] id: EDAM:0000078 name: Protein analysis namespace: topic alt_id: EDAM:0000586 def: "Processing and analysis of protein data, typically molecular sequence and structural data." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Protein informatics" EXACT [] synonym: "Protein bioinformatics" EXACT [] synonym: "Proteins" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002225 name: Protein databases namespace: topic def: "Data resources concerning proteins." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Protein data resources" EXACT [] is_a: EDAM:0003071 ! Biological data resources is_a: EDAM:0000078 ! Protein analysis [Term] id: EDAM:0000079 name: Metabolites namespace: topic def: "Informatics resources (typically structural data) concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." [EDAM:EBI "EMBRACE definition"] comment: This concept excludes macromolecules such as proteins and nucleic acids. subset: topic is_a: EDAM:0000154 ! Small molecules [Term] id: EDAM:0000080 name: Sequence analysis namespace: topic alt_id: EDAM:0002228 alt_id: EDAM:0000584 def: "Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Sequences" EXACT [] xref: BioCatalogue:Sequence Analysis is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0003041 name: Sequence databases namespace: topic def: "Data resources concerning molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Sequence data" EXACT [] synonym: "Sequence data resource" EXACT [] synonym: "Sequence data resources" EXACT [] is_a: EDAM:0003071 ! Biological data resources is_a: EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0000081 name: Structure analysis namespace: topic alt_id: EDAM:0000693 alt_id: EDAM:0002827 alt_id: EDAM:0000585 def: "Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids." [EDAM:EBI "EMBRACE definition"] comment: This includes related concepts such as structural properties, alignments and structural motifs. subset: topic synonym: "Structural bioinformatics" EXACT [] synonym: "Computation structural biology" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0003038 name: Structure databases namespace: topic alt_id: EDAM:0003059 def: "Data resources concerning molecular secondary or tertiary (3D) structural information, typically of proteins and nucleic acids." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Structure data resources" EXACT [] is_a: EDAM:0003071 ! Biological data resources is_a: EDAM:0000081 ! Structure analysis [Term] id: EDAM:0000082 name: Structure prediction namespace: topic alt_id: EDAM:0000171 def: "Resources concerning the prediction of molecular (secondary or tertiary) structure." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000081 ! Structure analysis [Term] id: EDAM:0000083 name: Alignment namespace: topic def: "Resources concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000182 ! Sequence alignment consider: EDAM:0000183 ! Structure alignment consider: EDAM:0000184 ! Threading [Term] id: EDAM:0000084 alt_id: EDAM:0000192 alt_id: EDAM:0000193 name: Phylogenetics namespace: topic alt_id: EDAM:0000636 def: "Resources concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc." [EDAM:EBI "EMBRACE definition"] comment: This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data. subset: topic xref: BioCatalogue:Phylogeny xref: BioCatalogue:Statistical Robustness synonym: "Phylogenetic simulation" EXACT [] synonym: "Phylogenetic clocks, dating and stratigraphy" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0000200 alt_id: EDAM:0000206 name: Microarrays namespace: topic def: "Informatics resources concerning microarrays, for example, to process microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Microarrays synonym: "DNA microarrays" EXACT [] is_a: EDAM:0000607 ! Laboratory resources [Term] id: EDAM:0000121 name: Proteomics namespace: topic alt_id: EDAM:0000764 def: "Informatics resources concerning the study of whole proteomes of organisms." [EDAM:EBI "EMBRACE definition"] comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues). subset: topic synonym: "Protein expression" EXACT [] xref: BioCatalogue:Proteomics is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0000085 name: Functional genomics namespace: topic def: "Informatics resources concerning the study of gene or protein functions and their interactions." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000622 ! Genomics [Term] id: EDAM:0000122 name: Structural genomics namespace: topic def: "Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Structural Genomics is_a: EDAM:0002226 ! Structure determination is_a: EDAM:0000622 ! Genomics [Term] id: EDAM:0003061 name: Documentation and help namespace: topic def: "Resources concerning documentation and getting help." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003068 ! Literature and reference [Term] id: EDAM:0003047 name: Molecular biology reference namespace: topic def: "Resources concerning general molecular biology information extracted from the literature." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue: Document Discovery xref: BioCatalogue: Literature retrieval is_a: EDAM:0000606 ! Literature data resources [Term] id: EDAM:0000089 name: Ontologies namespace: topic alt_id: EDAM:0002255 def: "Resources concerning ontologies of biological or bioinformatics concepts (terms and relations), controlled vocabularies, structured glossary or other related resource." [EDAM:EBI "EMBRACE definition"] comment: This includes the annotation of entities (typically biological database entries) with terms from a controlled vocabulary. subset: topic synonym: "Ontology" EXACT [] xref: BioCatalogue:Ontology xref: BioCatalogue:Ontology Lookup is_a: EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0000090 alt_id: EDAM:0000155 alt_id: EDAM:0002274 alt_id: EDAM:0000165 name: Data search and retrieval namespace: topic def: "Resources 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"] comment: This includes, for example, search, query and retrieval of molecular sequences and associated data. subset: topic synonym: "Data retrieval" EXACT [] xref: BioCatalogue:Sequence Retrieval xref: BioCatalogue:Data Retrieval xref: BioCatalogue:Identifier Retrieval xref: BioCatalogue:Image Retrieval xref: BioCatalogue:Structure Retrieval is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0000091 name: Data handling namespace: topic alt_id: EDAM:0002282 def: "Resources for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Data types, processing and visualisation" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0000092 name: Data visualisation namespace: topic def: "Resources for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Data rendering and visualisation" EXACT [] synonym: "Data rendering" EXACT [] synonym: "Data plotting" EXACT [] is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0002258 name: Chemoinformatics namespace: topic def: "Informatics resources for the application of information technology to chemistry." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Cheminformatics" EXACT [] synonym: "Chemical informatics" EXACT [] synonym: "Computational chemistry" EXACT [] xref: BioCatalogue:Chemoinformatics is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002269 name: Biostatistics namespace: topic def: "Informatics resources for the application of statistical methods to biological problems." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Biometry" EXACT [] synonym: "Biometrics" EXACT [] xref: BioCatalogue:Biostatistics is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0003077 alt_id: EDAM:0001779 name: Data acquisition and deposition namespace: topic def: "Resources concerning the acquisition and deposition of biological data." [EDAM:EBI "EMBRACE definition"] synonym: "Database submission" EXACT [] subset: topic is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0000094 name: Nucleic acid thermodynamics namespace: topic alt_id: EDAM:0000614 alt_id: EDAM:0000104 def: "Informatics resources concerning the study of the thermodynamic properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"] comment: This includes the study of thermal and conformational properties including DNA or DNA/RNA denaturation (melting). subset: topic synonym: "Nucleic acid physicochemistry" EXACT [] synonym: "Nucleic acid properties" EXACT [] synonym: "Nucleic acid denaturation" EXACT [] synonym: "DNA melting" EXACT [] is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0000097 name: Nucleic acid structure analysis namespace: topic alt_id: EDAM:0000699 alt_id: EDAM:0000106 def: "The processing and analysis of nucleic acid (secondary or tertiary) structural data." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000081 ! Structure analysis is_a: EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0003039 name: Nucleic acid structure namespace: topic alt_id: EDAM:0002833 def: "Data resources concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003038 ! Structure databases [Term] id: EDAM:0000099 name: RNA namespace: topic alt_id: EDAM:0000653 def: "Informatics resources concerning RNA sequences and structures." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003042 ! Nucleic acid sequences [Term] id: EDAM:0000100 name: Nucleic acid restriction namespace: topic def: "Informatics resources for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000640 ! Nucleic acid sequence analysis is_a: EDAM:0000821 ! Enzymes and reactions [Term] id: EDAM:0000107 name: Codon usage analysis namespace: topic def: "Resources concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000110 ! Transcription [Term] id: EDAM:0000109 name: Gene finding namespace: topic def: "Resources that aim to identify, predict, model or analyse genes or gene structure in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. subset: topic synonym: "Gene prediction" EXACT [] xref: BioCatalogue:Gene Prediction is_a: EDAM:0003073 ! Nucleic acid feature detection [Term] id: EDAM:0000110 name: Transcription namespace: topic def: "Informatics resources concerning the transcription of DNA into mRNA." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Transcription Factors is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0000108 name: Translation namespace: topic def: "Informatics resources concerning the translation of mRNA into protein." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0000111 name: Promoters namespace: topic def: "Informatics resources concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins)." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Promoter Prediction is_obsolete: true consider: EDAM:0000749 ! Transcription factors and regulatory sites [Term] id: EDAM:0000112 name: Nucleic acid folding namespace: topic def: "Informatics resources concerning the folding (in 3D space) of nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0000114 name: Gene structure and RNA splicing namespace: topic alt_id: EDAM:0000750 def: "Informatics resources concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [EDAM:EBI "EMBRACE definition"] comment: This includes splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. subset: topic synonym: "RNA splicing" EXACT [] synonym: "Gene structure" EXACT [] is_a: EDAM:0003062 ! Genetic organisation is_a: EDAM:0000747 ! Nucleic acid sites and features [Term] id: EDAM:0000123 name: Protein properties namespace: topic alt_id: EDAM:0000615 def: "Informatics resources for the study of the physical and biochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Protein physicochemistry" EXACT [] is_a: EDAM:0000639 ! Protein sequence analysis [Term] id: EDAM:0001775 name: Protein function analysis namespace: topic alt_id: EDAM:0003057 def: "Informatics resources for the study of protein function." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000078 ! Protein analysis [Term] id: EDAM:0000128 name: Protein interactions namespace: topic alt_id: EDAM:0000587 def: "Informatics resources concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Interaction is_a: EDAM:0001775 ! Protein function analysis is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000130 name: Protein folding and stability namespace: topic def: "Informatics resources concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002814 ! Protein structure analysis [Term] id: EDAM:0002232 name: Lipoproteins namespace: topic def: "Informatics resources concerning lipoproteins (protein-lipid assemblies)." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000635 ! Specific protein resources [Term] id: EDAM:0000137 name: Protein hydropathy namespace: topic def: "Informatics resources for the study of the hydrophobic, hydrophilic and charge properties of a protein." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000123 ! Protein properties [Term] id: EDAM:0000140 name: Protein targeting and localization namespace: topic alt_id: EDAM:0000588 def: "Informatics resources for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002276 ! Protein function prediction is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000143 name: Protein structure comparison namespace: topic def: "Resources 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. subset: topic is_obsolete: true consider: EDAM:0000698 ! Protein tertiary structure consider: EDAM:0001770 ! Structure comparison [Term] id: EDAM:0002280 name: Nucleic acid structure comparison namespace: topic def: "Resources 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. subset: topic is_obsolete: true consider: EDAM:0000097 ! Nucleic acid structure analysis consider: EDAM:0001770 ! Structure comparison [Term] id: EDAM:0000144 name: Protein residue interaction analysis namespace: topic def: "The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Protein residue interactions" EXACT [] is_a: EDAM:0002814 ! Protein structure analysis [Term] id: EDAM:0002276 name: Protein function prediction namespace: topic def: "Resources concerning the prediction of functional properties of a protein." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Function Prediction is_a: EDAM:0001775 ! Protein function analysis [Term] id: EDAM:0000147 name: Protein-protein interactions namespace: topic alt_id: EDAM:0000719 def: "Informatics resources concerning protein-protein interactions, protein complexes, protein functional coupling etc." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000128 ! Protein interactions [Term] id: EDAM:0000148 name: Protein-ligand interactions namespace: topic alt_id: EDAM:0000717 def: "Informatics resources concerning protein-ligand (small molecule) interactions." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Ligand Interaction is_a: EDAM:0000128 ! Protein interactions [Term] id: EDAM:0000149 name: Protein-nucleic acid interactions namespace: topic alt_id: EDAM:0000718 def: "Informatics resources concerning protein-DNA/RNA interactions." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000128 ! Protein interactions [Term] id: EDAM:0000150 name: Protein design namespace: topic def: "Informatics resources concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000172 ! Protein structure prediction [Term] id: EDAM:0000151 name: G protein-coupled receptors (GPCR) namespace: topic def: "Resources concerning G-protein coupled receptors (GPCRs)." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000820 ! Membrane proteins [Term] id: EDAM:0002278 name: Transmembrane protein prediction namespace: topic def: "Predict transmembrane domains and topology in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000820 ! Membrane proteins consider: EDAM:0000178 ! Protein secondary structure prediction [Term] id: EDAM:0000152 name: Carbohydrates namespace: topic alt_id: EDAM:0000695 def: "Informatics resources concerning carbohydrates, typically including structural information." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003038 ! Structure databases [Term] id: EDAM:0000153 name: Lipids namespace: topic alt_id: EDAM:0002624 def: "Informatics resources concerning lipids and their structures." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003038 ! Structure databases [Term] id: EDAM:0000154 name: Small molecules namespace: topic alt_id: EDAM:0000696 def: "Informatics resources concerning small molecules of biological significance, typically including structural information." [EDAM:EBI "EMBRACE definition"] comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. subset: topic is_a: EDAM:0003038 ! Structure databases [Term] id: EDAM:0000156 name: Sequence editing namespace: topic def: "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000080 ! Sequence analysis consider: EDAM:0000091 ! Data handling [Term] id: EDAM:0000157 name: Sequence composition analysis namespace: topic def: "Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0000158 alt_id: EDAM:0000161 alt_id: EDAM:0000162 name: Sequence motifs namespace: topic def: "Resources concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Motifs" EXACT [] is_a: EDAM:0000594 ! Sequence classification [Term] id: EDAM:0000188 name: Sequence profiles and HMMs namespace: topic alt_id: EDAM:0000744 alt_id: EDAM:0000746 alt_id: EDAM:0001763 def: "Resources concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. subset: topic is_a: EDAM:0000594 ! Sequence classification [Term] id: EDAM:0000159 alt_id: EDAM:0002260 alt_id: EDAM:0002261 name: Sequence comparison namespace: topic def: "Resources 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. subset: topic xref: BioCatalogue:Protein Sequence Similarity xref: BioCatalogue:Nucleotide Sequence Similarity is_a: EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0000160 name: Sequence sites and features namespace: topic alt_id: EDAM:0000600 def: "Data resources concerning the positional features, such as functional and other key sites, in molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003041 ! Sequence databases [Term] id: EDAM:0003072 name: Sequence feature detection namespace: topic def: "Resources concerning the detection of the positional features, such as functional and other key sites, in molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0000163 name: Sequence database search namespace: topic def: "Search 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. subset: topic is_obsolete: true consider: EDAM:0000159 ! Sequence comparison [Term] id: EDAM:0003052 name: Sequence clusters and classification namespace: topic def: "Data resources concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity." [EDAM:EBI "EMBRACE definition"] comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. subset: topic synonym: "Sequence clusters" EXACT [] synonym: "Sequence families" EXACT [] is_a: EDAM:0003041 ! Sequence databases [Term] id: EDAM:0000164 name: Sequence clustering namespace: topic def: "Resources concerning the comparison and grouping together of molecular sequences on the basis of their similarities." [EDAM:EBI "EMBRACE definition"] comment: This includes systems that generate, process and analyse sequence clusters. subset: topic is_a: EDAM:0000159 ! Sequence comparison [Term] id: EDAM:0000594 name: Sequence classification namespace: topic def: "Resources concerning the classification of molecular sequences based on some measure of their similarity." [EDAM:EBI "EMBRACE definition"] comment: Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. subset: topic is_a: EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0000166 name: Protein structural motifs and surfaces namespace: topic alt_id: EDAM:0000139 alt_id: EDAM:0000170 alt_id: EDAM:0000146 alt_id: EDAM:0000589 def: "Resources concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"] comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. subset: topic synonym: "Protein structural features" EXACT [] synonym: "Protein surfaces" EXACT [] synonym: "Protein structural motifs" EXACT [] synonym: "Structural motifs" EXACT [] is_a: EDAM:0000698 ! Protein tertiary structure [Term] id: EDAM:0000167 name: Structural (3D) profiles namespace: topic alt_id: EDAM:0000599 def: "The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Structural profiles" EXACT [] is_a: EDAM:0001770 ! Structure comparison [Term] id: EDAM:0001770 alt_id: EDAM:0000168 alt_id: EDAM:0000169 name: Structure comparison namespace: topic def: "Resources concerning the comparison of two or more molecular structures." [EDAM:EBI "EMBRACE definition"] comment: This might involve comparison of secondary or tertiary (3D) structural information. subset: topic is_a: EDAM:0000081 ! Structure analysis [Term] id: EDAM:0002844 name: Structural clustering namespace: topic def: "Resources concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Structure classification" EXACT [] is_a: EDAM:0001770 ! Structure comparison [Term] id: EDAM:0002271 name: Structure database search 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. subset: topic is_obsolete: true consider: EDAM:0001770 ! Structure comparison [Term] id: EDAM:0000172 name: Protein structure prediction namespace: topic def: "Resources concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Structure Prediction is_a: EDAM:0000082 ! Structure prediction is_a: EDAM:0002814 ! Protein structure analysis [Term] id: EDAM:0000173 name: Nucleic acid structure prediction namespace: topic alt_id: EDAM:0000181 def: "Resources concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Nucleic acid folding" EXACT [] synonym: "RNA/DNA structure prediction" EXACT [] xref: BioCatalogue:Nucleotide Structure Prediction xref: BioCatalogue:Nucleotide Secondary Structure xref: BioCatalogue:Nucleotide Tertiary Structure is_a: EDAM:0000082 ! Structure prediction is_a: EDAM:0000097 ! Nucleic acid structure analysis [Term] id: EDAM:0002953 name: Nucleic acid design namespace: topic def: "Resources for the design of nucleic acid sequences with specific conformations." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000174 name: Ab initio structure prediction namespace: topic def: "Resources for the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "de novo protein structure prediction" EXACT [] is_a: EDAM:0000082 ! Structure prediction [Term] id: EDAM:0002275 name: Molecular modelling namespace: topic def: "Resources for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. " [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000082 ! Structure prediction is_a: EDAM:0000172 ! Protein structure prediction [Term] id: EDAM:0000175 name: Homology modelling namespace: topic def: "Resources for the modelling of the three-dimensional structure of a protein using known sequence and structural data." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Comparative modelling" EXACT [] is_a: EDAM:0002275 ! Molecular modelling [Term] id: EDAM:0000176 alt_id: EDAM:0000145 name: Molecular dynamics namespace: topic def: "Resources concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [EDAM:EBI "EMBRACE definition"] comment: This includes resources concerning flexibility and motion in protein and other molecular structures. subset: topic synonym: "Molecular motions" EXACT [] synonym: "Molecular flexibility" EXACT [] is_a: EDAM:0002275 ! Molecular modelling [Term] id: EDAM:0000177 name: Molecular docking namespace: topic def: "Resources for modelling the structure of proteins in complex with small molecules or other macromolecules." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002275 ! Molecular modelling [Term] id: EDAM:0000178 name: Protein secondary structure prediction namespace: topic def: "Resources concerning the prediction of secondary or supersecondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Secondary Structure is_a: EDAM:0000172 ! Protein structure prediction [Term] id: EDAM:0000179 name: Protein tertiary structure prediction namespace: topic def: "Resources concerning the prediction of tertiary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Tertiary Structure is_a: EDAM:0000172 ! Protein structure prediction [Term] id: EDAM:0000180 name: Protein fold recognition namespace: topic def: "Resources concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000172 ! Protein structure prediction [Term] id: EDAM:0000182 name: Sequence alignment namespace: topic alt_id: EDAM:0002283 alt_id: EDAM:0000185 alt_id: EDAM:0000186 alt_id: EDAM:0000187 alt_id: EDAM:0000596 alt_id: EDAM:0000189 def: "Resources concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] comment: This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. subset: topic xref: BioCatalogue:Protein Sequence Alignment xref: BioCatalogue:Nucleotide Sequence Alignment xref: BioCatalogue:Protein Pairwise Alignment xref: BioCatalogue:Nucleotide Pairwise Alignment xref: BioCatalogue:Protein Multiple Alignment xref: BioCatalogue:Nucleotide Multiple Alignment is_a: EDAM:0000159 ! Sequence comparison is_a: EDAM:0003041 ! Sequence databases [Term] id: EDAM:0000183 alt_id: EDAM:0002272 alt_id: EDAM:0002273 name: Structure alignment namespace: topic alt_id: EDAM:0000597 alt_id: EDAM:0000190 def: "Resources concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] comment: This includes the generation, storage, analysis, rendering etc. of structure alignments. subset: topic synonym: "Structure alignment generation" EXACT [] is_a: EDAM:0001770 ! Structure comparison is_a: EDAM:0003038 ! Structure databases [Term] id: EDAM:0000184 name: Threading namespace: topic def: "Resources concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Sequence-structure alignment" EXACT [] is_a: EDAM:0000180 ! Protein fold recognition [Term] id: EDAM:0000191 name: Phylogeny reconstruction namespace: topic def: "Resources concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] comment: Currently too specific for the topic branch (but might be unobsoleted). subset: topic xref: BioCatalogue:Tree Inference xref: BioCatalogue:Evolutionary Distance Measurements is_a: EDAM:0000084 ! Phylogenetics [Term] id: EDAM:0002257 name: Phylogeny visualisation namespace: topic def: "Visualise a phylogeny, for example, render a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Tree Display is_obsolete: true consider: EDAM:0000084 ! Phylogenetics [Term] id: EDAM:0000194 name: Phylogenomics namespace: topic def: "Resources concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000084 ! Phylogenetics is_a: EDAM:0000622 ! Genomics [Term] id: EDAM:0002842 name: High-throughput sequencing namespace: topic def: "Informatics resources concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Next-generation sequencing" EXACT [] is_obsolete: true consider: EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0000195 name: Virtual PCR namespace: topic def: "Informatics resources concerning simulated polymerase chain reaction (PCR)." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "PCR" EXACT [] synonym: "Polymerase chain reaction" EXACT [] is_obsolete: true consider: EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000196 name: Sequence assembly namespace: topic def: "Resources concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0000133 name: Two-dimensional gel electrophoresis namespace: topic alt_id: EDAM:0000765 def: "Resources concerning two-dimensional gel electrophoresis image and related data." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000121 ! Proteomics [Term] id: EDAM:0000134 name: Mass spectrometry namespace: topic alt_id: EDAM:0000766 def: "Resources concerning mass spectrometry and related data." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000121 ! Proteomics [Term] id: EDAM:0000135 name: Protein microarrays namespace: topic def: "Resources concerning protein microarray data." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000121 ! Proteomics consider: EDAM:0000200 ! Microarrays [Term] id: EDAM:0000102 name: Sequencing and mapping namespace: topic def: "Informatics resources concerning the determination and mapping of complete (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0000197 name: Gene expression resources namespace: topic def: "Data resources concerning primarily raw or processed gene expression (typically microarray) data." [EDAM:EBI "EMBRACE definition"] comment: This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein. subset: topic is_a: EDAM:0002816 ! Gene resources is_a: EDAM:0000203 ! Transcriptomics [Term] id: EDAM:0003062 name: Genetic organisation namespace: topic def: "Data resources concerning the structural and functional organisation of genes and other genetic elements." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002816 ! Gene resources [Term] id: EDAM:0000204 name: Gene regulation resources namespace: topic alt_id: EDAM:0003049 alt_id: EDAM:0000631 def: "Data resources concerning primarily the regulation of gene expression." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002816 ! Gene resources [Term] id: EDAM:0000199 name: Genetic variation namespace: topic alt_id: EDAM:0000626 def: "Resources concerning DNA sequence variation (mutation and polymorphism) data." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Mutation and polymorphism" EXACT [] synonym: "DNA variation" EXACT [] is_a: EDAM:0000625 ! Genotype and phenotype resources is_a: EDAM:0003041 ! Sequence databases is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0000202 name: Pharmacoinformatics namespace: topic def: "Informatics resources for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Computational pharmacology" EXACT [] is_a: EDAM:0002258 ! Chemoinformatics [Term] id: EDAM:0000203 name: Transcriptomics namespace: topic def: "Informatics resources concerning the analysis of mRNA expression levels, by identifying, quantifying or comparing mRNA transcripts or interpreting (in functional terms) gene expression data." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Gene expression profiling" EXACT [] synonym: "Expression profiling" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002277 name: SNPs namespace: topic def: "Resources concerning single nucleotide polymorphisms (SNP) and associated data." [EDAM:EBI "EMBRACE definition"] comment: A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. subset: topic is_a: EDAM:0000199 ! Genetic variation [Term] id: EDAM:0000208 name: Pharmacogenomics namespace: topic def: "Informatics resources concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Pharmacogenetics" EXACT [] is_a: EDAM:0000202 ! Pharmacoinformatics is_a: EDAM:0000622 ! Genomics [Term] id: EDAM:0000209 name: Drug design namespace: topic def: "Informatics resources concerning the design of drugs or potential drug compounds." [EDAM:EBI "EMBRACE definition"] comment: This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. subset: topic is_a: EDAM:0000202 ! Pharmacoinformatics [Term] id: EDAM:0000210 name: Fish namespace: topic def: "Informatics resources concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a fish, a group of fish or all fish. subset: topic is_a: EDAM:0002820 ! Vertebrates [Term] id: EDAM:0000211 name: Flies namespace: topic def: "Informatics resources concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a fly, a group of flies or all flies. subset: topic synonym: "Fly" EXACT [] is_a: EDAM:0002819 ! Invertebrates [Term] id: EDAM:0003048 name: Mammals namespace: topic def: "Informatics resources concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002820 ! Vertebrates [Term] id: EDAM:0000213 name: Mice or rats namespace: topic def: "Informatics resources concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a group of mice / rats or all mice / rats. subset: topic synonym: "Mouse or rat" EXACT [] is_a: EDAM:0003048 ! Mammals [Term] id: EDAM:0000215 name: Worms namespace: topic def: "Informatics resources concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a worm, a group of worms or all worms. subset: topic synonym: "Worm" EXACT [] is_a: EDAM:0002819 ! Invertebrates [Term] id: EDAM:0000217 name: Literature analysis namespace: topic alt_id: EDAM:0000088 alt_id: EDAM:0003058 def: "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue: Document Discovery xref: BioCatalogue: Literature retrieval synonym: "Literature search and analysis" EXACT [] synonym: "Literature sources" EXACT [] is_a: EDAM:0003068 ! Literature and reference [Term] id: EDAM:0000606 name: Literature data resources namespace: topic def: "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003068 ! Literature and reference is_a: EDAM:0003071 ! Biological data resources [Term] id: EDAM:0003068 name: Literature and reference namespace: topic def: "Informatics resources concerning the scientific literature, reference information and documentation." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0000218 name: Text mining namespace: topic def: "Resources concerning the analysis of the biomedical and informatics literature." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Text data mining" EXACT [] xref: BioCatalogue:Text Mining xref: BioCatalogue:Document Similarity xref: BioCatalogue:Document Clustering xref: BioCatalogue:Named Entity Recognition is_a: EDAM:0000217 ! Literature analysis [Term] id: EDAM:0000219 alt_id: EDAM:0002256 name: Annotation namespace: topic def: "Resources for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Ontology annotation" EXACT [] xref: BioCatalogue:Genome Annotation xref: BioCatalogue:Ontology Annotation is_a: EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0000221 name: Sequence annotation namespace: topic def: "Annotate a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000219 ! Annotation [Term] id: EDAM:0000222 name: Genome annotation namespace: topic def: "Annotate a genome." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Genome Annotation is_obsolete: true consider: EDAM:0000219 ! Annotation consider: EDAM:0000621 ! Genome, proteome and model organisms [Term] id: EDAM:0002230 name: Classification namespace: topic def: "Resources that help to identify, group, or name things in a structured way according to some schema based on observable relationships." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0002829 name: Ontologies, nomenclature and classification namespace: topic def: "Informatics resources concerning conceptualisation, categorisation and naming, or that help to identify, group, or name things in a structured way according to some schema based on observable relationships." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002811 name: Nomenclature namespace: topic alt_id: EDAM:0000619 def: "Informatics resources concerning biological nomenclature (naming), symbols and terminology." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0002229 name: Cell biology resources namespace: topic def: "Informatics resources concerning cells, such as key genes and proteins involved in the cell cycle." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003070 ! Biological science resources [Term] id: EDAM:0003064 name: Developmental biology resources namespace: topic def: "Informatics resources concerning how organisms grow and develop." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003070 ! Biological science resources [Term] id: EDAM:0003067 name: Anatomy resources namespace: topic def: "Informatics resources concerning the structures of living organisms." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003070 ! Biological science resources [Term] id: EDAM:0003065 name: Embryology resources namespace: topic def: "Informatics resources concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003064 ! Developmental biology resources [Term] id: EDAM:0003053 name: Genetics namespace: topic alt_id: EDAM:0002227 def: "Informatics resources concerning the study of genes, genetic variation and heredity in living organisms." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Genetics data resources" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002226 name: Structure determination namespace: topic alt_id: EDAM:0000136 def: "Informatics resources concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, including the assignment or modelling of molecular structure from such data." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Structural determination" EXACT [] synonym: "Structural assignment" EXACT [] synonym: "Structure assignment" EXACT [] synonym: "Raw structural data analysis" EXACT [] is_a: EDAM:0000081 ! Structure analysis [Term] id: EDAM:0000595 name: Protein classification namespace: topic alt_id: EDAM:0000129 def: "Resources concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000078 ! Protein analysis is_a: EDAM:0002829 ! Ontologies, nomenclature and classification is_a: EDAM:0000594 ! Sequence classification [Term] id: EDAM:0000598 name: Sequence motif or profile namespace: topic def: "Resources concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [EDAM:EBI "EMBRACE definition"] comment: This includes comparison, discovery, recognition etc. of sequence motifs. subset: topic is_obsolete: true consider: EDAM:0000158 ! Sequence motifs consider: EDAM:0000188 ! Sequence profiles and HMMs [Term] id: EDAM:0000601 name: Protein modifications namespace: topic alt_id: EDAM:0000142 def: "Informatics resources concerning protein chemical modifications, e.g. post-translational modifications." [EDAM:EBI "EMBRACE definition"] comment: EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of term GO:0006464) and/or the Protein Modifications ontology (children of term MOD:00000) subset: topic xref: GO:0006464 ! protein modification process synonym: "Protein post-translation modification" EXACT [] is_a: EDAM:0000123 ! Protein properties is_a: EDAM:0002225 ! Protein databases seealso: GO:0006464 ! protein modification process seealso: MOD:00000 ! protein modification [Term] id: EDAM:0000602 name: Pathways, networks and models namespace: topic alt_id: EDAM:0000198 alt_id: EDAM:0000755 def: "Data resources concerning biological pathways, networks and other models." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Pathways xref: BioCatalogue:Pathway Retrieval is_a: EDAM:0002259 ! Systems biology is_a: EDAM:0003071 ! Biological data resources [Term] id: EDAM:0003075 name: Biological system modelling namespace: topic def: "Resources for modelling biological systems in mathematical terms." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Model Analysis xref: BioCatalogue:Model Execution is_a: EDAM:0002259 ! Systems biology [Term] id: EDAM:0003076 name: Network or pathway analysis namespace: topic def: "The processing (including construction) and analysis of biological networks and pathways." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002259 ! Systems biology [Term] id: EDAM:0002259 name: Systems biology namespace: topic def: "Informatics resources concerning the holistic modelling and analysis of biological systems and the interactions therein." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Systems Biology is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0000605 name: Informatics namespace: topic alt_id: EDAM:0002841 def: "A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000091 ! Data handling [Term] id: EDAM:0000607 name: Laboratory resources namespace: topic def: "Data resources concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003071 ! Biological data resources [Term] id: EDAM:0000608 name: Cell culture resources namespace: topic def: "Informatics resources concerning general cell culture or data on a specific cell lines." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000607 ! Laboratory resources [Term] id: EDAM:0000610 name: Ecoinformatics namespace: topic def: "Informatics resources concerning the application of information technology to the ecological and environmental sciences." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Computational ecology" EXACT [] synonym: "Ecological informatics" EXACT [] is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0003063 name: Medical informatics resources namespace: topic alt_id: EDAM:0000087 def: "Informatics resources for the application of information technology to health, disease and biomedicine." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Health and disease" EXACT [] synonym: "Healthcare informatics" EXACT [] synonym: "Health informatics" EXACT [] synonym: "Clinical informatics" EXACT [] synonym: "Biomedical informatics" EXACT [] is_a: EDAM:0000607 ! Laboratory resources [Term] id: EDAM:0003050 name: Biodiversity namespace: topic def: "Informatics resources concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Biodiversity data resource" EXACT [] synonym: "Biodiversity data resources" EXACT [] is_a: EDAM:0000610 ! Ecoinformatics [Term] id: EDAM:0002840 name: Toxicoinformatics namespace: topic def: "Informatics resources concerning the adverse effects of chemical substances on living organisms." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Computational toxicology" EXACT [] is_a: EDAM:0002258 ! Chemoinformatics [Term] id: EDAM:0002661 name: Toxins and targets namespace: topic def: "Informatics resources concerning structural and associated data for toxic chemical substances." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002840 ! Toxicoinformatics is_a: EDAM:0000154 ! Small molecules [Term] id: EDAM:0000611 name: Electron microscopy namespace: topic def: "Informatics resources concerning electron microscopy data." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0002226 ! Structure determination [Term] id: EDAM:0002828 name: X-ray crystallography namespace: topic def: "Resources concerning X-ray crystallography data." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0002226 ! Structure determination [Term] id: EDAM:0000593 name: NMR namespace: topic def: "Resources concerning raw NMR data." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0002226 ! Structure determination [Term] id: EDAM:0000612 name: Cell cycle namespace: topic alt_id: EDAM:0000609 def: "Resources concerning the cell cycle including key genes and proteins." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0002229 ! Cell biology resources [Term] id: EDAM:0000613 name: Peptides and amino acids namespace: topic alt_id: EDAM:0000604 def: "Informatics resources concerning the physicochemical, biochemical or structural properties of amino acids or peptides." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000154 ! Small molecules [Term] id: EDAM:0000616 name: Organelle genes and proteins namespace: topic def: "Informatics resources concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003078 ! Gene and protein resources [Term] id: EDAM:0000617 name: Ribosomal genes and proteins namespace: topic def: "Informatics resources concerning ribosomes, typically of ribosome-related genes and proteins." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Ribosome genes and proteins" EXACT [] is_a: EDAM:0000616 ! Organelle genes and proteins [Term] id: EDAM:0000621 name: Genome, proteome and model organisms namespace: topic alt_id: EDAM:0000086 alt_id: EDAM:0000591 alt_id: EDAM:0000643 alt_id: EDAM:0000800 alt_id: EDAM:0000795 def: "Informatics resources concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms." [EDAM:EBI "EMBRACE definition"] comment: General information on or more organisms, genomes (including molecular sequences and map, genes and annotation) and proteomes may be included. subset: topic synonym: "Genome map" EXACT [] is_a: EDAM:0000622 ! Genomics is_a: EDAM:0000121 ! Proteomics is_a: EDAM:0000625 ! Genotype and phenotype resources [Term] id: EDAM:0000622 name: Genomics namespace: topic alt_id: EDAM:0000093 alt_id: EDAM:0000794 def: "Informatics resources concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Genomics xref: BioCatalogue:Functional Genomics is_a: EDAM:0000003 ! Topic [Term] id: EDAM:0002816 name: Gene resources namespace: topic alt_id: EDAM:0000630 def: "Informatics resource (typically a database) primarily focussed on genes." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Gene database" EXACT [] synonym: "Gene resource" EXACT [] is_a: EDAM:0003071 ! Biological data resources is_a: EDAM:0003053 ! Genetics [Term] id: EDAM:0003054 name: Molecular genetics namespace: topic def: "Resources concerning the structure and function of genes at a molecular level." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0003053 ! Genetics [Term] id: EDAM:0003055 name: Quantitative genetics namespace: topic def: "Resources concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight)." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003053 ! Genetics [Term] id: EDAM:0003056 name: Population genetics namespace: topic def: "Resources concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003053 ! Genetics [Term] id: EDAM:0000623 name: Genes, gene family or system namespace: topic def: "Data resources concerning particular gene(s), gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003052 ! Sequence clusters and classification is_a: EDAM:0002816 ! Gene resources [Term] id: EDAM:0000624 name: Chromosomes namespace: topic def: "Informatics resources concerning chromosomes." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003062 ! Genetic organisation [Term] id: EDAM:0000625 name: Genotype and phenotype resources namespace: topic alt_id: EDAM:0002231 def: "Informatics resources concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002816 ! Gene resources [Term] id: EDAM:0003078 name: Gene and protein resources namespace: topic def: "Data resources concerning specific genes and their encoded proteins or a related group of such genes and proteins." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Genes and proteins resources" EXACT [] is_a: EDAM:0000635 ! Specific protein resources is_a: EDAM:0000623 ! Genes, gene family or system [Term] id: EDAM:0003070 name: Biological science resources namespace: topic alt_id: EDAM:0003066 def: "Informatics resources concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Phenotype resource" EXACT [] is_a: EDAM:0003071 ! Biological data resources [Term] id: EDAM:0000629 name: Gene expression and microarray namespace: topic def: "Resources concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000197 ! Gene expression resources consider: EDAM:0000200 ! Microarrays [Term] id: EDAM:0000634 name: Disease resources namespace: topic def: "Informatics resources concerning diseases." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000625 ! Genotype and phenotype resources [Term] id: EDAM:0002813 name: Disease genes and proteins namespace: topic alt_id: EDAM:0000819 def: "Informatics resources concerning the genes, gene variations and proteins involved in one or more specific diseases." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000634 ! Disease resources is_a: EDAM:0003078 ! Gene and protein resources [Term] id: EDAM:0000635 name: Specific protein resources namespace: topic def: "Informatics resources concerning a particular protein, protein family or other group of proteins." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Specific protein" EXACT [] is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000637 name: Taxonomy namespace: topic def: "Informatics resources concerning organism classification, identification and naming." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0000639 name: Protein sequence analysis namespace: topic alt_id: EDAM:0000125 def: "Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Sequence Analysis is_a: EDAM:0000080 ! Sequence analysis is_a: EDAM:0000078 ! Protein analysis [Term] id: EDAM:0003043 name: Protein sequences namespace: topic def: "Data resources concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Protein Sequence Analysis is_a: EDAM:0003041 ! Sequence databases is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000640 name: Nucleic acid sequence analysis namespace: topic alt_id: EDAM:0000096 def: "Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Nucleotide Sequence Analysis is_a: EDAM:0000080 ! Sequence analysis is_a: EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0003042 name: Nucleic acid sequences namespace: topic def: "Data resources concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003041 ! Sequence databases [Term] id: EDAM:0000641 name: Repeat sequences namespace: topic alt_id: EDAM:0002262 def: "Resources concerning the repetitive nature of molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Repeat sequence" EXACT [] xref: BioCatalogue:Repeats is_a: EDAM:0000157 ! Sequence composition analysis is_a: EDAM:0003041 ! Sequence databases [Term] id: EDAM:0000642 name: Low complexity sequences namespace: topic alt_id: EDAM:0002263 def: "Resources concerning the (character) complexity of molecular sequences, particularly regions of low complexity." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000157 ! Sequence composition analysis is_a: EDAM:0003041 ! Sequence databases [Term] id: EDAM:0000644 name: Proteome namespace: topic def: "Resources concerning a specific proteome including protein sequences and annotation." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0000646 name: BLAST namespace: resources def: "A BLAST-format database of sequences." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0003041 ! Sequence database [Term] id: EDAM:0000654 name: DNA namespace: topic alt_id: EDAM:0000098 alt_id: EDAM:0000666 alt_id: EDAM:0000627 alt_id: EDAM:0000628 def: "Resources concerning DNA sequences and structure, including processes such as methylation and replication." [EDAM:EBI "EMBRACE definition"] comment: The DNA sequences might be coding or non-coding sequences. subset: topic is_a: EDAM:0003042 ! Nucleic acid sequences [Term] id: EDAM:0000655 name: mRNA, EST or cDNA namespace: topic alt_id: EDAM:0000205 def: "Resources concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Transcriptome" EXACT [] is_a: EDAM:0000099 ! RNA [Term] id: EDAM:0000659 name: Functional RNA namespace: topic alt_id: EDAM:0000113 alt_id: EDAM:0000119 alt_id: EDAM:0000664 alt_id: EDAM:0000665 alt_id: EDAM:0000120 def: "Resources concerning functional or non-coding RNA sequences." [EDAM:EBI "EMBRACE definition"] comment: For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). subset: topic is_a: EDAM:0000099 ! RNA [Term] id: EDAM:0003060 name: Regulatory RNA namespace: topic alt_id: EDAM:0000661 alt_id: EDAM:0000662 alt_id: EDAM:0000117 alt_id: EDAM:0000118 def: "Resources concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA)." [EDAM:EBI "EMBRACE definition"] comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. subset: topic is_a: EDAM:0000659 ! Functional RNA [Term] id: EDAM:0000660 name: rRNA namespace: topic alt_id: EDAM:0000116 def: "Resources concerning one or more ribosomal RNA (rRNA) sequences." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000659 ! Functional RNA [Term] id: EDAM:0000663 name: tRNA namespace: topic alt_id: EDAM:0000115 def: "Resources concerning one or more transfer RNA (tRNA) sequences." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000659 ! Functional RNA [Term] id: EDAM:0002814 name: Protein structure analysis namespace: topic alt_id: EDAM:0000126 alt_id: EDAM:0000590 def: "Resources concerning protein secondary or tertiary structural data and/or associated annotation." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000078 ! Protein analysis is_a: EDAM:0000081 ! Structure analysis [Term] id: EDAM:0003040 name: Protein structure namespace: topic def: "Data resources concerning protein secondary or tertiary structural data and/or associated annotation." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003038 ! Structure databases is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000694 name: Protein secondary structure namespace: topic alt_id: EDAM:0002124 def: "Data resources concerning protein secondary structure or secondary structure alignments." [EDAM:EBI "EMBRACE definition"] comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. subset: topic synonym: "Protein secondary structure analysis" EXACT [] is_a: EDAM:0003040 ! Protein structure [Term] id: EDAM:0000698 name: Protein tertiary structure namespace: topic alt_id: EDAM:0002125 def: "Data resources concerning protein tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003040 ! Protein structure [Term] id: EDAM:0000697 name: RNA structure and alignment namespace: topic def: "Resources concerning RNA secondary or tertiary structure and alignments." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "RNA structure" EXACT [] synonym: "RNA structure alignment" EXACT [] synonym: "RNA alignment" EXACT [] is_a: EDAM:0000183 ! Structure alignment [Term] id: EDAM:0002826 name: Protein structure alignment namespace: topic def: "Resources concerning protein secondary or tertiary structure alignments." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000183 ! Structure alignment is_a: EDAM:0002814 ! Protein structure analysis [Term] id: EDAM:0000620 name: Drugs and targets namespace: topic def: "Informatics resources concerning the structures of drugs, drug target, their interactions and binding affinities." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000154 ! Small molecules is_a: EDAM:0000202 ! Pharmacoinformatics [Term] id: EDAM:0000618 name: Scents namespace: topic def: "A database about scents." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000154 ! Small molecules [Term] id: EDAM:0000722 name: Nucleic acid classification namespace: topic def: "Resources concerning nucleic acid classification (typically sequence classification)." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0002829 ! Ontologies, nomenclature and classification is_a: EDAM:0000077 ! Nucleic acid analysis is_a: EDAM:0000594 ! Sequence classification [Term] id: EDAM:0000723 name: Protein structure classification namespace: resources def: "Resources concerning protein structural classifications." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0001770 ! Structure comparison consider: EDAM:0000736 ! Protein domains and folds [Term] id: EDAM:0000724 name: Protein families namespace: topic def: "Data resources concerning primarily proteins that have been classified as members of a protein family (or other grouping)." [EDAM:EBI "EMBRACE definition"] comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. subset: topic synonym: "Protein sequence classification" EXACT [] synonym: "Protein secondary" EXACT [] is_a: EDAM:0003052 ! Sequence clusters and classification is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000736 name: Protein domains and folds namespace: topic alt_id: EDAM:0000703 alt_id: EDAM:0000700 alt_id: EDAM:0000127 def: "Resources concerning protein tertiary structural domains and folds." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Domains is_a: EDAM:0000698 ! Protein tertiary structure is_a: EDAM:0000724 ! Protein families [Term] id: EDAM:0000740 name: Nucleic acid sequence alignment namespace: topic def: "Resources concerning nucleotide sequence alignments." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000182 ! Sequence alignment is_a: EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0000741 name: Protein sequence alignment namespace: topic def: "Resources concerning protein sequence alignments." [EDAM:EBI "EMBRACE definition"] comment: A sequence profile typically represents a sequence alignment. subset: topic is_a: EDAM:0000182 ! Sequence alignment is_a: EDAM:0000639 ! Protein sequence analysis [Term] id: EDAM:0000742 name: Sequence motif or profile (nucleotide) namespace: resources def: "Resources concerning nucleotide sequence motifs, or sequence profiles derived from an nucleic acid sequence alignment." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0000743 name: Sequence motif or profile (protein) namespace: resources def: "Resources concerning protein sequence motifs, or sequence profiles derived from an protein sequence alignment." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0000747 name: Nucleic acid sites and features namespace: topic alt_id: EDAM:0000105 alt_id: EDAM:0000095 def: "Data resources concerning positional features such as functional sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Nucleic acid functional sites" EXACT [] synonym: "Nucleic acid features" EXACT [] is_a: EDAM:0000160 ! Sequence sites and features is_a: EDAM:0003042 ! Nucleic acid sequences [Term] id: EDAM:0003073 name: Nucleic acid feature detection namespace: topic def: "Resources concerning the detection of positional features such as functional sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000640 ! Nucleic acid sequence analysis is_a: EDAM:0003072 ! Sequence feature detection [Term] id: EDAM:0000748 name: Protein sites and features namespace: topic alt_id: EDAM:0000124 alt_id: EDAM:0000138 def: "Data resources concerning positional features such as functional sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Protein functional sites" EXACT [] synonym: "Protein sequence features" EXACT [] is_a: EDAM:0000160 ! Sequence sites and features is_a: EDAM:0003043 ! Protein sequences [Term] id: EDAM:0003074 name: Protein feature detection namespace: topic def: "Resources concerning the detection, identification and analysis of positional protein sequence features, such as functional sites." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000639 ! Protein sequence analysis is_a: EDAM:0003072 ! Sequence feature detection [Term] id: EDAM:0000749 name: Transcription factors and regulatory sites namespace: topic alt_id: EDAM:0000811 def: "Resources concerning transcription factors; proteins that bind to DNA and control transcription of DNA to mRNA, either promoting (as an activator) or blocking (as a repressor) the binding to DNA of RNA polymerase, and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes promoters, enhancers, silencers and boundary elements / insulators. This includes sequence and structural information, binding profiles etc, and may also include the transcription factor binding site in DNA. synonym: "Transcriptional regulatory sites" EXACT [] synonym: "Transcription factors" EXACT [] synonym: "Transcription factor and binding site" EXACT [] is_a: EDAM:0000204 ! Gene regulation resources is_a: EDAM:0000110 ! Transcription is_a: EDAM:0000635 ! Specific protein resources is_a: EDAM:0000747 ! Nucleic acid sites and features is_a: EDAM:0003062 ! Genetic organisation is_a: EDAM:0003073 ! Nucleic acid feature detection [Term] id: EDAM:0000751 name: Phosphorylation sites namespace: topic def: "Resources concerning protein phosphorylation and phosphorylation sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000601 ! Protein modifications is_a: EDAM:0000748 ! Protein sites and features [Term] id: EDAM:0000753 name: Metabolic pathways namespace: topic def: "Informatics resources concerning metabolic pathways." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000602 ! Pathways, networks and models [Term] id: EDAM:0000754 name: Signaling pathways namespace: topic def: "Informatics resources concerning signaling pathways." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000602 ! Pathways, networks and models [Term] id: EDAM:0003044 name: Protein interaction networks namespace: topic def: "Informatics resources concerning protein-protein interaction networks." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000602 ! Pathways, networks and models is_a: EDAM:0000147 ! Protein-protein interactions [Term] id: EDAM:0000771 name: Biological models namespace: topic alt_id: EDAM:0002267 alt_id: EDAM:0002268 def: "Informatics resources concerning mathematical or other models of biological processes." [EDAM:EBI "EMBRACE definition"] comment: This includes databases of models and methods to construct or analyse a model. subset: topic xref: BioCatalogue:Model Creation is_a: EDAM:0000602 ! Pathways, networks and models [Term] id: EDAM:0002846 name: Gene regulatory networks namespace: topic def: "Informatics resources concerning gene regulatory networks." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000602 ! Pathways, networks and models is_a: EDAM:0000204 ! Gene regulation resources [Term] id: EDAM:0000767 name: Protein and peptide identification namespace: topic alt_id: EDAM:0000603 def: "Informatics resources concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays." [EDAM:EBI "EMBRACE definition"] comment: This includes the results of any methods that separate, characterize and identify expressed proteins. subset: topic synonym: "Peptide identification and proteolysis" EXACT [] synonym: "Proteomics data" EXACT [] synonym: "Proteomics data resources" EXACT [] is_a: EDAM:0000121 ! Proteomics is_a: EDAM:0000639 ! Protein sequence analysis is_a: EDAM:0002225 ! Protein databases [Term] id: EDAM:0000141 name: Protein cleavage sites and proteolysis namespace: topic def: "Resources concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000639 ! Protein sequence analysis [Term] id: EDAM:0000769 name: Workflows namespace: topic def: "Resources concerning biological or biomedical analytical workflows or pipelines." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0000220 name: Data processing and validation namespace: topic alt_id: EDAM:0002286 alt_id: EDAM:0002270 alt_id: EDAM:0002834 def: "Resources concerning basic manipulations of files or reports of generic biological data." [EDAM:EBI "EMBRACE definition"] comment: This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. subset: topic synonym: "Report handling" EXACT [] synonym: "File handling" EXACT [] synonym: "Data file handling" EXACT [] synonym: "Report processing" EXACT [] is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0000770 name: Data types and objects namespace: topic def: "Resources concerning structuring data into basic types and (computational) objects." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000091 ! Data handling [Term] id: EDAM:0000632 name: Probes and primers namespace: topic alt_id: EDAM:0000207 def: "Resources concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR)." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000607 ! Laboratory resources is_a: EDAM:0003041 ! Sequence databases [Term] id: EDAM:0003032 name: Primer or probe design namespace: topic def: "Informatics resources concerning the design of primers for PCR and DNA amplification or the design of molecular probes." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0000779 name: Mitochondrial genes and proteins namespace: topic def: "Informatics resources concerning mitochondria, typically of mitochondrial genes and proteins." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Mitochondria genes and proteins" EXACT [] is_a: EDAM:0000616 ! Organelle genes and proteins [Term] id: EDAM:0002818 name: Eukaryotes namespace: topic alt_id: EDAM:0000669 def: "Informatics resources concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. subset: topic synonym: "Eukaryote" EXACT [] is_a: EDAM:0000621 ! Genome, proteome and model organisms [Term] id: EDAM:0002821 name: Unicellular eukaryotes namespace: topic alt_id: EDAM:0000675 def: "Informatics resources concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. subset: topic synonym: "Unicellular eukaryote" EXACT [] is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0002819 name: Invertebrates namespace: topic alt_id: EDAM:0000678 def: "Informatics resources concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. subset: topic is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0002820 name: Vertebrates namespace: topic alt_id: EDAM:0000679 def: "Informatics resources concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. subset: topic synonym: "Vertebrate" EXACT [] is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0002815 name: Humans namespace: topic alt_id: EDAM:0000692 alt_id: EDAM:0000687 def: "Informatics resources concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a human, a group of humans or all humans. subset: topic synonym: "Human" EXACT [] is_a: EDAM:0003048 ! Mammals [Term] id: EDAM:0000780 name: Plants namespace: topic alt_id: EDAM:0000677 alt_id: EDAM:0000785 alt_id: EDAM:0000784 alt_id: EDAM:0000214 def: "Informatics resources concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a plant, a group of plants or all plants. subset: topic synonym: "Plant" EXACT [] is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0000781 name: Viruses namespace: topic alt_id: EDAM:0000790 alt_id: EDAM:0000671 alt_id: EDAM:0000791 def: "Informatics resources concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a virus, a group of viruses or all viruses. subset: topic synonym: "Virus" EXACT [] is_a: EDAM:0000621 ! Genome, proteome and model organisms [Term] id: EDAM:0000782 name: Fungi namespace: topic alt_id: EDAM:0000792 alt_id: EDAM:0000793 alt_id: EDAM:0000676 def: "Informatics resources concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a fungus, a group of fungi or all fungi. synonym: "Fungal" EXACT [] subset: topic is_a: EDAM:0002818 ! Eukaryotes [Term] id: EDAM:0000783 name: Pathogens namespace: topic def: "Informatics resources concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a pathogen, a group of pathogens or all pathogens. subset: topic synonym: "Pathogen" EXACT [] is_a: EDAM:0000621 ! Genome, proteome and model organisms [Term] id: EDAM:0001811 name: Prokaryotes and archae namespace: topic alt_id: EDAM:0000691 alt_id: EDAM:0000670 alt_id: EDAM:0000212 def: "Informatics resources concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] comment: The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. subset: topic synonym: "Prokaryote and archae" EXACT [] is_a: EDAM:0000621 ! Genome, proteome and model organisms [Term] id: EDAM:0000786 name: Arabidopsis namespace: topic def: "Informatics resources concerning Arabidopsis-specific data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000780 ! Plants [Term] id: EDAM:0000787 name: Rice namespace: topic def: "Informatics resources concerning rice-specific data." [EDAM:EBI "EMBRACE definition"] is_a: EDAM:0000780 ! Plants [Term] id: EDAM:0002817 name: Yeast namespace: topic alt_id: EDAM:0000682 alt_id: EDAM:0000216 def: "Informatics resources concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000782 ! Fungi [Term] id: EDAM:0000796 name: Genetic mapping and linkage namespace: topic alt_id: EDAM:0000103 def: "Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Genetic linkage" EXACT [] synonym: "Linkage mapping" EXACT [] is_a: EDAM:0000102 ! Sequencing and mapping relationship: has_topic EDAM:0003053 ! Genetics [Term] id: EDAM:0000797 name: Comparative genomics namespace: topic alt_id: EDAM:0000101 def: "Informatics resources for the study (typically comparison) of the structure or function of multiple genomes." [EDAM:EBI "EMBRACE definition"] subset: topic xref: BioCatalogue:Comparative Genomics is_a: EDAM:0000622 ! Genomics [Term] id: EDAM:0000798 name: Mobile genetic elements namespace: topic def: "Resources concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0003062 ! Genetic organisation [Term] id: EDAM:0000801 name: Human genes namespace: resources def: "Resources concerning human genes." [EDAM:EBI "EMBRACE definition"] is_obsolete: true consider: EDAM:0000623 ! Genes, gene family or system [Term] id: EDAM:0000803 name: Human disease namespace: topic def: "Resources concerning human diseases, typically describing the genes, mutations and proteins implicated in disease." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000634 ! Disease resources [Term] id: EDAM:0000804 name: Immunoinformatics namespace: topic alt_id: EDAM:0000201 alt_id: EDAM:0000633 def: "Informatics resources for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Computational immunology" EXACT [] is_a: EDAM:0000003 ! Topics [Term] id: EDAM:0002830 name: Immunity genes, immunoproteins and antigens namespace: topic def: "Informatics resources concerning immunity-related genes, proteins and their ligands." [EDAM:EBI "EMBRACE definition"] comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." subset: topic synonym: "Immunoproteins and immunopeptides" EXACT [] is_a: EDAM:0000804 ! Immunoinformatics is_a: EDAM:0003078 ! Gene and protein resources [Term] id: EDAM:0002847 name: Disease (specific) namespace: topic def: "Informatics resources dedicated to one or more specific diseases (not diseases in general)." [EDAM:EBI "EMBRACE definition"] subset: topic is_obsolete: true consider: EDAM:0000634 ! Disease resources [Term] id: EDAM:0002640 name: Cancer resources namespace: topic alt_id: EDAM:0000805 def: "Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000634 ! Disease resources [Term] id: EDAM:0000820 name: Membrane proteins namespace: topic alt_id: EDAM:0000131 def: "Informatics resources concerning a protein or region of a protein that spans a membrane." [EDAM:EBI "EMBRACE definition"] subset: topic synonym: "Transmembrane proteins" EXACT [] is_a: EDAM:0000635 ! Specific protein resources [Term] id: EDAM:0000821 name: Enzymes and reactions namespace: topic alt_id: EDAM:0000132 def: "Informatics resources concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." [EDAM:EBI "EMBRACE definition"] subset: topic is_a: EDAM:0000635 ! Specific protein resources ! ! Operation ! [Term] id: EDAM:0000223 name: Undefined namespace: operation def: "Debugging." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true [Term] id: EDAM:0002945 name: Analysis namespace: operation def: "Apply analytical methods to existing data of a specific type." [EDAM:EBI "EMBRACE definition"] comment: For non-analytical operations, see the 'Processing' branch. subset: operation is_obsolete: true consider: EDAM:0002420 ! Analysis and processing [Term] id: EDAM:0002420 name: Analysis and processing namespace: operation def: "Process (read and / or write) data of a specific type, for example applying analytical methods." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Calculation" EXACT [] synonym: "Computation" EXACT [] is_a: EDAM:0000004 ! Operation relationship: has_input EDAM:0000006 ! Data {minCardinality=0} relationship: has_output EDAM:0000006 ! Data {minCardinality=0} [Term] id: EDAM:0002423 name: Prediction, detection and recognition namespace: operation def: "Predict, recognise, detect or identify some properties of a biomolecule." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation [Term] id: EDAM:0003023 name: Prediction, detection and recognition (protein) namespace: operation def: "Predict, recognise, detect or identify some properties of proteins." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002423 ! Prediction, detection and recognition [Term] id: EDAM:0003024 name: Prediction, detection and recognition (nucleic acid) namespace: operation def: "Predict, recognise, detect or identify some properties of nucleic acids." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002423 ! Prediction, detection and recognition [Term] id: EDAM:0002946 name: Alignment analysis namespace: operation def: "Analyse an existing alignment of two or more molecular sequences, structures or derived data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002951 ! Alignment processing relationship: has_input EDAM:0001916 ! Alignment {minCardinality=1} ! Extends cardinality constraint on parent. relationship: has_output EDAM:0002083 ! Alignment report {minCardinality=1} [Term] id: EDAM:0002947 name: Article analysis namespace: operation def: "Analyse a body of scientific text (typically a full text article from a scientific journal.)" [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002505 ! Text processing relationship: has_input EDAM:0000971 ! Article {minCardinality=1} relationship: has_output EDAM:0002954 ! Article report relationship: has_topic EDAM:0000217 ! Literature analysis [Term] id: EDAM:0002993 name: Molecular interaction data processing namespace: operation def: "Process (read and / or write) molecular interaction data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true [Term] id: EDAM:0002948 name: Molecular interaction analysis namespace: operation def: "Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true [Term] id: EDAM:0002949 name: Protein interaction analysis namespace: operation def: "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002405 ! Protein interaction data processing relationship: has_output EDAM:0000906 ! Protein report (interaction) {minCardinality=1} relationship: has_topic EDAM:0000128 ! Protein interactions [Term] id: EDAM:0003096 name: Editing namespace: operation def: "Edit, convert or otherwise change a data entity, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation [Term] id: EDAM:0002928 name: Alignment namespace: operation def: "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation is_a: EDAM:0002951 ! Alignment processing relationship: has_output EDAM:0001916 ! Alignment {minCardinality=1} [Term] id: EDAM:0002424 name: Comparison namespace: operation def: "Compare two or more things to identify similarities." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation [Term] id: EDAM:0002997 name: Protein comparison namespace: operation def: "Compare two or more proteins (or some aspect) to identify similarities." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002424 ! Comparison [Term] id: EDAM:0002998 name: Nucleic acid comparison namespace: operation def: "Compare two or more nucleic acids to identify similarities." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002424 ! Comparison [Term] id: EDAM:0002990 name: Classification namespace: operation def: "Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation relationship: has_output EDAM:0002987 ! Classification {minCardinality=1} [Term] id: EDAM:0002995 name: Sequence classification namespace: operation def: "Assign molecular sequence(s) to a group or category." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002990 ! Classification is_a: EDAM:0002403 ! Sequence analysis [Term] id: EDAM:0003093 name: Sequence screening namespace: operation def: "Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002995 ! Sequence classification [Term] id: EDAM:0002996 name: Structure classification namespace: operation def: "Assign molecular structure(s) to a group or category." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002990 ! Classification is_a: EDAM:0002480 ! Structure analysis [Term] id: EDAM:0002425 name: Optimisation and refinement namespace: operation def: "Refine or optimise some data model." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation [Term] id: EDAM:0002426 name: Modelling and simulation namespace: operation def: "Model or simulate some biological entity or system." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation relationship: has_topic EDAM:0002275 ! Molecular modelling [Term] id: EDAM:0002427 name: Data handling namespace: operation def: "Perform basic operations on some data or a database." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002420 ! Analysis and processing [Term] id: EDAM:0002428 name: Validation and standardisation namespace: operation def: "Validate or standardise some data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000004 ! Operation [Term] id: EDAM:0002429 name: Mapping and assembly namespace: operation def: "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." [EDAM:EBI "EMBRACE definition"] comment: This is a broad concept and is used a placeholder for other, more specific terms. subset: operation is_a: EDAM:0000004 ! Operation relationship: has_topic EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0002430 name: Design namespace: operation def: "Design a biological entity (typically a molecular sequence or structure) with specific properties." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) [Term] id: EDAM:0002238 name: Statistical calculation namespace: operation def: "Perform a statistical data operation of some type, e.g. calibration or validation." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000004 ! Operation [Term] id: EDAM:0000224 name: Search and retrieval namespace: operation def: "Search or query a data resource and retrieve entries and / or annotation." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Database retrieval" EXACT [] is_a: EDAM:0000004 ! Operation relationship: has_output EDAM:0000006 ! Data {minCardinality=0} relationship: has_topic EDAM:0000090 ! Data search and retrieval [Term] id: EDAM:0002501 name: Nucleic acid data processing namespace: operation def: "Process (read and / or write) nucleic acid sequence or structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0002084 ! Nucleic acid report {minCardinality=0} relationship: has_output EDAM:0002084 ! Nucleic acid report {minCardinality=0} relationship: has_topic EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0002502 name: Protein data processing namespace: operation def: "Process (read and / or write) protein sequence or structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000896 ! Protein report {minCardinality=0} relationship: has_output EDAM:0000896 ! Protein report {minCardinality=0} relationship: has_topic EDAM:0000078 ! Protein analysis [Term] id: EDAM:0002407 name: Annotation processing namespace: operation def: "Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002951 name: Alignment processing namespace: operation def: "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0001916 ! Alignment {minCardinality=0} relationship: has_output EDAM:0001916 ! Alignment {minCardinality=0} [Term] id: EDAM:0002412 name: Data index processing namespace: operation def: "Process (read and / or write) an index of (typically a file of) biological data." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Database index processing" EXACT [] is_a: EDAM:0002409 ! File processing relationship: has_input EDAM:0000955 ! Data index {minCardinality=0} relationship: has_output EDAM:0000955 ! Data index {minCardinality=0} relationship: has_topic EDAM:0000220 ! Data processing and validation [Term] id: EDAM:0002504 name: Structural data processing namespace: operation def: "Process (read and / or write) molecular structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002465 ! Structure processing [Term] id: EDAM:0002403 name: Sequence analysis namespace: operation alt_id: EDAM:0002477 def: "Analyse one or more known molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence analysis (general)" EXACT [] is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} relationship: has_output EDAM:0002955 ! Sequence report {minCardinality=1} relationship: has_topic EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0002408 name: Sequence feature analysis namespace: operation def: "Analyse features in molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000253 ! Sequence feature detection [Term] id: EDAM:0002404 name: Sequence motif processing namespace: operation def: "Process (read and / or write) molecular sequence motifs." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0001353 ! Sequence motif {minCardinality=0} relationship: has_output EDAM:0001353 ! Sequence motif {minCardinality=0} relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0002417 name: Physicochemical property data processing namespace: operation def: "Process (read and / or write) data on the physicochemical property of a molecule." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002420 ! Analysis and processing [Term] id: EDAM:0002414 name: Protein function analysis namespace: operation def: "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." [EDAM:EBI "EMBRACE definition"] comment: This is a broad concept and is used a placeholder for other, more specific terms. subset: operation is_a: EDAM:0002502 ! Protein data processing relationship: has_output EDAM:0000896 ! Protein report [Term] id: EDAM:0000258 name: Sequence alignment analysis namespace: operation def: "Analyse a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002463 ! Sequence alignment processing is_a: EDAM:0002946 ! Alignment analysis relationship: has_input EDAM:0000292 ! Sequence alignment {minCardinality=1} ! Extends cardinality constraint on parent. relationship: has_output EDAM:0000867 ! Sequence alignment report {minCardinality=1} relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0002506 name: Sequence alignment analysis (protein) namespace: operation def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002502 ! Protein data processing is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_input EDAM:0001384 ! Sequence alignment (protein) {minCardinality=1} relationship: has_topic EDAM:0000741 ! Protein sequence alignment [Term] id: EDAM:0002507 name: Sequence alignment analysis (nucleic acid) namespace: operation def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002501 ! Nucleic acid data processing is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_input EDAM:0001383 ! Sequence alignment (nucleic acid) {minCardinality=1} relationship: has_topic EDAM:0000740 ! Nucleic acid sequence alignment [Term] id: EDAM:0002416 name: Protein secondary structure analysis namespace: operation def: "Analyse known protein secondary structure data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002444 ! Protein secondary structure processing synonym: "Secondary structure analysis (protein)" EXACT [] relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} relationship: has_output EDAM:0002956 ! Protein secondary structure report relationship: has_topic EDAM:0000694 ! Protein secondary structure [Term] id: EDAM:0000270 name: Transmembrane protein analysis namespace: operation def: "Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions." [EDAM:EBI "EMBRACE definition"] comment: Use this (or child) term for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). subset: operation is_a: EDAM:0002502 ! Protein data processing relationship: has_output EDAM:0001456 ! Protein features (membrane regions) relationship: has_topic EDAM:0000820 ! Membrane proteins [Term] id: EDAM:0002476 name: Molecular dynamics simulation namespace: operation def: "Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002423 ! Prediction, detection and recognition is_a: EDAM:0002480 ! Structure analysis is_a: EDAM:0002426 ! Modelling and simulation relationship: has_output EDAM:0000883 ! Structure relationship: has_topic EDAM:0000082 ! Structure prediction relationship: has_topic EDAM:0000176 ! Molecular dynamics [Term] id: EDAM:0000271 name: Structure prediction namespace: operation def: "Predict tertiary structure of a molecular (biopolymer) sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002423 ! Prediction, detection and recognition is_a: EDAM:0002465 ! Structure processing relationship: has_output EDAM:0000883 ! Structure relationship: has_topic EDAM:0000082 ! Structure prediction [Term] id: EDAM:0002405 name: Protein interaction data processing namespace: operation def: "Process (read and / or write) protein interaction data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002502 ! Protein data processing relationship: has_input EDAM:0000906 ! Protein report (interaction) {minCardinality=0} relationship: has_output EDAM:0000906 ! Protein report (interaction) {minCardinality=0} relationship: has_topic EDAM:0000128 ! Protein interactions [Term] id: EDAM:0002521 name: Map data processing namespace: operation def: "Process (read and / or write) a DNA map of some type." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "DNA map data processing" EXACT [] is_a: EDAM:0002501 ! Nucleic acid data processing relationship: has_input EDAM:0001274 ! Map {minCardinality=0} relationship: has_output EDAM:0001274 ! Map {minCardinality=0} relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0002520 name: DNA mapping namespace: operation def: "Generate a map of a DNA sequence annotated with positional or non-positional features of some type." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002521 ! Map data processing is_a: EDAM:0002429 ! Mapping and assembly relationship: has_output EDAM:0001274 ! Map {minCardinality=1} relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0000282 name: Genetic mapping namespace: operation def: "Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances." [EDAM:EBI "EMBRACE definition"] comment: Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. subset: operation synonym: "Genetic map generation" EXACT [] synonym: "Linkage mapping" EXACT [] is_a: EDAM:0002520 ! DNA mapping relationship: has_output EDAM:0001278 ! Genetic map {minCardinality=1} relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0002944 name: Physical mapping namespace: operation def: "Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002520 ! DNA mapping relationship: has_output EDAM:0001280 ! Physical map {minCardinality=1} relationship: has_topic EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0002871 name: Sequence tagged site (STS) mapping namespace: operation def: "Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS)." [EDAM:EBI "EMBRACE definition"] comment: An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. subset: operation synonym: "Sequence mapping" EXACT [] is_a: EDAM:0002944 ! Physical mapping relationship: has_output EDAM:0001279 ! Sequence map {minCardinality=1} [Term] id: EDAM:0000283 name: Linkage analysis namespace: operation def: "Analyse genetic linkage." [EDAM:EBI "EMBRACE definition"] comment: For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. subset: operation is_a: EDAM:0002478 ! Nucleic acid sequence analysis relationship: has_output EDAM:0000927 ! Gene annotation (linkage) relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0002493 name: Codon usage data processing namespace: operation def: "Process (read and / or write) codon usage data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000286 ! Codon usage analysis [Term] id: EDAM:0002503 name: Sequence data processing namespace: operation def: "Process (read and / or write) molecular sequence data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002446 ! Sequence processing [Term] id: EDAM:0002463 name: Sequence alignment processing namespace: operation def: "Process (read and / or write) a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002951 ! Alignment processing relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=0} relationship: has_output EDAM:0000863 ! Sequence alignment {minCardinality=0} relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0002952 name: Structure alignment processing namespace: operation def: "Process (read and / or write) a molecular tertiary (3D) structure alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002951 ! Alignment processing relationship: has_input EDAM:0000886 ! Structure alignment {minCardinality=0} relationship: has_output EDAM:0000886 ! Structure alignment {minCardinality=0} relationship: has_topic EDAM:0000183 ! Structure alignment [Term] id: EDAM:0000292 name: Sequence alignment namespace: operation def: "Align (identify equivalent sites within) molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence alignment generation" EXACT [] is_a: EDAM:0002463 ! Sequence alignment processing is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002928 ! Alignment relationship: has_output EDAM:0000863 ! Sequence alignment {minCardinality=1} relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000293 name: Hybrid sequence alignment namespace: operation def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000292 ! Sequence alignment [Term] id: EDAM:0000294 name: Structure-based sequence alignment namespace: operation def: "Align molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000292 ! Sequence alignment relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0002480 name: Structure analysis namespace: operation alt_id: EDAM:0002431 def: "Analyse known molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002465 ! Structure processing relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} relationship: has_output EDAM:0002085 ! Structure report {minCardinality=1} relationship: has_topic EDAM:0000081 ! Structure analysis [Term] id: EDAM:0002931 name: Secondary structure comparison namespace: operation def: "Compare two or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002424 ! Comparison relationship: has_input EDAM:0002081 ! Secondary structure {minCardinality=2} relationship: has_output EDAM:0002881 ! Secondary structure report {minCardinality=1} relationship: has_topic EDAM:0001770 ! Structure comparison [Term] id: EDAM:0002483 name: Structure comparison namespace: operation def: "Compare two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002424 ! Comparison is_a: EDAM:0002480 ! Structure analysis relationship: has_topic EDAM:0001770 ! Structure comparison [Term] id: EDAM:0000295 name: Structure alignment namespace: operation def: "Align (superimpose) molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002928 ! Alignment is_a: EDAM:0002483 ! Structure comparison is_a: EDAM:0002952 ! Structure alignment processing relationship: has_output EDAM:0000886 ! Structure alignment {minCardinality=1} relationship: has_topic EDAM:0000183 ! Structure alignment [Term] id: EDAM:0002413 name: Sequence profile processing namespace: operation def: "Process (read and / or write) some type of sequence profile." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0001354 ! Sequence profile {minCardinality=0} relationship: has_output EDAM:0001354 ! Sequence profile {minCardinality=0} relationship: has_topic EDAM:0000188 ! Sequence profiles and HMMs [Term] id: EDAM:0002411 name: Structural (3D) profile processing namespace: operation def: "Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=0} relationship: has_output EDAM:0000889 ! Structural (3D) profile {minCardinality=0} relationship: has_topic EDAM:0000167 ! Structural (3D) profiles [Term] id: EDAM:0000303 name: Protein fold recognition namespace: operation def: "Recognize (predict and identify) known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. subset: operation synonym: "Protein domain prediction" EXACT [] synonym: "Protein fold prediction" EXACT [] is_a: EDAM:0000414 ! Protein feature detection (from sequence) is_a: EDAM:0000474 ! Protein structure prediction is_a: EDAM:0002997 ! Protein comparison relationship: has_output EDAM:0000901 ! Protein features (domains) {minCardinality=1} relationship: has_topic EDAM:0000184 ! Threading [Term] id: EDAM:0002246 name: Demonstration namespace: operation def: "An operation performing purely illustrative (pedagogical) purposes." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true [Term] id: EDAM:0002505 name: Text processing namespace: operation def: "Process (read and / or write) text." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0002048 ! Report {minCardinality=0} relationship: has_output EDAM:0002048 ! Report {minCardinality=0} [Term] id: EDAM:0000306 name: Text mining namespace: operation def: "Process and analyse text (typically the biomedical and informatics literature) to extract information from it." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Text data mining" EXACT [] is_a: EDAM:0002947 ! Article analysis relationship: has_input EDAM:0002048 ! Report {minCardinality=0} relationship: has_output EDAM:0000972 ! Text mining report relationship: has_topic EDAM:0000218 ! Text mining [Term] id: EDAM:0002419 name: Primer and probe design namespace: operation def: "Predict oligonucleotide primers or probes." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003095 ! Nucleic acid design is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) synonym: "Primer and probe prediction" EXACT [] relationship: has_topic EDAM:0003032 ! Primer or probe design [Term] id: EDAM:0000310 name: Sequence assembly namespace: operation def: "Assemble fragments of a DNA sequence to reconstruct the original sequence." [EDAM:EBI "EMBRACE definition"] comment: Typically, contigs (for example ESTs and genomic DNA fragments) are aligned and merged, depending on the detected fragment overlaps. Annotation of the assembled sequence might be generated. subset: operation is_a: EDAM:0002429 ! Mapping and assembly is_a: EDAM:0002446 ! Sequence processing is_a: EDAM:0002478 ! Nucleic acid sequence analysis relationship: has_output EDAM:0000925 ! Sequence assembly relationship: has_topic EDAM:0000196 ! Sequence assembly [Term] id: EDAM:0002432 name: Microarray data processing namespace: operation def: "Process (read and / or write) microarray data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0002495 name: Gene expression data processing namespace: operation def: "Process (read and / or write) gene expression (typically microarray) data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing synonym: "Gene expression (microarray) data processing" EXACT [] synonym: "Microarray data processing" EXACT [] relationship: has_input EDAM:0003117 ! Microarray hybridisation data {minCardinality=0} relationship: has_output EDAM:0003117 ! Microarray hybridisation data {minCardinality=0} relationship: has_topic EDAM:0000197 ! Gene expression resources relationship: has_topic EDAM:0000200 ! Microarrays [Term] id: EDAM:0002500 name: Microarray raw data analysis namespace: operation def: "Analyse raw microarray data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0000311 name: Microarray data standardization and normalization namespace: operation def: "Standardize or normalize microarray data." [EDAM:EBI "EMBRACE definition"] comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. subset: operation is_a: EDAM:0002495 ! Gene expression data processing is_a: EDAM:0002428 ! Validation and standardisation relationship: has_input EDAM:0003117 ! Microarray hybridisation data {minCardinality=1} relationship: has_output EDAM:0003117 ! Microarray hybridisation data {minCardinality=1} [Term] id: EDAM:0000318 name: Structural genomics target selection namespace: operation def: "Identify and select targets for protein structural determination." [EDAM:EBI "EMBRACE definition"] comment: Methods will typically navigate a graph of protein families of known structure. subset: operation is_obsolete: true consider: EDAM:0002406 ! Protein structure analysis [Term] id: EDAM:0002406 name: Protein structure analysis namespace: operation alt_id: EDAM:0002458 def: "Analyse protein tertiary structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002480 ! Structure analysis is_a: EDAM:0002459 ! Structure processing (protein) synonym: "Structure analysis (protein)" EXACT [] relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=1} relationship: has_output EDAM:0000897 ! Protein property [Term] id: EDAM:0002481 name: Nucleic acid structure analysis namespace: operation alt_id: EDAM:0002418 def: "Analyse nucleic acid tertiary structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002480 ! Structure analysis is_a: EDAM:0002519 ! Structure processing (nucleic acid) relationship: has_input EDAM:0001459 ! Nucleic acid structure {minCardinality=1} relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=1} [Term] id: EDAM:0000324 name: Phylogenetic tree analysis namespace: operation def: "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002443 ! Phylogenetic tree processing relationship: has_input EDAM:0000872 ! Phylogenetic tree {minCardinality=1} relationship: has_output EDAM:0001438 ! Phylogenetic tree report {minCardinality=1} [Term] id: EDAM:0002438 name: Pathway or network processing namespace: operation def: "Generate, analyse or handle a biological pathway or network." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0002600 ! Pathway or network {minCardinality=0} relationship: has_output EDAM:0002600 ! Pathway or network {minCardinality=0} relationship: has_topic EDAM:0000602 ! Pathways, networks and models [Term] id: EDAM:0003083 name: Pathway or network rendering namespace: operation def: "Render (visualise) a biological pathway or network." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002438 ! Pathway or network processing is_a: EDAM:0000337 ! Plotting and rendering relationship: has_input EDAM:0002600 ! Pathway or network {minCardinality=1} relationship: has_topic EDAM:0000602 ! Pathways, networks and models [Term] id: EDAM:0002497 name: Pathway or network analysis namespace: operation def: "Analyse a known biological pathway or network." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002438 ! Pathway or network processing relationship: has_input EDAM:0002600 ! Pathway or network {minCardinality=1} relationship: has_output EDAM:0002984 ! Pathway or network report {minCardinality=1} [Term] id: EDAM:0002415 name: Protein folding analysis namespace: operation def: "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." [EDAM:EBI "EMBRACE definition"] comment: This is a broad concept and is used a placeholder for other, more specific terms. subset: operation synonym: "Protein folding modelling" EXACT [] is_a: EDAM:0002502 ! Protein data processing is_a: EDAM:0002426 ! Modelling and simulation relationship: has_output EDAM:0000903 ! Protein folding report {minCardinality=1} relationship: has_topic EDAM:0000130 ! Protein folding and stability [Term] id: EDAM:0000331 name: Protein modelling (mutation) namespace: operation def: "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function." [EDAM:EBI "EMBRACE definition"] comment: Methods might predict silent or pathological mutations. subset: operation is_a: EDAM:0000477 ! Protein modelling is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) synonym: "Protein mutation modelling" EXACT [] relationship: has_topic EDAM:0000130 ! Protein folding and stability relationship: has_topic EDAM:0000199 ! Genetic variation [Term] id: EDAM:0000332 name: Immunogen design namespace: operation def: "Design molecules that elicit an immune response (immunogens)." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000559 ! Peptide immunogen prediction and optimisation [Term] id: EDAM:0002409 name: File processing namespace: operation def: "Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Report handling" EXACT [] synonym: "File handling" EXACT [] synonym: "Data file processing" EXACT [] is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000006 ! Data {minCardinality=0} relationship: has_output EDAM:0000006 ! Data {minCardinality=0} relationship: has_topic EDAM:0000220 ! Data processing and validation [Term] id: EDAM:0000337 name: Plotting and rendering namespace: operation def: "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Visualisation" EXACT [] is_a: EDAM:0000004 ! Operation relationship: has_input EDAM:0000006 ! Data {minCardinality=1} relationship: has_output EDAM:0002968 ! Image {minCardinality=0} relationship: has_topic EDAM:0000092 ! Data visualisation [Term] id: EDAM:0002121 name: Sequence file processing namespace: operation def: "Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002446 ! Sequence processing is_a: EDAM:0002409 ! File processing [Term] id: EDAM:0003081 name: Sequence alignment editing namespace: operation def: "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002122 ! Sequence alignment file processing is_a: EDAM:0003096 ! Editing [Term] id: EDAM:0002122 name: Sequence alignment file processing namespace: operation def: "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002409 ! File processing is_a: EDAM:0002463 ! Sequence alignment processing relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=1} relationship: has_output EDAM:0000863 ! Sequence alignment {minCardinality=1} [Term] id: EDAM:0003080 name: Structure editing namespace: operation def: "Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002234 ! Structure file processing is_a: EDAM:0003096 ! Editing relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} [Term] id: EDAM:0002234 name: Structure file processing namespace: operation def: "Perform basic (non-analytical) operations on a file of molecular tertiary structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002409 ! File processing is_a: EDAM:0002465 ! Structure processing [Term] id: EDAM:0002120 name: Listfile processing namespace: operation def: "Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002409 ! File processing relationship: has_input EDAM:0001111 ! EMBOSS listfile relationship: has_output EDAM:0001111 ! EMBOSS listfile [Term] id: EDAM:0001812 name: Data loading namespace: operation def: "Prepare or load a user-specified data file so that it is available for use." [EDAM:EBI "EMBRACE definition"] subset: operation xref: WHATIF:UploadPDB is_a: EDAM:0002409 ! File processing relationship: has_input EDAM:0000842 ! Identifier {minCardinality=1} [Term] id: EDAM:0000335 name: File reformatting namespace: operation def: "Reformat a file of data (or equivalent entity in memory)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002409 ! File processing [Term] id: EDAM:0000336 name: File validation namespace: operation def: "Test and validate the format and content of a data file." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002409 ! File processing is_a: EDAM:0002428 ! Validation and standardisation [Term] id: EDAM:0002421 name: Database search namespace: operation def: "Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query." [EDAM:EBI "EMBRACE definition"] comment: Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. subset: operation is_a: EDAM:0000224 ! Search and retrieval is_a: EDAM:0002424 ! Comparison relationship: has_output EDAM:0002080 ! Database hits {cardinality=0} [Term] id: EDAM:0002422 name: Data retrieval namespace: operation def: "Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000224 ! Search and retrieval relationship: has_input EDAM:0000842 ! Identifier {minCardinality=1} [Term] id: EDAM:0000343 name: Transmembrane protein database search namespace: operation def: "Search a database of transmembrane proteins, for example for sequence or structural similarities." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002421 ! Database search [Term] id: EDAM:0000304 name: Data retrieval (metadata and documentation) namespace: operation def: "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described." [EDAM:EBI "EMBRACE definition"] comment: This includes documentation, general information and other metadata on entities such as databases, database entries and tools. subset: operation synonym: "Data retrieval (documentation)" EXACT [] synonym: "Data retrieval (metadata)" EXACT [] relationship: has_output EDAM:0002337 ! Metadata {minCardinality=1} is_a: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0000225 name: Data retrieval (database cross-reference) namespace: operation def: "Search database to retrieve all relevant references to a particular entity or entry." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0001813 name: Sequence retrieval namespace: operation def: "Query a sequence data resource (typically a database) and retrieve sequences and / or annotation." [EDAM:EBI "EMBRACE definition"] comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. subset: operation synonym: "Data retrieval (sequences)" EXACT [] is_a: EDAM:0002422 ! Data retrieval is_a: EDAM:0002446 ! Sequence processing relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} [Term] id: EDAM:0001814 name: Structure retrieval namespace: operation def: "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation." [EDAM:EBI "EMBRACE definition"] comment: This includes direct retrieval methods but not those that perform calculations on the sequence or structure. subset: operation xref: WHATIF:DownloadPDB xref: WHATIF:EchoPDB is_a: EDAM:0002422 ! Data retrieval is_a: EDAM:0002465 ! Structure processing relationship: has_output EDAM:0000883 ! Structure {minCardinality=0} [Term] id: EDAM:0002237 name: Data retrieval (sequence profile) namespace: operation def: "Query a profile data resource and retrieve one or more profile(s) and / or associated annotation." [EDAM:EBI "EMBRACE definition"] comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002434 name: Data retrieval (codon usage table) namespace: operation def: "Retrieve a codon usage table and / or associated annotation." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002264 name: Data retrieval (pathway or network) namespace: operation def: "Query a biological pathways database and retrieve annotation on one or more pathways." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002265 name: Data retrieval (identifier) namespace: operation def: "Query a database and retrieve one or more data identifiers." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002224 name: Data retrieval (ontology concept) namespace: operation def: "Query an ontology and retrieve concepts or relations." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Ontology retrieval" EXACT [] is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002222 name: Data retrieval (ontology annotation) namespace: operation def: "Search and retrieve documentation on a bioinformatics ontology." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Ontology information retrieval" EXACT [] is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002468 name: Data retrieval (phylogenetic tree) namespace: operation def: "Retrieve a phylogenetic tree from a data resource." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0000257 name: Data retrieval (sequence alignment) namespace: operation def: "Display basic information about a sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002473 name: Data retrieval (genotype and phenotype annotation) namespace: operation def: "Retrieve information on a specific genotype or phenotype." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Genotype and phenotype information retrieval" EXACT [] is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002472 name: Data retrieval (gene annotation) namespace: operation def: "Retrieve information on a specific gene." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Gene information retrieval" EXACT [] is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002471 name: Data retrieval (RNA family annotation) namespace: operation def: "Retrieve information on an RNA family." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "RNA family information retrieval" EXACT [] is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002470 name: Data retrieval (protein family annotation) namespace: operation def: "Retrieve information on a protein family." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Protein family information retrieval" EXACT [] is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002469 name: Data retrieval (protein interaction annotation) namespace: operation def: "Retrieve information on a protein interaction." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0002467 name: Data retrieval (protein annotation) namespace: operation def: "Retrieve information on a protein." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Protein information retrieval" EXACT [] is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0000280 name: Data retrieval (restriction enzyme annotation) namespace: operation def: "Retrieve information on restriction enzymes or restriction enzyme sites." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Restriction enzyme information retrieval" EXACT [] is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0000515 name: Data retrieval (tool metadata) namespace: operation def: "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Tool information retrieval" EXACT [] synonym: "Data retrieval (tool annotation)" EXACT [] is_a: EDAM:0000304 ! Data retrieval (metadata and documentation) relationship: has_output EDAM:0000958 ! Tool metadata {minCardinality=0} [Term] id: EDAM:0000516 name: Data retrieval (database metadata) namespace: operation def: "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Database information retrieval" EXACT [] synonym: "Data retrieval (database annotation)" EXACT [] is_a: EDAM:0000304 ! Data retrieval (metadata and documentation) relationship: has_output EDAM:0000957 ! Database metadata {minCardinality=0} [Term] id: EDAM:0000344 name: Sequence retrieval (by code) namespace: operation def: "Query a database and retrieve sequences with a given entry code or accession number." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0001813 ! Sequence retrieval [Term] id: EDAM:0000345 name: Sequence retrieval (by keyword) namespace: operation def: "Query a database and retrieve sequences containing a given keyword." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0001813 ! Sequence retrieval [Term] id: EDAM:0001845 name: PDB file sequence retrieval namespace: operation def: "Extract a molecular sequence from a PDB file." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF: PDB_sequence is_obsolete: true consider: EDAM:0000344 ! Sequence retrieval (by code) [Term] id: EDAM:0000305 name: Literature search namespace: operation def: "Query the biomedical and informatics literature." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002421 ! Database search relationship: has_output EDAM:0000970 ! Bibliographic reference {minCardinality=0} relationship: has_topic EDAM:0000217 ! Literature analysis [Term] id: EDAM:0000338 name: Sequence database search namespace: operation def: "Search a sequence database by sequence comparison and retrieve similar sequences." [EDAM:EBI "EMBRACE definition"] comment: This excludes direct retrieval methods (e.g. the dbfetch program). subset: operation is_a: EDAM:0002421 ! Database search is_a: EDAM:0002403 ! Sequence analysis relationship: has_output EDAM:0000857 ! Database hits (sequence) {minCardinality=0} relationship: has_topic EDAM:0000159 ! Sequence comparison [Term] id: EDAM:0000339 name: Structure database search namespace: operation def: "Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002421 ! Database search is_a: EDAM:0002996 ! Structure classification relationship: has_output EDAM:0000885 ! Database hits (structure) {minCardinality=0} relationship: has_topic EDAM:0000081 ! Structure analysis [Term] id: EDAM:0000340 name: Protein secondary database search namespace: operation def: "Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group." [EDAM:EBI "EMBRACE definition"] comment: Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). subset: operation synonym: "Protein sequence classification" EXACT [] is_a: EDAM:0002421 ! Database search is_a: EDAM:0003093 ! Sequence screening relationship: has_output EDAM:0000858 ! Database hits (secondary) {minCardinality=0} relationship: has_topic EDAM:0000595 ! Protein classification [Term] id: EDAM:0000341 name: Motif database search namespace: operation def: "Screen a sequence against a motif or pattern database." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002421 ! Database search is_a: EDAM:0000239 ! Sequence motif recognition is_a: EDAM:0003093 ! Sequence screening relationship: has_output EDAM:0001298 ! Sequence features (motifs) {minCardinality=0} relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0000342 name: Sequence profile database search namespace: operation def: "Search a database of sequence profiles with a query sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002421 ! Database search is_a: EDAM:0000300 ! Sequence-profile alignment is_a: EDAM:0003093 ! Sequence screening relationship: has_output EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0000346 name: Sequence database search (by sequence) namespace: operation def: "Search a sequence database and retrieve sequences that are similar to a query sequence." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence similarity search" EXACT [] is_a: EDAM:0000338 ! Sequence database search is_a: EDAM:0003093 ! Sequence screening is_a: EDAM:0002451 ! Sequence comparison [Term] id: EDAM:0000347 name: Sequence database search (by motif or pattern) namespace: operation def: "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000338 ! Sequence database search is_a: EDAM:0000239 ! Sequence motif recognition relationship: has_input EDAM:0001353 ! Sequence motif {minCardinality=1} relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0000348 name: Sequence database search (by amino acid composition) namespace: operation def: "Search a sequence database and retrieve sequences of a given amino acid composition." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000338 ! Sequence database search relationship: has_input EDAM:0001267 ! Amino acid frequencies relationship: has_topic EDAM:0000157 ! Sequence composition analysis [Term] id: EDAM:0000349 name: Sequence database search (by physicochemical property) namespace: operation def: "Search a sequence database and retrieve sequences with a specified physicochemical property." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000338 ! Sequence database search [Term] id: EDAM:0000350 name: Sequence database search (by sequence using word-based methods) namespace: operation def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method." [EDAM:EBI "EMBRACE definition"] comment: Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. subset: operation synonym: "Sequence similarity search (word-based methods)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000288 ! Sequence word comparison [Term] id: EDAM:0000351 name: Sequence database search (by sequence using profile-based methods) namespace: operation def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query." [EDAM:EBI "EMBRACE definition"] comment: This includes tools based on PSI-BLAST. subset: operation synonym: "Sequence similarity search (profile-based methods)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000300 ! Sequence-profile alignment [Term] id: EDAM:0000352 name: Sequence database search (by sequence using local alignment-based methods) namespace: operation def: "Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method." [EDAM:EBI "EMBRACE definition"] comment: This includes tools based on the Smith-Waterman algorithm or FASTA. subset: operation synonym: "Sequence similarity search (local alignment-based methods) " EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000493 ! Pairwise sequence alignment (local) relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000353 name: Sequence database search (by sequence using global alignment-based methods) namespace: operation def: "Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method." [EDAM:EBI "EMBRACE definition"] comment: This includes tools based on the Needleman and Wunsch algorithm. subset: operation synonym: "Sequence similarity search (global alignment-based methods)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) is_a: EDAM:0000494 ! Pairwise sequence alignment (global) relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000354 name: Sequence database search (by sequence for primer sequences) namespace: operation def: "Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences." [EDAM:EBI "EMBRACE definition"] comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. subset: operation synonym: "Sequence similarity search (primer sequences)" EXACT [] is_a: EDAM:0000346 ! Sequence database search (by sequence) relationship: has_topic EDAM:0003032 ! Primer or probe design [Term] id: EDAM:0000355 name: Sequence database search (by molecular weight) namespace: operation def: "Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Protein fingerprinting" EXACT [] synonym: "Peptide mass fingerprinting" EXACT [] is_a: EDAM:0000349 ! Sequence database search (by physicochemical property) relationship: has_input EDAM:0000944 ! Peptide mass fingerprint relationship: has_topic EDAM:0000123 ! Protein properties relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0000356 name: Sequence database search (by isoelectric point) namespace: operation def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000349 ! Sequence database search (by physicochemical property) relationship: has_topic EDAM:0000123 ! Protein properties [Term] id: EDAM:0000357 name: Structure retrieval (by code) namespace: operation def: "Query a tertiary structure database and retrieve entries with a given entry code or accession number." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0001814 ! Structure retrieval [Term] id: EDAM:0000358 name: Structure retrieval (by keyword) namespace: operation def: "Query a tertiary structure database and retrieve entries containing a given keyword." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0001814 ! Structure retrieval [Term] id: EDAM:0001914 name: Structure retrieval (water) namespace: operation def: "Query a tertiary structure database and retrieve water molecules." [EDAM:EBI "EMBRACE definition"] subset: operation xref: WHATIF:MovedWaterPDB is_a: EDAM:0001814 ! Structure retrieval [Term] id: EDAM:0000359 name: Structure database search (by sequence) namespace: operation def: "Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Structure retrieval by sequence" EXACT [] is_a: EDAM:0000339 ! Structure database search is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0003093 ! Sequence screening [Term] id: EDAM:0000360 name: Structure database search (by structure) namespace: operation def: "Search a tertiary structure database and retrieve structures that are similar to a query structure." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Structure retrieval by structure" EXACT [] synonym: "Structural similarity search" EXACT [] is_a: EDAM:0000339 ! Structure database search relationship: has_topic EDAM:0001770 ! Structure comparison relationship: has_topic EDAM:0001770 ! Structure comparison [Term] id: EDAM:0000226 name: Annotation namespace: operation def: "Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] comment: This is a broad concept and is used a placeholder for other, more specific terms. subset: operation is_a: EDAM:0000004 ! Operation relationship: has_input EDAM:0000582 ! Ontology relationship: has_topic EDAM:0000089 ! Ontologies [Term] id: EDAM:0001774 name: Annotation retrieval namespace: operation def: "Retrieve existing annotation (or documentation), typically annotation on a database entity." [EDAM:EBI "EMBRACE definition"] comment: Use this terms for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0000361 name: Sequence annotation namespace: operation def: "Annotate a molecular sequence record with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000226 ! Annotation relationship: has_input EDAM:0000849 ! Sequence record {minCardinality=1} relationship: has_output EDAM:0000849 ! Sequence record {minCardinality=1} [Term] id: EDAM:0000362 name: Genome annotation namespace: operation def: "Annotate a genome sequence with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000361 ! Sequence annotation [Term] id: EDAM:0002466 name: Map annotation namespace: operation def: "Annotate a DNA map of some type with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000226 ! Annotation is_a: EDAM:0002521 ! Map data processing relationship: has_input EDAM:0001274 ! Map {minCardinality=1} relationship: has_output EDAM:0001274 ! Map {minCardinality=1} [Term] id: EDAM:0000227 name: Data indexing namespace: operation def: "Generate an index of (typically a file of) biological data." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Database indexing" EXACT [] is_a: EDAM:0002412 ! Data index processing relationship: has_output EDAM:0000955 ! Data index [Term] id: EDAM:0000228 name: Data index analysis namespace: operation def: "Analyse an index of biological data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002412 ! Data index processing is_a: EDAM:0002412 ! Data index processing synonym: "Database index analysis" EXACT [] relationship: has_input EDAM:0000955 ! Data index {minCardinality=1} relationship: has_output EDAM:0000956 ! Data index report {minCardinality=1} [Term] id: EDAM:0002478 name: Nucleic acid sequence analysis namespace: operation def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002448 ! Sequence processing (nucleic acid) relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=1} relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0003095 name: Nucleic acid design namespace: operation def: "Design (or predict) nucleic acid sequences with specific chemical or physical properties." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002478 ! Nucleic acid sequence analysis [Term] id: EDAM:0002479 name: Protein sequence analysis namespace: operation def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002447 ! Sequence processing (protein) synonym: "Sequence analysis (protein)" EXACT [] relationship: has_input EDAM:0002976 ! Protein sequence {minCardinality=1} relationship: has_topic EDAM:0000639 ! Protein sequence analysis [Term] id: EDAM:0002446 name: Sequence processing namespace: operation alt_id: EDAM:0002449 def: "Process (read and / or write) one or more molecular sequences and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence processing (general)" EXACT [] is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=0} relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} relationship: has_topic EDAM:0000080 ! Sequence analysis [Term] id: EDAM:0002447 name: Sequence processing (protein) namespace: operation def: "Process (read and / or write) a protein sequence and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002446 ! Sequence processing is_a: EDAM:0002502 ! Protein data processing relationship: has_input EDAM:0002976 ! Protein sequence {minCardinality=0} relationship: has_output EDAM:0002976 ! Protein sequence {minCardinality=0} [Term] id: EDAM:0002448 name: Sequence processing (nucleic acid) namespace: operation def: "Process (read and / or write) a nucleotide sequence and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002446 ! Sequence processing is_a: EDAM:0002501 ! Nucleic acid data processing relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=0} relationship: has_output EDAM:0002977 ! Nucleic acid sequence {minCardinality=0} [Term] id: EDAM:0000229 name: Annotation retrieval (sequence) namespace: operation def: "Retrieve basic information about a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0001813 ! Sequence retrieval [Term] id: EDAM:0000230 name: Sequence generation namespace: operation def: "Generate a molecular sequence by some means." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002121 ! Sequence file processing [Term] id: EDAM:0002513 name: Sequence generation (nucleic acid) namespace: operation def: "Generate a nucleic acid sequence by some means." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000230 ! Sequence generation is_a: EDAM:0002448 ! Sequence processing (nucleic acid) relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0002514 name: Sequence generation (protein) namespace: operation def: "Generate a protein sequence by some means." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000230 ! Sequence generation is_a: EDAM:0002447 ! Sequence processing (protein) relationship: has_topic EDAM:0000639 ! Protein sequence analysis [Term] id: EDAM:0000231 name: Sequence editing namespace: operation def: "Edit or change a molecular sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002121 ! Sequence file processing is_a: EDAM:0003096 ! Editing [Term] id: EDAM:0002511 name: Sequence editing (nucleic acid) namespace: operation def: "Edit or change a nucleic acid sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000231 ! Sequence editing is_a: EDAM:0002448 ! Sequence processing (nucleic acid) [Term] id: EDAM:0002512 name: Sequence editing (protein) namespace: operation def: "Edit or change a protein sequence, either randomly or specifically." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000231 ! Sequence editing is_a: EDAM:0002447 ! Sequence processing (protein) [Term] id: EDAM:0000232 name: Sequence merging namespace: operation def: "Merge two or more (typically overlapping) molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence splicing" EXACT [] is_a: EDAM:0000231 ! Sequence editing [Term] id: EDAM:0000233 name: Sequence conversion namespace: operation def: "Convert a molecular sequence from one type to another." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000231 ! Sequence editing [Term] id: EDAM:0001780 name: Sequence submission namespace: operation def: "Submit a molecular sequence to a database." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} relationship: has_topic EDAM:0000091 ! Data handling [Term] id: EDAM:0000234 name: Sequence complexity calculation namespace: operation alt_id: EDAM:0000373 alt_id: EDAM:0000374 def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000236 ! Sequence composition calculation relationship: has_output EDAM:0001259 ! Sequence complexity {minCardinality=1} relationship: has_topic EDAM:0000642 ! Low complexity sequences [Term] id: EDAM:0000235 name: Sequence ambiguity calculation namespace: operation alt_id: EDAM:0000375 alt_id: EDAM:0000376 def: "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000236 ! Sequence composition calculation relationship: has_output EDAM:0001260 ! Sequence ambiguity {minCardinality=1} relationship: has_topic EDAM:0000157 ! Sequence composition analysis [Term] id: EDAM:0000291 name: Sequence clustering namespace: operation def: "Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [EDAM:EBI "EMBRACE definition"] comment: The clusters may be output or used internally for some other purpose. subset: operation synonym: "Sequence cluster generation" EXACT [] is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002452 ! Sequence cluster processing is_a: EDAM:0002995 ! Sequence classification relationship: has_output EDAM:0001235 ! Sequence cluster {minCardinality=0} [Term] id: EDAM:0000236 name: Sequence composition calculation namespace: operation def: "Calculate character or word composition or frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002403 ! Sequence analysis relationship: has_output EDAM:0001261 ! Sequence composition relationship: has_topic EDAM:0000157 ! Sequence composition analysis relationship: has_topic EDAM:0000157 ! Sequence composition analysis [Term] id: EDAM:0000237 name: Repeat sequence analysis namespace: operation def: "Find and/or analyse repeat sequences in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] comment: Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. subset: operation is_a: EDAM:0002403 ! Sequence analysis relationship: has_topic EDAM:0000641 ! Repeat sequences [Term] id: EDAM:0000290 name: Sequence redundancy removal namespace: operation def: "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000291 ! Sequence clustering relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} relationship: has_topic EDAM:0000164 ! Sequence clustering [Term] id: EDAM:0002451 name: Sequence comparison namespace: operation def: "Compare two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002424 ! Comparison relationship: has_input EDAM:0002044 ! Sequence {minCardinality=2} relationship: has_output EDAM:0002955 ! Sequence report relationship: has_topic EDAM:0000159 ! Sequence comparison [Term] id: EDAM:0002508 name: Nucleic acid sequence comparison namespace: operation def: "Compare two or more nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence comparison (nucleic acid)" EXACT [] is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002478 ! Nucleic acid sequence analysis is_a: EDAM:0002998 ! Nucleic acid comparison [Term] id: EDAM:0002509 name: Protein sequence comparison namespace: operation def: "Compare two or more protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence comparison (protein)" EXACT [] is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002479 ! Protein sequence analysis is_a: EDAM:0002997 ! Protein comparison [Term] id: EDAM:0000288 name: Sequence word comparison namespace: operation def: "Find exact character or word matches between molecular sequences without full sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002451 ! Sequence comparison relationship: has_output EDAM:0000861 ! Sequence alignment (words) {minCardinality=1} [Term] id: EDAM:0000289 name: Sequence distance matrix generation namespace: operation def: "Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Phylogenetic distance matrix generation" EXACT [] is_a: EDAM:0002451 ! Sequence comparison relationship: has_output EDAM:0000870 ! Sequence distance matrix relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] id: EDAM:0000266 name: Vector sequence detection namespace: operation def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002508 ! Nucleic acid sequence comparison is_a: EDAM:0000415 ! Nucleic acid feature detection [Term] id: EDAM:0002233 name: Representative sequence identification namespace: operation def: "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000291 ! Sequence clustering relationship: has_topic EDAM:0000164 ! Sequence clustering [Term] id: EDAM:0000317 name: EST and cDNA sequence analysis namespace: operation def: "Analyse EST or cDNA sequences." [EDAM:EBI "EMBRACE definition"] comment: For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. subset: operation is_obsolete: true consider: EDAM:0002403 ! Sequence analysis [Term] id: EDAM:0000265 name: Frameshift error detection namespace: operation def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [EDAM:EBI "EMBRACE definition"] comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. subset: operation is_a: EDAM:0002508 ! Nucleic acid sequence comparison is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_topic EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0000241 name: Transcription regulatory sequence analysis namespace: operation def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. subset: operation is_obsolete: true consider: EDAM:0000438 ! Transcription regulatory element prediction [Term] id: EDAM:0000281 name: Genetic marker identification namespace: operation def: "Identify genetic markers in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. subset: operation is_obsolete: true consider: EDAM:0000415 ! Nucleic acid feature detection [Term] id: EDAM:0000363 name: Nucleic acid sequence reverse and complement namespace: operation def: "Generate the reverse and / or complement of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002513 ! Sequence generation (nucleic acid) [Term] id: EDAM:0000364 name: Random sequence generation namespace: operation def: "Generate a random sequence, for example, with a specific character composition." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000230 ! Sequence generation [Term] id: EDAM:0000365 name: Nucleic acid restriction digest namespace: operation def: "Generate digest fragments for a nucleotide sequence containing restriction sites." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002513 ! Sequence generation (nucleic acid) is_a: EDAM:0000262 ! Nucleic acid property calculation relationship: has_output EDAM:0001239 ! Restriction digest relationship: has_topic EDAM:0000100 ! Nucleic acid restriction [Term] id: EDAM:0000366 name: Protein sequence cleavage namespace: operation def: "Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002514 ! Sequence generation (protein) is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001238 ! Proteolytic digest relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0000367 name: Sequence mutation and randomization namespace: operation def: "Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000231 ! Sequence editing [Term] id: EDAM:0000368 name: Sequence masking namespace: operation def: "Mask characters in a molecular sequence (replacing those characters with a mask character)." [EDAM:EBI "EMBRACE definition"] comment: For example, SNPs or repeats in a DNA sequence might be masked. subset: operation is_a: EDAM:0000231 ! Sequence editing relationship: has_input EDAM:0000851 ! Sequence mask character {minCardinality=1} [Term] id: EDAM:0000369 name: Sequence cutting namespace: operation def: "Cut (remove) characters or a region from a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000231 ! Sequence editing [Term] id: EDAM:0000370 name: Restriction site creation namespace: operation def: "Create (or remove) restriction sites in sequences, for example using silent mutations." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002511 ! Sequence editing (nucleic acid) relationship: has_topic EDAM:0000100 ! Nucleic acid restriction [Term] id: EDAM:0000371 name: DNA translation namespace: operation def: "Translate a DNA sequence into protein." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000233 ! Sequence conversion relationship: has_topic EDAM:0000108 ! Translation [Term] id: EDAM:0000372 name: DNA transcription namespace: operation def: "Transcribe a nucleotide sequence into mRNA sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000233 ! Sequence conversion relationship: has_topic EDAM:0000110 ! Transcription [Term] id: EDAM:0002510 name: DNA back-translation namespace: operation def: "Back-translate a protein sequence into DNA." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000233 ! Sequence conversion relationship: has_topic EDAM:0000108 ! Translation [Term] id: EDAM:0000377 name: Sequence composition calculation (nucleic acid) namespace: operation def: "Calculate base frequency or word composition of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000236 ! Sequence composition calculation is_a: EDAM:0000262 ! Nucleic acid property calculation [Term] id: EDAM:0000378 name: Sequence composition calculation (protein) namespace: operation def: "Calculate amino acid frequency or word composition of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000236 ! Sequence composition calculation is_a: EDAM:0003088 ! Protein property calculation (from sequence) [Term] id: EDAM:0002284 name: Nucleic acid density plotting namespace: operation def: "Calculate a density plot (of base composition) for a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000377 ! Sequence composition calculation (nucleic acid) [Term] id: EDAM:0000379 name: Repeat sequence detection namespace: operation alt_id: EDAM:0002450 def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000237 ! Repeat sequence analysis is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001299 ! Sequence features (repeats) [Term] id: EDAM:0000380 name: Repeat sequence organisation analysis namespace: operation def: "Analyse repeat sequence organization such as periodicity." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000237 ! Repeat sequence analysis is_a: EDAM:0000236 ! Sequence composition calculation [Term] id: EDAM:0000490 name: Dotplot plotting namespace: operation def: "Draw a dotplot of sequence similarities identified from word-matching or character comparison." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000288 ! Sequence word comparison is_a: EDAM:0000565 ! Sequence alignment rendering relationship: has_output EDAM:0000862 ! Dotplot {minCardinality=1} [Term] id: EDAM:0000242 name: Conserved transcription regulatory sequence identification namespace: operation def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." [EDAM:EBI "EMBRACE definition"] comment: For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. subset: operation is_a: EDAM:0000438 ! Transcription regulatory element prediction is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001315 ! Gene features (TFBS) [Term] id: EDAM:0000238 name: Sequence motif discovery namespace: operation def: "Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery)." [EDAM:EBI "EMBRACE definition"] comment: Motifs and patterns might be conserved or over-represented (occur with improbable frequency). subset: operation synonym: "Motif discovery" EXACT [] is_a: EDAM:0000253 ! Sequence feature detection is_a: EDAM:0002404 ! Sequence motif processing relationship: has_output EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0000239 name: Sequence motif recognition namespace: operation def: "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequence motif detection" EXACT [] is_a: EDAM:0002404 ! Sequence motif processing is_a: EDAM:0000253 ! Sequence feature detection relationship: has_output EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0000240 name: Sequence motif comparison namespace: operation def: "Find motifs shared by molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002451 ! Sequence comparison is_a: EDAM:0002404 ! Sequence motif processing relationship: has_output EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0002123 name: Small molecule data processing namespace: operation def: "Process (read and / or write) physicochemical property data for small molecules." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002420 ! Analysis and processing [Term] id: EDAM:0000250 name: Protein property calculation namespace: operation alt_id: EDAM:0002933 def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [EDAM:EBI "EMBRACE definition"] comment: This includes methods to render and visualise the properties of a protein sequence. subset: operation synonym: "Protein property rendering" EXACT [] is_a: EDAM:0002502 ! Protein data processing is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_input EDAM:0000897 ! Protein property {minCardinality=0} relationship: has_output EDAM:0000897 ! Protein property {minCardinality=0} relationship: has_topic EDAM:0000123 ! Protein properties [Term] id: EDAM:0003088 name: Protein property calculation (from sequence) namespace: operation def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000250 ! Protein property calculation is_a: EDAM:0002479 ! Protein sequence analysis [Term] id: EDAM:0000261 name: Nucleic acid property processing namespace: operation def: "Process (read and / or write) physicochemical property data of nucleic acids." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000262 ! Nucleic acid property calculation [Term] id: EDAM:0000334 name: Enzyme kinetics calculation namespace: operation def: "Calculate Km, Vmax and derived data for an enzyme reaction." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0002024 ! Enzyme kinetics data {minCardinality=1} relationship: has_topic EDAM:0000821 ! Enzymes and reactions [Term] id: EDAM:0000398 name: Protein molecular weight calculation namespace: operation def: "Calculate the molecular weight of a protein sequence or fragments." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001519 ! Peptide molecular weights {minCardinality=1} relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0002930 name: Protein property comparison namespace: operation def: "Compare the physicochemical properties of two or more proteins (or reference data)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002997 ! Protein comparison relationship: has_output EDAM:0000897 ! Protein property {minCardinality=1} [Term] id: EDAM:0002929 name: Protein fragment weight comparison namespace: operation def: "Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000398 ! Protein molecular weight calculation is_a: EDAM:0002930 ! Protein property comparison [Term] id: EDAM:0000399 name: Protein extinction coefficient calculation namespace: operation def: "Predict extinction coefficients or optical density of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001531 ! Protein extinction coefficient {minCardinality=1} [Term] id: EDAM:0000400 name: Protein pH-dependent property calculation namespace: operation def: "Calculate pH-dependent properties from pKa calculations of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0000897 ! Protein property relationship: has_topic EDAM:0000137 ! Protein hydropathy [Term] id: EDAM:0000401 name: Protein hydropathy calculation (from sequence) namespace: operation def: "Hydropathy calculation on a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002574 ! Protein hydropathy calculation [Term] id: EDAM:0000252 name: Peptide immunogenicity prediction namespace: operation def: "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins." [EDAM:EBI "EMBRACE definition"] comment: This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. subset: operation is_a: EDAM:0002492 ! Protein interaction prediction is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001534 ! Peptide immunogenicity {minCardinality=1} relationship: has_topic EDAM:0000804 ! Immunoinformatics [Term] id: EDAM:0002932 name: Hopp and Woods plotting namespace: operation def: "Generate a Hopp and Woods plot of antigenicity of a protein." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000252 ! Peptide immunogenicity prediction [Term] id: EDAM:0000402 name: Protein titration curve plotting namespace: operation def: "Plot a protein titration curve." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000400 ! Protein pH-dependent property calculation relationship: has_output EDAM:0001527 ! Protein titration curve {minCardinality=1} [Term] id: EDAM:0000403 name: Protein isoelectric point calculation namespace: operation def: "Calculate isoelectric point of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000400 ! Protein pH-dependent property calculation relationship: has_output EDAM:0001528 ! Protein isoelectric point {minCardinality=1} [Term] id: EDAM:0000404 name: Protein hydrogen exchange rate calculation namespace: operation def: "Estimate hydrogen exchange rate of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000400 ! Protein pH-dependent property calculation relationship: has_output EDAM:0001530 ! Protein hydrogen exchange rate {minCardinality=1} [Term] id: EDAM:0000405 name: Protein hydrophobic region calculation namespace: operation def: "Calculate hydrophobic or hydrophilic / charged regions of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) [Term] id: EDAM:0000406 name: Protein aliphatic index calculation namespace: operation def: "Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM:0001521 ! Protein aliphatic index {minCardinality=1} [Term] id: EDAM:0000407 name: Protein hydrophobic moment plotting namespace: operation def: "Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity." [EDAM:EBI "EMBRACE definition"] comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM:0001520 ! Peptide hydrophobic moment {minCardinality=1} [Term] id: EDAM:0000408 name: Protein globularity prediction namespace: operation def: "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM:0001526 ! Protein globularity {minCardinality=1} [Term] id: EDAM:0000409 name: Protein solubility prediction namespace: operation def: "Predict the solubility or atomic solvation energy of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM:0001524 ! Protein solubility {minCardinality=1} [Term] id: EDAM:0000410 name: Protein crystallizability prediction namespace: operation def: "Predict crystallizability of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM:0001525 ! Protein crystallizability {minCardinality=1} [Term] id: EDAM:0000455 name: Nucleic acid thermodynamic property calculation namespace: operation def: "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000262 ! Nucleic acid property calculation relationship: has_output EDAM:0002985 ! Nucleic acid thermodynamic data {minCardinality=1} [Term] id: EDAM:0000456 name: Nucleic acid melting profile plotting namespace: operation def: "Calculate and plot a DNA or DNA/RNA melting profile." [EDAM:EBI "EMBRACE definition"] comment: A melting profile is used to visualise and analyse partly melted DNA conformations. subset: operation is_a: EDAM:0000262 ! Nucleic acid property calculation relationship: has_output EDAM:0001583 ! Nucleic acid melting profile {minCardinality=1} [Term] id: EDAM:0000262 name: Nucleic acid property calculation namespace: operation def: "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002478 ! Nucleic acid sequence analysis relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=1} [Term] id: EDAM:0002439 name: RNA secondary structure processing namespace: operation def: "Process (read and / or write) RNA secondary structure data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002482 ! Secondary structure processing is_a: EDAM:0002501 ! Nucleic acid data processing relationship: has_input EDAM:0000880 ! RNA secondary structure {minCardinality=0} relationship: has_output EDAM:0000880 ! RNA secondary structure {minCardinality=0} relationship: has_topic EDAM:0000097 ! Nucleic acid structure analysis relationship: has_topic EDAM:0000697 ! RNA structure and alignment [Term] id: EDAM:0002519 name: Structure processing (nucleic acid) namespace: operation def: "Process (read and / or write) nucleic acid tertiary structure data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002465 ! Structure processing is_a: EDAM:0002501 ! Nucleic acid data processing relationship: has_input EDAM:0001459 ! Nucleic acid structure {minCardinality=0} relationship: has_output EDAM:0001459 ! Nucleic acid structure {minCardinality=0} relationship: has_topic EDAM:0000097 ! Nucleic acid structure analysis [Term] id: EDAM:0002440 name: Structure processing (RNA) namespace: operation def: "Process (read and / or write) RNA tertiary structure data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002519 ! Structure processing (nucleic acid) [Term] id: EDAM:0000278 name: RNA secondary structure prediction namespace: operation def: "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." [EDAM:EBI "EMBRACE definition"] comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). subset: operation is_a: EDAM:0002439 ! RNA secondary structure processing is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0000880 ! RNA secondary structure {minCardinality=1} relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0002441 name: RNA structure prediction namespace: operation def: "Predict RNA tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000475 ! Nucleic acid structure prediction relationship: has_output EDAM:0001465 ! RNA structure {minCardinality=1} [Term] id: EDAM:0002442 name: DNA structure prediction namespace: operation def: "Predict DNA tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000475 ! Nucleic acid structure prediction relationship: has_output EDAM:0001464 ! DNA structure {minCardinality=1} [Term] id: EDAM:0000279 name: Nucleic acid folding analysis namespace: operation def: "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002426 ! Modelling and simulation is_a: EDAM:0002501 ! Nucleic acid data processing synonym: "Nucleic acid folding" EXACT [] synonym: "Nucleic acid folding modelling" EXACT [] relationship: has_output EDAM:0001596 ! Nucleic acid folding report relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0000461 name: Nucleic acid curvature calculation namespace: operation def: "Calculate curvature and flexibility / stiffness of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] comment: This includes properties such as. subset: operation is_a: EDAM:0000262 ! Nucleic acid property calculation relationship: has_output EDAM:0000912 ! Nucleic acid property {minCardinality=1} relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0001768 name: Nucleic acid folding family identification namespace: operation def: "Identify folding families of related RNAs." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000483 ! Structured RNA prediction and optimisation [Term] id: EDAM:0001769 name: Nucleic acid folding energy calculation namespace: operation def: "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000279 ! Nucleic acid folding analysis [Term] id: EDAM:0001777 name: Protein function prediction namespace: operation def: "Predict general functional properties of a protein." [EDAM:EBI "EMBRACE definition"] comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. subset: operation is_a: EDAM:0002414 ! Protein function analysis is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_topic EDAM:0002276 ! Protein function prediction [Term] id: EDAM:0003084 name: Protein function prediction (from sequence) namespace: operation def: "Predict general (non-positional) functional properties of a protein from analysing its sequence." [EDAM:EBI "EMBRACE definition"] comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. subset: operation is_a: EDAM:0001777 ! Protein function prediction is_a: EDAM:0002479 ! Protein sequence analysis is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_topic EDAM:0002276 ! Protein function prediction [Term] id: EDAM:0001778 name: Protein function comparison namespace: operation def: "Compare the functional properties of two or more proteins." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002414 ! Protein function analysis is_a: EDAM:0002997 ! Protein comparison relationship: has_topic EDAM:0001775 ! Protein function analysis [Term] id: EDAM:0000413 name: MHC peptide immunogenicity prediction namespace: operation def: "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000252 ! Peptide immunogenicity prediction [Term] id: EDAM:0000253 name: Sequence feature detection namespace: operation def: "Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002423 ! Prediction, detection and recognition relationship: has_output EDAM:0001255 ! Sequence features {minCardinality=1} relationship: has_topic EDAM:0003072 ! Sequence feature detection [Term] id: EDAM:0002453 name: Feature table processing namespace: operation def: "Process (read and / or write) a sequence feature table." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0001270 ! Sequence feature table {minCardinality=0} relationship: has_input EDAM:0002201 ! Sequence record full {minCardinality=0} relationship: has_output EDAM:0001255 ! Sequence features {minCardinality=0} relationship: has_topic EDAM:0000160 ! Sequence sites and features [Term] id: EDAM:0000254 name: Data retrieval (feature table) namespace: operation def: "Extract a sequence feature table from a sequence database entry." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002422 ! Data retrieval [Term] id: EDAM:0000255 name: Feature table query namespace: operation def: "Query the features (in a feature table) of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002453 ! Feature table processing relationship: has_input EDAM:0001270 ! Sequence feature table {minCardinality=0} relationship: has_input EDAM:0002201 ! Sequence record full {minCardinality=0} relationship: has_output EDAM:0001255 ! Sequence features [Term] id: EDAM:0000256 name: Feature table comparison namespace: operation def: "Compare the feature tables of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002453 ! Feature table processing is_a: EDAM:0002424 ! Comparison relationship: has_input EDAM:0001270 ! Sequence feature table {minCardinality=0} relationship: has_input EDAM:0002201 ! Sequence record full {minCardinality=0} [Term] id: EDAM:0003092 name: Protein feature detection namespace: operation def: "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002502 ! Protein data processing is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM:0001277 ! Protein features {minCardinality=1} relationship: has_topic EDAM:0003074 ! Protein feature detection [Term] id: EDAM:0000414 name: Protein feature detection (from sequence) namespace: operation def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." [EDAM:EBI "EMBRACE definition"] comment: Methods typically involve scanning for known motifs, patterns and regular expressions. subset: operation synonym: "Sequence feature detection (protein)" EXACT [] is_a: EDAM:0003092 ! Protein feature detection is_a: EDAM:0000253 ! Sequence feature detection is_a: EDAM:0002479 ! Protein sequence analysis [Term] id: EDAM:0003090 name: Protein feature detection (from structure) namespace: operation def: "Predict, recognise and identify positional features in proteins from analysing protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003092 ! Protein feature detection is_a: EDAM:0002406 ! Protein structure analysis [Term] id: EDAM:0003087 name: Protein site detection namespace: operation alt_id: EDAM:0000382 def: "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "name: Sequence motif recognition (protein)" EXACT [] is_a: EDAM:0000414 ! Protein feature detection (from sequence) is_a: EDAM:0000239 ! Sequence motif recognition [Term] id: EDAM:0000415 name: Nucleic acid feature detection namespace: operation alt_id: EDAM:0000381 def: "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions." [EDAM:EBI "EMBRACE definition"] comment: Methods typically involve scanning for known motifs, patterns and regular expressions. subset: operation synonym: "Sequence feature detection (nucleic acid)" EXACT [] is_a: EDAM:0000239 ! Sequence motif recognition is_a: EDAM:0002478 ! Nucleic acid sequence analysis is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM:0001276 ! Nucleic acid features {minCardinality=1} relationship: has_topic EDAM:0003073 ! Nucleic acid feature detection [Term] id: EDAM:0000416 name: Epitope mapping namespace: operation def: "Predict antigenic determinant sites (epitopes) in protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Epitope mapping is commonly done during vaccine design. subset: operation is_a: EDAM:0003087 ! Protein site detection is_a: EDAM:0002429 ! Mapping and assembly relationship: has_output EDAM:0001326 ! Protein features (binding sites) relationship: has_topic EDAM:0000804 ! Immunoinformatics [Term] id: EDAM:0000417 name: Protein post-translation modification site prediction namespace: operation def: "Predict post-translation modification sites in protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. subset: operation is_a: EDAM:0003087 ! Protein site detection relationship: has_output EDAM:0001324 ! Protein features (post-translation modifications) relationship: has_topic EDAM:0000601 ! Protein modifications [Term] id: EDAM:0002489 name: Protein subcellular localization prediction namespace: operation def: "Predict the subcellular localization of a protein sequence." [EDAM:EBI "EMBRACE definition"] comment: The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. subset: operation synonym: "Protein targeting prediction" EXACT [] is_a: EDAM:0003084 ! Protein function prediction (from sequence) is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_topic EDAM:0000140 ! Protein targeting and localization [Term] id: EDAM:0000418 name: Protein signal peptide detection namespace: operation def: "Detect or predict signal peptides and signal peptide cleavage sites in protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. subset: operation is_a: EDAM:0003087 ! Protein site detection is_a: EDAM:0002489 ! Protein subcellular localization prediction relationship: has_output EDAM:0001322 ! Protein features (signal peptides) relationship: has_topic EDAM:0000140 ! Protein targeting and localization [Term] id: EDAM:0000419 name: Binding site prediction (from sequence) namespace: operation def: "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Ligand-binding and active site prediction (from sequence)" EXACT [] is_a: EDAM:0003087 ! Protein site detection is_a: EDAM:0002575 ! Binding site prediction [Term] id: EDAM:0000420 name: Protein-nucleic acid binding prediction namespace: operation def: "Predict RNA and DNA-binding binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000419 ! Binding site prediction (from sequence) relationship: has_output EDAM:0001326 ! Protein features (binding sites) {minCardinality=0} [Term] id: EDAM:0000421 name: Protein folding site prediction namespace: operation def: "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003087 ! Protein site detection is_a: EDAM:0002415 ! Protein folding analysis relationship: has_output EDAM:0002989 ! Protein features (key folding sites) {minCardinality=1} [Term] id: EDAM:0000422 name: Protein cleavage site prediction namespace: operation def: "Detect or predict cleavage sites (enzymatic or chemical) in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003087 ! Protein site detection relationship: has_output EDAM:0001323 ! Protein features (cleavage sites) relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0000423 name: Epitope mapping (MHC Class I) namespace: operation def: "Predict epitopes that bind to MHC class I molecules." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000416 ! Epitope mapping [Term] id: EDAM:0000424 name: Epitope mapping (MHC Class II) namespace: operation def: "Predict epitopes that bind to MHC class II molecules." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000416 ! Epitope mapping [Term] id: EDAM:0000411 name: Protein signal peptide detection (eukaryotes) namespace: operation def: "Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000418 ! Protein signal peptide detection [Term] id: EDAM:0000412 name: Protein signal peptide detection (bacteria) namespace: operation def: "Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000418 ! Protein signal peptide detection [Term] id: EDAM:0002454 name: Gene and gene component prediction namespace: operation def: "Detect, predict and identify genes or components of genes in DNA sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Gene finding" EXACT [] is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001300 ! Nucleic acid features (gene structure) relationship: has_topic EDAM:0000109 ! Gene finding [Term] id: EDAM:0000425 name: Whole gene prediction namespace: operation def: "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002454 ! Gene and gene component prediction [Term] id: EDAM:0000426 name: Gene component prediction namespace: operation def: "Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. subset: operation is_a: EDAM:0002454 ! Gene and gene component prediction [Term] id: EDAM:0000427 name: Transposon prediction namespace: operation def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001301 ! Nucleic acid features (mobile genetic elements) [Term] id: EDAM:0000428 name: PolyA signal detection namespace: operation def: "Detect polyA signals in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001302 ! Nucleic acid features (PolyA signal or site) [Term] id: EDAM:0000429 name: Quadruplex formation site detection namespace: operation alt_id: EDAM:0002455 def: "Detect quadruplex-forming motifs in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. subset: operation is_a: EDAM:0000415 ! Nucleic acid feature detection synonym: "Quadruplex structure prediction" EXACT [] relationship: has_output EDAM:0001303 ! Nucleic acid features (quadruplexes) relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0000430 name: CpG island and isochore detection namespace: operation alt_id: EDAM:0000576 def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences." [EDAM:EBI "EMBRACE definition"] comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. subset: operation synonym: "CpG island and isochores detection" EXACT [] synonym: "CpG island and isochores rendering" EXACT [] is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001304 ! Nucleic acid features (CpG island and isochore) relationship: has_topic EDAM:0000157 ! Sequence composition analysis [Term] id: EDAM:0000431 name: Restriction site recognition namespace: operation def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001305 ! Nucleic acid features (restriction sites) relationship: has_topic EDAM:0000100 ! Nucleic acid restriction [Term] id: EDAM:0000433 name: Splice site prediction namespace: operation def: "Identify, predict or analyse splice sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might require a pre-mRNA or genomic DNA sequence. subset: operation is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001307 ! Nucleic acid features (splice sites) relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing [Term] id: EDAM:0000453 name: Nucleosome formation potential prediction namespace: operation def: "Predict nucleosome formation potential of DNA sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000432 ! Nucleosome formation or exclusion sequence prediction [Term] id: EDAM:0000432 name: Nucleosome formation or exclusion sequence prediction namespace: operation def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000415 ! Nucleic acid feature detection relationship: has_output EDAM:0001306 ! Nucleic acid features (nucleosome exclusion sequences) [Term] id: EDAM:0000434 name: Integrated gene prediction namespace: operation def: "Predict whole gene structure using a combination of multiple methods to achieve better predictions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000425 ! Whole gene prediction [Term] id: EDAM:0000435 name: Operon prediction namespace: operation def: "Find operons (operators, promoters and genes) in bacteria genes." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000425 ! Whole gene prediction [Term] id: EDAM:0000464 name: tRNA gene prediction namespace: operation def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000425 ! Whole gene prediction relationship: has_topic EDAM:0000663 ! tRNA [Term] id: EDAM:0000436 name: Coding region prediction namespace: operation def: "Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000426 ! Gene component prediction relationship: has_output EDAM:0001313 ! Nucleic acid features (coding sequence) [Term] id: EDAM:0000437 name: Selenocysteine insertion sequence (SECIS) prediction namespace: operation def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. subset: operation is_a: EDAM:0000426 ! Gene component prediction relationship: has_output EDAM:0001300 ! Nucleic acid features (gene structure) [Term] id: EDAM:0000438 name: Transcription regulatory element prediction namespace: operation def: "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. subset: operation is_a: EDAM:0000426 ! Gene component prediction relationship: has_topic EDAM:0000110 ! Transcription relationship: has_topic EDAM:0000749 ! Transcription factors and regulatory sites [Term] id: EDAM:0000439 name: Translation initiation site prediction namespace: operation def: "Predict translation initiation sites, possibly by searching a database of sites." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000436 ! Coding region prediction relationship: has_topic EDAM:0000108 ! Translation [Term] id: EDAM:0000440 name: Promoter prediction namespace: operation def: "Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. subset: operation is_a: EDAM:0000438 ! Transcription regulatory element prediction relationship: has_output EDAM:0001312 ! Gene features (promoter) [Term] id: EDAM:0000441 name: Transcription regulatory element prediction (DNA-cis) namespace: operation def: "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. subset: operation is_a: EDAM:0000438 ! Transcription regulatory element prediction [Term] id: EDAM:0000442 name: Transcription regulatory element prediction (RNA-cis) namespace: operation def: "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." [EDAM:EBI "EMBRACE definition"] comment: Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. subset: operation is_a: EDAM:0000438 ! Transcription regulatory element prediction [Term] id: EDAM:0000443 name: Transcription regulatory element prediction (trans) namespace: operation def: "Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets." [EDAM:EBI "EMBRACE definition"] comment: Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. subset: operation synonym: "Functional RNA identification" EXACT [] is_a: EDAM:0000438 ! Transcription regulatory element prediction relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] id: EDAM:0000444 name: Matrix/scaffold attachment site prediction namespace: operation def: "Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. subset: operation is_a: EDAM:0000438 ! Transcription regulatory element prediction relationship: has_output EDAM:0001308 ! Nucleic acid features (matrix/scaffold attachment sites) [Term] id: EDAM:0000445 name: Transcription factor binding site prediction namespace: operation def: "Identify or predict transcription factor binding sites in DNA sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000440 ! Promoter prediction relationship: has_output EDAM:0001315 ! Gene features (TFBS) [Term] id: EDAM:0000446 name: Exonic splicing enhancer prediction namespace: operation def: "Identify or predict exonic splicing enhancers (ESE) in exons." [EDAM:EBI "EMBRACE definition"] comment: An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. subset: operation is_a: EDAM:0000440 ! Promoter prediction relationship: has_output EDAM:0002397 ! Nucleic acid features (exon) relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing [Term] id: EDAM:0002008 name: siRNA duplex prediction namespace: operation def: "Identify or predict siRNA duplexes in RNA." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) relationship: has_output EDAM:0002169 ! Nucleic acid features (siRNA) relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] id: EDAM:0000465 name: siRNA binding specificity prediction namespace: operation def: "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] id: EDAM:0000463 name: microRNA detection namespace: operation def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000443 ! Transcription regulatory element prediction (trans) relationship: has_output EDAM:0001310 ! Nucleic acid features (microRNA) [Term] id: EDAM:0000259 name: Sequence alignment comparison namespace: operation def: "Compare (typically by aligning) two molecular sequence alignments." [EDAM:EBI "EMBRACE definition"] comment: See also 'Sequence profile alignment'. subset: operation is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002424 ! Comparison [Term] id: EDAM:0000260 name: Sequence alignment conversion namespace: operation def: "Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003081 ! Sequence alignment editing [Term] id: EDAM:0000447 name: Sequence alignment quality evaluation namespace: operation def: "Evaluate molecular sequence alignment accuracy." [EDAM:EBI "EMBRACE definition"] comment: Evaluation might be purely sequence-based or use structural information. subset: operation is_a: EDAM:0002428 ! Validation and standardisation is_a: EDAM:0000258 ! Sequence alignment analysis [Term] id: EDAM:0000448 name: Sequence alignment analysis (conservation) namespace: operation def: "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. subset: operation is_a: EDAM:0000258 ! Sequence alignment analysis relationship: has_output EDAM:0001415 ! Sequence alignment report (site conservation) [Term] id: EDAM:0000449 name: Sequence alignment analysis (site correlation) namespace: operation def: "Analyse correlations between sites in a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. subset: operation is_a: EDAM:0000258 ! Sequence alignment analysis relationship: has_output EDAM:0001416 ! Sequence alignment report (site correlation) [Term] id: EDAM:0000450 name: Sequence alignment analysis (chimeric sequence detection) namespace: operation def: "Detects chimeric sequences (chimeras) from a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. subset: operation is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) relationship: has_topic EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000451 name: Sequence alignment analysis (recombination detection) namespace: operation def: "Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. subset: operation is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) [Term] id: EDAM:0000452 name: Sequence alignment analysis (indel detection) namespace: operation def: "Identify insertion, deletion and duplication events from a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. subset: operation is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) [Term] id: EDAM:0000457 name: Nucleic acid stitch profile plotting namespace: operation def: "Calculate and plot a DNA or DNA/RNA stitch profile." [EDAM:EBI "EMBRACE definition"] comment: A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. subset: operation is_a: EDAM:0000456 ! Nucleic acid melting profile plotting relationship: has_output EDAM:0001587 ! Nucleic acid stitch profile [Term] id: EDAM:0000458 name: Nucleic acid melting curve plotting namespace: operation def: "Calculate and plot a DNA or DNA/RNA melting curve." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000456 ! Nucleic acid melting profile plotting relationship: has_output EDAM:0002958 ! Nucleic acid melting curve [Term] id: EDAM:0000459 name: Nucleic acid probability profile plotting namespace: operation def: "Calculate and plot a DNA or DNA/RNA probability profile." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000456 ! Nucleic acid melting profile plotting relationship: has_output EDAM:0002959 ! Nucleic acid probability profile [Term] id: EDAM:0000460 name: Nucleic acid temperature profile plotting namespace: operation def: "Calculate and plot a DNA or DNA/RNA temperature profile." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000456 ! Nucleic acid melting profile plotting relationship: has_output EDAM:0002960 ! Nucleic acid temperature profile [Term] id: EDAM:0002444 name: Protein secondary structure processing namespace: operation def: "Process (read and / or write) protein secondary structure data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002482 ! Secondary structure processing is_a: EDAM:0002502 ! Protein data processing relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=0} relationship: has_output EDAM:0000876 ! Protein features (secondary structure) {minCardinality=0} relationship: has_topic EDAM:0000694 ! Protein secondary structure [Term] id: EDAM:0000319 name: Protein secondary structure assignment namespace: operation def: "Assign secondary structure from protein coordinate or experimental data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002444 ! Protein secondary structure processing is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} relationship: has_topic EDAM:0002226 ! Structure determination [Term] id: EDAM:0000267 name: Protein secondary structure prediction namespace: operation def: "Predict secondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. subset: operation synonym: "Secondary structure prediction (protein)" EXACT [] is_a: EDAM:0002444 ! Protein secondary structure processing is_a: EDAM:0000414 ! Protein feature detection (from sequence) is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} relationship: has_topic EDAM:0000178 ! Protein secondary structure prediction [Term] id: EDAM:0000268 name: Protein super-secondary structure prediction namespace: operation def: "Predict super-secondary structure of protein sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. subset: operation is_a: EDAM:0000267 ! Protein secondary structure prediction relationship: has_output EDAM:0000877 ! Protein features (super-secondary) [Term] id: EDAM:0000534 name: Protein secondary structure assignment (from coordinate data) namespace: operation def: "Assign secondary structure from protein coordinate data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000319 ! Protein secondary structure assignment is_a: EDAM:0003090 ! Protein feature detection (from structure) [Term] id: EDAM:0000535 name: Protein secondary structure assignment (from CD data) namespace: operation def: "Assign secondary structure from circular dichroism (CD) spectroscopic data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000319 ! Protein secondary structure assignment relationship: has_input EDAM:0000939 ! Protein circular dichroism (CD) spectroscopic data [Term] id: EDAM:0001847 name: DSSP secondary structure assignment namespace: operation def: "Determine for residue the DSSP determined secondary structure in three-state (HSC)." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF: ResidueDSSP is_obsolete: true consider: EDAM:0000534 ! Protein secondary structure assignment (from coordinate data) [Term] id: EDAM:0000467 name: Protein secondary structure prediction (integrated) namespace: operation def: "Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000267 ! Protein secondary structure prediction [Term] id: EDAM:0000468 name: Protein secondary structure prediction (helices) namespace: operation def: "Predict helical secondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000267 ! Protein secondary structure prediction [Term] id: EDAM:0000469 name: Protein secondary structure prediction (turns) namespace: operation def: "Predict turn structure (for example beta hairpin turns) of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000267 ! Protein secondary structure prediction [Term] id: EDAM:0000470 name: Protein secondary structure prediction (coils) namespace: operation def: "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000267 ! Protein secondary structure prediction [Term] id: EDAM:0000471 name: Protein secondary structure prediction (disulfide bonds) namespace: operation def: "Predict cysteine bonding state and disulfide bond partners in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000267 ! Protein secondary structure prediction [Term] id: EDAM:0000269 name: Transmembrane protein prediction namespace: operation def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000270 ! Transmembrane protein analysis is_a: EDAM:0000267 ! Protein secondary structure prediction relationship: has_output EDAM:0001456 ! Protein features (membrane regions) {minCardinality=1} [Term] id: EDAM:0002456 name: GPCR classification namespace: operation def: "Classify G-protein coupled receptors (GPCRs) into families and subfamilies." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "G protein-coupled receptor (GPCR) classification" EXACT [] is_a: EDAM:0000473 ! GPCR analysis is_a: EDAM:0002995 ! Sequence classification relationship: has_output EDAM:0000907 ! Protein family {minCardinality=1} [Term] id: EDAM:0002457 name: GPCR coupling selectivity prediction namespace: operation def: "Predict G-protein coupled receptor (GPCR) coupling selectivity." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000473 ! GPCR analysis is_a: EDAM:0002492 ! Protein interaction prediction is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0000896 ! Protein report {minCardinality=1} [Term] id: EDAM:0000473 name: GPCR analysis namespace: operation def: "Analyse G-protein coupled receptor proteins (GPCRs)." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "G protein-coupled receptor (GPCR) analysis" EXACT [] is_a: EDAM:0000270 ! Transmembrane protein analysis relationship: has_output EDAM:0001456 ! Protein features (membrane regions) relationship: has_topic EDAM:0000820 ! Membrane proteins [Term] id: EDAM:0000472 name: GPCR prediction namespace: operation def: "Predict G protein-coupled receptors (GPCR)." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "G protein-coupled receptor (GPCR) prediction" EXACT [] is_a: EDAM:0000269 ! Transmembrane protein prediction is_a: EDAM:0000473 ! GPCR analysis [Term] id: EDAM:0000474 name: Protein structure prediction namespace: operation def: "Predict tertiary structure (backbone and side-chain conformation) of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000271 ! Structure prediction is_a: EDAM:0002459 ! Structure processing (protein) is_a: EDAM:0002479 ! Protein sequence analysis is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM:0001460 ! Protein structure {minCardinality=1} relationship: has_topic EDAM:0000179 ! Protein tertiary structure prediction [Term] id: EDAM:0000475 name: Nucleic acid structure prediction namespace: operation def: "Predict tertiary structure of DNA or RNA." [EDAM:EBI "EMBRACE definition"] comment: Methods might identify thermodynamically stable or evolutionarily conserved structures. subset: operation is_a: EDAM:0000271 ! Structure prediction is_a: EDAM:0002519 ! Structure processing (nucleic acid) is_a: EDAM:0002478 ! Nucleic acid sequence analysis is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM:0001459 ! Nucleic acid structure {minCardinality=1} relationship: has_topic EDAM:0000173 ! Nucleic acid structure prediction [Term] id: EDAM:0000476 name: Ab initio structure prediction namespace: operation def: "Predict tertiary structure of protein sequence(s) without homologs of known structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000474 ! Protein structure prediction relationship: has_topic EDAM:0000174 ! Ab initio structure prediction [Term] id: EDAM:0000477 name: Protein modelling namespace: operation def: "Build a three-dimensional protein model based on known (for example homologs) structures." [EDAM:EBI "EMBRACE definition"] comment: The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. subset: operation synonym: "Comparative modelling" EXACT [] synonym: "Homology modelling" EXACT [] synonym: "Homology structure modelling" EXACT [] synonym: "Protein structure comparative modelling" EXACT [] is_a: EDAM:0002406 ! Protein structure analysis is_a: EDAM:0000474 ! Protein structure prediction is_a: EDAM:0002426 ! Modelling and simulation relationship: has_topic EDAM:0000175 ! Homology modelling [Term] id: EDAM:0000478 name: Protein docking namespace: operation def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [EDAM:EBI "EMBRACE definition"] comment: This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. subset: operation is_a: EDAM:0000477 ! Protein modelling is_a: EDAM:0002492 ! Protein interaction prediction relationship: has_output EDAM:0001461 ! Protein-ligand complex {minCardinality=0} relationship: has_output EDAM:0002877 ! Protein complex {minCardinality=0} relationship: has_topic EDAM:0000177 ! Molecular docking [Term] id: EDAM:0000302 name: Protein threading namespace: operation def: "Align molecular sequence to structure in 3D space (threading)." [EDAM:EBI "EMBRACE definition"] comment: Use this term for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: operation synonym: "Sequence-structure alignment" EXACT [] is_a: EDAM:0000303 ! Protein fold recognition is_a: EDAM:0002928 ! Alignment relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=1} relationship: has_output EDAM:0000893 ! Sequence-structure alignment {minCardinality=1} relationship: has_topic EDAM:0000175 ! Homology modelling relationship: has_topic EDAM:0000184 ! Threading [Term] id: EDAM:0000479 name: Protein modelling (backbone) namespace: operation def: "Model protein backbone conformation." [EDAM:EBI "EMBRACE definition"] comment: Methods might require a preliminary C(alpha) trace. subset: operation is_a: EDAM:0000477 ! Protein modelling [Term] id: EDAM:0000480 name: Protein modelling (side chains) namespace: operation def: "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc." [EDAM:EBI "EMBRACE definition"] comment: Methods might use a residue rotamer library. subset: operation is_a: EDAM:0000477 ! Protein modelling [Term] id: EDAM:0000481 name: Protein modelling (loops) namespace: operation def: "Model loop conformation in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000477 ! Protein modelling [Term] id: EDAM:0001841 name: Rotamer likelihood prediction namespace: operation def: "Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure." [EDAM:WHATIF "EMBRACE definition"] comment: Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. subset: operation xref: WHATIF:ShowLikelyRotamers xref: WHATIF:ShowLikelyRotamers100 xref: WHATIF:ShowLikelyRotamers200 xref: WHATIF:ShowLikelyRotamers300 xref: WHATIF:ShowLikelyRotamers400 xref: WHATIF:ShowLikelyRotamers500 xref: WHATIF:ShowLikelyRotamers600 xref: WHATIF:ShowLikelyRotamers700 xref: WHATIF:ShowLikelyRotamers800 xref: WHATIF:ShowLikelyRotamers900 is_a: EDAM:0000480 ! Protein modelling (side chains) [Term] id: EDAM:0000482 name: Protein-ligand docking namespace: operation def: "Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques." [EDAM:EBI "EMBRACE definition"] comment: Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. subset: operation synonym: "Virtual ligand screening" EXACT [] is_a: EDAM:0000478 ! Protein docking relationship: has_output EDAM:0001461 ! Protein-ligand complex {minCardinality=1} relationship: has_topic EDAM:0000148 ! Protein-ligand interactions [Term] id: EDAM:0000483 name: Structured RNA prediction and optimisation namespace: operation def: "Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "RNA inverse folding" EXACT [] synonym: "Nucleic acid folding family identification" EXACT [] is_a: EDAM:0003095 ! Nucleic acid design is_a: EDAM:0002425 ! Optimisation and refinement relationship: has_output EDAM:0001234 ! Sequence set (nucleic acid) relationship: has_topic EDAM:0002953 ! Nucleic acid design [Term] id: EDAM:0000273 name: Protein interaction raw data analysis namespace: operation def: "Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002949 ! Protein interaction analysis relationship: has_input EDAM:0000905 ! Protein interaction raw data relationship: has_topic EDAM:0000147 ! Protein-protein interactions [Term] id: EDAM:0002492 name: Protein interaction prediction namespace: operation def: "Predict the interactions of proteins with other molecules." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002405 ! Protein interaction data processing is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM:0000906 ! Protein report (interaction) {minCardinality=1} [Term] id: EDAM:0002464 name: Protein-protein interaction prediction namespace: operation def: "Identify or predict protein-protein interactions, interfaces, binding sites etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002492 ! Protein interaction prediction relationship: has_output EDAM:0001565 ! Protein-protein interaction {minCardinality=1} relationship: has_topic EDAM:0000147 ! Protein-protein interactions [Term] id: EDAM:0000274 name: Protein-protein interaction prediction (from protein sequence) namespace: operation def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002464 ! Protein-protein interaction prediction is_a: EDAM:0003084 ! Protein function prediction (from sequence) [Term] id: EDAM:0000275 name: Protein-protein interaction prediction (from protein structure) namespace: operation def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002464 ! Protein-protein interaction prediction is_a: EDAM:0003090 ! Protein feature detection (from structure) [Term] id: EDAM:0002445 name: Protein interaction network processing namespace: operation def: "Process (read and / or write) a network of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002405 ! Protein interaction data processing is_a: EDAM:0002438 ! Pathway or network processing relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=0} relationship: has_output EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=0} relationship: has_topic EDAM:0003044 ! Protein interaction networks [Term] id: EDAM:0000333 name: Zinc finger protein domain prediction and optimisation namespace: operation def: "Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000420 ! Protein-nucleic acid binding prediction is_a: EDAM:0002425 ! Optimisation and refinement relationship: has_output EDAM:0001567 ! Protein-nucleic acid interaction relationship: has_topic EDAM:0000150 ! Protein design [Term] id: EDAM:0000276 name: Protein interaction network analysis namespace: operation def: "Analyse a network of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002445 ! Protein interaction network processing is_a: EDAM:0002949 ! Protein interaction analysis is_a: EDAM:0002497 ! Pathway or network analysis relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=1} relationship: has_output EDAM:0002984 ! Pathway or network report [Term] id: EDAM:0000277 name: Protein interaction network comparison namespace: operation def: "Compare two or more networks of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000276 ! Protein interaction network analysis is_a: EDAM:0001778 ! Protein function comparison relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=2} [Term] id: EDAM:0000484 name: SNP detection namespace: operation def: "Find single nucleotide polymorphisms (SNPs) between sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. subset: operation synonym: "Single nucleotide polymorphism detection" EXACT [] is_a: EDAM:0002508 ! Nucleic acid sequence comparison is_a: EDAM:0002508 ! Nucleic acid sequence comparison relationship: has_output EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0000485 name: Radiation Hybrid Mapping namespace: operation def: "Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002944 ! Physical mapping relationship: has_output EDAM:0002870 ! Radiation hybrid map {minCardinality=1} [Term] id: EDAM:0000486 name: Functional mapping namespace: operation def: "Map the genetic architecture of dynamic complex traits." [EDAM:EBI "EMBRACE definition"] comment: This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). subset: operation is_obsolete: true consider: EDAM:0000282 ! Genetic mapping [Term] id: EDAM:0000487 name: Haplotype inference namespace: operation def: "Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated." [EDAM:EBI "EMBRACE definition"] comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). subset: operation synonym: "Haplotype mapping" EXACT [] is_a: EDAM:0000283 ! Linkage analysis relationship: has_output EDAM:0001863 ! Haplotype map {minCardinality=1} [Term] id: EDAM:0000488 name: Linkage disequilibrium calculation namespace: operation def: "Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [EDAM:EBI "EMBRACE definition"] comment: Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. subset: operation is_a: EDAM:0000283 ! Linkage analysis relationship: has_output EDAM:0001634 ! Gene annotation (linkage disequilibrium) {minCardinality=1} [Term] id: EDAM:0000286 name: Codon usage analysis namespace: operation alt_id: EDAM:0002494 def: "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "synon: Codon usage table analysis" EXACT [] synonym: "synon: Codon usage data analysis" EXACT [] is_a: EDAM:0002501 ! Nucleic acid data processing relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=0} relationship: has_input EDAM:0001597 ! Codon usage table {minCardinality=0} relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=0} relationship: has_output EDAM:0000914 ! Codon usage report {minCardinality=0} relationship: has_topic EDAM:0000107 ! Codon usage analysis [Term] id: EDAM:0002433 name: Codon usage table processing namespace: operation def: "Process (read and / or write) a codon usage table." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000286 ! Codon usage analysis relationship: has_input EDAM:0001597 ! Codon usage table {minCardinality=0} relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=0} [Term] id: EDAM:0000287 name: Base position variability plotting namespace: operation def: "Identify and plot third base position variability in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000286 ! Codon usage analysis relationship: has_output EDAM:0001263 ! Sequence composition (base position variability) {minCardinality=1} relationship: has_topic EDAM:0000109 ! Gene finding [Term] id: EDAM:0000489 name: Genetic code prediction namespace: operation def: "Predict genetic code from analysis of codon usage data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000286 ! Codon usage analysis is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM:0001598 ! Genetic code {minCardinality=1} [Term] id: EDAM:0002962 name: Codon usage bias calculation namespace: operation def: "Calculate codon usage bias." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000286 ! Codon usage analysis relationship: has_output EDAM:0002865 ! Codon usage bias {minCardinality=1} [Term] id: EDAM:0002963 name: Codon usage bias plotting namespace: operation def: "Generate a codon usage bias plot." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002962 ! Codon usage bias calculation relationship: has_output EDAM:0001600 ! Codon usage bias plot {minCardinality=1} [Term] id: EDAM:0002964 name: Codon usage fraction calculation namespace: operation def: "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000286 ! Codon usage analysis relationship: has_output EDAM:0001602 ! Codon usage fraction difference {minCardinality=1} [Term] id: EDAM:0000284 name: Codon usage table generation namespace: operation def: "Calculate codon usage statistics and create a codon usage table." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002433 ! Codon usage table processing relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=1} [Term] id: EDAM:0000285 name: Codon usage table comparison namespace: operation def: "Compare two or more codon usage tables." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002433 ! Codon usage table processing is_a: EDAM:0002998 ! Nucleic acid comparison [Term] id: EDAM:0000491 name: Pairwise sequence alignment namespace: operation def: "Align exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: operation is_a: EDAM:0000292 ! Sequence alignment relationship: has_output EDAM:0001381 ! Sequence alignment (pair) {minCardinality=1} [Term] id: EDAM:0000492 name: Multiple sequence alignment namespace: operation def: "Align two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. subset: operation is_a: EDAM:0000292 ! Sequence alignment [Term] id: EDAM:0002089 name: Sequence alignment refinement namespace: operation def: "Refine an existing sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000258 ! Sequence alignment analysis is_a: EDAM:0002425 ! Optimisation and refinement [Term] id: EDAM:0000493 name: Pairwise sequence alignment (local) namespace: operation def: "Locally align exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Local alignment methods identify regions of local similarity. subset: operation is_a: EDAM:0000491 ! Pairwise sequence alignment [Term] id: EDAM:0000494 name: Pairwise sequence alignment (global) namespace: operation def: "Globally align exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Global alignment methods identify similarity across the entire length of the sequences. subset: operation is_a: EDAM:0000491 ! Pairwise sequence alignment [Term] id: EDAM:0000495 name: Multiple sequence alignment (local) namespace: operation def: "Locally align two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Local alignment methods identify regions of local similarity. subset: operation is_a: EDAM:0000492 ! Multiple sequence alignment [Term] id: EDAM:0000496 name: Multiple sequence alignment (global) namespace: operation def: "Globally align two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Global alignment methods identify similarity across the entire length of the sequences. subset: operation is_a: EDAM:0000492 ! Multiple sequence alignment [Term] id: EDAM:0000497 name: Multiple sequence alignment (constrained) namespace: operation def: "Align two or more molecular sequences with user-defined constraints." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000492 ! Multiple sequence alignment [Term] id: EDAM:0000498 name: Multiple sequence alignment (consensus) namespace: operation def: "Align two or more molecular sequences using multiple methods to achieve higher quality." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000492 ! Multiple sequence alignment [Term] id: EDAM:0000499 name: Multiple sequence alignment (phylogenetic tree-based) namespace: operation def: "Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree." [EDAM:EBI "EMBRACE definition"] comment: This is supposed to give a more biologically meaningful alignment than standard alignments. subset: operation is_a: EDAM:0000492 ! Multiple sequence alignment relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] id: EDAM:0000500 name: Secondary structure alignment namespace: operation def: "Align molecular secondary structure (represented as a 1D string)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002482 ! Secondary structure processing is_a: EDAM:0002931 ! Secondary structure comparison is_a: EDAM:0000294 ! Structure-based sequence alignment relationship: has_output EDAM:0002366 ! Secondary structure alignment {minCardinality=1} relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000501 name: Protein secondary structure alignment namespace: operation def: "Align protein secondary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000500 ! Secondary structure alignment is_a: EDAM:0002488 ! Protein secondary structure comparison synonym: "Secondary structure alignment (protein)" EXACT [] relationship: has_output EDAM:0000878 ! Secondary structure alignment (protein) {minCardinality=1} [Term] id: EDAM:0000502 name: RNA secondary structure alignment namespace: operation def: "Align RNA secondary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002439 ! RNA secondary structure processing is_a: EDAM:0000500 ! Secondary structure alignment synonym: "Secondary structure alignment (RNA)" EXACT [] relationship: has_input EDAM:0000880 ! RNA secondary structure {minCardinality=2} relationship: has_output EDAM:0000881 ! Secondary structure alignment (RNA) {minCardinality=1} [Term] id: EDAM:0000503 name: Pairwise structure alignment namespace: operation def: "Align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000295 ! Structure alignment [Term] id: EDAM:0000504 name: Multiple structure alignment namespace: operation def: "Align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: This includes methods that use an existing alignment. subset: operation is_a: EDAM:0000295 ! Structure alignment [Term] id: EDAM:0002488 name: Protein secondary structure comparison namespace: operation def: "Compare protein secondary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002416 ! Protein secondary structure analysis is_a: EDAM:0002931 ! Secondary structure comparison is_a: EDAM:0002997 ! Protein comparison synonym: "Secondary structure comparison (protein)" EXACT [] relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=2} [Term] id: EDAM:0002487 name: Protein structure comparison namespace: operation def: "Compare protein tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Methods might identify structural neighbors, find structural similarities or define a structural core. subset: operation is_a: EDAM:0002459 ! Structure processing (protein) is_a: EDAM:0002483 ! Structure comparison is_a: EDAM:0002997 ! Protein comparison synonym: "Structure comparison (protein)" EXACT [] relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=2} relationship: has_output EDAM:0000897 ! Protein property [Term] id: EDAM:0002518 name: Nucleic acid structure comparison namespace: operation def: "Compare nucleic acid tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Structure comparison (nucleic acid)" EXACT [] is_a: EDAM:0002483 ! Structure comparison is_a: EDAM:0002481 ! Nucleic acid structure analysis is_a: EDAM:0002998 ! Nucleic acid comparison [Term] id: EDAM:0000505 name: Structure alignment (protein) namespace: operation def: "Align protein tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000295 ! Structure alignment [Term] id: EDAM:0000506 name: Structure alignment (RNA) namespace: operation def: "Align RNA tertiary structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000295 ! Structure alignment [Term] id: EDAM:0000507 name: Pairwise structure alignment (local) namespace: operation def: "Locally align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Local alignment methods identify regions of local similarity, common substructures etc. subset: operation is_a: EDAM:0000503 ! Pairwise structure alignment [Term] id: EDAM:0000508 name: Pairwise structure alignment (global) namespace: operation def: "Globally align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Global alignment methods identify similarity across the entire structures. subset: operation is_a: EDAM:0000503 ! Pairwise structure alignment [Term] id: EDAM:0000509 name: Multiple structure alignment (local) namespace: operation def: "Locally align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Local alignment methods identify regions of local similarity, common substructures etc. subset: operation is_a: EDAM:0000504 ! Multiple structure alignment [Term] id: EDAM:0000510 name: Multiple structure alignment (global) namespace: operation def: "Globally align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"] comment: Global alignment methods identify similarity across the entire structures. subset: operation is_a: EDAM:0000504 ! Multiple structure alignment [Term] id: EDAM:0000296 name: Sequence profile generation namespace: operation def: "Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002413 ! Sequence profile processing is_a: EDAM:0002463 ! Sequence alignment processing relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=1} relationship: has_output EDAM:0001354 ! Sequence profile {minCardinality=1} [Term] id: EDAM:0000298 name: Sequence profile alignment namespace: operation def: "Align sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"] comment: See also 'Sequence alignment comparison'. subset: operation is_a: EDAM:0002413 ! Sequence profile processing is_a: EDAM:0002928 ! Alignment relationship: has_input EDAM:0001354 ! Sequence profile {minCardinality=2} relationship: has_output EDAM:0000868 ! Sequence profile alignment {minCardinality=1} [Term] id: EDAM:0000300 name: Sequence-profile alignment namespace: operation def: "Align molecular sequence(s) to sequence profile(s)." [EDAM:EBI "EMBRACE definition"] comment: A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: operation is_a: EDAM:0002413 ! Sequence profile processing is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002928 ! Alignment relationship: has_input EDAM:0001354 ! Sequence profile {minCardinality=1} relationship: has_output EDAM:0000869 ! Sequence-profile alignment {minCardinality=1} [Term] id: EDAM:0000511 name: Sequence profile alignment (pairwise) namespace: operation def: "Align exactly two molecular profiles." [EDAM:EBI "EMBRACE definition"] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: operation is_a: EDAM:0000298 ! Sequence profile alignment [Term] id: EDAM:0000512 name: Sequence profile alignment (multiple) namespace: operation def: "Align two or more molecular profiles." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000298 ! Sequence profile alignment [Term] id: EDAM:0000297 name: Structural (3D) profile generation namespace: operation def: "Generate some type of structural (3D) profile or template from a structure or structure alignment." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Structural profile generation" EXACT [] is_a: EDAM:0002411 ! Structural (3D) profile processing is_a: EDAM:0002952 ! Structure alignment processing is_a: EDAM:0002465 ! Structure processing relationship: has_input EDAM:0000886 ! Structure alignment {minCardinality=1} relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} relationship: has_output EDAM:0000889 ! Structural (3D) profile {minCardinality=1} [Term] id: EDAM:0000299 name: Structural (3D) profile alignment namespace: operation def: "Align structural (3D) profiles or templates (representing structures or structure alignments)." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Structural profile alignment" EXACT [] is_a: EDAM:0002411 ! Structural (3D) profile processing is_a: EDAM:0002928 ! Alignment relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=2} relationship: has_output EDAM:0000890 ! Structural (3D) profile alignment {minCardinality=1} relationship: has_topic EDAM:0000183 ! Structure alignment [Term] id: EDAM:0000513 name: Structural (3D) profile alignment (pairwise) namespace: operation def: "Align exactly two molecular Structural (3D) profiles." [EDAM:EBI "EMBRACE definition"] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: operation is_a: EDAM:0000299 ! Structural (3D) profile alignment [Term] id: EDAM:0000514 name: Structural (3D) profile alignment (multiple) namespace: operation def: "Align two or more molecular 3D profiles." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000299 ! Structural (3D) profile alignment [Term] id: EDAM:0000301 name: Sequence-3D profile alignment namespace: operation def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: operation is_a: EDAM:0000303 ! Protein fold recognition is_a: EDAM:0002928 ! Alignment is_a: EDAM:0002403 ! Sequence analysis relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=2} relationship: has_output EDAM:0000891 ! Sequence-3D profile alignment {minCardinality=1} relationship: has_topic EDAM:0000184 ! Threading [Term] id: EDAM:0000308 name: PCR primer design namespace: operation def: "Design or predict oligonucleotide primers for PCR and DNA amplification etc." [EDAM:EBI "EMBRACE definition"] comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. subset: operation synonym: "PCR primer prediction" EXACT [] is_a: EDAM:0002419 ! Primer and probe design relationship: has_input EDAM:0002977 ! Nucleic acid sequence relationship: has_output EDAM:0001240 ! PCR primers {minCardinality=0} relationship: has_topic EDAM:0003032 ! Primer or probe design [Term] id: EDAM:0000309 name: Microarray probe design namespace: operation def: "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Microarray probe prediction" EXACT [] is_a: EDAM:0002419 ! Primer and probe design is_a: EDAM:0002425 ! Optimisation and refinement relationship: has_input EDAM:0002977 ! Nucleic acid sequence relationship: has_output EDAM:0002717 ! Oligonucleotide probe annotation {minCardinality=1} relationship: has_topic EDAM:0000200 ! Microarrays relationship: has_topic EDAM:0003032 ! Primer or probe design [Term] id: EDAM:0000307 name: Virtual PCR namespace: operation def: "Perform in-silico (virtual) PCR." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002478 ! Nucleic acid sequence analysis relationship: has_topic EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000517 name: PCR primer design (for large scale sequencing) namespace: operation def: "Predict primers for large scale sequencing." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design relationship: has_topic EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0000518 name: PCR primer design (for genotyping polymorphisms) namespace: operation def: "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design [Term] id: EDAM:0000519 name: PCR primer design (for gene transcription profiling) namespace: operation def: "Predict primers for gene transcription profiling." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design relationship: has_topic EDAM:0000203 ! Transcriptomics [Term] id: EDAM:0000520 name: PCR primer design (for conserved primers) namespace: operation def: "Predict primers that are conserved across multiple genomes or species." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design [Term] id: EDAM:0000521 name: PCR primer design (based on gene structure) namespace: operation def: "Predict primers based on gene structure, promoters, exon-exon junctions etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design relationship: has_topic EDAM:0000109 ! Gene finding [Term] id: EDAM:0000522 name: PCR primer design (for methylation PCRs) namespace: operation def: "Predict primers for methylation PCRs." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000308 ! PCR primer design [Term] id: EDAM:0000523 name: Sequence assembly (mapping assembly) namespace: operation def: "Sequence assembly by combining fragments using an existing backbone sequence." [EDAM:EBI "EMBRACE definition"] comment: The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. subset: operation is_a: EDAM:0000310 ! Sequence assembly [Term] id: EDAM:0000524 name: Sequence assembly (de-novo assembly) namespace: operation def: "Sequence assembly by combining fragments into a new, previously unknown sequence." [EDAM:EBI "EMBRACE definition"] comment: De-novo assemblers are much slower and more memory intensive than mapping assemblers. subset: operation is_a: EDAM:0000310 ! Sequence assembly [Term] id: EDAM:0000525 name: Sequence assembly (genome assembly) namespace: operation def: "Sequence assembly capable on a very large scale such as assembly of whole genomes." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000310 ! Sequence assembly [Term] id: EDAM:0000526 name: Sequence assembly (EST assembly) namespace: operation def: "Sequence assembly for EST sequences (transcribed mRNA)." [EDAM:EBI "EMBRACE definition"] comment: Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. subset: operation is_a: EDAM:0000310 ! Sequence assembly [Term] id: EDAM:0002410 name: Gene expression analysis namespace: operation def: "Analyse gene expression and regulation data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0002435 name: Gene expression profile processing namespace: operation def: "Process (read and / or write) a gene expression profile." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002495 ! Gene expression data processing relationship: has_input EDAM:0000928 ! Gene expression profile {minCardinality=0} relationship: has_output EDAM:0000928 ! Gene expression profile {minCardinality=0} relationship: has_topic EDAM:0000203 ! Transcriptomics relationship: has_topic EDAM:0000200 ! Microarrays [Term] id: EDAM:0000312 name: Sequencing-based expression profile data processing namespace: operation def: "Process (read and / or write) SAGE, MPSS or SBS experimental data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0002498 name: Sequencing-based expression profile data analysis namespace: operation def: "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0002496 name: Gene regulatory network processing namespace: operation def: "Process (read and / or write) a network of gene regulation." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002438 ! Pathway or network processing relationship: has_input EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=0} relationship: has_output EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=0} relationship: has_topic EDAM:0000197 ! Gene expression resources relationship: has_topic EDAM:0002846 ! Gene regulatory networks [Term] id: EDAM:0001781 name: Gene regulatory network analysis namespace: operation def: "Analyse a known network of gene regulation." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002496 ! Gene regulatory network processing is_a: EDAM:0002497 ! Pathway or network analysis relationship: has_input EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=1} [Term] id: EDAM:0002437 name: Gene regulatory network prediction namespace: operation def: "Predict a network of gene regulation." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002496 ! Gene regulatory network processing is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM:0002961 ! Pathway or network (gene regulation) {minCardinality=1} [Term] id: EDAM:0003094 name: Protein interaction network prediction namespace: operation def: "Predict a network of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002445 ! Protein interaction network processing relationship: has_output EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=1} [Term] id: EDAM:0000316 name: Functional profiling namespace: operation def: "Interpret (in functional terms) and annotate gene expression data." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000532 ! Gene expression profile analysis [Term] id: EDAM:0000264 name: Splice transcript prediction namespace: operation def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002499 ! Splicing modelling relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing [Term] id: EDAM:0002499 name: Splicing analysis namespace: operation def: "Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Splicing modelling" EXACT [] is_a: EDAM:0002508 ! Nucleic acid sequence comparison is_a: EDAM:0002426 ! Modelling and simulation is_a: EDAM:0003024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM:0001307 ! Nucleic acid features (splice sites) {minCardinality=1} relationship: has_topic EDAM:0000114 ! Gene structure and RNA splicing [Term] id: EDAM:0000313 name: Gene expression profile clustering namespace: operation def: "Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000315 ! Gene expression profile comparison relationship: has_output EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0000314 name: Gene expression profile generation namespace: operation def: "Generate a gene expression profile or pattern, for example from microarray data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002435 ! Gene expression profile processing relationship: has_output EDAM:0000928 ! Gene expression profile {minCardinality=1} [Term] id: EDAM:0000315 name: Gene expression profile comparison namespace: operation def: "Compare gene expression profiles or patterns." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000532 ! Gene expression profile analysis is_a: EDAM:0002998 ! Nucleic acid comparison relationship: has_output EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0002436 name: Gene expression profile annotation namespace: operation def: "Annotate a gene expression profile with terms from an ontology of gene functions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000532 ! Gene expression profile analysis is_a: EDAM:0000226 ! Annotation relationship: has_output EDAM:0000928 ! Gene expression profile {minCardinality=1} [Term] id: EDAM:0000532 name: Gene expression profile analysis namespace: operation def: "Analyse one or more gene expression profiles, typically to interpret them in functional terms." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Functional profiling" EXACT [] is_a: EDAM:0002435 ! Gene expression profile processing relationship: has_input EDAM:0000928 ! Gene expression profile {minCardinality=1} [Term] id: EDAM:0000533 name: Gene expression profile pathway mapping namespace: operation def: "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000532 ! Gene expression profile analysis is_a: EDAM:0002497 ! Pathway or network analysis relationship: has_output EDAM:0002984 ! Pathway or network report [Term] id: EDAM:0000527 name: Tag mapping namespace: operation def: "Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology terms." [EDAM:EBI "EMBRACE definition"] comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. subset: operation synonym: "Tag to gene assignment" EXACT [] is_a: EDAM:0002436 ! Gene expression profile annotation relationship: has_output EDAM:0000936 ! Sequence tag profile (with gene assignment) {minCardinality=0} [Term] id: EDAM:0000528 name: SAGE data processing namespace: operation def: "Process (read and / or write) serial analysis of gene expression (SAGE) data." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Serial analysis of gene expression data processing" EXACT [] is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0000529 name: MPSS data processing namespace: operation def: "Process (read and / or write) massively parallel signature sequencing (MPSS) data." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Massively parallel signature sequencing data processing" EXACT [] is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0000530 name: SBS data processing namespace: operation def: "Process (read and / or write) sequencing by synthesis (SBS) data." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Sequencing by synthesis data processing" EXACT [] is_obsolete: true consider: EDAM:0002495 ! Gene expression data processing [Term] id: EDAM:0000531 name: Heat map generation namespace: operation def: "Generate a heat map of gene expression from microarray data." [EDAM:EBI "EMBRACE definition"] comment: The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. subset: operation is_a: EDAM:0000571 ! Microarray data rendering relationship: has_output EDAM:0001636 ! Heat map {minCardinality=1} [Term] id: EDAM:0002934 name: Microarray cluster textual view rendering def: "Visualise gene clusters with gene names." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002935 name: Microarray wave graph rendering namespace: operation synonym: "Microarray cluster temporal graph rendering" EXACT [] def: "Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis." [EDAM:EBI "EMBRACE definition"] comment: This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002936 name: Microarray dendrograph rendering synonym: "Microarray checks view rendering" EXACT [] synonym: "Microarray view rendering" EXACT [] def: "Generate a dendrograph of raw, preprocessed or clustered microarray data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002937 name: Microarray proximity map rendering synonym: "Microarray distance map rendering" EXACT [] def: "Generate a plot of distances (distance matrix) between genes." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002938 name: Microarray tree or dendrogram view rendering synonym: "Microarray matrix tree plot rendering" EXACT [] synonym: "Microarray 2-way dendrogram rendering" EXACT [] def: "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002939 name: Microarray principal component rendering def: "Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002940 name: Microarray scatter plot rendering def: "Generate a scatter plot of microarray data, typically after principal component analysis." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002941 name: Whole microarray graph view rendering def: "Visualise gene expression data where each band (or line graph) corresponds to a sample." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002942 name: Microarray tree-map rendering def: "Visualise gene expression data after hierarchical clustering for representing hierarchical relationships." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002943 name: Microarray Box-Whisker plot rendering def: "Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000571 ! Microarray data rendering [Term] id: EDAM:0002459 name: Structure processing (protein) namespace: operation def: "Process (read and / or write) a protein tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002465 ! Structure processing is_a: EDAM:0002502 ! Protein data processing relationship: has_input EDAM:0001460 ! Protein structure {minCardinality=0} relationship: has_output EDAM:0001460 ! Protein structure {minCardinality=0} relationship: has_topic EDAM:0000698 ! Protein tertiary structure [Term] id: EDAM:0000243 name: Protein property calculation (from structure) namespace: operation alt_id: EDAM:0003089 def: "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." [EDAM:EBI "EMBRACE definition"] comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. subset: operation is_a: EDAM:0002406 ! Protein structure analysis is_a: EDAM:0000250 ! Protein property calculation synonym: "Protein structural property calculation" EXACT [] relationship: has_output EDAM:0000897 ! Protein property {minCardinality=0} relationship: has_topic EDAM:0000123 ! Protein properties relationship: has_topic EDAM:0002814 ! Protein structure analysis [Term] id: EDAM:0000244 name: Protein flexibility and motion analysis namespace: operation def: "Analyse flexibility and motion in protein structure." [EDAM:EBI "EMBRACE definition"] comment: Use this term for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. subset: operation is_a: EDAM:0000243 ! Protein property calculation (from structure) is_a: EDAM:0002476 ! Molecular dynamics simulation relationship: has_output EDAM:0001541 ! Protein flexibility or motion report {minCardinality=1} [Term] id: EDAM:0000245 name: Protein structural motif recognition namespace: operation def: "Identify or screen for 3D structural motifs in protein structure(s)." [EDAM:EBI "EMBRACE definition"] comment: This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. subset: operation synonym: "Protein structural feature identification" EXACT [] is_a: EDAM:0003090 ! Protein feature detection (from structure) relationship: has_output EDAM:0000899 ! Protein features (3D motif) {minCardinality=1} relationship: has_topic EDAM:0000166 ! Protein structural motifs and surfaces [Term] id: EDAM:0000246 name: Protein domain recognition namespace: operation def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003090 ! Protein feature detection (from structure) relationship: has_output EDAM:0000901 ! Protein features (domains) {minCardinality=1} relationship: has_topic EDAM:0000736 ! Protein domains and folds [Term] id: EDAM:0000247 name: Protein architecture analysis namespace: operation def: "Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002406 ! Protein structure analysis relationship: has_output EDAM:0000902 ! Protein architecture report {minCardinality=1} [Term] id: EDAM:0002474 name: Protein architecture comparison namespace: operation def: "Compare the architecture of two or more protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000247 ! Protein architecture analysis is_a: EDAM:0002488 ! Protein secondary structure comparison relationship: has_output EDAM:0000902 ! Protein architecture report {minCardinality=1} [Term] id: EDAM:0002475 name: Protein architecture recognition namespace: operation def: "Identify the architecture of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000247 ! Protein architecture analysis is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) is_a: EDAM:0002996 ! Structure classification relationship: has_output EDAM:0000902 ! Protein architecture report {minCardinality=1} [Term] id: EDAM:0000248 name: Residue interaction calculation namespace: operation def: "Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s)." [EDAM:EBI "EMBRACE definition"] subset: operation xref: WHATIF:ListContactsNormal xref: WHATIF:ListContactsRelaxed xref: WHATIF:ListSideChainContactsNormal xref: WHATIF:ListSideChainContactsRelaxed xref: WHATIF: SymShellOneXML xref: WHATIF: SymShellTwoXML xref: WHATIF: SymShellFiveXML xref: WHATIF: SymShellTenXML is_a: EDAM:0000243 ! Protein property calculation (from structure) relationship: has_output EDAM:0001540 ! Protein residue interactions {minCardinality=1} relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis [Term] id: EDAM:0000272 name: Residue interaction prediction namespace: operation def: "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods usually involve multiple sequence alignment analysis. subset: operation is_a: EDAM:0000243 ! Protein property calculation (from structure) is_a: EDAM:0002506 ! Sequence alignment analysis (protein) relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis [Term] id: EDAM:0000249 name: Torsion angle calculation namespace: operation def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000243 ! Protein property calculation (from structure) relationship: has_output EDAM:0002991 ! Protein torsion angle data [Term] id: EDAM:0000320 name: Protein structure assignment namespace: operation def: "Assign a protein tertiary structure (3D coordinates) from raw experimental data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002459 ! Structure processing (protein) relationship: has_output EDAM:0001460 ! Protein structure {minCardinality=1} relationship: has_topic EDAM:0002226 ! Structure determination [Term] id: EDAM:0000321 name: Protein model evaluation namespace: operation def: "Evaluate the quality or correctness a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] comment: Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. subset: operation xref: WHATIF: UseFileDB is_a: EDAM:0000477 ! Protein modelling is_a: EDAM:0002428 ! Validation and standardisation relationship: has_output EDAM:0001539 ! Protein structural quality report {minCardinality=1} relationship: has_topic EDAM:0002275 ! Molecular modelling relationship: has_topic EDAM:0000175 ! Homology modelling relationship: has_topic EDAM:0000179 ! Protein tertiary structure prediction [Term] id: EDAM:0000322 name: Protein model refinement namespace: operation def: "Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc." [EDAM:EBI "EMBRACE definition"] comment: The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. subset: operation xref: WHATIF: CorrectedPDBasXML is_a: EDAM:0000321 ! Protein model evaluation is_a: EDAM:0002425 ! Optimisation and refinement [Term] id: EDAM:0002239 name: 3D-1D scoring matrix generation namespace: operation def: "Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data." [EDAM:EBI "EMBRACE definition"] comment: A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. subset: operation is_a: EDAM:0000243 ! Protein property calculation (from structure) is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001499 ! 3D-1D scoring matrix {minCardinality=1} relationship: has_topic EDAM:0000167 ! Structural (3D) profiles [Term] id: EDAM:0002574 name: Protein hydropathy calculation namespace: operation def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000250 ! Protein property calculation relationship: has_output EDAM:0002970 ! Protein hydropathy data {minCardinality=1} relationship: has_topic EDAM:0000137 ! Protein hydropathy [Term] id: EDAM:0000383 name: Protein hydropathy calculation (from structure) namespace: operation def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002574 ! Protein hydropathy calculation is_a: EDAM:0000243 ! Protein property calculation (from structure) [Term] id: EDAM:0000384 name: Protein solvent accessibility calculation namespace: operation def: "Calculate solvent accessible or buried surface areas in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000243 ! Protein property calculation (from structure) relationship: has_output EDAM:0001542 ! Protein solvent accessibility relationship: has_topic EDAM:0000137 ! Protein hydropathy [Term] id: EDAM:0001850 name: Protein cysteine and disulfide bond assignment namespace: operation def: "Assign cysteine bonding state and disulfide bond partners in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000534 ! Protein secondary structure assignment (from coordinate data) relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis [Term] id: EDAM:0000385 name: Protein hydropathy cluster calculation namespace: operation def: "Identify clusters of hydrophobic or charged residues in a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000383 ! Protein hydropathy calculation (from structure) is_a: EDAM:0000393 ! Protein residue cluster calculation [Term] id: EDAM:0000386 name: Protein dipole moment calculation namespace: operation def: "Calculate whether a protein structure has an unusually large net charge (dipole moment)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003088 ! Protein property calculation (from sequence) relationship: has_output EDAM:0001545 ! Protein dipole moment {minCardinality=1} [Term] id: EDAM:0000387 name: Protein surface and interior calculation namespace: operation def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000384 ! Protein solvent accessibility calculation relationship: has_output EDAM:0001543 ! Protein surface report {minCardinality=1} relationship: has_topic EDAM:0000166 ! Protein structural motifs and surfaces [Term] id: EDAM:0001816 name: Surface rendering namespace: operation def: "Calculate the positions of dots that are homogeneously distributed over the surface of a molecule." [EDAM:WHATIF "EMBRACE definition"] comment: A dot has three coordinates (x,y,z) and (typically) a color. subset: operation xref: WHATIF:GetSurfaceDots is_a: EDAM:0002462 ! Protein surface calculation is_a: EDAM:0000570 ! Structure rendering [Term] id: EDAM:0002460 name: Protein atom surface calculation namespace: operation def: "Calculate the solvent accessibility for each atom in a structure." [EDAM:WHATIF "EMBRACE definition"] comment: Waters are not considered. subset: operation is_a: EDAM:0000387 ! Protein surface and interior calculation [Term] id: EDAM:0001817 name: Protein atom surface calculation (accessible) namespace: operation def: "Calculate the solvent accessibility ('accessible surface') for each atom in a structure." [EDAM:WHATIF "EMBRACE definition"] comment: Waters are not considered. subset: operation xref: WHATIF:AtomAccessibilitySolvent xref: WHATIF:AtomAccessibilitySolventPlus is_a: EDAM:0002460 ! Protein atom surface calculation [Term] id: EDAM:0001818 name: Protein atom surface calculation (accessible molecular) namespace: operation def: "Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure." [EDAM:WHATIF "EMBRACE definition"] comment: Waters are not considered. subset: operation xref: WHATIF:AtomAccessibilityMolecular xref: WHATIF:AtomAccessibilityMolecularPlus is_a: EDAM:0002460 ! Protein atom surface calculation [Term] id: EDAM:0002461 name: Protein residue surface calculation namespace: operation def: "Calculate the solvent accessibility for each residue in a structure." [EDAM:WHATIF "EMBRACE definition"] subset: operation is_a: EDAM:0000387 ! Protein surface and interior calculation [Term] id: EDAM:0001819 name: Protein residue surface calculation (accessible) namespace: operation def: "Calculate the solvent accessibility ('accessible surface') for each residue in a structure." [EDAM:WHATIF "EMBRACE definition"] comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). subset: operation xref: WHATIF:ResidueAccessibilitySolvent is_a: EDAM:0002461 ! Protein residue surface calculation [Term] id: EDAM:0001820 name: Protein residue surface calculation (vacuum accessible) namespace: operation def: "Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [EDAM:WHATIF "EMBRACE definition"] comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). subset: operation xref: WHATIF:ResidueAccessibilityVacuum is_a: EDAM:0002461 ! Protein residue surface calculation [Term] id: EDAM:0001821 name: Protein residue surface calculation (accessible molecular) namespace: operation def: "Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure." [EDAM:WHATIF "EMBRACE definition"] comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). subset: operation xref: WHATIF:ResidueAccessibilityMolecular is_a: EDAM:0002461 ! Protein residue surface calculation [Term] id: EDAM:0001822 name: Protein residue surface calculation (vacuum molecular) namespace: operation def: "Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [EDAM:WHATIF "EMBRACE definition"] comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). subset: operation xref: WHATIF:ResidueAccessibilityVacuumMolecular is_a: EDAM:0002461 ! Protein residue surface calculation [Term] id: EDAM:0002462 name: Protein surface calculation namespace: operation def: "Calculate the solvent accessibility of a structure as a whole." [EDAM:WHATIF "EMBRACE definition"] subset: operation is_a: EDAM:0000387 ! Protein surface and interior calculation [Term] id: EDAM:0001823 name: Protein surface calculation (accessible molecular) namespace: operation def: "Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:TotAccessibilityMolecular is_a: EDAM:0002462 ! Protein surface calculation [Term] id: EDAM:0001824 name: Protein surface calculation (accessible) namespace: operation def: "Calculate the solvent accessibility ('accessible surface') for a structure as a whole." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:TotAccessibilitySolvent is_a: EDAM:0002462 ! Protein surface calculation [Term] id: EDAM:0001829 name: Cysteine bridge detection namespace: operation def: "Detect cysteine bridges (from coordinate data) in a protein structure." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:ShowCysteineBridge is_a: EDAM:0001850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM:0001830 name: Free cysteine detection namespace: operation def: "Detect free cysteines in a protein structure." [EDAM:WHATIF "EMBRACE definition"] comment: A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. subset: operation xref: WHATIF:ShowCysteineFree is_a: EDAM:0001850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM:0001831 name: Metal-bound cysteine detection namespace: operation def: "Detect cysteines that are bound to metal in a protein structure." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:ShowCysteineMetal is_a: EDAM:0001850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM:0002575 name: Binding site prediction namespace: operation def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Ligand-binding and active site prediction" EXACT [] is_a: EDAM:0002492 ! Protein interaction prediction relationship: has_output EDAM:0001325 ! Protein features (active sites) {minCardinality=0} relationship: has_output EDAM:0001326 ! Protein features (binding sites) {minCardinality=0} relationship: has_topic EDAM:0000148 ! Protein-ligand interactions [Term] id: EDAM:0000388 name: Binding site prediction (from structure) namespace: operation def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Ligand-binding and active site prediction (from structure)" EXACT [] is_a: EDAM:0000245 ! Protein structural motif recognition is_a: EDAM:0002575 ! Binding site prediction [Term] id: EDAM:0000389 name: Protein-nucleic acid binding site analysis namespace: operation def: "Analyse RNA or DNA-binding sites in protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002949 ! Protein interaction analysis relationship: has_input EDAM:0001567 ! Protein-nucleic acid interaction relationship: has_topic EDAM:0000149 ! Protein-nucleic acid interactions [Term] id: EDAM:0000390 name: Protein peeling namespace: operation def: "Decompose a structure into compact or globular fragments (protein peeling)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000246 ! Protein domain recognition relationship: has_output EDAM:0000901 ! Protein features (domains) {minCardinality=1} [Term] id: EDAM:0000391 name: Protein distance matrix calculation namespace: operation def: "Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000248 ! Residue interaction calculation relationship: has_output EDAM:0001546 ! Protein distance matrix {minCardinality=1} [Term] id: EDAM:0000394 name: Hydrogen bond calculation namespace: operation def: "Identify potential hydrogen bonds between amino acids and other groups." [EDAM:WHATIF "EMBRACE definition"] comment: The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. subset: operation xref: WHATIF:ShowHydrogenBondsM xref: WHATIF:ShowHydrogenBonds xref: WHATIF:ShowHydrogenBonds xref: WHATIF:HasHydrogenBonds is_a: EDAM:0000248 ! Residue interaction calculation relationship: has_output EDAM:0001549 ! Protein hydrogen bonds {minCardinality=1} [Term] id: EDAM:0002491 name: Hydrogen bond calculation (inter-residue) namespace: operation def: "Identify potential hydrogen bonds between amino acid residues." [EDAM:WHATIF "EMBRACE definition"] subset: operation is_a: EDAM:0000394 ! Hydrogen bond calculation is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) [Term] id: EDAM:0001839 name: Salt bridge calculation namespace: operation def: "Calculate (and possibly score) salt bridges in a protein structure." [EDAM:WHATIF "EMBRACE definition"] comment: Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. subset: operation xref: WHATIF:HasSaltBridge xref: WHATIF:HasSaltBridgePlus xref: WHATIF:ShowSaltBridges xref: WHATIF:ShowSaltBridgesH is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) [Term] id: EDAM:0001846 name: HET group detection namespace: operation def: "Identify HET groups in PDB files." [EDAM:WHATIF "EMBRACE definition"] comment: A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. subset: operation xref: WHATIF: HETGroupNames is_a: EDAM:0001838 ! Residue contact calculation (residue-ligand) [Term] id: EDAM:0002950 alt_id: EDAM:0001833 name: Residue contact calculation namespace: operation def: "Calculate contacts between residues and some other group in a protein structure." [EDAM:WHATIF "EMBRACE definition"] subset: operation is_a: EDAM:0000248 ! Residue interaction calculation [Term] id: EDAM:0001838 name: Residue contact calculation (residue-ligand) namespace: operation def: "Calculate contacts between residues and ligands in a protein structure." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:ShowLigandContacts xref: WHATIF:ShowDrugContacts xref: WHATIF:ShowDrugContactsShort is_a: EDAM:0002950 ! Residue contact calculation is_a: EDAM:0000388 ! Binding site prediction (from structure) [Term] id: EDAM:0002490 name: Residue contact calculation (residue-residue) namespace: operation def: "Calculate contacts between residues in a protein structure." [EDAM:WHATIF "EMBRACE definition"] subset: operation is_a: EDAM:0002950 ! Residue contact calculation [Term] id: EDAM:0000392 name: Protein contact map calculation namespace: operation def: "Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) relationship: has_output EDAM:0001547 ! Protein contact map {minCardinality=1} [Term] id: EDAM:0000393 name: Protein residue cluster calculation namespace: operation def: "Calculate clusters of contacting residues in protein structures." [EDAM:EBI "EMBRACE definition"] comment: Cluster of contacting residues might be key structural residues. subset: operation is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) relationship: has_output EDAM:0001548 ! Protein residue 3D cluster {minCardinality=1} [Term] id: EDAM:0001832 name: Residue contact calculation (residue-nucleic acid) namespace: operation def: "Calculate protein residue contacts with nucleic acids in a structure." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:HasNucleicContacts xref: WHATIF:ShowProteiNucleicContacts is_a: EDAM:0002950 ! Residue contact calculation is_a: EDAM:0000389 ! Protein-nucleic acid binding site data analysis is_a: EDAM:0000245 ! Protein structural motif recognition [Term] id: EDAM:0001834 name: Residue contact calculation (residue-metal) namespace: operation def: "Calculate protein residue contacts with metal in a structure." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:HasMetalContacts xref: WHATIF:HasMetalContactsPlus is_a: EDAM:0002950 ! Residue contact calculation is_a: EDAM:0000388 ! Binding site prediction (from structure) [Term] id: EDAM:0001835 name: Residue contact calculation (residue-negative ion) namespace: operation def: "Calculate ion contacts in a structure (all ions for all side chain atoms)." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:HasNegativeIonContacts xref: WHATIF:HasNegativeIonContactsPlus is_a: EDAM:0002950 ! Residue contact calculation [Term] id: EDAM:0001837 name: Residue symmetry contact calculation namespace: operation def: "Calculate the number of symmetry contacts made by residues in a protein structure." [EDAM:WHATIF "EMBRACE definition"] comment: A symmetry contact is a contact between two atoms in different asymmetric unit. subset: operation xref: WHATIF:SymmetryContact is_a: EDAM:0002490 ! Residue contact calculation (residue-residue) [Term] id: EDAM:0000396 name: Ramachandran plot calculation namespace: operation def: "Calculate a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000249 ! Torsion angle calculation relationship: has_output EDAM:0001544 ! Ramachandran plot {minCardinality=1} [Term] id: EDAM:0000397 name: Ramachandran plot evaluation namespace: operation def: "Analyse (typically to validate) a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0001844 ! Dihedral angle validation relationship: has_input EDAM:0001544 ! Ramachandran plot {minCardinality=1} relationship: has_output EDAM:0001539 ! Protein structural quality report [Term] id: EDAM:0001825 name: Backbone torsion angle calculation namespace: operation def: "Calculate for each residue in a protein structure all its backbone torsion angles." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:ResidueTorsionsBB is_a: EDAM:0000249 ! Torsion angle calculation [Term] id: EDAM:0001826 name: Full torsion angle calculation namespace: operation def: "Calculate for each residue in a protein structure all its torsion angles." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:ResidueTorsions is_a: EDAM:0000249 ! Torsion angle calculation [Term] id: EDAM:0001827 name: Cysteine torsion angle calculation namespace: operation def: "Calculate for each cysteine (bridge) all its torsion angles." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:CysteineTorsions is_a: EDAM:0000249 ! Torsion angle calculation [Term] id: EDAM:0001828 name: Tau angle calculation namespace: operation def: "For each amino acid in a protein structure calculate the backbone angle tau." [EDAM:WHATIF "EMBRACE definition"] comment: Tau is the backbone angle N-Calpha-C (angle over the C-alpha). subset: operation xref: WHATIF:ShowTauAngle is_a: EDAM:0000249 ! Torsion angle calculation [Term] id: EDAM:0000536 name: Protein structure assignment (from X-ray crystallographic data) namespace: operation def: "Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000320 ! Protein structure assignment relationship: has_input EDAM:0000937 ! Protein X-ray crystallographic data {minCardinality=1} [Term] id: EDAM:0000537 name: Protein structure assignment (from NMR data) namespace: operation def: "Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000320 ! Protein structure assignment relationship: has_input EDAM:0000938 ! Protein NMR data {minCardinality=1} [Term] id: EDAM:0000395 name: Residue non-canonical interaction detection namespace: operation def: "Calculate non-canonical atomic interactions in protein structures." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000248 ! Residue interaction calculation is_a: EDAM:0000321 ! Protein model evaluation relationship: has_output EDAM:0001550 ! Protein non-canonical interactions {minCardinality=1} [Term] id: EDAM:0001913 name: Residue validation namespace: operation def: "Identify poor quality amino acid positions in protein structures." [EDAM:WHATIF "EMBRACE definition"] comment: The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). subset: operation xref: WHATIF: UseResidueDB is_a: EDAM:0000321 ! Protein model evaluation [Term] id: EDAM:0001843 name: Residue packing validation namespace: operation def: "Identify poorly packed residues in protein structures." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF: PackingQuality is_a: EDAM:0000395 ! Residue non-canonical interaction detection [Term] id: EDAM:0001844 name: Dihedral angle validation namespace: operation def: "Identify for each residue in a protein structure any improper dihedral (phi/psi) angles." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF: ImproperQualitySum xref: WHATIF: ImproperQualityMax is_a: EDAM:0000321 ! Protein model evaluation [Term] id: EDAM:0001836 name: Residue bump detection namespace: operation def: "Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:ShowBumps is_a: EDAM:0000395 ! Residue non-canonical interaction detection [Term] id: EDAM:0002443 name: Phylogenetic tree processing namespace: operation def: "Process (read and / or write) a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000872 ! Phylogenetic tree {minCardinality=0} relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=0} relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] id: EDAM:0000550 name: Sequence alignment analysis (phylogenetic modelling) namespace: operation def: "Identify a plausible model of DNA substitution that explains a DNA sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002507 ! Sequence alignment analysis (nucleic acid) is_a: EDAM:0002426 ! Modelling and simulation relationship: has_output EDAM:0001439 ! DNA substitution model relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] id: EDAM:0000554 name: Phylogenetic tree analysis (natural selection) namespace: operation def: "Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive)." [EDAM:EBI "EMBRACE definition"] comment: Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. subset: operation is_a: EDAM:0000324 ! Phylogenetic tree analysis [Term] id: EDAM:0000323 name: Phylogenetic tree construction namespace: operation def: "Construct a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] comment: Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. subset: operation synonym: "Phylogenetic tree generation" EXACT [] is_a: EDAM:0002443 ! Phylogenetic tree processing is_a: EDAM:0002995 ! Sequence classification relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=1} relationship: has_topic EDAM:0000080 ! Sequence analysis relationship: has_topic EDAM:0000084 ! Phylogenetics [Term] id: EDAM:0000325 name: Phylogenetic tree comparison namespace: operation def: "Compare two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] comment: For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. subset: operation is_a: EDAM:0000324 ! Phylogenetic tree analysis is_a: EDAM:0002424 ! Comparison [Term] id: EDAM:0000326 name: Phylogenetic tree editing namespace: operation def: "Edit a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002443 ! Phylogenetic tree processing is_a: EDAM:0003096 ! Editing relationship: has_input EDAM:0000872 ! Phylogenetic tree {minCardinality=1} relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=1} [Term] id: EDAM:0000551 name: Phylogenetic tree analysis (shape) namespace: operation def: "Analyse the shape (topology) of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "Phylogenetic tree topology analysis" EXACT [] is_a: EDAM:0000324 ! Phylogenetic tree analysis relationship: has_output EDAM:0001440 ! Phylogenetic tree report (tree shape) {minCardinality=1} [Term] id: EDAM:0000552 name: Phylogenetic tree bootstrapping namespace: operation def: "Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000324 ! Phylogenetic tree analysis is_a: EDAM:0002428 ! Validation and standardisation relationship: has_output EDAM:0001441 ! Phylogenetic tree report (tree evaluation) {minCardinality=1} [Term] id: EDAM:0000553 name: Phylogenetic tree analysis (gene family prediction) namespace: operation def: "Predict families of genes and gene function based on their position in a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000324 ! Phylogenetic tree analysis relationship: has_output EDAM:0000916 ! Gene annotation relationship: has_topic EDAM:0000194 ! Phylogenomics [Term] id: EDAM:0000538 name: Phylogenetic tree construction (data centric) namespace: operation def: "Construct a phylogenetic tree from a specific type of data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000323 ! Phylogenetic tree construction [Term] id: EDAM:0000539 name: Phylogenetic tree construction (method centric) namespace: operation def: "Construct a phylogenetic tree using a specific method." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000323 ! Phylogenetic tree construction [Term] id: EDAM:0000540 name: Phylogenetic tree construction (from molecular sequences) namespace: operation def: "Phylogenetic tree construction from molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. subset: operation is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) is_a: EDAM:0002403 ! Sequence analysis [Term] id: EDAM:0000541 name: Phylogenetic tree construction (from continuous quantitative characters) namespace: operation def: "Phylogenetic tree construction from continuous quantitative character data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) relationship: has_input EDAM:0001426 ! Phylogenetic continuous quantitative data {minCardinality=1} [Term] id: EDAM:0000542 name: Phylogenetic tree construction (from gene frequencies) namespace: operation def: "Phylogenetic tree construction from gene frequency data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) relationship: has_input EDAM:0002873 ! Phylogenetic gene frequencies data {minCardinality=1} relationship: has_topic EDAM:0000197 ! Gene expression resources [Term] id: EDAM:0000543 name: Phylogenetic tree construction (from polymorphism data) namespace: operation def: "Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000538 ! Phylogenetic tree construction (data centric) relationship: has_topic EDAM:0000199 ! Genetic variation [Term] id: EDAM:0000544 name: Phylogenetic species tree construction namespace: operation def: "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000540 ! Phylogenetic tree construction (from molecular sequences) [Term] id: EDAM:0000327 name: Phylogenetic footprinting / shadowing namespace: operation def: "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing)." [EDAM:EBI "EMBRACE definition"] comment: A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. subset: operation is_a: EDAM:0000540 ! Phylogenetic tree construction (from molecular sequences) relationship: has_topic EDAM:0000194 ! Phylogenomics [Term] id: EDAM:0000545 name: Phylogenetic tree construction (parsimony methods) namespace: operation def: "Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment." [EDAM:EBI "EMBRACE definition"] comment: This includes evolutionary parsimony (invariants) methods. subset: operation is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM:0000546 name: Phylogenetic tree construction (minimum distance methods) namespace: operation def: "Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances." [EDAM:EBI "EMBRACE definition"] comment: This includes neighbor joining (NJ) clustering method. subset: operation is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM:0000547 name: Phylogenetic tree construction (maximum likelihood and Bayesian methods) namespace: operation def: "Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution." [EDAM:EBI "EMBRACE definition"] comment: Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. subset: operation is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM:0000548 name: Phylogenetic tree construction (quartet methods) namespace: operation def: "Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM:0000549 name: Phylogenetic tree construction (AI methods) namespace: operation def: "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM:0000555 name: Phylogenetic tree construction (consensus) namespace: operation def: "Compare two or more phylogenetic trees to produce a consensus tree." [EDAM:EBI "EMBRACE definition"] comment: Methods typically test for topological similarity between trees using for example a congruence index. subset: operation is_a: EDAM:0000325 ! Phylogenetic tree comparison is_a: EDAM:0000323 ! Phylogenetic tree construction [Term] id: EDAM:0000556 name: Phylogenetic sub/super tree detection namespace: operation def: "Compare two or more phylogenetic trees to detect subtrees or supertrees." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000325 ! Phylogenetic tree comparison [Term] id: EDAM:0000557 name: Phylogenetic tree distances calculation namespace: operation def: "Compare two or more phylogenetic trees to calculate distances between trees." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000325 ! Phylogenetic tree comparison relationship: has_output EDAM:0001442 ! Phylogenetic tree report (tree distances) {minCardinality=1} [Term] id: EDAM:0000558 name: Phylogenetic tree annotation namespace: operation def: "Annotate a phylogenetic tree with terms from a controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000326 ! Phylogenetic tree editing is_a: EDAM:0000226 ! Annotation [Term] id: EDAM:0000328 name: Protein folding simulation namespace: operation def: "Simulate the folding of a protein." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002415 ! Protein folding analysis [Term] id: EDAM:0000329 name: Protein folding pathway prediction namespace: operation def: "Predict the folding pathway(s) or non-native structural intermediates of a protein." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002415 ! Protein folding analysis is_a: EDAM:0003023 ! Prediction, detection and recognition (protein) [Term] id: EDAM:0001842 name: Proline mutation value calculation namespace: operation def: "Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF:ProlineMutationValue is_a: EDAM:0000331 ! Protein modelling (mutation) [Term] id: EDAM:0000330 name: Protein SNP mapping namespace: operation def: "Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000331 ! Protein modelling (mutation) relationship: has_output EDAM:0002885 ! Nucleic acid features (polymorphism annotation) relationship: has_topic EDAM:0002277 ! SNPs [Term] id: EDAM:0000559 name: Peptide immunogen prediction and optimisation namespace: operation def: "Predict and optimise peptide ligands that elicit an immunological response." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000252 ! Peptide immunogenicity prediction is_a: EDAM:0002425 ! Optimisation and refinement relationship: has_output EDAM:0001460 ! Protein structure relationship: has_topic EDAM:0000150 ! Protein design relationship: has_topic EDAM:0000804 ! Immunoinformatics [Term] id: EDAM:0000560 name: DNA vaccine prediction and optimisation namespace: operation def: "Predict or optimise DNA to elicit (via DNA vaccination) an immunological response." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003095 ! Nucleic acid design is_a: EDAM:0002425 ! Optimisation and refinement relationship: has_topic EDAM:0000804 ! Immunoinformatics relationship: has_topic EDAM:0002953 ! Nucleic acid design [Term] id: EDAM:0000561 name: Sequence reformatting namespace: operation def: "Reformat (a file or other report of) molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000335 ! File reformatting is_a: EDAM:0002121 ! Sequence file processing [Term] id: EDAM:0000562 name: Sequence alignment reformatting namespace: operation def: "Reformat (a file or other report of) molecular sequence alignment(s)." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000335 ! File reformatting is_a: EDAM:0002122 ! Sequence alignment editing [Term] id: EDAM:0000563 name: Codon usage table reformatting namespace: operation def: "Reformat a codon usage table." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000335 ! File reformatting is_a: EDAM:0002433 ! Codon usage table processing relationship: has_input EDAM:0001597 ! Codon usage table {minCardinality=1} relationship: has_output EDAM:0001597 ! Codon usage table {minCardinality=1} [Term] id: EDAM:0001848 name: Structure reformatting namespace: operation def: "Reformat (a file or other report of) tertiary structure data." [EDAM:WHATIF "EMBRACE definition"] subset: operation xref: WHATIF: PDBasXML is_a: EDAM:0002234 ! Structure file processing is_a: EDAM:0000335 ! File reformatting [Term] id: EDAM:0000564 name: Sequence rendering namespace: operation def: "Visualise, format or render a molecular sequence, possibly with sequence features or properties shown." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} relationship: has_output EDAM:0002969 ! Sequence image {minCardinality=1} [Term] id: EDAM:0002515 name: Sequence rendering (nucleic acid) namespace: operation def: "Visualise, format or render a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] comment: Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. subset: operation is_a: EDAM:0000564 ! Sequence rendering is_a: EDAM:0002448 ! Sequence processing (nucleic acid) relationship: has_topic EDAM:0000640 ! Nucleic acid sequence analysis [Term] id: EDAM:0002516 name: Sequence rendering (protein) namespace: operation def: "Visualise, format or render a protein sequence." [EDAM:EBI "EMBRACE definition"] comment: Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. subset: operation is_a: EDAM:0000564 ! Sequence rendering is_a: EDAM:0002447 ! Sequence processing (protein) [Term] id: EDAM:0000565 name: Sequence alignment rendering namespace: operation def: "Visualise, format or print a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002463 ! Sequence alignment processing relationship: has_input EDAM:0000863 ! Sequence alignment {minCardinality=1} relationship: has_output EDAM:0001711 ! Sequence alignment image {minCardinality=1} [Term] id: EDAM:0002452 name: Sequence cluster processing namespace: operation def: "Process (read and / or write) a sequence cluster." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0001235 ! Sequence cluster {minCardinality=0} relationship: has_output EDAM:0001235 ! Sequence cluster {minCardinality=0} relationship: has_topic EDAM:0000164 ! Sequence clustering [Term] id: EDAM:0000566 name: Sequence cluster rendering namespace: operation def: "Visualise, format or render sequence clusters." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002452 ! Sequence cluster processing relationship: has_input EDAM:0001235 ! Sequence cluster {minCardinality=1} [Term] id: EDAM:0000567 name: Phylogenetic tree rendering namespace: operation def: "Visualise or plot a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002443 ! Phylogenetic tree processing is_a: EDAM:0000337 ! Plotting and rendering relationship: has_output EDAM:0000872 ! Phylogenetic tree {minCardinality=1} [Term] id: EDAM:0000568 name: RNA secondary structure rendering namespace: operation def: "Visualise RNA secondary structure, knots, pseudoknots etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002439 ! RNA secondary structure processing relationship: has_input EDAM:0000880 ! RNA secondary structure {minCardinality=1} [Term] id: EDAM:0000569 name: Protein secondary structure rendering namespace: operation def: "Render and visualise protein secondary structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002444 ! Protein secondary structure processing relationship: has_input EDAM:0000876 ! Protein features (secondary structure) {minCardinality=1} [Term] id: EDAM:0002485 name: Helical wheel rendering namespace: operation def: "Render a helical wheel representation of protein secondary structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000569 ! Protein secondary structure rendering relationship: has_output EDAM:0002162 ! Helical wheel {minCardinality=1} [Term] id: EDAM:0002486 name: Topology diagram rendering namespace: operation def: "Render a topology diagram of protein secondary structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000569 ! Protein secondary structure rendering relationship: has_output EDAM:0002992 ! Protein structure image [Term] id: EDAM:0002241 name: Transmembrane protein rendering namespace: operation def: "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000569 ! Protein secondary structure rendering is_a: EDAM:0000270 ! Transmembrane protein analysis relationship: has_input EDAM:0001456 ! Protein features (membrane regions) {minCardinality=1} relationship: has_output EDAM:0002992 ! Protein structure image [Term] id: EDAM:0002482 name: Secondary structure processing namespace: operation def: "Process (read and / or write) a molecular secondary structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0002081 ! Secondary structure {minCardinality=0} relationship: has_output EDAM:0002081 ! Secondary structure {minCardinality=0} relationship: has_topic EDAM:0000081 ! Structure analysis [Term] id: EDAM:0002465 name: Structure processing namespace: operation alt_id: EDAM:0002484 def: "Process (read and / or write) a molecular tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0002420 ! Analysis and processing relationship: has_input EDAM:0000883 ! Structure {minCardinality=0} relationship: has_output EDAM:0000883 ! Structure {minCardinality=0} relationship: has_topic EDAM:0000081 ! Structure analysis [Term] id: EDAM:0000570 name: Structure rendering namespace: operation def: "Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002465 ! Structure processing relationship: has_input EDAM:0000883 ! Structure {minCardinality=1} relationship: has_output EDAM:0001710 ! Structure image [Term] id: EDAM:0000571 name: Microarray data rendering namespace: operation def: "Visualise microarray data." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002435 ! Gene expression profile processing relationship: has_input EDAM:0003117 ! Microarray hybridisation data {minCardinality=1} relationship: has_output EDAM:0002967 ! Microarray image {minCardinality=1} [Term] id: EDAM:0000572 name: Protein interaction network rendering namespace: operation def: "Identify and analyse networks of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0003083 ! Pathway or network rendering is_a: EDAM:0002445 ! Protein interaction network processing relationship: has_input EDAM:0001663 ! Pathway or network (protein-protein interaction) {minCardinality=1} [Term] id: EDAM:0000573 name: Map rendering namespace: operation def: "Render and visualise a DNA map." [EDAM:EBI "EMBRACE definition"] subset: operation synonym: "DNA map rendering" EXACT [] is_a: EDAM:0002515 ! Sequence rendering (nucleic acid) is_a: EDAM:0002521 ! Map data processing relationship: has_input EDAM:0001274 ! Map {minCardinality=1} [Term] id: EDAM:0000574 name: Sequence motif rendering namespace: operation def: "Render a sequence with motifs." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000564 ! Sequence rendering [Term] id: EDAM:0000577 name: DNA linear map rendering namespace: operation def: "Draw a linear maps of DNA." [EDAM:EBI "EMBRACE definition"] subset: operation is_obsolete: true consider: EDAM:0000573 ! Map rendering [Term] id: EDAM:0000578 name: DNA circular map rendering namespace: operation def: "Draw a circular maps of DNA, for example a plasmid map." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000573 ! Map rendering [Term] id: EDAM:0000579 name: Operon rendering namespace: operation def: "Visualise operon structure etc." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000573 ! Map rendering relationship: has_topic EDAM:0000109 ! Gene finding [Term] id: EDAM:0000575 name: Restriction map rendering namespace: operation def: "Visualise restriction maps in DNA sequences." [EDAM:EBI "EMBRACE definition"] subset: operation is_a: EDAM:0000573 ! Map rendering is_a: EDAM:0000431 ! Restriction site recognition relationship: has_output EDAM:0001289 ! Restriction map [Term] id: EDAM:0000005 name: Resource type namespace: data def: "A type of computational resource used in bioinformatics." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0002831 name: Databank namespace: data def: "A flat-file (textual) data archive." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0002832 name: Web portal namespace: data def: "A web site providing data (web pages) on a common theme to a HTTP client." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0000581 name: Database namespace: data def: "A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0000007 name: Tool namespace: data def: "A bioinformatics package or tool, e.g. a standalone application or web service." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0001884 name: UniProt keywords namespace: data def: "A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000582 ! Ontology [Term] id: EDAM:0000831 name: MeSH vocabulary namespace: data def: "Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000582 ! Ontology [Term] id: EDAM:0000832 name: HGNC vocabulary namespace: data def: "Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000582 ! Ontology [Term] id: EDAM:0000835 name: UMLS vocabulary namespace: data def: "Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000582 ! Ontology ! ! Data ! [Term] id: EDAM:0000841 name: Undefined namespace: data def: "Debugging." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0002100 name: Type namespace: data alt_id: EDAM:0002864 def: "A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0001866 name: Map type namespace: data def: "A designation of the type of map (genetic map, physical map, sequence map etc) or map set." [EDAM:EBI "EMBRACE definition"] comment: Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. subset: data is_a: EDAM:0002100 ! Type is_a: EDAM:0002019 ! Map attribute [Term] id: EDAM:0001094 name: Sequence type namespace: data def: "A label (text token) describing a type of molecular sequence." [EDAM:EBI "EMBRACE definition"] comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). subset: data is_a: EDAM:0002100 ! Type is_a: EDAM:0002534 ! Sequence parameter relationship: is_identifier_of EDAM:0002044 ! Sequence relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0002132 name: Mutation type namespace: data def: "A type of point or block mutation, including insertion, deletion, change, duplication and moves." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002100 ! Type [Term] id: EDAM:0000985 name: Molecule type namespace: data def: "A label (text token) describing the type a molecule." [EDAM:EBI "EMBRACE definition"] comment: For example, 'Protein', 'DNA', 'RNA' etc. subset: data is_a: EDAM:0002100 ! Type [Term] id: EDAM:0001122 name: Phylogenetic tree type namespace: data def: "A label (text token) describing the type of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] comment: For example 'nj', 'upgmp' etc. subset: data is_a: EDAM:0002100 ! Type relationship: is_identifier_of EDAM:0000872 ! Phylogenetic tree [Term] id: EDAM:0002592 name: Cancer type namespace: data def: "A type (represented as a string) of cancer." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002100 ! Type [Term] id: EDAM:0002524 name: Protein data namespace: data def: "Data concerning one or more protein molecules." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0000896 ! Protein report [Term] id: EDAM:0002525 name: Nucleic acid data namespace: data def: "Data concerning one or more nucleic acid molecules." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0002084 ! Nucleic acid report [Term] id: EDAM:0002248 name: Schema namespace: data def: "A data schema for organising or transforming data of some type." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0000843 name: Database entry namespace: data def: "An entry (retrievable via URL) from a biological database." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000006 ! Data [Term] id: EDAM:0002767 name: Identifier with metadata namespace: data def: "Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000842 ! Identifier [Term] id: EDAM:0002768 name: Gene symbol annotation namespace: data def: "Annotation about a gene symbol." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002767 ! Identifier with metadata [Term] id: EDAM:0002087 name: Molecular property namespace: data def: "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Physicochemical property" EXACT [] is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0001917 name: Atomic property namespace: data def: "Data for an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "General atomic property" EXACT [] is_a: EDAM:0002087 ! Molecular property [Term] id: EDAM:0002050 name: Molecular property (general) namespace: data def: "General data for a molecule." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "General molecular property" EXACT [] is_a: EDAM:0002087 ! Molecular property [Term] id: EDAM:0002925 name: Sequence data namespace: data def: "Data concerning molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0002044 ! Sequence consider: EDAM:0002955 ! Sequence report [Term] id: EDAM:0002044 name: Sequence namespace: data def: "One or more molecular sequences, possibly with associated annotation." [EDAM:EBI "EMBRACE definition"] comment: This term is a placeholder of terms for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. subset: data relationship: has_topic EDAM:0000080 ! Sequence analysis is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002976 name: Protein sequence namespace: data def: "One or more protein sequences, possibly with associated annotation." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002044 ! Sequence [Term] id: EDAM:0002977 name: Nucleic acid sequence namespace: data def: "One or more nucleic acid sequences, possibly with associated annotation." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002044 ! Sequence [Term] id: EDAM:0002955 name: Sequence report namespace: data def: "An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence-derived report" EXACT [] is_a: EDAM:0002048 ! Report [Term] id: EDAM:0000855 name: Sequence metadata namespace: data def: "Basic or general information concerning molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: This is used for such things as a report including the sequence identifier, type and length. subset: data is_a: EDAM:0001254 ! Sequence property is_a: EDAM:0002955 ! Sequence report is_a: EDAM:0002337 ! Metadata [Term] id: EDAM:0002522 name: Map data namespace: data def: "Data concerning a map of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0001274 ! Map consider: EDAM:0002019 ! Map attribute [Term] id: EDAM:0001274 name: Map namespace: data def: "A map of (typically one) DNA sequence annotated with positional or non-positional features." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "DNA map" EXACT [] relationship: has_topic EDAM:0000102 ! Sequencing and mapping is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0001864 name: Map set namespace: data def: "Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby:GCP_CorrelatedMapSet xref: Moby:GCP_CorrelatedLinkageMapSet is_a: EDAM:0002019 ! Map attribute [Term] id: EDAM:0002019 name: Map attribute namespace: data def: "An attribute of a molecular map (genetic or physical)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002337 ! Metadata relationship: has_topic EDAM:0000102 ! Sequencing and mapping [Term] id: EDAM:0002080 name: Database hits namespace: data def: "A report of hits from searching a database of some type." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002093 ! Data reference [Term] id: EDAM:0000860 name: Sequence signature namespace: data def: "A classifier of sequences such as a sequence motif, profile or other diagnostic element." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001353 ! Sequence motif consider: EDAM:0001354 ! Sequence profile [Term] id: EDAM:0002981 name: Sequence motif data namespace: data def: "Data concerning specific or conserved pattern in molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0001353 ! Sequence motif [Term] id: EDAM:0001353 name: Sequence motif namespace: data def: "Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0002762 name: Sequence motif metadata namespace: data def: "Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002337 ! Metadata relationship: has_topic EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0002982 name: Sequence profile data namespace: data def: "Data concerning models representing a (typically multiple) sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0001354 ! Sequence profile [Term] id: EDAM:0001354 name: Sequence profile namespace: data def: "Some type of statistical model representing a (typically multiple) sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000188 ! Sequence profiles and HMMs [Term] id: EDAM:0002788 name: Sequence profile metadata namespace: data def: "Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002337 ! Metadata relationship: has_topic EDAM:0000188 ! Sequence profiles and HMMs [Term] id: EDAM:0001355 name: Protein signature namespace: data def: "An entry (sequence classifier and associated data) from the InterPro database." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "InterPro entry" EXACT [] is_a: EDAM:0000907 ! Protein family [Term] id: EDAM:0002161 name: Sequence similarity plot namespace: data def: "A plot of sequence similarities identified from word-matching or character comparison." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000867 ! Sequence alignment report [Term] id: EDAM:0000862 name: Dotplot namespace: data def: "A dotplot of sequence similarities identified from word-matching or character comparison." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002161 ! Sequence similarity plot [Term] id: EDAM:0002539 name: Alignment data namespace: data def: "Data concerning an alignment of two or more molecular sequences, structures or derived data." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. subset: data is_obsolete: true consider: EDAM:0001916 ! Alignment consider: EDAM:0002083 ! Alignment report [Term] id: EDAM:0001916 name: Alignment namespace: data def: "An alignment of molecular sequences, structures or profiles derived from them." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002083 name: Alignment report namespace: data def: "An informative report about a molecular alignment of some type, including alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_a: EDAM:0002048 ! Report [Term] id: EDAM:0002711 name: Genome metadata namespace: data def: "Provenance metadata or other general information concerning a genome as a whole." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000855 ! Sequence metadata [Term] id: EDAM:0000867 name: Sequence alignment report namespace: data def: "An informative report of molecular sequence alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_a: EDAM:0002083 ! Alignment report [Term] id: EDAM:0002598 name: Secondary structure alignment metadata namespace: data def: "An informative report on protein secondary structure alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002083 ! Alignment report [Term] id: EDAM:0000879 name: Secondary structure alignment metadata (protein) namespace: data def: "An informative report on protein secondary structure alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002083 ! Alignment report [Term] id: EDAM:0000882 name: Secondary structure alignment metadata (RNA) namespace: data def: "An informative report of RNA secondary structure alignment-derived data or metadata." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002083 ! Alignment report [Term] id: EDAM:0002082 name: Matrix namespace: data def: "An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002855 name: Distance matrix namespace: data def: "A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002082 ! Matrix [Term] id: EDAM:0000870 name: Sequence distance matrix namespace: data def: "A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation." [EDAM:EBI "EMBRACE definition"] comment: Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. subset: data synonym: "Phylogenetic distance matrix" EXACT [] xref: Moby:phylogenetic_distance_matrix is_a: EDAM:0002855 ! Distance matrix [Term] id: EDAM:0002856 name: Structural distance matrix namespace: data def: "Distances (values representing similarity) between a group of molecular structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002855 ! Distance matrix ! Phylogenetic character data! Also molecular sequences, microsatellites), polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments [Term] id: EDAM:0002523 name: Phylogenetic raw data namespace: data def: "Data concerning phylogeny, typically of molecular sequences." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Phylogenetic data" EXACT [] is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0000871 name: Phylogenetic character data namespace: data def: "Data from which a phylogenetic tree may be generated." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002523 ! Phylogenetic raw data [Term] id: EDAM:0000872 name: Phylogenetic tree namespace: data def: "The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length." [EDAM:EBI "EMBRACE definition"] comment: A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. subset: data xref: Moby:Tree xref: Moby:phylogenetic_tree xref: Moby:myTree relationship: has_topic EDAM:0000084 ! Phylogenetics is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0001438 name: Phylogenetic tree report namespace: data alt_id: EDAM:0000873 def: "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Phylogenetic tree-derived report" EXACT [] is_a: EDAM:0002048 ! Report [Term] id: EDAM:0000874 name: Comparison matrix namespace: data def: "Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison." [EDAM:EBI "EMBRACE definition"] comment: The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). subset: data synonym: "Substitution matrix" EXACT [] is_a: EDAM:0002082 ! Matrix [Term] id: EDAM:0002053 name: Structural data namespace: data def: "Data concerning molecular structural data." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0000883 ! Structure consider: EDAM:0002085 ! Structure report [Term] id: EDAM:0002085 name: Structure report namespace: data def: "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Structure-derived report" EXACT [] is_a: EDAM:0002048 ! Report [Term] id: EDAM:0002973 name: Secondary structure data namespace: data def: "Data concerning molecular secondary structure data." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002081 ! Secondary structure consider: EDAM:0002881 ! Secondary structure report [Term] id: EDAM:0002881 name: Secondary structure report namespace: data def: "An informative report on general information, properties or features of one or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Secondary structure-derived report" EXACT [] is_a: EDAM:0002048 ! Report [Term] id: EDAM:0002956 name: Protein secondary structure report namespace: data def: "An informative report about the properties or features of one or more protein secondary structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002881 ! Secondary structure report [Term] id: EDAM:0001494 name: Structural transformation matrix namespace: data def: "Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002082 ! Matrix [Term] id: EDAM:0000887 name: Structure alignment report namespace: data def: "An informative report on molecular tertiary structure alignment-derived data." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_a: EDAM:0002083 ! Alignment report [Term] id: EDAM:0000889 name: Structural (3D) profile namespace: data def: "Some type of structural (3D) profile or template (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "3D profile" EXACT [] is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000167 ! Structural (3D) profiles [Term] id: EDAM:0000892 name: Protein sequence-structure scoring matrix namespace: data def: "Matrix of values used for scoring sequence-structure compatibility." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002082 ! Matrix [Term] id: EDAM:0002528 name: Molecular data namespace: data def: "Data concerning a specific type of molecule." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Molecule-specific data" EXACT [] is_obsolete: true consider: EDAM:0002529 ! Molecule report [Term] id: EDAM:0002599 name: Molecular interaction namespace: data def: "Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Molecular interaction data" EXACT [] is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002601 name: Small molecule data namespace: data def: "Data concerning one or more small molecules." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002016 name: Amino acid property namespace: data def: "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Amino acid data" EXACT [] is_a: EDAM:0002087 ! Molecular property [Term] id: EDAM:0002979 name: Peptide property namespace: data def: "Data concerning small peptides." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Peptide data" EXACT [] is_a: EDAM:0002087 ! Molecular property [Term] id: EDAM:0000895 name: Peptide annotation namespace: data def: "An informative report about a specific peptide." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000962 ! Small molecule annotation is_a: EDAM:0002979 ! Peptide property relationship: has_topic EDAM:0000613 ! Peptides and amino acids [Term] id: EDAM:0002399 name: Gene annotation (transcript) namespace: data alt_id: EDAM:0002703 def: "An informative report on a specific gene transcript, clone or EST." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene transcript annotation" EXACT [] synonym: "Gene annotation (clone or EST)" EXACT [] is_a: EDAM:0000916 ! Gene annotation [Term] id: EDAM:0000896 name: Protein report namespace: data def: "An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene product annotation" EXACT [] is_a: EDAM:0002529 ! Molecule report relationship: has_topic EDAM:0000078 ! Protein analysis [Term] id: EDAM:0000897 name: Protein property namespace: data def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model." [EDAM:EBI "EMBRACE definition"] comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Protein physicochemical property" EXACT [] is_a: EDAM:0000896 ! Protein report is_a: EDAM:0002087 ! Molecular property [Term] id: EDAM:0001537 name: Protein structure report namespace: data def: "Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains." [EDAM:EBI "EMBRACE definition"] subset: data alt_id: EDAM:0000898 alt_id: EDAM:0001538 alt_id: EDAM:0002377 synonym: "Protein structure report (domain)" EXACT [] synonym: "Protein structure-derived report" EXACT [] synonym: "Protein structural property" EXACT [] synonym: "Protein report (structure)" EXACT [] synonym: "Protein property (structural)" EXACT [] is_a: EDAM:0000896 ! Protein report is_a: EDAM:0002085 ! Structure report [Term] id: EDAM:0003151 name: Protein property (physicochemical) namespace: data def: "A report of primarily non-positional data describing intrinsic physicochemical properties of a protein molecule." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein physicochemical property" EXACT [] is_obsolete: true consider: EDAM:0000897 ! Protein property [Term] id: EDAM:0003152 name: Protein property (sequence) namespace: data def: "A non-positional property of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein sequence property" EXACT [] is_obsolete: true consider: EDAM:0000897 ! Protein property [Term] id: EDAM:0002313 name: Carbohydrate structure report namespace: data def: "Annotation on or information derived from one or more specific carbohydrate 3D structure(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002085 ! Structure report [Term] id: EDAM:0002879 name: Lipid structure report namespace: data def: "Annotation on or information derived from one or more specific lipid 3D structure(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002085 ! Structure report [Term] id: EDAM:0002987 name: Classification namespace: data def: "Data concerning a classification of molecular sequences, structures or other entities." [EDAM:EBI "EMBRACE definition"] comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. subset: data synonym: "Classification data" EXACT [] is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0002829 ! Ontologies, nomenclature and classification [Term] id: EDAM:0003028 name: Taxonomy namespace: data def: "Data concerning the classification, identification and naming of organisms." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Taxonomic data" EXACT [] is_a: EDAM:0002987 ! Classification relationship: has_topic EDAM:0000637 ! Taxonomy [Term] id: EDAM:0002986 name: Nucleic acid classification namespace: data def: "Data concerning the classification of nucleic acid sequences or structures." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Nucleic acid classification data" EXACT [] is_a: EDAM:0002084 ! Nucleic acid report is_a: EDAM:0002987 ! Classification relationship: has_topic EDAM:0000722 ! Nucleic acid classification [Term] id: EDAM:0002980 name: Protein classification namespace: data def: "Data concerning the classification of protein sequences or structures." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Protein classification data" EXACT [] is_a: EDAM:0000896 ! Protein report is_a: EDAM:0002987 ! Classification relationship: has_topic EDAM:0000595 ! Protein classification [Term] id: EDAM:0000900 name: Protein domain classification namespace: data def: "Data concerning the classification of the sequences and/or structures of protein structural domain(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002980 ! Protein classification relationship: has_topic EDAM:0000736 ! Protein domains and folds [Term] id: EDAM:0003101 name: Protein domain classification node namespace: data def: "A node from a classification of protein structural domain(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000900 ! Protein domain classification [Term] id: EDAM:0000906 name: Protein interaction namespace: data def: "An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein report (interaction)" EXACT [] is_a: EDAM:0002599 ! Molecular interaction is_a: EDAM:0000896 ! Protein report relationship: has_topic EDAM:0000128 ! Protein interactions [Term] id: EDAM:0000907 name: Protein family namespace: data def: "An informative report on a specific protein family or other group of classified proteins." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein family annotation" EXACT [] is_a: EDAM:0002980 ! Protein classification relationship: has_topic EDAM:0000724 ! Protein families [Term] id: EDAM:0002354 name: RNA family annotation namespace: data def: "An informative report on a specific RNA family or other group of classified RNA sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002986 ! Nucleic acid classification [Term] id: EDAM:0002978 name: Reaction data namespace: data alt_id: EDAM:0000908 def: "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Reaction annotation" EXACT [] synonym: "Enzyme kinetics annotation" EXACT [] subset: data is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002024 name: Enzyme kinetics data namespace: data def: "Data concerning chemical reaction(s) catalysed by enzyme(s)." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_a: EDAM:0002978 ! Reaction data [Term] id: EDAM:0000911 name: Nucleotide base annotation namespace: data def: "An informative report about a specific nucleotide base." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002116 name: Nucleic acid features (codon) namespace: data def: "An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0002084 name: Nucleic acid report namespace: data def: "An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002529 ! Molecule report [Term] id: EDAM:0000912 name: Nucleic acid property namespace: data def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] comment: The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Nucleic acid physicochemical property" EXACT [] is_a: EDAM:0002084 ! Nucleic acid report is_a: EDAM:0002087 ! Molecular property [Term] id: EDAM:0002086 name: Nucleic acid structure report namespace: data alt_id: EDAM:0000913 def: "A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s)." [EDAM:EBI "EMBRACE definition"] comment: This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. subset: data synonym: "Nucleic acid structural property" EXACT [] synonym: "Nucleic acid property (structural)" EXACT [] is_a: EDAM:0000912 ! Nucleic acid property is_a: EDAM:0002085 ! Structure report [Term] id: EDAM:0002927 name: Codon usage data namespace: data def: "Data concerning codon usage." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0001597 ! Codon usage table consider: EDAM:0000914 ! Codon usage report [Term] id: EDAM:0001597 name: Codon usage table namespace: data def: "Table of codon usage data calculated from one or more nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] comment: A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000107 ! Codon usage analysis [Term] id: EDAM:0000914 name: Codon usage report namespace: data def: "Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_a: EDAM:0002048 ! Report relationship: has_topic EDAM:0000107 ! Codon usage analysis [Term] id: EDAM:0002603 name: Microarray data namespace: data alt_id: EDAM:0002541 def: "Image or hybridisation data for a microarray, typically a study of gene expression." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. See also EDAM:0000931 ! Experiment annotation (microarray) subset: data synonym: "Gene expression data" EXACT [] is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0003110 name: Raw microarray data namespace: data def: "Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment." [EDAM:EBI "EMBRACE definition"] comment: Such data as found in Affymetrix CEL or GPR files. subset: data is_a: EDAM:0003117 ! Microarray hybridisation data is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0003111 name: Processed microarray data namespace: data alt_id: EDAM:0000929 def: "Data generated from processing and analysis of probe set data from a microarray experiment." [EDAM:EBI "EMBRACE definition"] comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. subset: data synonym: "Microarray probe set data" EXACT [] synonym: "Gene expression report" EXACT [] synonym: "Gene annotation (expression)" EXACT [] is_a: EDAM:0003117 ! Microarray hybridisation data is_a: EDAM:0000928 ! Gene expression profile relationship: has_topic EDAM:0000197 ! Gene expression resources [Term] id: EDAM:0003117 name: Microarray hybridisation data namespace: data def: "Data concerning the hybridisations measured during a microarray experiment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002603 ! Microarray data relationship: has_topic EDAM:0000197 ! Gene expression resources [Term] id: EDAM:0003112 name: Normalised microarray data namespace: data def: "The final processed (normalised) data for a set of hybridisations in a microarray experiment." [EDAM:EBI "EMBRACE definition"] comment: This combines data from all hybridisations. subset: data synonym: "Gene expression matrix" EXACT [] synonym: "Gene expression data matrix" EXACT [] is_a: EDAM:0003117 ! Microarray hybridisation data [Term] id: EDAM:0003113 name: Sample annotation namespace: data def: "Annotation on a biological sample, for example experimental factors and their values." [EDAM:EBI "EMBRACE definition"] comment: This might include compound and dose in a dose response experiment. subset: data is_a: EDAM:0000931 ! Experiment annotation (microarray) [Term] id: EDAM:0003115 name: Microarray annotation namespace: data def: "Annotation on the array itself used in a microarray experiment." [EDAM:EBI "EMBRACE definition"] comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. subset: data is_a: EDAM:0000931 ! Experiment annotation (microarray) [Term] id: EDAM:0003116 name: Microarray protocol annotation namespace: data def: "Annotation on laboratory and/or data processing protocols used in an microarray experiment." [EDAM:EBI "EMBRACE definition"] comment: This might describe e.g. the normalisation methods used to process the raw data. subset: data is_a: EDAM:0000931 ! Experiment annotation (microarray) [Term] id: EDAM:0002763 name: Locus annotation namespace: data def: "An informative report on a particular locus." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Locus report" EXACT [] is_obsolete: true consider: EDAM:0000916 ! Gene annotation [Term] id: EDAM:0000916 name: Gene annotation namespace: data alt_id: EDAM:0002394 alt_id: EDAM:0002361 def: "An informative report on a particular locus, gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] comment: This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). subset: data synonym: "Gene report" EXACT [] synonym: "Gene annotation (functional)" EXACT [] xref: Moby:gene xref: Moby:GeneInfo xref: Moby_namespace:Human_Readable_Description is_a: EDAM:0001276 ! Nucleic acid features relationship: has_topic EDAM:0000623 ! Genes, gene family or system [Term] id: EDAM:0003148 name: Gene family annotation namespace: data def: "An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002986 ! Nucleic acid classification is_a: EDAM:0000916 ! Gene annotation [Term] id: EDAM:0000918 name: Nucleic acid features (variation) namespace: data def: "A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence variation annotation" EXACT [] is_a: EDAM:0003122 ! Nucleic acid features (difference and change) relationship: has_topic EDAM:0000199 ! Genetic variation [Term] id: EDAM:0000919 name: Gene annotation (chromosome) namespace: data def: "An informative report on a specific chromosome." [EDAM:EBI "EMBRACE definition"] comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. subset: data is_a: EDAM:0000916 ! Gene annotation relationship: has_topic EDAM:0000624 ! Chromosomes [Term] id: EDAM:0002602 name: Genotype and phenotype data namespace: data def: "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000920 ! Genotype/phenotype annotation [Term] id: EDAM:0000920 name: Genotype/phenotype annotation namespace: data alt_id: EDAM:0002890 def: "An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002048 ! Report [Term] id: EDAM:0002531 name: Experiment annotation namespace: data def: "Annotation on a wet lab experiment, such as experimental conditions." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002048 ! Report [Term] id: EDAM:0003109 name: Experimental measurement annotation namespace: data def: "Annotation on the result of a wet lab experiment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0003108 ! Experimental measurement consider: EDAM:0002531 ! Experiment annotation [Term] id: EDAM:0002381 name: Experiment annotation (genotype) namespace: data def: "Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002531 ! Experiment annotation [Term] id: EDAM:0000925 name: Sequence assembly namespace: data def: "An assembly of fragments of a (typically genomic) DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. subset: data xref: SO:0001248 is_a: EDAM:0001234 ! Sequence set (nucleic acid) [Term] id: EDAM:0002028 name: Experimental data namespace: data def: "Raw data from or annotation on laboratory experiments." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data synonym: "Experimental measurement data" EXACT [] is_obsolete: true consider: EDAM:0003108 ! Experimental measurement consider: EDAM:0002531 ! Experiment annotation [Term] id: EDAM:0003108 name: Experimental measurement namespace: data def: "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data synonym: "Raw experimental data" EXACT [] synonym: "Experimental measurement data" EXACT [] is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002042 name: Evidence namespace: data def: "Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0000941 name: Electron microscopy model namespace: data def: "Annotation on a structural 3D model (volume map) from electron microscopy." [EDAM:EBI "EMBRACE definition"] comment: This might include the location in the model of the known features of a particular macromolecule. subset: data is_a: EDAM:0000940 ! Electron microscopy volume map relationship: has_topic EDAM:0002226 ! Structure determination [Term] id: EDAM:0002971 name: Workflow data namespace: data def: "Data concerning a computational workflow." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000949 ! Workflow metadata consider: EDAM:0002972 ! Workflow [Term] id: EDAM:0000949 name: Workflow metadata namespace: data def: "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002337 ! Metadata relationship: has_topic EDAM:0000769 ! Workflows [Term] id: EDAM:0002972 name: Workflow namespace: data def: "A computational workflow." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000769 ! Workflows [Term] id: EDAM:0000950 name: Biological model namespace: data def: "A biological model which can be represented in mathematical terms." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000771 ! Biological models [Term] id: EDAM:0002983 name: Pathway or network data namespace: data def: "Data concerning a specific biological pathway or network." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002600 ! Pathway or network consider: EDAM:0002984 ! Pathway or network report [Term] id: EDAM:0002984 name: Pathway or network report namespace: data def: "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002048 ! Report relationship: has_topic EDAM:0000602 ! Pathways, networks and models [Term] id: EDAM:0002600 name: Pathway or network namespace: data def: "Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000602 ! Pathways, networks and models [Term] id: EDAM:0001883 name: Annotated URI namespace: data def: "A URI along with annotation describing the data found at the address." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby:DescribedLink is_a: EDAM:0002337 ! Metadata is_a: EDAM:0002093 ! Data reference [Term] id: EDAM:0000954 name: Database cross-mapping namespace: data def: "A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases." [EDAM:EBI "EMBRACE definition"] comment: The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. subset: data is_a: EDAM:0002093 ! Data reference [Term] id: EDAM:0002872 name: ID list namespace: data def: "A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002093 ! Data reference [Term] id: EDAM:0002765 name: Term ID list namespace: data def: "One or more terms from one or more controlled vocabularies which are annotations on an entity." [EDAM:EBI "EMBRACE definition"] comment: The terms are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. subset: data is_a: EDAM:0002872 ! ID list [Term] id: EDAM:0001111 name: EMBOSS listfile namespace: data def: "List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002872 ! ID list [Term] id: EDAM:0002093 name: Data reference namespace: data def: "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology." [EDAM:EBI "EMBRACE definition"] comment: A list of database accessions or identifiers are usually included. subset: data is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002540 name: Data index data namespace: data def: "Data concerning an index of data." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Database index" EXACT [] is_obsolete: true consider: EDAM:0000955 ! Data index consider: EDAM:0000956 ! Data index report [Term] id: EDAM:0000955 name: Data index namespace: data def: "An index of data of biological relevance." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000220 ! Data processing and validation [Term] id: EDAM:0000956 name: Data index report namespace: data def: "A report of an analysis of an index of biological data." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Database index annotation" EXACT [] is_a: EDAM:0002048 ! Report relationship: has_topic EDAM:0000220 ! Data processing and validation [Term] id: EDAM:0002048 name: Report namespace: data alt_id: EDAM:0000969 alt_id: EDAM:0003037 def: "A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing. subset: data synonym: "Text" EXACT [] synonym: "Textual data" EXACT [] synonym: "Document" EXACT [] is_a: EDAM:0000006 ! Data [Term] id: EDAM:0001772 name: Score or penalty namespace: data alt_id: EDAM:0002138 def: "A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0002529 name: Molecule report namespace: data def: "An informative report on a specific molecule." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Molecular report" EXACT [] is_a: EDAM:0002048 ! Report [Term] id: EDAM:0000962 name: Small molecule annotation namespace: data def: "An informative report on a specific chemical compound." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Chemical compound annotation" EXACT [] synonym: "Small molecule report" EXACT [] is_a: EDAM:0002085 ! Structure report is_a: EDAM:0002529 ! Molecule report relationship: has_topic EDAM:0000154 ! Small molecules [Term] id: EDAM:0000963 name: Cell line annotation namespace: data def: "Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Organism strain data" EXACT [] is_a: EDAM:0002530 ! Organism annotation [Term] id: EDAM:0002530 name: Organism annotation namespace: data def: "An informative report on a specific organism." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002048 ! Report [Term] id: EDAM:0002307 name: Virus annotation namespace: data def: "An informative report on a specific virus." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002530 ! Organism annotation [Term] id: EDAM:0002395 name: Fungi annotation namespace: data def: "An informative report on a specific fungus." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002530 ! Organism annotation [Term] id: EDAM:0000964 name: Scent annotation namespace: data def: "An informative report about a specific scent." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002968 name: Image namespace: data alt_id: EDAM:0000965 def: "Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002884 name: Plot namespace: data def: "Biological data that is plotted as a graph of some type." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002968 ! Image [Term] id: EDAM:0002353 name: Ontological data namespace: data def: "Data concerning an ontology." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0002223 ! Ontology metadata consider: EDAM:0000582 ! Ontology [Term] id: EDAM:0002849 name: Abstract namespace: data def: "An abstract of a scientific article." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002857 ! Article metadata [Term] id: EDAM:0000970 name: Bibliographic reference namespace: data def: "Bibliographic data that uniquely identifies a scientific article, book or other published material." [EDAM:EBI "EMBRACE definition"] comment: A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. subset: data synonym: "Reference" EXACT [] synonym: "Citation" EXACT [] xref: Moby:GCP_SimpleCitation xref: Moby:Publication is_a: EDAM:0002857 ! Article metadata is_a: EDAM:0002093 ! Data reference [Term] id: EDAM:0002526 name: Article data namespace: data def: "Data concerning the scientific literature." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. subset: data is_obsolete: true consider: EDAM:0000971 ! Article [Term] id: EDAM:0000971 name: Article namespace: data def: "A body of scientific text, typically a full text article from a scientific journal." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0003068 ! Literature data resources [Term] id: EDAM:0002857 name: Article metadata namespace: data def: "Bibliographic data concerning scientific article(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002954 ! Article report is_a: EDAM:0002337 ! Metadata relationship: has_topic EDAM:0003068 ! Literature data resources [Term] id: EDAM:0002954 name: Article report namespace: data def: "Data concerning or derived from the analysis of a scientific article." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002048 ! Report [Term] id: EDAM:0000972 name: Text mining report namespace: data def: "An abstract of the results of text mining." [EDAM:EBI "EMBRACE definition"] comment: A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. subset: data is_a: EDAM:0002954 ! Article report [Term] id: EDAM:0002143 name: EMBOSS report namespace: data def: "An application report generated by the EMBOSS suite." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002048 ! Report [Term] id: EDAM:0002176 name: Cardinality namespace: data def: "The number of a certain thing." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0002527 name: Parameter namespace: data alt_id: EDAM:0002029 alt_id: EDAM:0001773 alt_id: EDAM:0000961 def: "Typically a simple numerical or string value that controls the operation of a tool." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Parameter or primitive" EXACT [] synonym: "Tool parameter" EXACT [] synonym: "Tool-specific parameter" EXACT [] synonym: "Generic parameter" EXACT [] is_a: EDAM:0000006 ! Data [Term] id: EDAM:0002190 name: Sequence checksum namespace: data def: "A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Hash code" EXACT [] synonym: "Hash sum" EXACT [] synonym: "Hash" EXACT [] synonym: "Hash value" EXACT [] is_a: EDAM:0002534 ! Sequence parameter is_a: EDAM:0000855 ! Sequence metadata [Term] id: EDAM:0002192 name: Error namespace: data def: "Data on an error generated by computer system or tool." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000959 ! Job metadata [Term] id: EDAM:0002249 name: DTD namespace: data def: "A DTD (document type definition)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002248 ! Schema [Term] id: EDAM:0002250 name: XSD schema namespace: data def: "An XSD schema." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002248 ! Schema [Term] id: EDAM:0002251 name: Relax-NG schema namespace: data def: "A relax-NG schema." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002248 ! Schema [Term] id: EDAM:0002252 name: XSLT stylesheet namespace: data def: "An XSLT stylesheet." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002248 ! Schema [Term] id: EDAM:0001743 name: Atomic coordinate namespace: data def: "Cartesian coordinate of an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Cartesian coordinate" EXACT [] is_a: EDAM:0001917 ! Atomic property [Term] id: EDAM:0001857 name: Atomic occupancy namespace: data def: "The fraction of an atom type present at a site in a molecular structure." [EDAM:EBI "EMBRACE definition"] comment: The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. subset: data xref: WHATIF: PDBx_occupancy is_a: EDAM:0001917 ! Atomic property [Term] id: EDAM:0001858 name: Isotropic B factor namespace: data def: "Isotropic B factor (atomic displacement parameter) for an atom from a PDB file." [EDAM:EBI "EMBRACE definition"] subset: data xref: WHATIF: PDBx_B_iso_or_equiv is_a: EDAM:0001917 ! Atomic property [Term] id: EDAM:0001744 name: Atomic x coordinate namespace: data def: "Cartesian x coordinate of an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Cartesian x coordinate" EXACT [] xref: WHATIF: PDBx_Cartn_x is_a: EDAM:0001743 ! Atomic coordinate ! _atom_site.Cartn_x in PDBML [Term] id: EDAM:0001745 name: Atomic y coordinate namespace: data def: "Cartesian y coordinate of an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Cartesian y coordinate" EXACT [] xref: WHATIF: PDBx_Cartn_y is_a: EDAM:0001743 ! Atomic coordinate ! _atom_site.Cartn_y in PDBML [Term] id: EDAM:0001746 name: Atomic z coordinate namespace: data def: "Cartesian z coordinate of an atom (in a molecular structure)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Cartesian z coordinate" EXACT [] xref: WHATIF: PDBx_Cartn_z is_a: EDAM:0001743 ! Atomic coordinate ! _atom_site.Cartn_z in PDBML [Term] id: EDAM:0000844 name: Molecular mass namespace: data def: "Mass of a molecule." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002050 ! Molecular property (general) [Term] id: EDAM:0000845 name: Molecular charge namespace: data def: "Net charge of a molecule." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002050 ! Molecular property (general) ! pdbx_formal_charge in PDBML [Term] id: EDAM:0000846 name: Chemical formula namespace: data def: "A specification of a chemical structure." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Chemical structure specification" EXACT [] is_a: EDAM:0002050 ! Molecular property (general) [Term] id: EDAM:0000847 name: QSAR descriptor namespace: data def: "A QSAR quantitative descriptor (name-value pair) of chemical structure." [EDAM:EBI "EMBRACE definition"] comment: QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. subset: data is_a: EDAM:0002050 ! Molecular property (general) [Term] id: EDAM:0002301 name: SMILES string namespace: data def: "A specification of a chemical structure in SMILES format." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000846 ! Chemical formula ! Many subtypes of the individual descriptors below (not included here) cover all types of protein properties. [Term] id: EDAM:0001201 name: QSAR descriptor (constitutional) namespace: data def: "A QSAR constitutional descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR constitutional descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor [Term] id: EDAM:0001202 name: QSAR descriptor (electronic) namespace: data def: "A QSAR electronic descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR electronic descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor [Term] id: EDAM:0001203 name: QSAR descriptor (geometrical) namespace: data def: "A QSAR geometrical descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR geometrical descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor [Term] id: EDAM:0001204 name: QSAR descriptor (topological) namespace: data def: "A QSAR topological descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR topological descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor [Term] id: EDAM:0001205 name: QSAR descriptor (molecular) namespace: data def: "A QSAR molecular descriptor." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "QSAR molecular descriptor" EXACT [] is_a: EDAM:0000847 ! QSAR descriptor [Term] id: EDAM:0000848 name: Raw sequence namespace: data def: "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] comment: Non-sequence characters may be used for example for gaps and translation stop. subset: data is_a: EDAM:0002044 ! Sequence [Term] id: EDAM:0002201 name: Sequence record full namespace: data def: "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] subset: data xref: SO:2000061 is_a: EDAM:0000849 ! Sequence record [Term] id: EDAM:0002888 name: Sequence record full (protein) namespace: data def: "A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] subset: data xref: SO:2000061 is_a: EDAM:0002201 ! Sequence record full is_a: EDAM:0002886 ! Sequence record (protein) [Term] id: EDAM:0002889 name: Sequence record full (nucleic acid) namespace: data def: "A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] subset: data xref: SO:2000061 is_a: EDAM:0002201 ! Sequence record full is_a: EDAM:0002887 ! Sequence record (nucleic acid) [Term] id: EDAM:0000849 name: Sequence record namespace: data alt_id: EDAM:0001220 alt_id: EDAM:0001224 alt_id: EDAM:0001225 alt_id: EDAM:0001226 alt_id: EDAM:0001227 alt_id: EDAM:0001229 alt_id: EDAM:0001230 alt_id: EDAM:0001231 alt_id: EDAM:0001232 def: "A molecular sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002044 ! Sequence [Term] id: EDAM:0002886 name: Sequence record (protein) namespace: data alt_id: EDAM:0001222 def: "A protein sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein sequence record" EXACT [] is_a: EDAM:0000849 ! Sequence record is_a: EDAM:0002976 ! Protein sequence [Term] id: EDAM:0002887 name: Sequence record (nucleic acid) namespace: data alt_id: EDAM:0001221 def: "A nucleic acid sequence and associated metadata." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Nucleic acid sequence record" EXACT [] synonym: "Nucleotide sequence record" EXACT [] is_a: EDAM:0000849 ! Sequence record is_a: EDAM:0002977 ! Nucleic acid sequence [Term] id: EDAM:0000850 name: Sequence set namespace: data def: "A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for arbitrary sequence sets and associated data arising from processing. subset: data is_a: EDAM:0002955 ! Sequence report [Term] id: EDAM:0002974 name: Raw sequence (protein) namespace: data def: "A raw protein sequence (string of characters)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000848 ! Raw sequence is_a: EDAM:0002976 ! Protein sequence [Term] id: EDAM:0002975 name: Raw sequence (nucleic acid) namespace: data def: "A raw nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000848 ! Raw sequence is_a: EDAM:0002977 ! Nucleic acid sequence [Term] id: EDAM:0002046 name: Sequence record lite (nucleic acid) namespace: data def: "A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002043 ! Sequence record lite is_a: EDAM:0002887 ! Sequence record (nucleic acid) [Term] id: EDAM:0002047 name: Sequence record lite (protein) namespace: data def: "A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002043 ! Sequence record lite is_a: EDAM:0002886 ! Sequence record (protein) [Term] id: EDAM:0002043 name: Sequence record lite namespace: data alt_id: EDAM:0001223 def: "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000849 ! Sequence record [Term] id: EDAM:0002173 name: Sequence set (stream) namespace: data def: "A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for sequence sets that are expected to be read and processed a single sequence at a time. subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set [Term] id: EDAM:0002245 name: Sequence set (bootstrapped) namespace: data def: "A collection of sequences output from a bootstrapping (resampling) procedure." [EDAM:EBI "EMBRACE definition"] comment: Bootstrapping is often performed in phylogenetic analysis. subset: data is_a: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001233 name: Sequence set (protein) namespace: data def: "Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001234 name: Sequence set (nucleic acid) namespace: data def: "Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000850 ! Sequence set is_a: EDAM:0002977 ! Nucleic acid sequence [Term] id: EDAM:0001235 name: Sequence cluster namespace: data def: "A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information." [EDAM:EBI "EMBRACE definition"] comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information. subset: data is_a: EDAM:0000850 ! Sequence set relationship: has_topic EDAM:0003052 ! Sequence clusters and classification relationship: has_topic EDAM:0000724 ! Protein families [Term] id: EDAM:0001236 name: Psiblast checkpoint file namespace: data def: "A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration." [EDAM:EBI "EMBRACE definition"] comment: A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001237 name: HMMER synthetic sequences set namespace: data def: "Sequences generated by HMMER package in FASTA-style format." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001238 name: Proteolytic digest namespace: data def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001233 ! Sequence set (protein) relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0001766 name: CATH domain sequences (ATOM) namespace: data def: "FASTA sequence database for all CATH domains (based on PDB ATOM records)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001767 name: CATH domain sequences (COMBS) namespace: data def: "FASTA sequence database for all CATH domains (based on COMBS sequence data)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001239 name: Restriction digest namespace: data def: "Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease." [EDAM:EBI "EMBRACE definition"] subset: data xref: SO:0000412 is_a: EDAM:0001234 ! Sequence set (nucleic acid) [Term] id: EDAM:0002874 name: Sequence set (polymorphic) namespace: data def: "A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001234 ! Sequence set (nucleic acid) [Term] id: EDAM:0001240 name: PCR primers namespace: data def: "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001234 ! Sequence set (nucleic acid) [Term] id: EDAM:0001241 name: vectorstrip cloning vector definition file namespace: data def: "File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001242 name: Primer3 internal oligo mishybridizing library namespace: data def: "A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001243 name: Primer3 mispriming library file namespace: data def: "A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001244 name: primersearch primer pairs sequence record namespace: data def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001245 name: Sequence cluster (protein) namespace: data def: "A cluster of protein sequences." [EDAM:EBI "EMBRACE definition"] comment: The sequences are typically related, for example a family of sequences. subset: data synonym: "Protein sequence cluster" EXACT [] is_a: EDAM:0001233 ! Sequence set (protein) is_a: EDAM:0001235 ! Sequence cluster [Term] id: EDAM:0001246 name: Sequence cluster (nucleic acid) namespace: data def: "A cluster of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] comment: The sequences are typically related, for example a family of sequences. subset: data synonym: "Nucleotide sequence cluster" EXACT [] is_a: EDAM:0001234 ! Sequence set (nucleic acid) is_a: EDAM:0001235 ! Sequence cluster [Term] id: EDAM:0001764 name: CATH representative domain sequences (ATOM) namespace: data def: "FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001235 ! Sequence cluster [Term] id: EDAM:0001765 name: CATH representative domain sequences (COMBS) namespace: data def: "FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001235 ! Sequence cluster [Term] id: EDAM:0002198 name: Gene cluster namespace: data def: "A cluster of similar genes." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001246 ! Sequence cluster (nucleic acid) [Term] id: EDAM:0001253 name: Sequence information report namespace: data def: "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002043 ! Sequence record lite consider: EDAM:0000855 ! Sequence metadata [Term] id: EDAM:0001254 name: Sequence property namespace: data def: "An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence properties report" EXACT [] is_a: EDAM:0002955 ! Sequence report [Term] id: EDAM:0001255 name: Sequence features namespace: data alt_id: EDAM:0001271 alt_id: EDAM:0001275 def: "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence." [EDAM:EBI "EMBRACE definition"] comment: This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. subset: data synonym: "Sequence features report" EXACT [] synonym: "General sequence features" EXACT [] is_a: EDAM:0002955 ! Sequence report [Term] id: EDAM:0002914 name: Sequence features metadata namespace: data def: "Metadata on sequence features." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000855 ! Sequence metadata [Term] id: EDAM:0001020 name: Sequence feature key namespace: data def: "The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key." [EDAM:EBI "EMBRACE definition"] comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. subset: data synonym: "Sequence feature type" EXACT [] synonym: "Sequence feature method" EXACT [] is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0001021 name: Sequence feature qualifier namespace: data def: "Typically one of the EMBL or Swiss-Prot feature qualifiers." [EDAM:EBI "EMBRACE definition"] comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location. subset: data is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0001022 name: Sequence feature label namespace: data def: "Typically an EMBL or Swiss-Prot feature label." [EDAM:EBI "EMBRACE definition"] comment: A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. subset: data synonym: "Sequence feature name" EXACT [] is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0001278 name: Genetic map namespace: data def: "A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies." [EDAM:EBI "EMBRACE definition"] comment: A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. subset: data synonym: "Linkage map" EXACT [] xref: Moby:GeneticMap is_a: EDAM:0001274 ! Map relationship: has_topic EDAM:0000796 ! Genetic mapping and linkage [Term] id: EDAM:0001283 name: Cytogenetic map namespace: data alt_id: EDAM:0001287 def: "A map showing banding patterns derived from direct observation of a stained chromosome." [EDAM:EBI "EMBRACE definition"] comment: This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. subset: data synonym: "Cytologic map" EXACT [] synonym: "Cytogenic map" EXACT [] synonym: "Chromosome map" EXACT [] is_a: EDAM:0001280 ! Physical map [Term] id: EDAM:0002870 name: Radiation hybrid map namespace: data def: "A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome." [EDAM:EBI "EMBRACE definition"] comment: The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. subset: data synonym: "RH map" EXACT [] is_a: EDAM:0001280 ! Physical map [Term] id: EDAM:0001279 name: Sequence map namespace: data def: "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs." [EDAM:EBI "EMBRACE definition"] comment: A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. subset: data is_a: EDAM:0001280 ! Physical map [Term] id: EDAM:0001280 name: Physical map namespace: data def: "A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them." [EDAM:EBI "EMBRACE definition"] comment: Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. subset: data is_a: EDAM:0001274 ! Map [Term] id: EDAM:0001284 name: DNA transduction map namespace: data def: "A gene map showing distances between loci based on relative cotransduction frequencies." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001278 ! Genetic map [Term] id: EDAM:0001860 name: QTL map namespace: data def: "A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Quantitative trait locus map" EXACT [] is_a: EDAM:0001278 ! Genetic map [Term] id: EDAM:0001859 name: Deletion map namespace: data def: "A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type." [EDAM:EBI "EMBRACE definition"] comment: A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. subset: data synonym: "Deletion-based cytogenetic map" EXACT [] is_a: EDAM:0001283 ! Cytogenetic map [Term] id: EDAM:0001863 name: Haplotype map namespace: data def: "A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby:Haplotyping_Study_obj is_a: EDAM:0001278 ! Genetic map [Term] id: EDAM:0001285 name: Gene map namespace: data def: "Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001279 ! Sequence map [Term] id: EDAM:0001286 name: Plasmid map namespace: data def: "Sequence map of a plasmid (circular DNA)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001279 ! Sequence map [Term] id: EDAM:0001288 name: Genome map namespace: data def: "Sequence map of a whole genome." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001279 ! Sequence map [Term] id: EDAM:0001865 name: Map feature namespace: data def: "A feature which may mapped (positioned) on a genetic or other type of map." [EDAM:EBI "EMBRACE definition"] comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. subset: data xref: Moby:MapFeature is_obsolete: true consider: EDAM:0001255 ! Sequence features consider: EDAM:0002019 ! Map attribute consider: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0001257 name: Sequence property (protein) namespace: data def: "A report of general sequence properties derived from protein sequence data." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000897 ! Protein property [Term] id: EDAM:0001258 name: Sequence property (nucleic acid) namespace: data def: "A report of general sequence properties derived from nucleotide sequence data." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000912 ! Nucleic acid property [Term] id: EDAM:0001259 name: Sequence complexity namespace: data def: "A report on sequence complexity, for example low-complexity or repeat regions in sequences." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence property (complexity)" EXACT [] is_a: EDAM:0001254 ! Sequence property [Term] id: EDAM:0001260 name: Sequence ambiguity namespace: data def: "A report on ambiguity in molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence property (ambiguity)" EXACT [] is_a: EDAM:0001254 ! Sequence property [Term] id: EDAM:0001261 name: Sequence composition namespace: data def: "A report (typically a table) on character or word composition / frequency of a molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence property (composition)" EXACT [] is_a: EDAM:0001254 ! Sequence property [Term] id: EDAM:0003119 name: Sequence features (compositionally-biased regions) namespace: data def: "A report of regions in a molecular sequence that are biased to certain characters." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001261 ! Sequence composition [Term] id: EDAM:0003085 name: Protein sequence composition namespace: data def: "A report (typically a table) on character or word composition / frequency of protein sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence property (protein composition)" EXACT [] is_a: EDAM:0001261 ! Sequence composition [Term] id: EDAM:0003086 name: Nucleic acid sequence composition namespace: data def: "A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence property (nucleic acid composition)" EXACT [] is_a: EDAM:0001261 ! Sequence composition is_a: EDAM:0000912 ! Nucleic acid property [Term] id: EDAM:0001262 name: Peptide molecular weight hits namespace: data def: "A report on peptide fragments of certain molecular weight(s) in one or more protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001233 ! Sequence set (protein) [Term] id: EDAM:0001263 name: Sequence composition (base position variability) namespace: data def: "Report on or plot of third base position variability in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003086 ! Nucleic acid sequence composition [Term] id: EDAM:0002157 name: Word composition namespace: data def: "Word composition data for a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001268 ! Amino acid word frequencies consider: EDAM:0001266 ! Sequence composition (base words) [Term] id: EDAM:0001264 name: Sequence composition table namespace: data def: "A table of character or word composition / frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001261 ! Sequence composition [Term] id: EDAM:0002166 name: Sequence composition plot namespace: data def: "A plot of character or word composition / frequency of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001261 ! Sequence composition [Term] id: EDAM:0001265 name: Sequence composition (base frequencies) namespace: data def: "A table of base frequencies of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003086 ! Nucleic acid sequence composition [Term] id: EDAM:0001267 name: Amino acid frequencies namespace: data def: "A table of amino acid frequencies of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence composition (amino acid frequencies)" EXACT [] is_a: EDAM:0003085 ! Protein sequence composition [Term] id: EDAM:0001266 name: Sequence composition (base words) namespace: data def: "A table of word composition of a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003086 ! Nucleic acid sequence composition [Term] id: EDAM:0001268 name: Amino acid word frequencies namespace: data def: "A table of amino acid word composition of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence composition (amino acid words)" EXACT [] is_a: EDAM:0003085 ! Protein sequence composition [Term] id: EDAM:0001269 name: DAS sequence feature annotation namespace: data def: "Annotation of a molecular sequence in DAS format." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001978 ! DASGFF feature [Term] id: EDAM:0003002 name: Sequence annotation track namespace: data def: "Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Annotation track" EXACT [] synonym: "Genome track" EXACT [] synonym: "Genomic track" EXACT [] synonym: "Genome-browser track" EXACT [] synonym: "Genome annotation track" EXACT [] is_a: EDAM:0001255 ! Sequence features [Term] id: EDAM:0001270 name: Sequence feature table namespace: data def: "Annotation of positional sequence features, organized into a standard feature table." [EDAM:EBI "EMBRACE definition"] synonym: "Feature table" EXACT [] is_a: EDAM:0001255 ! Sequence feature annotation [Term] id: EDAM:0001276 name: Nucleic acid features namespace: data alt_id: EDAM:0001273 def: "Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence)." [EDAM:EBI "EMBRACE definition"] comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. subset: data synonym: "Nucleic acid feature table" EXACT [] synonym: "Feature table (nucleic acid)" EXACT [] is_a: EDAM:0002084 ! Nucleic acid report is_a: EDAM:0001255 ! Sequence features [Term] id: EDAM:0003139 name: Nucleic acid features (STS) namespace: data def: "A report on sequence tagged sites (STS) in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] comment: Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. subset: data is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0003122 name: Nucleic acid features (difference and change) namespace: data def: "A report on features in a nucleic acid sequence that indicate changes to or differences between sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0003123 name: Nucleic acid features (expression signal) namespace: data def: "A report on regions within a nucleic acid sequence containing a signal that alters a biological function." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0003125 name: Nucleic acid features (binding) namespace: data def: "A report on regions of a nucleic acid sequence that bind some other molecule." [EDAM:EBI "EMBRACE definition"] comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). subset: data is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0003126 name: Nucleic acid features (repeats) namespace: data def: "A report on repetitive elements within a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] comment: This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. subset: data is_a: EDAM:0001299 ! Sequence features (repeats) is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0003127 name: Nucleic acid features (replication and recombination) namespace: data def: "A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination." [EDAM:EBI "EMBRACE definition"] comment: This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. subset: data is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0003128 name: Nucleic acid features (structure) namespace: data def: "A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0003132 name: Nucleic acid features (d-loop) namespace: data def: "A report on displacement loops in a mitochondrial DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. subset: data is_a: EDAM:0003128 ! Nucleic acid features (structure) [Term] id: EDAM:0003133 name: Nucleic acid features (stem loop) namespace: data def: "A report on stem loops in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. subset: data is_a: EDAM:0003128 ! Nucleic acid features (structure) [Term] id: EDAM:0002882 name: DNA features namespace: data def: "DNA sequence-specific feature annotation (not in a feature table)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0002883 name: Nucleic acid features (RNA features) namespace: data def: "Features concerning RNA or regions of DNA that encode an RNA molecule." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "RNA features" EXACT [] is_a: EDAM:0001300 ! Nucleic acid features (gene structure) [Term] id: EDAM:0003134 name: Nucleic acid features (mRNA features) namespace: data def: "Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules." [EDAM:EBI "EMBRACE definition"] comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). subset: data synonym: "mRNA features" EXACT [] is_a: EDAM:0002883 ! Nucleic acid features (RNA features) [Term] id: EDAM:0003137 name: Nucleic acid features (non-coding RNA) namespace: data def: "Features concerning non-coding or functional RNA molecules, including tRNA and rRNA." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "ncRNA features" EXACT [] synonym: "Non-coding RNA features" EXACT [] is_a: EDAM:0002883 ! Nucleic acid features (RNA features) [Term] id: EDAM:0003138 name: Nucleic acid features (transcriptional) namespace: data def: "Features concerning transcription of DNA into RNA including the regulation of transcription." [EDAM:EBI "EMBRACE definition"] comment: This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. subset: data is_a: EDAM:0002883 ! Nucleic acid features (RNA features) [Term] id: EDAM:0001277 name: Protein features namespace: data alt_id: EDAM:0001272 def: "Protein sequence-specific feature annotation (positional features of a protein sequence)." [EDAM:EBI "EMBRACE definition"] comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. subset: data synonym: "Feature table (protein)" EXACT [] synonym: "Protein feature table" EXACT [] is_a: EDAM:0001255 ! Sequence features is_a: EDAM:0000896 ! Protein report [Term] id: EDAM:0001256 name: Sequence features (comparative) namespace: data def: "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data is_obsolete: true consider: EDAM:0001255 ! Sequence features [Term] id: EDAM:0001298 name: Sequence features (motifs) namespace: data def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." [EDAM:EBI "EMBRACE definition"] comment: Use this term if another, more specific term is not available. subset: data is_a: EDAM:0001255 ! Sequence features [Term] id: EDAM:0003130 name: Protein features (motifs) namespace: data def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." [EDAM:EBI "EMBRACE definition"] comment: Use this term if another, more specific term is not available. subset: data is_a: EDAM:0001277 ! Protein features is_a: EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0003131 name: Nucleic acid features (motifs) namespace: data def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences." [EDAM:EBI "EMBRACE definition"] comment: Use this term if another, more specific term is not available. subset: data is_a: EDAM:0001276 ! Nucleic acid features is_a: EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0000858 name: Database hits (secondary) namespace: data def: "A report of hits from a search of a protein secondary or domain database." [EDAM:EBI "EMBRACE definition"] comment: Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See terms under 'Protein features'. subset: data is_a: EDAM:0002080 ! Database hits [Term] id: EDAM:0000901 name: Protein features (domains) namespace: data def: "Summary of structural domains or 3D folds in a protein or polypeptide chain." [EDAM:EBI "EMBRACE definition"] comment: The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. subset: data synonym: "Protein domain assignment" EXACT [] synonym: "Protein structural domains" EXACT [] is_a: EDAM:0001277 ! Protein features relationship: has_topic EDAM:0000736 ! Protein domains and folds [Term] id: EDAM:0003118 name: Protein features (topological domains) namespace: data def: "Summary of topological domains such as cytoplasmic regions in a protein." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein topological domains" EXACT [] is_a: EDAM:0001277 ! Protein features relationship: has_topic EDAM:0000736 ! Protein domains and folds [Term] id: EDAM:0001299 name: Sequence features (repeats) namespace: data alt_id: EDAM:0001282 def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] comment: The report might include derived data map such as classification, annotation, organization, periodicity etc. subset: data synonym: "Repeat sequence map" EXACT [] is_a: EDAM:0001255 ! Sequence features [Term] id: EDAM:0003129 name: Protein features (repeats) namespace: data def: "Location of short repetitive subsequences (repeat sequences) in a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001299 ! Sequence features (repeats) is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001281 name: Sequence signature map namespace: data def: "Image of a sequence with matches to signatures, motifs or profiles." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0001290 name: InterPro compact match image namespace: data def: "Image showing matches between protein sequence(s) and InterPro Entries." [EDAM:EBI "EMBRACE definition"] comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. subset: data is_obsolete: true consider: EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0001291 name: InterPro detailed match image namespace: data def: "Image showing detailed information on matches between protein sequence(s) and InterPro Entries." [EDAM:EBI "EMBRACE definition"] comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. subset: data is_obsolete: true consider: EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0001292 name: InterPro architecture image namespace: data def: "Image showing the architecture of InterPro domains in a protein sequence." [EDAM:EBI "EMBRACE definition"] comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. subset: data is_obsolete: true consider: EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0001293 name: SMART protein schematic namespace: data def: "SMART protein schematic in PNG format." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0001294 name: GlobPlot domain image namespace: data def: "Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001298 ! Sequence features (motifs) [Term] id: EDAM:0001564 name: Protein fold recognition report namespace: data def: "A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. subset: data is_obsolete: true consider: EDAM:0000901 ! Protein features (domains) [Term] id: EDAM:0001300 name: Nucleic acid features (gene and transcript structure) namespace: data def: "A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene annotation (structure)" EXACT [] is_a: EDAM:0000916 ! Gene annotation is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0003140 name: Nucleic acid features (immunoglobulin gene structure) namespace: data def: "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001300 ! Nucleic acid features (gene structure) [Term] id: EDAM:0001301 name: Nucleic acid features (mobile genetic elements) namespace: data def: "A report on a region of a nucleic acid sequence containin mobile genetic elements." [EDAM:EBI "EMBRACE definition"] comment: This includes transposons, Plasmids, Bacteriophage elements and Group II introns. subset: data synonym: "Nucleic acid features (transposons)" EXACT [] is_a: EDAM:0001276 ! Nucleic acid features [Term] id: EDAM:0001302 name: Nucleic acid features (PolyA signal or site) namespace: data def: "A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript." [EDAM:EBI "EMBRACE definition"] comment: A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. subset: data synonym: "PolyA signal" EXACT [] synonym: "PolyA site" EXACT [] is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) [Term] id: EDAM:0003135 name: Nucleic acid features (signal or transit peptide) namespace: data def: "A report on a coding sequence for a signal or transit peptide." [EDAM:EBI "EMBRACE definition"] comment: A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. subset: data is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) [Term] id: EDAM:0001303 name: Nucleic acid features (quadruplexes) namespace: data def: "A report on quadruplex-forming motifs in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003128 ! Nucleic acid features (structure) [Term] id: EDAM:0001304 name: Nucleic acid features (CpG island and isochore) namespace: data def: "A report or plot of CpG rich regions (isochores) in a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003138 ! Nucleic acid features (transcriptional) [Term] id: EDAM:0001305 name: Nucleic acid features (restriction sites) namespace: data def: "Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003125 ! Nucleic acid features (binding) [Term] id: EDAM:0001306 name: Nucleic acid features (nucleosome exclusion sequences) namespace: data def: "A report on nucleosome formation potential or exclusion sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003127 ! Nucleic acid features (replication and recombination) [Term] id: EDAM:0001307 name: Nucleic acid features (splice sites) namespace: data alt_id: EDAM:0000915 def: "A report on splice sites in a nucleotide sequence or alternative RNA splicing events." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Nucleic acid report (RNA splice model)" EXACT [] synonym: "Nucleic acid report (RNA splicing)" EXACT [] is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) [Term] id: EDAM:0001308 name: Nucleic acid features (matrix/scaffold attachment sites) namespace: data def: "A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003138 ! Nucleic acid features (transcriptional) [Term] id: EDAM:0001309 name: Gene features (exonic splicing enhancer) namespace: data def: "A report on exonic splicing enhancers (ESE) in an exon." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002397 ! Nucleic acid features (exon) [Term] id: EDAM:0001310 name: Nucleic acid features (microRNA) namespace: data def: "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003137 ! Nucleic acid features (non-coding RNA) relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] id: EDAM:0002169 name: Nucleic acid features (siRNA) namespace: data def: "A report on siRNA duplexes in mRNA." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003137 ! Nucleic acid features (non-coding RNA) relationship: has_topic EDAM:0003060 ! Regulatory RNA [Term] id: EDAM:0000922 name: Nucleic acid features (primers) namespace: data def: "Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003127 ! Nucleic acid features (replication and recombination) relationship: has_topic EDAM:0000632 ! Probes and primers [Term] id: EDAM:0001311 name: Nucleic acid features (operon) namespace: data def: "A report on operons (operators, promoters and genes) from a bacterial genome." [EDAM:EBI "EMBRACE definition"] comment: The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. subset: data synonym: "Gene features (operon)" EXACT [] is_a: EDAM:0001300 ! Nucleic acid features (gene structure) [Term] id: EDAM:0001312 name: Gene features (promoter) namespace: data def: "A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003138 ! Nucleic acid features (transcriptional) [Term] id: EDAM:0001313 name: Nucleic acid features (coding sequence) namespace: data alt_id: EDAM:0001317 def: "A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene features (coding sequence)" EXACT [] synonym: "Gene features (coding region)" EXACT [] synonym: "Gene annotation (translation)" EXACT [] is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) [Term] id: EDAM:0001314 name: Gene features (SECIS element) namespace: data def: "A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001300 ! Nucleic acid features (gene structure) [Term] id: EDAM:0001315 name: Gene features (TFBS) namespace: data def: "A report on the transcription factor binding sites (TFBS) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001312 ! Gene features (promoter) is_a: EDAM:0003125 ! Nucleic acid features (binding) relationship: has_topic EDAM:0000749 ! Transcription factors and regulatory sites [Term] id: EDAM:0002397 name: Nucleic acid features (exon) namespace: data def: "An informative report on an exon in a nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene features (exon)" EXACT [] is_a: EDAM:0001313 ! Nucleic acid features (coding sequence) [Term] id: EDAM:0002754 name: Nucleic acid features (intron) namespace: data def: "An informative report on an intron in a nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene features (intron)" EXACT [] is_a: EDAM:0003134 ! Nucleic acid features (mRNA features) [Term] id: EDAM:0002160 name: Fickett testcode plot namespace: data def: "A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001313 ! Nucleic acid features (coding sequence) [Term] id: EDAM:0001289 name: Restriction map namespace: data def: "Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001305 ! Nucleic acid features (restriction sites) is_a: EDAM:0001279 ! Sequence map is_a: EDAM:0002969 ! Sequence image [Term] id: EDAM:0001321 name: Protein features (sites) namespace: data def: "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites." [EDAM:EBI "EMBRACE definition"] comment: Use this term for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. subset: data is_obsolete: true consider: EDAM:0001277 ! Protein features [Term] id: EDAM:0001322 name: Protein features (signal peptides) namespace: data def: "A report on the location of signal peptides or signal peptide cleavage sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0003120 name: Protein features (sequence variants) namespace: data def: "A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001323 name: Protein features (cleavage sites) namespace: data def: "A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001277 ! Protein features relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0001324 name: Protein features (post-translation modifications) namespace: data def: "A report on post-translation modifications in a protein sequence, typically describing the specific sites involved." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein features (post-translation modification sites)" EXACT [] synonym: "Post-translation modification" EXACT [] is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001325 name: Protein features (active sites) namespace: data def: "A report on catalytic residues (active site) of an enzyme." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Enzyme active site" EXACT [] is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001326 name: Protein features (binding sites) namespace: data def: "A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0002989 name: Protein features (key folding sites) namespace: data def: "A report on key residues involved in protein folding." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001327 name: Protein features (epitopes) namespace: data def: "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data." [EDAM:EBI "EMBRACE definition"] comment: Epitope mapping is commonly done during vaccine design. subset: data is_obsolete: true consider: EDAM:0001326 ! Protein features (binding sites) [Term] id: EDAM:0001328 name: Protein features (nucleic acid binding sites) namespace: data def: "A report on RNA and DNA-binding proteins and binding sites in protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001329 name: MHC Class I epitopes report namespace: data def: "A report on epitopes that bind to MHC class I molecules." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001326 ! Protein features (binding sites) [Term] id: EDAM:0001330 name: MHC Class II epitopes report namespace: data def: "A report on predicted epitopes that bind to MHC class II molecules." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001326 ! Protein features (binding sites) [Term] id: EDAM:0001331 name: Protein features (PEST sites) namespace: data def: "A report or plot of PEST sites in a protein sequence." [EDAM:EBI "EMBRACE definition"] comment: 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. subset: data is_obsolete: true consider: EDAM:0001323 ! Protein features (cleavage sites) [Term] id: EDAM:0000857 name: Database hits (sequence) namespace: data def: "A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits." [EDAM:EBI "EMBRACE definition"] comment: The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. subset: data is_a: EDAM:0002080 ! Database hits [Term] id: EDAM:0000885 name: Database hits (structure) namespace: data def: "Results (hits) from searching a database of tertiary structure." [EDAM:EBI "EMBRACE definition"] comment: This includes alignment and score data. subset: data is_a: EDAM:0002080 ! Database hits [Term] id: EDAM:0001338 name: Sequence database hits scores list namespace: data def: "Scores from a sequence database search (for example a BLAST search)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000857 ! Database hits (sequence) [Term] id: EDAM:0001339 name: Sequence database hits alignments list namespace: data def: "Alignments from a sequence database search (for example a BLAST search)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000857 ! Database hits (sequence) [Term] id: EDAM:0001340 name: Sequence database hits evaluation data namespace: data def: "A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000857 ! Database hits (sequence) [Term] id: EDAM:0001358 name: Prosite nucleotide pattern namespace: data def: "A nucleotide regular expression pattern from the Prosite database." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001353 ! Sequence motif [Term] id: EDAM:0001359 name: Prosite protein pattern namespace: data def: "A protein regular expression pattern from the Prosite database." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001353 ! Sequence motif [Term] id: EDAM:0001352 name: Regular expression namespace: data def: "Regular expression pattern." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0002070 name: Sequence motif (nucleic acid) namespace: data def: "A nucleotide sequence motif." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001353 ! Sequence motif [Term] id: EDAM:0002071 name: Sequence motif (protein) namespace: data def: "An amino acid sequence motif." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001353 ! Sequence motif [Term] id: EDAM:0002854 name: Position-specific scoring matrix namespace: data def: "A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001354 ! Sequence profile is_a: EDAM:0002082 ! Matrix [Term] id: EDAM:0001361 name: Position frequency matrix namespace: data def: "A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "PFM" EXACT [] is_a: EDAM:0002854 ! Position-specific scoring matrix [Term] id: EDAM:0001362 name: Position weight matrix namespace: data def: "A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position." [EDAM:EBI "EMBRACE definition"] comment: Contributions of individual sequences to the matrix might be uneven (weighted). subset: data synonym: "PWM" EXACT [] is_a: EDAM:0002854 ! Position-specific scoring matrix [Term] id: EDAM:0001363 name: Information content matrix namespace: data def: "A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "ICM" EXACT [] is_a: EDAM:0002854 ! Position-specific scoring matrix [Term] id: EDAM:0001364 name: Hidden Markov model namespace: data def: "A hidden Markov model representation of a set or alignment of sequences." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "HMM" EXACT [] is_a: EDAM:0001354 ! Sequence profile [Term] id: EDAM:0001365 name: Fingerprint namespace: data def: "One or more fingerprints (sequence classifiers) as used in the PRINTS database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002854 ! Position-specific scoring matrix [Term] id: EDAM:0001368 name: Domainatrix signature namespace: data def: "A protein signature of the type used in the EMBASSY Signature package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001354 ! Sequence profile [Term] id: EDAM:0001371 name: HMMER NULL hidden Markov model namespace: data def: "NULL hidden Markov model representation used by the HMMER package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001364 ! Hidden Markov model [Term] id: EDAM:0001372 name: Protein family signature namespace: data def: "A protein family signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. subset: data is_a: EDAM:0001355 ! Protein signature [Term] id: EDAM:0001373 name: Protein domain signature namespace: data def: "A protein domain signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries. subset: data is_a: EDAM:0001355 ! Protein signature [Term] id: EDAM:0001374 name: Protein region signature namespace: data def: "A protein region signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein region signature defines a region which cannot be described as a protein family or domain signature. subset: data is_a: EDAM:0001355 ! Protein signature [Term] id: EDAM:0001375 name: Protein repeat signature namespace: data def: "A protein repeat signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. subset: data is_a: EDAM:0001355 ! Protein signature [Term] id: EDAM:0001376 name: Protein site signature namespace: data def: "A protein site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein site signature is a classifier for a specific site in a protein. subset: data is_a: EDAM:0001355 ! Protein signature [Term] id: EDAM:0001377 name: Protein conserved site signature namespace: data def: "A protein conserved site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. subset: data is_a: EDAM:0001376 ! Protein site signature [Term] id: EDAM:0001378 name: Protein active site signature namespace: data def: "A protein active site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. subset: data is_a: EDAM:0001376 ! Protein site signature [Term] id: EDAM:0001379 name: Protein binding site signature namespace: data def: "A protein binding site signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. subset: data is_a: EDAM:0001376 ! Protein site signature [Term] id: EDAM:0001380 name: Protein post-translational modification signature namespace: data def: "A protein post-translational modification signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] comment: A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. subset: data is_a: EDAM:0001376 ! Protein site signature [Term] id: EDAM:0000861 name: Sequence alignment (words) namespace: data def: "Alignment of exact matches between subsequences (words) within two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence word alignment" EXACT [] is_a: EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0000863 name: Sequence alignment namespace: data def: "Alignment of multiple molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001916 ! Alignment relationship: has_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0000868 name: Sequence profile alignment namespace: data def: "A profile-profile alignment (each profile typically representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001916 ! Alignment [Term] id: EDAM:0000869 name: Sequence-profile alignment namespace: data def: "Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] comment: Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. subset: data is_a: EDAM:0001916 ! Alignment [Term] id: EDAM:0002366 name: Secondary structure alignment namespace: data def: "Alignment of the (1D representations of) secondary structure of two or more molecules." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001916 ! Alignment [Term] id: EDAM:0000878 name: Secondary structure alignment (protein) namespace: data def: "Alignment of the (1D representations of) secondary structure of two or more proteins." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002366 ! Secondary structure alignment is_a: EDAM:0003154 ! Protein alignment [Term] id: EDAM:0000881 name: Secondary structure alignment (RNA) namespace: data def: "Alignment of the (1D representations of) secondary structure of two or more RNA molecules." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby:RNAStructAlignmentML is_a: EDAM:0002366 ! Secondary structure alignment [Term] id: EDAM:0000886 name: Structure alignment namespace: data def: "Alignment (superimposition) of molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] comment: A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. subset: data is_a: EDAM:0001916 ! Alignment relationship: has_topic EDAM:0000183 ! Structure alignment [Term] id: EDAM:0000890 name: Structural (3D) profile alignment namespace: data def: "A 3D profile-3D profile alignment (each profile representing structures or a structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Structural profile alignment" EXACT [] is_a: EDAM:0001916 ! Alignment [Term] id: EDAM:0000891 name: Sequence-3D profile alignment namespace: data def: "An alignment of a sequence to a 3D profile (representing structures or a structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence-structural profile alignment" EXACT [] is_a: EDAM:0000893 ! Sequence-structure alignment [Term] id: EDAM:0000893 name: Sequence-structure alignment namespace: data def: "An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s))." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001916 ! Alignment [Term] id: EDAM:0001381 name: Sequence alignment (pair) namespace: data def: "Alignment of exactly two molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0001382 name: Sequence alignment (multiple) namespace: data def: "Alignment of more than two molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0001383 name: Sequence alignment (nucleic acid) namespace: data def: "Alignment of multiple nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000863 ! Sequence alignment is_a: EDAM:0002084 ! Nucleic acid report [Term] id: EDAM:0001384 name: Sequence alignment (protein) namespace: data def: "Alignment of multiple protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000863 ! Sequence alignment is_a: EDAM:0003154 ! Protein alignment [Term] id: EDAM:0001385 name: Sequence alignment (hybrid) namespace: data def: "Alignment of multiple molecular sequences of different types." [EDAM:EBI "EMBRACE definition"] comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. subset: data is_a: EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0001386 name: Sequence alignment (nucleic acid pair) namespace: data def: "Alignment of exactly two nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001381 ! Sequence alignment (pair) is_a: EDAM:0001383 ! Sequence alignment (nucleic acid) [Term] id: EDAM:0001387 name: Sequence alignment (protein pair) namespace: data def: "Alignment of exactly two protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001381 ! Sequence alignment (pair) is_a: EDAM:0001384 ! Sequence alignment (protein) [Term] id: EDAM:0001389 name: Multiple nucleotide sequence alignment namespace: data def: "Alignment of more than two nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0001390 name: Multiple protein sequence alignment namespace: data def: "Alignment of more than two protein sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0001388 name: Hybrid sequence alignment (pair) namespace: data def: "Alignment of exactly two molecular sequences of different types." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001385 ! Sequence alignment (hybrid) [Term] id: EDAM:0001417 name: Sequence-profile alignment (Domainatrix signature) namespace: data def: "Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000869 ! Sequence-profile alignment [Term] id: EDAM:0001418 name: Sequence-profile alignment (HMM) namespace: data def: "Alignment of molecular sequence(s) to a hidden Markov model(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000869 ! Sequence-profile alignment [Term] id: EDAM:0001420 name: Sequence-profile alignment (fingerprint) namespace: data def: "Alignment of molecular sequences to a protein fingerprint from the PRINTS database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000869 ! Sequence-profile alignment [Term] id: EDAM:0001479 name: Structure alignment (pair) namespace: data def: "Alignment (superimposition) of exactly two molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000886 ! Structure alignment [Term] id: EDAM:0001480 name: Structure alignment (multiple) namespace: data def: "Alignment (superimposition) of more than two molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000886 ! Structure alignment [Term] id: EDAM:0001481 name: Structure alignment (protein) namespace: data def: "Alignment (superimposition) of protein tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000886 ! Structure alignment is_a: EDAM:0003154 ! Protein alignment [Term] id: EDAM:0001482 name: Structure alignment (nucleic acid) namespace: data def: "Alignment (superimposition) of nucleic acid tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000886 ! Structure alignment is_a: EDAM:0002084 ! Nucleic acid report [Term] id: EDAM:0001483 name: Structure alignment (protein pair) namespace: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001481 ! Structure alignment (protein) is_a: EDAM:0001479 ! Structure alignment (pair) [Term] id: EDAM:0001484 name: Multiple protein tertiary structure alignment namespace: data def: "Alignment (superimposition) of more than two protein tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001481 ! Structure alignment (protein) [Term] id: EDAM:0001485 name: Structure alignment (protein all atoms) namespace: data def: "Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001481 ! Structure alignment (protein) [Term] id: EDAM:0001486 name: Structure alignment (protein C-alpha atoms) namespace: data def: "Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered)." [EDAM:EBI "EMBRACE definition"] comment: C-beta atoms from amino acid side-chains may be considered. subset: data is_a: EDAM:0001481 ! Structure alignment (protein) [Term] id: EDAM:0001487 name: Pairwise protein tertiary structure alignment (all atoms) namespace: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001485 ! Structure alignment (protein all atoms) [Term] id: EDAM:0001488 name: Pairwise protein tertiary structure alignment (C-alpha atoms) namespace: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [EDAM:EBI "EMBRACE definition"] comment: C-beta atoms from amino acid side-chains may be included. subset: data is_obsolete: true consider: EDAM:0001486 ! Structure alignment (protein C-alpha atoms) [Term] id: EDAM:0001489 name: Multiple protein tertiary structure alignment (all atoms) namespace: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001485 ! Structure alignment (protein all atoms) [Term] id: EDAM:0001490 name: Multiple protein tertiary structure alignment (C-alpha atoms) namespace: data def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [EDAM:EBI "EMBRACE definition"] comment: C-beta atoms from amino acid side-chains may be included. subset: data is_obsolete: true consider: EDAM:0001486 ! Structure alignment (protein C-alpha atoms) [Term] id: EDAM:0001491 name: Structure alignment (nucleic acid pair) namespace: data def: "Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001482 ! Structure alignment (nucleic acid) is_a: EDAM:0001479 ! Structure alignment (pair) [Term] id: EDAM:0001492 name: Multiple nucleic acid tertiary structure alignment namespace: data def: "Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001482 ! Structure alignment (nucleic acid) [Term] id: EDAM:0001493 name: Structure alignment (RNA) namespace: data def: "Alignment (superimposition) of RNA tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001482 ! Structure alignment (nucleic acid) [Term] id: EDAM:0000866 name: Sequence alignment metadata namespace: data def: "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000867 ! Sequence alignment report is_a: EDAM:0002337 ! Metadata [Term] id: EDAM:0001414 name: Sequence alignment metadata (quality report) namespace: data def: "Data on molecular sequence alignment quality (estimated accuracy)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000867 ! Sequence alignment report [Term] id: EDAM:0001415 name: Sequence alignment report (site conservation) namespace: data def: "Data on character conservation in a molecular sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this term for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. subset: data is_a: EDAM:0000867 ! Sequence alignment report [Term] id: EDAM:0001416 name: Sequence alignment report (site correlation) namespace: data def: "Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000867 ! Sequence alignment report [Term] id: EDAM:0002242 name: Phylogenetic property values namespace: data def: "Phylogenetic property values data." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000871 ! Phylogenetic character data [Term] id: EDAM:0001444 name: Phylogenetic character contrasts namespace: data def: "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Phylogenetic report (character contrasts)" EXACT [] is_a: EDAM:0002523 ! Phylogenetic raw data [Term] id: EDAM:0001426 name: Phylogenetic continuous quantitative data namespace: data def: "Continuous quantitative data that may be read during phylogenetic tree calculation." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Quantitative traits" EXACT [] synonym: "Phylogenetic continuous quantitative characters" EXACT [] is_a: EDAM:0000871 ! Phylogenetic character data [Term] id: EDAM:0002873 name: Phylogenetic gene frequencies data namespace: data def: "Gene frequencies data that may be read during phylogenetic tree calculation." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001426 ! Phylogenetic continuous quantitative data [Term] id: EDAM:0001427 name: Phylogenetic discrete data namespace: data def: "Character data with discrete states that may be read during phylogenetic tree calculation." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Discretely coded characters" EXACT [] synonym: "Discrete characters" EXACT [] synonym: "Phylogenetic discrete states" EXACT [] is_a: EDAM:0000871 ! Phylogenetic character data [Term] id: EDAM:0002994 name: Phylogenetic character weights namespace: data def: "Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002523 ! Phylogenetic raw data [Term] id: EDAM:0001428 name: Phylogenetic character cliques namespace: data def: "One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Phylogenetic report (cliques)" EXACT [] is_a: EDAM:0002523 ! Phylogenetic raw data [Term] id: EDAM:0001429 name: Phylogenetic invariants namespace: data def: "Phylogenetic invariants data for testing alternative tree topologies." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Phylogenetic report (invariants)" EXACT [] is_a: EDAM:0002523 ! Phylogenetic raw data [Term] id: EDAM:0002247 name: Phylogenetic consensus tree namespace: data def: "A consensus phylogenetic tree derived from comparison of multiple trees." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000872 ! Phylogenetic tree [Term] id: EDAM:0001439 name: DNA substitution model namespace: data def: "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequence alignment report (DNA substitution model)" EXACT [] synonym: "Phylogenetic tree report (DNA substitution model)" EXACT [] is_a: EDAM:0001438 ! Phylogenetic tree report is_a: EDAM:0000950 ! Biological model is_a: EDAM:0000867 ! Sequence alignment report [Term] id: EDAM:0001440 name: Phylogenetic tree report (tree shape) namespace: data def: "Data about the shape of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001438 ! Phylogenetic tree report [Term] id: EDAM:0001441 name: Phylogenetic tree report (tree evaluation) namespace: data def: "Data on the confidence of a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001438 ! Phylogenetic tree report [Term] id: EDAM:0001442 name: Phylogenetic tree report (tree distances) namespace: data def: "Distances, such as Branch Score distance, between two or more phylogenetic trees." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001438 ! Phylogenetic tree report [Term] id: EDAM:0001443 name: Phylogenetic tree report (tree stratigraphic) namespace: data def: "Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001438 ! Phylogenetic tree report [Term] id: EDAM:0001446 name: Comparison matrix (integers) namespace: data def: "Matrix of integer numbers for sequence comparison." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Substitution matrix (integers)" EXACT [] is_obsolete: true consider: EDAM:0000874 ! Comparison matrix [Term] id: EDAM:0001447 name: Comparison matrix (floats) namespace: data def: "Matrix of floating point numbers for sequence comparison." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Substitution matrix (floats)" EXACT [] is_obsolete: true consider: EDAM:0000874 ! Comparison matrix [Term] id: EDAM:0001448 name: Comparison matrix (nucleotide) namespace: data def: "Matrix of integer or floating point numbers for nucleotide comparison." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Nucleotide substitution matrix" EXACT [] is_a: EDAM:0000874 ! Comparison matrix [Term] id: EDAM:0001449 name: Comparison matrix (amino acid) namespace: data def: "Matrix of integer or floating point numbers for amino acid comparison." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Amino acid substitution matrix" EXACT [] is_a: EDAM:0002016 ! Amino acid property is_a: EDAM:0000874 ! Comparison matrix [Term] id: EDAM:0001450 name: Nucleotide comparison matrix (integers) namespace: data def: "Matrix of integer numbers for nucleotide comparison." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Nucleotide substitution matrix (integers)" EXACT [] is_obsolete: true consider: EDAM:0001448 ! Comparison matrix (nucleotide) [Term] id: EDAM:0001451 name: Nucleotide comparison matrix (floats) namespace: data def: "Matrix of floating point numbers for nucleotide comparison." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Nucleotide substitution matrix (floats)" EXACT [] is_obsolete: true consider: EDAM:0001448 ! Comparison matrix (nucleotide) [Term] id: EDAM:0001452 name: Amino acid comparison matrix (integers) namespace: data def: "Matrix of integer numbers for amino acid comparison." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Amino acid substitution matrix (integers)" EXACT [] is_obsolete: true consider: EDAM:0001449 ! Comparison matrix (amino acid) [Term] id: EDAM:0001453 name: Amino acid comparison matrix (floats) namespace: data def: "Matrix of floating point numbers for amino acid comparison." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Amino acid substitution matrix (floats)" EXACT [] is_obsolete: true consider: EDAM:0001449 ! Comparison matrix (amino acid) [Term] id: EDAM:0001540 name: Protein residue interactions namespace: data def: "Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Residue interaction data" EXACT [] synonym: "Atom interaction data" EXACT [] is_a: EDAM:0002599 ! Molecular interaction is_a: EDAM:0000906 ! Protein interaction relationship: has_topic EDAM:0000144 ! Protein residue interaction analysis [Term] id: EDAM:0001543 name: Protein surface report namespace: data def: "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data synonym: "Protein structure report (surface)" EXACT [] is_a: EDAM:0001542 ! Protein solvent accessibility is_a: EDAM:0001537 ! Protein structure report [Term] id: EDAM:0000875 name: Protein topology namespace: data def: "Predicted or actual protein topology represented as a string of protein secondary structure elements." [EDAM:EBI "EMBRACE definition"] comment: The location and size of the secondary structure elements and intervening loop regions is usually indicated. subset: data is_obsolete: true consider: EDAM:0000876 ! Protein features (secondary structure) [Term] id: EDAM:0002081 name: Secondary structure namespace: data def: "The secondary structure assignment (predicted or real) of a nucleic acid or protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0000877 name: Protein features (super-secondary) namespace: data def: "A report of predicted or actual super-secondary structure of protein sequence(s)." [EDAM:EBI "EMBRACE definition"] comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. subset: data synonym: "Protein structure report (super-secondary)" EXACT [] is_a: EDAM:0001277 ! Protein features is_a: EDAM:0001537 ! Protein structure report [Term] id: EDAM:0000902 name: Protein architecture report namespace: data def: "An informative report on architecture (spatial arrangement of secondary structure) of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein structure report (architecture)" EXACT [] synonym: "Protein property (architecture)" EXACT [] is_a: EDAM:0000897 ! Protein property is_a: EDAM:0001537 ! Protein structure report [Term] id: EDAM:0000883 name: Structure namespace: data def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [EDAM:EBI "EMBRACE definition"] comment: The coordinate data may be predicted or real. subset: data relationship: has_topic EDAM:0000081 ! Structure analysis is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0000884 name: Tertiary structure record namespace: data def: "An entry from a molecular tertiary (3D) structure database." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000883 ! Structure [Term] id: EDAM:0001546 name: Protein distance matrix namespace: data def: "A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001540 ! Protein residue interactions [Term] id: EDAM:0001547 name: Protein contact map namespace: data def: "An amino acid residue contact map for a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001540 ! Protein residue interactions [Term] id: EDAM:0001548 name: Protein residue 3D cluster namespace: data def: "Report on clusters of contacting residues in protein structures such as a key structural residue network." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001540 ! Protein residue interactions [Term] id: EDAM:0001549 name: Protein hydrogen bonds namespace: data def: "Patterns of hydrogen bonding in protein structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001540 ! Protein residue interactions [Term] id: EDAM:0001550 name: Protein non-canonical interactions namespace: data def: "Non-canonical atomic interactions in protein structures." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein non-canonical interactions report" EXACT [] is_a: EDAM:0001540 ! Protein residue interactions is_a: EDAM:0001539 ! Protein structural quality report [Term] id: EDAM:0001542 name: Protein solvent accessibility namespace: data def: "Data on the solvent accessible or buried surface area of a protein structure." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This term covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. subset: data is_a: EDAM:0001540 ! Protein residue interactions [Term] id: EDAM:0000876 name: Protein features (secondary structure) namespace: data def: "Secondary structure assignment (predicted or real) of a protein." [EDAM:EBI "EMBRACE definition"] comment: The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). subset: data synonym: "Protein secondary structure" EXACT [] is_a: EDAM:0002081 ! Secondary structure is_a: EDAM:0001277 ! Protein features relationship: has_topic EDAM:0000694 ! Protein secondary structure [Term] id: EDAM:0000880 name: RNA secondary structure namespace: data def: "An informative report of secondary structure (predicted or real) of an RNA molecule." [EDAM:EBI "EMBRACE definition"] comment: This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. subset: data xref: Moby:RNAStructML is_a: EDAM:0002081 ! Secondary structure relationship: has_topic EDAM:0000697 ! RNA structure and alignment [Term] id: EDAM:0001456 name: Protein features (membrane regions) namespace: data def: "An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." [EDAM:EBI "EMBRACE definition"] comment: This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. subset: data synonym: "Transmembrane region report" EXACT [] synonym: "Intramembrane region report" EXACT [] synonym: "Protein report (membrane protein)" EXACT [] is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0001755 name: Protein atom namespace: data def: "Data on a single atom from a protein structure." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data synonym: "Atom data" EXACT [] is_a: EDAM:0001460 ! Protein structure [Term] id: EDAM:0001756 name: Protein residue namespace: data def: "Data on a single amino acid residue position in a protein structure." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data synonym: "Residue" EXACT [] is_a: EDAM:0001460 ! Protein structure [Term] id: EDAM:0001459 name: Nucleic acid structure namespace: data def: "3D coordinate and associated data for a nucleic acid tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000883 ! Structure relationship: has_topic EDAM:0000097 ! Nucleic acid structure analysis [Term] id: EDAM:0001460 name: Protein structure namespace: data def: "3D coordinate and associated data for a protein tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000883 ! Structure relationship: has_topic EDAM:0002814 ! Protein structure analysis relationship: has_topic EDAM:0000698 ! Protein tertiary structure [Term] id: EDAM:0001461 name: Protein-ligand complex namespace: data def: "The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule." [EDAM:EBI "EMBRACE definition"] comment: This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. subset: data is_a: EDAM:0001460 ! Protein structure [Term] id: EDAM:0001462 name: Carbohydrate structure namespace: data def: "3D coordinate and associated data for a carbohydrate (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000883 ! Structure relationship: has_topic EDAM:0000152 ! Carbohydrates relationship: has_topic EDAM:0000153 ! Lipids [Term] id: EDAM:0002850 name: Lipid structure namespace: data def: "3D coordinate and associated data for a lipid structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000883 ! Structure [Term] id: EDAM:0001463 name: Small molecule structure namespace: data def: "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000883 ! Structure relationship: has_topic EDAM:0000154 ! Small molecules [Term] id: EDAM:0002851 name: Drug structure namespace: data def: "3D coordinate and associated data for the (3D) structure of a drug." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001463 ! Small molecule structure [Term] id: EDAM:0002852 name: Toxin structure namespace: data def: "3D coordinate and associated data for the (3D) structure of a toxin." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001463 ! Small molecule structure [Term] id: EDAM:0001464 name: DNA structure namespace: data def: "3D coordinate and associated data for a DNA tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001459 ! Nucleic acid structure [Term] id: EDAM:0001465 name: RNA structure namespace: data def: "3D coordinate and associated data for an RNA tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001459 ! Nucleic acid structure relationship: has_topic EDAM:0000697 ! RNA structure and alignment [Term] id: EDAM:0001466 name: tRNA structure namespace: data def: "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001465 ! RNA structure [Term] id: EDAM:0001467 name: Protein chain namespace: data def: "3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001460 ! Protein structure [Term] id: EDAM:0001468 name: Protein domain namespace: data def: "3D coordinate and associated data for the tertiary (3D) structure of a protein domain." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001460 ! Protein structure relationship: has_topic EDAM:0000736 ! Protein domains and folds [Term] id: EDAM:0002877 name: Protein complex namespace: data def: "3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001460 ! Protein structure [Term] id: EDAM:0002878 name: Protein structural motif namespace: data def: "3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001460 ! Protein structure [Term] id: EDAM:0001469 name: Protein structure (all atoms) namespace: data def: "3D coordinate and associated data for a protein tertiary (3D) structure (all atoms)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001460 ! Protein structure [Term] id: EDAM:0001470 name: Protein structure (C-alpha atoms) namespace: data def: "3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only)." [EDAM:EBI "EMBRACE definition"] comment: C-beta atoms from amino acid side-chains may be included. subset: data is_a: EDAM:0001460 ! Protein structure [Term] id: EDAM:0001471 name: Protein chain (all atoms) namespace: data def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001467 ! Protein chain consider: EDAM:0001469 ! Protein structure (all atoms) [Term] id: EDAM:0001472 name: Protein chain (C-alpha atoms) namespace: data def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only)." [EDAM:EBI "EMBRACE definition"] comment: C-beta atoms from amino acid side-chains may be included. subset: data is_obsolete: true consider: EDAM:0001467 ! Protein chain consider: EDAM:0001470 ! Protein structure (C-alpha atoms) [Term] id: EDAM:0001473 name: Protein domain (all atoms) namespace: data def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001468 ! Protein domain consider: EDAM:0001469 ! Protein structure (all atoms) [Term] id: EDAM:0001474 name: Protein domain (C-alpha atoms) namespace: data def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only)." [EDAM:EBI "EMBRACE definition"] comment: C-beta atoms from amino acid side-chains may be included. subset: data is_obsolete: true consider: EDAM:0001468 ! Protein domain consider: EDAM:0001470 ! Protein structure (C-alpha atoms) [Term] id: EDAM:0001495 name: DaliLite hit table namespace: data def: "DaliLite hit table of protein chain tertiary structure alignment data." [EDAM:EBI "EMBRACE definition"] comment: The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. subset: data is_obsolete: true consider: EDAM:0000887 ! Structure alignment report [Term] id: EDAM:0001499 name: 3D-1D scoring matrix namespace: data def: "A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000892 ! Protein sequence-structure scoring matrix [Term] id: EDAM:0000894 name: Amino acid annotation namespace: data def: "An informative report about a specific amino acid." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002016 ! Amino acid property is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0001501 name: Amino acid index namespace: data def: "A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002016 ! Amino acid property is_a: EDAM:0002082 ! Matrix [Term] id: EDAM:0001503 name: Amino acid pair-wise contact potentials namespace: data def: "Statistical protein contact potentials." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002016 ! Amino acid property [Term] id: EDAM:0001502 name: Amino acid index (chemical classes) namespace: data def: "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001501 ! Amino acid index [Term] id: EDAM:0001505 name: Amino acid index (molecular weight) namespace: data def: "Molecular weights of amino acids." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001501 ! Amino acid index [Term] id: EDAM:0001506 name: Amino acid index (hydropathy) namespace: data def: "Hydrophobic, hydrophilic or charge properties of amino acids." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001501 ! Amino acid index [Term] id: EDAM:0001507 name: Amino acid index (White-Wimley data) namespace: data def: "Experimental free energy values for the water-interface and water-octanol transitions for the amino acids." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001501 ! Amino acid index [Term] id: EDAM:0001508 name: Amino acid index (van der Waals radii) namespace: data def: "Van der Waals radii of atoms for different amino acid residues." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001501 ! Amino acid index [Term] id: EDAM:0001509 name: Enzyme property namespace: data def: "An informative report on a specific enzyme." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Enzyme report" EXACT [] synonym: "Protein report (enzyme)" EXACT [] is_a: EDAM:0000897 ! Protein property relationship: has_topic EDAM:0000821 ! Enzymes and reactions [Term] id: EDAM:0001776 name: Protein report (function) namespace: data def: "Report on general functional properties of specific protein(s)." [EDAM:EBI "EMBRACE definition"] comment: For properties that can be mapped to a sequence, use 'Sequence report' instead. subset: data is_obsolete: true consider: EDAM:0000896 ! Protein report [Term] id: EDAM:0002722 name: Protein features (disordered structure) namespace: data def: "An informative report about disordered structure in a protein." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein structure report (disordered structure)" EXACT [] is_a: EDAM:0001277 ! Protein features is_a: EDAM:0001537 ! Protein structure report [Term] id: EDAM:0002147 name: Protein report (transcription factor) namespace: data def: "An informative report on a transcription factor protein." [EDAM:EBI "EMBRACE definition"] comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. subset: data synonym: "Transcription factor binding site data" EXACT [] is_obsolete: true consider: EDAM:0000896 ! Protein report [Term] id: EDAM:0002401 name: Protein report (membrane protein) namespace: data def: "An informative report on a membrane protein." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001456 ! Protein features (membrane regions) [Term] id: EDAM:0001517 name: Restriction enzyme property namespace: data alt_id: EDAM:0001510 alt_id: EDAM:0001518 def: "An informative report on a specific restriction enzyme such as enzyme reference data." [EDAM:EBI "EMBRACE definition"] comment: This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. subset: data synonym: "Restriction enzyme report" EXACT [] synonym: "Restriction enzyme pattern data" EXACT [] synonym: "Protein report (restriction enzyme)" EXACT [] is_a: EDAM:0001509 ! Enzyme property [Term] id: EDAM:0001533 name: Protein subcellular localization namespace: data def: "An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein report (subcellular localization)" EXACT [] is_obsolete: true consider: EDAM:0000896 ! Protein report [Term] id: EDAM:0002191 name: Protein features (checmical modification) namespace: data def: "Data on a chemical modification of a protein." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein modification annotation" EXACT [] is_a: EDAM:0001277 ! Protein features [Term] id: EDAM:0002991 name: Protein torsion angle data namespace: data def: "Torsion angle data for a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Torsion angle data" EXACT [] is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001544 name: Ramachandran plot namespace: data def: "Phi/psi angle data or a Ramachandran plot of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002991 ! Protein torsion angle data [Term] id: EDAM:0001545 name: Protein dipole moment namespace: data def: "Data on the net charge distribution (dipole moment) of a protein structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001519 name: Peptide molecular weights namespace: data alt_id: EDAM:0001535 def: "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents." [EDAM:EBI "EMBRACE definition"] comment: The report might include associated data such as frequency of peptide fragment molecular weights. subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001520 name: Peptide hydrophobic moment namespace: data def: "Report on the hydrophobic moment of a polypeptide sequence." [EDAM:EBI "EMBRACE definition"] comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: data is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0002970 name: Protein hydropathy data namespace: data def: "A report on protein properties concerning hydropathy." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein hydropathy report" EXACT [] is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001521 name: Protein aliphatic index namespace: data def: "The aliphatic index of a protein." [EDAM:EBI "EMBRACE definition"] comment: The aliphatic index is the relative protein volume occupied by aliphatic side chains. subset: data is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0002164 name: Protein sequence properties plot namespace: data def: "A plot of general physicochemical properties of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000897 ! Protein property [Term] id: EDAM:0002165 name: Protein ionization curve namespace: data def: "A plot of pK versus pH for a protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001522 name: Protein sequence hydropathy plot namespace: data def: "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc." [EDAM:EBI "EMBRACE definition"] comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: data is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0001523 name: Protein charge plot namespace: data def: "A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001524 name: Protein solubility namespace: data def: "The solubility or atomic solvation energy of a protein sequence or structure." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein solubility data" EXACT [] is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0001525 name: Protein crystallizability namespace: data def: "Data on the crystallizability of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein crystallizability data" EXACT [] is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0001526 name: Protein globularity namespace: data def: "Data on the stability, intrinsic disorder or globularity of a protein sequence." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein globularity data" EXACT [] is_a: EDAM:0002970 ! Protein hydropathy data [Term] id: EDAM:0001527 name: Protein titration curve namespace: data def: "The titration curve of a protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001528 name: Protein isoelectric point namespace: data def: "The isoelectric point of one proteins." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001529 name: Protein pKa value namespace: data def: "The pKa value of a protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001530 name: Protein hydrogen exchange rate namespace: data def: "The hydrogen exchange rate of a protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001531 name: Protein extinction coefficient namespace: data def: "The extinction coefficient of a protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001532 name: Protein optical density namespace: data def: "The optical density of a protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001534 name: Peptide immunogenicity data namespace: data def: "An report on allergenicity / immunogenicity of peptides and proteins." [EDAM:EBI "EMBRACE definition"] comment: This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. subset: data synonym: "Peptide immunogenicity report" EXACT [] synonym: "Peptide immunogenicity" EXACT [] is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0002957 name: Hopp and Woods plot namespace: data def: "A Hopp and Woods plot of predicted antigenicity of a peptide or protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001534 ! Peptide immunogenicity data [Term] id: EDAM:0001536 name: MHC peptide immunogenicity report namespace: data def: "A report on the immunogenicity of MHC class I or class II binding peptides." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001534 ! Peptide immunogenicity data [Term] id: EDAM:0002753 name: Carbohydrate conformational map namespace: data def: "A conformational energy map of the glycosidic linkages in a carbohydrate molecule." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002313 ! Carbohydrate structure report [Term] id: EDAM:0000899 name: Protein features (3D motif) namespace: data def: "An informative report on the 3D structural motifs in a protein." [EDAM:EBI "EMBRACE definition"] comment: This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. subset: data synonym: "Protein structure report (3D motif)" EXACT [] is_a: EDAM:0001277 ! Protein features is_a: EDAM:0001537 ! Protein structure report relationship: has_topic EDAM:0000166 ! Protein structural motifs and surfaces [Term] id: EDAM:0001539 name: Protein structural quality report namespace: data def: "Report on the quality of a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] comment: Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. subset: data synonym: "Protein structure report (quality evaluation)" EXACT [] synonym: "Protein report (structural quality)" EXACT [] synonym: "Protein property (structural quality)" EXACT [] is_a: EDAM:0000897 ! Protein property is_a: EDAM:0001537 ! Protein structure report [Term] id: EDAM:0001541 name: Protein flexibility or motion report namespace: data def: "Informative report on flexibility or motion of a protein structure." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data synonym: "Protein structure report (flexibility or motion)" EXACT [] synonym: "Protein property (flexibility or motion)" EXACT [] synonym: "Protein flexibility or motion" EXACT [] is_a: EDAM:0000897 ! Protein property is_a: EDAM:0001537 ! Protein structure report [Term] id: EDAM:0002235 name: Raw SCOP domain classification namespace: data def: "Raw SCOP domain classification data files." [EDAM:EBI "EMBRACE definition"] comment: These are the parsable data files provided by SCOP. subset: data is_obsolete: true consider: EDAM:0000900 ! Protein domain classification [Term] id: EDAM:0002236 name: Raw CATH domain classification namespace: data def: "Raw CATH domain classification data files." [EDAM:EBI "EMBRACE definition"] comment: These are the parsable data files provided by CATH. subset: data is_obsolete: true consider: EDAM:0000900 ! Protein domain classification [Term] id: EDAM:0001762 name: CATH domain report namespace: data def: "Summary of domain classification information for a CATH domain." [EDAM:EBI "EMBRACE definition"] comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. subset: data is_obsolete: true consider: EDAM:0000900 ! Protein domain classification [Term] id: EDAM:0001553 name: CATH node namespace: data def: "Information on a node from the CATH database." [EDAM:EBI "EMBRACE definition"] comment: The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. subset: data synonym: "CATH classification node report" EXACT [] is_a: EDAM:0003101 ! Protein domain classification node [Term] id: EDAM:0001554 name: SCOP node namespace: data def: "Information on a node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "SCOP classification node" EXACT [] is_a: EDAM:0003101 ! Protein domain classification node [Term] id: EDAM:0003141 name: SCOP class namespace: data def: "Information on a 'class' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001554 ! SCOP node [Term] id: EDAM:0003142 name: SCOP fold namespace: data def: "Information on a 'fold' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001554 ! SCOP node [Term] id: EDAM:0003143 name: SCOP superfamily namespace: data def: "Information on a 'superfamily' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001554 ! SCOP node [Term] id: EDAM:0003144 name: SCOP family namespace: data def: "Information on a 'family' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001554 ! SCOP node [Term] id: EDAM:0003145 name: SCOP protein namespace: data def: "Information on a 'protein' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001554 ! SCOP node [Term] id: EDAM:0003146 name: SCOP species namespace: data def: "Information on a 'species' node from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001554 ! SCOP node [Term] id: EDAM:0001555 name: EMBASSY domain classification namespace: data def: "An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000900 ! Protein domain classification [Term] id: EDAM:0001556 name: CATH class namespace: data def: "Information on a protein 'class' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node [Term] id: EDAM:0001557 name: CATH architecture namespace: data def: "Information on a protein 'architecture' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node [Term] id: EDAM:0001558 name: CATH topology namespace: data def: "Information on a protein 'topology' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node [Term] id: EDAM:0001559 name: CATH homologous superfamily namespace: data def: "Information on a protein 'homologous superfamily' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node [Term] id: EDAM:0001560 name: CATH structurally similar group namespace: data def: "Information on a protein 'structurally similar group' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node [Term] id: EDAM:0001561 name: CATH functional category namespace: data def: "Information on a protein 'functional category' node from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001553 ! CATH node [Term] id: EDAM:0001565 name: Protein-protein interaction namespace: data alt_id: EDAM:0002712 def: "Data on protein-protein interaction(s)." [EDAM:EBI "EMBRACE definition"] comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains). subset: data synonym: "Protein structure report (protein complex)" EXACT [] is_a: EDAM:0000906 ! Protein report (interaction) relationship: has_topic EDAM:0000147 ! Protein-protein interactions [Term] id: EDAM:0001566 name: Protein-ligand interaction namespace: data def: "Data on protein-ligand (small molecule) interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000906 ! Protein report (interaction) relationship: has_topic EDAM:0000148 ! Protein-ligand interactions [Term] id: EDAM:0001567 name: Protein-nucleic acid interaction namespace: data def: "Data on protein-DNA/RNA interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000906 ! Protein report (interaction) relationship: has_topic EDAM:0000149 ! Protein-nucleic acid interactions [Term] id: EDAM:0002359 name: Domain-domain interaction namespace: data def: "Data on protein domain-protein domain interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001565 ! Protein-protein interaction [Term] id: EDAM:0002378 name: Protein-motif interaction namespace: data def: "Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001565 ! Protein-protein interaction [Term] id: EDAM:0002360 name: Domain-domain interaction (indirect) namespace: data def: "Data on indirect protein domain-protein domain interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002359 ! Domain-domain interaction [Term] id: EDAM:0002402 name: Protein-drug interaction namespace: data def: "Informative report on protein-drug interaction(s) including binding affinity data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001566 ! Protein ligand interaction [Term] id: EDAM:0002358 name: Domain-nucleic acid interaction namespace: data def: "Data on protein domain-DNA/RNA interaction(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001567 ! Protein-nucleic acid interaction [Term] id: EDAM:0002025 name: Michaelis Menten plot namespace: data def: "A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002024 ! Enzyme kinetics data [Term] id: EDAM:0002026 name: Hanes Woolf plot namespace: data def: "A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002024 ! Enzyme kinetics data [Term] id: EDAM:0000909 name: Vmax namespace: data def: "The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002024 ! Enzyme kinetics data [Term] id: EDAM:0000910 name: Km namespace: data def: "Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002024 ! Enzyme kinetics data [Term] id: EDAM:0002720 name: Dinucleotide property namespace: data def: "Physicochemical property data for one or more dinucleotides." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002088 ! DNA base structural data [Term] id: EDAM:0003149 name: Nucleic acid property (sequence) namespace: data def: "A non-positional property of a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Nucleic acid sequence property" EXACT [] is_obsolete: true consider: EDAM:0000912 ! Nucleic acid property [Term] id: EDAM:0002985 name: Nucleic acid thermodynamic data namespace: data def: "A thermodynamic or kinetic property of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Nucleic acid property (thermodynamic or kinetic)" EXACT [] synonym: "Nucleic acid thermodynamic property" EXACT [] is_a: EDAM:0000912 ! Nucleic acid property [Term] id: EDAM:0001583 name: Nucleic acid melting profile namespace: data def: "Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating." [EDAM:EBI "EMBRACE definition"] comment: A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. subset: data synonym: "Nucleic acid stability profile" EXACT [] is_a: EDAM:0002985 ! Nucleic acid thermodynamic data [Term] id: EDAM:0001584 name: Nucleic acid enthalpy namespace: data def: "Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002985 ! Nucleic acid thermodynamic data [Term] id: EDAM:0001585 name: Nucleic acid entropy namespace: data def: "Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002985 ! Nucleic acid thermodynamic data [Term] id: EDAM:0001586 name: Nucleic acid melting temperature namespace: data def: "Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002139 ! Nucleic acid melting temperature [Term] id: EDAM:0002088 name: DNA base structural data namespace: data def: "Structural data for DNA base pairs or runs of bases, such as energy or angle data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000912 ! Nucleic acid property is_a: EDAM:0002086 ! Nucleic acid structure report [Term] id: EDAM:0002167 name: Nucleic acid density plot namespace: data def: "Density plot (of base composition) for a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000912 ! Nucleic acid property [Term] id: EDAM:0001587 name: Nucleic acid stitch profile namespace: data def: "Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [EDAM:EBI "EMBRACE definition"] comment: A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. subset: data is_a: EDAM:0001583 ! Nucleic acid melting profile [Term] id: EDAM:0002958 name: Nucleic acid melting curve namespace: data def: "A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [EDAM:EBI "EMBRACE definition"] comment: Shows the proportion of nucleic acid which are double-stranded versus temperature. subset: data is_a: EDAM:0001583 ! Nucleic acid melting profile [Term] id: EDAM:0002959 name: Nucleic acid probability profile namespace: data def: "A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [EDAM:EBI "EMBRACE definition"] comment: Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature subset: data is_a: EDAM:0001583 ! Nucleic acid melting profile [Term] id: EDAM:0002960 name: Nucleic acid temperature profile namespace: data def: "A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [EDAM:EBI "EMBRACE definition"] comment: Plots melting temperature versus base position. subset: data synonym: "Melting map" EXACT [] is_a: EDAM:0001583 ! Nucleic acid melting profile [Term] id: EDAM:0001594 name: Vienna RNA calculated energy namespace: data def: "RNA calculated energy data generated by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001584 ! Nucleic acid enthalpy [Term] id: EDAM:0001588 name: DNA base pair stacking energies data namespace: data def: "DNA base pair stacking energies data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002088 ! DNA base structural data [Term] id: EDAM:0001589 name: DNA base pair twist angle data namespace: data def: "DNA base pair twist angle data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002088 ! DNA base structural data [Term] id: EDAM:0001590 name: DNA base trimer roll angles data namespace: data def: "DNA base trimer roll angles data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002088 ! DNA base structural data [Term] id: EDAM:0001595 name: Base pairing probability matrix dotplot namespace: data def: "Dotplot of RNA base pairing probability matrix." [EDAM:EBI "EMBRACE definition"] comment: Such as generated by the Vienna package. subset: data is_a: EDAM:0002088 ! DNA base structural data [Term] id: EDAM:0001598 name: Genetic code namespace: data def: "A genetic code for an organism." [EDAM:EBI "EMBRACE definition"] comment: A genetic code need not include detailed codon usage information. subset: data is_a: EDAM:0001597 ! Codon usage table [Term] id: EDAM:0002865 name: Codon usage bias namespace: data def: "A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000914 ! Codon usage report [Term] id: EDAM:0001599 name: Codon adaptation index namespace: data def: "A simple measure of synonymous codon usage bias often used to predict gene expression levels." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "CAI" EXACT [] is_obsolete: true consider: EDAM:0002865 ! Codon usage bias [Term] id: EDAM:0001600 name: Codon usage bias plot namespace: data def: "A plot of the synonymous codon usage calculated for windows over a nucleotide sequence." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Synonymous codon usage statistic plot" EXACT [] is_a: EDAM:0002865 ! Codon usage bias [Term] id: EDAM:0001601 name: Nc statistic namespace: data def: "The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002865 ! Codon usage bias [Term] id: EDAM:0001602 name: Codon usage fraction difference namespace: data def: "The differences in codon usage fractions between two codon usage tables." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000914 ! Codon usage report [Term] id: EDAM:0000917 name: Gene classification namespace: data def: "A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000916 ! Gene annotation [Term] id: EDAM:0000927 name: Gene annotation (linkage) namespace: data def: "An informative report on the linkage of alleles." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000916 ! Gene annotation [Term] id: EDAM:0001634 name: Gene annotation (linkage disequilibrium) namespace: data def: "A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000927 ! Gene annotation (linkage) [Term] id: EDAM:0000928 name: Gene expression profile namespace: data def: "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene expression pattern" EXACT [] is_a: EDAM:0003031 ! Core data [Term] id: EDAM:0002579 name: Expressed gene list namespace: data def: "A simple summary of expressed genes." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene annotation (expressed gene list)" EXACT [] is_a: EDAM:0002872 ! ID list [Term] id: EDAM:0002586 name: Northern blot image namespace: data def: "An image arising from a Northern Blot experiment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0001636 name: Heat map namespace: data def: "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." [EDAM:EBI "EMBRACE definition"] comment: A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. subset: data is_a: EDAM:0002967 ! Microarray image [Term] id: EDAM:0002092 name: Nucleic acid features (SNP) namespace: data def: "Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: An SNP is an individual point mutation or substitution of a single nucleotide. subset: data synonym: "Single nucleotide polymorphism" EXACT [] synonym: "SNP annotation" EXACT [] is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0002867 name: Nucleic acid features (VNTR) namespace: data def: "Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. subset: data synonym: "Variable number of tandem repeat polymorphism" EXACT [] synonym: "VNTR annotation" EXACT [] is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0002868 name: Nucleic acid features (microsatellite) namespace: data def: "Annotation on a microsatellite polymorphism in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. subset: data synonym: "Microsatellite annotation" EXACT [] is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0002869 name: Nucleic acid features (RFLP) namespace: data def: "Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence." [EDAM:EBI "EMBRACE definition"] comment: An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. subset: data synonym: "RFLP annotation" EXACT [] is_a: EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0001853 name: Chromosome annotation (aberration) namespace: data def: "A report on a chromosome aberration such as abnormalities in chromosome structure." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000919 ! Nucleic acid features (chromosome) [Term] id: EDAM:0001621 name: Pharmacogenomic annotation namespace: data def: "Data on the influence of genotype on drug response." [EDAM:EBI "EMBRACE definition"] comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. subset: data is_a: EDAM:0000920 ! Genotype and phenotype annotation [Term] id: EDAM:0001622 name: Disease annotation namespace: data def: "An informative report on a specific disease." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000920 ! Genotype/phenotype annotation relationship: has_topic EDAM:0000634 ! Disease resources [Term] id: EDAM:0002533 name: Nucleic acid features (mutation) namespace: data def: "Annotation on a mutation." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Mutation annotation" EXACT [] is_a: EDAM:0000918 ! Nucleic acid features (variation) [Term] id: EDAM:0002885 name: Nucleic acid features (polymorphism annotation) namespace: data def: "Annotation on a polymorphism." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Polymorphism annotation" EXACT [] is_a: EDAM:0000918 ! Nucleic acid features (variation) [Term] id: EDAM:0002212 name: Mutation annotation (basic) namespace: data def: "Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002533 ! Nucleic acid features (mutation) [Term] id: EDAM:0002213 name: Mutation annotation (prevalence) namespace: data def: "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002533 ! Nucleic acid features (mutation) [Term] id: EDAM:0002214 name: Mutation annotation (prognostic) namespace: data def: "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002533 ! Nucleic acid features (mutation) [Term] id: EDAM:0002215 name: Mutation annotation (functional) namespace: data def: "An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002533 ! Nucleic acid features (mutation) [Term] id: EDAM:0002217 name: Tumor annotation namespace: data def: "An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001622 ! Disease annotation [Term] id: EDAM:0001852 name: Sequence assembly component namespace: data def: "A component of a larger sequence assembly." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000925 ! Sequence assembly [Term] id: EDAM:0000923 name: Experiment annotation (PCR assay data) namespace: data def: "Data on a PCR assay or electronic / virtual PCR." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "PCR assay data" EXACT [] is_a: EDAM:0002531 ! Experiment annotation relationship: has_topic EDAM:0000077 ! Nucleic acid analysis [Term] id: EDAM:0000924 name: Sequence trace namespace: data def: "A molecular sequence (reads) with associated sequencing metadata (such as base-call quality scores or raw sequencing data)." [EDAM:EBI "EMBRACE definition"] comment: This is the raw data produced by a DNA sequencing machine. subset: data is_a: EDAM:0003108 ! Experimental measurement is_a: EDAM:0002887 ! Sequence record (nucleic acid) [Term] id: EDAM:0000926 name: Radiation Hybrid (RH) scores namespace: data def: "Radiation hybrid scores (RH) scores for one or more markers." [EDAM:EBI "EMBRACE definition"] comment: Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. subset: data is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0002363 name: 2D PAGE data namespace: data def: "Data concerning two-dimensional polygel electrophoresis." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data is_obsolete: true consider: EDAM:0000942 ! 2D PAGE image consider: EDAM:0002364 ! Experiment annotation (2D PAGE) [Term] id: EDAM:0002838 name: Experimental data (proteomics) namespace: data def: "Data concerning a proteomics experiment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0003147 ! Experiment annotation (mass spectrometry) [Term] id: EDAM:0002536 name: Mass spectrometry data namespace: data def: "Data concerning a mass spectrometry experiment." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data is_obsolete: true consider: EDAM:0000943 ! Mass spectrometry spectra consider: EDAM:0000944 ! Peptide mass fingerprint consider: EDAM:0003147 ! Experiment annotation (mass spectrometry) [Term] id: EDAM:0000943 name: Mass spectrometry spectra namespace: data def: "Spectra from mass spectrometry." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003108 ! Experimental measurement relationship: has_topic EDAM:0000121 ! Proteomics [Term] id: EDAM:0000944 name: Peptide mass fingerprint namespace: data def: "A set of peptide masses (peptide mass fingerprint) from mass spectrometry." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Protein fingerprint" EXACT [] synonym: "Peak list" EXACT [] is_a: EDAM:0002979 ! Peptide property is_a: EDAM:0003108 ! Experimental measurement relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0000945 name: Peptide identification namespace: data def: "Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002979 ! Peptide property relationship: has_topic EDAM:0000767 ! Protein and peptide identification [Term] id: EDAM:0002537 name: Protein structure raw data namespace: data def: "Raw data from experimental methods for determining protein structure." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0000937 name: Protein X-ray crystallographic data namespace: data def: "X-ray crystallography data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002537 ! Protein structure raw data [Term] id: EDAM:0000938 name: Protein NMR data namespace: data def: "Protein nuclear magnetic resonance (NMR) raw data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002537 ! Protein structure raw data [Term] id: EDAM:0000939 name: Protein circular dichroism (CD) spectroscopic data namespace: data def: "Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002537 ! Protein structure raw data [Term] id: EDAM:0000940 name: Electron microscopy volume map namespace: data def: "Volume map data from electron microscopy." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "EM volume map" EXACT [] is_a: EDAM:0003108 ! Experimental measurement relationship: has_topic EDAM:0002226 ! Structure determination [Term] id: EDAM:0000905 name: Protein interaction raw data namespace: data def: "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0000931 name: Experiment annotation (microarray) namespace: data alt_id: EDAM:0003114 def: "Information on a microarray experiment such as conditions, protocol, sample:data relationships etc." [EDAM:EBI "EMBRACE definition"] comment: This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. subset: data synonym: "Experimental design annotation" EXACT [] is_a: EDAM:0002531 ! Experiment annotation relationship: has_topic EDAM:0000197 ! Gene expression resources [Term] id: EDAM:0002866 name: Experiment annotation (Northern blot) namespace: data def: "General annotation on a Northern Blot experiment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002531 ! Experiment annotation [Term] id: EDAM:0003147 name: Experiment annotation (mass spectrometry) namespace: data def: "General annotation on a mass spectrometry experiment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002531 ! Experiment annotation [Term] id: EDAM:0000932 name: Oligonucleotide probe data namespace: data def: "Data on oligonucleotide probes (typically for use with DNA microarrays)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002717 ! Oligonucleotide probe annotation [Term] id: EDAM:0002535 name: Sequence tag profile namespace: data def: "Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed." [EDAM:EBI "EMBRACE definition"] comment: SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. subset: data synonym: "Sequencing-based expression profile" EXACT [] is_a: EDAM:0000928 ! Gene expression profile [Term] id: EDAM:0000933 name: SAGE experimental data namespace: data def: "Output from a serial analysis of gene expression (SAGE) experiment." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Serial analysis of gene expression (SAGE) experimental data" EXACT [] is_obsolete: true consider: EDAM:0002535 ! Sequence tag profile [Term] id: EDAM:0000934 name: MPSS experimental data namespace: data def: "Massively parallel signature sequencing (MPSS) data." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Massively parallel signature sequencing (MPSS) experimental data" EXACT [] is_obsolete: true consider: EDAM:0002535 ! Sequence tag profile [Term] id: EDAM:0000935 name: SBS experimental data namespace: data def: "Sequencing by synthesis (SBS) data." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Sequencing by synthesis (SBS) experimental data" EXACT [] is_obsolete: true consider: EDAM:0002535 ! Sequence tag profile [Term] id: EDAM:0000936 name: Sequence tag profile (with gene assignment) namespace: data def: "Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002535 ! Sequence tag profile [Term] id: EDAM:0000942 name: 2D PAGE image namespace: data def: "Two-dimensional gel electrophoresis image." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Two-dimensional gel electrophoresis image" EXACT [] is_a: EDAM:0002968 ! Image is_a: EDAM:0003108 ! Experimental measurement relationship: has_topic EDAM:0000121 ! Proteomics [Term] id: EDAM:0002364 name: Experiment annotation (2D PAGE) namespace: data def: "An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002531 ! Experiment annotation relationship: has_topic EDAM:0000121 ! Proteomics [Term] id: EDAM:0002965 name: 2D PAGE image (annotated) namespace: data def: "An informative report on a two-dimensional (2D PAGE) gel." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "2D PAGE image annotation" EXACT [] is_a: EDAM:0000942 ! 2D PAGE image [Term] id: EDAM:0002372 name: 2D PAGE spot (annotated) namespace: data def: "An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "2D PAGE spot annotation" EXACT [] is_a: EDAM:0002965 ! 2D PAGE image (annotated) [Term] id: EDAM:0001646 name: Molecular weights standard fingerprint namespace: data def: "Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000944 ! Peptide mass fingerprint [Term] id: EDAM:0002717 name: Oligonucleotide probe annotation namespace: data def: "General annotation on an oligonucleotide probe." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003115 ! Microarray annotation relationship: has_topic EDAM:0000632 ! Probes and primers [Term] id: EDAM:0002966 name: Oligonucleotide probe sets annotation namespace: data def: "General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002717 ! Oligonucleotide probe annotation [Term] id: EDAM:0001642 name: Affymetrix probe sets library file namespace: data def: "Affymetrix library file of information about which probes belong to which probe set." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002966 ! Oligonucleotide probe sets annotation ! synonym: "CDF file" EXACT [] [Term] id: EDAM:0001643 name: Affymetrix probe sets information library file namespace: data def: "Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002966 ! Oligonucleotide probe sets annotation ! synonym: "GIN file" EXACT [] [Term] id: EDAM:0000856 name: Sequence feature source namespace: data def: "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived." [EDAM:EBI "EMBRACE definition"] comment: This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). subset: data is_a: EDAM:0002042 ! Evidence is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0000859 name: Sequence signature model namespace: data def: "Data files used by motif or profile methods." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000950 ! Biological model [Term] id: EDAM:0000946 name: Pathway or network annotation namespace: data def: "An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002984 ! Pathway or network report [Term] id: EDAM:0002589 name: Hierarchy namespace: data def: "A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Hierarchy annotation" EXACT [] is_a: EDAM:0002987 ! Classification [Term] id: EDAM:0000904 name: Protein features (mutation) namespace: data def: "Data on the effect of (typically point) mutation on protein folding, stability, structure and function." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data synonym: "Protein property (mutation)" EXACT [] synonym: "Protein report (mutation)" EXACT [] synonym: "Protein structure report (mutation)" EXACT [] is_obsolete: true consider: EDAM:0000896 ! Protein report [Term] id: EDAM:0000903 name: Protein folding report namespace: data def: "A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data synonym: "Protein report (folding)" EXACT [] synonym: "Protein property (folding)" EXACT [] is_a: EDAM:0000897 ! Protein property [Term] id: EDAM:0001596 name: Nucleic acid folding report namespace: data def: "A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. subset: data synonym: "Nucleic acid report (folding model)" EXACT [] synonym: "Nucleic acid report (folding)" EXACT [] is_a: EDAM:0000912 ! Nucleic acid property [Term] id: EDAM:0001344 name: MEME motif alphabet namespace: data def: "Alphabet for the motifs (patterns) that MEME will search for." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000950 ! Biological model [Term] id: EDAM:0001345 name: MEME background frequencies file namespace: data def: "MEME background frequencies file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000950 ! Biological model [Term] id: EDAM:0001346 name: MEME motifs directive file namespace: data def: "File of directives for ordering and spacing of MEME motifs." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000950 ! Biological model [Term] id: EDAM:0001347 name: Dirichlet distribution namespace: data def: "Dirichlet distribution used by hidden Markov model analysis programs." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000950 ! Biological model [Term] id: EDAM:0001348 name: HMM emission and transition counts namespace: data def: "Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000950 ! Biological model [Term] id: EDAM:0000947 name: Biological pathway map namespace: data def: "A map (typically a diagram) of a biological pathway." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002600 ! Pathway or network [Term] id: EDAM:0001656 name: Pathway or network (metabolic) namespace: data def: "A report typically including a map (diagram) of a metabolic pathway." [EDAM:EBI "EMBRACE definition"] comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. subset: data is_a: EDAM:0002600 ! Pathway or network [Term] id: EDAM:0001657 name: Pathway or network (genetic information processing) namespace: data def: "A report typically including a map (diagram) of a genetic information processing pathway." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002600 ! Pathway or network [Term] id: EDAM:0002961 name: Pathway or network (gene regulation) namespace: data def: "A report typically including a map (diagram) of a gene regulatory network." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002600 ! Pathway or network relationship: has_topic EDAM:0002846 ! Gene regulatory networks [Term] id: EDAM:0001658 name: Pathway or network (environmental information processing) namespace: data def: "A report typically including a map (diagram) of an environmental information processing pathway." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002600 ! Pathway or network [Term] id: EDAM:0001659 name: Pathway or network (signal transduction) namespace: data def: "A report typically including a map (diagram) of a signal transduction pathway." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002600 ! Pathway or network [Term] id: EDAM:0001660 name: Pathway or network (cellular process) namespace: data def: "A report typically including a map (diagram) of a cellular process pathway." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002600 ! Pathway or network [Term] id: EDAM:0001661 name: Pathway or network (disease) namespace: data def: "A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002600 ! Pathway or network [Term] id: EDAM:0001662 name: Pathway or network (drug structure relationship) namespace: data def: "A report typically including a map (diagram) of drug structure relationships." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002600 ! Pathway or network [Term] id: EDAM:0001663 name: Pathway or network (protein-protein interaction) namespace: data def: "A report typically including a map (diagram) of a network of protein interactions." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002600 ! Pathway or network [Term] id: EDAM:0000951 name: Statistical estimate score namespace: data def: "A value representing estimated statistical significance of some observed data; typically sequence database hits." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001772 ! Score or penalty is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0000865 name: Sequence similarity score namespace: data def: "A value representing molecular sequence similarity." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001772 ! Score or penalty [Term] id: EDAM:0000888 name: Structure similarity score namespace: data def: "A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001772 ! Score or penalty [Term] id: EDAM:0002146 name: Threshold namespace: data def: "A value that serves as a threshold for a tool (usually to control scoring or output)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001772 ! Score or penalty [Term] id: EDAM:0001667 name: E-value namespace: data def: "A simple floating point number defining the lower or upper limit of an expectation value (E-value)." [EDAM:EBI "EMBRACE definition"] comment: An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. subset: data synonym: "Expectation value" EXACT [] is_a: EDAM:0000951 ! Statistical estimate score [Term] id: EDAM:0001668 name: Z-value namespace: data def: "The z-value is the number of standard deviations a data value is above or below a mean value." [EDAM:EBI "EMBRACE definition"] comment: A z-value might be specified as a threshold for reporting hits from database searches. subset: data is_a: EDAM:0000951 ! Statistical estimate score [Term] id: EDAM:0001669 name: P-value namespace: data def: "The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true." [EDAM:EBI "EMBRACE definition"] comment: A z-value might be specified as a threshold for reporting hits from database searches. subset: data is_a: EDAM:0000951 ! Statistical estimate score [Term] id: EDAM:0001412 name: Sequence identity namespace: data def: "Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000865 ! Sequence similarity score [Term] id: EDAM:0001413 name: Sequence similarity namespace: data def: "Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension." [EDAM:EBI "EMBRACE definition"] comment: Data Type is float probably. subset: data is_a: EDAM:0000865 ! Sequence similarity score [Term] id: EDAM:0002335 name: Bit score namespace: data def: "A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system." [EDAM:EBI "EMBRACE definition"] comment: Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. subset: data is_a: EDAM:0001413 ! Sequence similarity [Term] id: EDAM:0001496 name: Molecular similarity score namespace: data def: "A score reflecting structural similarities of two molecules." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000888 ! Structure similarity score [Term] id: EDAM:0001497 name: Root-mean-square deviation namespace: data def: "Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "RMSD" EXACT [] is_a: EDAM:0000888 ! Structure similarity score [Term] id: EDAM:0001498 name: Tanimoto similarity score namespace: data def: "A measure of the similarity between two ligand fingerprints." [EDAM:EBI "EMBRACE definition"] comment: A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. subset: data is_a: EDAM:0000888 ! Structure similarity score [Term] id: EDAM:0001673 name: Swiss-Prot to PDB mapping namespace: data def: "Cross-mapping of Swiss-Prot codes to PDB identifiers." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000954 ! Database cross-mapping [Term] id: EDAM:0001674 name: Sequence database cross-references namespace: data def: "Cross-references from a sequence record to other databases." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002093 ! Data reference [Term] id: EDAM:0002337 name: Metadata namespace: data alt_id: EDAM:0002853 def: "Data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data synonym: "Provenance metadata" EXACT [] is_a: EDAM:0002048 ! Report [Term] id: EDAM:0002018 name: Annotation namespace: data def: "A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it." [EDAM:EBI "EMBRACE definition"] comment: This is a broad data type and is used a placeholder for other, more specific types. subset: data is_obsolete: true consider: EDAM:0002048 ! Report [Term] id: EDAM:0000948 name: Data resource definition namespace: data def: "A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001883 ! Annotated URI [Term] id: EDAM:0000957 name: Database metadata namespace: data def: "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003106 ! System metadata [Term] id: EDAM:0002223 name: Ontology metadata namespace: data def: "Data concerning a biological ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002337 ! Metadata relationship: has_topic EDAM:0000089 ! Ontologies [Term] id: EDAM:0002193 name: Database entry metadata namespace: data def: "Basic information on any arbitrary database entry." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000957 ! Database metadata [Term] id: EDAM:0000958 name: Tool metadata namespace: data def: "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003106 ! System metadata [Term] id: EDAM:0002218 name: Server metadata namespace: data def: "Basic information about a server on the web, such as an SRS server." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003106 ! System metadata [Term] id: EDAM:0000959 name: Job metadata namespace: data def: "Textual metadata on a submitted or completed job." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby:PDGJOB is_a: EDAM:0003106 ! System metadata [Term] id: EDAM:0000960 name: User metadata namespace: data def: "Textual metadata on a software author or end-user, for example a person or other software." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003106 ! System metadata [Term] id: EDAM:0003106 name: System metadata namespace: data def: "Metadata concerning the software, hardware or other aspects of a computer system." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002337 ! Metadata [Term] id: EDAM:0000583 name: Directory metadata namespace: data def: "A directory on disk from which files are read." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003106 ! System metadata [Term] id: EDAM:0000953 name: Version information namespace: data def: "Information on a version of software or data, for example name, version number and release date." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002337 ! Metadata [Term] id: EDAM:0002724 name: Embryo annotation namespace: data def: "Annotation on an embryo or concerning embryological development." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002530 ! Organism annotation relationship: has_topic EDAM:0003065 ! Embryology resources [Term] id: EDAM:0001664 name: MIRIAM datatype namespace: data def: "An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources." [EDAM:EBI "EMBRACE definition"] comment: A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. subset: data is_a: EDAM:0000948 ! Data resource definition [Term] id: EDAM:0002875 name: DRCAT resource namespace: data def: "An entry (resource) from the DRCAT bioinformatics resource catalogue." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000948 ! Data resource definition [Term] id: EDAM:0000952 name: EMBOSS database resource definition namespace: data def: "Resource definition for an EMBOSS database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000957 ! Database metadata [Term] id: EDAM:0001675 name: Job status namespace: data def: "Metadata on the status of a submitted job." [EDAM:EBI "EMBRACE definition"] comment: Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). subset: data is_a: EDAM:0000959 ! Job metadata [Term] id: EDAM:0001678 name: Tool log namespace: data def: "A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000959 ! Job metadata [Term] id: EDAM:0001677 name: Job type namespace: data def: "A label (text token) describing the type of job, for example interactive or non-interactive." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002100 ! Type [Term] id: EDAM:0001679 name: DaliLite log file namespace: data def: "DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001680 name: STRIDE log file namespace: data def: "STRIDE log file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001681 name: NACCESS log file namespace: data def: "NACCESS log file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001682 name: EMBOSS wordfinder log file namespace: data def: "EMBOSS wordfinder log file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001683 name: EMBOSS domainatrix log file namespace: data def: "EMBOSS (EMBASSY) domainatrix application log file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001684 name: EMBOSS sites log file namespace: data def: "EMBOSS (EMBASSY) sites application log file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001685 name: EMBOSS supermatcher error file namespace: data def: "EMBOSS (EMBASSY) supermatcher error file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001686 name: EMBOSS megamerger log file namespace: data def: "EMBOSS megamerger log file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001687 name: EMBOSS whichdb log file namespace: data def: "EMBOSS megamerger log file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001688 name: EMBOSS vectorstrip log file namespace: data def: "EMBOSS vectorstrip log file." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001678 ! Tool log [Term] id: EDAM:0001670 name: Database version information namespace: data def: "Information on a database (or ontology) version, for example name, version number and release date." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Ontology version information" EXACT [] is_a: EDAM:0000953 ! Version information is_a: EDAM:0000957 ! Database metadata [Term] id: EDAM:0002090 name: Database entry version information namespace: data def: "Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000953 ! Version information is_a: EDAM:0002193 ! Database entry metadata [Term] id: EDAM:0001671 name: Tool version information namespace: data def: "Information on an application version, for example name, version number and release date." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000953 ! Version information is_a: EDAM:0000958 ! Tool metadata [Term] id: EDAM:0001771 name: Sequence version information namespace: data def: "Information on an molecular sequence version." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000953 ! Version information is_a: EDAM:0000855 ! Sequence metadata [Term] id: EDAM:0002041 name: Genome version information namespace: data def: "Information on a genome version." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000953 ! Version information is_a: EDAM:0002711 ! Genome metadata [Term] id: EDAM:0001672 name: CATH version information namespace: data def: "Information on a version of the CATH database." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001670 ! Database version information [Term] id: EDAM:0001047 name: URI namespace: data def: "A string of characters that name or otherwise identify a resource on the Internet." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0002079 name: Search parameter namespace: data def: "Some simple value controlling a search operation, typically a search of a database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0002534 name: Sequence parameter namespace: data def: "A parameter concerning calculations on molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0002130 name: Sequence profile type namespace: data def: "A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002534 ! Sequence parameter is_a: EDAM:0002100 ! Type [Term] id: EDAM:0002023 name: Sequence mask parameter namespace: data def: "Data used to replace (mask) characters in a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002534 ! Sequence parameter [Term] id: EDAM:0000853 name: DNA sense specification namespace: data def: "The strand of a DNA sequence (forward or reverse)." [EDAM:EBI "EMBRACE definition"] comment: The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. subset: data synonym: "DNA strand specification" EXACT [] synonym: "Strand" EXACT [] is_a: EDAM:0002534 ! Sequence parameter is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0002126 name: Translation frame specification namespace: data def: "Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002534 ! Sequence parameter3 [Term] id: EDAM:0002336 name: Translation phase specification namespace: data def: "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Phase" EXACT [] is_a: EDAM:0002534 ! Sequence parameter is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0001014 name: Sequence position specification namespace: data def: "A specification (partial or complete) of one or more positions or regions of a molecular sequence or map." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002534 ! Sequence parameter [Term] id: EDAM:0000854 name: Sequence length specification namespace: data def: "A specification of sequence length(s)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002534 ! Sequence parameter [Term] id: EDAM:0002357 name: Protein signature type namespace: data def: "A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002534 ! Sequence parameter is_a: EDAM:0002100 ! Type [Term] id: EDAM:0000864 name: Sequence alignment parameter namespace: data def: "Some simple value controlling a sequence alignment (or similar 'match') operation." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002534 ! Sequence parameter [Term] id: EDAM:0001120 name: Sequence alignment type namespace: data def: "A label (text token) describing the type of a sequence alignment." [EDAM:EBI "EMBRACE definition"] comment: Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. subset: data is_a: EDAM:0000864 ! Sequence alignment parameter is_a: EDAM:0002100 ! Type [Term] id: EDAM:0001052 name: URL namespace: data alt_id: EDAM:0001054 alt_id: EDAM:0001168 alt_id: EDAM:0001169 def: "A Uniform Resource Locator (URL)." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby:URL xref: Moby:Link is_a: EDAM:0001047 ! URI [Term] id: EDAM:0001053 name: URN namespace: data def: "A Uniform Resource Name (URN)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001047 ! URI [Term] id: EDAM:0001055 name: LSID namespace: data def: "A Life Science Identifier (LSID) - a unique identifier of some data." [EDAM:EBI "EMBRACE definition"] comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:::[:] subset: data synonym: "Life Science Identifier" EXACT [] is_a: EDAM:0001053 ! URN [Term] id: EDAM:0000968 name: Keyword namespace: data def: "Keyword(s) or phrase(s) used (typically) for text-searching purposes." [EDAM:EBI "EMBRACE definition"] comment: Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. subset: data xref: Moby:Global_Keyword xref: Moby:QueryString xref: Moby:Wildcard_Query xref: Moby:BooleanQueryString is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0002022 name: Vienna RNA structural data namespace: data def: "Data used by the Vienna RNA analysis package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002527 ! Parameter [Term] id: EDAM:0002134 name: Results sort order namespace: data def: "A control of the order of data that is output, for example the order of sequences in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002079 ! Search parameter [Term] id: EDAM:0002135 name: Toggle namespace: data def: "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002527 ! Parameter [Term] id: EDAM:0002139 name: Nucleic acid melting temperature namespace: data def: "A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Melting temperature" EXACT [] is_a: EDAM:0002985 ! Nucleic acid thermodynamic data [Term] id: EDAM:0002140 name: Concentration namespace: data def: "The concentration of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002050 ! Molecular property (general) [Term] id: EDAM:0002151 name: Color namespace: data def: "Specification of one or more colors." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002152 ! Rendering parameter [Term] id: EDAM:0002152 name: Rendering parameter namespace: data def: "A parameter that is used to control rendering (drawing) to a device or image." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Graphics parameter" EXACT [] synonym: "Graphical parameter" EXACT [] is_a: EDAM:0002527 ! Parameter [Term] id: EDAM:0003105 name: Geotemporal metadata namespace: data def: "Basic information concerning geographical location or time." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002337 ! Metadata [Term] id: EDAM:0002156 name: Date namespace: data def: "A temporal date." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003105 ! Geotemporal metadata [Term] id: EDAM:0001693 name: Number of iterations namespace: data def: "Number of iterations of an algorithm." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002079 ! Search parameter [Term] id: EDAM:0001694 name: Number of output entities namespace: data def: "Number of entities (for example database hits, sequences, alignments etc) to write to an output file." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002079 ! Search parameter ! Possible values include: 'SC' (score) or 'RF' (rank), pvalue (sort by increasing P-value (probability). i.e. most statistically significant hits given first), count (sort hits by increasing number of submatches (for example HSP) in each hit, score (sort hits in order of increasing score [Term] id: EDAM:0001695 name: Hit sort order namespace: data def: "Controls the order of hits (reported matches) in an output file from a database search." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002134 ! Results sort order [Term] id: EDAM:0000851 name: Sequence mask character namespace: data def: "A character used to replace (mask) other characters in a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002023 ! Sequence mask parameter [Term] id: EDAM:0000852 name: Sequence mask type namespace: data def: "A label (text token) describing the type of sequence masking to perform." [EDAM:EBI "EMBRACE definition"] comment: Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. subset: data is_a: EDAM:0002023 ! Sequence mask parameter is_a: EDAM:0002100 ! Type [Term] id: EDAM:0001016 name: Sequence position namespace: data def: "A position of a single point (base or residue) in a sequence, or part of such a specification." [EDAM:EBI "EMBRACE definition"] subset: data xref: WHATIF: number xref: WHATIF: PDBx_atom_site is_a: EDAM:0001014 ! Sequence position specification ! _atom_site.id in PDBML [Term] id: EDAM:0002145 name: Sequence offset namespace: data def: "An offset for a single-point sequence position." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001016 ! Sequence position is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0001017 name: Sequence range namespace: data def: "Specification of range(s) of sequence positions." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001014 ! Sequence position specification [Term] id: EDAM:0002012 name: Map position namespace: data alt_id: EDAM:0001894 def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval." [EDAM:EBI "EMBRACE definition"] comment: This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. subset: data synonym: "Locus" EXACT [] xref: Moby:GCP_MapPoint xref: Moby:GCP_MapPosition xref: Moby:HitPosition xref: Moby:GenePosition xref: Moby:MapPosition xref: Moby:Position xref: Moby:GCP_MapInterval xref: Moby:Locus is_a: EDAM:0001016 ! Sequence position is_a: EDAM:0001017 ! Sequence range is_a: EDAM:0002019 ! Map attribute ! seealso: XXX:0000000 ! All the different types of locus ! _atom_site.id in PDBML [Term] id: EDAM:0002216 name: Codon number namespace: data def: "The number of a codon, for instance, at which a mutation is located." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001016 ! Sequence position [Term] id: EDAM:0001742 name: PDB residue number namespace: data def: "A residue identifier (a string) from a PDB file." [EDAM:EBI "EMBRACE definition"] subset: data xref: WHATIF: pdb_number is_a: EDAM:0001016 ! Sequence position ! PDB_residue_no in PDBML [Term] id: EDAM:0001856 name: PDB insertion code namespace: data def: "An insertion code (part of the residue number) for an amino acid residue from a PDB file." [EDAM:EBI "EMBRACE definition"] subset: data xref: WHATIF: insertion_code is_a: EDAM:0001016 ! Sequence position ! pdbx_PDB_ins_code in PDBML [Term] id: EDAM:0001906 name: Quantitative trait locus namespace: data def: "A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment)." [EDAM:EBI "EMBRACE definition"] comment: A QTL sometimes but does not necessarily correspond to a gene. subset: data synonym: "QTL" EXACT [] xref: Moby:SO_QTL is_obsolete: true consider: EDAM:0002012 ! Map position [Term] id: EDAM:0001249 name: Sequence length namespace: data def: "The size (length) of a sequence, subsequence or region in a sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000854 ! Sequence length specification [Term] id: EDAM:0001252 name: Sequence length range namespace: data def: "Specification of range(s) of length of sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000854 ! Sequence length specification [Term] id: EDAM:0001250 name: Word size namespace: data def: "Size of a sequence word." [EDAM:EBI "EMBRACE definition"] comment: Word size is used for example in word-based sequence database search methods. subset: data synonym: "Word length" EXACT [] is_a: EDAM:0001249 ! Sequence length [Term] id: EDAM:0001251 name: Window size namespace: data def: "Size of a sequence window." [EDAM:EBI "EMBRACE definition"] comment: A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. subset: data is_a: EDAM:0001249 ! Sequence length [Term] id: EDAM:0002141 name: Window step size namespace: data def: "Size of the incremental 'step' a sequence window is moved over a sequence." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001249 ! Sequence length [Term] id: EDAM:0001125 name: Comparison matrix type namespace: data def: "A label (text token) describing the type of a comparison matrix." [EDAM:EBI "EMBRACE definition"] comment: For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. subset: data synonym: "Substitution matrix type" EXACT [] is_a: EDAM:0000864 ! Sequence alignment parameter is_a: EDAM:0002100 ! Type [Term] id: EDAM:0001394 name: Alignment score or penalty namespace: data def: "A simple floating point number defining the penalty for opening or extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000864 ! Sequence alignment parameter is_a: EDAM:0001772 ! Score or penalty [Term] id: EDAM:0001395 name: Score end gaps control namespace: data def: "Whether end gaps are scored or not." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002527 ! Parameter [Term] id: EDAM:0001396 name: Aligned sequence order namespace: data def: "Controls the order of sequences in an output sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002134 ! Results sort order [Term] id: EDAM:0002136 name: Sequence width namespace: data def: "The width of an output sequence or alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001249 ! Sequence length [Term] id: EDAM:0002137 name: Gap penalty namespace: data def: "A penalty for introducing or extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001394 ! Alignment score or penalty [Term] id: EDAM:0001401 name: Match reward score namespace: data def: "The score for a 'match' used in various sequence database search applications with simple scoring schemes." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001394 ! Alignment score or penalty [Term] id: EDAM:0001402 name: Mismatch penalty score namespace: data def: "The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001394 ! Alignment score or penalty [Term] id: EDAM:0001403 name: Drop off score namespace: data def: "This is the threshold drop in score at which extension of word alignment is halted." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001394 ! Alignment score or penalty [Term] id: EDAM:0001397 name: Gap opening penalty namespace: data def: "A penalty for opening a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002137 ! Gap penalty [Term] id: EDAM:0001398 name: Gap extension penalty namespace: data def: "A penalty for extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002137 ! Gap penalty [Term] id: EDAM:0001399 name: Gap separation penalty namespace: data def: "A penalty for gaps that are close together in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002137 ! Gap penalty [Term] id: EDAM:0001400 name: Terminal gap penalty namespace: data def: "A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001410 ! Terminal gap opening penalty consider: EDAM:0001411 ! Terminal gap extension penalty [Term] id: EDAM:0001404 name: Gap opening penalty (integer) namespace: data def: "A simple floating point number defining the penalty for opening a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001397 ! Gap opening penalty [Term] id: EDAM:0001405 name: Gap opening penalty (float) namespace: data def: "A simple floating point number defining the penalty for opening a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001397 ! Gap opening penalty [Term] id: EDAM:0001406 name: Gap extension penalty (integer) namespace: data def: "A simple floating point number defining the penalty for extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001398 ! Gap extension penalty [Term] id: EDAM:0001407 name: Gap extension penalty (float) namespace: data def: "A simple floating point number defining the penalty for extending a gap in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001398 ! Gap extension penalty [Term] id: EDAM:0001408 name: Gap separation penalty (integer) namespace: data def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001399 ! Gap separation penalty [Term] id: EDAM:0001409 name: Gap separation penalty (float) namespace: data def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0001399 ! Gap separation penalty [Term] id: EDAM:0001410 name: Terminal gap opening penalty namespace: data def: "A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001397 ! Gap opening penalty [Term] id: EDAM:0001411 name: Terminal gap extension penalty namespace: data def: "A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001398 ! Gap extension penalty [Term] id: EDAM:0002007 name: UniProt keyword namespace: data def: "A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database." [EDAM:EBI "EMBRACE definition"] subset: data xref: Moby_namespace:SP_KW xref: http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW is_a: EDAM:0000968 ! Keyword [Term] id: EDAM:0001877 name: Synonym namespace: data def: "An alternative for a word." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Alternative name" EXACT [] is_obsolete: true consider: EDAM:0000968 ! Keyword [Term] id: EDAM:0001878 name: Misspelling namespace: data def: "A common misspelling of a word." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000968 ! Keyword [Term] id: EDAM:0001879 name: Acronym namespace: data def: "An abbreviation of a phrase or word." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000968 ! Keyword [Term] id: EDAM:0001880 name: Misnomer namespace: data def: "A term which is likely to be misleading of its meaning." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000968 ! Keyword [Term] id: EDAM:0001591 name: Vienna RNA parameters namespace: data def: "RNA parameters used by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002527 ! Parameter [Term] id: EDAM:0001592 name: Vienna RNA structure constraints namespace: data def: "Structure constraints used by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002527 ! Parameter [Term] id: EDAM:0001593 name: Vienna RNA concentration data namespace: data def: "RNA concentration data used by the Vienna package." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002527 ! Parameter [Term] id: EDAM:0001696 name: Drug annotation namespace: data def: "An informative report on a specific drug." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000962 ! Small molecule annotation relationship: has_topic EDAM:0000620 ! Drugs and targets [Term] id: EDAM:0002400 name: Toxin annotation namespace: data def: "An informative report on a specific toxin." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002240 name: Heterogen annotation namespace: data def: "An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002726 name: Inhibitor annotation namespace: data def: "An informative report on one or more small molecules that are enzyme inhibitors." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002396 name: Fungi annotation (anamorph) namespace: data def: "An informative report on a specific fungus anamorph." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002395 ! Fungi annotation [Term] id: EDAM:0002142 name: EMBOSS graph namespace: data def: "An image of a graph generated by the EMBOSS suite." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002968 ! Image [Term] id: EDAM:0001707 name: Phylogenetic tree image namespace: data def: "An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information." [EDAM:EBI "EMBRACE definition"] comment: See also 'Phylogenetic tree' subset: data is_a: EDAM:0002968 ! Image is_a: EDAM:0001438 ! Phylogenetic tree report [Term] id: EDAM:0001708 name: RNA secondary structure image namespace: data def: "Image of RNA secondary structure, knots, pseudoknots etc." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002880 ! Secondary structure image [Term] id: EDAM:0001709 name: Protein secondary structure image namespace: data def: "Image of protein secondary structure." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002880 ! Secondary structure image is_a: EDAM:0002956 ! Protein secondary structure report [Term] id: EDAM:0001710 name: Structure image namespace: data alt_id: EDAM:0002604 def: "Image of one or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002085 ! Structure report is_a: EDAM:0002968 ! Image [Term] id: EDAM:0002880 name: Secondary structure image namespace: data def: "Image of one or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002881 ! Secondary structure report [Term] id: EDAM:0001711 name: Sequence alignment image namespace: data def: "Image of two or more aligned molecular sequences possibly annotated with alignment features." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002968 ! Image is_a: EDAM:0000867 ! Sequence alignment report [Term] id: EDAM:0002168 name: Sequence trace image namespace: data def: "Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases)." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002969 ! Sequence image [Term] id: EDAM:0002969 name: Sequence image namespace: data def: "Image of a molecular sequence, possibly with sequence features or properties shown." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002968 ! Image is_a: EDAM:0002955 ! Sequence report [Term] id: EDAM:0001712 name: Structure image (small molecule) namespace: data def: "An image of the structure of a small chemical compound." [EDAM:EBI "EMBRACE definition"] comment: The molecular identifier and formula are typically included. subset: data synonym: "Chemical structure image" EXACT [] synonym: "Small molecule structure image" EXACT [] is_a: EDAM:0001710 ! Structure image is_a: EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002992 name: Protein structure image namespace: data def: "An image of protein structure." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Structure image (protein)" EXACT [] is_a: EDAM:0001710 ! Structure image is_a: EDAM:0003153 ! Protein image [Term] id: EDAM:0003154 name: Protein alignment namespace: data def: "An alignment of protein sequences and/or structures." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000896 ! Protein report is_a: EDAM:0001916 ! Alignment [Term] id: EDAM:0003153 name: Protein image namespace: data def: "An image of a protein." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000896 ! Protein report [Term] id: EDAM:0001713 name: Fate map namespace: data def: " A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002724 ! Embryo annotation [Term] id: EDAM:0002967 name: Microarray image namespace: data alt_id: EDAM:0001635 def: "An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene expression image" EXACT [] is_a: EDAM:0002603 ! Microarray data is_a: EDAM:0002968 ! Image relationship: has_topic EDAM:0000197 ! Gene expression resources [Term] id: EDAM:0001714 name: Microarray spots image namespace: data def: "An image of spots from a microarray experiment." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002967 ! Microarray image is_a: EDAM:0003108 ! Experimental measurement [Term] id: EDAM:0002162 name: Helical wheel namespace: data def: "An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0001709 ! Protein secondary structure image [Term] id: EDAM:0002163 name: Helical net namespace: data def: "An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix." [EDAM:EBI "EMBRACE definition"] comment: Useful for highlighting amphipathicity and other properties. subset: data is_a: EDAM:0001709 ! Protein secondary structure image [Term] id: EDAM:0002308 name: Virus annotation (taxonomy) namespace: data def: "An informative report on the taxonomy of a specific virus." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002307 ! Virus annotation [Term] id: EDAM:0000582 name: Ontology namespace: data alt_id: EDAM:0000829 alt_id: EDAM:0000830 alt_id: EDAM:0000834 alt_id: EDAM:0000836 alt_id: EDAM:0000837 alt_id: EDAM:0000838 alt_id: EDAM:0000839 alt_id: EDAM:0000840 alt_id: EDAM:0002221 def: "An ontology of biological or bioinformatics terms and relations, a controlled vocabulary, structured glossary etc." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000089 ! Ontologies [Term] id: EDAM:0002858 name: Ontology concept namespace: data def: "A concept from a biological ontology." [EDAM:EBI "EMBRACE definition"] comment: This includes any fields from the term definition such as term name, definition, comments and so on. subset: data is_a: EDAM:0003031 ! Core data relationship: has_topic EDAM:0000089 ! Ontologies [Term] id: EDAM:0000966 name: Ontology term namespace: data def: "A term (name) from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000967 ! Ontology concept metadata [Term] id: EDAM:0000967 name: Ontology concept metadata namespace: data def: "Data concerning or derived from a concept from a biological ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0002337 ! Metadata relationship: has_topic EDAM:0000089 ! Ontologies [Term] id: EDAM:0001715 name: BioPax namespace: data def: "A term from the BioPax ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001716 name: GO namespace: data def: "A term definition from The Gene Ontology (GO)." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "Gene Ontology term" EXACT [] xref: Moby:GO_Term xref: Moby:GOTerm xref: Moby:Annotated_GO_Term xref: Moby:Annotated_GO_Term_With_Probability is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001717 name: MeSH namespace: data def: "A term from the MeSH vocabulary." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001718 name: HGNC namespace: data def: "A term from the HGNC controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001719 name: NCBI taxonomy vocabulary namespace: data def: "A term from the NCBI taxonomy vocabulary." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001720 name: Plant ontology term namespace: data def: "A term from the Plant Ontology (PO)." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001721 name: UMLS namespace: data def: "A term from the UMLS vocabulary." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001722 name: FMA namespace: data def: "A term from Foundational Model of Anatomy." [EDAM:EBI "EMBRACE definition"] comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001723 name: EMAP namespace: data def: "A term from the EMAP mouse ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001724 name: ChEBI namespace: data def: "A term from the ChEBI ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001725 name: MGED namespace: data def: "A term from the MGED ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001726 name: myGrid namespace: data def: "A term from the myGrid ontology." [EDAM:EBI "EMBRACE definition"] comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides terms for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. subset: data is_obsolete: true consider: EDAM:0000966 ! Ontology term [Term] id: EDAM:0001727 name: GO (biological process) namespace: data def: "A term definition for a biological process from the Gene Ontology (GO)." [EDAM:EBI "EMBRACE definition"] comment: Data Type is an enumerated string. subset: data is_obsolete: true consider: EDAM:0002858 ! Ontology concept [Term] id: EDAM:0001728 name: GO (molecular function) namespace: data def: "A term definition for a molecular function from the Gene Ontology (GO)." [EDAM:EBI "EMBRACE definition"] comment: Data Type is an enumerated string. subset: data is_obsolete: true consider: EDAM:0002858 ! Ontology concept [Term] id: EDAM:0001729 name: GO (cellular component) namespace: data def: "A term definition for a cellular component from the Gene Ontology (GO)." [EDAM:EBI "EMBRACE definition"] comment: Data Type is an enumerated string. subset: data is_obsolete: true consider: EDAM:0002858 ! Ontology concept [Term] id: EDAM:0001730 name: Ontology relation namespace: data def: "A relation defined for a term from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000967 ! Ontology concept metadata [Term] id: EDAM:0001731 name: Ontology term definition namespace: data def: "The definition of a term from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000967 ! Ontology concept metadata [Term] id: EDAM:0001732 name: Ontology term comment namespace: data def: "A comment on a term from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_a: EDAM:0000967 ! Ontology concept metadata [Term] id: EDAM:0001733 name: Ontology term cross-reference namespace: data def: "Cross-references for a term from an ontology." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true consider: EDAM:0002093 ! Data reference [Term] id: EDAM:0001738 name: doc2loc document information namespace: data def: "Information on a published article provided by the doc2loc program." [EDAM:EBI "EMBRACE definition"] comment: The doc2loc output includes the url, format, type and availability code of a document for every service provider. subset: data is_obsolete: true consider: EDAM:0000970 ! Bibliographic reference [Term] id: EDAM:0002177 name: Exactly 1 namespace: data def: "A single thing." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0002178 name: 1 or more namespace: data def: "One or more things." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0002179 name: Exactly 2 namespace: data def: "Exactly two things." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true [Term] id: EDAM:0002180 name: 2 or more namespace: data def: "Two or more things." [EDAM:EBI "EMBRACE definition"] subset: data is_obsolete: true ! Identifier [Term] id: EDAM:0000973 name: Undefined namespace: identifier def: "Debugging." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true [Term] id: EDAM:0001121 name: BLAST sequence alignment type namespace: identifier def: "The type of a BLAST sequence alignment." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001120 ! Sequence alignment type [Term] id: EDAM:0000974 name: Entity identifier namespace: identifier def: "An identifier of a biological entity or phenomenon." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0000842 ! Identifier [Term] id: EDAM:0000975 name: Data resource identifier namespace: identifier def: "An identifier of a data resource." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0000842 ! Identifier [Term] id: EDAM:0000978 name: Discrete entity identifier namespace: identifier def: "Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0000842 ! Identifier [Term] id: EDAM:0000979 name: Entity feature identifier namespace: identifier def: "Name or other identifier of an entity feature (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"] subset: identifier is_obsolete: true consider: EDAM:0000842 ! Identifier [Term] id: EDAM:0000980 name: Entity collection identifier namespace: identifier def: "Name or other identifier of a collection of discrete biological entities." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0000842 ! Identifier [Term] id: EDAM:0000981 name: Phenomenon identifier namespace: identifier def: "Name or other identifier of a physical, observable biological occurrence or event." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0000842 ! Identifier [Term] id: EDAM:0002091 name: Accession namespace: identifier alt_id: EDAM:0002862 def: "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000842 ! Identifier [Term] id: EDAM:0002099 name: Name namespace: identifier alt_id: EDAM:0002863 def: "A name of a thing, which need not necessarily uniquely identify it." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Symbolic name" EXACT [] is_a: EDAM:0000842 ! Identifier [Term] id: EDAM:0000976 name: Identifier (typed) namespace: identifier def: "An identifier that identifies a particular type of data." [EDAM:EBI "EMBRACE definition"] comment: This term exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the terms nested under 'Accession' and 'Name'. All terms under here are already included under 'Accession' or 'Name'. subset: identifier is_a: EDAM:0000842 ! Identifier [Term] id: EDAM:0002109 name: Identifier (hybrid) namespace: identifier def: "An identifier that is re-used for data objects of fundamentally different types (typically served from a single database)." [EDAM:EBI "EMBRACE definition"] comment: This branch provides an alternative organisation of the terms nested under 'Accession' and 'Name'. All terms under here are already included under 'Accession' or 'Name'. subset: identifier is_a: EDAM:0000842 ! Identifier [Term] id: EDAM:0000977 name: Tool identifier namespace: identifier def: "An identifier of a bioinformatics tool, e.g. an application or web service." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0001190 name: Tool name namespace: identifier def: "The name of a computer package, application, method or function." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000977 ! Tool identifier [Term] id: EDAM:0001191 name: Tool name (signature) namespace: identifier def: "The unique name of a signature (sequence classifier) method." [EDAM:EBI "EMBRACE definition"] comment: Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. subset: identifier is_a: EDAM:0001190 ! Tool name [Term] id: EDAM:0001192 name: Tool name (BLAST) namespace: identifier def: "The name of a BLAST tool." [EDAM:EBI "EMBRACE definition"] comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. subset: identifier synonym: "BLAST name" EXACT [] is_a: EDAM:0001190 ! Tool name [Term] id: EDAM:0001193 name: Tool name (FASTA) namespace: identifier def: "The name of a FASTA tool." [EDAM:EBI "EMBRACE definition"] comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. subset: identifier is_a: EDAM:0001190 ! Tool name [Term] id: EDAM:0001194 name: Tool name (EMBOSS) namespace: identifier def: "The name of an EMBOSS application." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001190 ! Tool name [Term] id: EDAM:0001195 name: Tool name (EMBASSY package) namespace: identifier def: "The name of an EMBASSY package." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001190 ! Tool name [Term] id: EDAM:0002098 name: Job identifier namespace: identifier def: "An identifier of a submitted job." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0001676 name: Job ID namespace: identifier def: "The (typically numeric) unique identifier of a submitted job." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002098 ! Job identifier [Term] id: EDAM:0002118 name: Person identifier namespace: identifier def: "An identifier of a software end-user (typically a person)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002101 name: User ID namespace: identifier def: "An identifier of a software end-user (typically a person)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002118 ! Person identifier [Term] id: EDAM:0001689 name: Username namespace: identifier def: "A username on a computer system." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002101 ! User ID [Term] id: EDAM:0001690 name: Password namespace: identifier def: "A password on a computer system." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002101 ! User ID [Term] id: EDAM:0001691 name: Email address namespace: identifier def: "A valid email address of an end-user." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby:Email xref: Moby:EmailAddress is_a: EDAM:0002101 ! User ID [Term] id: EDAM:0001692 name: Person name namespace: identifier def: "The name of a person." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002118 ! Person identifier [Term] id: EDAM:0001881 name: Author ID namespace: identifier def: "Information on the authors of a published work." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby:Author is_a: EDAM:0002118 ! Person identifier [Term] id: EDAM:0001882 name: DragonDB author identifier namespace: identifier def: "An identifier representing an author in the DragonDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001881 ! Author ID [Term] id: EDAM:0002596 name: Catalogue identifier namespace: identifier def: "An identifier of a catalogue of biological resources." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002779 name: Stock number namespace: identifier def: "An identifier of stock from a catalogue of biological resources." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0003022 name: NCBI genetic code ID namespace: identifier def: "Identifier of a genetic code in the NCBI list of genetic codes." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[1-9][0-9]?" ! example: 16 is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0000982 name: Molecule identifier namespace: identifier def: "Name or other identifier of a molecule." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0002529 ! Molecule report [Term] id: EDAM:0001015 name: Sequence feature ID namespace: identifier def: "A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0003034 ! Sequence feature identifier [Term] id: EDAM:0003107 name: Sequence feature name namespace: identifier def: "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002099 ! Name is_a: EDAM:0003034 ! Sequence feature identifier [Term] id: EDAM:0003034 name: Sequence feature identifier namespace: identifier def: "Name or other identifier of molecular sequence feature(s)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002914 ! Sequence feature metadata relationship: is_identifier_of EDAM:0001255 ! Sequence features [Term] id: EDAM:0001023 name: EMBOSS Uniform Feature Object namespace: data def: "The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "UFO" EXACT [] is_a: EDAM:0003034 ! Sequence feature identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001893 name: Locus ID namespace: identifier def: "A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Locus name" EXACT [] synonym: "Locus identifier" EXACT [] is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0002012 ! Map position [Term] id: EDAM:0002340 name: Genome build identifier namespace: identifier def: "An identifier of a build of a particular genome." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002749 ! Genome identifier [Term] id: EDAM:0002749 name: Genome identifier namespace: identifier def: "An identifier of a particular genome." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002903 name: Genome accession namespace: identifier def: "An accession of a particular genome (in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002749 ! Genome identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001025 name: Gene identifier namespace: identifier def: "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby:GeneAccessionList is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0000916 ! Gene annotation [Term] id: EDAM:0002795 name: ORF identifier namespace: identifier def: "An identifier of an open reading frame." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002727 name: Promoter ID namespace: identifier def: "An identifier of a promoter of a gene that is catalogued in a database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby:GeneAccessionList is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002630 name: Mobile genetic element ID namespace: identifier def: "An identifier of a mobile genetic element." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002127 name: Genetic code identifier namespace: identifier def: "An identifier of a genetic code." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0001598 ! Genetic code [Term] id: EDAM:0001038 name: Protein domain ID namespace: identifier def: "Identifier of a protein structural domain." [EDAM:EBI "EMBRACE definition"] comment: This is typically a character or string concatenated with a PDB identifier and a chain identifier. subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0001468 ! Protein domain [Term] id: EDAM:0002618 name: Protein modification ID namespace: identifier def: "Identifier of a protein modification catalogued in a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001867 name: Protein fold name namespace: identifier def: "The name of a protein fold." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002655 name: Cell type identifier namespace: identifier def: "A unique identifier of a type or group of cells." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002893 name: Cell type accession namespace: identifier def: "Accession of a type or group of cells (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002655 ! Cell type identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001869 name: Organism identifier namespace: identifier def: "A unique identifier of a (group of) organisms." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0002530 ! Organism annotation [Term] id: EDAM:0002908 name: Organism accession namespace: identifier def: "An accession of annotation on a (group of) organisms (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001869 ! Organism identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002909 name: Organism name namespace: identifier def: "The name of an organism (or group of organisms)." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby:Organism_Name xref: Moby:OrganismsLongName xref: Moby:OrganismsShortName xref: Moby:FirstEpithet xref: Moby:InfraspecificEpithet xref: Moby:OccurrenceRecord xref: Moby:BriefOccurrenceRecord is_a: EDAM:0001869 ! Organism identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001048 name: Database identifier namespace: identifier def: "An identifier of a biological or bioinformatics database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0000957 ! Database metadata [Term] id: EDAM:0001049 name: Directory name namespace: identifier def: "The name of a directory." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002099 ! Name is_a: EDAM:0000583 ! Directory metadata [Term] id: EDAM:0001050 name: File name namespace: identifier def: "The name (or part of a name) of a file (of any type)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001051 name: Ontology name namespace: identifier def: "Name of an ontology of biological or bioinformatics terms and relations." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002099 ! Name is_a: EDAM:0002338 ! Ontology identifier relationship: is_identifier_of EDAM:0000582 ! Ontology [Term] id: EDAM:0002110 name: Molecular property identifier namespace: identifier def: "Identifier of a molecular property." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0002087 ! Molecular property [Term] id: EDAM:0001062 name: Database entry identifier namespace: identifier def: "An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type." [EDAM:EBI "EMBRACE definition"] comment: This term is required for completeness. It should never have child terms. subset: identifier is_obsolete: true consider: EDAM:0000842 ! Identifier [Term] id: EDAM:0002117 name: Map identifier namespace: identifier def: "An identifier of a map of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0001274 ! Map [Term] id: EDAM:0002904 name: Map accession namespace: identifier def: "An accession of a map of a molecular sequence (deposited in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002117 ! Map identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001063 name: Sequence identifier namespace: identifier def: "An identifier of molecular sequence(s) or entries from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0000855 ! Sequence metadata relationship: is_identifier_of EDAM:0002044 ! Sequence [Term] id: EDAM:0002294 name: Sequence variation ID namespace: identifier def: "An identifier of an entry from a database of molecular sequence variation." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001064 name: Sequence set ID namespace: identifier def: "An identifier of a set of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000850 ! Sequence set [Term] id: EDAM:0001065 name: Sequence signature identifier namespace: identifier def: "Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001114 ! Sequence motif identifier consider: EDAM:0001115 ! Sequence profile ID [Term] id: EDAM:0001066 name: Sequence alignment ID namespace: identifier def: "Identifier of a molecular sequence alignment, for example a record from an alignment database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0001067 name: Phylogenetic distance matrix identifier namespace: identifier def: "Identifier of a phylogenetic distance matrix." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0001068 name: Phylogenetic tree ID namespace: identifier def: "Identifier of a phylogenetic tree for example from a phylogenetic tree database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000872 ! Phylogenetic tree [Term] id: EDAM:0003036 name: Matrix identifier namespace: identifier def: "An identifier of an array of numerical values, such as a comparison matrix." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0002082 ! Matrix [Term] id: EDAM:0001069 name: Comparison matrix identifier namespace: identifier def: "An identifier of a comparison matrix." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Substitution matrix identifier" EXACT [] is_a: EDAM:0003036 ! Matrix identifier relationship: is_identifier_of EDAM:0000874 ! Comparison matrix [Term] id: EDAM:0003035 name: Structure identifier namespace: identifier def: "An identifier of a molecular tertiary structure, typically an entry from a structure database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0000883 ! Structure [Term] id: EDAM:0001070 name: Structure ID namespace: identifier def: "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0003035 ! Structure identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001759 name: PDB model number namespace: identifier def: "Identifier of a model structure from a PDB file." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Model number" EXACT [] xref: WHATIF: model_number is_a: EDAM:0003035 ! Structure identifier ! pdbx_PDB_model_num in PDBML [Term] id: EDAM:0001071 name: Structural (3D) profile ID namespace: identifier def: "Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Structural profile identifier" EXACT [] is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000889 ! Structural (3D) profile [Term] id: EDAM:0001072 name: Structure alignment ID namespace: identifier def: "Identifier of an entry from a database of tertiary structure alignments." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000886 ! Structure alignment [Term] id: EDAM:0001073 name: Amino acid index ID namespace: identifier def: "Identifier of an index of amino acid physicochemical and biochemical property data." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0003036 ! Matrix identifier is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0001501 ! Amino acid index [Term] id: EDAM:0002627 name: Molecular interaction ID namespace: identifier def: "Identifier of a report of molecular interactions from a database (typically)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0002599 ! Molecular interaction [Term] id: EDAM:0001075 name: Protein family identifier namespace: identifier def: "Identifier of a protein family." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Protein secondary database record identifier" EXACT [] is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0000907 ! Protein family [Term] id: EDAM:0002910 name: Protein family accession namespace: identifier def: "Accession of a protein family (that is deposited in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0001075 ! Protein family identifier [Term] id: EDAM:0001131 name: Protein family name namespace: identifier def: "Name of a protein family." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001075 ! Protein family identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002355 name: RNA family identifier namespace: identifier def: "Identifier of an RNA family, typically an entry from a RNA sequence classification database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0002354 ! RNA family annotation [Term] id: EDAM:0002111 name: Codon usage table identifier namespace: identifier def: "Identifier of a codon usage table, for example a genetic code." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0001597 ! Codon usage table relationship: is_identifier_of EDAM:0001598 ! Genetic code [Term] id: EDAM:0001077 name: Transcription factor identifier namespace: identifier def: "Identifier of a transcription factor (or a TF binding site)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0000989 ! Protein identifier relationship: is_identifier_of EDAM:0001315 ! Gene features (TFBS) [Term] id: EDAM:0002911 name: Transcription factor accession namespace: identifier def: "Accession of an entry from a database of transcription factors or binding sites." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001077 ! Transcription factor identifier is_a: EDAM:0002907 ! Protein accession is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001078 name: Microarray experiment annotation ID namespace: identifier def: "Identifier of an entry from a database of microarray data." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0000931 ! Microarray experiment annotation [Term] id: EDAM:0001079 name: Electron microscopy model ID namespace: identifier def: "Identifier of an entry from a database of electron microscopy data." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000941 ! Electron microscopy model [Term] id: EDAM:0001080 name: Gene expression report ID namespace: identifier alt_id: EDAM:0002708 def: "Accession of a report of gene expression (e.g. a gene expression profile) from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Gene expression profile identifier" EXACT [] is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0001081 name: Genotype and phenotype annotation ID namespace: identifier def: "Identifier of an entry from a database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000920 ! Genotype and phenotype annotation [Term] id: EDAM:0002382 name: Genotype experiment ID namespace: identifier def: "Identifier of an entry from a database of genotype experiment metadata." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0002381 ! Experiment annotation (genotype) [Term] id: EDAM:0002638 name: PubChem bioassay ID namespace: identifier def: "Identifier of an assay from the PubChem database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002639 ! PubChem identifier [Term] id: EDAM:0001082 name: Pathway or network identifier namespace: identifier def: "Identifier of an entry from a database of biological pathways or networks." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0002600 ! Pathway or network [Term] id: EDAM:0002590 name: Hierarchy identifier namespace: identifier def: "Identifier of an entry from a database of biological hierarchies." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0002891 ! Biological model accession [Term] id: EDAM:0002108 name: Reaction ID namespace: identifier def: "Identifier of a biological reaction from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0002978 ! Reaction data [Term] id: EDAM:0001083 name: Workflow ID namespace: identifier def: "Identifier of a biological or biomedical workflow, typically from a database of workflows." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0002972 ! Workflow [Term] id: EDAM:0001084 name: Data resource definition identifier namespace: identifier def: "Identifier of a data type definition from some provider." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002219 name: Database field name namespace: identifier def: "The name of a field in a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001085 name: Biological model identifier namespace: identifier def: "Identifier of a mathematical model, typically an entry from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0000950 ! Biological model [Term] id: EDAM:0002891 name: Biological model accession namespace: identifier def: "Accession of a mathematical model, typically an entry from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001085 ! Biological model identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001086 name: Compound identifier namespace: identifier def: "Identifier of an entry from a database of chemicals." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Small molecule identifier" EXACT [] synonym: "Chemical compound identifier" EXACT [] is_a: EDAM:0000982 ! Molecule identifier relationship: is_identifier_of EDAM:0000962 ! Small molecule annotation relationship: is_identifier_of EDAM:0001712 ! Structure image (small molecule) relationship: is_identifier_of EDAM:0000846 ! Chemical formula [Term] id: EDAM:0002894 name: Compound accession namespace: identifier def: "Accession of an entry from a database of chemicals." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Small molecule accession" EXACT [] synonym: "Chemical compound accession" EXACT [] is_a: EDAM:0001086 ! Compound identifier is_a: EDAM:0002901 ! Molecule accession [Term] id: EDAM:0002338 name: Ontology identifier namespace: identifier def: "Any arbitrary identifier of an ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0000582 ! Ontology [Term] id: EDAM:0003025 name: Ontology term identifier namespace: identifier def: "Identifier of a term in an ontology of biological or bioinformatics terms and relations." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0002858 ! Ontology concept [Term] id: EDAM:0001087 name: Ontology term ID namespace: identifier def: "A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics terms and relations." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Ontology concept ID" EXACT [] is_a: EDAM:0003025 ! Ontology term identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001088 name: Article ID namespace: identifier def: "Unique identifier of a scientific article." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0000971 ! Article [Term] id: EDAM:0002633 name: Book ID namespace: identifier def: "Unique identifier of a book." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002790 name: Gel identifier namespace: identifier def: "Identifier of a two-dimensional (protein) gel." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002791 name: Reference map name (SWISS-2DPAGE) namespace: identifier def: "Name of a reference map gel from the SWISS-2DPAGE database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002790 ! Gel identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002373 name: Spot ID namespace: identifier def: "Unique identifier of a spot from a two-dimensional (protein) gel." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002587 name: Blot ID namespace: identifier def: "Unique identifier of a blot from a Northern Blot." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002379 name: Strain identifier namespace: identifier def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001869 ! Organism identifier [Term] id: EDAM:0002912 name: Strain accession namespace: identifier def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002379 ! Strain identifier is_a: EDAM:0002908 ! Organism accession relationship: is_identifier_of EDAM:0000963 ! Cell line annotation [Term] id: EDAM:0002917 name: ConsensusPathDB identifier namespace: identifier def: "An identifier of an entity from the ConsensusPathDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002109 ! Identifier (hybrid) [Term] id: EDAM:0002776 name: ConsensusPathDB entity ID namespace: identifier def: "Identifier of a physical entity from the ConsensusPathDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002917 ! ConsensusPathDB identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002777 name: ConsensusPathDB entity name namespace: identifier def: "Name of a physical entity from the ConsensusPathDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002917 ! ConsensusPathDB identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002639 name: PubChem identifier namespace: identifier def: "Identifier of an entry from the PubChem database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002367 name: ASTD ID namespace: identifier def: "Identifier of an object from the ASTD database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001089 name: FlyBase ID namespace: identifier def: "Identifier of an object from the FlyBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "FB[a-zA-Z_0-9]{2}[0-9]{7}" is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002113 name: WormBase identifier namespace: identifier def: "Identifier of an object from the WormBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002109 ! Identifier (hybrid) [Term] id: EDAM:0002104 name: BioCyc ID namespace: identifier def: "Identifier of an object from one of the BioCyc databases." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001154 name: KEGG object identifier namespace: identifier def: "Unique identifier of an object from one of the KEGG databases (excluding the GENES division)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002380 name: CABRI accession namespace: identifier def: "A unique identifier of an item from the CABRI database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002387 name: TAIR accession namespace: identifier def: "Identifier of an entry from the TAIR database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002610 name: Ensembl ID namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENS[A-Z]*[FPTG][0-9]{11}" is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002620 name: RGD ID namespace: identifier def: "Identifier of an entry from the RGD database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]{4,7}" is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002632 name: SGD ID namespace: identifier def: "Identifier of an entry from the Saccharomyces genome database (SGD)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PWY[a-zA-Z_0-9]{2}\-[0-9]{3}" is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002649 name: PharmGKB ID namespace: identifier def: "Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PA[0-9]+" is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002368 name: ASTD ID (exon) namespace: identifier def: "Identifier of an exon from the ASTD database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002367 ! ASTD ID [Term] id: EDAM:0002369 name: ASTD ID (intron) namespace: identifier def: "Identifier of an intron from the ASTD database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002367 ! ASTD ID [Term] id: EDAM:0002370 name: ASTD ID (polya) namespace: identifier def: "Identifier of a polyA signal from the ASTD database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002367 ! ASTD ID [Term] id: EDAM:0002371 name: ASTD ID (tss) namespace: identifier def: "Identifier of a transcription start site from the ASTD database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002367 ! ASTD ID [Term] id: EDAM:0002671 name: Ensembl ID (Homo sapiens) namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENS([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002672 name: Ensembl ID ("Bos taurus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Bos taurus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSBTA([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002673 name: Ensembl ID ("Canis familiaris") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Canis familiaris" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSCAF([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002674 name: Ensembl ID ("Cavia porcellus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Cavia porcellus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSCPO([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002675 name: Ensembl ID ("Ciona intestinalis") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Ciona intestinalis" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSCIN([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002676 name: Ensembl ID ("Ciona savignyi") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Ciona savignyi" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSCSAV([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002677 name: Ensembl ID ("Danio rerio") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Danio rerio" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSDAR([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002678 name: Ensembl ID ("Dasypus novemcinctus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Dasypus novemcinctus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSDNO([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002679 name: Ensembl ID ("Echinops telfairi") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Echinops telfairi" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSETE([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002680 name: Ensembl ID ("Erinaceus europaeus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Erinaceus europaeus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSEEU([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002681 name: Ensembl ID ("Felis catus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Felis catus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSFCA([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002682 name: Ensembl ID ("Gallus gallus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Gallus gallus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSGAL([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002683 name: Ensembl ID ("Gasterosteus aculeatus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Gasterosteus aculeatus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSGAC([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002684 name: Ensembl ID ("Homo sapiens") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Homo sapiens" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSHUM([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002685 name: Ensembl ID ("Loxodonta africana") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Loxodonta africana" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSLAF([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002686 name: Ensembl ID ("Macaca mulatta") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Macaca mulatta" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSMMU([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002687 name: Ensembl ID ("Monodelphis domestica") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Monodelphis domestica" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSMOD([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002688 name: Ensembl ID ("Mus musculus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Mus musculus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSMUS([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002689 name: Ensembl ID ("Myotis lucifugus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Myotis lucifugus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSMLU([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002690 name: Ensembl ID ("Ornithorhynchus anatinus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Ornithorhynchus anatinus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSOAN([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002691 name: Ensembl ID ("Oryctolagus cuniculus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Oryctolagus cuniculus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSOCU([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002692 name: Ensembl ID ("Oryzias latipes") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Oryzias latipes" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSORL([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002693 name: Ensembl ID ("Otolemur garnettii") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Otolemur garnettii" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSSAR([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002694 name: Ensembl ID ("Pan troglodytes") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Pan troglodytes" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSPTR([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002695 name: Ensembl ID ("Rattus norvegicus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Rattus norvegicus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSRNO([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002696 name: Ensembl ID ("Spermophilus tridecemlineatus") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Spermophilus tridecemlineatus" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSSTO([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002697 name: Ensembl ID ("Takifugu rubripes") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Takifugu rubripes" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSFRU([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002698 name: Ensembl ID ("Tupaia belangeri") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Tupaia belangeri" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSTBE([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002699 name: Ensembl ID ("Xenopus tropicalis") namespace: identifier def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Xenopus tropicalis" division)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ENSXET([EGTP])[0-9]{11}" is_obsolete: true consider: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002725 name: Transcript ID (Ensembl) namespace: identifier def: "Unique identifier for a gene transcript from the Ensembl database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Ensembl Transcript ID" EXACT [] is_a: EDAM:0002610 ! Ensembl ID is_a: EDAM:0002769 ! Transcript ID [Term] id: EDAM:0002597 name: CABRI catalogue name namespace: identifier def: "The name of a catalogue of biological resources from the CABRI database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002596 ! Catalogue identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002780 name: Stock number (TAIR) namespace: identifier def: "A stock number from The Arabidopsis information resource (TAIR)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002779 ! Stock number [Term] id: EDAM:0002129 name: File format name namespace: identifier def: "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002131 name: Operating system name namespace: identifier def: "Name of a computer operating system such as Linux, PC or Mac." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002538 name: Mutation identifier namespace: identifier def: "An identifier of a mutation." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0002209 name: Mutation ID namespace: identifier def: "A unique identifier of a specific mutation catalogued in a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002538 ! Mutation identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002133 name: Logical operator namespace: identifier def: "A logical operator such as OR, AND, XOR, and NOT." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001114 name: Sequence motif identifier namespace: identifier def: "Identifier of a sequence motif, for example an entry from a motif database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0001353 ! Sequence motif [Term] id: EDAM:0001115 name: Sequence profile ID namespace: identifier def: "Identifier of a sequence profile." [EDAM:EBI "EMBRACE definition"] comment: A sequence profile typically represents a sequence alignment. subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0001354 ! Sequence profile [Term] id: EDAM:0002660 name: BioNumbers ID namespace: identifier def: "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0000983 name: Atom identifier namespace: identifier def: "Identifier (e.g. character symbol) of a specific atom." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) [Term] id: EDAM:0000984 name: Molecule name namespace: identifier def: "Name of a specific molecule." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000982 ! Molecule identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002901 name: Molecule accession namespace: identifier def: "Accession of a specific molecule (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000982 ! Molecule identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0000986 name: Chemical identifier namespace: identifier def: "Unique identifier of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001086 ! Compound identifier [Term] id: EDAM:0002119 name: Nucleic acid identifier namespace: identifier def: "Name or other identifier of a nucleic acid molecule." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000982 ! Molecule identifier relationship: is_identifier_of EDAM:0002084 ! Nucleic acid report [Term] id: EDAM:0000988 name: Peptide identifier namespace: identifier def: "Identifier of a peptide chain." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000982 ! Molecule identifier [Term] id: EDAM:0002906 name: Peptide ID namespace: identifier def: "Accession of a peptide deposited in a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000988 ! Peptide identifier is_a: EDAM:0002901 ! Molecule accession [Term] id: EDAM:0001008 name: Polypeptide chain ID namespace: identifier def: "Identifier of a polypeptide chain from a protein." [EDAM:EBI "EMBRACE definition"] comment: This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA subset: identifier synonym: "Polypeptide chain identifier" EXACT [] synonym: "Protein chain identifier" EXACT [] synonym: "PDB chain identifier" EXACT [] synonym: "Chain identifier" EXACT [] synonym: "PDB strand id" EXACT [] xref: WHATIF: chain is_a: EDAM:0000988 ! Peptide identifier relationship: is_identifier_of EDAM:0001467 ! Protein chain ! pdbx_PDB_strand_id in PDBML [Term] id: EDAM:0000989 name: Protein identifier namespace: identifier def: "Identifier of a protein." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000982 ! Molecule identifier relationship: is_identifier_of EDAM:0000896 ! Protein report [Term] id: EDAM:0002907 name: Protein accession namespace: identifier def: "Accession of a protein deposited in a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000989 ! Protein identifier is_a: EDAM:0002901 ! Molecule accession [Term] id: EDAM:0001757 name: Atom name namespace: identifier def: "Name of an atom." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000983 ! Atom identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001748 name: PDB atom name namespace: identifier def: "Identifier (a string) of a specific atom from a PDB file for a molecular structure." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: WHATIF: atom_type xref: WHATIF: alternate_atom xref: WHATIF: PDBx_auth_atom_id xref: WHATIF: PDBx_type_symbol is_a: EDAM:0001757 ! Atom name ! pdbx_PDB_atom_name in PDBML [Term] id: EDAM:0000990 name: Compound name namespace: identifier def: "Unique name of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Chemical name" EXACT [] is_a: EDAM:0001086 ! Compound identifier is_a: EDAM:0000984 ! Molecule name [Term] id: EDAM:0000991 name: Chemical registry number namespace: identifier def: "Unique registry number of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002894 ! Compound accession [Term] id: EDAM:0000992 name: Ligand identifier namespace: identifier def: "Code word for a ligand, for example from a PDB file." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001086 ! Compound identifier [Term] id: EDAM:0000993 name: Drug identifier namespace: identifier def: "Identifier of a drug." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001086 ! Compound identifier relationship: is_identifier_of EDAM:0002851 ! Drug structure [Term] id: EDAM:0002895 name: Drug accession namespace: identifier def: "Accession of a drug." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000993 ! Drug identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002899 name: Drug name namespace: identifier def: "Common name of a drug." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000993 ! Drug identifier is_a: EDAM:0000990 ! Compound name [Term] id: EDAM:0002576 name: Toxin identifier namespace: identifier def: "Identifier of a toxin." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001086 ! Compound identifier relationship: is_identifier_of EDAM:0002852 ! Toxin structure [Term] id: EDAM:0002896 name: Toxin name namespace: identifier def: "Name of a toxin." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002576 ! Toxin identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002897 name: Toxin accession namespace: identifier def: "Accession of a toxin (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002576 ! Toxin identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0000994 name: Amino acid identifier namespace: identifier def: "Identifier of an amino acid." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Residue identifier" EXACT [] is_a: EDAM:0001086 ! Compound identifier relationship: is_identifier_of EDAM:0002016 ! Amino acid property [Term] id: EDAM:0000995 name: Nucleotide identifier namespace: identifier def: "Name or other identifier of a nucleotide." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001086 ! Compound identifier [Term] id: EDAM:0000996 name: Monosaccharide identifier namespace: identifier def: "Identifier of a monosaccharide." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001086 ! Compound identifier [Term] id: EDAM:0002898 name: Monosaccharide accession namespace: identifier def: "Accession of a monosaccharide (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000996 ! Monosaccharide identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002812 name: Lipid identifier namespace: identifier def: "Identifier of a lipid." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000982 ! Molecule identifier relationship: is_identifier_of EDAM:0002850 ! Lipid structure relationship: is_identifier_of EDAM:0002879 ! Lipid structure report [Term] id: EDAM:0002905 name: Lipid accession namespace: identifier def: "Accession of an entry from a database of lipids." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002812 ! Lipid identifier is_a: EDAM:0002901 ! Molecule accession [Term] id: EDAM:0002663 name: Carbohydrate identifier namespace: identifier def: "Identifier of a carbohydrate." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001086 ! Compound identifier relationship: is_identifier_of EDAM:0002313 ! Carbohydrate structure report relationship: is_identifier_of EDAM:0001462 ! Carbohydrate structure [Term] id: EDAM:0002900 name: Carbohydrate accession namespace: identifier def: "Accession of an entry from a database of carbohydrates." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002663 ! Carbohydrate identifier is_a: EDAM:0002901 ! Molecule accession [Term] id: EDAM:0002605 name: Compound ID (KEGG) namespace: identifier def: "Unique identifier of a chemical compound from the KEGG database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "KEGG compound ID" EXACT [] synonym: "KEGG compound identifier" EXACT [] regex: "C[0-9]+" is_a: EDAM:0002894 ! Compound accession is_a: EDAM:0001154 ! KEGG object identifier [Term] id: EDAM:0002580 name: BindingDB Monomer ID namespace: identifier def: "Unique identifier of a monomer from the BindingDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002894 ! Compound accession [Term] id: EDAM:0001172 name: PubChem CID namespace: identifier def: "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "PubChem compound accession identifier" EXACT [] regex: "[0-9]+" is_a: EDAM:0002894 ! Compound accession is_a: EDAM:0002639 ! PubChem identifier [Term] id: EDAM:0001173 name: ChemSpider ID namespace: identifier def: "Identifier of an entry from the ChemSpider database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002894 ! Compound accession [Term] id: EDAM:0001174 name: ChEBI ID namespace: identifier def: "Identifier of an entry from the ChEBI database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "ChEBI identifier" EXACT [] regex: "CHEBI:[0-9]+" is_a: EDAM:0002894 ! Compound accession [Term] id: EDAM:0002105 name: Compound ID (BioCyc) namespace: identifier def: "Identifier of a compound from the BioCyc chemical compounds database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "BioCyc compound ID" EXACT [] synonym: "BioCyc compound identifier" EXACT [] is_a: EDAM:0002104 ! BioCyc ID is_a: EDAM:0002894 ! Compound accession [Term] id: EDAM:0002622 name: Compound ID (HMDB) namespace: identifier def: "Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB)." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "HMDB ID" EXACT [] regex: "HMDB[0-9]{5}" is_a: EDAM:0002894 ! Compound accession [Term] id: EDAM:0002635 name: Compound ID (3DMET) namespace: identifier def: "Identifier of a metabolite from the 3DMET database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "3DMET ID" EXACT [] regex: "B[0-9]{5}" is_a: EDAM:0002894 ! Compound accession [Term] id: EDAM:0002646 name: Compound ID (ChEMBL) namespace: identifier def: "Identifier of a small molecular from the ChEMBL database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "ChEMBL ID" EXACT [] regex: "[0-9]+" is_a: EDAM:0002894 ! Compound accession [Term] id: EDAM:0002658 name: Compound ID (ChemIDplus) namespace: identifier def: "Identifier of a chemical from the ChemIDplus database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "ChemIDplus ID" EXACT [] regex: "[0-9]+" is_a: EDAM:0002894 ! Compound accession [Term] id: EDAM:0000997 name: Chemical name (ChEBI) namespace: identifier def: "Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound." [EDAM:EBI "EMBRACE definition"] comment: This is the recommended chemical name for use for example in database annotation. subset: identifier synonym: "ChEBI chemical name" EXACT [] is_a: EDAM:0000990 ! Compound name [Term] id: EDAM:0000998 name: Chemical name (IUPAC) namespace: identifier def: "IUPAC recommended name of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "IUPAC chemical name" EXACT [] is_a: EDAM:0000990 ! Compound name [Term] id: EDAM:0000999 name: Chemical name (INN) namespace: identifier def: "International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO)." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "INN chemical name" EXACT [] is_a: EDAM:0000990 ! Compound name [Term] id: EDAM:0001000 name: Chemical name (brand) namespace: identifier def: "Brand name of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Brand chemical name" EXACT [] is_a: EDAM:0000990 ! Compound name [Term] id: EDAM:0001001 name: Chemical name (synonymous) namespace: identifier def: "Synonymous name of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Synonymous chemical name" EXACT [] is_a: EDAM:0000990 ! Compound name [Term] id: EDAM:0001002 name: Chemical registry number (CAS) namespace: identifier def: "CAS registry number of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "CAS chemical registry number" EXACT [] is_a: EDAM:0000991 ! Chemical registry number [Term] id: EDAM:0001003 name: Chemical registry number (Beilstein) namespace: identifier def: "Beilstein registry number of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Beilstein chemical registry number" EXACT [] is_a: EDAM:0000991 ! Chemical registry number [Term] id: EDAM:0001004 name: Chemical registry number (Gmelin) namespace: identifier def: "Gmelin registry number of a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Gmelin chemical registry number" EXACT [] is_a: EDAM:0000991 ! Chemical registry number [Term] id: EDAM:0001005 name: HET group name namespace: identifier def: "3-letter code word for a ligand (HET group) from a PDB file, for example ATP." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Short ligand name" EXACT [] synonym: "Component identifier code" EXACT [] is_a: EDAM:0000990 ! Compound name [Term] id: EDAM:0002613 name: KEGG Glycan ID namespace: identifier def: "Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "G[0-9]+" is_a: EDAM:0002900 ! Carbohydrate accession is_a: EDAM:0001154 ! KEGG object identifier [Term] id: EDAM:0002326 name: DrugBank ID namespace: identifier def: "Unique identifier of a drug from the DrugBank database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "DB[0-9]{5}" is_a: EDAM:0002895 ! Drug accession [Term] id: EDAM:0002609 name: Drug ID (KEGG) namespace: identifier def: "Unique identifier of a drug from the KEGG Drug database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "D[0-9]+" is_a: EDAM:0002895 ! Drug accession is_a: EDAM:0001154 ! KEGG object identifier [Term] id: EDAM:0002652 name: Drug ID (PharmGKB) namespace: identifier def: "Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PA[0-9]+" is_a: EDAM:0002895 ! Drug accession is_a: EDAM:0002649 ! PharmGKB ID [Term] id: EDAM:0002653 name: Drug ID (TTD) namespace: identifier def: "Identifier of a drug from the Therapeutic Target Database (TTD)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "DAP[0-9]+" is_a: EDAM:0002895 ! Drug accession [Term] id: EDAM:0003102 name: CAS number namespace: identifier def: "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "CAS registry number" EXACT [] is_a: EDAM:0002895 ! Drug accession [Term] id: EDAM:0003103 name: ATC code namespace: identifier def: "Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002895 ! Drug accession [Term] id: EDAM:0003104 name: UNII namespace: identifier def: "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Unique Ingredient Identifier" EXACT [] is_a: EDAM:0001086 ! Compound identifier [Term] id: EDAM:0002578 name: ArachnoServer ID namespace: identifier def: "Unique identifier of a toxin from the ArachnoServer database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002897 ! Toxin accession [Term] id: EDAM:0002662 name: T3DB ID namespace: identifier def: "Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "T3D[0-9]+" is_a: EDAM:0002897 ! Toxin accession [Term] id: EDAM:0001006 name: Amino acid name namespace: identifier def: "String of one or more ASCII characters representing an amino acid." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000994 ! Amino acid identifier [Term] id: EDAM:0002563 name: Amino acid name (single letter) namespace: identifier def: "Single letter amino acid identifier, e.g. G." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001006 ! Amino acid name [Term] id: EDAM:0002564 name: Amino acid name (three letter) namespace: identifier def: "Three letter amino acid identifier, e.g. GLY." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001006 ! Amino acid name [Term] id: EDAM:0001758 name: PDB residue name namespace: identifier def: "Three-letter amino acid residue names as used in PDB files." [EDAM:EBI "EMBRACE definition"] subset: format xref: WHATIF: type is_a: EDAM:0002564 ! Amino acid name (three letter) [Term] id: EDAM:0002565 name: Amino acid name (full name) namespace: identifier def: "Full name of an amino acid, e.g. Glycine." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001006 ! Amino acid name [Term] id: EDAM:0001007 name: Nucleotide code namespace: identifier def: "String of one or more ASCII characters representing a nucleotide." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000995 ! Nucleotide identifier is_a: EDAM:0000990 ! Compound name [Term] id: EDAM:0002746 name: MonosaccharideDB ID namespace: identifier def: "Unique identifier of a monosaccharide from the MonosaccharideDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002898 ! Monosaccharide accession [Term] id: EDAM:0002625 name: LIPID MAPS ID namespace: identifier def: "Identifier of an entry from the LIPID MAPS database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "LM ID" EXACT [] regex: "LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?" is_a: EDAM:0002905 ! Lipid accession [Term] id: EDAM:0002665 name: LipidBank ID namespace: identifier def: "Identifier of an entry from the LipidBank database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[a-zA-Z_0-9]+[0-9]+" is_a: EDAM:0002905 ! Lipid accession [Term] id: EDAM:0002664 name: GlycomeDB ID namespace: identifier def: "Identifier of an entry from the GlycomeDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002900 ! Carbohydrate accession [Term] id: EDAM:0002752 name: GlycoMap ID namespace: identifier def: "Identifier of an entry from the GlycosciencesDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002900 ! Carbohydrate accession [Term] id: EDAM:0002796 name: Linucs ID namespace: identifier def: "Identifier of an entry from the GlycosciencesDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002900 ! Carbohydrate accession [Term] id: EDAM:0000987 name: Chromosome name namespace: identifier def: "Name of a chromosome." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002119 ! Nucleic acid identifier is_a: EDAM:0000984 ! Molecule name relationship: is_identifier_of EDAM:0000919 ! Nucleic acid features (chromosome) [Term] id: EDAM:0002208 name: Plasmid identifier namespace: identifier def: "An identifier of a plasmid in a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002119 ! Nucleic acid identifier [Term] id: EDAM:0002718 name: Oligonucleotide ID namespace: identifier def: "Identifier of an oligonucleotide from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002119 ! Nucleic acid identifier is_a: EDAM:0002901 ! Molecule accession [Term] id: EDAM:0002769 name: Transcript ID namespace: identifier def: "Identifier of a RNA transcript." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002119 ! Nucleic acid identifier is_a: EDAM:0002901 ! Molecule accession relationship: is_identifier_of EDAM:0002399 ! Gene annotation (transcript) [Term] id: EDAM:0002706 name: Chromosome name (BioCyc) namespace: identifier def: "Name of a chromosome as used in the BioCyc database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000987 ! Chromosome name [Term] id: EDAM:0002719 name: dbProbe ID namespace: identifier def: "Identifier of an oligonucleotide probe from the dbProbe database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002718 ! Oligonucleotide ID [Term] id: EDAM:0002721 name: DiProDB ID namespace: identifier def: "Identifier of an dinucleotide property from the DiProDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002718 ! Oligonucleotide ID [Term] id: EDAM:0002770 name: HIT ID namespace: identifier def: "Identifier of an RNA transcript from the H-InvDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002769 ! Transcript ID [Term] id: EDAM:0002626 name: PeptideAtlas ID namespace: identifier def: "Identifier of a peptide from the PeptideAtlas peptide databases." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PAp[0-9]{8}" is_a: EDAM:0002906 ! Peptide ID ! pdbx_PDB_strand_id in PDBML [Term] id: EDAM:0001009 name: Protein name namespace: identifier def: "Name of a protein." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000989 ! Protein identifier is_a: EDAM:0000984 ! Molecule name [Term] id: EDAM:0001010 name: Enzyme identifier namespace: identifier def: "Name or other identifier of an enzyme or record from a database of enzymes." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000989 ! Protein identifier relationship: is_identifier_of EDAM:0001509 ! Enzyme property [Term] id: EDAM:0002114 name: WormBase wormpep ID namespace: identifier def: "Protein identifier used by WormBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "CE[0-9]{5}" is_a: EDAM:0002907 ! Protein accession is_a: EDAM:0002113 ! WormBase identifier [Term] id: EDAM:0002804 name: Protein ID (ConoServer) namespace: identifier def: "Unique identifier for a cone snail toxin protein from the ConoServer database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002802 name: Protein ID (EcID) namespace: identifier def: "Unique identifier for a protein from the EcID database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0003029 name: Protein ID (EMBL/GenBank/DDBJ) namespace: identifier def: "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators." [EDAM:EBI "EMBRACE definition"] comment: This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. subset: identifier is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002398 name: Protein ID (Ensembl) namespace: identifier def: "Unique identifier for a protein from the Ensembl database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Ensembl protein ID" EXACT [] is_a: EDAM:0002907 ! Protein accession is_a: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0002713 name: Protein ID (CORUM) namespace: identifier def: "Unique identifier for a protein complex from the CORUM database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "CORUM complex ID" EXACT [] is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002715 name: Protein ID (CuticleDB) namespace: identifier def: "Unique identifier for a protein from the CuticleDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "CuticleDB ID" EXACT [] is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002723 name: Protein ID (DisProt) namespace: identifier def: "Unique identifier for a protein from the DisProt database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "DisProt ID" EXACT [] is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002789 name: Protein ID (TopDB) namespace: identifier def: "Unique identifier for a membrane protein from the TopDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "TopDB ID" EXACT [] is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002792 name: Protein ID (PeroxiBase) namespace: identifier def: "Unique identifier for a peroxidase protein from the PeroxiBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "PeroxiBase ID" EXACT [] is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002797 name: Protein ID (LGICdb) namespace: identifier def: "Unique identifier for a ligand-gated ion channel protein from the LGICdb database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "LGICdb ID" EXACT [] is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002617 name: Signaling Gateway protein ID namespace: identifier def: "Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "A[0-9]{6}" is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002647 name: LGICdb identifier namespace: identifier def: "Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[a-zA-Z_0-9]+" is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002654 name: Target ID (TTD) namespace: identifier def: "Identifier of a target protein from the Therapeutic Target Database (TTD)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "TTDS[0-9]+" is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002756 name: TCID namespace: identifier def: "Identifier of a membrane transport proteins from the transport classification database (TCDB)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002772 name: HPA antibody id namespace: identifier def: "Identifier of a antibody from the HPA database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002773 name: IMGT/HLA ID namespace: identifier def: "Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0002764 name: Protein name (UniProt) namespace: identifier def: "Official name of a protein as used in the UniProt database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001009 ! Protein name [Term] id: EDAM:0002775 name: Kinase name namespace: identifier def: "The name of a kinase protein." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001009 ! Protein name [Term] id: EDAM:0002321 name: Enzyme ID namespace: identifier def: "A unique, persistent identifier of an enzyme." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Enzyme accession" EXACT [] is_a: EDAM:0001010 ! Enzyme identifier is_a: EDAM:0002907 ! Protein accession [Term] id: EDAM:0001012 name: Enzyme name namespace: identifier def: "Name of an enzyme." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001010 ! Enzyme identifier is_a: EDAM:0001009 ! Protein name [Term] id: EDAM:0001011 name: EC number namespace: identifier def: "An Enzyme Commission (EC) number of an enzyme." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "EC code" EXACT [] synonym: "EC" EXACT [] synonym: "Enzyme Commission number" EXACT [] xref: Moby:EC_Number xref: Moby:Annotated_EC_Number regex: "[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+" is_a: EDAM:0002321 ! Enzyme accession [Term] id: EDAM:0002107 name: Enzyme ID (BioCyc) namespace: identifier def: "Identifier of an enzyme from the BioCyc enzymes database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "BioCyc enzyme ID" EXACT [] is_a: EDAM:0002104 ! BioCyc ID is_a: EDAM:0002321 ! Enzyme ID [Term] id: EDAM:0002629 name: Enzyme ID (MEROPS) namespace: identifier def: "Unique identifier of a peptidase enzyme from the MEROPS database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "MEROPS ID" EXACT [] regex: "S[0-9]{2}\.[0-9]{3}" is_a: EDAM:0002321 ! Enzyme ID [Term] id: EDAM:0002702 name: Enzyme ID (CAZy) namespace: identifier def: "Identifier of an enzyme from the CAZy enzymes database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "CAZy ID" EXACT [] is_a: EDAM:0002321 ! Enzyme ID [Term] id: EDAM:0002325 name: REBASE enzyme number namespace: identifier def: "Identifier of an enzyme from the REBASE enzymes database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002091 ! Enzyme accession [Term] id: EDAM:0001013 name: Restriction enzyme name namespace: identifier def: "Name of a restriction enzyme." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001012 ! Enzyme name relationship: is_identifier_of EDAM:0001517 ! Restriction enzyme property [Term] id: EDAM:0001018 name: Nucleic acid feature identifier namespace: identifier def: "Name or other identifier of an nucleic acid feature." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001015 ! Sequence feature ID [Term] id: EDAM:0001019 name: Protein feature identifier namespace: identifier def: "Name or other identifier of a protein feature." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001015 ! Sequence feature ID [Term] id: EDAM:0002736 name: Sequence feature ID (SwissRegulon) namespace: identifier def: "A feature identifier as used in the SwissRegulon database." [EDAM:EBI "EMBRACE definition"] comment: This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". subset: identifier is_a: EDAM:0001015 ! Sequence feature ID [Term] id: EDAM:0001024 name: Codon name namespace: identifier def: "String of one or more ASCII characters representing a codon." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001276 ! Nucleic acid features ! Don't know whether the loci identifiers listed here are 'ordered' or not. [Term] id: EDAM:0002009 name: Ordered locus name namespace: identifier def: "A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001895 name: Locus ID (AGI) namespace: identifier def: "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "AGI locus code" EXACT [] synonym: "AGI ID" EXACT [] synonym: "AGI identifier" EXACT [] synonym: "Arabidopsis gene loci number" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode regex: "AT[1-5]G[0-9]{5}" is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001896 name: Locus ID (ASPGD) namespace: identifier def: "Identifier for loci from ASPGD (Aspergillus Genome Database)." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001897 name: Locus ID (MGG) namespace: identifier def: "Identifier for loci from Magnaporthe grisea Database at the Broad Institute." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001898 name: Locus ID (CGD) namespace: identifier def: "Identifier for loci from CGD (Candida Genome Database)." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "CGD locus identifier" EXACT [] synonym: "CGDID" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGD xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGDID is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001899 name: Locus ID (CMR) namespace: identifier def: "Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR xref: http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001900 name: NCBI locus tag namespace: identifier def: "Identifier for loci from NCBI database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Locus ID (NCBI)" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag xref: Moby_namespace:LocusID is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001901 name: Locus ID (SGD) namespace: identifier def: "Identifier for loci from SGD (Saccharomyces Genome Database)." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "SGDID" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGD xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGDID is_a: EDAM:0001893 ! Locus ID is_a: EDAM:0002632 ! SGD ID [Term] id: EDAM:0001902 name: Locus ID (MMP) namespace: identifier def: "Identifier of loci from Maize Mapping Project." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:MMP_Locus is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001903 name: Locus ID (DictyBase) namespace: identifier def: "Identifier of locus from DictyBase (Dictyostelium discoideum)." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:DDB_gene is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001904 name: Locus ID (EntrezGene) namespace: identifier def: "Identifier of a locus from EntrezGene database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:EntrezGene_EntrezGeneID xref: Moby_namespace:EntrezGene_ID is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001905 name: Locus ID (MaizeGDB) namespace: identifier def: "Identifier of locus from MaizeGDB (Maize genome database)." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:MaizeGDB_Locus is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001908 name: Locus ID (Tropgene) namespace: identifier def: "Identifier of a locus from the Tropgene database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby:Tropgene_locus is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0002744 name: Locus ID (PseudoCAP) namespace: identifier def: "Identifier of a locus from the PseudoCAP database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0002745 name: Locus ID (UTR) namespace: identifier def: "Identifier of a locus from the UTR database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0002794 name: ORF ID namespace: identifier def: "Accession of an open reading frame (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002795 ! ORF identifier is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001026 name: Gene symbol namespace: identifier def: "The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:Global_GeneSymbol xref: Moby_namespace:Global_GeneCommonName is_a: EDAM:0002299 ! Gene name [Term] id: EDAM:0002299 name: Gene name namespace: identifier def: "The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001025 ! Gene identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002295 name: Gene ID namespace: identifier def: "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Gene code" EXACT [] synonym: "Gene accession" EXACT [] is_a: EDAM:0001025 ! Gene identifier is_a: EDAM:0001893 ! Locus ID [Term] id: EDAM:0001891 name: iHOP symbol namespace: identifier def: "A unique identifier of a protein or gene used in the iHOP database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:iHOPsymbol is_a: EDAM:0002295 ! Gene ID is_a: EDAM:0002907 ! Protein accession is_a: EDAM:0002109 ! Identifier (hybrid) ! Suspect this identifiers more than just genes [Term] id: EDAM:0001036 name: TIGR identifier namespace: identifier def: "Identifier of an entry from the TIGR database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002295 ! Gene ID is_a: EDAM:0002109 ! Identifier (hybrid) [Term] id: EDAM:0001037 name: TAIR accession (gene) namespace: identifier def: "Identifier of an gene from the TAIR database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "Gene:[0-9]{7}" is_a: EDAM:0002295 ! Gene ID is_a: EDAM:0002387 ! TAIR accession [Term] id: EDAM:0002388 name: TAIR accession (At gene) namespace: identifier def: "Identifier of an Arabidopsis thaliana gene from the TAIR database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001037 ! TAIR accession (gene) [Term] id: EDAM:0001806 name: Gene synonym namespace: identifier def: "Any name (other than the recommended one) for a gene." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Gene name synonym" EXACT [] is_obsolete: true consider: EDAM:0001026 ! Gene name [Term] id: EDAM:0001807 name: ORF name namespace: identifier def: "The name of an open reading frame attributed by a sequencing project." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002795 ! ORF identifier is_a: EDAM:0002099 ! Name ! GeneFarm gene ID is also given [Term] id: EDAM:0001892 name: Gene name (GeneFarm) namespace: identifier def: "Name of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:GENEFARM_GeneName is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001889 name: Gene name (DragonDB) namespace: identifier def: "The name of an Antirrhinum Gene from the DragonDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:DragonDB_Gene is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001890 name: Gene name (Arabidopsis) namespace: identifier def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:ArabidopsisGeneSymbol is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001783 name: Gene name (ASPGD) namespace: identifier def: "Name of a gene from Aspergillus Genome Database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001784 name: Gene name (CGD) namespace: identifier def: "Name of a gene from Candida Genome Database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001785 name: Gene name (dictyBase) namespace: identifier def: "Name of a gene from dictyBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001786 name: Gene name (EcoGene primary) namespace: identifier def: "Primary name of a gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "EcoGene primary gene name" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001787 name: Gene name (MaizeGDB) namespace: identifier def: "Name of a gene from MaizeGDB (maize genes) database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001788 name: Gene name (SGD) namespace: identifier def: "Name of a gene from Saccharomyces Genome Database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS is_a: EDAM:0001026 ! Gene symbol is_a: EDAM:0002632 ! SGD ID [Term] id: EDAM:0001789 name: Gene name (TGD) namespace: identifier def: "Name of a gene from Tetrahymena Genome Database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001790 name: Gene name (CGSC) namespace: identifier def: "Symbol of a gene from E.coli Genetic Stock Center." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001791 name: Gene name (HGNC) namespace: identifier def: "Symbol of a gene approved by the HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Official gene name" EXACT [] synonym: "Gene name (HUGO)" EXACT [] synonym: "HGNC symbol" EXACT [] synonym: "HUGO symbol" EXACT [] synonym: "HGNC gene symbol" EXACT [] synonym: "HUGO gene symbol" EXACT [] synonym: "HUGO gene name" EXACT [] synonym: "HGNC gene name" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene regex: "HGNC:[0-9]{1,5}" is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001792 name: Gene name (MGD) namespace: identifier def: "Symbol of a gene from the Mouse Genome Database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD regex: "MGI:[0-9]+" is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0001793 name: Gene name (Bacillus subtilis) namespace: identifier def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0002103 name: Gene name (KEGG GENES) namespace: identifier def: "Name of an entry (gene) from the KEGG GENES database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "KEGG GENES entry name" EXACT [] xref: Moby_namespace:GeneId regex: "[a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*" is_a: EDAM:0001026 ! Gene symbol is_a: EDAM:0001154 ! KEGG object identifier [Term] id: EDAM:0002296 name: Gene name (AceView) namespace: identifier def: "Name of an entry (gene) from the AceView genes database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "AceView gene name" EXACT [] is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0002300 name: Gene name (NCBI) namespace: identifier def: "Name of an entry (gene) from the NCBI genes database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "NCBI gene name" EXACT [] is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0002740 name: Gene name (Genolist) namespace: identifier def: "Name of an entry (gene) from the Genolist genes database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Genolist gene name" EXACT [] is_a: EDAM:0001026 ! Gene symbol [Term] id: EDAM:0002743 name: Gene name (HUGO) namespace: identifier def: "Name of an entry (gene) from the HUGO database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001791 ! Gene name (HGNC) [Term] id: EDAM:0002771 name: HIX ID namespace: identifier def: "A unique identifier of gene cluster in the H-InvDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002737 name: FIG ID namespace: identifier def: "A unique identifier of gene in the NMPDR database." [EDAM:EBI "EMBRACE definition"] comment: A FIG ID consists of four parts: a prefix, genome id, locus type and id number. subset: identifier is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002774 name: Gene ID (JCVI) namespace: identifier def: "A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002738 name: Gene ID (Xenbase) namespace: identifier def: "A unique identifier of gene in the Xenbase database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002799 name: Gene ID (MfunGD) namespace: identifier def: "A unique identifier of gene in the MfunGD database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002739 name: Gene ID (Genolist) namespace: identifier def: "A unique identifier of gene in the Genolist database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001028 name: Gene identifier (NCBI RefSeq) namespace: identifier def: "An NCBI RefSeq unique identifier of a gene." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001027 ! NCBI gene ID [Term] id: EDAM:0001029 name: Gene identifier (NCBI UniGene) namespace: identifier def: "An NCBI UniGene unique identifier of a gene." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001104 ! Sequence cluster ID (UniGene) [Term] id: EDAM:0001030 name: Gene identifier (Entrez) namespace: identifier def: "An Entrez unique identifier of a gene." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_obsolete: true consider: EDAM:0001027 ! NCBI gene ID [Term] id: EDAM:0001886 name: Blattner number namespace: identifier def: "The blattner identifier for a gene." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:Blattner_number is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001027 name: Gene ID (NCBI) namespace: identifier def: "An NCBI unique identifier of a gene." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Gene identifier (NCBI)" EXACT [] synonym: "NCBI gene ID" EXACT [] synonym: "NCBI geneid" EXACT [] synonym: "Gene identifier (Entrez)" EXACT [] synonym: "Entrez gene ID" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID is_a: EDAM:0002295 ! Gene ID is_a: EDAM:0001098 ! RefSeq accession [Term] id: EDAM:0001031 name: Gene ID (CGD) namespace: identifier def: "Identifier of a gene or feature from the CGD database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "CGD ID" EXACT [] is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001032 name: Gene ID (DictyBase) namespace: identifier def: "Identifier of a gene from DictyBase." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001033 name: Gene ID (Ensembl) namespace: identifier def: "Unique identifier for a gene (or other feature) from the Ensembl database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Ensembl Gene ID" EXACT [] is_a: EDAM:0002295 ! Gene ID is_a: EDAM:0002610 ! Ensembl ID [Term] id: EDAM:0001034 name: Gene ID (SGD) namespace: identifier def: "Identifier of an entry from the SGD database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "SGD identifier" EXACT [] regex: "S[0-9]+" is_a: EDAM:0002295 ! Gene ID is_a: EDAM:0002632 ! SGD ID [Term] id: EDAM:0001885 name: Gene ID (GeneFarm) namespace: identifier def: "Identifier of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:GENEFARM_GeneID is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001907 name: Gene ID (KOME) namespace: identifier def: "Identifier of a gene from the KOME database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:GeneId is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001794 name: Gene ID (PlasmoDB) namespace: identifier def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001795 name: Gene ID (EcoGene) namespace: identifier def: "Identifier of a gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "EcoGene Accession" EXACT [] synonym: "EcoGene ID" EXACT [] is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002297 name: Gene ID (ECK) namespace: identifier def: "Identifier of an E. coli K-12 gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "E. coli K-12 gene identifier" EXACT [] synonym: "ECK accession" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK is_a: EDAM:0001795 ! Gene ID (EcoGene) [Term] id: EDAM:0001796 name: Gene ID (FlyBase) namespace: identifier def: "Gene identifier from FlyBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001802 name: Gene ID (Gramene) namespace: identifier def: "Gene identifier from Gramene database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001803 name: Gene ID (Virginia microbial) namespace: identifier def: "Gene identifier from Virginia Bioinformatics Institute microbial database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001804 name: Gene ID (SGN) namespace: identifier def: "Gene identifier from Sol Genomics Network." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001805 name: Gene ID (WormBase) namespace: identifier def: "Gene identifier used by WormBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase regex: "WBGene[0-9]{8}" is_a: EDAM:0002295 ! Gene ID is_a: EDAM:0002113 ! WormBase identifier [Term] id: EDAM:0001035 name: Gene ID (GeneDB) namespace: identifier def: "Identifier of a gene from the GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "GeneDB identifier" EXACT [] xref: Moby_namespace:GeneDB regex: "[a-zA-Z_0-9\.-]*" is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002285 name: Gene ID (MIPS) namespace: identifier def: "Identifier for genetic elements in MIPS database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "MIPS genetic element identifier" EXACT [] is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002298 name: Gene ID (HGNC) namespace: identifier def: "Identifier for a gene approved by the HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "HGNC ID" EXACT [] is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002642 name: Gene ID (miRBase) namespace: identifier def: "Identifier for a gene from the miRBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "miRNA name" EXACT [] synonym: "miRNA identifier" EXACT [] synonym: "miRNA ID" EXACT [] regex: "MI[0-9]{7}" is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002643 name: Gene ID (ZFIN) namespace: identifier def: "Identifier for a gene from the Zebrafish information network genome (ZFIN) database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "ZDB\-GENE\-[0-9]+\-[0-9]+" is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002759 name: Gene ID (VectorBase) namespace: identifier def: "Identifier for a gene from the VectorBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "VectorBase ID" EXACT [] is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002835 name: Gene ID (VBASE2) namespace: identifier def: "Identifier for a gene from the VBASE2 database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "VBASE2 ID" EXACT [] is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0001797 name: Gene ID (GeneDB Glossina morsitans) namespace: identifier def: "Gene identifier from Glossina morsitans GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans is_obsolete: true consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] id: EDAM:0001798 name: Gene ID (GeneDB Leishmania major) namespace: identifier def: "Gene identifier from Leishmania major GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor is_obsolete: true consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] id: EDAM:0001799 name: Gene ID (GeneDB Plasmodium falciparum) namespace: identifier def: "Gene identifier from Plasmodium falciparum GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum is_obsolete: true consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] id: EDAM:0001800 name: Gene ID (GeneDB Schizosaccharomyces pombe) namespace: identifier def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe is_obsolete: true consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] id: EDAM:0001801 name: Gene ID (GeneDB Trypanosoma brucei) namespace: identifier def: "Gene identifier from Trypanosoma brucei GeneDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei is_obsolete: true consider: EDAM:0001035 ! Gene ID (GeneDB) [Term] id: EDAM:0001887 name: Gene ID (MIPS Maize) namespace: identifier def: "Identifier for genetic elements in MIPS Maize database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "MIPS genetic element identifier (Maize)" EXACT [] xref: Moby_namespace:MIPS_GE_Maize is_obsolete: true consider: EDAM:0002285 ! Gene ID (MIPS) [Term] id: EDAM:0001888 name: Gene ID (MIPS Medicago) namespace: identifier def: "Identifier for genetic elements in MIPS Medicago database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "MIPS genetic element identifier (Medicago)" EXACT [] xref: Moby_namespace:MIPS_GE_Medicago is_obsolete: true consider: EDAM:0002285 ! Gene ID (MIPS) [Term] id: EDAM:0002751 name: GenomeReviews ID namespace: identifier def: "An identifier of a particular genome." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002903 ! Genome accession [Term] id: EDAM:0002786 name: NCBI Genome Project ID namespace: identifier def: "An identifier of a genome project assigned by NCBI." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002903 ! Genome accession [Term] id: EDAM:0002787 name: NCBI genome accession namespace: identifier def: "A unique identifier of a whole genome assigned by the NCBI." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002903 ! Genome accession [Term] id: EDAM:0002631 name: ACLAME ID namespace: identifier def: "An identifier of a mobile genetic element from the Aclame database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "mge:[0-9]+" is_a: EDAM:0002630 ! Mobile genetic element ID [Term] id: EDAM:0002128 name: Genetic code name namespace: identifier def: "Informal name for a genetic code, typically an organism name." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002127 ! Genetic code identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001039 name: SCOP domain identifier namespace: identifier def: "Identifier of a protein domain (or other node) from the SCOP database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001038 ! Protein domain ID relationship: is_identifier_of EDAM:0001554 ! SCOP node [Term] id: EDAM:0002700 name: CATH identifier namespace: identifier def: "Identifier of a protein domain (or other node) from the CATH database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001038 ! Protein domain ID relationship: is_identifier_of EDAM:0001553 ! CATH node [Term] id: EDAM:0002666 name: CDD ID namespace: identifier def: "Identifier of a conserved domain from the Conserved Domain Database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "cd[0-9]{5}" is_a: EDAM:0001038 ! Protein domain ID [Term] id: EDAM:0001041 name: SCOP concise classification string (sccs) namespace: identifier def: "A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification." [EDAM:EBI "EMBRACE definition"] comment: An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. subset: identifier is_a: EDAM:0001039 ! SCOP domain identifier [Term] id: EDAM:0001042 name: SCOP sunid namespace: identifier def: "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229." [EDAM:EBI "EMBRACE definition"] comment: A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. subset: identifier synonym: "sunid" EXACT [] synonym: "SCOP unique identifier" EXACT [] is_a: EDAM:0001039 ! SCOP domain identifier [Term] id: EDAM:0001040 name: CATH domain ID namespace: identifier def: "Identifier of a protein domain from CATH." [EDAM:EBI "EMBRACE definition"] comment: For example '1nr3A00'. subset: identifier synonym: "CATH domain identifier" EXACT [] is_a: EDAM:0002700 ! CATH identifier [Term] id: EDAM:0001043 name: CATH node ID namespace: identifier def: "A code number identifying a node from the CATH database." [EDAM:EBI "EMBRACE definition"] comment: For example '3.30.1190.10.1.1.1.1.1'. subset: identifier synonym: "CATH code" EXACT [] synonym: "CATH node identifier" EXACT [] is_a: EDAM:0002700 ! CATH identifier [Term] id: EDAM:0002701 name: CATH node ID (family) namespace: identifier def: "A code number identifying a family from the CATH database." [EDAM:EBI "EMBRACE definition"] comment: For example '2.10.10.10'. subset: identifier is_a: EDAM:0001043 ! CATH node ID relationship: is_identifier_of EDAM:0001553 ! CATH node [Term] id: EDAM:0002619 name: RESID ID namespace: identifier def: "Identifier of a protein modification catalogued in the RESID database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "AA[0-9]{4}" is_a: EDAM:0002618 ! Protein modification ID [Term] id: EDAM:0002892 name: Cell type name namespace: identifier def: "The name of a type or group of cells." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002655 ! Cell type identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002656 name: NeuronDB ID namespace: identifier def: "A unique identifier of a neuron from the NeuronDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002893 ! Cell type accession [Term] id: EDAM:0002657 name: NeuroMorpho ID namespace: identifier def: "A unique identifier of a neuron from the NeuroMorpho database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[a-zA-Z_0-9]+" is_a: EDAM:0002893 ! Cell type accession [Term] id: EDAM:0001868 name: Taxon namespace: identifier def: "The name of a group of organisms belonging to the same taxonomic rank." [EDAM:EBI "EMBRACE definition"] comment: For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. subset: identifier synonym: "Taxonomy rank" EXACT [] synonym: "Taxonomic rank" EXACT [] xref: Moby:BriefTaxonConcept xref: Moby:PotentialTaxon is_a: EDAM:0002909 ! Organism name [Term] id: EDAM:0001872 name: Taxonomic classification namespace: identifier def: "The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature." [EDAM:EBI "EMBRACE definition"] comment: Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. subset: identifier synonym: "Taxonomic name" EXACT [] synonym: "Taxonomic information" EXACT [] xref: Moby:GCP_Taxon xref: Moby:TaxonName xref: Moby:TaxonTCS xref: Moby:TaxonScientificName xref: Moby:iANT_organism-xml is_a: EDAM:0002909 ! Organism name [Term] id: EDAM:0001874 name: Genbank common name namespace: identifier def: "Common name for an organism as used in the GenBank database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002909 ! Organism name [Term] id: EDAM:0001873 name: iHOP organism ID namespace: identifier def: "A unique identifier for an organism used in the iHOP database." [EDAM:EBI "EMBRACE definition"] subset: identifier xref: Moby_namespace:iHOPorganism is_a: EDAM:0002908 ! Organism accession [Term] id: EDAM:0002102 name: KEGG organism code namespace: identifier def: "A three-letter code used in the KEGG databases to uniquely identify organisms." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002909 ! Organism name is_a: EDAM:0001154 ! KEGG object identifier [Term] id: EDAM:0002593 name: BRENDA organism ID namespace: identifier def: "A unique identifier for an organism used in the BRENDA database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002908 ! Organism accession [Term] id: EDAM:0002913 name: Virus identifier namespace: identifier def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001869 ! Organism identifier relationship: is_identifier_of EDAM:0002307 ! Virus annotation [Term] id: EDAM:0002785 name: Virus ID namespace: identifier def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002913 ! Virus identifier is_a: EDAM:0002908 ! Organism accession [Term] id: EDAM:0002836 name: DPVweb ID namespace: identifier def: "A unique identifier for a virus from the DPVweb database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "DPVweb virus ID" EXACT [] is_a: EDAM:0002785 ! Virus ID [Term] id: EDAM:0002784 name: RNAVirusDB ID namespace: identifier def: "A unique identifier for a virus from the RNAVirusDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002785 ! Virus ID ! Could list (or cross-reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. [Term] id: EDAM:0001875 name: NCBI taxon namespace: identifier def: "The name of a taxon from the NCBI taxonomy database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001868 ! Taxon [Term] id: EDAM:0002594 name: UniGene taxon namespace: identifier def: "The name of a taxon using the controlled vocabulary of the UniGene database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "UniGene organism abbreviation" EXACT [] is_a: EDAM:0001868 ! Taxon [Term] id: EDAM:0002595 name: UTRdb taxon namespace: identifier def: "The name of a taxon using the controlled vocabulary of the UTRdb database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001868 ! Taxon [Term] id: EDAM:0001044 name: Kingdom name namespace: identifier def: "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001868 ! Taxon [Term] id: EDAM:0001870 name: Genus name namespace: identifier def: "The name of a genus of organism." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001868 ! Taxon [Term] id: EDAM:0002732 name: Family name namespace: identifier def: "The name of a family of organism." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001868 ! Taxon [Term] id: EDAM:0001045 name: Species name namespace: identifier def: "The name of a species (typically a taxonomic group) of organism." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Organism species" EXACT [] is_a: EDAM:0001868 ! Taxon [Term] id: EDAM:0002733 name: Genus name (virus) namespace: identifier def: "The name of a genus of viruses." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001870 ! Genus name [Term] id: EDAM:0002734 name: Family name (virus) namespace: identifier def: "The name of a family of viruses." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0002732 ! Family name [Term] id: EDAM:0002317 name: Cell line name (exact) namespace: identifier def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002316 ! Cell line name [Term] id: EDAM:0002318 name: Cell line name (truncated) namespace: identifier def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002316 ! Cell line name [Term] id: EDAM:0002319 name: Cell line name (no punctuation) namespace: identifier def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002316 ! Cell line name [Term] id: EDAM:0002320 name: Cell line name (assonant) namespace: identifier def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002316 ! Cell line name [Term] id: EDAM:0001056 name: Database name namespace: identifier def: "The name of a biological or bioinformatics database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001048 ! Database identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002149 name: Database category name namespace: identifier def: "The name of a category of biological or bioinformatics database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001056 ! Database name [Term] id: EDAM:0001057 name: Sequence database name namespace: identifier def: "The name of a molecular sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001056 ! Database name [Term] id: EDAM:0002735 name: Database name (SwissRegulon) namespace: identifier def: "The name of a SwissRegulon database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001056 ! Database name [Term] id: EDAM:0002747 name: Database name (CMD) namespace: identifier def: "The name of a subdivision of the Collagen Mutation Database (CMD) database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001056 ! Database name [Term] id: EDAM:0002748 name: Database name (Osteogenesis) namespace: identifier def: "The name of a subdivision of the Osteogenesis database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001056 ! Database name [Term] id: EDAM:0001058 name: Enumerated file name namespace: identifier def: "The name of a file (of any type) with restricted possible values." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001050 ! File name [Term] id: EDAM:0001059 name: File name extension namespace: identifier def: "The extension of a file name." [EDAM:EBI "EMBRACE definition"] comment: A file extension is the characters appearing after the final '.' in the file name. subset: identifier is_a: EDAM:0001050 ! File name [Term] id: EDAM:0001060 name: File base name namespace: identifier def: "The base name of a file." [EDAM:EBI "EMBRACE definition"] comment: A file base name is the file name stripped of its directory specification and extension. subset: identifier is_a: EDAM:0001050 ! File name [Term] id: EDAM:0001061 name: QSAR descriptor name namespace: identifier def: "Name of a QSAR descriptor." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002110 ! Molecular property identifier is_a: EDAM:0002099 ! Name relationship: is_identifier_of EDAM:0000847 ! QSAR descriptor [Term] id: EDAM:0002288 name: Sequence identifier (protein) namespace: identifier def: "An identifier of protein sequence(s) or protein sequence database entries." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001096 ! Sequence accession (protein) [Term] id: EDAM:0002289 name: Sequence identifier (nucleic acid) namespace: identifier def: "An identifier of nucleotide sequence(s) or nucleotide sequence database entries." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001097 ! Sequence accession (nucleic acid) [Term] id: EDAM:0001093 name: Sequence accession namespace: identifier def: "A persistent, unique identifier of a molecular sequence database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Sequence accession number" EXACT [] is_a: EDAM:0001063 ! Sequence identifier is_a: EDAM:0002091 ! Accession is_a: EDAM:0002914 ! Sequence feature metadata [Term] id: EDAM:0002154 name: Sequence name namespace: identifier def: "Any arbitrary name of a molecular sequence." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001063 ! Sequence identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001095 name: EMBOSS Uniform Sequence Address namespace: identifier def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"] subset: data synonym: "USA" EXACT [] is_a: EDAM:0001063 ! Sequence identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002291 name: UniProt ID namespace: identifier def: "An identifier of a polypeptide in the UniProt database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "UniProt identifier" EXACT [] is_a: EDAM:0001096 ! Sequence accession (protein) relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0001100 name: PIR identifier namespace: identifier def: "An identifier of PIR sequence database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "PIR accession number" EXACT [] synonym: "PIR ID" EXACT [] is_a: EDAM:0001096 ! Sequence identifier (protein) relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0001101 name: TREMBL accession namespace: identifier def: "Identifier of a TREMBL sequence database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0003021 ! UniProt accession synonym: "TREMBL accession number" EXACT [] synonym: "TREMBL ID" EXACT [] relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0002621 name: TAIR accession (protein) namespace: identifier def: "Identifier of a protein sequence from the TAIR database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "AASequence:[0-9]{10}" is_a: EDAM:0001096 ! Sequence identifier (protein) is_a: EDAM:0002387 ! TAIR accession relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0002290 name: EMBL accession namespace: identifier alt_id: EDAM:0001107 def: "An accession number of an entry from the EMBL sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "EMBL accession number" EXACT [] synonym: "EMBL identifier" EXACT [] synonym: "EMBL ID" EXACT [] is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ ID [Term] id: EDAM:0002292 name: GenBank accession namespace: identifier alt_id: EDAM:0001108 def: "Accession number of an entry from the GenBank sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ ID synonym: "GenBank accession number" EXACT [] synonym: "GenBank identifier" EXACT [] synonym: "GenBank ID" EXACT [] [Term] id: EDAM:0002916 name: DDBJ accession namespace: identifier alt_id: EDAM:0001109 def: "An identifier of an entry from the DDBJ sequence database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ ID synonym: "DDBJ accession number" EXACT [] synonym: "DDBJ identifier" EXACT [] synonym: "DDBJ ID" EXACT [] [Term] id: EDAM:0001855 name: Clone ID namespace: identifier def: "An identifier of a clone (cloned molecular sequence) from a database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002769 ! Transcript ID [Term] id: EDAM:0002386 name: EPD ID namespace: identifier def: "Identifier of an entry (promoter) from the EPD database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "EPD identifier" EXACT [] is_a: EDAM:0002727 ! Promoter ID [Term] id: EDAM:0002741 name: ABS ID namespace: identifier def: "Identifier of an entry (promoter) from the ABS database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "ABS identifier" EXACT [] is_a: EDAM:0002727 ! Promoter ID [Term] id: EDAM:0001096 name: Sequence accession (protein) namespace: identifier def: "Accession number of a protein sequence database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Protein sequence accession number" EXACT [] is_a: EDAM:0001093 ! Sequence accession relationship: is_identifier_of EDAM:0002976 ! Protein sequence [Term] id: EDAM:0001097 name: Sequence accession (nucleic acid) namespace: identifier def: "Accession number of a nucleotide sequence database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Nucleotide sequence accession number" EXACT [] is_a: EDAM:0001093 ! Sequence accession relationship: is_identifier_of EDAM:0002977 ! Nucleotide sequence [Term] id: EDAM:0002362 name: Sequence accession (hybrid) namespace: identifier def: "Accession number of a nucleotide or protein sequence database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001093 ! Sequence accession relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0001098 name: RefSeq accession namespace: identifier def: "Accession number of a RefSeq database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+" is_a: EDAM:0002362 ! Sequence accession (hybrid) synonym: "RefSeq ID" EXACT [] [Term] id: EDAM:0002314 name: GI number namespace: identifier def: "A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record." [EDAM:EBI "EMBRACE definition"] comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. subset: identifier synonym: "NCBI GI number" EXACT [] synonym: "gi number" EXACT [] is_a: EDAM:0002362 ! Sequence accession (hybrid) [Term] id: EDAM:0002315 name: NCBI version namespace: identifier def: "An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number." [EDAM:EBI "EMBRACE definition"] comment: Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. subset: identifier synonym: "accession.version" EXACT [] synonym: "NCBI accession.version" EXACT [] is_a: EDAM:0002362 ! Sequence accession (hybrid) [Term] id: EDAM:0002385 name: RefSeq accession (protein) namespace: identifier def: "Accession number of a protein from the RefSeq database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001098 ! RefSeq accession synonym: "RefSeq protein ID" EXACT [] [Term] id: EDAM:0002327 name: GI number (protein) namespace: identifier def: "A unique identifier assigned to NCBI protein sequence records." [EDAM:EBI "EMBRACE definition"] comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. subset: identifier synonym: "protein gi number" EXACT [] synonym: "protein gi" EXACT [] is_a: EDAM:0002314 ! GI number [Term] id: EDAM:0001099 name: UniProt accession (extended) namespace: identifier def: "Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0 ! regex: "([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9])" ! example: Q7M1G0 P43353-2 P01012.107 ! Q9C199 A5A6J6 is_a: EDAM:0003021 ! UniProt accession relationship: is_identifier_of EDAM:0001208 ! Protein sequence relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0003021 name: UniProt accession namespace: identifier def: "Accession number of a UniProt (protein sequence) database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier ! regex: "([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9])" ! example: P43353 Q9C199 A5A6J6 synonym: "UniProtKB accession number" EXACT [] synonym: "UniProtKB entry accession" EXACT [] synonym: "UniProt accession number" EXACT [] synonym: "Swiss-Prot accession" EXACT [] is_a: EDAM:0002291 ! UniProt ID [Term] id: EDAM:0002392 name: UniParc accession namespace: identifier def: "Accession number of a UniParc (protein sequence) database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "UniParc ID" EXACT [] synonym: "UPI" EXACT [] regex: "UPI[A-F0-9]{10}" is_a: EDAM:0002291 ! UniProt ID [Term] id: EDAM:0002915 name: Gramene identifier namespace: identifier def: "Identifier of a Gramene database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001096 ! Sequence accession (protein) [Term] id: EDAM:0001102 name: Gramene primary identifier namespace: identifier def: "Primary identifier of a Gramene database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Gramene primary ID" EXACT [] is_a: EDAM:0002915 ! Gramene identifier [Term] id: EDAM:0002293 name: Gramene secondary identifier namespace: identifier def: "Secondary (internal) identifier of a Gramene database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Gramene secondary ID" EXACT [] synonym: "Gramene internal ID" EXACT [] synonym: "Gramene internal identifier" EXACT [] is_a: EDAM:0002915 ! Gramene identifier [Term] id: EDAM:0002384 name: IPI protein ID namespace: identifier def: "Identifier of a protein entry catalogued in the International Protein Index (IPI) database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "IPI[0-9]{8}" is_a: EDAM:0001096 ! Sequence accession (protein) [Term] id: EDAM:0002728 name: EST accession namespace: identifier def: "Identifier of an EST sequence." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001855 ! Clone ID [Term] id: EDAM:0001103 name: EMBL/GenBank/DDBJ ID namespace: identifier def: "Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001097 ! Sequence accession (nucleic acid) [Term] id: EDAM:0002389 name: UniSTS accession namespace: identifier def: "Identifier of an entry from the UniSTS database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001097 ! Sequence accession (nucleic acid) [Term] id: EDAM:0002390 name: UNITE accession namespace: identifier def: "Identifier of an entry from the UNITE database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001097 ! Sequence accession (nucleic acid) [Term] id: EDAM:0002391 name: UTR accession namespace: identifier def: "Identifier of an entry from the UTR database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001097 ! Sequence accession (nucleic acid) [Term] id: EDAM:0002393 name: mFLJ/mKIAA number namespace: identifier def: "Identifier of an entry from the Rouge or HUGE databases." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002295 ! Gene ID [Term] id: EDAM:0002781 name: REDIdb ID namespace: identifier def: "Identifier of an entry from the RNA editing database (REDIdb)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001097 ! Sequence accession (nucleic acid) [Term] id: EDAM:0002729 name: COGEME EST ID namespace: identifier def: "Identifier of an EST sequence from the COGEME database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002728 ! EST accession [Term] id: EDAM:0002730 name: COGEME unisequence ID namespace: identifier def: "Identifier of a unisequence from the COGEME database." [EDAM:EBI "EMBRACE definition"] comment: A unisequence is a single sequence assembled from ESTs. subset: identifier is_a: EDAM:0002728 ! EST accession [Term] id: EDAM:0002798 name: MaizeDB ID namespace: identifier def: "Identifier of an EST sequence from the MaizeDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002728 ! EST accession [Term] id: EDAM:0001105 name: dbEST accession namespace: identifier def: "Identifier of a dbEST database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "dbEST ID" EXACT [] is_a: EDAM:0002292 ! GenBank accession is_a: EDAM:0002728 ! EST accession [Term] id: EDAM:0002704 name: Clone ID (IMAGE) namespace: identifier def: "A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence)." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "I.M.A.G.E. cloneID" EXACT [] synonym: "IMAGE cloneID" EXACT [] is_a: EDAM:0001855 ! Clone ID [Term] id: EDAM:0002803 name: Clone ID (RefSeq) namespace: identifier def: "A unique identifier of a cDNA molecule catalogued in the RefSeq database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001855 ! Clone ID is_a: EDAM:0001098 ! RefSeq accession [Term] id: EDAM:0001110 name: EMBOSS sequence type namespace: identifier def: "The EMBOSS type of a molecular sequence." [EDAM:EBI "EMBRACE definition"] comment: See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. subset: identifier is_obsolete: true consider: EDAM:0001094 ! Sequence type [Term] id: EDAM:0001106 name: dbSNP ID namespace: identifier def: "Identifier of a dbSNP database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "dbSNP identifier" EXACT [] is_a: EDAM:0002294 ! Sequence variation ID [Term] id: EDAM:0002805 name: GeneSNP ID namespace: identifier def: "Identifier of a GeneSNP database entry." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002294 ! Sequence variation ID [Term] id: EDAM:0001112 name: Sequence cluster ID namespace: identifier def: "An identifier of a cluster of molecular sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001064 ! Sequence set ID relationship: is_identifier_of EDAM:0001235 ! Sequence cluster [Term] id: EDAM:0002346 name: Sequence cluster ID (UniRef) namespace: identifier def: "Unique identifier of an entry from the UniRef database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "UniRef entry accession" EXACT [] synonym: "UniRef cluster id" EXACT [] is_a: EDAM:0001112 ! Sequence cluster ID [Term] id: EDAM:0001113 name: Sequence cluster ID (COG) namespace: identifier def: "Unique identifier of an entry from the COG database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "COG ID" EXACT [] is_a: EDAM:0001112 ! Sequence cluster ID [Term] id: EDAM:0001104 name: Sequence cluster ID (UniGene) namespace: identifier def: "A unique identifier of an entry (gene cluster) from the NCBI UniGene database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "UniGene ID" EXACT [] synonym: "UniGene identifier" EXACT [] synonym: "UniGene cluster ID" EXACT [] synonym: "UniGene cluster id" EXACT [] is_a: EDAM:0001112 ! Sequence cluster ID [Term] id: EDAM:0002220 name: Sequence cluster ID (SYSTERS) namespace: identifier def: "Unique identifier of a sequence cluster from the SYSTERS database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "SYSTERS cluster ID" EXACT [] is_a: EDAM:0001112 ! Sequence cluster ID [Term] id: EDAM:0002612 name: Sequence cluster ID (CluSTr) namespace: identifier def: "Unique identifier of a sequence cluster from the CluSTr database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "CluSTr cluster ID" EXACT [] synonym: "CluSTr ID" EXACT [] regex: "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?" is_a: EDAM:0001112 ! Sequence cluster ID [Term] id: EDAM:0002347 name: Sequence cluster ID (UniRef100) namespace: identifier def: "Unique identifier of an entry from the UniRef100 database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "UniRef100 entry accession" EXACT [] synonym: "UniRef100 cluster id" EXACT [] is_a: EDAM:0002346 ! Sequence cluster ID (UniRef) [Term] id: EDAM:0002348 name: Sequence cluster ID (UniRef90) namespace: identifier def: "Unique identifier of an entry from the UniRef90 database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "UniRef90 entry accession" EXACT [] synonym: "UniRef90 cluster id" EXACT [] is_a: EDAM:0002346 ! Sequence cluster ID (UniRef) [Term] id: EDAM:0002349 name: Sequence cluster ID (UniRef50) namespace: identifier def: "Unique identifier of an entry from the UniRef50 database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "UniRef50 entry accession" EXACT [] synonym: "UniRef50 cluster id" EXACT [] is_a: EDAM:0002346 ! Sequence cluster ID (UniRef) [Term] id: EDAM:0002761 name: UTRSite ID namespace: identifier def: "Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001114 ! Sequence motif identifier [Term] id: EDAM:0001116 name: ELM ID namespace: identifier def: "Identifier of an entry from the ELMdb database of protein functional sites." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001114 ! Sequence motif identifier [Term] id: EDAM:0001117 name: Prosite accession number namespace: identifier def: "Accession number of an entry from the Prosite database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Prosite ID" EXACT [] regex: "PS[0-9]{5}" is_a: EDAM:0001114 ! Sequence motif identifier [Term] id: EDAM:0002714 name: CDD PSSM-ID namespace: identifier def: "Unique identifier of a position-specific scoring matrix from the CDD database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001115 ! Sequence profile ID [Term] id: EDAM:0001118 name: HMMER hidden Markov model ID namespace: identifier def: "Unique identifier or name of a HMMER hidden Markov model." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001115 ! Sequence profile ID relationship: is_identifier_of EDAM:0001364 ! Hidden Markov model [Term] id: EDAM:0001119 name: JASPAR profile ID namespace: identifier def: "Unique identifier or name of a profile from the JASPAR database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001115 ! Sequence profile ID [Term] id: EDAM:0002150 name: Sequence profile name namespace: identifier def: "Name of a sequence profile." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0001115 ! Sequence profile ID [Term] id: EDAM:0001123 name: TreeBASE study accession number namespace: identifier def: "Accession number of an entry from the TreeBASE database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001068 ! Phylogenetic tree ID [Term] id: EDAM:0001124 name: TreeFam accession number namespace: identifier def: "Accession number of an entry from the TreeFam database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001068 ! Phylogenetic tree ID [Term] id: EDAM:0001126 name: Comparison matrix name namespace: identifier def: "Unique name or identifier of a comparison matrix." [EDAM:EBI "EMBRACE definition"] comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. subset: identifier synonym: "Substitution matrix name" EXACT [] is_a: EDAM:0001069 ! Comparison matrix identifier is_a: EDAM:0002099 ! Name relationship: is_identifier_of EDAM:0000874 ! Comparison matrix [Term] id: EDAM:0001127 name: PDB ID namespace: identifier def: "An identifier of an entry from the PDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "PDB identifier" EXACT [] synonym: "PDBID" EXACT [] regex: "[a-zA-Z_0-9]{4}" is_a: EDAM:0001070 ! Structure ID [Term] id: EDAM:0002667 name: MMDB ID namespace: identifier def: "An identifier of an entry from the MMDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "MMDB accession" EXACT [] regex: "[0-9]{1,5}" is_a: EDAM:0001070 ! Structure ID [Term] id: EDAM:0002793 name: SISYPHUS ID namespace: identifier def: "Identifier of an entry from the SISYPHUS database of tertiary structure alignments." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001072 ! Structure alignment ID [Term] id: EDAM:0001128 name: AAindex ID namespace: identifier def: "Identifier of an entry from the AAindex database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001073 ! Amino acid index ID [Term] id: EDAM:0001074 name: Protein interaction ID namespace: identifier def: "Identifier of a report of protein interactions from a protein interaction database (typically)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002627 ! Molecular interaction ID [Term] id: EDAM:0002628 name: BioGRID interaction ID namespace: identifier def: "A unique identifier of an interaction from the BioGRID database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002627 ! Molecular interaction ID [Term] id: EDAM:0002636 name: MatrixDB interaction ID namespace: identifier def: "A unique identifier of an interaction from the MatrixDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)" is_a: EDAM:0002627 ! Molecular interaction ID [Term] id: EDAM:0001129 name: BIND accession number namespace: identifier def: "Accession number of an entry from the BIND database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001074 ! Protein interaction ID [Term] id: EDAM:0001130 name: IntAct accession number namespace: identifier def: "Accession number of an entry from the IntAct database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "EBI\-[0-9]+" is_a: EDAM:0001074 ! Protein interaction ID [Term] id: EDAM:0002302 name: STRING ID namespace: identifier def: "Unique identifier of an entry from the STRING database of protein-protein interactions." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001074 ! Protein interaction ID [Term] id: EDAM:0002615 name: MINT ID namespace: identifier def: "Unique identifier of an entry from the MINT database of protein-protein interactions." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "MINT\-[0-9]{1,5}" is_a: EDAM:0001074 ! Protein interaction ID [Term] id: EDAM:0002616 name: DIP ID namespace: identifier def: "Unique identifier of an entry from the DIP database of protein-protein interactions." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "DIP[\:\-][0-9]{3}[EN]" is_a: EDAM:0001074 ! Protein interaction ID [Term] id: EDAM:0002668 name: iRefIndex ID namespace: identifier def: "Unique identifier of an entry from the iRefIndex database of protein-protein interactions." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0001074 ! Protein interaction ID [Term] id: EDAM:0001076 name: Codon usage table name namespace: identifier def: "Unique name of a codon usage table." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002111 ! Codon usage table identifier is_a: EDAM:0002099 ! Name relationship: is_identifier_of EDAM:0001597 ! Codon usage table relationship: is_identifier_of EDAM:0001598 ! Genetic code [Term] id: EDAM:0002356 name: RFAM accession namespace: identifier def: "Stable accession number of an entry (RNA family) from the RFAM database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002355 ! RNA family identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002606 name: RFAM name namespace: identifier def: "Name (not necessarily stable) an entry (RNA family) from the RFAM database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002355 ! RNA family identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002766 name: HAMAP ID namespace: identifier def: "Name of a protein family from the HAMAP database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0001132 name: InterPro entry name namespace: identifier def: "Name of an InterPro entry, usually indicating the type of protein matches for that entry." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001131 ! Protein family name relationship: is_identifier_of EDAM:0001355 ! Protein signature [Term] id: EDAM:0001133 name: InterPro accession namespace: identifier def: "Primary accession number of an InterPro entry." [EDAM:EBI "EMBRACE definition"] comment: Every InterPro entry has a unique accession number to provide a persistent citation of database records. subset: identifier synonym: "InterPro primary accession number" EXACT [] synonym: "InterPro primary accession" EXACT [] regex: "IPR[0-9]{6}" ! example: IPR015590 is_a: EDAM:0002910 ! Protein family accession relationship: is_identifier_of EDAM:0001355 ! Protein signature [Term] id: EDAM:0001134 name: InterPro secondary accession namespace: identifier def: "Secondary accession number of an InterPro entry." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "InterPro secondary accession number" EXACT [] is_a: EDAM:0001133 ! InterPro accession relationship: is_identifier_of EDAM:0001355 ! Protein signature [Term] id: EDAM:0001135 name: Gene3D ID namespace: identifier def: "Unique identifier of an entry from the Gene3D database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0001136 name: PIRSF ID namespace: identifier def: "Unique identifier of an entry from the PIRSF database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PIRSF[0-9]{6}" is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0001137 name: PRINTS code namespace: identifier def: "The unique identifier of an entry in the PRINTS database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PR[0-9]{5}" is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0001138 name: Pfam accession number namespace: identifier def: "Accession number of a Pfam entry." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PF[0-9]{5}" is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0002758 name: Pfam clan ID namespace: identifier def: "Accession number of a Pfam clan." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "CL[0-9]{4}" is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0002757 name: Pfam domain name namespace: identifier def: "Name of a domain from the Pfam database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PF[0-9]{5}" is_a: EDAM:0001131 ! Protein family name [Term] id: EDAM:0002782 name: SMART domain name namespace: identifier def: "Name of a domain from the SMART database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001131 ! Protein family name [Term] id: EDAM:0001139 name: SMART accession number namespace: identifier def: "Accession number of an entry from the SMART database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "SM[0-9]{5}" is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0001140 name: Superfamily hidden Markov model number namespace: identifier def: "Unique identifier (number) of a hidden Markov model from the Superfamily database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0001141 name: TIGRFam ID namespace: identifier def: "Accession number of an entry (family) from the TIGRFam database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "TIGRFam accession number" EXACT [] is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0001142 name: ProDom accession number namespace: identifier def: "A ProDom domain family accession number." [EDAM:EBI "EMBRACE definition"] comment: ProDom is a protein domain family database. subset: identifier regex: "PD[0-9]+" is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0002614 name: TCDB ID namespace: identifier def: "A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins." [EDAM:EBI "EMBRACE definition"] comment: OBO file for regular expression. subset: identifier synonym: "TC number" EXACT [] regex: "[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+" is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0002731 name: Protein family ID (GeneFarm) namespace: identifier def: "Accession number of an entry (family) from the TIGRFam database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "GeneFarm family ID" EXACT [] is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0002783 name: Protein family ID (PANTHER) namespace: identifier def: "Accession number of an entry (family) from the PANTHER database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Panther family ID" EXACT [] is_a: EDAM:0002910 ! Protein family accession [Term] id: EDAM:0001143 name: TRANSFAC accession number namespace: identifier def: "Identifier of an entry from the TRANSFAC database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002911 ! Transcription factor accession [Term] id: EDAM:0002716 name: DBD ID namespace: identifier def: "Identifier of a predicted transcription factor from the DBD database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002911 ! Transcription factor accession [Term] id: EDAM:0002742 name: AraC-XylS ID namespace: identifier def: "Identifier of a transcription factor from the AraC-XylS database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002911 ! Transcription factor accession [Term] id: EDAM:0002755 name: Transcription factor name namespace: identifier def: "The name of a transcription factor." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001077 ! Transcription factor identifier is_a: EDAM:0001009 ! Protein name [Term] id: EDAM:0001144 name: ArrayExpress accession number namespace: identifier def: "Accession number of an entry from the ArrayExpress database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "ArrayExpress experiment ID" EXACT [] regex: "[AEP]-[a-zA-Z_0-9]{4}-[0-9]+" is_a: EDAM:0001078 ! Microarray experiment annotation ID [Term] id: EDAM:0001145 name: PRIDE experiment accession number namespace: identifier def: "PRIDE experiment accession number." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0001078 ! Microarray experiment annotation ID [Term] id: EDAM:0002710 name: CleanEx dataset code namespace: identifier def: "An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001078 ! Microarray experiment annotation ID [Term] id: EDAM:0001146 name: EMDB ID namespace: identifier def: "Identifier of an entry from the EMDB electron microscopy database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001079 ! Electron microscopy model ID [Term] id: EDAM:0001147 name: GEO accession number namespace: identifier def: "Accession number of an entry from the GEO database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "o^GDS[0-9]+" is_a: EDAM:0001080 ! Gene expression report ID [Term] id: EDAM:0001148 name: GermOnline ID namespace: identifier def: "Identifier of an entry from the GermOnline database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001080 ! Gene expression report ID [Term] id: EDAM:0001149 name: EMAGE ID namespace: identifier def: "Identifier of an entry from the EMAGE database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001080 ! Gene expression report ID [Term] id: EDAM:0002709 name: CleanEx entry name namespace: identifier def: "An identifier of a gene expression profile from the CleanEx database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001080 ! Gene expression report ID [Term] id: EDAM:0001150 name: Disease ID namespace: identifier def: "Identifier of an entry from a database of disease." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0001622 ! Disease annotation [Term] id: EDAM:0001151 name: HGVbase ID namespace: identifier def: "Identifier of an entry from the HGVbase database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001081 ! Genotype and phenotype annotation ID [Term] id: EDAM:0001152 name: HIVDB identifier namespace: identifier def: "Identifier of an entry from the HIVDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0000842 ! Identifier [Term] id: EDAM:0001153 name: OMIM ID namespace: identifier def: "Identifier of an entry from the OMIM database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[*#+%^]?[0-9]{6}" is_a: EDAM:0001081 ! Genotype and phenotype annotation ID [Term] id: EDAM:0002611 name: ICD identifier namespace: identifier def: "An identifier of a disease from the International Classification of Diseases (ICD) database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[A-Z][0-9]+(\.[-[0-9]+])?" is_a: EDAM:0001150 ! Disease ID relationship: is_identifier_of EDAM:0001622 ! Disease annotation [Term] id: EDAM:0002800 name: Orpha number namespace: identifier def: "An identifier of a disease from the Orpha database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001150 ! Disease ID relationship: is_identifier_of EDAM:0001622 ! Disease annotation [Term] id: EDAM:0002651 name: Disease ID (PharmGKB) namespace: identifier def: "Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PA[0-9]+" is_a: EDAM:0001150 ! Disease ID is_a: EDAM:0002649 ! PharmGKB ID [Term] id: EDAM:0002383 name: EGA accession namespace: identifier def: "Identifier of an entry from the EGA database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002382 ! Genotype experiment ID [Term] id: EDAM:0002342 name: Pathway or network name namespace: identifier def: "The name of a biological pathway or network." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001082 ! Pathway or network identifier [Term] id: EDAM:0002365 name: Pathway or network accession namespace: identifier def: "A persistent, unique identifier of a biological pathway or network (typically a database entry)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001082 ! Pathway or network identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0002637 name: cPath ID namespace: identifier def: "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database." [EDAM:EBI "EMBRACE definition"] comment: These identifiers are unique within the cPath database, however, they are not stable between releases. subset: identifier regex: "[0-9]+" is_a: EDAM:0002109 ! Identifier (hybrid) is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0002659 name: Pathway ID (SMPDB) namespace: identifier def: "Identifier of a pathway from the Small Molecule Pathway Database (SMPDB)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "SMP[0-9]{5}" is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0002837 name: Pathway ID (BioSystems) namespace: identifier def: "Identifier of a pathway from the BioSystems pathway database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0002650 name: Pathway ID (PharmGKB) namespace: identifier def: "Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "PA[0-9]+" is_a: EDAM:0002365 ! Pathway or network accession is_a: EDAM:0002649 ! PharmGKB ID [Term] id: EDAM:0002345 name: Pathway ID (ConsensusPathDB) namespace: identifier def: "Identifier of a pathway from the ConsensusPathDB pathway database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002917 ! ConsensusPathDB identifier is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0002343 name: Pathway ID (KEGG) namespace: identifier def: "Identifier of a pathway from the KEGG pathway database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "KEGG pathway ID" EXACT [] regex: "[a-zA-Z_0-9]{2,3}[0-9]{5}" is_a: EDAM:0002365 ! Pathway or network accession is_a: EDAM:0001154 ! KEGG object identifier [Term] id: EDAM:0002344 name: Pathway ID (NCI-Nature) namespace: identifier def: "Identifier of a pathway from the NCI-Nature pathway database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[a-zA-Z_0-9]+" is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0001155 name: Pathway ID (reactome) namespace: identifier def: "Identifier of an entry from the Reactome database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Reactome ID" EXACT [] regex: "REACT_[0-9]+(\.[0-9]+)?" is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0001156 name: Pathway ID (aMAZE) namespace: identifier def: "Identifier of an entry from the aMAZE database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "aMAZE ID" EXACT [] is_obsolete: true consider: EDAM:0001082 ! Pathway or network identifier [Term] id: EDAM:0001157 name: Pathway ID (BioCyc) namespace: identifier def: "Identifier of an pathway from the BioCyc biological pathways database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "BioCyc pathway ID" EXACT [] is_a: EDAM:0002365 ! Pathway or network accession is_a: EDAM:0002104 ! BioCyc ID [Term] id: EDAM:0001158 name: Pathway ID (INOH) namespace: identifier def: "Identifier of an entry from the INOH database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "INOH identifier" EXACT [] is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0001159 name: Pathway ID (PATIKA) namespace: identifier def: "Identifier of an entry from the PATIKA database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "PATIKA ID" EXACT [] is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0001160 name: Pathway ID (CPDB) namespace: identifier def: "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB." [EDAM:EBI "EMBRACE definition"] comment: This term refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. subset: identifier synonym: "CPDB ID" EXACT [] is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0001161 name: Pathway ID (Panther) namespace: identifier def: "Identifier of a biological pathway from the Panther Pathways database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "Panther Pathways ID" EXACT [] regex: "PTHR[0-9]{5}" is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0002645 name: Pathway ID (Unipathway) namespace: identifier def: "Identifier of a biological pathway from the Unipathway database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "upaid" EXACT [] regex: "UPA[0-9]{5}" is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0002670 name: Pathway ID (DQCS) namespace: identifier def: "Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS)." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002365 ! Pathway or network accession [Term] id: EDAM:0002591 name: Brite hierarchy ID namespace: identifier def: "Identifier of an entry from the Brite database of biological hierarchies." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002891 ! Biological model accession [Term] id: EDAM:0001162 name: MIRIAM identifier namespace: identifier def: "Unique identifier of a MIRIAM data resource." [EDAM:EBI "EMBRACE definition"] comment: This is the identifier used internally by MIRIAM for a data type. For example 'MIR:00100005'. subset: identifier regex: "MIR:[0-9]{8}" is_a: EDAM:0002902 ! Data resource definition accession relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype [Term] id: EDAM:0001163 name: MIRIAM data type name namespace: identifier def: "The name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002253 ! Data resource definition name relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype [Term] id: EDAM:0002253 name: Data resource definition name namespace: identifier def: "The name of a data type." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001084 ! Data resource definition identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0002902 name: Data resource definition accession namespace: identifier def: "Accession of a data definition (catalogued in a database)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001084 ! Data resource definition identifier is_a: EDAM:0002091 ! Accession [Term] id: EDAM:0001164 name: MIRIAM URI namespace: identifier def: "The URI (URL or URN) of a data entity from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] comment: A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. For example: urn:miriam:pubmed:16333295 is the MIRIAM URI of the publication about MIRIAM, whereas 'urn:miriam:obo.go:GO%3A0045202' refers to GO. subset: identifier is_a: EDAM:0002902 ! Data resource definition accession is_a: EDAM:0001047 ! URI relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype [Term] id: EDAM:0001165 name: MIRIAM data type primary name namespace: identifier def: "The primary name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] comment: The primary name of a MIRIAM data type is taken from a controlled vocabulary. For example, a protein entity has the data type 'UniProt', an enzyme has the type 'Enzyme Nomenclature' etc. subset: identifier is_a: EDAM:0001163 ! MIRIAM data type name [Term] id: EDAM:0001166 name: MIRIAM data type synonymous name namespace: identifier def: "A synonymous name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"] comment: A synonymous name for a MIRIAM data type taken from a controlled vocabulary. subset: identifier is_a: EDAM:0001163 ! MIRIAM data type name [Term] id: EDAM:0002106 name: Reaction ID (BioCyc) namespace: identifier def: "Identifier of a biological reaction from the BioCyc reactions database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002108 ! Reaction ID is_a: EDAM:0002104 ! BioCyc ID relationship: has_topic EDAM:0000613 ! Peptides and amino acids [Term] id: EDAM:0002309 name: Reaction ID (SABIO-RK) namespace: identifier def: "Identifier of a biological reaction from the SABIO-RK reactions database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002108 ! Reaction ID [Term] id: EDAM:0002648 name: Reaction kinetics ID (SABIO-RK) namespace: identifier def: "Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002309 ! Reaction ID (SABIO-RK) [Term] id: EDAM:0002608 name: Reaction ID (KEGG) namespace: identifier def: "Identifier of a biological reaction from the KEGG reactions database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "R[0-9]+" is_a: EDAM:0002108 ! Reaction ID is_a: EDAM:0001154 ! KEGG object identifier [Term] id: EDAM:0002641 name: Reaction ID (MACie) namespace: identifier def: "Identifier of an enzyme reaction mechanism from the MACie database." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "MACie entry number" EXACT [] regex: "M[0-9]{4}" is_a: EDAM:0002108 ! Reaction ID [Term] id: EDAM:0002644 name: Reaction ID (Rhea) namespace: identifier def: "Identifier of an enzyme-catalysed reaction from the Rhea database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]{5}" is_a: EDAM:0002108 ! Reaction ID [Term] id: EDAM:0001167 name: Taverna workflow ID namespace: identifier def: "Unique identifier of a Taverna workflow." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001083 ! Workflow ID [Term] id: EDAM:0001170 name: Biological model name namespace: identifier def: "Name of a biological (mathematical) model." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001085 ! Biological model identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001171 name: BioModel ID namespace: identifier def: "Unique identifier of an entry from the BioModel database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "(BIOMD|MODEL)[0-9]{10}" is_a: EDAM:0002891 ! Biological model accession [Term] id: EDAM:0002669 name: ModelDB ID namespace: identifier def: "Unique identifier of an entry from the ModelDB database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]+" is_a: EDAM:0002891 ! Biological model accession [Term] id: EDAM:0002339 name: Ontology term name namespace: identifier def: "The name of a term in an ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0003025 ! Ontology term identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001175 name: BioPax term ID namespace: identifier def: "An identifier of a term from the BioPax ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001176 name: GO term ID namespace: identifier def: "An identifier of a term from The Gene Ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "GO term identifier" EXACT [] regex: "[0-9]{7}" "GO:[0-9]{7}" ! Isn't the string with "GO:" not an ID but an ontology reference + ID, in GO-style format? Check that with GO. Check the same with other ids having "regex.+:" (doi & ISBN should probably work both with & without(?)) ! regex: "GO:[0-9]{7}" is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001177 name: MeSH term ID namespace: identifier def: "An identifier of a term from the MeSH vocabulary." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001178 name: HGNC term ID namespace: identifier def: "An identifier of a term from the HGNC controlled vocabulary." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001179 name: NCBI taxonomy ID namespace: identifier def: "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[1-9][0-9]{0,8}" ! regex: "[0-9]+" synonym: "NCBI taxonomy term identifier" EXACT [] synonym: "NCBI tax ID" EXACT [] is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001180 name: Plant Ontology term ID namespace: identifier def: "An identifier of a term from the Plant Ontology (PO)." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001181 name: UMLS term ID namespace: identifier def: "An identifier of a term from the UMLS vocabulary." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001182 name: FMA term ID namespace: identifier def: "An identifier of a term from Foundational Model of Anatomy." [EDAM:EBI "EMBRACE definition"] comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. subset: identifier regex: "FMA:[0-9]+" is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001183 name: EMAP term ID namespace: identifier def: "An identifier of a term from the EMAP mouse ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001184 name: ChEBI term ID namespace: identifier def: "An identifier of a term from the ChEBI ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001185 name: MGED term ID namespace: identifier def: "An identifier of a term from the MGED ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0001186 name: myGrid term ID namespace: identifier def: "An identifier of a term from the myGrid ontology." [EDAM:EBI "EMBRACE definition"] comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides terms for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. subset: identifier is_a: EDAM:0001087 ! Ontology term ID [Term] id: EDAM:0002705 name: GO term ID (cellular compartment) namespace: identifier def: "An identifier of a 'cellular compartment' term from the Gene Ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "GO term identifier (cellular compartment)" EXACT [] regex: "[0-9]{7}" "GO:[0-9]{7}" is_a: EDAM:0001176 ! GO term ID [Term] id: EDAM:0002582 name: GO term ID (biological process) namespace: identifier def: "An identifier of a 'biological process' term from the the Gene Ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]{7}" "GO:[0-9]{7}" is_a: EDAM:0001176 ! GO term ID [Term] id: EDAM:0002583 name: GO term ID (molecular function) namespace: identifier def: "An identifier of a 'molecular function' term from the the Gene Ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "[0-9]{7}" "GO:[0-9]{7}" is_a: EDAM:0001176 ! GO term ID [Term] id: EDAM:0002581 name: GO term name namespace: identifier def: "The name of a term from the GO ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0002339 ! Ontology term name [Term] id: EDAM:0003026 name: GO term name (biological process) namespace: identifier def: "The name of a term for a biological process from the GO ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0002339 ! Ontology term name [Term] id: EDAM:0003027 name: GO term name (molecular function) namespace: identifier def: "The name of a term for a molecular function from the GO ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0002339 ! Ontology term name [Term] id: EDAM:0002584 name: GO term name (cellular component) namespace: identifier def: "The name of a term for a cellular component from the GO ontology." [EDAM:EBI "EMBRACE definition"] subset: identifier is_obsolete: true consider: EDAM:0002339 ! Ontology term name ! Different biological types of signature are listed below. Bioinformatics types (motif, profile, HMM etc) are given elsewhere [Term] id: EDAM:0001187 name: PubMed ID namespace: identifier def: "PubMed unique identifier of an article." [EDAM:EBI "EMBRACE definition"] subset: identifier synonym: "PMID" EXACT [] regex: "[1-9][0-9]{0,8}" ! regex: "^[0-9]+" is_a: EDAM:0001088 ! Article ID [Term] id: EDAM:0001188 name: Digital Object Identifier namespace: identifier def: "Digital Object Identifier (DOI) of a published article." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "(doi\:)?[0-9]{2}\.[0-9]{4}/.*" is_a: EDAM:0001088 ! Article ID [Term] id: EDAM:0001189 name: Medline UI namespace: identifier def: "Medline UI (unique identifier) of an article." [EDAM:EBI "EMBRACE definition"] comment: The use of Medline UI has been replaced by the PubMed unique identifier. subset: identifier synonym: "Medline unique identifier" EXACT [] is_a: EDAM:0001088 ! Article ID [Term] id: EDAM:0002634 name: ISBN namespace: identifier def: "The International Standard Book Number (ISBN) is for identifying printed books." [EDAM:EBI "EMBRACE definition"] subset: identifier regex: "(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)" is_a: EDAM:0002633 ! Book ID [Term] id: EDAM:0002374 name: Spot serial number namespace: identifier def: "Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002373 ! Spot ID [Term] id: EDAM:0002375 name: Spot ID (HSC-2DPAGE) namespace: identifier def: "Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002373 ! Spot ID [Term] id: EDAM:0002588 name: BlotBase blot ID namespace: identifier def: "Unique identifier of a blot from a Northern Blot from the BlotBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002587 ! Blot ID [Term] id: EDAM:0001046 name: Strain name namespace: identifier def: "The name of a strain of an organism variant, typically a plant, virus or bacterium." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002909 ! Organism name is_a: EDAM:0002379 ! Strain identifier [Term] id: EDAM:0002778 name: CCAP strain number namespace: identifier def: "The number of a strain of algae and protozoa from the CCAP database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002912 ! Strain accession [Term] id: EDAM:0002316 name: Cell line name namespace: identifier def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001046 ! Strain name [Term] id: EDAM:0002112 name: FlyBase primary identifier namespace: identifier def: "Primary identifier of an object from the FlyBase database." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0001089 ! FlyBase ID [Term] id: EDAM:0002174 name: FlyBase secondary identifier namespace: identifier def: "Secondary identifier of an object from the FlyBase database." [EDAM:EBI "EMBRACE definition"] comment: Secondary identifier are used to handle entries that were merged with or split from other entries in the database. subset: identifier is_a: EDAM:0001089 ! FlyBase ID [Term] id: EDAM:0001091 name: WormBase name namespace: identifier def: "Name of an object from the WormBase database, usually a human-readable name." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002113 ! WormBase identifier is_a: EDAM:0002099 ! Name [Term] id: EDAM:0001092 name: WormBase class namespace: identifier def: "Class of an object from the WormBase database." [EDAM:EBI "EMBRACE definition"] comment: A WormBase class describes the type of object such as 'sequence' or 'protein'. subset: identifier is_a: EDAM:0002113 ! WormBase identifier [Term] id: EDAM:0002254 name: OBO file format name namespace: identifier def: "Name of an OBO file format such as OBO-XML, plain and so on." [EDAM:EBI "EMBRACE definition"] subset: identifier is_a: EDAM:0002129 ! File format name ! Format [Term] id: EDAM:0002351 name: Undefined namespace: format def: "Debugging." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true [Term] id: EDAM:0002350 name: Format (typed) namespace: format def: "A broad class of format distinguished by the scientific nature of the data that is identified." [EDAM:EBI "EMBRACE definition"] comment: This term exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The term branch under 'Format (typed)' provides an alternative organisation of the terms nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All terms under here are already included under those branches. subset: format is_a: EDAM:0001915 ! Format [Term] id: EDAM:0002330 name: Text ! synonym: "Tabular format" SPECIALISATION WITHOUT WELL-DEFINED BORDERS(to find this for users who search for 'tabular format') [] namespace: format def: "Text format." [EDAM:EBI "EMBRACE definition"] comment: Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. subset: format is_a: EDAM:0001915 ! Format [Term] id: EDAM:0002331 name: HTML namespace: format def: "HTML format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001915 ! Format [Term] id: EDAM:0002332 name: XML namespace: format def: "Extensible Markup Language (XML) format." [EDAM:EBI "EMBRACE definition"] comment: Data in XML format can be serialised into text, or binary format. subset: format is_a: EDAM:0001915 ! Format [Term] id: EDAM:0002333 name: Binary namespace: format def: "Binary format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001915 ! Format [Term] id: EDAM:0002352 name: BioXSD synonym: "BioXSD XML format" EXACT [] namespace: format def: "BioXSD XML format of some of basic bioinformatics data types (sequences, sequence records, annotated sequences, sequence alignments, references to resources, and more)." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://bioxsd.org is_a: EDAM:0002332 ! XML [Term] id: EDAM:0002376 name: RDF namespace: format def: "Resource Description Framework (RDF) format." [EDAM:EBI "EMBRACE definition"] comment: Data in RDF format can be serialised into XML, text, or binary format. subset: format is_a: EDAM:0001915 ! Format [Term] id: EDAM:0002921 name: Sequence variation annotation format namespace: format def: "Format of sequence variation annotation." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000918 ! Nucleic acid features (variation) [Term] id: EDAM:0002919 name: Sequence annotation track format namespace: format def: "Format of a sequence annotation track." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0003002 ! Sequence annotation track [Term] id: EDAM:0002848 name: Bibliographic reference format namespace: format def: "Format of a bibliographic reference." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000970 ! Bibliographic reference relationship: is_format_of EDAM:0002849 ! Abstract [Term] id: EDAM:0002334 name: URI format namespace: format def: "Typical textual representation of a URI." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001047 ! URI [Term] id: EDAM:0001918 name: Atomic data format namespace: format def: "Data format for an individual atom." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001475 ! PDB database entry format [Term] id: EDAM:0001919 name: Sequence record format namespace: format def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0001920 name: Sequence feature annotation format namespace: format def: "Data format for molecular sequence feature information." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001255 ! Sequence features [Term] id: EDAM:0001921 name: Alignment format namespace: format def: "Data format for molecular sequence alignment information." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0002920 name: Alignment format (pair only) namespace: format def: "Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001921 ! Alignment format relationship: is_format_of EDAM:0001381 ! Sequence alignment (pair) [Term] id: EDAM:0002006 name: Phylogenetic tree format namespace: format def: "Data format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000872 ! Phylogenetic tree [Term] id: EDAM:0002033 name: Tertiary structure format namespace: format def: "Data format for a molecular tertiary structure." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) [Term] id: EDAM:0002034 name: Biological model format namespace: format def: "Data format for a biological model." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000950 ! Biological model [Term] id: EDAM:0002014 name: Sequence-profile alignment format namespace: format def: "Data format for a sequence-profile alignment." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000869 ! Sequence-profile alignment [Term] id: EDAM:0002562 name: Amino acid identifier format namespace: format def: "Text format (representation) of amino acid residues." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0000994 ! Amino acid identifier [Term] id: EDAM:0002017 name: Amino acid index format namespace: format def: "Data format for an amino acid index." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0003033 ! Matrix format relationship: is_format_of EDAM:0001501 ! Amino acid index [Term] id: EDAM:0002020 name: Article format namespace: format def: "Data format for a full-text scientific article." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Literature format" EXACT [] is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000971 ! Article [Term] id: EDAM:0002021 name: Text mining report format namespace: format def: "Data format for an abstract (report) from text mining." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000972 ! Text mining report [Term] id: EDAM:0002027 name: Enzyme kinetics report format namespace: format def: "Data format for reports on enzyme kinetics." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0002024 ! Enzyme kinetics data [Term] id: EDAM:0002030 name: Small molecule report format namespace: format def: "Format of a report on a chemical compound." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Chemical compound annotation format" EXACT [] is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000962 ! Small molecule annotation [Term] id: EDAM:0002031 name: Gene annotation format namespace: format def: "Format of a report on a particular locus, gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000916 ! Gene annotation [Term] id: EDAM:0002032 name: Workflow format namespace: format def: "Format of a workflow." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0002972 ! Workflow [Term] id: EDAM:0002035 name: Chemical formula format namespace: format def: "Text format of a chemical formula." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000846 ! Chemical formula [Term] id: EDAM:0002036 name: Phylogenetic character data format namespace: format def: "Format of raw (unplotted) phylogenetic data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000871 ! Phylogenetic character data [Term] id: EDAM:0003097 name: Protein domain classification format namespace: format def: "Format of data concerning the classification of the sequences and/or structures of protein structural domain(s)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000900 ! Protein domain classification [Term] id: EDAM:0003098 name: Raw SCOP domain classification format namespace: data def: "Format of raw SCOP domain classification data files." [EDAM:EBI "EMBRACE definition"] comment: These are the parsable data files provided by SCOP. subset: format is_a: EDAM:0003097 ! Protein domain classification format [Term] id: EDAM:0003099 name: Raw CATH domain classification format namespace: data def: "Format of raw CATH domain classification data files." [EDAM:EBI "EMBRACE definition"] comment: These are the parsable data files provided by CATH. subset: format is_a: EDAM:0003097 ! Protein domain classification format [Term] id: EDAM:0003100 name: CATH domain report format namespace: data def: "Format of summary of domain classification information for a CATH domain." [EDAM:EBI "EMBRACE definition"] comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. subset: data is_a: EDAM:0003097 ! Protein domain classification format [Term] id: EDAM:0002045 name: Electron microscopy model format namespace: format def: "Annotation format for electron microscopy models." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002350 ! Format (typed) [Term] id: EDAM:0002049 name: Phylogenetic tree report (tree distances) format namespace: format def: "Format for phylogenetic tree distance data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001442 ! Phylogenetic tree report (tree distances) [Term] id: EDAM:0002051 name: Polymorphism report format namespace: format def: "Format for sequence polymorphism data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0002885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM:0002052 name: Protein family report format namespace: format def: "Format for reports on a protein family." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000907 ! Protein family [Term] id: EDAM:0002054 name: Protein interaction format namespace: format def: "Format for protein interaction data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000906 ! Protein report (interaction) [Term] id: EDAM:0002055 name: Sequence assembly format namespace: format def: "Format for sequence assembly data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000925 ! Sequence assembly [Term] id: EDAM:0002056 name: Microarray experiment data format namespace: format def: "Format for microarray experimental data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000931 ! Experiment annotation (microarray) [Term] id: EDAM:0002058 name: Gene expression report format namespace: format def: "Format for a report on gene expression." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002031 ! Gene annotation format relationship: is_format_of EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0002059 name: Genotype and phenotype annotation format namespace: format def: "Format of a report on genotype / phenotype information." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000920 ! Genotype and phenotype annotation [Term] id: EDAM:0002060 name: Map format namespace: format def: "Format of a map of (typically one) molecular sequence annotated with features." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001274 ! Map [Term] id: EDAM:0002061 name: Nucleic acid features (primers) format namespace: format def: "Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000922 ! Nucleic acid features (primers) [Term] id: EDAM:0002062 name: Protein report format namespace: format def: "Format of a report of general information about a specific protein." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000896 ! Protein report [Term] id: EDAM:0003033 name: Matrix format namespace: format def: "Format of a matrix (array) of numerical values." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0002082 ! Matrix [Term] id: EDAM:0002064 name: 3D-1D scoring matrix format namespace: format def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0003033 ! Matrix format relationship: is_format_of EDAM:0001499 ! 3D-1D scoring matrix [Term] id: EDAM:0002065 name: Protein structure report (quality evaluation) format namespace: format def: "Format of a report on the quality of a protein three-dimensional model." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001539 ! Protein structural quality report [Term] id: EDAM:0002066 name: Database hits (sequence) format namespace: format def: "Format of a report on sequence hits and associated data from searching a sequence database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000857 ! Database hits (sequence) [Term] id: EDAM:0002067 name: Sequence distance matrix format namespace: format def: "Format of a matrix of genetic distances between molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000870 ! Sequence distance matrix [Term] id: EDAM:0002068 name: Sequence motif format namespace: format def: "Format of a sequence motif." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001353 ! Sequence motif [Term] id: EDAM:0002069 name: Sequence profile format namespace: format def: "Format of a sequence profile." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001354 ! Sequence profile [Term] id: EDAM:0002074 name: Dirichlet distribution format namespace: format def: "Data format of a dirichlet distribution." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001347 ! Dirichlet distribution [Term] id: EDAM:0002075 name: HMM emission and transition counts format namespace: format def: "Data format for the emission and transition counts of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001348 ! HMM emission and transition counts [Term] id: EDAM:0002077 name: Protein secondary structure format namespace: format def: "Format for secondary structure (predicted or real) of a protein molecule." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000876 ! Protein features (secondary structure) [Term] id: EDAM:0002076 name: RNA secondary structure format namespace: format def: "Format for secondary structure (predicted or real) of an RNA molecule." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000880 ! RNA secondary structure [Term] id: EDAM:0002078 name: Sequence range format namespace: format def: "Format used to specify range(s) of sequence positions." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001017 ! Sequence range [Term] id: EDAM:0002155 name: Sequence features (repeats) format namespace: format def: "Format used for map of repeats in molecular (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001299 ! Sequence features (repeats) [Term] id: EDAM:0002158 name: Nucleic acid features (restriction sites) format namespace: format def: "Format used for report on restriction enzyme recognition sites in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001305 ! Nucleic acid features (restriction sites) [Term] id: EDAM:0002159 name: Gene features (coding region) format namespace: format def: "Format used for report on coding regions in nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002031 ! Gene annotation format relationship: is_format_of EDAM:0001313 ! Nucleic acid features (coding sequence) [Term] id: EDAM:0002170 name: Sequence cluster format namespace: format def: "Format used for clusters of molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001235 ! Sequence cluster [Term] id: EDAM:0002195 name: Ontology format namespace: format def: "Format used for ontologies." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000582 ! Ontology [Term] id: EDAM:0002210 name: Strain data format namespace: format def: "Format of a report on organism strain data / cell line." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000963 ! Cell line annotation [Term] id: EDAM:0002542 name: Protein features (domains) format namespace: format def: "Format of a report on protein features (domain composition)." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002350 ! Format (typed) [Term] id: EDAM:0002571 name: Raw sequence format namespace: format def: "Format of a raw molecular sequence (i.e. the alphabet used)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000848 ! Raw sequence [Term] id: EDAM:0001734 name: PubMed citation namespace: format def: "Format of bibliographic reference as used by the PubMed database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002848 ! Bibliographic reference format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001735 name: Medline Display Format namespace: format def: "Format for abstracts of scientific articles from the Medline database." [EDAM:EBI "EMBRACE definition"] comment: Bibliographic reference information including citation information is included subset: format xref: Moby:PubMed-MEDLINE is_a: EDAM:0002848 ! Bibliographic reference format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001736 name: CiteXplore-core namespace: format def: "CiteXplore 'core' citation format including title, journal, authors and abstract." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002848 ! Bibliographic reference format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001737 name: CiteXplore-all namespace: format def: "CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002848 ! Bibliographic reference format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001747 name: PDB atom record format namespace: format def: "Format of an ATOM record (describing data for an individual atom) from a PDB file." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001476 ! PDB format [Term] id: EDAM:0002551 name: Sequence record format (text) namespace: format def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0002552 name: Sequence record format (XML) namespace: format def: "Data format for a molecular sequence record." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001919 ! Sequence record format [Term] id: EDAM:0002203 name: Sequence record lite format namespace: format def: "Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001919 ! Sequence record format relationship: is_format_of EDAM:0002043 ! Sequence record lite [Term] id: EDAM:0002202 name: Sequence record full format namespace: format def: "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001919 ! Sequence record format relationship: is_format_of EDAM:0002201 ! Sequence record full [Term] id: EDAM:0002057 name: Sequence trace format namespace: format def: "Format for sequence trace data (i.e. including base call information)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001919 ! Sequence record format relationship: is_format_of EDAM:0000924 ! Sequence trace [Term] id: EDAM:0001923 name: acedb namespace: format def: "ACEDB sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) [Term] id: EDAM:0001924 name: clustal sequence format namespace: format def: "Clustalw output format." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001982 ! clustal alignment format [Term] id: EDAM:0001925 name: codata namespace: format def: "Codata entry format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001928 name: experiment namespace: format def: "Staden experiment file format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001934 name: fitch namespace: format def: "Fitch program format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001935 name: gcg namespace: format def: "GCG sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001938 name: GFF2-seq namespace: format def: "GFF feature file format with sequence in the header." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0001974 ! GFF2 [Term] id: EDAM:0001939 name: GFF3-seq namespace: format def: "GFF3 feature file format with sequence." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0001975 ! GFF2 [Term] id: EDAM:0001941 name: hennig86 namespace: format def: "Hennig86 output sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001942 name: ig namespace: format def: "Intelligenetics sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001943 name: igstrict namespace: format def: "Intelligenetics sequence format (strict version)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001944 name: jackknifer namespace: format def: "Jackknifer interleaved and non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001945 name: mase namespace: format def: "Mase program sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001946 name: mega-seq namespace: format def: "Mega interleaved and non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001947 name: msf namespace: format def: "GCG MSF (multiple sequence file) file format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001949 name: nexus-seq namespace: format def: "Nexus/paup interleaved sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001950 name: pdbatom namespace: format def: "PDB sequence format (ATOM lines)." [EDAM:EBI "EMBRACE definition"] comment: pdb format in EMBOSS. subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0001475 ! PDB database entry format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001951 name: pdbatomnuc namespace: format def: "PDB nucleotide sequence format (ATOM lines)." [EDAM:EBI "EMBRACE definition"] comment: pdbnuc format in EMBOSS. subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0001475 ! PDB database entry format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001952 name: pdbseqresnuc namespace: format def: "PDB nucleotide sequence format (SEQRES lines)." [EDAM:EBI "EMBRACE definition"] comment: pdbnucseq format in EMBOSS. subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0001475 ! PDB database entry format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001953 name: pdbseqres namespace: format def: "PDB sequence format (SEQRES lines)." [EDAM:EBI "EMBRACE definition"] comment: pdbseq format in EMBOSS. subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0001475 ! PDB database entry format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001955 name: phylip sequence format namespace: format def: "Phylip interleaved sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001997 ! phylip [Term] id: EDAM:0001956 name: phylipnon sequence format namespace: format def: "Phylip non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001998 ! phylipnon [Term] id: EDAM:0001957 name: raw namespace: format def: "Raw sequence format with no non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001958 name: refseqp namespace: format def: "Refseq protein entry sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001959 name: selex sequence format namespace: format def: "Selex sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002000 ! selex alignment format [Term] id: EDAM:0001960 name: Staden format namespace: format def: "Staden suite sequence format." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001961 name: stockholm namespace: format def: "Stockholm multiple sequence alignment format (used by Pfam and Rfam)." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://en.wikipedia.org/wiki/Stockholm_format is_a: EDAM:0002330 ! Text is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001962 name: strider namespace: format def: "DNA strider output sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001964 name: text namespace: format def: "Plain text sequence format (essentially unformatted)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001965 name: treecon sequence format namespace: format def: "Treecon output sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002005 ! treecon-seq [Term] id: EDAM:0001966 name: asn1 sequence format namespace: format def: "NCBI ASN.1 sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001969 name: debug-seq namespace: format def: "EMBOSS debugging trace sequence format of full internal data content." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001970 name: jackknifernon namespace: format def: "Jackknifer output sequence non-interleaved format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001971 name: meganon sequence format namespace: format def: "Mega non-interleaved output sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001992 ! meganon [Term] id: EDAM:0001973 name: nexusnon namespace: format def: "Nexus/paup non-interleaved sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001967 name: das namespace: format def: "DAS sequence (XML) format (any type)." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "das sequence format" EXACT [] is_a: EDAM:0002552 ! Sequence record format (XML) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001968 name: dasdna namespace: format def: "DAS sequence (XML) format (nucleotide-only)." [EDAM:EBI "EMBRACE definition"] comment: The use of this format is deprecated. subset: format is_a: EDAM:0002552 ! Sequence record format (XML) is_a: EDAM:0002332 ! XML [Term] id: EDAM:0002546 name: FASTA-like namespace: format def: "A format resembling FASTA format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the many non-standard FASTA-like formats. subset: format is_a: EDAM:0002203 ! Sequence record lite format [Term] id: EDAM:0002200 name: FASTA-like (text) namespace: format def: "A text format resembling FASTA format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the many non-standard FASTA-like formats. subset: format is_a: EDAM:0002546 ! FASTA-like is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002310 name: FASTA-HTML namespace: format def: "FASTA format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002546 ! FASTA-like is_a: EDAM:0002331 ! HTML [Term] id: EDAM:0001929 name: FASTA format namespace: format def: "FASTA format including NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "FASTA" EXACT [] synonym: "FASTA sequence format" EXACT [] is_a: EDAM:0002200 ! FASTA-like (text) is_a: EDAM:0002554 ! Alignment format (text) [Term] id: EDAM:0001926 name: dbid namespace: format def: "Fasta format variant with database name before ID." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002200 ! FASTA-like (text) [Term] id: EDAM:0001940 name: giFASTA format namespace: format def: "FASTA sequence format including NCBI-style GIs." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002200 ! FASTA-like (text) [Term] id: EDAM:0001954 name: Pearson format namespace: format def: "Plain old FASTA sequence format (unspecified format for IDs)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002200 ! FASTA-like (text) [Term] id: EDAM:0001972 name: NCBI format namespace: format def: "NCBI FASTA sequence format with NCBI-style IDs." [EDAM:EBI "EMBRACE definition"] comment: There are several variants of this. subset: format is_a: EDAM:0002200 ! FASTA-like (text) [Term] id: EDAM:0002543 name: EMBL-like format namespace: format def: "A format resembling EMBL entry (plain text) format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the many non-standard EMBL-like formats. subset: format is_a: EDAM:0002202 ! Sequence record full format [Term] id: EDAM:0002559 name: GenBank-like format namespace: format def: "A format resembling GenBank entry (plain text) format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the non-standard GenBank-like formats. subset: format is_a: EDAM:0002202 ! Sequence record full format [Term] id: EDAM:0002547 name: uniprotkb-like format namespace: format def: "A sequence format resembling uniprotkb entry format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002202 ! Sequence record full format is_a: EDAM:0002206 ! Sequence feature table format (text) [Term] id: EDAM:0001948 name: nbrf namespace: format def: "NBRF/PIR entry sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002202 ! Sequence record full format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002181 name: EMBL-like (text) namespace: format def: "A text format resembling EMBL entry format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the many non-standard EMBL-like text formats. subset: format is_a: EDAM:0002543 ! EMBL-like is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002558 name: EMBL-like (XML) namespace: format def: "An XML format resembling EMBL entry format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the any non-standard EMBL-like XML formats. subset: format is_a: EDAM:0002543 ! EMBL-like is_a: EDAM:0002332 ! XML [Term] id: EDAM:0002311 name: EMBL-HTML namespace: format def: "EMBL entry format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002543 ! EMBL-like is_a: EDAM:0002331 ! HTML [Term] id: EDAM:0001927 name: EMBL format namespace: format def: "EMBL entry format." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "EMBL sequence format" EXACT [] synonym: "EMBL" EXACT [] is_a: EDAM:0002181 ! EMBL-like (text) is_a: EDAM:0002206 ! Sequence feature table format (text) [Term] id: EDAM:0002186 name: geneseq namespace: format def: "Geneseq sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002181 ! EMBL-like (text) [Term] id: EDAM:0002204 name: EMBL format (XML) namespace: format def: "An XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] comment: This is a placeholder for other more specific terms. It should not normally be used for annotation. subset: format is_a: EDAM:0002558 ! EMBL-like (XML) [Term] id: EDAM:0002183 name: EMBLXML namespace: format def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002204 ! EMBL (XML) [Term] id: EDAM:0002184 name: cdsxml namespace: format def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002204 ! EMBL (XML) [Term] id: EDAM:0002185 name: insdxml namespace: format def: "XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002204 ! EMBL (XML) [Term] id: EDAM:0002205 name: GenBank-like format (text) namespace: format def: "A text format resembling GenBank entry (plain text) format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for the non-standard GenBank-like text formats. subset: format is_a: EDAM:0002559 ! GenBank-like is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002532 name: GenBank-HTML namespace: format def: "Genbank entry format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002559 ! GenBank-like is_a: EDAM:0002331 ! HTML [Term] id: EDAM:0001936 name: GenBank format namespace: format def: "Genbank entry format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002205 ! GenBank-like (text) is_a: EDAM:0002206 ! Sequence feature table format (text) [Term] id: EDAM:0001937 name: genpept namespace: format def: "Genpept protein entry format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002205 ! GenBank-like (text) [Term] id: EDAM:0002187 name: uniprotkb-like (text) namespace: format def: "A text sequence format resembling uniprotkb entry format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002547 ! uniprotkb-like is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001963 name: Swiss-Prot format namespace: format def: "Swiss-Prot entry sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002187 ! uniprotkb-like (text) [Term] id: EDAM:0002188 name: uniprot namespace: format def: "UniProt entry sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002187 ! uniprotkb-like (text) [Term] id: EDAM:0002189 name: ipi namespace: format def: "ipi sequence format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002187 ! uniprotkb-like (text) [Term] id: EDAM:0001628 name: ABI namespace: format def: "A format of raw sequence read data from an Applied Biosystems sequencing machine." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0002333 ! Binary [Term] id: EDAM:0001629 name: mira namespace: format def: "Format of MIRA sequence trace information file." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002545 name: FASTQ-like format namespace: format def: "A format resembling FASTQ short read format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for non-standard FASTQ short read-like formats. subset: format is_a: EDAM:0002057 ! Sequence trace format [Term] id: EDAM:0002572 name: BAM namespace: format def: "BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://samtools.sourceforge.net/SAM-1.3.pdf is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0001921 ! Alignment format is_a: EDAM:0002333 ! Binary [Term] id: EDAM:0002573 name: SAM namespace: format def: "Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [EDAM:EBI "EMBRACE definition"] comment: The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. subset: format spec: http://samtools.sourceforge.net/SAM-1.3.pdf is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0002920 ! Alignment format (pair only) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002182 name: FASTQ-like format (text) namespace: format def: "A text format resembling FASTQ short read format." [EDAM:EBI "EMBRACE definition"] comment: This term may be used for non-standard FASTQ short read-like formats. subset: format is_a: EDAM:0002545 ! FASTQ-like is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001930 name: FASTQ namespace: format def: "FASTQ short read format ignoring quality scores." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002182 ! FASTQ-like (text) [Term] id: EDAM:0001931 name: FASTQ-illumina namespace: format def: "FASTQ Illumina 1.3 short read format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002182 ! FASTQ-like (text) [Term] id: EDAM:0001932 name: FASTQ-sanger namespace: format def: "FASTQ short read format with phred quality." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002182 ! FASTQ-like (text) [Term] id: EDAM:0001933 name: FASTQ-solexa namespace: format def: "FASTQ Solexa/Illumina 1.0 short read format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002182 ! FASTQ-like (text) [Term] id: EDAM:0002548 name: Sequence feature table format namespace: format def: "Format for a sequence feature table." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001920 ! Sequence feature annotation format relationship: is_format_of EDAM:0001255 ! Sequence features [Term] id: EDAM:0001979 name: debug-feat namespace: format def: "EMBOSS debugging trace feature format of full internal data content." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001920 ! Sequence feature annotation format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002206 name: Sequence feature table format (text) namespace: format def: "Text format for a sequence feature table." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002548 ! Sequence feature table format [Term] id: EDAM:0002553 name: Sequence feature table format (XML) namespace: format def: "XML format for a sequence feature table." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002548 ! Sequence feature table format [Term] id: EDAM:0002305 name: GFF namespace: format def: "GFF feature format (of indeterminate version)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002206 ! Sequence feature table format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001976 name: pir namespace: format def: "PIR feature format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002206 ! Sequence feature table format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001977 name: swiss feature namespace: format def: "Swiss-Prot feature format." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001963 ! swiss [Term] id: EDAM:0001980 name: EMBL feature namespace: format def: "EMBL feature format." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001927 ! EMBL [Term] id: EDAM:0001981 name: GenBank feature namespace: format def: "Genbank feature format." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001936 ! GenBank [Term] id: EDAM:0001974 name: GFF2 namespace: format def: "General Feature Format (GFF) of sequence features." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://www.sanger.ac.uk/resources/software/gff/spec.html is_a: EDAM:0002305 ! GFF [Term] id: EDAM:0001975 name: GFF3 namespace: format def: "Generic Feature Format version 3 (GFF3) of sequence features." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://sequenceontology.org/resources/gff3.html is_a: EDAM:0002305 ! GFF [Term] id: EDAM:0002306 name: GTF namespace: format def: "Gene Transfer Format (GTF), a restricted version of GFF." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://mblab.wustl.edu/GTF22.html http://genome.ucsc.edu/FAQ/FAQformat#format4 is_a: EDAM:0002305 ! GFF [Term] id: EDAM:0001978 name: DASGFF namespace: format def: "DAS GFF (XML) feature format." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "DASGFF feature" EXACT [] synonym: "das feature" EXACT [] is_a: EDAM:0002553 ! Sequence feature table format (XML) is_a: EDAM:0002332 ! XML [Term] id: EDAM:0002554 name: Alignment format (text) namespace: format def: "Text format for molecular sequence alignment information." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0002555 name: Alignment format (XML) namespace: format def: "XML format for molecular sequence alignment information." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001921 ! Alignment format [Term] id: EDAM:0001982 name: clustal namespace: format def: "Clustalw format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001983 name: debug namespace: format def: "EMBOSS alignment format for debugging trace of full internal data content." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001984 name: FASTA-aln namespace: format def: "Fasta format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002200 ! FASTA-like (text) [Term] id: EDAM:0002922 name: markx0 variant namespace: format def: "Some variant of Pearson MARKX alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001985 name: markx0 namespace: format def: "Pearson MARKX0 alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002922 ! markx0 variant [Term] id: EDAM:0001986 name: markx1 namespace: format def: "Pearson MARKX1 alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002922 ! markx0 variant [Term] id: EDAM:0001987 name: markx10 namespace: format def: "Pearson MARKX10 alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002922 ! markx0 variant [Term] id: EDAM:0001988 name: markx2 namespace: format def: "Pearson MARKX2 alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002922 ! markx0 variant [Term] id: EDAM:0001989 name: markx3 namespace: format def: "Pearson MARKX3 alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002922 ! markx0 variant [Term] id: EDAM:0001990 name: match namespace: format def: "Alignment format for start and end of matches between sequence pairs." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002923 name: mega variant namespace: format def: "Some variant of Mega format for (typically aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001991 name: mega namespace: format def: "Mega format for (typically aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002923 ! mega variant [Term] id: EDAM:0001992 name: meganon namespace: format def: "Mega non-interleaved format for (typically aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002923 ! mega variant [Term] id: EDAM:0001993 name: msf alignment format namespace: format def: "MSF format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001947 ! msf [Term] id: EDAM:0001994 name: nexus alignment format namespace: format def: "Nexus/paup format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001949 ! nexus [Term] id: EDAM:0001995 name: nexusnon alignment format namespace: format def: "Nexus/paup non-interleaved format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0001973 ! nexusnon [Term] id: EDAM:0001996 name: pair namespace: format def: "EMBOSS simple sequence pair alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) [Term] id: EDAM:0002924 name: phylip variant namespace: format def: "Some variant of Phylip format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001997 name: phylip namespace: format def: "Phylip format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002924 ! phylip variant [Term] id: EDAM:0001998 name: phylipnon namespace: format def: "Phylip non-interleaved format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002924 ! phylip variant [Term] id: EDAM:0001999 name: score namespace: format def: "Alignment format for score values for pairs of sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002000 name: selex namespace: format def: "SELEX format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002001 name: simple namespace: format def: "EMBOSS simple multiple alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002002 name: srs namespace: format def: "Simple multiple sequence (alignment) format for SRS." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002003 name: srspair namespace: format def: "Simple sequence pair (alignment) format for SRS." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002920 ! Alignment format (pair only) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002004 name: tcoffee namespace: format def: "TCOFFEE program alignment format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002005 name: treecon-seq namespace: format def: "Treecon format for (aligned) sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002551 ! Sequence record format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001391 name: hmmer-aln namespace: format def: "FASTA-style format for multiple sequences aligned by HMMER package to an HMM." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001392 name: dialign namespace: format def: "Multiple sequences aligned by DIALIGN package." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001393 name: daf namespace: format def: "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family." [EDAM:EBI "EMBRACE definition"] comment: The format is clustal-like and includes annotation of domain family classification information. subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002556 name: Phylogenetic tree format (text) namespace: format def: "Text format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002006 ! Phylogenetic tree format [Term] id: EDAM:0002557 name: Phylogenetic tree format (XML) namespace: format def: "XML format for a phylogenetic tree." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002006 ! Phylogenetic tree format [Term] id: EDAM:0001435 name: phylip tree namespace: format def: "Phylogenetic tree data format used by the PHYLIP program." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002556 ! Phylogenetic tree format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001425 name: Phylip tree raw namespace: format def: "Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002556 ! Phylogenetic tree format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001424 name: Clustalw dendrogram namespace: format def: "Dendrogram (tree file) format generated by Clustalw." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002556 ! Phylogenetic tree format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001436 name: treebase namespace: format def: "The format of an entry from the TreeBASE database of phylogenetic data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002556 ! Phylogenetic tree format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001437 name: treefam namespace: format def: "The format of an entry from the TreeFam database of phylogenetic data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002556 ! Phylogenetic tree format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001910 name: newick namespace: format def: "Phylogenetic tree Newick (text) format." [EDAM:EBI "EMBRACE definition"] subset: format xref: Moby:Newick_Text is_a: EDAM:0002556 ! Phylogenetic tree format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001911 name: treecon namespace: format def: "Phylogenetic tree TreeCon (text) format." [EDAM:EBI "EMBRACE definition"] subset: format xref: Moby:TreeCon is_a: EDAM:0002556 ! Phylogenetic tree format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001912 name: nexus namespace: format def: "Phylogenetic tree Nexus (text) format." [EDAM:EBI "EMBRACE definition"] subset: format xref: Moby:Nexus_Text is_a: EDAM:0002556 ! Phylogenetic tree format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001475 name: PDB database entry format namespace: format def: "Format of an entry (or part of an entry) from the PDB database." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "PDB entry" EXACT [] is_a: EDAM:0002033 ! Tertiary structure format [Term] id: EDAM:0001476 name: PDB format namespace: format def: "Entry format of PDB database in PDB format." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "PDB" EXACT [] xref: Moby:PDB-formatted-text xref: Moby:PDB-Text is_a: EDAM:0001475 ! PDB database entry format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001477 name: mmCIF namespace: format def: "Entry format of PDB database in mmCIF format." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "mmcif" EXACT [] xref: Moby:mmCIF-Text xref: Moby:mmCIF_Text is_a: EDAM:0001475 ! PDB database entry format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001478 name: PDBML namespace: format def: "Entry format of PDB database in PDBML (XML) format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001475 ! PDB database entry format is_a: EDAM:0002332 ! XML [Term] id: EDAM:0002013 name: Biological pathway or network format namespace: format def: "Data format for a biological pathway or network." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002034 ! Biological model format relationship: is_format_of EDAM:0002600 ! Pathway or network [Term] id: EDAM:0002585 name: SBML namespace: format def: "XML format for models of biological processes such as metabolism, cell signaling and so on." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002034 ! Biological model format is_a: EDAM:0002332 ! XML [Term] id: EDAM:0001666 name: BioModel mathematical model format namespace: format def: "Format of mathematical models from the BioModel database." [EDAM:EBI "EMBRACE definition"] comment: Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001647 name: KEGG PATHWAY entry format namespace: format def: "The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001648 name: MetaCyc entry format namespace: format def: "The format of an entry from the MetaCyc metabolic pathways database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001649 name: HumanCyc entry format namespace: format def: "The format of a report from the HumanCyc metabolic pathways database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001650 name: INOH entry format namespace: format def: "The format of an entry from the INOH signal transduction pathways database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001651 name: PATIKA entry format namespace: format def: "The format of an entry from the PATIKA biological pathways database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001652 name: Reactome entry format namespace: format def: "The format of an entry from the reactome biological pathways database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001653 name: aMAZE entry format namespace: format def: "The format of an entry from the aMAZE biological pathways and molecular interactions database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001654 name: CPDB entry format namespace: format def: "The format of an entry from the CPDB database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001655 name: Panther Pathways entry format namespace: format def: "The format of an entry from the Panther Pathways database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002341 name: NCI-Nature pathway entry format namespace: format def: "The format of an entry from the NCI-Nature pathways database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002015 name: Sequence-profile alignment (HMM) format namespace: format def: "Data format for a sequence-HMM profile alignment." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002014 ! Sequence-profile alignment format [Term] id: EDAM:0001419 name: Sequence-MEME profile alignment namespace: format def: "Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002014 ! Sequence-profile alignment format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001421 name: HMMER profile alignment (sequences versus HMMs) namespace: format def: "Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002014 ! Sequence-profile alignment format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001422 name: HMMER profile alignment (HMM versus sequences) namespace: format def: "Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002014 ! Sequence-profile alignment format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001504 name: aaindex namespace: format def: "Amino acid index format used by the AAindex database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002017 ! Amino acid index format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001739 name: pmc namespace: format def: "Article format of the PubMed Central database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002020 ! Article format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002194 name: medline namespace: format def: "Abstract format used by MedLine database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002020 ! Article format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001740 name: iHOP text mining abstract format namespace: format def: "iHOP abstract format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002021 ! Text mining report format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001741 name: Oscar3 namespace: format def: "Text mining abstract format from the Oscar 3 application." [EDAM:EBI "EMBRACE definition"] comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology terms and chemical data from a document. subset: format is_a: EDAM:0002021 ! Text mining report format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001582 name: findkm namespace: format def: "A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002027 ! Enzyme kinetics report format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001697 name: KEGG LIGAND entry format namespace: format def: "The format of an entry from the KEGG LIGAND chemical database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001698 name: KEGG COMPOUND entry format namespace: format def: "The format of an entry from the KEGG COMPOUND database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001699 name: KEGG PLANT entry format namespace: format def: "The format of an entry from the KEGG PLANT database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001700 name: KEGG GLYCAN entry format namespace: format def: "The format of an entry from the KEGG GLYCAN database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001706 name: KEGG DRUG entry format namespace: format def: "The format of an entry from the KEGG DRUG database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001701 name: PubChem entry format namespace: format def: "The format of an entry from PubChem." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001702 name: ChemSpider entry format namespace: format def: "The format of an entry from a database of chemical structures and property predictions." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001703 name: ChEBI entry format namespace: format def: "The format of an entry from Chemical Entities of Biological Interest (ChEBI)." [EDAM:EBI "EMBRACE definition"] comment: ChEBI includes an ontological classification defining relations between entities or classes of entities. subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001704 name: MSDchem ligand dictionary entry format namespace: format def: "The format of an entry from the MSDchem ligand dictionary." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001705 name: HET group dictionary entry format namespace: format def: "The format of an entry from the HET group dictionary (HET groups from PDB files)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002030 ! Small molecule report format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001808 name: GeneIlluminator gene report format namespace: format def: "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service." [EDAM:EBI "EMBRACE definition"] comment: This includes a gene name and abbreviation of the name which may be in a namespace indicating the gene status and relevant organisation. subset: format xref: Moby:GI_Gene is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001809 name: BacMap gene card format namespace: format def: "Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database." [EDAM:EBI "EMBRACE definition"] subset: format xref: Moby:BacMapGeneCard is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001810 name: ColiCard report format namespace: format def: "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [EDAM:EBI "EMBRACE definition"] subset: format xref: Moby:ColiCard is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002328 name: PseudoCAP gene report format namespace: format def: "Format of a report on a gene from the PseudoCAP database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002329 name: GeneCards gene report format namespace: format def: "Format of a report on a gene from the GeneCards database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001603 name: Ensembl gene report format namespace: format def: "Entry format of Ensembl genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001604 name: DictyBase gene report format namespace: format def: "Entry format of DictyBase genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001605 name: CGD gene report format namespace: format def: "Entry format of Candida Genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001606 name: DragonDB gene report format namespace: format def: "Entry format of DragonDB genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001607 name: EcoCyc gene report format namespace: format def: "Entry format of EcoCyc genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001608 name: FlyBase gene report format namespace: format def: "Entry format of FlyBase genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001609 name: Gramene gene report format namespace: format def: "Entry format of Gramene genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001610 name: KEGG GENES gene report format namespace: format def: "Entry format of KEGG GENES genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001611 name: MaizeGDB gene report format namespace: format def: "Entry format of the Maize genetics and genomics database (MaizeGDB)." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001612 name: MGD gene report format namespace: format def: "Entry format of the Mouse Genome Database (MGD)." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001613 name: RGD gene report format namespace: format def: "Entry format of the Rat Genome Database (RGD)." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001614 name: SGD gene report format namespace: format def: "Entry format of the Saccharomyces Genome Database (SGD)." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001615 name: GeneDB gene report format namespace: format def: "Entry format of the Sanger GeneDB genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001616 name: TAIR gene report format namespace: format def: "Entry format of The Arabidopsis Information Resource (TAIR) genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001617 name: WormBase gene report format namespace: format def: "Entry format of the WormBase genomes database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001618 name: ZFIN gene report format namespace: format def: "Entry format of the Zebrafish Information Network (ZFIN) genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001619 name: TIGR gene report format namespace: format def: "Entry format of the TIGR genome database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001782 name: NCBI gene report format namespace: format def: "Entry (gene) format of the NCBI database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001665 name: Taverna workflow format namespace: format def: "Format of Taverna workflows." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002032 ! Workflow format is_a: EDAM:0002332 ! XML [Term] id: EDAM:0001196 name: smiles namespace: format def: "Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002035 ! Chemical formula format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001197 name: inchi namespace: format def: "Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002035 ! Chemical formula format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001198 name: mf namespace: format def: "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound." [EDAM:EBI "EMBRACE definition"] comment: The general MF query format consists of a series of valid atomic symbols, with an optional number or range. subset: format is_a: EDAM:0002035 ! Chemical formula format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001199 name: inchikey namespace: format def: "The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound." [EDAM:EBI "EMBRACE definition"] comment: An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. subset: format is_a: EDAM:0002035 ! Chemical formula format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001200 name: smarts namespace: format def: "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001196 ! smiles [Term] id: EDAM:0002037 name: Phylogenetic continuous quantitative character format namespace: format def: "Format of phylogenetic continuous quantitative character data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002036 ! Phylogenetic character data format relationship: is_format_of EDAM:0001426 ! Phylogenetic continuous quantitative data [Term] id: EDAM:0001431 name: Phylogenetic property values format namespace: format def: "Format of phylogenetic property data." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002036 ! Phylogenetic character data format [Term] id: EDAM:0002038 name: Phylogenetic discrete states format namespace: format def: "Format of phylogenetic discrete states data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002036 ! Phylogenetic character data format relationship: is_format_of EDAM:0001427 ! Phylogenetic discrete data [Term] id: EDAM:0002039 name: Phylogenetic tree report (cliques) format namespace: format def: "Format of phylogenetic cliques data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002036 ! Phylogenetic character data format relationship: is_format_of EDAM:0001428 ! Phylogenetic tree report (cliques) [Term] id: EDAM:0002040 name: Phylogenetic tree report (invariants) format namespace: format def: "Format of phylogenetic invariants data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002036 ! Phylogenetic character data format relationship: is_format_of EDAM:0001429 ! Phylogenetic tree report (invariants) [Term] id: EDAM:0001430 name: phylip continuous quantitative characters namespace: format def: "PHYLIP file format for continuous quantitative character data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001432 name: phylip character frequencies namespace: format def: "PHYLIP file format for phylogenetics character frequency data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002243 name: phylip property values namespace: format def: "PHYLIP file format for phylogenetic property data." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002036 ! Phylogenetic character data format [Term] id: EDAM:0001433 name: phylip discrete states namespace: format def: "Format of PHYLIP discrete states data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002038 ! Phylogenetic discrete states format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001434 name: phylip cliques namespace: format def: "Format of PHYLIP cliques data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002039 ! Phylogenetic tree report (cliques) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001645 name: EMDB entry format namespace: format def: "Format of an entry from the Electron Microscopy DataBase (EMDB)." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001445 name: phylip tree distance namespace: format def: "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002049 ! Phylogenetic tree report (tree distances) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001620 name: dbSNP polymorphism report format namespace: format def: "Entry format for the dbSNP database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001570 name: InterPro entry format namespace: format def: "Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences." [EDAM:EBI "EMBRACE definition"] comment: This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001571 name: InterPro entry abstract format namespace: format def: "Entry format for the textual abstract of signatures in an InterPro entry and its protein matches." [EDAM:EBI "EMBRACE definition"] comment: References are included and a functional inference is made where possible. subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001572 name: Gene3D entry format namespace: format def: "Entry format for the Gene3D protein secondary database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001573 name: PIRSF entry format namespace: format def: "Entry format for the PIRSF protein secondary database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001574 name: PRINTS entry format namespace: format def: "Entry format for the PRINTS protein secondary database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001575 name: Panther Families and HMMs entry format namespace: format def: "Entry format for the Panther library of protein families and subfamilies." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001576 name: Pfam entry format namespace: format def: "Entry format for the Pfam protein secondary database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001577 name: SMART entry format namespace: format def: "Entry format for the SMART protein secondary database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001578 name: Superfamily entry format namespace: format def: "Entry format for the Superfamily protein secondary database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001579 name: TIGRFam entry format namespace: format def: "Entry format for the TIGRFam protein secondary database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001580 name: ProDom entry format namespace: format def: "Entry format for the ProDom protein domain classification database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001581 name: FSSP entry format namespace: format def: "Entry format for the FSSP database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001568 name: BIND entry format namespace: format def: "Entry format for the BIND database of protein interaction." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001569 name: IntAct entry format namespace: format def: "Entry format for the IntAct database of protein interaction." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002560 name: STRING entry format namespace: format def: "Entry format for the STRING database of protein interaction." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002303 name: STRING entry format (HTML) namespace: format def: "Entry format (HTML) for the STRING database of protein interaction." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002304 name: STRING entry format (XML) namespace: format def: "Entry format (XML) for the STRING database of protein interaction." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002054 ! Protein interaction format is_a: EDAM:0002332 ! XML [Term] id: EDAM:0002561 name: Sequence assembly format (text) namespace: format def: "Text format for sequence assembly data." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002055 ! Sequence assembly format [Term] id: EDAM:0001630 name: CAF namespace: format def: "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://www.sanger.ac.uk/resources/software/caf/ is_a: EDAM:0002561 ! Sequence assembly format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001631 name: exp namespace: format def: "Sequence assembly project file EXP format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002561 ! Sequence assembly format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001632 name: SCF namespace: format def: "Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://staden.sourceforge.net/manual/formats_unix_2.html is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0002333 ! Binary [Term] id: EDAM:0001633 name: PHD namespace: format def: "PHD sequence trace format to store serialised chromatogram data (reads)." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://www.bioperl.org/wiki/PHD_sequence_format is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001640 name: ArrayExpress entry format namespace: format def: "Entry format for the ArrayExpress microarrays database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001641 name: affymetrix-exp namespace: format def: "Affymetrix data file format for information about experimental conditions and protocols." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Affymetrix experimental conditions data file format" EXACT [] is_a: EDAM:0002056 ! Microarray experiment data format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001638 name: cel namespace: format def: "Format of Affymetrix data file of information about (raw) expression levels of the individual probes." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Affymetrix probe raw data format" EXACT [] is_a: EDAM:0002058 ! Gene expression report format is_a: EDAM:0002330 ! Text relationship: is_format_of EDAM:0003110 ! Raw microarray data [Term] id: EDAM:0001644 name: chp namespace: format def: "Format of Affymetrix data file of information about (normalised) expression levels of the individual probes." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Affymetrix probe normalised data format" EXACT [] is_a: EDAM:0002058 ! Gene expression report format is_a: EDAM:0002330 ! Text relationship: is_format_of EDAM:0003111 ! Processed microarray data [Term] id: EDAM:0001637 name: dat namespace: format def: "Format of Affymetrix data file of raw image data." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Affymetrix image data file format" EXACT [] is_a: EDAM:0002058 ! Gene expression report format is_a: EDAM:0002330 ! Text relationship: is_format_of EDAM:0001714 ! Microarray spots image [Term] id: EDAM:0001623 name: OMIM entry format namespace: format def: "Format of an entry from the OMIM database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001624 name: HGVbase entry format namespace: format def: "Format of a record from the HGVbase database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001625 name: HIVDB entry format namespace: format def: "Format of a record from the HIVDB database of genotypes and phenotypes." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001626 name: KEGG DISEASE entry format namespace: format def: "Format of an entry from the KEGG DISEASE database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001861 name: PlasMapper TextMap namespace: format def: "Map of a plasmid (circular DNA) in PlasMapper TextMap format." [EDAM:EBI "EMBRACE definition"] subset: format xref: Moby:PlasMapperTextMap is_a: EDAM:0002060 ! Map format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001627 name: Primer3 primer namespace: format def: "Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002061 ! Nucleic acid features (primers) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002063 name: Protein report (enzyme) format namespace: format def: "Format of a report of general information about a specific enzyme." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002350 ! Format (typed) [Term] id: EDAM:0001511 name: IntEnz enzyme report format namespace: format def: "Format of an entry from IntEnz (The Integrated Relational Enzyme Database)." [EDAM:EBI "EMBRACE definition"] comment: IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001512 name: BRENDA enzyme report format namespace: format def: "Format of an entry from the BRENDA enzyme database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002322 name: BioCyc enzyme report format namespace: format def: "Format of an entry from the BioCyc enzyme database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002323 name: ENZYME enzyme report format namespace: format def: "Format of an entry from the Enzyme nomenclature database (ENZYME)." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001513 name: KEGG REACTION enzyme report format namespace: format def: "Format of an entry from the KEGG REACTION database of biochemical reactions." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001514 name: KEGG ENZYME enzyme report format namespace: format def: "Format of an entry from the KEGG ENZYME database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001515 name: REBASE proto enzyme report format namespace: format def: "Format of an entry from the proto section of the REBASE enzyme database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001516 name: REBASE withrefm enzyme report format namespace: format def: "Format of an entry from the withrefm section of the REBASE enzyme database." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001500 name: Domainatrix 3D-1D scoring matrix format namespace: format def: "Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true [Term] id: EDAM:0001551 name: Pcons report format namespace: format def: "Format of output of the Pcons Model Quality Assessment Program (MQAP)." [EDAM:EBI "EMBRACE definition"] comment: Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. subset: format is_a: EDAM:0002065 ! Protein structure report (quality evaluation) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001552 name: ProQ report format namespace: format def: "Format of output of the ProQ protein model quality predictor." [EDAM:EBI "EMBRACE definition"] comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. subset: format is_a: EDAM:0002065 ! Protein structure report (quality evaluation) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001341 name: InterPro hits format namespace: format def: "Results format for searches of the InterPro database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002066 ! Database hits (sequence) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001342 name: InterPro protein view report format namespace: format def: "Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries." [EDAM:EBI "EMBRACE definition"] comment: The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. subset: format is_a: EDAM:0001341 ! InterPro hits format [Term] id: EDAM:0001343 name: InterPro match table format namespace: format def: "Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry." [EDAM:EBI "EMBRACE definition"] comment: The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. subset: format is_a: EDAM:0001341 ! InterPro hits format [Term] id: EDAM:0001332 name: FASTA search results format namespace: format def: "Format of results of a sequence database search using FASTA." [EDAM:EBI "EMBRACE definition"] comment: This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) subset: format is_a: EDAM:0002066 ! Database hits (sequence) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001333 name: BLAST results namespace: format def: "Format of results of a sequence database search using some variant of BLAST." [EDAM:EBI "EMBRACE definition"] comment: This includes score data, alignment data and summary table. subset: format is_a: EDAM:0002066 ! Database hits (sequence) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001334 name: mspcrunch namespace: format def: "Format of results of a sequence database search using some variant of MSPCrunch." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002066 ! Database hits (sequence) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001335 name: smith-waterman namespace: format def: "Format of results of a sequence database search using some variant of Smith Waterman." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002066 ! Database hits (sequence) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001336 name: dhf namespace: format def: "Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information." [EDAM:EBI "EMBRACE definition"] comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. subset: format is_a: EDAM:0002066 ! Database hits (sequence) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001337 name: lhf namespace: format def: "Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information." [EDAM:EBI "EMBRACE definition"] comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database. subset: format is_a: EDAM:0002066 ! Database hits (sequence) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001423 name: phylip distance matrix namespace: format def: "Format of PHYLIP phylogenetic distance matrix data." [EDAM:EBI "EMBRACE definition"] comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). subset: format is_a: EDAM:0002067 ! Sequence distance matrix format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001360 name: meme-motif namespace: format def: "A motif in the format generated by the MEME program." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002068 ! Sequence motif format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001356 name: prosite-pattern namespace: format def: "Format of a regular expression pattern from the Prosite database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002068 ! Sequence motif format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001357 name: EMBOSS sequence pattern namespace: format def: "Format of an EMBOSS sequence pattern." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002068 ! Sequence motif format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002072 name: Hidden Markov model format namespace: format def: "Format of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002069 ! Sequence profile format relationship: is_format_of EDAM:0001364 ! Hidden Markov model [Term] id: EDAM:0001367 name: jaspar namespace: format def: "A profile (sequence classifier) in the format used in the JASPAR database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002069 ! Sequence profile format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001366 name: prosite-profile namespace: format def: "Sequence profile (sequence classifier) format used in the PROSITE database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002069 ! Sequence profile format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001369 name: MEME background Markov model namespace: format def: "Format of the model of random sequences used by MEME." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002072 ! Hidden Markov model format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001370 name: hmmer namespace: format def: "Format of a hidden Markov model representation used by the HMMER package." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002072 ! Hidden Markov model format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001349 name: HMMER Dirichlet prior namespace: format def: "Dirichlet distribution HMMER format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002074 ! Dirichlet distribution format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001350 name: MEME Dirichlet prior namespace: format def: "Dirichlet distribution MEME format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002074 ! Dirichlet distribution format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001351 name: HMMER emission and transition namespace: format def: "Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002075 ! HMM emission and transition counts format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001454 name: dssp namespace: format def: "Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins)." [EDAM:EBI "EMBRACE definition"] comment: The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. subset: format is_a: EDAM:0002077 ! Protein secondary structure format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001455 name: hssp namespace: format def: "Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002077 ! Protein secondary structure format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001457 name: Vienna RNA secondary structure namespace: format def: "Format of RNA secondary structure (in bracket notation) with free energy values, generated by the Vienna program." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002076 ! RNA secondary structure format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001458 name: Vienna local RNA secondary structure namespace: format def: "Format of local RNA secondary structure components with free energy values, generated by the Vienna program." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002076 ! RNA secondary structure format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001248 name: EMBL feature location namespace: format def: "Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database." [EDAM:EBI "EMBRACE definition"] subset: format synonym: "Feature location" EXACT [] is_a: EDAM:0002078 ! Sequence range format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001295 name: quicktandem namespace: format def: "Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002155 ! Sequence features (repeats) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001296 name: Sanger inverted repeats namespace: format def: "Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002155 ! Sequence features (repeats) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001297 name: EMBOSS repeat namespace: format def: "Report format for tandem repeats in a sequence (an EMBOSS report format)." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002155 ! Sequence features (repeats) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001318 name: restrict namespace: format def: "Report format for restriction enzyme recognition sites used by EMBOSS restrict program." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002158 ! Nucleic acid features (restriction sites) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001319 name: restover namespace: format def: "Report format for restriction enzyme recognition sites used by EMBOSS restover program." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002158 ! Nucleic acid features (restriction sites) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001320 name: REBASE restriction sites namespace: format def: "Report format for restriction enzyme recognition sites used by REBASE database." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002158 ! Nucleic acid features (restriction sites) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001316 name: est2genome namespace: format def: "Format of a report on exon-intron structure generated by EMBOSS est2genome." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002159 ! Gene features (coding region) format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002171 name: Sequence cluster format (protein) namespace: format def: "Format used for clusters of protein sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002170 ! Sequence cluster format [Term] id: EDAM:0002172 name: Sequence cluster format (nucleic acid) namespace: format def: "Format used for clusters of nucleotide sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002170 ! Sequence cluster format [Term] id: EDAM:0001247 name: COG sequence cluster format namespace: format def: "Format of an entry from the COG database of clusters of (related) protein sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0002175 name: Gene cluster format namespace: format alt_id: EDAM:0002918 def: "Format used for clusters of genes." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002172 ! Sequence cluster format (nucleic acid) [Term] id: EDAM:0001228 name: UniGene entry format namespace: format def: "Format of an entry from UniGene." [EDAM:EBI "EMBRACE definition"] comment: A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001639 name: affymetrix namespace: format def: "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002330 ! Text is_a: EDAM:0002172 ! Sequence cluster format (nucleic acid) [Term] id: EDAM:0002196 name: OBO format namespace: format def: "OBO ontology format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002195 ! Ontology format [Term] id: EDAM:0002549 name: OBO namespace: format def: "OBO ontology text format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002196 ! OBO format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002197 name: OWL namespace: format def: "OWL ontology format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002195 ! Ontology format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002550 name: OBO-XML namespace: format def: "OBO ontology XML format." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002196 ! OBO format is_a: EDAM:0002332 ! XML [Term] id: EDAM:0002211 name: CIP strain data format namespace: format def: "Format for a report of strain data as used for CIP database entries." [EDAM:EBI "EMBRACE definition"] subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001760 name: CATH chain report format namespace: format def: "Format of CATH domain classification information for a polypeptide chain." [EDAM:EBI "EMBRACE definition"] comment: The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001761 name: CATH PDB report format namespace: format def: "Format of CATH domain classification information for a protein PDB file." [EDAM:EBI "EMBRACE definition"] comment: The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0001563 name: SMART domain assignment report format namespace: format def: "Format of SMART domain assignment data." [EDAM:EBI "EMBRACE definition"] comment: The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. subset: format is_obsolete: true consider: EDAM:0002331 ! HTML [Term] id: EDAM:0003000 name: AB1 namespace: format def: "AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence." [http://www.fileinfo.com/extension/ab1 EDAM:EBI "EMBRACE definition"] comment: AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). subset: format is_a: EDAM:0002333 ! Binary is_a: EDAM:0002057 ! Sequence trace format [Term] id: EDAM:0003001 name: ACE namespace: format def: "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt is_a: EDAM:0002330 ! Text is_a: EDAM:0002055 ! Sequence assembly format [Term] id: EDAM:0003003 name: BED namespace: format def: "BED format of sequence annotation track, typically to be displayed in a genome browser." [EDAM:EBI "EMBRACE definition"] comment: BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). subset: format spec: http://genome.ucsc.edu/FAQ/FAQformat#format1 is_a: EDAM:0002919 ! Sequence annotation track format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0003004 name: bigBed namespace: format def: "bigBed format for large sequence annotation tracks, similar to textual BED format." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://genome.ucsc.edu/FAQ/FAQformat#format1.5 is_a: EDAM:0002919 ! Sequence annotation track format is_a: EDAM:0002333 ! Binary [Term] id: EDAM:0003005 name: WIG namespace: format def: "Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://genome.ucsc.edu/goldenPath/help/wiggle.html is_a: EDAM:0002919 ! Sequence annotation track format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0003006 name: bigWig namespace: format def: "bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://genome.ucsc.edu/FAQ/FAQformat#format6.1 is_a: EDAM:0002919 ! Sequence annotation track format is_a: EDAM:0002333 ! Binary [Term] id: EDAM:0003007 name: PSL namespace: format def: "PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://genome.ucsc.edu/FAQ/FAQformat#format2 is_a: EDAM:0002919 ! Sequence annotation track format is_a: EDAM:0002920 ! Alignment format (pair only) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0003008 name: MAF namespace: format def: "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth." [EDAM:EBI "EMBRACE definition"] comment: Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. subset: format spec: http://genome.ucsc.edu/FAQ/FAQformat#format5 is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002919 ! Sequence annotation track format [Term] id: EDAM:0003009 name: 2bit namespace: format def: "2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://jcomeau.freeshell.org/www/genome/2bitformat.html http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002333 ! Binary [Term] id: EDAM:0003010 name: .nib namespace: format def: ".nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://genome.ucsc.edu/FAQ/FAQformat#format8 is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002333 ! Binary [Term] id: EDAM:0002094 name: pure namespace: format def: "EMBOSS alphabet for molecular sequence with possible unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002095 name: unpure namespace: format def: "EMBOSS alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002096 name: unambiguous sequence namespace: format def: "EMBOSS alphabet for a molecular sequence with possible unknown positions but without ambiguity characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002566 name: completely unambiguous namespace: format def: "EMBOSS alphabet for a molecular sequence without any unknown positions or ambiguity characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0002097 name: ambiguous namespace: format def: "EMBOSS alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001207 name: nucleotide namespace: format def: "EMBOSS alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] comment: Non-sequence characters may be used for example for gaps. subset: format is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001208 name: protein namespace: format def: "EMBOSS alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] comment: Non-sequence characters may be used for gaps and translation stop. subset: format synonym: "Amino acid sequence" EXACT [] is_a: EDAM:0002571 ! Raw sequence format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0001206 name: unambiguous pure namespace: format def: "EMBOSS alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002094 ! pure is_a: EDAM:0002096 ! unambiguous [Term] id: EDAM:0002567 name: completely unambiguous pure namespace: format def: "EMBOSS alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002094 ! pure is_a: EDAM:0002566 ! completely unambiguous [Term] id: EDAM:0001209 name: consensus namespace: format def: "EMBOSS alphabet for the consensus of two or more molecular sequences." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002097 ! ambiguous is_a: EDAM:0002095 ! unpure [Term] id: EDAM:0001210 name: pure nucleotide namespace: format def: "EMBOSS alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002094 ! pure is_a: EDAM:0001207 ! nucleotide [Term] id: EDAM:0001211 name: unambiguous pure nucleotide namespace: format def: "EMBOSS alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters ." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001207 ! nucleotide is_a: EDAM:0001206 ! unambiguous pure [Term] id: EDAM:0002568 name: completely unambiguous pure nucleotide namespace: format def: "EMBOSS alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters ." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001207 ! nucleotide is_a: EDAM:0002567 ! completely unambiguous pure [Term] id: EDAM:0001212 name: dna namespace: format def: "EMBOSS alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001207 ! nucleotide [Term] id: EDAM:0001213 name: rna namespace: format def: "EMBOSS alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001207 ! nucleotide [Term] id: EDAM:0001214 name: unambiguous pure dna namespace: format def: "EMBOSS alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001206 ! unambiguous pure is_a: EDAM:0001212 ! dna [Term] id: EDAM:0002569 name: completely unambiguous pure dna namespace: format def: "EMBOSS alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002567 ! completely unambiguous pure is_a: EDAM:0001212 ! dna [Term] id: EDAM:0001215 name: pure dna namespace: format def: "EMBOSS alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001210 ! pure nucleotide is_a: EDAM:0001212 ! dna [Term] id: EDAM:0001216 name: unambiguous pure rna sequence namespace: format def: "EMBOSS alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001206 ! unambiguous pure is_a: EDAM:0001213 ! rna [Term] id: EDAM:0002570 name: completely unambiguous pure rna sequence namespace: format def: "EMBOSS alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002567 ! completely unambiguous pure is_a: EDAM:0001213 ! rna [Term] id: EDAM:0001217 name: pure rna namespace: format def: "EMBOSS alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001210 ! pure nucleotide is_a: EDAM:0001213 ! rna [Term] id: EDAM:0001218 name: unambiguous pure protein namespace: format def: "EMBOSS alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0001206 ! unambiguous pure is_a: EDAM:0001208 ! protein [Term] id: EDAM:0002607 name: completely unambiguous pure protein namespace: format def: "EMBOSS alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002567 ! completely unambiguous pure is_a: EDAM:0001208 ! protein [Term] id: EDAM:0001219 name: pure protein namespace: format def: "EMBOSS alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters." [EDAM:EBI "EMBRACE definition"] subset: format is_a: EDAM:0002094 ! pure is_a: EDAM:0001208 ! protein [Term] id: EDAM:0003011 name: genePred namespace: format def: "genePred table format for gene prediction tracks." [EDAM:EBI "EMBRACE definition"] comment: genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. subset: format spec: http://genome.ucsc.edu/FAQ/FAQformat#format9 is_a: EDAM:0002919 ! Sequence annotation track format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0003012 name: pgSnp namespace: format def: "Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser." [EDAM:EBI "EMBRACE definition"] ! UCSC-specific,but also for custom tracks & useful subset: format spec: http://genome.ucsc.edu/FAQ/FAQformat#format10 is_a: EDAM:0002919 ! Sequence annotation track format is_a: EDAM:0002330 ! Text ! [Term] ! id: EDAM:000todo if desired (but then we could include 100 ucsc db tables) At least, this one is used also in IGV (for importing genome cytobands) ! name: Cytoband format ! namespace: format ! def: "Cytoband format for chromosome cytobands." [EDAM:EBI "EMBRACE definition"] ! comment: Reflects a UCSC Browser DB table. ! subset: format ! spec: http://www.broadinstitute.org/software/igv/Cytoband [Term] id: EDAM:0003013 name: axt namespace: format def: "axt format of alignments, typically produced from BLASTZ." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://genome.ucsc.edu/goldenPath/help/axt.html is_a: EDAM:0002920 ! Alignment format (pair only) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0003014 name: LAV namespace: format def: "LAV format of alignments generated by BLASTZ and LASTZ." [http://genome.ucsc.edu/goldenPath/help/axt.html] ! Can be used by UCSC and Galaxy subset: format spec: http://www.bx.psu.edu/miller_lab/dist/lav_format.html is_a: EDAM:0002920 ! Alignment format (pair only) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0003015 name: Pileup namespace: format def: "Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s)." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://samtools.sourceforge.net/pileup.shtml is_a: EDAM:0002920 ! Alignment format (pair only) is_a: EDAM:0002330 ! Text ! and of track? (encoded as points, but could be 'function', like wig) [Term] id: EDAM:0003016 name: VCF namespace: format def: "Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://vcftools.sourceforge.net/specs.html is_a: EDAM:0002921 ! Sequence variation annotation format is_a: EDAM:0002330 ! Text [Term] id: EDAM:0003017 name: SRF namespace: format def: "Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive." [EDAM:EBI "EMBRACE definition" http://srf.sourceforge.net/ShortSequenceFormatDec18th_v_1_3.htm] subset: format spec: http://srf.sourceforge.net/ is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0002333 ! Binary [Term] id: EDAM:0003018 name: ZTR namespace: format def: "ZTR format for storing chromatogram data from DNA sequencing instruments." [http://staden.sourceforge.net/manual/formats_unix_12.html EDAM:EBI "EMBRACE definition"] subset: format spec: http://staden.sourceforge.net/manual/formats_unix_12.html is_a: EDAM:0002057 ! Sequence trace format is_a: EDAM:0002333 ! Binary [Term] id: EDAM:0003019 name: GVF namespace: format def: "Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://sequenceontology.org/gvf.html is_a: EDAM:0001975 ! GFF3 ! is_format_of (1255, Sequence feature annotation) is defined in parent (+ here has special tags for a particular class of seqfeatures: variation (indels,polymphs,structvar)) [Term] id: EDAM:0003020 name: BCF namespace: format def: "BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [EDAM:EBI "EMBRACE definition"] subset: format spec: http://samtools.sourceforge.net/mpileup.shtml ! BCF described on this site is_a: EDAM:0002921 ! Sequence variation annotation format is_a: EDAM:0002333 ! Binary