format-version: 1.2 ontology: http://edamontology.org subsetdef: bioinformatics "Bioinformatics" subsetdef: concept_properties "EDAM concept properties" subsetdef: data "EDAM types of data" subsetdef: edam "EDAM" subsetdef: formats "EDAM data formats" subsetdef: identifiers "EDAM types of identifiers" subsetdef: operations "EDAM operations" subsetdef: relations "EDAM relations" subsetdef: topics "EDAM topics" data-version: 1.2 date: 13:12:2012 00:00 default-relationship-id-prefix: EDAM idspace: EDAM http://edamontology.org/ "EDAM relations and concept properties" idspace: EDAM_data http://edamontology.org/data_ "EDAM types of data" idspace: EDAM_format http://edamontology.org/format_ "EDAM data formats" idspace: EDAM_operation http://edamontology.org/operation_ "EDAM operations" idspace: EDAM_topic http://edamontology.org/topic_ "EDAM topics" remark: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web. remark: EDAM editors: Jon Ison and Matus Kalas. Co-authors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE (FP6, EU), EMBOSS (BBSRC, UK), eSysbio and FUGE Bioinformatics Platform (both Research Council of Norway). See http://edamontology.org for documentation and licence. page: http://edamontology.org/page definedBy: EDAM_1.2.owl next_id: 3263 saved-by: Jon Ison, Matus Kalas ![Term] !id: ObsoleteClass !name: Obsolete concept (EDAM) !comment: Needed for conversion to the OBO format. !created_in: "1.2 / http://www.geneontology.org/formats/oboInOwl" !def: "An obsolete concept (redefined in EDAM)." [http://edamontology.org] !is_a: ObsoleteClass ! Obsolete concept (EDAM) !is_a: owl:DeprecatedClass !is_obsolete: true [Term] id: EDAM_data:0005 name: Resource type subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A type of computational resource used in bioinformatics." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:0006 name: Data subset: bioinformatics subset: data subset: edam synonym: "Continuant" BROAD [] synonym: "Data record" EXACT [] synonym: "Data set" NARROW [] synonym: "WSIO_data:002" EXACT [] synonym: "Datum" NARROW [] synonym: "DigitalEntity" RELATED [] synonym: "IAO:0000027" RELATED [] synonym: "IAO:0000030" RELATED [] synonym: "Perpetuant" RELATED [] synonym: "SIO:000069" RELATED [] synonym: "SIO:000088" RELATED [] created_in: "beta12orEarlier" def: "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output." [http://edamontology.org] namespace: data disjoint_from: EDAM_format:1915 ! Format disjoint_from: EDAM_operation:0004 ! Operation disjoint_from: EDAM_topic:0003 ! Topic [Term] id: EDAM_data:0007 name: Tool subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A bioinformatics package or tool, e.g. a standalone application or web service." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:0581 name: Database subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:0582 name: Ontology subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_data:0583 name: Directory metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A directory on disk from which files are read." [http://edamontology.org] namespace: data is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:0831 name: MeSH vocabulary subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0582 ! Ontology [Term] id: EDAM_data:0832 name: HGNC vocabulary subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0582 ! Ontology [Term] id: EDAM_data:0835 name: UMLS vocabulary subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0582 ! Ontology [Term] id: EDAM_data:0842 name: Identifier subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "WSIO_data:005" EXACT [] synonym: "http://purl.org/dc/elements/1.1/identifier" NARROW [] synonym: "ID" EXACT [] synonym: "SIO:000115" EXACT [] created_in: "beta12orEarlier" def: "A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0006 ! Data disjoint_from: EDAM_data:2048 ! Report disjoint_from: EDAM_data:2527 ! Parameter disjoint_from: EDAM_data:3031 ! Core data relationship: is_identifier_of EDAM_data:0006 ! Data [Term] id: EDAM_data:0843 name: Database entry subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An entry (retrievable via URL) from a biological database." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0006 ! Data [Term] id: EDAM_data:0844 name: Molecular mass subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Mass of a molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:2050 ! Molecular property (general) [Term] id: EDAM_data:0845 name: Molecular charge subset: bioinformatics subset: data subset: edam xref: PDBML:pdbx_formal_charge created_in: "beta12orEarlier" def: "Net charge of a molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:2050 ! Molecular property (general) [Term] id: EDAM_data:0846 name: Chemical formula subset: bioinformatics subset: data subset: edam synonym: "Chemical structure specification" EXACT [] created_in: "beta12orEarlier" def: "A specification of a chemical structure." [http://edamontology.org] namespace: data is_a: EDAM_data:2050 ! Molecular property (general) [Term] id: EDAM_data:0847 name: QSAR descriptor 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. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A QSAR quantitative descriptor (name-value pair) of chemical structure." [http://edamontology.org] namespace: data is_a: EDAM_data:2050 ! Molecular property (general) [Term] id: EDAM_data:0848 name: Raw sequence comment: Non-sequence characters may be used for example for gaps and translation stop. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] namespace: data is_a: EDAM_data:2044 ! Sequence [Term] id: EDAM_data:0849 name: Sequence record subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A molecular sequence and associated metadata." [http://edamontology.org] namespace: data is_a: EDAM_data:2044 ! Sequence [Term] id: EDAM_data:0850 name: Sequence set comment: This concept may be used for arbitrary sequence sets and associated data arising from processing. subset: bioinformatics subset: data subset: edam synonym: "SO:0001260" RELATED [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:0851 name: Sequence mask character subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A character used to replace (mask) other characters in a molecular sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2023 ! Sequence mask parameter [Term] id: EDAM_data:0852 name: Sequence mask type 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A label (text token) describing the type of sequence masking to perform." [http://edamontology.org] namespace: data is_a: EDAM_data:2023 ! Sequence mask parameter is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:0853 name: DNA sense specification 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: bioinformatics subset: data subset: edam synonym: "DNA strand specification" EXACT [] synonym: "Strand" EXACT [] created_in: "beta12orEarlier" def: "The strand of a DNA sequence (forward or reverse)." [http://edamontology.org] namespace: data is_a: EDAM_data:2534 ! Sequence parameter is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:0854 name: Sequence length specification subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A specification of sequence length(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:0855 name: Sequence metadata comment: This is used for such things as a report including the sequence identifier, type and length. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Basic or general information concerning molecular sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1254 ! Sequence property is_a: EDAM_data:2337 ! Metadata is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:0856 name: Sequence feature source 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived." [http://edamontology.org] namespace: data is_a: EDAM_data:2042 ! Evidence is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:0857 name: Database hits (sequence) 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2080 ! Database hits [Term] id: EDAM_data:0858 name: Database hits (secondary) 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 concepts under 'Protein features'. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report of hits from a search of a protein secondary or domain database." [http://edamontology.org] namespace: data is_a: EDAM_data:2080 ! Database hits [Term] id: EDAM_data:0859 name: Sequence signature model subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data files used by motif or profile methods." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:0860 name: Sequence signature subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A classifier of sequences such as a sequence motif, profile or other diagnostic element." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1353 ! Sequence motif consider: EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:0861 name: Sequence alignment (words) subset: bioinformatics subset: data subset: edam synonym: "Sequence word alignment" EXACT [] created_in: "beta12orEarlier" def: "Alignment of exact matches between subsequences (words) within two or more molecular sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:0862 name: Dotplot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] namespace: data is_a: EDAM_data:2161 ! Sequence similarity plot [Term] id: EDAM_data:0863 name: Sequence alignment subset: bioinformatics subset: data subset: edam synonym: "http://purl.bioontology.org/ontology/MSH/D016415" EXACT [] synonym: "Sequence:alignment" EXACT [] synonym: "SIO:010066" EXACT [] created_in: "beta12orEarlier" def: "Alignment of multiple molecular sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1916 ! Alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_data:0864 name: Sequence alignment parameter subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Some simple value controlling a sequence alignment (or similar 'match') operation." [http://edamontology.org] namespace: data is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:0865 name: Sequence similarity score subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A value representing molecular sequence similarity." [http://edamontology.org] namespace: data is_a: EDAM_data:1772 ! Score or penalty [Term] id: EDAM_data:0866 name: Sequence alignment metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." [http://edamontology.org] namespace: data is_a: EDAM_data:0867 ! Sequence alignment report is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:0867 name: Sequence alignment report comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report of molecular sequence alignment-derived data or metadata." [http://edamontology.org] namespace: data is_a: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:0868 name: Sequence profile alignment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A profile-profile alignment (each profile typically representing a sequence alignment)." [http://edamontology.org] namespace: data is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:0869 name: Sequence-profile alignment 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment)." [http://edamontology.org] namespace: data is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:0870 name: Sequence distance matrix comment: Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. subset: bioinformatics subset: data subset: edam synonym: "Phylogenetic distance matrix" EXACT [] xref: Moby:phylogenetic_distance_matrix created_in: "beta12orEarlier" def: "A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation." [http://edamontology.org] namespace: data is_a: EDAM_data:2855 ! Distance matrix [Term] id: EDAM_data:0871 name: Phylogenetic character data comment: As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments subset: bioinformatics subset: data subset: edam synonym: "Character" RELATED [] created_in: "beta12orEarlier" def: "Basic character data from which a phylogenetic tree may be generated." [http://edamontology.org] namespace: data is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] id: EDAM_data:0872 name: Phylogenetic tree 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: bioinformatics subset: data subset: edam synonym: "http://purl.bioontology.org/ontology/MSH/D010802" RELATED [] synonym: "Phylogeny" EXACT [] synonym: "Tree" RELATED [] xref: Moby:myTree xref: Moby:phylogenetic_tree xref: Moby:Tree created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_data:0874 name: Comparison matrix 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: bioinformatics subset: data subset: edam synonym: "Substitution matrix" EXACT [] created_in: "beta12orEarlier" def: "Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison." [http://edamontology.org] namespace: data is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:0875 name: Protein topology comment: The location and size of the secondary structure elements and intervening loop regions is usually indicated. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Predicted or actual protein topology represented as a string of protein secondary structure elements." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0876 ! Protein features (secondary structure) [Term] id: EDAM_data:0876 name: Protein features (secondary structure) 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: bioinformatics subset: data subset: edam synonym: "Protein secondary structure" EXACT [] created_in: "beta12orEarlier" def: "Secondary structure assignment (predicted or real) of a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:2081 ! Secondary structure relationship: has_topic EDAM_topic:0694 ! Protein secondary structure [Term] id: EDAM_data:0877 name: Protein features (super-secondary) comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. subset: bioinformatics subset: data subset: edam synonym: "Protein structure report (super-secondary)" EXACT [] created_in: "beta12orEarlier" def: "A report of predicted or actual super-secondary structure of protein sequence(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:0878 name: Secondary structure alignment (protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of the (1D representations of) secondary structure of two or more proteins." [http://edamontology.org] namespace: data is_a: EDAM_data:2366 ! Secondary structure alignment is_a: EDAM_data:3154 ! Protein alignment [Term] id: EDAM_data:0879 name: Secondary structure alignment metadata (protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:0880 name: RNA secondary structure record comment: This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. subset: bioinformatics subset: data subset: edam xref: Moby:RNAStructML created_in: "beta12orEarlier" def: "An informative report of secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:2081 ! Secondary structure relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] id: EDAM_data:0881 name: Secondary structure alignment (RNA) subset: bioinformatics subset: data subset: edam xref: Moby:RNAStructAlignmentML created_in: "beta12orEarlier" def: "Alignment of the (1D representations of) secondary structure of two or more RNA molecules." [http://edamontology.org] namespace: data is_a: EDAM_data:2366 ! Secondary structure alignment [Term] id: EDAM_data:0882 name: Secondary structure alignment metadata (RNA) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report of RNA secondary structure alignment-derived data or metadata." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:0883 name: Structure comment: The coordinate data may be predicted or real. subset: bioinformatics subset: data subset: edam synonym: "http://purl.bioontology.org/ontology/MSH/D015394" RELATED [] synonym: "Structure data" EXACT [] created_in: "beta12orEarlier" def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_data:0884 name: Tertiary structure record subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An entry from a molecular tertiary (3D) structure database." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0883 ! Structure [Term] id: EDAM_data:0885 name: Database hits (structure) comment: This includes alignment and score data. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Results (hits) from searching a database of tertiary structure." [http://edamontology.org] namespace: data is_a: EDAM_data:2080 ! Database hits [Term] id: EDAM_data:0886 name: Structure alignment 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of molecular tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:0883 ! Structure is_a: EDAM_data:1916 ! Alignment relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] id: EDAM_data:0887 name: Structure alignment report comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on molecular tertiary structure alignment-derived data." [http://edamontology.org] namespace: data is_a: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:0888 name: Structure similarity score subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison." [http://edamontology.org] namespace: data is_a: EDAM_data:1772 ! Score or penalty [Term] id: EDAM_data:0889 name: Structural (3D) profile subset: bioinformatics subset: data subset: edam synonym: "3D profile" EXACT [] created_in: "beta12orEarlier" def: "Some type of structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] id: EDAM_data:0890 name: Structural (3D) profile alignment subset: bioinformatics subset: data subset: edam synonym: "Structural profile alignment" EXACT [] created_in: "beta12orEarlier" def: "A 3D profile-3D profile alignment (each profile representing structures or a structure alignment)." [http://edamontology.org] namespace: data is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:0891 name: Sequence-3D profile alignment subset: bioinformatics subset: data subset: edam synonym: "Sequence-structural profile alignment" EXACT [] created_in: "beta12orEarlier" def: "An alignment of a sequence to a 3D profile (representing structures or a structure alignment)." [http://edamontology.org] namespace: data is_a: EDAM_data:0893 ! Sequence-structure alignment [Term] id: EDAM_data:0892 name: Protein sequence-structure scoring matrix subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Matrix of values used for scoring sequence-structure compatibility." [http://edamontology.org] namespace: data is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:0893 name: Sequence-structure alignment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s))." [http://edamontology.org] namespace: data is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:0894 name: Amino acid annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report about a specific amino acid." [http://edamontology.org] namespace: data is_a: EDAM_data:0962 ! Small molecule annotation is_a: EDAM_data:2016 ! Amino acid property [Term] id: EDAM_data:0895 name: Peptide annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report about a specific peptide." [http://edamontology.org] namespace: data is_a: EDAM_data:0962 ! Small molecule annotation is_a: EDAM_data:2979 ! Peptide property relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids [Term] id: EDAM_data:0896 name: Protein report subset: bioinformatics subset: data subset: edam synonym: "Gene product annotation" EXACT [] created_in: "beta12orEarlier" def: "An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data." [http://edamontology.org] namespace: data is_a: EDAM_data:2529 ! Molecule report relationship: has_topic EDAM_topic:0078 ! Protein analysis [Term] id: EDAM_data:0897 name: Protein property 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: bioinformatics subset: data subset: edam synonym: "Protein physicochemical property" EXACT [] created_in: "beta12orEarlier" def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model." [http://edamontology.org] namespace: data is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:0899 name: Protein features (3D motif) comment: This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. subset: bioinformatics subset: data subset: edam synonym: "Protein structure report (3D motif)" EXACT [] created_in: "beta12orEarlier" def: "An informative report on the 3D structural motifs in a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:1537 ! Protein structure report relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces [Term] id: EDAM_data:0900 name: Protein domain classification subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:2980 ! Protein classification relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_data:0901 name: Protein features (domains) 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: bioinformatics subset: data subset: edam synonym: "Protein domain assignment" EXACT [] synonym: "Protein structural domains" EXACT [] created_in: "beta12orEarlier" def: "Summary of structural domains or 3D folds in a protein or polypeptide chain." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_data:0902 name: Protein architecture report subset: bioinformatics subset: data subset: edam synonym: "Protein property (architecture)" EXACT [] synonym: "Protein structure report (architecture)" EXACT [] created_in: "beta12orEarlier" def: "An informative report on architecture (spatial arrangement of secondary structure) of a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:0903 name: Protein folding report 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: bioinformatics subset: data subset: edam synonym: "Protein property (folding)" EXACT [] synonym: "Protein report (folding)" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:0904 name: Protein features (mutation) 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: bioinformatics subset: data subset: edam synonym: "Protein property (mutation)" EXACT [] synonym: "Protein report (mutation)" EXACT [] synonym: "Protein structure report (mutation)" EXACT [] created_in: "beta12orEarlier" def: "Data on the effect of (typically point) mutation on protein folding, stability, structure and function." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:0905 name: Protein interaction raw data 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [http://edamontology.org] namespace: data is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:0906 name: Protein interaction subset: bioinformatics subset: data subset: edam synonym: "Protein report (interaction)" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:2599 ! Molecular interaction relationship: has_topic EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_data:0907 name: Protein family subset: bioinformatics subset: data subset: edam synonym: "Protein family annotation" EXACT [] created_in: "beta12orEarlier" def: "An informative report on a specific protein family or other group of classified proteins." [http://edamontology.org] namespace: data is_a: EDAM_data:2980 ! Protein classification relationship: has_topic EDAM_topic:0724 ! Protein families [Term] id: EDAM_data:0909 name: Vmax subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large." [http://edamontology.org] namespace: data is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_data:0910 name: Km subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction." [http://edamontology.org] namespace: data is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_data:0911 name: Nucleotide base annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report about a specific nucleotide base." [http://edamontology.org] namespace: data is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:0912 name: Nucleic acid property 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: bioinformatics subset: data subset: edam synonym: "Nucleic acid physicochemical property" EXACT [] created_in: "beta12orEarlier" def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:2084 ! Nucleic acid report is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:0914 name: Codon usage report comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] id: EDAM_data:0916 name: Gene annotation 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: bioinformatics subset: data subset: edam synonym: "Gene annotation (functional)" EXACT [] synonym: "Gene report" EXACT [] xref: Moby:gene xref: Moby:GeneInfo xref: Moby_namespace:Human_Readable_Description created_in: "beta12orEarlier" def: "An informative report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features relationship: has_topic EDAM_topic:0623 ! Genes, gene family or system [Term] id: EDAM_data:0917 name: Gene classification subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:0918 name: Nucleic acid features (variation) subset: bioinformatics subset: data subset: edam synonym: "Sequence variation annotation" EXACT [] synonym: "SO:0001059" RELATED [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:3122 ! Nucleic acid features (difference and change) relationship: has_topic EDAM_topic:0199 ! Genetic variation [Term] id: EDAM_data:0919 name: Gene annotation (chromosome) comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a specific chromosome." [http://edamontology.org] namespace: data is_a: EDAM_data:0916 ! Gene annotation relationship: has_topic EDAM_topic:0624 ! Chromosomes [Term] id: EDAM_data:0920 name: Genotype/phenotype annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:0922 name: Nucleic acid features (primers) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination) relationship: has_topic EDAM_topic:0632 ! Probes and primers [Term] id: EDAM_data:0923 name: Experiment annotation (PCR assay data) subset: bioinformatics subset: data subset: edam synonym: "PCR assay data" EXACT [] created_in: "beta12orEarlier" def: "Data on a PCR assay or electronic / virtual PCR." [http://edamontology.org] namespace: data is_a: EDAM_data:2531 ! Experiment annotation relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_data:0924 name: Sequence trace comment: This is the raw data produced by a DNA sequencing machine. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores." [http://edamontology.org] namespace: data is_a: EDAM_data:2887 ! Sequence record (nucleic acid) is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:0925 name: Sequence assembly 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: bioinformatics subset: data subset: edam synonym: "Sequence:assembly" EXACT [] synonym: "SO:0000353" EXACT [] synonym: "SO:0001248" NARROW [] created_in: "beta12orEarlier" def: "An assembly of fragments of a (typically genomic) DNA sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:0926 name: Radiation Hybrid (RH) scores comment: Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Radiation hybrid scores (RH) scores for one or more markers." [http://edamontology.org] namespace: data is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:0927 name: Gene annotation (linkage) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on the linkage of alleles." [http://edamontology.org] namespace: data is_a: EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:0928 name: Gene expression profile subset: bioinformatics subset: data subset: edam synonym: "Gene expression pattern" EXACT [] created_in: "beta12orEarlier" def: "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:0931 name: Experiment annotation (microarray) 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: bioinformatics subset: data subset: edam synonym: "Experimental design annotation" EXACT [] created_in: "beta12orEarlier" def: "Information on a microarray experiment such as conditions, protocol, sample:data relationships etc." [http://edamontology.org] namespace: data is_a: EDAM_data:2531 ! Experiment annotation relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:0932 name: Oligonucleotide probe data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on oligonucleotide probes (typically for use with DNA microarrays)." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2717 ! Oligonucleotide probe annotation [Term] id: EDAM_data:0933 name: SAGE experimental data subset: bioinformatics subset: data subset: edam synonym: "Serial analysis of gene expression (SAGE) experimental data" EXACT [] created_in: "beta12orEarlier" def: "Output from a serial analysis of gene expression (SAGE) experiment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2535 ! Sequence tag profile [Term] id: EDAM_data:0934 name: MPSS experimental data subset: bioinformatics subset: data subset: edam synonym: "Massively parallel signature sequencing (MPSS) experimental data" EXACT [] created_in: "beta12orEarlier" def: "Massively parallel signature sequencing (MPSS) data." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2535 ! Sequence tag profile [Term] id: EDAM_data:0935 name: SBS experimental data subset: bioinformatics subset: data subset: edam synonym: "Sequencing by synthesis (SBS) experimental data" EXACT [] created_in: "beta12orEarlier" def: "Sequencing by synthesis (SBS) data." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2535 ! Sequence tag profile [Term] id: EDAM_data:0936 name: Sequence tag profile (with gene assignment) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2535 ! Sequence tag profile [Term] id: EDAM_data:0937 name: Protein X-ray crystallographic data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "X-ray crystallography data." [http://edamontology.org] namespace: data is_a: EDAM_data:2537 ! Protein structure raw data [Term] id: EDAM_data:0938 name: Protein NMR data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Protein nuclear magnetic resonance (NMR) raw data." [http://edamontology.org] namespace: data is_a: EDAM_data:2537 ! Protein structure raw data [Term] id: EDAM_data:0939 name: Protein circular dichroism (CD) spectroscopic data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data." [http://edamontology.org] namespace: data is_a: EDAM_data:2537 ! Protein structure raw data [Term] id: EDAM_data:0940 name: Electron microscopy volume map subset: bioinformatics subset: data subset: edam synonym: "EM volume map" EXACT [] created_in: "beta12orEarlier" def: "Volume map data from electron microscopy." [http://edamontology.org] namespace: data is_a: EDAM_data:3108 ! Experimental measurement relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] id: EDAM_data:0941 name: Electron microscopy model comment: This might include the location in the model of the known features of a particular macromolecule. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Annotation on a structural 3D model (volume map) from electron microscopy." [http://edamontology.org] namespace: data is_a: EDAM_data:0940 ! Electron microscopy volume map relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] id: EDAM_data:0942 name: 2D PAGE image subset: bioinformatics subset: data subset: edam synonym: "Two-dimensional gel electrophoresis image" EXACT [] created_in: "beta12orEarlier" def: "Two-dimensional gel electrophoresis image." [http://edamontology.org] namespace: data is_a: EDAM_data:2968 ! Image is_a: EDAM_data:3108 ! Experimental measurement relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] id: EDAM_data:0943 name: Mass spectrometry spectra subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Spectra from mass spectrometry." [http://edamontology.org] namespace: data is_a: EDAM_data:2536 ! Mass spectrometry data relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] id: EDAM_data:0944 name: Peptide mass fingerprint subset: bioinformatics subset: data subset: edam synonym: "Peak list" EXACT [] synonym: "Protein fingerprint" EXACT [] created_in: "beta12orEarlier" def: "A set of peptide masses (peptide mass fingerprint) from mass spectrometry." [http://edamontology.org] namespace: data is_a: EDAM_data:2536 ! Mass spectrometry data is_a: EDAM_data:2979 ! Peptide property relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:0945 name: Peptide identification subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database." [http://edamontology.org] namespace: data is_a: EDAM_data:2979 ! Peptide property relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:0946 name: Pathway or network annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_data:0947 name: Biological pathway map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A map (typically a diagram) of a biological pathway." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:0948 name: Data resource definition subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper." [http://edamontology.org] namespace: data is_a: EDAM_data:1883 ! Annotated URI [Term] id: EDAM_data:0949 name: Workflow metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:0950 name: Biological model subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A biological model which can be represented in mathematical terms." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0771 ! Biological models [Term] id: EDAM_data:0951 name: Statistical estimate score subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A value representing estimated statistical significance of some observed data; typically sequence database hits." [http://edamontology.org] namespace: data is_a: EDAM_data:1772 ! Score or penalty is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:0952 name: EMBOSS database resource definition subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Resource definition for an EMBOSS database." [http://edamontology.org] namespace: data is_a: EDAM_data:0957 ! Database metadata [Term] id: EDAM_data:0953 name: Version information comment: Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. subset: bioinformatics subset: data subset: edam synonym: "IAO:0000129" NARROW [] synonym: "SIO:000653" NARROW [] synonym: "SWO:9000061" NARROW [] synonym: "Version" EXACT [] created_in: "beta12orEarlier" def: "Information on a version of software or data, for example name, version number and release date." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:0954 name: Database cross-mapping 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases." [http://edamontology.org] namespace: data is_a: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:0955 name: Data index subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An index of data of biological relevance." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] id: EDAM_data:0956 name: Data index report subset: bioinformatics subset: data subset: edam synonym: "Database index annotation" EXACT [] created_in: "beta12orEarlier" def: "A report of an analysis of an index of biological data." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] id: EDAM_data:0957 name: Database metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." [http://edamontology.org] namespace: data is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:0958 name: Tool metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." [http://edamontology.org] namespace: data is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:0959 name: Job metadata subset: bioinformatics subset: data subset: edam xref: Moby:PDGJOB created_in: "beta12orEarlier" def: "Textual metadata on a submitted or completed job." [http://edamontology.org] namespace: data is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:0960 name: User metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Textual metadata on a software author or end-user, for example a person or other software." [http://edamontology.org] namespace: data is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:0962 name: Small molecule annotation subset: bioinformatics subset: data subset: edam synonym: "Chemical compound annotation" EXACT [] synonym: "Small molecule report" EXACT [] created_in: "beta12orEarlier" def: "An informative report on a specific chemical compound." [http://edamontology.org] namespace: data is_a: EDAM_data:2085 ! Structure report is_a: EDAM_data:2529 ! Molecule report relationship: has_topic EDAM_topic:0154 ! Small molecules [Term] id: EDAM_data:0963 name: Cell line annotation subset: bioinformatics subset: data subset: edam synonym: "Organism strain data" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2530 ! Organism annotation [Term] id: EDAM_data:0964 name: Scent annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report about a specific scent." [http://edamontology.org] namespace: data is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:0966 name: Ontology term subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term (name) from an ontology." [http://edamontology.org] namespace: data is_a: EDAM_data:0967 ! Ontology concept metadata [Term] id: EDAM_data:0967 name: Ontology concept metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning or derived from a concept from a biological ontology." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_data:0968 name: Keyword comment: Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. subset: bioinformatics subset: data subset: edam xref: Moby:BooleanQueryString xref: Moby:Global_Keyword xref: Moby:QueryString xref: Moby:Wildcard_Query created_in: "beta12orEarlier" def: "Keyword(s) or phrase(s) used (typically) for text-searching purposes." [http://edamontology.org] namespace: data is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:0970 name: Bibliographic reference 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: bioinformatics subset: data subset: edam synonym: "Citation" EXACT [] synonym: "Reference" EXACT [] xref: Moby:GCP_SimpleCitation xref: Moby:Publication created_in: "beta12orEarlier" def: "Bibliographic data that uniquely identifies a scientific article, book or other published material." [http://edamontology.org] namespace: data is_a: EDAM_data:2093 ! Data reference is_a: EDAM_data:2857 ! Article metadata [Term] id: EDAM_data:0971 name: Article subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A body of scientific text, typically a full text article from a scientific journal." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:3068 ! Literature and reference [Term] id: EDAM_data:0972 name: Text mining report comment: A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An abstract of the results of text mining." [http://edamontology.org] namespace: data is_a: EDAM_data:2954 ! Article report [Term] id: EDAM_data:0974 name: Entity identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a biological entity or phenomenon." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0975 name: Data resource identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a data resource." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0976 name: Identifier (typed) comment: This concept 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 concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier that identifies a particular type of data." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0977 name: Tool identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a bioinformatics tool, e.g. an application or web service." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:0978 name: Discrete entity identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence)." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0979 name: Entity feature identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0980 name: Entity collection identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name or other identifier of a collection of discrete biological entities." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0981 name: Phenomenon identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name or other identifier of a physical, observable biological occurrence or event." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:0982 name: Molecule identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name or other identifier of a molecule." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2529 ! Molecule report [Term] id: EDAM_data:0983 name: Atom identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier (e.g. character symbol) of a specific atom." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:0984 name: Molecule name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a specific molecule." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0982 ! Molecule identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:0985 name: Molecule type comment: For example, 'Protein', 'DNA', 'RNA' etc. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A label (text token) describing the type a molecule." [http://edamontology.org] example: "Protein|DNA|RNA" namespace: data is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:0986 name: Chemical identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a chemical compound." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:0987 name: Chromosome name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a chromosome." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0984 ! Molecule name is_a: EDAM_data:2119 ! Nucleic acid identifier relationship: is_identifier_of EDAM_data:0919 ! Gene annotation (chromosome) [Term] id: EDAM_data:0988 name: Peptide identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a peptide chain." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0982 ! Molecule identifier [Term] id: EDAM_data:0989 name: Protein identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a protein." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0982 ! Molecule identifier relationship: is_identifier_of EDAM_data:0896 ! Protein report [Term] id: EDAM_data:0990 name: Compound name subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Chemical name" EXACT [] created_in: "beta12orEarlier" def: "Unique name of a chemical compound." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0984 ! Molecule name is_a: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:0991 name: Chemical registry number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique registry number of a chemical compound." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:0992 name: Ligand identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Code word for a ligand, for example from a PDB file." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:0993 name: Drug identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a drug." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1086 ! Compound identifier relationship: is_identifier_of EDAM_data:2851 ! Drug structure [Term] id: EDAM_data:0994 name: Amino acid identifier subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Residue identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an amino acid." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1086 ! Compound identifier relationship: is_identifier_of EDAM_data:2016 ! Amino acid property [Term] id: EDAM_data:0995 name: Nucleotide identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name or other identifier of a nucleotide." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:0996 name: Monosaccharide identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a monosaccharide." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:0997 name: Chemical name (ChEBI) comment: This is the recommended chemical name for use for example in database annotation. subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "ChEBI chemical name" EXACT [] created_in: "beta12orEarlier" def: "Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:0998 name: Chemical name (IUPAC) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "IUPAC chemical name" EXACT [] created_in: "beta12orEarlier" def: "IUPAC recommended name of a chemical compound." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:0999 name: Chemical name (INN) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "INN chemical name" EXACT [] created_in: "beta12orEarlier" def: "International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:1000 name: Chemical name (brand) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Brand chemical name" EXACT [] created_in: "beta12orEarlier" def: "Brand name of a chemical compound." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:1001 name: Chemical name (synonymous) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Synonymous chemical name" EXACT [] created_in: "beta12orEarlier" def: "Synonymous name of a chemical compound." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:1002 name: Chemical registry number (CAS) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CAS chemical registry number" EXACT [] created_in: "beta12orEarlier" def: "CAS registry number of a chemical compound." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0991 ! Chemical registry number [Term] id: EDAM_data:1003 name: Chemical registry number (Beilstein) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Beilstein chemical registry number" EXACT [] created_in: "beta12orEarlier" def: "Beilstein registry number of a chemical compound." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0991 ! Chemical registry number [Term] id: EDAM_data:1004 name: Chemical registry number (Gmelin) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Gmelin chemical registry number" EXACT [] created_in: "beta12orEarlier" def: "Gmelin registry number of a chemical compound." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0991 ! Chemical registry number [Term] id: EDAM_data:1005 name: HET group name subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Component identifier code" EXACT [] synonym: "Short ligand name" EXACT [] created_in: "beta12orEarlier" def: "3-letter code word for a ligand (HET group) from a PDB file, for example ATP." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0990 ! Compound name [Term] id: EDAM_data:1006 name: Amino acid name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "String of one or more ASCII characters representing an amino acid." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0994 ! Amino acid identifier [Term] id: EDAM_data:1007 name: Nucleotide code subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "String of one or more ASCII characters representing a nucleotide." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0990 ! Compound name is_a: EDAM_data:0995 ! Nucleotide identifier [Term] id: EDAM_data:1008 name: Polypeptide chain ID comment: This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Chain identifier" EXACT [] synonym: "PDB chain identifier" EXACT [] synonym: "PDB strand id" EXACT [] synonym: "Polypeptide chain identifier" EXACT [] synonym: "Protein chain identifier" EXACT [] xref: PDBML:pdbx_PDB_strand_id xref: WHATIF: chain created_in: "beta12orEarlier" def: "Identifier of a polypeptide chain from a protein." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0988 ! Peptide identifier relationship: is_identifier_of EDAM_data:1467 ! Protein chain [Term] id: EDAM_data:1009 name: Protein name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a protein." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0984 ! Molecule name is_a: EDAM_data:0989 ! Protein identifier [Term] id: EDAM_data:1010 name: Enzyme identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name or other identifier of an enzyme or record from a database of enzymes." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0989 ! Protein identifier relationship: is_identifier_of EDAM_data:1509 ! Enzyme property [Term] id: EDAM_data:1011 name: EC number subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "EC" EXACT [] synonym: "EC code" EXACT [] synonym: "Enzyme Commission number" EXACT [] xref: Moby:Annotated_EC_Number xref: Moby:EC_Number created_in: "beta12orEarlier" def: "An Enzyme Commission (EC) number of an enzyme." [http://edamontology.org] regex: "[0-9]+\\.-\\.-\\.-|[0-9]+\\.[0-9]+\\.-\\.-|[0-9]+\\.[0-9]+\\.[0-9]+\\.-|[0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+" namespace: identifier is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:1012 name: Enzyme name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of an enzyme." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1009 ! Protein name is_a: EDAM_data:1010 ! Enzyme identifier [Term] id: EDAM_data:1013 name: Restriction enzyme name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a restriction enzyme." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1012 ! Enzyme name relationship: is_identifier_of EDAM_data:1517 ! Restriction enzyme property [Term] id: EDAM_data:1014 name: Sequence position specification subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A specification (partial or complete) of one or more positions or regions of a molecular sequence or map." [http://edamontology.org] namespace: data is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:1015 name: Sequence feature ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:3034 ! Sequence feature identifier [Term] id: EDAM_data:1016 name: Sequence position subset: bioinformatics subset: data subset: edam synonym: "SO:0000735" RELATED [] xref: PDBML:_atom_site.id xref: WHATIF: number xref: WHATIF: PDBx_atom_site created_in: "beta12orEarlier" def: "A position of a single point (base or residue) in a sequence, or part of such a specification." [http://edamontology.org] namespace: data is_a: EDAM_data:1014 ! Sequence position specification [Term] id: EDAM_data:1017 name: Sequence range subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Specification of range(s) of sequence positions." [http://edamontology.org] namespace: data is_a: EDAM_data:1014 ! Sequence position specification [Term] id: EDAM_data:1018 name: Nucleic acid feature identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name or other identifier of an nucleic acid feature." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1015 ! Sequence feature ID [Term] id: EDAM_data:1019 name: Protein feature identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name or other identifier of a protein feature." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1015 ! Sequence feature ID [Term] id: EDAM_data:1020 name: Sequence feature key comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. subset: bioinformatics subset: data subset: edam synonym: "Sequence feature method" EXACT [] synonym: "Sequence feature type" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1021 name: Sequence feature qualifier comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Typically one of the EMBL or Swiss-Prot feature qualifiers." [http://edamontology.org] namespace: data is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1022 name: Sequence feature label 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: bioinformatics subset: data subset: edam synonym: "Sequence feature name" EXACT [] created_in: "beta12orEarlier" def: "Typically an EMBL or Swiss-Prot feature label." [http://edamontology.org] namespace: data is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1023 name: EMBOSS Uniform Feature Object subset: bioinformatics subset: data subset: edam synonym: "UFO" EXACT [] created_in: "beta12orEarlier" def: "The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications." [http://edamontology.org] namespace: data is_a: EDAM_data:2099 ! Name is_a: EDAM_data:3034 ! Sequence feature identifier [Term] id: EDAM_data:1024 name: Codon name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "String of one or more ASCII characters representing a codon." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:1025 name: Gene identifier subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby:GeneAccessionList created_in: "beta12orEarlier" def: "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:1026 name: Gene symbol subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:Global_GeneCommonName xref: Moby_namespace:Global_GeneSymbol created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2299 ! Gene name [Term] id: EDAM_data:1027 name: Gene ID (NCBI) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Entrez gene ID" EXACT [] synonym: "Gene identifier (Entrez)" EXACT [] synonym: "Gene identifier (NCBI)" EXACT [] synonym: "NCBI gene ID" EXACT [] synonym: "NCBI geneid" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene created_in: "beta12orEarlier" def: "An NCBI unique identifier of a gene." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1098 ! RefSeq accession is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1028 name: Gene identifier (NCBI RefSeq) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An NCBI RefSeq unique identifier of a gene." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1027 ! Gene ID (NCBI) [Term] id: EDAM_data:1029 name: Gene identifier (NCBI UniGene) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An NCBI UniGene unique identifier of a gene." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1104 ! Sequence cluster ID (UniGene) [Term] id: EDAM_data:1030 name: Gene identifier (Entrez) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An Entrez unique identifier of a gene." [http://edamontology.org] regex: "[0-9]+" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1027 ! Gene ID (NCBI) [Term] id: EDAM_data:1031 name: Gene ID (CGD) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CGD ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a gene or feature from the CGD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1032 name: Gene ID (DictyBase) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a gene from DictyBase." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1033 name: Gene ID (Ensembl) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Ensembl Gene ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier for a gene (or other feature) from the Ensembl database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:1034 name: Gene ID (SGD) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "SGD identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry from the SGD database." [http://edamontology.org] regex: "S[0-9]+" namespace: identifier is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2632 ! SGD ID [Term] id: EDAM_data:1035 name: Gene ID (GeneDB) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "GeneDB identifier" EXACT [] xref: Moby_namespace:GeneDB created_in: "beta12orEarlier" def: "Identifier of a gene from the GeneDB database." [http://edamontology.org] regex: "[a-zA-Z_0-9\\.-]*" namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1036 name: TIGR identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the TIGR database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1037 name: TAIR accession (gene) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an gene from the TAIR database." [http://edamontology.org] regex: "Gene:[0-9]{7}" namespace: identifier is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2387 ! TAIR accession [Term] id: EDAM_data:1038 name: Protein domain ID comment: This is typically a character or string concatenated with a PDB identifier and a chain identifier. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a protein structural domain." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:1468 ! Protein domain [Term] id: EDAM_data:1039 name: SCOP domain identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a protein domain (or other node) from the SCOP database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1038 ! Protein domain ID relationship: is_identifier_of EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:1040 name: CATH domain ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CATH domain identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a protein domain from CATH." [http://edamontology.org] example: "1nr3A00" namespace: identifier is_a: EDAM_data:2700 ! CATH identifier [Term] id: EDAM_data:1041 name: SCOP concise classification string (sccs) comment: An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1039 ! SCOP domain identifier [Term] id: EDAM_data:1042 name: SCOP sunid 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: bioinformatics subset: data subset: edam subset: identifiers synonym: "SCOP unique identifier" EXACT [] synonym: "sunid" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229." [http://edamontology.org] example: "33229" namespace: identifier is_a: EDAM_data:1039 ! SCOP domain identifier [Term] id: EDAM_data:1043 name: CATH node ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CATH code" EXACT [] synonym: "CATH node identifier" EXACT [] created_in: "beta12orEarlier" def: "A code number identifying a node from the CATH database." [http://edamontology.org] example: "3.30.1190.10.1.1.1.1.1" namespace: identifier is_a: EDAM_data:2700 ! CATH identifier [Term] id: EDAM_data:1044 name: Kingdom name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:1045 name: Species name subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Organism species" EXACT [] created_in: "beta12orEarlier" def: "The name of a species (typically a taxonomic group) of organism." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:1046 name: Strain name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2379 ! Strain identifier is_a: EDAM_data:2909 ! Organism name [Term] id: EDAM_data:1047 name: URI subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A string of characters that name or otherwise identify a resource on the Internet." [http://edamontology.org] namespace: data is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:1048 name: Database identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a biological or bioinformatics database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0957 ! Database metadata [Term] id: EDAM_data:1049 name: Directory name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a directory." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1050 name: File name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name (or part of a name) of a file (of any type)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1051 name: Ontology name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2338 ! Ontology identifier relationship: is_identifier_of EDAM_data:0582 ! Ontology [Term] id: EDAM_data:1052 name: URL subset: bioinformatics subset: data subset: edam xref: Moby:Link xref: Moby:URL created_in: "beta12orEarlier" def: "A Uniform Resource Locator (URL)." [http://edamontology.org] namespace: data is_a: EDAM_data:1047 ! URI [Term] id: EDAM_data:1053 name: URN subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A Uniform Resource Name (URN)." [http://edamontology.org] namespace: data is_a: EDAM_data:1047 ! URI [Term] id: EDAM_data:1055 name: LSID comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following EDAM_format: URN:LSID:::[:] subset: bioinformatics subset: data subset: edam synonym: "Life Science Identifier" EXACT [] created_in: "beta12orEarlier" def: "A Life Science Identifier (LSID) - a unique identifier of some data." [http://edamontology.org] namespace: data is_a: EDAM_data:1053 ! URN [Term] id: EDAM_data:1056 name: Database name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a biological or bioinformatics database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1048 ! Database identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1057 name: Sequence database name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a molecular sequence database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:1058 name: Enumerated file name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a file (of any type) with restricted possible values." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1050 ! File name [Term] id: EDAM_data:1059 name: File name extension comment: A file extension is the characters appearing after the final '.' in the file name. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The extension of a file name." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1050 ! File name [Term] id: EDAM_data:1060 name: File base name comment: A file base name is the file name stripped of its directory specification and extension. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The base name of a file." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1050 ! File name [Term] id: EDAM_data:1061 name: QSAR descriptor name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a QSAR descriptor." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2110 ! Molecular property identifier relationship: is_identifier_of EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1062 name: Database entry identifier comment: This concept is required for completeness. It should never have child concepts. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:1063 name: Sequence identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of molecular sequence(s) or entries from a molecular sequence database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2044 ! Sequence [Term] id: EDAM_data:1064 name: Sequence set ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a set of molecular sequence(s)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1065 name: Sequence signature identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1114 ! Sequence motif identifier consider: EDAM_data:1115 ! Sequence profile ID [Term] id: EDAM_data:1066 name: Sequence alignment ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a molecular sequence alignment, for example a record from an alignment database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1067 name: Phylogenetic distance matrix identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a phylogenetic distance matrix." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:1068 name: Phylogenetic tree ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a phylogenetic tree for example from a phylogenetic tree database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0872 ! Phylogenetic tree [Term] id: EDAM_data:1069 name: Comparison matrix identifier subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Substitution matrix identifier" EXACT [] created_in: "beta12orEarlier" def: "An identifier of a comparison matrix." [http://edamontology.org] namespace: identifier is_a: EDAM_data:3036 ! Matrix identifier relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1070 name: Structure ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:3035 ! Structure identifier [Term] id: EDAM_data:1071 name: Structural (3D) profile ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Structural profile identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0889 ! Structural (3D) profile [Term] id: EDAM_data:1072 name: Structure alignment ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from a database of tertiary structure alignments." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0886 ! Structure alignment [Term] id: EDAM_data:1073 name: Amino acid index ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an index of amino acid physicochemical and biochemical property data." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:3036 ! Matrix identifier relationship: is_identifier_of EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1074 name: Protein interaction ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a report of protein interactions from a protein interaction database (typically)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2627 ! Molecular interaction ID [Term] id: EDAM_data:1075 name: Protein family identifier subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Protein secondary database record identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a protein family." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0907 ! Protein family [Term] id: EDAM_data:1076 name: Codon usage table name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique name of a codon usage table." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2111 ! Codon usage table identifier relationship: is_identifier_of EDAM_data:1597 ! Codon usage table relationship: is_identifier_of EDAM_data:1598 ! Genetic code [Term] id: EDAM_data:1077 name: Transcription factor identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a transcription factor (or a TF binding site)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:0989 ! Protein identifier relationship: is_identifier_of EDAM_data:1315 ! Gene features (TFBS) [Term] id: EDAM_data:1078 name: Microarray experiment annotation ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from a database of microarray data." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_data:1079 name: Electron microscopy model ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from a database of electron microscopy data." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0941 ! Electron microscopy model [Term] id: EDAM_data:1080 name: Gene expression report ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Gene expression profile identifier" EXACT [] created_in: "beta12orEarlier" def: "Accession of a report of gene expression (e.g. a gene expression profile) from a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_data:1081 name: Genotype and phenotype annotation ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from a database of genotypes and phenotypes." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0920 ! Genotype/phenotype annotation [Term] id: EDAM_data:1082 name: Pathway or network identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from a database of biological pathways or networks." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1083 name: Workflow ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a biological or biomedical workflow, typically from a database of workflows." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:2972 ! Workflow [Term] id: EDAM_data:1084 name: Data resource definition identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a data type definition from some provider." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:1085 name: Biological model identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a mathematical model, typically an entry from a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1086 name: Compound identifier subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Chemical compound identifier" EXACT [] synonym: "Small molecule identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry from a database of chemicals." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0982 ! Molecule identifier relationship: is_identifier_of EDAM_data:0846 ! Chemical formula relationship: is_identifier_of EDAM_data:0962 ! Small molecule annotation relationship: is_identifier_of EDAM_data:1712 ! Structure image (small molecule) [Term] id: EDAM_data:1087 name: Ontology concept ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Ontology concept ID" EXACT [] created_in: "beta12orEarlier" def: "A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:3025 ! Ontology concept identifier [Term] id: EDAM_data:1088 name: Article ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a scientific article." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0971 ! Article [Term] id: EDAM_data:1089 name: FlyBase ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an object from the FlyBase database." [http://edamontology.org] regex: "FB[a-zA-Z_0-9]{2}[0-9]{7}" namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:1091 name: WormBase name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of an object from the WormBase database, usually a human-readable name." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2113 ! WormBase identifier [Term] id: EDAM_data:1092 name: WormBase class comment: A WormBase class describes the type of object such as 'sequence' or 'protein'. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Class of an object from the WormBase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2113 ! WormBase identifier [Term] id: EDAM_data:1093 name: Sequence accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Sequence accession number" EXACT [] created_in: "beta12orEarlier" def: "A persistent, unique identifier of a molecular sequence database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1063 ! Sequence identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1094 name: Sequence type comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A label (text token) describing a type of molecular sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2100 ! Type is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:1095 name: EMBOSS Uniform Sequence Address subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "EMBOSS USA" EXACT [] created_in: "beta12orEarlier" def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1063 ! Sequence identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1096 name: Sequence accession (protein) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Protein sequence accession number" EXACT [] created_in: "beta12orEarlier" def: "Accession number of a protein sequence database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1093 ! Sequence accession relationship: is_identifier_of EDAM_data:2976 ! Protein sequence [Term] id: EDAM_data:1097 name: Sequence accession (nucleic acid) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Nucleotide sequence accession number" EXACT [] created_in: "beta12orEarlier" def: "Accession number of a nucleotide sequence database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1093 ! Sequence accession relationship: is_identifier_of EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:1098 name: RefSeq accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "RefSeq ID" EXACT [] created_in: "beta12orEarlier" def: "Accession number of a RefSeq database entry." [http://edamontology.org] regex: "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+" namespace: identifier is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] id: EDAM_data:1099 name: UniProt accession (extended) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number." [http://edamontology.org] example: "Q7M1G0|P43353-2|P01012.107" 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]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+" namespace: identifier obsolete_since: "1.0" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:3021 ! UniProt accession [Term] id: EDAM_data:1100 name: PIR identifier subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "PIR accession number" EXACT [] synonym: "PIR ID" EXACT [] created_in: "beta12orEarlier" def: "An identifier of PIR sequence database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1096 ! Sequence accession (protein) relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:1101 name: TREMBL accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a TREMBL sequence database entry." [http://edamontology.org] namespace: identifier obsolete_since: "1.2" replaced_by: EDAM_data:3021 !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:1102 name: Gramene primary identifier subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Gramene primary ID" EXACT [] created_in: "beta12orEarlier" def: "Primary identifier of a Gramene database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2915 ! Gramene identifier [Term] id: EDAM_data:1103 name: EMBL/GenBank/DDBJ ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:1104 name: Sequence cluster ID (UniGene) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "UniGene cluster ID" EXACT [] synonym: "UniGene cluster id" EXACT [] synonym: "UniGene ID" EXACT [] synonym: "UniGene identifier" EXACT [] created_in: "beta12orEarlier" def: "A unique identifier of an entry (gene cluster) from the NCBI UniGene database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:1105 name: dbEST accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "dbEST ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a dbEST database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2292 ! GenBank accession is_a: EDAM_data:2728 ! EST accession [Term] id: EDAM_data:1106 name: dbSNP ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "dbSNP identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a dbSNP database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2294 ! Sequence variation ID [Term] id: EDAM_data:1110 name: EMBOSS sequence type comment: See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The EMBOSS type of a molecular sequence." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1094 ! Sequence type [Term] id: EDAM_data:1111 name: EMBOSS listfile subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile)." [http://edamontology.org] namespace: data is_a: EDAM_data:2872 ! ID list [Term] id: EDAM_data:1112 name: Sequence cluster ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a cluster of molecular sequence(s)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1064 ! Sequence set ID relationship: is_identifier_of EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1113 name: Sequence cluster ID (COG) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "COG ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier of an entry from the COG database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:1114 name: Sequence motif identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a sequence motif, for example an entry from a motif database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:1115 name: Sequence profile ID comment: A sequence profile typically represents a sequence alignment. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a sequence profile." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:1116 name: ELM ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the ELMdb database of protein functional sites." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1114 ! Sequence motif identifier [Term] id: EDAM_data:1117 name: Prosite accession number subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Prosite ID" EXACT [] created_in: "beta12orEarlier" def: "Accession number of an entry from the Prosite database." [http://edamontology.org] regex: "PS[0-9]{5}" namespace: identifier is_a: EDAM_data:1114 ! Sequence motif identifier [Term] id: EDAM_data:1118 name: HMMER hidden Markov model ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier or name of a HMMER hidden Markov model." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1115 ! Sequence profile ID relationship: is_identifier_of EDAM_data:1364 ! Hidden Markov model [Term] id: EDAM_data:1119 name: JASPAR profile ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier or name of a profile from the JASPAR database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1115 ! Sequence profile ID [Term] id: EDAM_data:1120 name: Sequence alignment type comment: Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A label (text token) describing the type of a sequence alignment." [http://edamontology.org] namespace: data is_a: EDAM_data:0864 ! Sequence alignment parameter is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1121 name: BLAST sequence alignment type subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The type of a BLAST sequence alignment." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1120 ! Sequence alignment type [Term] id: EDAM_data:1122 name: Phylogenetic tree type comment: For example 'nj', 'upgmp' etc. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A label (text token) describing the type of a phylogenetic tree." [http://edamontology.org] example: "nj|upgmp" namespace: data is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1123 name: TreeBASE study accession number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of an entry from the TreeBASE database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1068 ! Phylogenetic tree ID [Term] id: EDAM_data:1124 name: TreeFam accession number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of an entry from the TreeFam database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1068 ! Phylogenetic tree ID [Term] id: EDAM_data:1125 name: Comparison matrix type 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: bioinformatics subset: data subset: edam synonym: "Substitution matrix type" EXACT [] created_in: "beta12orEarlier" def: "A label (text token) describing the type of a comparison matrix." [http://edamontology.org] example: "blosum|pam|gonnet|id" namespace: data is_a: EDAM_data:0864 ! Sequence alignment parameter is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1126 name: Comparison matrix name comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Substitution matrix name" EXACT [] created_in: "beta12orEarlier" def: "Unique name or identifier of a comparison matrix." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1069 ! Comparison matrix identifier is_a: EDAM_data:2099 ! Name relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1127 name: PDB ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "PDB identifier" EXACT [] synonym: "PDBID" EXACT [] created_in: "beta12orEarlier" def: "An identifier of an entry from the PDB database." [http://edamontology.org] regex: "[a-zA-Z_0-9]{4}" namespace: identifier is_a: EDAM_data:1070 ! Structure ID [Term] id: EDAM_data:1128 name: AAindex ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the AAindex database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1073 ! Amino acid index ID [Term] id: EDAM_data:1129 name: BIND accession number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of an entry from the BIND database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:1130 name: IntAct accession number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of an entry from the IntAct database." [http://edamontology.org] regex: "EBI\\-[0-9]+" namespace: identifier is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:1131 name: Protein family name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a protein family." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1075 ! Protein family identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1132 name: InterPro entry name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of an InterPro entry, usually indicating the type of protein matches for that entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1131 ! Protein family name relationship: is_identifier_of EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1133 name: InterPro accession comment: Every InterPro entry has a unique accession number to provide a persistent citation of database records. subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "InterPro primary accession" EXACT [] synonym: "InterPro primary accession number" EXACT [] created_in: "beta12orEarlier" def: "Primary accession number of an InterPro entry." [http://edamontology.org] example: "IPR015590" regex: "IPR[0-9]{6}" namespace: identifier is_a: EDAM_data:2910 ! Protein family accession relationship: is_identifier_of EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1134 name: InterPro secondary accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "InterPro secondary accession number" EXACT [] created_in: "beta12orEarlier" def: "Secondary accession number of an InterPro entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1133 ! InterPro accession relationship: is_identifier_of EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1135 name: Gene3D ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an entry from the Gene3D database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1136 name: PIRSF ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an entry from the PIRSF database." [http://edamontology.org] regex: "PIRSF[0-9]{6}" namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1137 name: PRINTS code subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The unique identifier of an entry in the PRINTS database." [http://edamontology.org] regex: "PR[0-9]{5}" namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1138 name: Pfam accession number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of a Pfam entry." [http://edamontology.org] regex: "PF[0-9]{5}" namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1139 name: SMART accession number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of an entry from the SMART database." [http://edamontology.org] regex: "SM[0-9]{5}" namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1140 name: Superfamily hidden Markov model number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier (number) of a hidden Markov model from the Superfamily database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1141 name: TIGRFam ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "TIGRFam accession number" EXACT [] created_in: "beta12orEarlier" def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1142 name: ProDom accession number comment: ProDom is a protein domain family database. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A ProDom domain family accession number." [http://edamontology.org] regex: "PD[0-9]+" namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:1143 name: TRANSFAC accession number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the TRANSFAC database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2911 ! Transcription factor accession [Term] id: EDAM_data:1144 name: ArrayExpress accession number subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "ArrayExpress experiment ID" EXACT [] created_in: "beta12orEarlier" def: "Accession number of an entry from the ArrayExpress database." [http://edamontology.org] regex: "[AEP]-[a-zA-Z_0-9]{4}-[0-9]+" namespace: identifier is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] id: EDAM_data:1145 name: PRIDE experiment accession number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "PRIDE experiment accession number." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] id: EDAM_data:1146 name: EMDB ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the EMDB electron microscopy database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1079 ! Electron microscopy model ID [Term] id: EDAM_data:1147 name: GEO accession number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of an entry from the GEO database." [http://edamontology.org] regex: "o^GDS[0-9]+" namespace: identifier is_a: EDAM_data:1080 ! Gene expression report ID [Term] id: EDAM_data:1148 name: GermOnline ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the GermOnline database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1080 ! Gene expression report ID [Term] id: EDAM_data:1149 name: EMAGE ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the EMAGE database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1080 ! Gene expression report ID [Term] id: EDAM_data:1150 name: Disease ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from a database of disease." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:1622 ! Disease annotation [Term] id: EDAM_data:1151 name: HGVbase ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the HGVbase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID [Term] id: EDAM_data:1152 name: HIVDB identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the HIVDB database." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:1153 name: OMIM ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the OMIM database." [http://edamontology.org] regex: "[*#+%^]?[0-9]{6}" namespace: identifier is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID [Term] id: EDAM_data:1154 name: KEGG object identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an object from one of the KEGG databases (excluding the GENES division)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:1155 name: Pathway ID (reactome) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Reactome ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry from the Reactome database." [http://edamontology.org] regex: "REACT_[0-9]+(\\.[0-9]+)?" namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1156 name: Pathway ID (aMAZE) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "aMAZE ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry from the aMAZE database." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1082 ! Pathway or network identifier [Term] id: EDAM_data:1157 name: Pathway ID (BioCyc) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "BioCyc pathway ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an pathway from the BioCyc biological pathways database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2104 ! BioCyc ID is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1158 name: Pathway ID (INOH) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "INOH identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry from the INOH database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1159 name: Pathway ID (PATIKA) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "PATIKA ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry from the PATIKA database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1160 name: Pathway ID (CPDB) comment: This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CPDB ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1161 name: Pathway ID (Panther) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Panther Pathways ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a biological pathway from the Panther Pathways database." [http://edamontology.org] regex: "PTHR[0-9]{5}" namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:1162 name: MIRIAM identifier comment: This is the identifier used internally by MIRIAM for a data type. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a MIRIAM data resource." [http://edamontology.org] example: MIR:00100005 regex: "MIR:[0-9]{8}" namespace: identifier is_a: EDAM_data:2902 ! Data resource definition accession relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype [Term] id: EDAM_data:1163 name: MIRIAM data type name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a data type from the MIRIAM database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2253 ! Data resource definition name relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype [Term] id: EDAM_data:1164 name: MIRIAM URI 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. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The URI (URL or URN) of a data entity from the MIRIAM database." [http://edamontology.org] example: urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 namespace: identifier is_a: EDAM_data:1047 ! URI is_a: EDAM_data:2902 ! Data resource definition accession relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype [Term] id: EDAM_data:1165 name: MIRIAM data type primary name comment: The primary name of a MIRIAM data type is taken from a controlled vocabulary. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The primary name of a data type from the MIRIAM database." [http://edamontology.org] example: "UniProt|Enzyme Nomenclature" namespace: identifier is_a: EDAM_data:1163 ! MIRIAM data type name [Term] id: EDAM_data:1166 name: MIRIAM data type synonymous name comment: A synonymous name for a MIRIAM data type taken from a controlled vocabulary. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A synonymous name of a data type from the MIRIAM database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1163 ! MIRIAM data type name [Term] id: EDAM_data:1167 name: Taverna workflow ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a Taverna workflow." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1083 ! Workflow ID [Term] id: EDAM_data:1170 name: Biological model name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a biological (mathematical) model." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1085 ! Biological model identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1171 name: BioModel ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an entry from the BioModel database." [http://edamontology.org] regex: "(BIOMD|MODEL)[0-9]{10}" namespace: identifier is_a: EDAM_data:2891 ! Biological model accession [Term] id: EDAM_data:1172 name: PubChem CID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "PubChem compound accession identifier" EXACT [] created_in: "beta12orEarlier" def: "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2639 ! PubChem identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:1173 name: ChemSpider ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the ChemSpider database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:1174 name: ChEBI ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "ChEBI identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry from the ChEBI database." [http://edamontology.org] regex: "CHEBI:[0-9]+" namespace: identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:1175 name: BioPax concept ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from the BioPax ontology." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1176 name: GO concept ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "GO concept identifier" EXACT [] created_in: "beta12orEarlier" def: "An identifier of a concept from The Gene Ontology." [http://edamontology.org] regex: "[0-9]{7}|GO:[0-9]{7}" namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1177 name: MeSH concept ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from the MeSH vocabulary." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1178 name: HGNC concept ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from the HGNC controlled vocabulary." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1179 name: NCBI taxonomy ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "NCBI tax ID" EXACT [] synonym: "NCBI taxonomy identifier" EXACT [] created_in: "beta12orEarlier" def: "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." [http://edamontology.org] example: "9662|3483|182682" regex: "[1-9][0-9]{0,8}" namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1180 name: Plant Ontology concept ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from the Plant Ontology (PO)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1181 name: UMLS concept ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from the UMLS vocabulary." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1182 name: FMA concept ID 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: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from Foundational Model of Anatomy." [http://edamontology.org] regex: "FMA:[0-9]+" namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1183 name: EMAP concept ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from the EMAP mouse ontology." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1184 name: ChEBI concept ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from the ChEBI ontology." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1185 name: MGED concept ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from the MGED ontology." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1186 name: myGrid concept ID comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a concept from the myGrid ontology." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID [Term] id: EDAM_data:1187 name: PubMed ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "PMID" EXACT [] created_in: "beta12orEarlier" def: "PubMed unique identifier of an article." [http://edamontology.org] example: "4963447" regex: "[1-9][0-9]{0,8}" namespace: identifier is_a: EDAM_data:1088 ! Article ID [Term] id: EDAM_data:1188 name: Digital Object Identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Digital Object Identifier (DOI) of a published article." [http://edamontology.org] regex: "(doi\\:)?[0-9]{2}\\.[0-9]{4}/.*" namespace: identifier is_a: EDAM_data:1088 ! Article ID [Term] id: EDAM_data:1189 name: Medline UI comment: The use of Medline UI has been replaced by the PubMed unique identifier. subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Medline unique identifier" EXACT [] created_in: "beta12orEarlier" def: "Medline UI (unique identifier) of an article." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1088 ! Article ID [Term] id: EDAM_data:1190 name: Tool name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a computer package, application, method or function." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0977 ! Tool identifier [Term] id: EDAM_data:1191 name: Tool name (signature) 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: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The unique name of a signature (sequence classifier) method." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:1192 name: Tool name (BLAST) comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "BLAST name" EXACT [] created_in: "beta12orEarlier" def: "The name of a BLAST tool." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:1193 name: Tool name (FASTA) comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a FASTA tool." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:1194 name: Tool name (EMBOSS) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of an EMBOSS application." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:1195 name: Tool name (EMBASSY package) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of an EMBASSY package." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1190 ! Tool name [Term] id: EDAM_data:1201 name: QSAR descriptor (constitutional) subset: bioinformatics subset: data subset: edam synonym: "QSAR constitutional descriptor" EXACT [] created_in: "beta12orEarlier" def: "A QSAR constitutional descriptor." [http://edamontology.org] namespace: data is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1202 name: QSAR descriptor (electronic) subset: bioinformatics subset: data subset: edam synonym: "QSAR electronic descriptor" EXACT [] created_in: "beta12orEarlier" def: "A QSAR electronic descriptor." [http://edamontology.org] namespace: data is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1203 name: QSAR descriptor (geometrical) subset: bioinformatics subset: data subset: edam synonym: "QSAR geometrical descriptor" EXACT [] created_in: "beta12orEarlier" def: "A QSAR geometrical descriptor." [http://edamontology.org] namespace: data is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1204 name: QSAR descriptor (topological) subset: bioinformatics subset: data subset: edam synonym: "QSAR topological descriptor" EXACT [] created_in: "beta12orEarlier" def: "A QSAR topological descriptor." [http://edamontology.org] namespace: data is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1205 name: QSAR descriptor (molecular) subset: bioinformatics subset: data subset: edam synonym: "QSAR molecular descriptor" EXACT [] created_in: "beta12orEarlier" def: "A QSAR molecular descriptor." [http://edamontology.org] namespace: data is_a: EDAM_data:0847 ! QSAR descriptor [Term] id: EDAM_data:1233 name: Sequence set (protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] namespace: data is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1234 name: Sequence set (nucleic acid) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] namespace: data is_a: EDAM_data:0850 ! Sequence set is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:1235 name: Sequence cluster comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information." [http://edamontology.org] namespace: data is_a: EDAM_data:0850 ! Sequence set relationship: has_topic EDAM_topic:0724 ! Protein families relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification [Term] id: EDAM_data:1236 name: Psiblast checkpoint file comment: A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1237 name: HMMER synthetic sequences set subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Sequences generated by HMMER package in FASTA-style format." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1238 name: Proteolytic digest subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses." [http://edamontology.org] namespace: data is_a: EDAM_data:1233 ! Sequence set (protein) relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:1239 name: Restriction digest subset: bioinformatics subset: data subset: edam xref: SO:0000412 created_in: "beta12orEarlier" def: "Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease." [http://edamontology.org] namespace: data is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:1240 name: PCR primers subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." [http://edamontology.org] namespace: data is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:1241 name: vectorstrip cloning vector definition file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1242 name: Primer3 internal oligo mishybridizing library subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1243 name: Primer3 mispriming library file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1244 name: primersearch primer pairs sequence record subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1245 name: Sequence cluster (protein) comment: The sequences are typically related, for example a family of sequences. subset: bioinformatics subset: data subset: edam synonym: "Protein sequence cluster" EXACT [] created_in: "beta12orEarlier" def: "A cluster of protein sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1233 ! Sequence set (protein) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1246 name: Sequence cluster (nucleic acid) comment: The sequences are typically related, for example a family of sequences. subset: bioinformatics subset: data subset: edam synonym: "Nucleotide sequence cluster" EXACT [] created_in: "beta12orEarlier" def: "A cluster of nucleotide sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1234 ! Sequence set (nucleic acid) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1249 name: Sequence length subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The size (length) of a sequence, subsequence or region in a sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:0854 ! Sequence length specification [Term] id: EDAM_data:1250 name: Word size comment: Word size is used for example in word-based sequence database search methods. subset: bioinformatics subset: data subset: edam synonym: "Word length" EXACT [] created_in: "beta12orEarlier" def: "Size of a sequence word." [http://edamontology.org] namespace: data is_a: EDAM_data:1249 ! Sequence length [Term] id: EDAM_data:1251 name: Window size 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Size of a sequence window." [http://edamontology.org] namespace: data is_a: EDAM_data:1249 ! Sequence length [Term] id: EDAM_data:1252 name: Sequence length range subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Specification of range(s) of length of sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:0854 ! Sequence length specification [Term] id: EDAM_data:1253 name: Sequence information report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0855 ! Sequence metadata consider: EDAM_data:2043 ! Sequence record lite [Term] id: EDAM_data:1254 name: Sequence property subset: bioinformatics subset: data subset: edam synonym: "Sequence properties report" EXACT [] created_in: "beta12orEarlier" def: "An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." [http://edamontology.org] namespace: data is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:1255 name: Feature record 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: bioinformatics subset: data subset: edam synonym: "Features" EXACT [] synonym: "General sequence features" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D058977" RELATED [] synonym: "Sequence features" EXACT [] synonym: "Sequence features report" EXACT [] synonym: "SO:0000110" RELATED [] created_in: "beta12orEarlier" def: "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:1256 name: Sequence features (comparative) 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1257 name: Sequence property (protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report of general sequence properties derived from protein sequence data." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1258 name: Sequence property (nucleic acid) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report of general sequence properties derived from nucleotide sequence data." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:1259 name: Sequence complexity subset: bioinformatics subset: data subset: edam synonym: "Sequence property (complexity)" EXACT [] created_in: "beta12orEarlier" def: "A report on sequence complexity, for example low-complexity or repeat regions in sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1254 ! Sequence property [Term] id: EDAM_data:1260 name: Sequence ambiguity subset: bioinformatics subset: data subset: edam synonym: "Sequence property (ambiguity)" EXACT [] created_in: "beta12orEarlier" def: "A report on ambiguity in molecular sequence(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:1254 ! Sequence property [Term] id: EDAM_data:1261 name: Sequence composition subset: bioinformatics subset: data subset: edam synonym: "Sequence property (composition)" EXACT [] created_in: "beta12orEarlier" def: "A report (typically a table) on character or word composition / frequency of a molecular sequence(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:1254 ! Sequence property [Term] id: EDAM_data:1262 name: Peptide molecular weight hits subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on peptide fragments of certain molecular weight(s) in one or more protein sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1233 ! Sequence set (protein) [Term] id: EDAM_data:1263 name: Sequence composition (base position variability) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Report on or plot of third base position variability in a nucleotide sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] id: EDAM_data:1264 name: Sequence composition table subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A table of character or word composition / frequency of a molecular sequence." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1261 ! Sequence composition [Term] id: EDAM_data:1265 name: Sequence composition (base frequencies) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A table of base frequencies of a nucleotide sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] id: EDAM_data:1266 name: Sequence composition (base words) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A table of word composition of a nucleotide sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3086 ! Nucleic acid sequence composition [Term] id: EDAM_data:1267 name: Amino acid frequencies subset: bioinformatics subset: data subset: edam synonym: "Sequence composition (amino acid frequencies)" EXACT [] created_in: "beta12orEarlier" def: "A table of amino acid frequencies of a protein sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3085 ! Protein sequence composition [Term] id: EDAM_data:1268 name: Amino acid word frequencies subset: bioinformatics subset: data subset: edam synonym: "Sequence composition (amino acid words)" EXACT [] created_in: "beta12orEarlier" def: "A table of amino acid word composition of a protein sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3085 ! Protein sequence composition [Term] id: EDAM_data:1269 name: DAS sequence feature annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Annotation of a molecular sequence in DAS format." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1978 ! DASGFF [Term] id: EDAM_data:1270 name: Sequence feature table subset: bioinformatics subset: data subset: edam synonym: "Feature table" EXACT [] created_in: "beta12orEarlier" def: "Annotation of positional sequence features, organized into a standard feature table." [http://edamontology.org] namespace: data is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1274 name: Map subset: bioinformatics subset: data subset: edam synonym: "DNA map" EXACT [] created_in: "beta12orEarlier" def: "A map of (typically one) DNA sequence annotated with positional or non-positional features." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0102 ! Mapping [Term] id: EDAM_data:1276 name: Nucleic acid features comment: This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. subset: bioinformatics subset: data subset: edam synonym: "Feature table (nucleic acid)" EXACT [] synonym: "Nucleic acid feature table" EXACT [] created_in: "beta12orEarlier" def: "Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence)." [http://edamontology.org] namespace: data is_a: EDAM_data:1255 ! Feature record is_a: EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:1277 name: Protein features comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. subset: bioinformatics subset: data subset: edam synonym: "Feature table (protein)" EXACT [] synonym: "Protein feature table" EXACT [] created_in: "beta12orEarlier" def: "Protein sequence-specific feature annotation (positional features of a protein sequence)." [http://edamontology.org] namespace: data is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1278 name: Genetic map 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: bioinformatics subset: data subset: edam synonym: "Linkage map" EXACT [] xref: Moby:GeneticMap created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1274 ! Map relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] id: EDAM_data:1279 name: Sequence map 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs." [http://edamontology.org] namespace: data is_a: EDAM_data:1280 ! Physical map [Term] id: EDAM_data:1280 name: Physical map 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1274 ! Map [Term] id: EDAM_data:1281 name: Sequence signature map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image of a sequence with matches to signatures, motifs or profiles." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1283 name: Cytogenetic map 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: bioinformatics subset: data subset: edam synonym: "Chromosome map" EXACT [] synonym: "Cytogenic map" EXACT [] synonym: "Cytologic map" EXACT [] created_in: "beta12orEarlier" def: "A map showing banding patterns derived from direct observation of a stained chromosome." [http://edamontology.org] namespace: data is_a: EDAM_data:1280 ! Physical map [Term] id: EDAM_data:1284 name: DNA transduction map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A gene map showing distances between loci based on relative cotransduction frequencies." [http://edamontology.org] namespace: data is_a: EDAM_data:1278 ! Genetic map [Term] id: EDAM_data:1285 name: Gene map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1279 ! Sequence map [Term] id: EDAM_data:1286 name: Plasmid map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Sequence map of a plasmid (circular DNA)." [http://edamontology.org] namespace: data is_a: EDAM_data:1279 ! Sequence map [Term] id: EDAM_data:1288 name: Genome map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Sequence map of a whole genome." [http://edamontology.org] namespace: data is_a: EDAM_data:1279 ! Sequence map [Term] id: EDAM_data:1289 name: Restriction map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:1279 ! Sequence map is_a: EDAM_data:1305 ! Nucleic acid features (restriction sites) is_a: EDAM_data:2969 ! Sequence image [Term] id: EDAM_data:1290 name: InterPro compact match image 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image showing matches between protein sequence(s) and InterPro Entries." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1291 name: InterPro detailed match image comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image showing detailed information on matches between protein sequence(s) and InterPro Entries." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1292 name: InterPro architecture image 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image showing the architecture of InterPro domains in a protein sequence." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1293 name: SMART protein schematic subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "SMART protein schematic in PNG format." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1294 name: GlobPlot domain image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:1298 name: Sequence features (motifs) comment: Use this concept if another, more specific concept is not available. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1299 name: Sequence features (repeats) comment: The report might include derived data map such as classification, annotation, organization, periodicity etc. subset: bioinformatics subset: data subset: edam synonym: "Repeat sequence map" EXACT [] created_in: "beta12orEarlier" def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1300 name: Nucleic acid features (gene and transcript structure) subset: bioinformatics subset: data subset: edam synonym: "Gene annotation (structure)" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0916 ! Gene annotation is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:1301 name: Nucleic acid features (mobile genetic elements) comment: This includes transposons, Plasmids, Bacteriophage elements and Group II introns. subset: bioinformatics subset: data subset: edam synonym: "Nucleic acid features (transposons)" EXACT [] created_in: "beta12orEarlier" def: "A report on a region of a nucleic acid sequence containin mobile genetic elements." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:1302 name: Nucleic acid features (PolyA signal or site) 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: bioinformatics subset: data subset: edam synonym: "PolyA signal" EXACT [] synonym: "PolyA site" EXACT [] created_in: "beta12orEarlier" def: "A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript." [http://edamontology.org] namespace: data is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:1303 name: Nucleic acid features (quadruplexes) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on quadruplex-forming motifs in a nucleotide sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] id: EDAM_data:1304 name: Nucleic acid features (CpG island and isochore) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report or plot of CpG rich regions (isochores) in a nucleotide sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) [Term] id: EDAM_data:1305 name: Nucleic acid features (restriction sites) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3125 ! Nucleic acid features (binding) [Term] id: EDAM_data:1306 name: Nucleic acid features (nucleosome exclusion sequences) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on nucleosome formation potential or exclusion sequence(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination) [Term] id: EDAM_data:1307 name: Nucleic acid features (splice sites) subset: bioinformatics subset: data subset: edam synonym: "Nucleic acid report (RNA splice model)" EXACT [] synonym: "Nucleic acid report (RNA splicing)" EXACT [] created_in: "beta12orEarlier" def: "A report on splice sites in a nucleotide sequence or alternative RNA splicing events." [http://edamontology.org] namespace: data is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:1308 name: Nucleic acid features (matrix/scaffold attachment sites) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) [Term] id: EDAM_data:1309 name: Gene features (exonic splicing enhancer) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on exonic splicing enhancers (ESE) in an exon." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2397 ! Nucleic acid features (exon) [Term] id: EDAM_data:1310 name: Nucleic acid features (microRNA) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." [http://edamontology.org] namespace: data is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA) relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_data:1311 name: Nucleic acid features (operon) 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: bioinformatics subset: data subset: edam synonym: "Gene features (operon)" EXACT [] created_in: "beta12orEarlier" def: "A report on operons (operators, promoters and genes) from a bacterial genome." [http://edamontology.org] namespace: data is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:1312 name: Gene features (promoter) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional) [Term] id: EDAM_data:1313 name: Nucleic acid features (coding sequence) subset: bioinformatics subset: data subset: edam synonym: "Gene annotation (translation)" EXACT [] synonym: "Gene features (coding region)" EXACT [] synonym: "Gene features (coding sequence)" EXACT [] created_in: "beta12orEarlier" def: "A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." [http://edamontology.org] namespace: data is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:1314 name: Gene features (SECIS element) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:1315 name: Gene features (TFBS) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on the transcription factor binding sites (TFBS) in a DNA sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:1312 ! Gene features (promoter) is_a: EDAM_data:3125 ! Nucleic acid features (binding) relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites [Term] id: EDAM_data:1321 name: Protein features (sites) comment: Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1322 name: Protein features (signal peptides) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on the location of signal peptides or signal peptide cleavage sites in protein sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1323 name: Protein features (cleavage sites) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:1324 name: Protein features (post-translation modifications) subset: bioinformatics subset: data subset: edam synonym: "Post-translation modification" EXACT [] synonym: "Protein features (post-translation modification sites)" EXACT [] created_in: "beta12orEarlier" def: "A report on post-translation modifications in a protein sequence, typically describing the specific sites involved." [http://edamontology.org] namespace: data is_a: EDAM_data:2191 ! Protein features (chemical modification) [Term] id: EDAM_data:1325 name: Protein features (active sites) subset: bioinformatics subset: data subset: edam synonym: "Enzyme active site" EXACT [] created_in: "beta12orEarlier" def: "A report on catalytic residues (active site) of an enzyme." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1326 name: Protein features (binding sites) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1327 name: Protein features (epitopes) comment: Epitope mapping is commonly done during vaccine design. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1326 ! Protein features (binding sites) [Term] id: EDAM_data:1328 name: Protein features (nucleic acid binding sites) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on RNA and DNA-binding proteins and binding sites in protein sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1329 name: MHC Class I epitopes report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on epitopes that bind to MHC class I molecules." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1326 ! Protein features (binding sites) [Term] id: EDAM_data:1330 name: MHC Class II epitopes report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on predicted epitopes that bind to MHC class II molecules." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1326 ! Protein features (binding sites) [Term] id: EDAM_data:1331 name: Protein features (PEST sites) comment: 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report or plot of PEST sites in a protein sequence." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1323 ! Protein features (cleavage sites) [Term] id: EDAM_data:1338 name: Sequence database hits scores list subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Scores from a sequence database search (for example a BLAST search)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0857 ! Database hits (sequence) [Term] id: EDAM_data:1339 name: Sequence database hits alignments list subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignments from a sequence database search (for example a BLAST search)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0857 ! Database hits (sequence) [Term] id: EDAM_data:1340 name: Sequence database hits evaluation data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0857 ! Database hits (sequence) [Term] id: EDAM_data:1344 name: MEME motif alphabet subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alphabet for the motifs (patterns) that MEME will search for." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1345 name: MEME background frequencies file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "MEME background frequencies file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1346 name: MEME motifs directive file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "File of directives for ordering and spacing of MEME motifs." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1347 name: Dirichlet distribution subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Dirichlet distribution used by hidden Markov model analysis programs." [http://edamontology.org] namespace: data is_a: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1348 name: HMM emission and transition counts subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0950 ! Biological model [Term] id: EDAM_data:1352 name: Regular expression subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Regular expression pattern." [http://edamontology.org] namespace: data is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1353 name: Sequence motif subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_data:1354 name: Sequence profile subset: bioinformatics subset: data subset: edam synonym: "SIO:010531" EXACT [] created_in: "beta12orEarlier" def: "Some type of statistical model representing a (typically multiple) sequence alignment." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_data:1355 name: Protein signature subset: bioinformatics subset: data subset: edam synonym: "InterPro entry" EXACT [] created_in: "beta12orEarlier" def: "An entry (sequence classifier and associated data) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:0907 ! Protein family [Term] id: EDAM_data:1358 name: Prosite nucleotide pattern subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A nucleotide regular expression pattern from the Prosite database." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:1359 name: Prosite protein pattern subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein regular expression pattern from the Prosite database." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:1361 name: Position frequency matrix subset: bioinformatics subset: data subset: edam synonym: "PFM" EXACT [] created_in: "beta12orEarlier" def: "A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org] namespace: data is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1362 name: Position weight matrix comment: Contributions of individual sequences to the matrix might be uneven (weighted). subset: bioinformatics subset: data subset: edam synonym: "PWM" EXACT [] created_in: "beta12orEarlier" def: "A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org] namespace: data is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1363 name: Information content matrix subset: bioinformatics subset: data subset: edam synonym: "ICM" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1364 name: Hidden Markov model subset: bioinformatics subset: data subset: edam synonym: "HMM" EXACT [] created_in: "beta12orEarlier" def: "A hidden Markov model representation of a set or alignment of sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:1365 name: Fingerprint subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "One or more fingerprints (sequence classifiers) as used in the PRINTS database." [http://edamontology.org] namespace: data is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1368 name: Domainatrix signature subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein signature of the type used in the EMBASSY Signature package." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:1371 name: HMMER NULL hidden Markov model subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "NULL hidden Markov model representation used by the HMMER package." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1364 ! Hidden Markov model [Term] id: EDAM_data:1372 name: Protein family signature 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1373 name: Protein domain signature comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein domain signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1374 name: Protein region signature comment: A protein region signature defines a region which cannot be described as a protein family or domain signature. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein region signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1375 name: Protein repeat signature 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein repeat signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1376 name: Protein site signature comment: A protein site signature is a classifier for a specific site in a protein. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein site signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:1355 ! Protein signature [Term] id: EDAM_data:1377 name: Protein conserved site signature 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein conserved site signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:1376 ! Protein site signature [Term] id: EDAM_data:1378 name: Protein active site signature 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein active site signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:1376 ! Protein site signature [Term] id: EDAM_data:1379 name: Protein binding site signature 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein binding site signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:1376 ! Protein site signature [Term] id: EDAM_data:1380 name: Protein post-translational modification signature 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein post-translational modification signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:1376 ! Protein site signature [Term] id: EDAM_data:1381 name: Sequence alignment (pair) subset: bioinformatics subset: data subset: edam synonym: "SIO:010068" RELATED [] created_in: "beta12orEarlier" def: "Alignment of exactly two molecular sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1382 name: Sequence alignment (multiple) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of more than two molecular sequences." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1383 name: Sequence alignment (nucleic acid) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of multiple nucleotide sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:0863 ! Sequence alignment is_a: EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:1384 name: Sequence alignment (protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of multiple protein sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:0863 ! Sequence alignment is_a: EDAM_data:3154 ! Protein alignment [Term] id: EDAM_data:1385 name: Sequence alignment (hybrid) comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of multiple molecular sequences of different types." [http://edamontology.org] namespace: data is_a: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1386 name: Sequence alignment (nucleic acid pair) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of exactly two nucleotide sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1381 ! Sequence alignment (pair) is_a: EDAM_data:1383 ! Sequence alignment (nucleic acid) [Term] id: EDAM_data:1387 name: Sequence alignment (protein pair) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of exactly two protein sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1381 ! Sequence alignment (pair) is_a: EDAM_data:1384 ! Sequence alignment (protein) [Term] id: EDAM_data:1388 name: Hybrid sequence alignment (pair) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of exactly two molecular sequences of different types." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1385 ! Sequence alignment (hybrid) [Term] id: EDAM_data:1389 name: Multiple nucleotide sequence alignment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of more than two nucleotide sequences." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1390 name: Multiple protein sequence alignment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of more than two protein sequences." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1394 name: Alignment score or penalty subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A simple floating point number defining the penalty for opening or extending a gap in an alignment." [http://edamontology.org] namespace: data is_a: EDAM_data:0864 ! Sequence alignment parameter is_a: EDAM_data:1772 ! Score or penalty [Term] id: EDAM_data:1395 name: Score end gaps control subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Whether end gaps are scored or not." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1396 name: Aligned sequence order subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Controls the order of sequences in an output sequence alignment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2134 ! Results sort order [Term] id: EDAM_data:1397 name: Gap opening penalty subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A penalty for opening a gap in an alignment." [http://edamontology.org] namespace: data is_a: EDAM_data:2137 ! Gap penalty [Term] id: EDAM_data:1398 name: Gap extension penalty subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A penalty for extending a gap in an alignment." [http://edamontology.org] namespace: data is_a: EDAM_data:2137 ! Gap penalty [Term] id: EDAM_data:1399 name: Gap separation penalty subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A penalty for gaps that are close together in an alignment." [http://edamontology.org] namespace: data is_a: EDAM_data:2137 ! Gap penalty [Term] id: EDAM_data:1400 name: Terminal gap penalty subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1410 ! Terminal gap opening penalty consider: EDAM_data:1411 ! Terminal gap extension penalty [Term] id: EDAM_data:1401 name: Match reward score subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The score for a 'match' used in various sequence database search applications with simple scoring schemes." [http://edamontology.org] namespace: data is_a: EDAM_data:1394 ! Alignment score or penalty [Term] id: EDAM_data:1402 name: Mismatch penalty score subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes." [http://edamontology.org] namespace: data is_a: EDAM_data:1394 ! Alignment score or penalty [Term] id: EDAM_data:1403 name: Drop off score subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "This is the threshold drop in score at which extension of word alignment is halted." [http://edamontology.org] namespace: data is_a: EDAM_data:1394 ! Alignment score or penalty [Term] id: EDAM_data:1404 name: Gap opening penalty (integer) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1397 ! Gap opening penalty [Term] id: EDAM_data:1405 name: Gap opening penalty (float) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1397 ! Gap opening penalty [Term] id: EDAM_data:1406 name: Gap extension penalty (integer) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1398 ! Gap extension penalty [Term] id: EDAM_data:1407 name: Gap extension penalty (float) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1398 ! Gap extension penalty [Term] id: EDAM_data:1408 name: Gap separation penalty (integer) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1399 ! Gap separation penalty [Term] id: EDAM_data:1409 name: Gap separation penalty (float) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1399 ! Gap separation penalty [Term] id: EDAM_data:1410 name: Terminal gap opening penalty subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1397 ! Gap opening penalty [Term] id: EDAM_data:1411 name: Terminal gap extension penalty subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1398 ! Gap extension penalty [Term] id: EDAM_data:1412 name: Sequence identity subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:0865 ! Sequence similarity score [Term] id: EDAM_data:1413 name: Sequence similarity comment: Data Type is float probably. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0865 ! Sequence similarity score [Term] id: EDAM_data:1414 name: Sequence alignment metadata (quality report) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on molecular sequence alignment quality (estimated accuracy)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:1415 name: Sequence alignment report (site conservation) 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 concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on character conservation in a molecular sequence alignment." [http://edamontology.org] namespace: data is_a: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:1416 name: Sequence alignment report (site correlation) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:1417 name: Sequence-profile alignment (Domainatrix signature) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_data:1418 name: Sequence-profile alignment (HMM) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of molecular sequence(s) to a hidden Markov model(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_data:1420 name: Sequence-profile alignment (fingerprint) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of molecular sequences to a protein fingerprint from the PRINTS database." [http://edamontology.org] namespace: data is_a: EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_data:1426 name: Phylogenetic continuous quantitative data subset: bioinformatics subset: data subset: edam synonym: "Phylogenetic continuous quantitative characters" EXACT [] synonym: "Quantitative traits" EXACT [] created_in: "beta12orEarlier" def: "Continuous quantitative data that may be read during phylogenetic tree calculation." [http://edamontology.org] namespace: data is_a: EDAM_data:0871 ! Phylogenetic character data [Term] id: EDAM_data:1427 name: Phylogenetic discrete data subset: bioinformatics subset: data subset: edam synonym: "Discrete characters" EXACT [] synonym: "Discretely coded characters" EXACT [] synonym: "Phylogenetic discrete states" EXACT [] created_in: "beta12orEarlier" def: "Character data with discrete states that may be read during phylogenetic tree calculation." [http://edamontology.org] namespace: data is_a: EDAM_data:0871 ! Phylogenetic character data [Term] id: EDAM_data:1428 name: Phylogenetic character cliques subset: bioinformatics subset: data subset: edam synonym: "Phylogenetic report (cliques)" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] id: EDAM_data:1429 name: Phylogenetic invariants subset: bioinformatics subset: data subset: edam synonym: "Phylogenetic report (invariants)" EXACT [] created_in: "beta12orEarlier" def: "Phylogenetic invariants data for testing alternative tree topologies." [http://edamontology.org] namespace: data is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] id: EDAM_data:1438 name: Phylogenetic tree report comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam synonym: "Phylogenetic tree-derived report" EXACT [] created_in: "beta12orEarlier" def: "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:1439 name: DNA substitution model subset: bioinformatics subset: data subset: edam synonym: "Phylogenetic tree report (DNA substitution model)" EXACT [] synonym: "Sequence alignment report (DNA substitution model)" EXACT [] created_in: "beta12orEarlier" def: "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." [http://edamontology.org] namespace: data is_a: EDAM_data:0867 ! Sequence alignment report is_a: EDAM_data:0950 ! Biological model is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1440 name: Phylogenetic tree report (tree shape) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data about the shape of a phylogenetic tree." [http://edamontology.org] namespace: data is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1441 name: Phylogenetic tree report (tree evaluation) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on the confidence of a phylogenetic tree." [http://edamontology.org] namespace: data is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1442 name: Phylogenetic tree report (tree distances) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Distances, such as Branch Score distance, between two or more phylogenetic trees." [http://edamontology.org] namespace: data is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1443 name: Phylogenetic tree report (tree stratigraphic) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis." [http://edamontology.org] namespace: data is_a: EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_data:1444 name: Phylogenetic character contrasts subset: bioinformatics subset: data subset: edam synonym: "Phylogenetic report (character contrasts)" EXACT [] created_in: "beta12orEarlier" def: "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." [http://edamontology.org] namespace: data is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] id: EDAM_data:1446 name: Comparison matrix (integers) subset: bioinformatics subset: data subset: edam synonym: "Substitution matrix (integers)" EXACT [] created_in: "beta12orEarlier" def: "Matrix of integer numbers for sequence comparison." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1447 name: Comparison matrix (floats) subset: bioinformatics subset: data subset: edam synonym: "Substitution matrix (floats)" EXACT [] created_in: "beta12orEarlier" def: "Matrix of floating point numbers for sequence comparison." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1448 name: Comparison matrix (nucleotide) subset: bioinformatics subset: data subset: edam synonym: "Nucleotide substitution matrix" EXACT [] created_in: "beta12orEarlier" def: "Matrix of integer or floating point numbers for nucleotide comparison." [http://edamontology.org] namespace: data is_a: EDAM_data:0874 ! Comparison matrix [Term] id: EDAM_data:1449 name: Comparison matrix (amino acid) subset: bioinformatics subset: data subset: edam synonym: "Amino acid substitution matrix" EXACT [] created_in: "beta12orEarlier" def: "Matrix of integer or floating point numbers for amino acid comparison." [http://edamontology.org] namespace: data is_a: EDAM_data:0874 ! Comparison matrix is_a: EDAM_data:2016 ! Amino acid property [Term] id: EDAM_data:1450 name: Nucleotide comparison matrix (integers) subset: bioinformatics subset: data subset: edam synonym: "Nucleotide substitution matrix (integers)" EXACT [] created_in: "beta12orEarlier" def: "Matrix of integer numbers for nucleotide comparison." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1448 ! Comparison matrix (nucleotide) [Term] id: EDAM_data:1451 name: Nucleotide comparison matrix (floats) subset: bioinformatics subset: data subset: edam synonym: "Nucleotide substitution matrix (floats)" EXACT [] created_in: "beta12orEarlier" def: "Matrix of floating point numbers for nucleotide comparison." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1448 ! Comparison matrix (nucleotide) [Term] id: EDAM_data:1452 name: Amino acid comparison matrix (integers) subset: bioinformatics subset: data subset: edam synonym: "Amino acid substitution matrix (integers)" EXACT [] created_in: "beta12orEarlier" def: "Matrix of integer numbers for amino acid comparison." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1449 ! Comparison matrix (amino acid) [Term] id: EDAM_data:1453 name: Amino acid comparison matrix (floats) subset: bioinformatics subset: data subset: edam synonym: "Amino acid substitution matrix (floats)" EXACT [] created_in: "beta12orEarlier" def: "Matrix of floating point numbers for amino acid comparison." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1449 ! Comparison matrix (amino acid) [Term] id: EDAM_data:1456 name: Protein features (membrane regions) 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: bioinformatics subset: data subset: edam synonym: "Intramembrane region report" EXACT [] synonym: "Protein report (membrane protein)" EXACT [] synonym: "Transmembrane region report" EXACT [] created_in: "beta12orEarlier" def: "An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:1459 name: Nucleic acid structure subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a nucleic acid tertiary (3D) structure." [http://edamontology.org] namespace: data is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis [Term] id: EDAM_data:1460 name: Protein structure subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a protein tertiary (3D) structure." [http://edamontology.org] namespace: data is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure relationship: has_topic EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_data:1461 name: Protein-ligand complex 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1462 name: Carbohydrate structure subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a carbohydrate (3D) structure." [http://edamontology.org] namespace: data is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0152 ! Carbohydrates relationship: has_topic EDAM_topic:0153 ! Lipids [Term] id: EDAM_data:1463 name: Small molecule structure subset: bioinformatics subset: data subset: edam synonym: "CHEBI:23367" RELATED [] created_in: "beta12orEarlier" def: "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." [http://edamontology.org] namespace: data is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0154 ! Small molecules [Term] id: EDAM_data:1464 name: DNA structure subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a DNA tertiary (3D) structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1459 ! Nucleic acid structure [Term] id: EDAM_data:1465 name: RNA structure record subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for an RNA tertiary (3D) structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1459 ! Nucleic acid structure relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] id: EDAM_data:1466 name: tRNA structure record subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." [http://edamontology.org] namespace: data is_a: EDAM_data:1465 ! RNA structure record [Term] id: EDAM_data:1467 name: Protein chain subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain." [http://edamontology.org] namespace: data is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1468 name: Protein domain subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for the tertiary (3D) structure of a protein domain." [http://edamontology.org] namespace: data is_a: EDAM_data:1460 ! Protein structure relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_data:1469 name: Protein structure (all atoms) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a protein tertiary (3D) structure (all atoms)." [http://edamontology.org] namespace: data is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1470 name: Protein structure (C-alpha atoms) comment: C-beta atoms from amino acid side-chains may be included. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] namespace: data is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1471 name: Protein chain (all atoms) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1467 ! Protein chain consider: EDAM_data:1469 ! Protein structure (all atoms) [Term] id: EDAM_data:1472 name: Protein chain (C-alpha atoms) comment: C-beta atoms from amino acid side-chains may be included. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1467 ! Protein chain consider: EDAM_data:1470 ! Protein structure (C-alpha atoms) [Term] id: EDAM_data:1473 name: Protein domain (all atoms) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1468 ! Protein domain consider: EDAM_data:1469 ! Protein structure (all atoms) [Term] id: EDAM_data:1474 name: Protein domain (C-alpha atoms) comment: C-beta atoms from amino acid side-chains may be included. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1468 ! Protein domain consider: EDAM_data:1470 ! Protein structure (C-alpha atoms) [Term] id: EDAM_data:1479 name: Structure alignment (pair) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of exactly two molecular tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:0886 ! Structure alignment [Term] id: EDAM_data:1480 name: Structure alignment (multiple) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of more than two molecular tertiary (3D) structures." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0886 ! Structure alignment [Term] id: EDAM_data:1481 name: Structure alignment (protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of protein tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:0886 ! Structure alignment is_a: EDAM_data:3154 ! Protein alignment [Term] id: EDAM_data:1482 name: Structure alignment (nucleic acid) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of nucleic acid tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:0886 ! Structure alignment is_a: EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:1483 name: Structure alignment (protein pair) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:1479 ! Structure alignment (pair) is_a: EDAM_data:1481 ! Structure alignment (protein) [Term] id: EDAM_data:1484 name: Multiple protein tertiary structure alignment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of more than two protein tertiary (3D) structures." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1481 ! Structure alignment (protein) [Term] id: EDAM_data:1485 name: Structure alignment (protein all atoms) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] namespace: data is_a: EDAM_data:1481 ! Structure alignment (protein) [Term] id: EDAM_data:1486 name: Structure alignment (protein C-alpha atoms) comment: C-beta atoms from amino acid side-chains may be considered. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] namespace: data is_a: EDAM_data:1481 ! Structure alignment (protein) [Term] id: EDAM_data:1487 name: Pairwise protein tertiary structure alignment (all atoms) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1485 ! Structure alignment (protein all atoms) [Term] id: EDAM_data:1488 name: Pairwise protein tertiary structure alignment (C-alpha atoms) comment: C-beta atoms from amino acid side-chains may be included. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms) [Term] id: EDAM_data:1489 name: Multiple protein tertiary structure alignment (all atoms) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1485 ! Structure alignment (protein all atoms) [Term] id: EDAM_data:1490 name: Multiple protein tertiary structure alignment (C-alpha atoms) comment: C-beta atoms from amino acid side-chains may be included. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms) [Term] id: EDAM_data:1491 name: Structure alignment (nucleic acid pair) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:1479 ! Structure alignment (pair) is_a: EDAM_data:1482 ! Structure alignment (nucleic acid) [Term] id: EDAM_data:1492 name: Multiple nucleic acid tertiary structure alignment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1482 ! Structure alignment (nucleic acid) [Term] id: EDAM_data:1493 name: Structure alignment (RNA) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment (superimposition) of RNA tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:1482 ! Structure alignment (nucleic acid) [Term] id: EDAM_data:1494 name: Structural transformation matrix subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures." [http://edamontology.org] namespace: data is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:1495 name: DaliLite hit table 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "DaliLite hit table of protein chain tertiary structure alignment data." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0887 ! Structure alignment report [Term] id: EDAM_data:1496 name: Molecular similarity score subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A score reflecting structural similarities of two molecules." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0888 ! Structure similarity score [Term] id: EDAM_data:1497 name: Root-mean-square deviation subset: bioinformatics subset: data subset: edam synonym: "RMSD" EXACT [] created_in: "beta12orEarlier" def: "Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates." [http://edamontology.org] namespace: data is_a: EDAM_data:0888 ! Structure similarity score [Term] id: EDAM_data:1498 name: Tanimoto similarity score 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A measure of the similarity between two ligand fingerprints." [http://edamontology.org] namespace: data is_a: EDAM_data:0888 ! Structure similarity score [Term] id: EDAM_data:1499 name: 3D-1D scoring matrix subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments." [http://edamontology.org] namespace: data is_a: EDAM_data:0892 ! Protein sequence-structure scoring matrix [Term] id: EDAM_data:1501 name: Amino acid index subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids." [http://edamontology.org] namespace: data is_a: EDAM_data:2016 ! Amino acid property is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:1502 name: Amino acid index (chemical classes) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." [http://edamontology.org] namespace: data is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1503 name: Amino acid pair-wise contact potentials subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Statistical protein contact potentials." [http://edamontology.org] namespace: data is_a: EDAM_data:2016 ! Amino acid property [Term] id: EDAM_data:1505 name: Amino acid index (molecular weight) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Molecular weights of amino acids." [http://edamontology.org] namespace: data is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1506 name: Amino acid index (hydropathy) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Hydrophobic, hydrophilic or charge properties of amino acids." [http://edamontology.org] namespace: data is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1507 name: Amino acid index (White-Wimley data) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Experimental free energy values for the water-interface and water-octanol transitions for the amino acids." [http://edamontology.org] namespace: data is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1508 name: Amino acid index (van der Waals radii) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Van der Waals radii of atoms for different amino acid residues." [http://edamontology.org] namespace: data is_a: EDAM_data:1501 ! Amino acid index [Term] id: EDAM_data:1509 name: Enzyme property subset: bioinformatics subset: data subset: edam synonym: "Enzyme report" EXACT [] synonym: "Protein report (enzyme)" EXACT [] created_in: "beta12orEarlier" def: "An informative report on a specific enzyme." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions [Term] id: EDAM_data:1517 name: Restriction enzyme property 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: bioinformatics subset: data subset: edam synonym: "Protein report (restriction enzyme)" EXACT [] synonym: "Restriction enzyme pattern data" EXACT [] synonym: "Restriction enzyme report" EXACT [] created_in: "beta12orEarlier" def: "An informative report on a specific restriction enzyme such as enzyme reference data." [http://edamontology.org] namespace: data is_a: EDAM_data:1509 ! Enzyme property [Term] id: EDAM_data:1519 name: Peptide molecular weights comment: The report might include associated data such as frequency of peptide fragment molecular weights. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1520 name: Peptide hydrophobic moment comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Report on the hydrophobic moment of a polypeptide sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1521 name: Protein aliphatic index comment: The aliphatic index is the relative protein volume occupied by aliphatic side chains. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The aliphatic index of a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1522 name: Protein sequence hydropathy plot comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc." [http://edamontology.org] namespace: data is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1523 name: Protein charge plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1524 name: Protein solubility subset: bioinformatics subset: data subset: edam synonym: "Protein solubility data" EXACT [] created_in: "beta12orEarlier" def: "The solubility or atomic solvation energy of a protein sequence or structure." [http://edamontology.org] namespace: data is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1525 name: Protein crystallizability subset: bioinformatics subset: data subset: edam synonym: "Protein crystallizability data" EXACT [] created_in: "beta12orEarlier" def: "Data on the crystallizability of a protein sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1526 name: Protein globularity subset: bioinformatics subset: data subset: edam synonym: "Protein globularity data" EXACT [] created_in: "beta12orEarlier" def: "Data on the stability, intrinsic disorder or globularity of a protein sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2970 ! Protein hydropathy data [Term] id: EDAM_data:1527 name: Protein titration curve subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The titration curve of a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1528 name: Protein isoelectric point subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The isoelectric point of one proteins." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1529 name: Protein pKa value subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The pKa value of a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1530 name: Protein hydrogen exchange rate subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The hydrogen exchange rate of a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1531 name: Protein extinction coefficient subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The extinction coefficient of a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1532 name: Protein optical density subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The optical density of a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1533 name: Protein subcellular localization subset: bioinformatics subset: data subset: edam synonym: "Protein report (subcellular localization)" EXACT [] created_in: "beta12orEarlier" def: "An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:1534 name: Peptide immunogenicity data 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: bioinformatics subset: data subset: edam synonym: "Peptide immunogenicity" EXACT [] synonym: "Peptide immunogenicity report" EXACT [] created_in: "beta12orEarlier" def: "An report on allergenicity / immunogenicity of peptides and proteins." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1536 name: MHC peptide immunogenicity report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on the immunogenicity of MHC class I or class II binding peptides." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1534 ! Peptide immunogenicity data [Term] id: EDAM_data:1537 name: Protein structure report subset: bioinformatics subset: data subset: edam synonym: "Protein property (structural)" EXACT [] synonym: "Protein report (structure)" EXACT [] synonym: "Protein structural property" EXACT [] synonym: "Protein structure report (domain)" EXACT [] synonym: "Protein structure-derived report" EXACT [] created_in: "beta12orEarlier" def: "Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains." [http://edamontology.org] namespace: data is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:2085 ! Structure report [Term] id: EDAM_data:1539 name: Protein structural quality report comment: Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. subset: bioinformatics subset: data subset: edam synonym: "Protein property (structural quality)" EXACT [] synonym: "Protein report (structural quality)" EXACT [] synonym: "Protein structure report (quality evaluation)" EXACT [] created_in: "beta12orEarlier" def: "Report on the quality of a protein three-dimensional model." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:1540 name: Protein residue interactions subset: bioinformatics subset: data subset: edam synonym: "Atom interaction data" EXACT [] synonym: "Residue interaction data" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0906 ! Protein interaction is_a: EDAM_data:2599 ! Molecular interaction relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] id: EDAM_data:1541 name: Protein flexibility or motion report 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: bioinformatics subset: data subset: edam synonym: "Protein flexibility or motion" EXACT [] synonym: "Protein property (flexibility or motion)" EXACT [] synonym: "Protein structure report (flexibility or motion)" EXACT [] created_in: "beta12orEarlier" def: "Informative report on flexibility or motion of a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:1542 name: Protein solvent accessibility 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 concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on the solvent accessible or buried surface area of a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1543 name: Protein surface report 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: bioinformatics subset: data subset: edam synonym: "Protein structure report (surface)" EXACT [] created_in: "beta12orEarlier" def: "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1537 ! Protein structure report is_a: EDAM_data:1542 ! Protein solvent accessibility [Term] id: EDAM_data:1544 name: Ramachandran plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Phi/psi angle data or a Ramachandran plot of a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:2991 ! Protein torsion angle data [Term] id: EDAM_data:1545 name: Protein dipole moment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on the net charge distribution (dipole moment) of a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:1546 name: Protein distance matrix subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1547 name: Protein contact map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An amino acid residue contact map for a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1548 name: Protein residue 3D cluster subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Report on clusters of contacting residues in protein structures such as a key structural residue network." [http://edamontology.org] namespace: data is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1549 name: Protein hydrogen bonds subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Patterns of hydrogen bonding in protein structures." [http://edamontology.org] namespace: data is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1550 name: Protein non-canonical interactions subset: bioinformatics subset: data subset: edam synonym: "Protein non-canonical interactions report" EXACT [] created_in: "beta12orEarlier" def: "Non-canonical atomic interactions in protein structures." [http://edamontology.org] namespace: data is_a: EDAM_data:1539 ! Protein structural quality report is_a: EDAM_data:1540 ! Protein residue interactions [Term] id: EDAM_data:1553 name: CATH node 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: bioinformatics subset: data subset: edam synonym: "CATH classification node report" EXACT [] created_in: "beta12orEarlier" def: "Information on a node from the CATH database." [http://edamontology.org] namespace: data is_a: EDAM_data:3101 ! Protein domain classification node [Term] id: EDAM_data:1554 name: SCOP node subset: bioinformatics subset: data subset: edam synonym: "SCOP classification node" EXACT [] created_in: "beta12orEarlier" def: "Information on a node from the SCOP database." [http://edamontology.org] namespace: data is_a: EDAM_data:3101 ! Protein domain classification node [Term] id: EDAM_data:1555 name: EMBASSY domain classification subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:1556 name: CATH class subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on a protein 'class' node from the CATH database." [http://edamontology.org] namespace: data is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1557 name: CATH architecture subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on a protein 'architecture' node from the CATH database." [http://edamontology.org] namespace: data is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1558 name: CATH topology subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on a protein 'topology' node from the CATH database." [http://edamontology.org] namespace: data is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1559 name: CATH homologous superfamily subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on a protein 'homologous superfamily' node from the CATH database." [http://edamontology.org] namespace: data is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1560 name: CATH structurally similar group subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on a protein 'structurally similar group' node from the CATH database." [http://edamontology.org] namespace: data is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1561 name: CATH functional category subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on a protein 'functional category' node from the CATH database." [http://edamontology.org] namespace: data is_a: EDAM_data:1553 ! CATH node [Term] id: EDAM_data:1564 name: Protein fold recognition report 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0901 ! Protein features (domains) [Term] id: EDAM_data:1565 name: Protein-protein interaction comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains). subset: bioinformatics subset: data subset: edam synonym: "Protein structure report (protein complex)" EXACT [] created_in: "beta12orEarlier" def: "Data on protein-protein interaction(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] id: EDAM_data:1566 name: Protein-ligand interaction subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on protein-ligand (small molecule) interaction(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] id: EDAM_data:1567 name: Protein-nucleic acid interaction subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on protein-DNA/RNA interaction(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions [Term] id: EDAM_data:1583 name: Nucleic acid melting profile 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: bioinformatics subset: data subset: edam synonym: "Nucleic acid stability profile" EXACT [] created_in: "beta12orEarlier" def: "Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating." [http://edamontology.org] namespace: data is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] id: EDAM_data:1584 name: Nucleic acid enthalpy subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] namespace: data is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] id: EDAM_data:1585 name: Nucleic acid entropy subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] namespace: data is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] id: EDAM_data:1586 name: Nucleic acid melting temperature subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2139 ! Nucleic acid melting temperature [Term] id: EDAM_data:1587 name: Nucleic acid stitch profile 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org] namespace: data is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] id: EDAM_data:1588 name: DNA base pair stacking energies data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "DNA base pair stacking energies data." [http://edamontology.org] namespace: data is_a: EDAM_data:2088 ! DNA base structural data [Term] id: EDAM_data:1589 name: DNA base pair twist angle data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "DNA base pair twist angle data." [http://edamontology.org] namespace: data is_a: EDAM_data:2088 ! DNA base structural data [Term] id: EDAM_data:1590 name: DNA base trimer roll angles data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "DNA base trimer roll angles data." [http://edamontology.org] namespace: data is_a: EDAM_data:2088 ! DNA base structural data [Term] id: EDAM_data:1591 name: Vienna RNA parameters subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "RNA parameters used by the Vienna package." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1592 name: Vienna RNA structure constraints subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Structure constraints used by the Vienna package." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1593 name: Vienna RNA concentration data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "RNA concentration data used by the Vienna package." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1594 name: Vienna RNA calculated energy subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "RNA calculated energy data generated by the Vienna package." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1584 ! Nucleic acid enthalpy [Term] id: EDAM_data:1595 name: Base pairing probability matrix dotplot comment: Such as generated by the Vienna package. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Dotplot of RNA base pairing probability matrix." [http://edamontology.org] namespace: data is_a: EDAM_data:2088 ! DNA base structural data [Term] id: EDAM_data:1596 name: Nucleic acid folding report 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: bioinformatics subset: data subset: edam synonym: "Nucleic acid report (folding model)" EXACT [] synonym: "Nucleic acid report (folding)" EXACT [] created_in: "beta12orEarlier" def: "A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." [http://edamontology.org] namespace: data is_a: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:1597 name: Codon usage table 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Table of codon usage data calculated from one or more nucleic acid sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] id: EDAM_data:1598 name: Genetic code comment: A genetic code need not include detailed codon usage information. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A genetic code for an organism." [http://edamontology.org] namespace: data is_a: EDAM_data:1597 ! Codon usage table [Term] id: EDAM_data:1599 name: Codon adaptation index subset: bioinformatics subset: data subset: edam synonym: "CAI" EXACT [] created_in: "beta12orEarlier" def: "A simple measure of synonymous codon usage bias often used to predict gene expression levels." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2865 ! Codon usage bias [Term] id: EDAM_data:1600 name: Codon usage bias plot subset: bioinformatics subset: data subset: edam synonym: "Synonymous codon usage statistic plot" EXACT [] created_in: "beta12orEarlier" def: "A plot of the synonymous codon usage calculated for windows over a nucleotide sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2865 ! Codon usage bias [Term] id: EDAM_data:1601 name: Nc statistic subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2865 ! Codon usage bias [Term] id: EDAM_data:1602 name: Codon usage fraction difference subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The differences in codon usage fractions between two codon usage tables." [http://edamontology.org] namespace: data is_a: EDAM_data:0914 ! Codon usage report [Term] id: EDAM_data:1621 name: Pharmacogenomic annotation comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on the influence of genotype on drug response." [http://edamontology.org] namespace: data is_a: EDAM_data:0920 ! Genotype/phenotype annotation [Term] id: EDAM_data:1622 name: Disease annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a specific disease." [http://edamontology.org] namespace: data is_a: EDAM_data:0920 ! Genotype/phenotype annotation relationship: has_topic EDAM_topic:0634 ! Disease resources [Term] id: EDAM_data:1634 name: Gene annotation (linkage disequilibrium) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: data is_a: EDAM_data:0927 ! Gene annotation (linkage) [Term] id: EDAM_data:1636 name: Heat map 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:2967 ! Microarray image [Term] id: EDAM_data:1642 name: Affymetrix probe sets library file subset: bioinformatics subset: data subset: edam synonym: "CDF file" RELATED [] created_in: "beta12orEarlier" def: "Affymetrix library file of information about which probes belong to which probe set." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation [Term] id: EDAM_data:1643 name: Affymetrix probe sets information library file subset: bioinformatics subset: data subset: edam synonym: "GIN file" RELATED [] created_in: "beta12orEarlier" def: "Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation [Term] id: EDAM_data:1646 name: Molecular weights standard fingerprint subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS." [http://edamontology.org] namespace: data is_a: EDAM_data:0944 ! Peptide mass fingerprint [Term] id: EDAM_data:1656 name: Pathway or network (metabolic) comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report typically including a map (diagram) of a metabolic pathway." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1657 name: Pathway or network (genetic information processing) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report typically including a map (diagram) of a genetic information processing pathway." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1658 name: Pathway or network (environmental information processing) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report typically including a map (diagram) of an environmental information processing pathway." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1659 name: Pathway or network (signal transduction) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report typically including a map (diagram) of a signal transduction pathway." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1660 name: Pathway or network (cellular process) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report typically including a map (diagram) of a cellular process pathway." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1661 name: Pathway or network (disease) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1662 name: Pathway or network (drug structure relationship) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report typically including a map (diagram) of drug structure relationships." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1663 name: Pathway or network (protein-protein interaction) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report typically including a map (diagram) of a network of protein interactions." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_data:1664 name: MIRIAM datatype 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources." [http://edamontology.org] namespace: data is_a: EDAM_data:0948 ! Data resource definition [Term] id: EDAM_data:1667 name: E-value 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: bioinformatics subset: data subset: edam synonym: "Expectation value" EXACT [] created_in: "beta12orEarlier" def: "A simple floating point number defining the lower or upper limit of an expectation value (E-value)." [http://edamontology.org] namespace: data is_a: EDAM_data:0951 ! Statistical estimate score [Term] id: EDAM_data:1668 name: Z-value comment: A z-value might be specified as a threshold for reporting hits from database searches. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The z-value is the number of standard deviations a data value is above or below a mean value." [http://edamontology.org] namespace: data is_a: EDAM_data:0951 ! Statistical estimate score [Term] id: EDAM_data:1669 name: P-value comment: A z-value might be specified as a threshold for reporting hits from database searches. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0951 ! Statistical estimate score [Term] id: EDAM_data:1670 name: Database version information subset: bioinformatics subset: data subset: edam synonym: "Ontology version information" EXACT [] created_in: "beta12orEarlier" def: "Information on a database (or ontology) version, for example name, version number and release date." [http://edamontology.org] namespace: data is_a: EDAM_data:0953 ! Version information is_a: EDAM_data:0957 ! Database metadata [Term] id: EDAM_data:1671 name: Tool version information subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on an application version, for example name, version number and release date." [http://edamontology.org] namespace: data is_a: EDAM_data:0953 ! Version information is_a: EDAM_data:0958 ! Tool metadata [Term] id: EDAM_data:1672 name: CATH version information subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on a version of the CATH database." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1670 ! Database version information [Term] id: EDAM_data:1673 name: Swiss-Prot to PDB mapping subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Cross-mapping of Swiss-Prot codes to PDB identifiers." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0954 ! Database cross-mapping [Term] id: EDAM_data:1674 name: Sequence database cross-references subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Cross-references from a sequence record to other databases." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:1675 name: Job status 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Metadata on the status of a submitted job." [http://edamontology.org] namespace: data is_a: EDAM_data:0959 ! Job metadata [Term] id: EDAM_data:1676 name: Job ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The (typically numeric) unique identifier of a submitted job." [http://edamontology.org] namespace: identifier obsolete_since: "1.0" replaced_by: EDAM_data:2098 !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:1677 name: Job type subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A label (text token) describing the type of job, for example interactive or non-interactive." [http://edamontology.org] namespace: data is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1678 name: Tool log subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages." [http://edamontology.org] namespace: data is_a: EDAM_data:0959 ! Job metadata [Term] id: EDAM_data:1679 name: DaliLite log file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1680 name: STRIDE log file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "STRIDE log file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1681 name: NACCESS log file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "NACCESS log file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1682 name: EMBOSS wordfinder log file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "EMBOSS wordfinder log file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1683 name: EMBOSS domainatrix log file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "EMBOSS (EMBASSY) domainatrix application log file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1684 name: EMBOSS sites log file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "EMBOSS (EMBASSY) sites application log file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1685 name: EMBOSS supermatcher error file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "EMBOSS (EMBASSY) supermatcher error file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1686 name: EMBOSS megamerger log file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "EMBOSS megamerger log file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1687 name: EMBOSS whichdb log file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "EMBOSS megamerger log file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1688 name: EMBOSS vectorstrip log file subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "EMBOSS vectorstrip log file." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1678 ! Tool log [Term] id: EDAM_data:1689 name: Username subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A username on a computer system." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2101 ! User ID [Term] id: EDAM_data:1690 name: Password subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A password on a computer system." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2101 ! User ID [Term] id: EDAM_data:1691 name: Email address subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby:Email xref: Moby:EmailAddress created_in: "beta12orEarlier" def: "A valid email address of an end-user." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2101 ! User ID [Term] id: EDAM_data:1692 name: Person name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a person." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2118 ! Person identifier [Term] id: EDAM_data:1693 name: Number of iterations subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Number of iterations of an algorithm." [http://edamontology.org] namespace: data is_a: EDAM_data:2079 ! Search parameter [Term] id: EDAM_data:1694 name: Number of output entities subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Number of entities (for example database hits, sequences, alignments etc) to write to an output file." [http://edamontology.org] namespace: data is_a: EDAM_data:2079 ! Search parameter [Term] id: EDAM_data:1695 name: Hit sort order subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Controls the order of hits (reported matches) in an output file from a database search." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2134 ! Results sort order [Term] id: EDAM_data:1696 name: Drug annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a specific drug." [http://edamontology.org] namespace: data is_a: EDAM_data:0962 ! Small molecule annotation relationship: has_topic EDAM_topic:0620 ! Drugs and targets [Term] id: EDAM_data:1707 name: Phylogenetic tree image comment: See also 'Phylogenetic tree' subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1438 ! Phylogenetic tree report is_a: EDAM_data:2968 ! Image [Term] id: EDAM_data:1708 name: RNA secondary structure image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image of RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] namespace: data is_a: EDAM_data:2880 ! Secondary structure image [Term] id: EDAM_data:1709 name: Protein secondary structure image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image of protein secondary structure." [http://edamontology.org] namespace: data is_a: EDAM_data:2880 ! Secondary structure image is_a: EDAM_data:2956 ! Protein secondary structure report [Term] id: EDAM_data:1710 name: Structure image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image of one or more molecular tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:2085 ! Structure report is_a: EDAM_data:2968 ! Image [Term] id: EDAM_data:1711 name: Sequence alignment image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image of two or more aligned molecular sequences possibly annotated with alignment features." [http://edamontology.org] namespace: data is_a: EDAM_data:0867 ! Sequence alignment report is_a: EDAM_data:2968 ! Image [Term] id: EDAM_data:1712 name: Structure image (small molecule) comment: The molecular identifier and formula are typically included. subset: bioinformatics subset: data subset: edam synonym: "Chemical structure image" EXACT [] synonym: "Small molecule structure image" EXACT [] created_in: "beta12orEarlier" def: "An image of the structure of a small chemical compound." [http://edamontology.org] namespace: data is_a: EDAM_data:0962 ! Small molecule annotation is_a: EDAM_data:1710 ! Structure image [Term] id: EDAM_data:1713 name: Fate map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: " A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development." [http://edamontology.org] namespace: data is_a: EDAM_data:2724 ! Embryo annotation [Term] id: EDAM_data:1714 name: Microarray spots image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An image of spots from a microarray experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:2967 ! Microarray image is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:1715 name: BioPax subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the BioPax ontology." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1716 name: GO subset: bioinformatics subset: data subset: edam synonym: "Gene Ontology term" EXACT [] xref: Moby:Annotated_GO_Term xref: Moby:Annotated_GO_Term_With_Probability xref: Moby:GO_Term xref: Moby:GOTerm created_in: "beta12orEarlier" def: "A term definition from The Gene Ontology (GO)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1717 name: MeSH subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the MeSH vocabulary." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1718 name: HGNC subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the HGNC controlled vocabulary." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1719 name: NCBI taxonomy vocabulary subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the NCBI taxonomy vocabulary." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1720 name: Plant ontology term subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the Plant Ontology (PO)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1721 name: UMLS subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the UMLS vocabulary." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1722 name: FMA 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from Foundational Model of Anatomy." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1723 name: EMAP subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the EMAP mouse ontology." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1724 name: ChEBI subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the ChEBI ontology." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1725 name: MGED subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the MGED ontology." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1726 name: myGrid comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term from the myGrid ontology." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0966 ! Ontology term [Term] id: EDAM_data:1727 name: GO (biological process) comment: Data Type is an enumerated string. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term definition for a biological process from the Gene Ontology (GO)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2858 ! Ontology concept [Term] id: EDAM_data:1728 name: GO (molecular function) comment: Data Type is an enumerated string. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term definition for a molecular function from the Gene Ontology (GO)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2858 ! Ontology concept [Term] id: EDAM_data:1729 name: GO (cellular component) comment: Data Type is an enumerated string. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term definition for a cellular component from the Gene Ontology (GO)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2858 ! Ontology concept [Term] id: EDAM_data:1730 name: Ontology relation type subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A relation type defined in an ontology." [http://edamontology.org] namespace: data is_a: EDAM_data:0967 ! Ontology concept metadata [Term] id: EDAM_data:1731 name: Ontology concept definition subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The definition of a concept from an ontology." [http://edamontology.org] namespace: data is_a: EDAM_data:0967 ! Ontology concept metadata [Term] id: EDAM_data:1732 name: Ontology concept comment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A comment on a concept from an ontology." [http://edamontology.org] namespace: data is_a: EDAM_data:0967 ! Ontology concept metadata [Term] id: EDAM_data:1733 name: Ontology concept reference subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Reference for a concept from an ontology." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:1738 name: doc2loc document information comment: The doc2loc output includes the url, format, type and availability code of a document for every service provider. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on a published article provided by the doc2loc program." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0970 ! Bibliographic reference [Term] id: EDAM_data:1742 name: PDB residue number subset: bioinformatics subset: data subset: edam xref: PDBML:PDB_residue_no xref: WHATIF: pdb_number created_in: "beta12orEarlier" def: "A residue identifier (a string) from a PDB file." [http://edamontology.org] namespace: data is_a: EDAM_data:1016 ! Sequence position [Term] id: EDAM_data:1743 name: Atomic coordinate subset: bioinformatics subset: data subset: edam synonym: "Cartesian coordinate" EXACT [] created_in: "beta12orEarlier" def: "Cartesian coordinate of an atom (in a molecular structure)." [http://edamontology.org] namespace: data is_a: EDAM_data:1917 ! Atomic property [Term] id: EDAM_data:1744 name: Atomic x coordinate subset: bioinformatics subset: data subset: edam synonym: "Cartesian x coordinate" EXACT [] xref: PDBML:_atom_site.Cartn_x in PDBML xref: WHATIF: PDBx_Cartn_x created_in: "beta12orEarlier" def: "Cartesian x coordinate of an atom (in a molecular structure)." [http://edamontology.org] namespace: data is_a: EDAM_data:1743 ! Atomic coordinate [Term] id: EDAM_data:1745 name: Atomic y coordinate subset: bioinformatics subset: data subset: edam synonym: "Cartesian y coordinate" EXACT [] xref: PDBML:_atom_site.Cartn_y in PDBML xref: WHATIF: PDBx_Cartn_y created_in: "beta12orEarlier" def: "Cartesian y coordinate of an atom (in a molecular structure)." [http://edamontology.org] namespace: data is_a: EDAM_data:1743 ! Atomic coordinate [Term] id: EDAM_data:1746 name: Atomic z coordinate subset: bioinformatics subset: data subset: edam synonym: "Cartesian z coordinate" EXACT [] xref: PDBML:_atom_site.Cartn_z xref: WHATIF: PDBx_Cartn_z created_in: "beta12orEarlier" def: "Cartesian z coordinate of an atom (in a molecular structure)." [http://edamontology.org] namespace: data is_a: EDAM_data:1743 ! Atomic coordinate [Term] id: EDAM_data:1748 name: PDB atom name subset: bioinformatics subset: data subset: edam subset: identifiers xref: PDBML:pdbx_PDB_atom_name xref: WHATIF: alternate_atom xref: WHATIF: atom_type xref: WHATIF: PDBx_auth_atom_id xref: WHATIF: PDBx_type_symbol created_in: "beta12orEarlier" def: "Identifier (a string) of a specific atom from a PDB file for a molecular structure." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1757 ! Atom name [Term] id: EDAM_data:1755 name: Protein atom 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: bioinformatics subset: data subset: edam synonym: "Atom data" EXACT [] synonym: "CHEBI:33250" RELATED [] created_in: "beta12orEarlier" def: "Data on a single atom from a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1756 name: Protein residue 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: bioinformatics subset: data subset: edam synonym: "Residue" EXACT [] created_in: "beta12orEarlier" def: "Data on a single amino acid residue position in a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:1757 name: Atom name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of an atom." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0983 ! Atom identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1758 name: PDB residue name subset: bioinformatics subset: data subset: edam subset: identifiers xref: WHATIF: type created_in: "beta12orEarlier" def: "Three-letter amino acid residue names as used in PDB files." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2564 ! Amino acid name (three letter) [Term] id: EDAM_data:1759 name: PDB model number subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Model number" EXACT [] xref: PDBML:pdbx_PDB_model_num xref: WHATIF: model_number created_in: "beta12orEarlier" def: "Identifier of a model structure from a PDB file." [http://edamontology.org] namespace: identifier is_a: EDAM_data:3035 ! Structure identifier [Term] id: EDAM_data:1762 name: CATH domain report 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Summary of domain classification information for a CATH domain." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:1764 name: CATH representative domain sequences (ATOM) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1765 name: CATH representative domain sequences (COMBS) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1766 name: CATH domain sequences (ATOM) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "FASTA sequence database for all CATH domains (based on PDB ATOM records)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1767 name: CATH domain sequences (COMBS) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "FASTA sequence database for all CATH domains (based on COMBS sequence data)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1771 name: Sequence version information subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on an molecular sequence version." [http://edamontology.org] namespace: data is_a: EDAM_data:0855 ! Sequence metadata is_a: EDAM_data:0953 ! Version information [Term] id: EDAM_data:1772 name: Score or penalty subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: data is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:1776 name: Protein report (function) comment: For properties that can be mapped to a sequence, use 'Sequence report' instead. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Report on general functional properties of specific protein(s)." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:1783 name: Gene name (ASPGD) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS created_in: "beta12orEarlier" def: "Name of a gene from Aspergillus Genome Database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1784 name: Gene name (CGD) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS created_in: "beta12orEarlier" def: "Name of a gene from Candida Genome Database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1785 name: Gene name (dictyBase) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase created_in: "beta12orEarlier" def: "Name of a gene from dictyBase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1786 name: Gene name (EcoGene primary) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "EcoGene primary gene name" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G created_in: "beta12orEarlier" def: "Primary name of a gene from EcoGene Database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1787 name: Gene name (MaizeGDB) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus created_in: "beta12orEarlier" def: "Name of a gene from MaizeGDB (maize genes) database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1788 name: Gene name (SGD) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS created_in: "beta12orEarlier" def: "Name of a gene from Saccharomyces Genome Database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol is_a: EDAM_data:2632 ! SGD ID [Term] id: EDAM_data:1789 name: Gene name (TGD) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS created_in: "beta12orEarlier" def: "Name of a gene from Tetrahymena Genome Database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1790 name: Gene name (CGSC) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC created_in: "beta12orEarlier" def: "Symbol of a gene from E.coli Genetic Stock Center." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1791 name: Gene name (HGNC) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Gene name (HUGO)" EXACT [] synonym: "HGNC gene name" EXACT [] synonym: "HGNC gene symbol" EXACT [] synonym: "HGNC symbol" EXACT [] synonym: "HUGO gene name" EXACT [] synonym: "HUGO gene symbol" EXACT [] synonym: "HUGO symbol" EXACT [] synonym: "Official gene name" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene created_in: "beta12orEarlier" def: "Symbol of a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org] regex: "HGNC:[0-9]{1,5}" namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1792 name: Gene name (MGD) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD created_in: "beta12orEarlier" def: "Symbol of a gene from the Mouse Genome Database." [http://edamontology.org] regex: "MGI:[0-9]+" namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1793 name: Gene name (Bacillus subtilis) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG created_in: "beta12orEarlier" def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1794 name: Gene ID (PlasmoDB) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB created_in: "beta12orEarlier" def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1795 name: Gene ID (EcoGene) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "EcoGene Accession" EXACT [] synonym: "EcoGene ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a gene from EcoGene Database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1796 name: Gene ID (FlyBase) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase created_in: "beta12orEarlier" def: "Gene identifier from FlyBase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1797 name: Gene ID (GeneDB Glossina morsitans) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans created_in: "beta12orEarlier" def: "Gene identifier from Glossina morsitans GeneDB database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1798 name: Gene ID (GeneDB Leishmania major) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor created_in: "beta12orEarlier" def: "Gene identifier from Leishmania major GeneDB database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1799 name: Gene ID (GeneDB Plasmodium falciparum) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum created_in: "beta12orEarlier" def: "Gene identifier from Plasmodium falciparum GeneDB database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1800 name: Gene ID (GeneDB Schizosaccharomyces pombe) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe created_in: "beta12orEarlier" def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1801 name: Gene ID (GeneDB Trypanosoma brucei) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei created_in: "beta12orEarlier" def: "Gene identifier from Trypanosoma brucei GeneDB database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1035 ! Gene ID (GeneDB) [Term] id: EDAM_data:1802 name: Gene ID (Gramene) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene created_in: "beta12orEarlier" def: "Gene identifier from Gramene database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1803 name: Gene ID (Virginia microbial) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD created_in: "beta12orEarlier" def: "Gene identifier from Virginia Bioinformatics Institute microbial database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1804 name: Gene ID (SGN) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN created_in: "beta12orEarlier" def: "Gene identifier from Sol Genomics Network." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1805 name: Gene ID (WormBase) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase created_in: "beta12orEarlier" def: "Gene identifier used by WormBase database." [http://edamontology.org] regex: "WBGene[0-9]{8}" namespace: identifier is_a: EDAM_data:2113 ! WormBase identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1806 name: Gene synonym subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Gene name synonym" EXACT [] created_in: "beta12orEarlier" def: "Any name (other than the recommended one) for a gene." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1807 name: ORF name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of an open reading frame attributed by a sequencing project." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2795 ! ORF identifier [Term] id: EDAM_data:1852 name: Sequence assembly component subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A component of a larger sequence assembly." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0925 ! Sequence assembly [Term] id: EDAM_data:1853 name: Chromosome annotation (aberration) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on a chromosome aberration such as abnormalities in chromosome structure." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0919 ! Gene annotation (chromosome) [Term] id: EDAM_data:1855 name: Clone ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a clone (cloned molecular sequence) from a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2769 ! Transcript ID [Term] id: EDAM_data:1856 name: PDB insertion code subset: bioinformatics subset: data subset: edam xref: PDBML:pdbx_PDB_ins_code xref: WHATIF: insertion_code created_in: "beta12orEarlier" def: "An insertion code (part of the residue number) for an amino acid residue from a PDB file." [http://edamontology.org] namespace: data is_a: EDAM_data:1016 ! Sequence position [Term] id: EDAM_data:1857 name: Atomic occupancy comment: The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. subset: bioinformatics subset: data subset: edam xref: WHATIF: PDBx_occupancy created_in: "beta12orEarlier" def: "The fraction of an atom type present at a site in a molecular structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1917 ! Atomic property [Term] id: EDAM_data:1858 name: Isotropic B factor subset: bioinformatics subset: data subset: edam xref: WHATIF: PDBx_B_iso_or_equiv created_in: "beta12orEarlier" def: "Isotropic B factor (atomic displacement parameter) for an atom from a PDB file." [http://edamontology.org] namespace: data is_a: EDAM_data:1917 ! Atomic property [Term] id: EDAM_data:1859 name: Deletion map 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: bioinformatics subset: data subset: edam synonym: "Deletion-based cytogenetic map" EXACT [] created_in: "beta12orEarlier" def: "A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type." [http://edamontology.org] namespace: data is_a: EDAM_data:1283 ! Cytogenetic map [Term] id: EDAM_data:1860 name: QTL map subset: bioinformatics subset: data subset: edam synonym: "Quantitative trait locus map" EXACT [] created_in: "beta12orEarlier" def: "A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers." [http://edamontology.org] namespace: data is_a: EDAM_data:1278 ! Genetic map [Term] id: EDAM_data:1863 name: Haplotype map subset: bioinformatics subset: data subset: edam xref: Moby:Haplotyping_Study_obj created_in: "beta12orEarlier" def: "A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation." [http://edamontology.org] namespace: data is_a: EDAM_data:1278 ! Genetic map [Term] id: EDAM_data:1864 name: Map set subset: bioinformatics subset: data subset: edam xref: Moby:GCP_CorrelatedLinkageMapSet xref: Moby:GCP_CorrelatedMapSet created_in: "beta12orEarlier" def: "Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped." [http://edamontology.org] namespace: data is_a: EDAM_data:2019 ! Map attribute [Term] id: EDAM_data:1865 name: Map feature comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. subset: bioinformatics subset: data subset: edam xref: Moby:MapFeature created_in: "beta12orEarlier" def: "A feature which may mapped (positioned) on a genetic or other type of map." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1255 ! Feature record consider: EDAM_data:1276 ! Nucleic acid features consider: EDAM_data:2019 ! Map attribute [Term] id: EDAM_data:1866 name: Map type 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A designation of the type of map (genetic map, physical map, sequence map etc) or map set." [http://edamontology.org] namespace: data is_a: EDAM_data:2019 ! Map attribute is_a: EDAM_data:2100 ! Type [Term] id: EDAM_data:1867 name: Protein fold name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a protein fold." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:1868 name: Taxon comment: For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Taxonomic rank" EXACT [] synonym: "Taxonomy rank" EXACT [] xref: Moby:BriefTaxonConcept xref: Moby:PotentialTaxon created_in: "beta12orEarlier" def: "The name of a group of organisms belonging to the same taxonomic rank." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2909 ! Organism name [Term] id: EDAM_data:1869 name: Organism identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of a (group of) organisms." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2530 ! Organism annotation [Term] id: EDAM_data:1870 name: Genus name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a genus of organism." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:1872 name: Taxonomic classification 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: bioinformatics subset: data subset: edam subset: identifiers synonym: "Taxonomic information" EXACT [] synonym: "Taxonomic name" EXACT [] xref: Moby:GCP_Taxon xref: Moby:iANT_organism-xml xref: Moby:TaxonName xref: Moby:TaxonScientificName xref: Moby:TaxonTCS created_in: "beta12orEarlier" def: "The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2909 ! Organism name [Term] id: EDAM_data:1873 name: iHOP organism ID subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:iHOPorganism created_in: "beta12orEarlier" def: "A unique identifier for an organism used in the iHOP database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2908 ! Organism accession [Term] id: EDAM_data:1874 name: Genbank common name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Common name for an organism as used in the GenBank database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2909 ! Organism name [Term] id: EDAM_data:1875 name: NCBI taxon subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a taxon from the NCBI taxonomy database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:1877 name: Synonym subset: bioinformatics subset: data subset: edam synonym: "Alternative name" EXACT [] created_in: "beta12orEarlier" def: "An alternative for a word." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:1878 name: Misspelling subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A common misspelling of a word." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:1879 name: Acronym subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An abbreviation of a phrase or word." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:1880 name: Misnomer subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A term which is likely to be misleading of its meaning." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:1881 name: Author ID subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby:Author created_in: "beta12orEarlier" def: "Information on the authors of a published work." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2118 ! Person identifier [Term] id: EDAM_data:1882 name: DragonDB author identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier representing an author in the DragonDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1881 ! Author ID [Term] id: EDAM_data:1883 name: Annotated URI subset: bioinformatics subset: data subset: edam xref: Moby:DescribedLink created_in: "beta12orEarlier" def: "A URI along with annotation describing the data found at the address." [http://edamontology.org] namespace: data is_a: EDAM_data:2093 ! Data reference is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:1884 name: UniProt keywords subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0582 ! Ontology [Term] id: EDAM_data:1885 name: Gene ID (GeneFarm) subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:GENEFARM_GeneID created_in: "beta12orEarlier" def: "Identifier of a gene from the GeneFarm database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1886 name: Blattner number subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:Blattner_number created_in: "beta12orEarlier" def: "The blattner identifier for a gene." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1887 name: Gene ID (MIPS Maize) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "MIPS genetic element identifier (Maize)" EXACT [] xref: Moby_namespace:MIPS_GE_Maize created_in: "beta12orEarlier" def: "Identifier for genetic elements in MIPS Maize database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2285 ! Gene ID (MIPS) [Term] id: EDAM_data:1888 name: Gene ID (MIPS Medicago) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "MIPS genetic element identifier (Medicago)" EXACT [] xref: Moby_namespace:MIPS_GE_Medicago created_in: "beta12orEarlier" def: "Identifier for genetic elements in MIPS Medicago database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2285 ! Gene ID (MIPS) [Term] id: EDAM_data:1889 name: Gene name (DragonDB) subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:DragonDB_Gene created_in: "beta12orEarlier" def: "The name of an Antirrhinum Gene from the DragonDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1890 name: Gene name (Arabidopsis) subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:ArabidopsisGeneSymbol created_in: "beta12orEarlier" def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1891 name: iHOP symbol subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:iHOPsymbol created_in: "beta12orEarlier" def: "A unique identifier of a protein or gene used in the iHOP database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2295 ! Gene ID is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:1892 name: Gene name (GeneFarm) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "GeneFarm gene ID" EXACT [] xref: Moby_namespace:GENEFARM_GeneName created_in: "beta12orEarlier" def: "Name of a gene from the GeneFarm database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:1893 name: Locus ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Locus identifier" EXACT [] synonym: "Locus name" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:2012 ! Map position [Term] id: EDAM_data:1895 name: Locus ID (AGI) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "AGI ID" EXACT [] synonym: "AGI identifier" EXACT [] synonym: "AGI locus code" EXACT [] synonym: "Arabidopsis gene loci number" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode created_in: "beta12orEarlier" def: "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" [http://edamontology.org] regex: "AT[1-5]G[0-9]{5}" namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1896 name: Locus ID (ASPGD) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID created_in: "beta12orEarlier" def: "Identifier for loci from ASPGD (Aspergillus Genome Database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1897 name: Locus ID (MGG) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG created_in: "beta12orEarlier" def: "Identifier for loci from Magnaporthe grisea Database at the Broad Institute." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1898 name: Locus ID (CGD) subset: bioinformatics subset: data subset: edam subset: identifiers 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 created_in: "beta12orEarlier" def: "Identifier for loci from CGD (Candida Genome Database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1899 name: Locus ID (CMR) subset: bioinformatics subset: data subset: edam subset: identifiers xref: http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR xref: http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR created_in: "beta12orEarlier" def: "Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1900 name: NCBI locus tag subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Locus ID (NCBI)" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag xref: Moby_namespace:LocusID created_in: "beta12orEarlier" def: "Identifier for loci from NCBI database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1901 name: Locus ID (SGD) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "SGDID" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGD xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGDID created_in: "beta12orEarlier" def: "Identifier for loci from SGD (Saccharomyces Genome Database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID is_a: EDAM_data:2632 ! SGD ID [Term] id: EDAM_data:1902 name: Locus ID (MMP) subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:MMP_Locus created_in: "beta12orEarlier" def: "Identifier of loci from Maize Mapping Project." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1903 name: Locus ID (DictyBase) subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:DDB_gene created_in: "beta12orEarlier" def: "Identifier of locus from DictyBase (Dictyostelium discoideum)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1904 name: Locus ID (EntrezGene) subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:EntrezGene_EntrezGeneID xref: Moby_namespace:EntrezGene_ID created_in: "beta12orEarlier" def: "Identifier of a locus from EntrezGene database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1905 name: Locus ID (MaizeGDB) subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:MaizeGDB_Locus created_in: "beta12orEarlier" def: "Identifier of locus from MaizeGDB (Maize genome database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1906 name: Quantitative trait locus comment: A QTL sometimes but does not necessarily correspond to a gene. subset: bioinformatics subset: data subset: edam synonym: "QTL" EXACT [] xref: Moby:SO_QTL created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2012 ! Map position [Term] id: EDAM_data:1907 name: Gene ID (KOME) subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby_namespace:GeneId created_in: "beta12orEarlier" def: "Identifier of a gene from the KOME database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:1908 name: Locus ID (Tropgene) subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby:Tropgene_locus created_in: "beta12orEarlier" def: "Identifier of a locus from the Tropgene database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:1916 name: Alignment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An alignment of molecular sequences, structures or profiles derived from them." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:1917 name: Atomic property subset: bioinformatics subset: data subset: edam synonym: "General atomic property" EXACT [] created_in: "beta12orEarlier" def: "Data for an atom (in a molecular structure)." [http://edamontology.org] namespace: data is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:2007 name: UniProt keyword subset: bioinformatics subset: data subset: edam xref: http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW xref: Moby_namespace:SP_KW created_in: "beta12orEarlier" def: "A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org] namespace: data is_a: EDAM_data:0968 ! Keyword [Term] id: EDAM_data:2009 name: Ordered locus name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:2012 name: Map position 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: bioinformatics subset: data subset: edam synonym: "Locus" EXACT [] xref: Moby:GCP_MapInterval xref: Moby:GCP_MapPoint xref: Moby:GCP_MapPosition xref: Moby:GenePosition xref: Moby:HitPosition xref: Moby:Locus xref: Moby:MapPosition xref: Moby:Position xref: PDBML:_atom_site.id created_in: "beta12orEarlier" def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval." [http://edamontology.org] namespace: data is_a: EDAM_data:1016 ! Sequence position is_a: EDAM_data:1017 ! Sequence range is_a: EDAM_data:2019 ! Map attribute [Term] id: EDAM_data:2016 name: Amino acid property subset: bioinformatics subset: data subset: edam synonym: "Amino acid data" EXACT [] created_in: "beta12orEarlier" def: "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." [http://edamontology.org] namespace: data is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:2018 name: Annotation comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2048 ! Report [Term] id: EDAM_data:2019 name: Map attribute subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An attribute of a molecular map (genetic or physical)." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0102 ! Mapping [Term] id: EDAM_data:2022 name: Vienna RNA structural data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data used by the Vienna RNA analysis package." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2023 name: Sequence mask parameter subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data used to replace (mask) characters in a molecular sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:2024 name: Enzyme kinetics data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning chemical reaction(s) catalysed by enzyme(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:2978 ! Reaction data [Term] id: EDAM_data:2025 name: Michaelis Menten plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_data:2026 name: Hanes Woolf plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: data is_a: EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_data:2028 name: Experimental data 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: bioinformatics subset: data subset: edam synonym: "Experimental measurement data" EXACT [] created_in: "beta12orEarlier" def: "Raw data from or annotation on laboratory experiments." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2531 ! Experiment annotation consider: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:2041 name: Genome version information subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Information on a genome version." [http://edamontology.org] namespace: data is_a: EDAM_data:0953 ! Version information is_a: EDAM_data:2711 ! Genome metadata [Term] id: EDAM_data:2042 name: Evidence subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2043 name: Sequence record lite subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] namespace: data is_a: EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2044 name: Sequence comment: This concept is a placeholder of concepts 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: bioinformatics subset: data subset: edam synonym: "BioMolecularSequenceInformation" RELATED [] synonym: "http://purl.bioontology.org/ontology/MSH/D008969" NARROW [] created_in: "beta12orEarlier" def: "One or more molecular sequences, possibly with associated annotation." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_data:2046 name: Sequence record lite (nucleic acid) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] namespace: data is_a: EDAM_data:2043 ! Sequence record lite is_a: EDAM_data:2887 ! Sequence record (nucleic acid) [Term] id: EDAM_data:2047 name: Sequence record lite (protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org] namespace: data is_a: EDAM_data:2043 ! Sequence record lite is_a: EDAM_data:2886 ! Sequence record (protein) [Term] id: EDAM_data:2048 name: Report 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: bioinformatics subset: data subset: edam synonym: "Document" EXACT [] synonym: "document" EXACT [] synonym: "SIO:000148" RELATED [] synonym: "Text" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0006 ! Data [Term] id: EDAM_data:2050 name: Molecular property (general) subset: bioinformatics subset: data subset: edam synonym: "General molecular property" EXACT [] created_in: "beta12orEarlier" def: "General data for a molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:2053 name: Structural data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning molecular structural data." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0883 ! Structure consider: EDAM_data:2085 ! Structure report [Term] id: EDAM_data:2070 name: Sequence motif (nucleic acid) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A nucleotide sequence motif." [http://edamontology.org] namespace: data is_a: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:2071 name: Sequence motif (protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An amino acid sequence motif." [http://edamontology.org] namespace: data is_a: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:2079 name: Search parameter subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Some simple value controlling a search operation, typically a search of a database." [http://edamontology.org] namespace: data is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2080 name: Database hits subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report of hits from searching a database of some type." [http://edamontology.org] namespace: data is_a: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:2081 name: Secondary structure subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The secondary structure assignment (predicted or real) of a nucleic acid or protein." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2082 name: Matrix comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2083 name: Alignment report comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report about a molecular alignment of some type, including alignment-derived data or metadata." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2084 name: Nucleic acid report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data." [http://edamontology.org] namespace: data is_a: EDAM_data:2529 ! Molecule report [Term] id: EDAM_data:2085 name: Structure report subset: bioinformatics subset: data subset: edam synonym: "Structure-derived report" EXACT [] created_in: "beta12orEarlier" def: "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2086 name: Nucleic acid structure report comment: This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. subset: bioinformatics subset: data subset: edam synonym: "Nucleic acid property (structural)" EXACT [] synonym: "Nucleic acid structural property" EXACT [] created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: data is_a: EDAM_data:0912 ! Nucleic acid property is_a: EDAM_data:2085 ! Structure report [Term] id: EDAM_data:2087 name: Molecular property subset: bioinformatics subset: data subset: edam synonym: "Physicochemical property" EXACT [] synonym: "SO:0000400" RELATED [] created_in: "beta12orEarlier" def: "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2088 name: DNA base structural data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Structural data for DNA base pairs or runs of bases, such as energy or angle data." [http://edamontology.org] namespace: data is_a: EDAM_data:0912 ! Nucleic acid property is_a: EDAM_data:2086 ! Nucleic acid structure report [Term] id: EDAM_data:2090 name: Database entry version information subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0953 ! Version information is_a: EDAM_data:2193 ! Database entry metadata [Term] id: EDAM_data:2091 name: Accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "SIO:000675" BROAD [] synonym: "SIO:000731" BROAD [] created_in: "beta12orEarlier" def: "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:2092 name: Nucleic acid features (SNP) comment: An SNP is an individual point mutation or substitution of a single nucleotide. subset: bioinformatics subset: data subset: edam synonym: "Single nucleotide polymorphism" EXACT [] synonym: "SNP annotation" EXACT [] created_in: "beta12orEarlier" def: "Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_data:2093 name: Data reference comment: A list of database accessions or identifiers are usually included. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2098 name: Job identifier subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "WSIO_data:009" EXACT [] created_in: "beta12orEarlier" def: "An identifier of a submitted job." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2099 name: Name subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "label" BROAD [] synonym: "name" EXACT [] synonym: "SIO:000116" EXACT [] synonym: "Symbolic name" EXACT [] created_in: "beta12orEarlier" def: "A name of a thing, which need not necessarily uniquely identify it." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:2100 name: Type subset: bioinformatics subset: data subset: edam synonym: "http://purl.org/dc/elements/1.1/type" EXACT [] created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: data is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2101 name: User ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2118 ! Person identifier [Term] id: EDAM_data:2102 name: KEGG organism code subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A three-letter code used in the KEGG databases to uniquely identify organisms." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1154 ! KEGG object identifier is_a: EDAM_data:2909 ! Organism name [Term] id: EDAM_data:2103 name: Gene name (KEGG GENES) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "KEGG GENES entry name" EXACT [] xref: Moby_namespace:GeneId created_in: "beta12orEarlier" def: "Name of an entry (gene) from the KEGG GENES database." [http://edamontology.org] regex: "[a-zA-Z_0-9]+:[a-zA-Z_0-9\\.-]*" namespace: identifier is_a: EDAM_data:1026 ! Gene symbol is_a: EDAM_data:1154 ! KEGG object identifier [Term] id: EDAM_data:2104 name: BioCyc ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an object from one of the BioCyc databases." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2105 name: Compound ID (BioCyc) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "BioCyc compound ID" EXACT [] synonym: "BioCyc compound identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a compound from the BioCyc chemical compounds database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2104 ! BioCyc ID is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2106 name: Reaction ID (BioCyc) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a biological reaction from the BioCyc reactions database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2104 ! BioCyc ID is_a: EDAM_data:2108 ! Reaction ID relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids [Term] id: EDAM_data:2107 name: Enzyme ID (BioCyc) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "BioCyc enzyme ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an enzyme from the BioCyc enzymes database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2104 ! BioCyc ID is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:2108 name: Reaction ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a biological reaction from a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:2978 ! Reaction data [Term] id: EDAM_data:2109 name: Identifier (hybrid) comment: This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier that is re-used for data objects of fundamentally different types (typically served from a single database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:2110 name: Molecular property identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a molecular property." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:2111 name: Codon usage table identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a codon usage table, for example a genetic code." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:1597 ! Codon usage table relationship: is_identifier_of EDAM_data:1598 ! Genetic code [Term] id: EDAM_data:2112 name: FlyBase primary identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Primary identifier of an object from the FlyBase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1089 ! FlyBase ID [Term] id: EDAM_data:2113 name: WormBase identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an object from the WormBase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2114 name: WormBase wormpep ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Protein identifier used by WormBase database." [http://edamontology.org] regex: "CE[0-9]{5}" namespace: identifier is_a: EDAM_data:2113 ! WormBase identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2116 name: Nucleic acid features (codon) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:2117 name: Map identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a map of a molecular sequence." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:1274 ! Map [Term] id: EDAM_data:2118 name: Person identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a software end-user (typically a person)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2119 name: Nucleic acid identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name or other identifier of a nucleic acid molecule." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0982 ! Molecule identifier relationship: is_identifier_of EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:2126 name: Translation frame specification subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome)." [http://edamontology.org] namespace: data is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:2127 name: Genetic code identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a genetic code." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:1598 ! Genetic code [Term] id: EDAM_data:2128 name: Genetic code name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Informal name for a genetic code, typically an organism name." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2127 ! Genetic code identifier [Term] id: EDAM_data:2129 name: File format name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2130 name: Sequence profile type subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc." [http://edamontology.org] namespace: data is_a: EDAM_data:2100 ! Type is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:2131 name: Operating system name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a computer operating system such as Linux, PC or Mac." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2132 name: Mutation type subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A type of point or block mutation, including insertion, deletion, change, duplication and moves." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2100 ! Type [Term] id: EDAM_data:2133 name: Logical operator subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A logical operator such as OR, AND, XOR, and NOT." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2134 name: Results sort order comment: Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A control of the order of data that is output, for example the order of sequences in an alignment." [http://edamontology.org] namespace: data is_a: EDAM_data:2079 ! Search parameter [Term] id: EDAM_data:2135 name: Toggle subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2136 name: Sequence width subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The width of an output sequence or alignment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1249 ! Sequence length [Term] id: EDAM_data:2137 name: Gap penalty subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A penalty for introducing or extending a gap in an alignment." [http://edamontology.org] namespace: data is_a: EDAM_data:1394 ! Alignment score or penalty [Term] id: EDAM_data:2139 name: Nucleic acid melting temperature subset: bioinformatics subset: data subset: edam synonym: "Melting temperature" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] id: EDAM_data:2140 name: Concentration subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The concentration of a chemical compound." [http://edamontology.org] namespace: data is_a: EDAM_data:2050 ! Molecular property (general) [Term] id: EDAM_data:2141 name: Window step size subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Size of the incremental 'step' a sequence window is moved over a sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:1249 ! Sequence length [Term] id: EDAM_data:2142 name: EMBOSS graph subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An image of a graph generated by the EMBOSS suite." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2968 ! Image [Term] id: EDAM_data:2143 name: EMBOSS report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An application report generated by the EMBOSS suite." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2048 ! Report [Term] id: EDAM_data:2145 name: Sequence offset subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An offset for a single-point sequence position." [http://edamontology.org] namespace: data is_a: EDAM_data:1016 ! Sequence position is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:2146 name: Threshold subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A value that serves as a threshold for a tool (usually to control scoring or output)." [http://edamontology.org] namespace: data is_a: EDAM_data:1772 ! Score or penalty [Term] id: EDAM_data:2147 name: Protein report (transcription factor) comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. subset: bioinformatics subset: data subset: edam synonym: "Transcription factor binding site data" EXACT [] created_in: "beta12orEarlier" def: "An informative report on a transcription factor protein." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:2149 name: Database category name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a category of biological or bioinformatics database." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:2150 name: Sequence profile name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a sequence profile." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1115 ! Sequence profile ID [Term] id: EDAM_data:2151 name: Color subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Specification of one or more colors." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2152 ! Rendering parameter [Term] id: EDAM_data:2152 name: Rendering parameter subset: bioinformatics subset: data subset: edam synonym: "Graphical parameter" EXACT [] synonym: "Graphics parameter" EXACT [] created_in: "beta12orEarlier" def: "A parameter that is used to control rendering (drawing) to a device or image." [http://edamontology.org] namespace: data is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2154 name: Sequence name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Any arbitrary name of a molecular sequence." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1063 ! Sequence identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2156 name: Date subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A temporal date." [http://edamontology.org] namespace: data is_a: EDAM_data:3105 ! Geotemporal metadata [Term] id: EDAM_data:2157 name: Word composition subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Word composition data for a molecular sequence." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1266 ! Sequence composition (base words) consider: EDAM_data:1268 ! Amino acid word frequencies [Term] id: EDAM_data:2160 name: Fickett testcode plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] id: EDAM_data:2161 name: Sequence similarity plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A plot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] namespace: data is_a: EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_data:2162 name: Helical wheel subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties." [http://edamontology.org] namespace: data is_a: EDAM_data:1709 ! Protein secondary structure image [Term] id: EDAM_data:2163 name: Helical net comment: Useful for highlighting amphipathicity and other properties. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1709 ! Protein secondary structure image [Term] id: EDAM_data:2164 name: Protein sequence properties plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A plot of general physicochemical properties of a protein sequence." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:2165 name: Protein ionization curve subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A plot of pK versus pH for a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:2166 name: Sequence composition plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A plot of character or word composition / frequency of a molecular sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:1261 ! Sequence composition [Term] id: EDAM_data:2167 name: Nucleic acid density plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Density plot (of base composition) for a nucleotide sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:2168 name: Sequence trace image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases)." [http://edamontology.org] namespace: data is_a: EDAM_data:2969 ! Sequence image [Term] id: EDAM_data:2169 name: Nucleic acid features (siRNA) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on siRNA duplexes in mRNA." [http://edamontology.org] namespace: data is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA) relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_data:2173 name: Sequence set (stream) comment: This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:2174 name: FlyBase secondary identifier comment: Secondary identifier are used to handle entries that were merged with or split from other entries in the database. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Secondary identifier of an object from the FlyBase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1089 ! FlyBase ID [Term] id: EDAM_data:2176 name: Cardinality subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The number of a certain thing." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:2177 name: Exactly 1 subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A single thing." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:2178 name: 1 or more subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "One or more things." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:2179 name: Exactly 2 subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Exactly two things." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:2180 name: 2 or more subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Two or more things." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:2190 name: Sequence checksum subset: bioinformatics subset: data subset: edam synonym: "Hash" EXACT [] synonym: "Hash code" EXACT [] synonym: "Hash sum" EXACT [] synonym: "Hash value" EXACT [] created_in: "beta12orEarlier" def: "A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing." [http://edamontology.org] namespace: data is_a: EDAM_data:0855 ! Sequence metadata is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:2191 name: Protein features (chemical modification) subset: bioinformatics subset: data subset: edam synonym: "GO:0006464" RELATED [] synonym: "MOD:00000" RELATED [] synonym: "Protein modification annotation" EXACT [] created_in: "beta12orEarlier" def: "Data on a chemical modification of a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:2192 name: Error subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on an error generated by computer system or tool." [http://edamontology.org] namespace: data is_a: EDAM_data:0959 ! Job metadata [Term] id: EDAM_data:2193 name: Database entry metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Basic information on any arbitrary database entry." [http://edamontology.org] namespace: data is_a: EDAM_data:0957 ! Database metadata [Term] id: EDAM_data:2198 name: Gene cluster subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A cluster of similar genes." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1246 ! Sequence cluster (nucleic acid) [Term] id: EDAM_data:2201 name: Sequence record full subset: bioinformatics subset: data subset: edam synonym: "http://purl.bioontology.org/ontology/MSH/D058977" RELATED [] xref: SO:2000061 created_in: "beta12orEarlier" def: "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] namespace: data is_a: EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2208 name: Plasmid identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a plasmid in a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2119 ! Nucleic acid identifier [Term] id: EDAM_data:2209 name: Mutation ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of a specific mutation catalogued in a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2538 ! Mutation identifier [Term] id: EDAM_data:2212 name: Mutation annotation (basic) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] id: EDAM_data:2213 name: Mutation annotation (prevalence) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] id: EDAM_data:2214 name: Mutation annotation (prognostic) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] id: EDAM_data:2215 name: Mutation annotation (functional) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2533 ! Nucleic acid features (mutation) [Term] id: EDAM_data:2216 name: Codon number subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "The number of a codon, for instance, at which a mutation is located." [http://edamontology.org] namespace: data is_a: EDAM_data:1016 ! Sequence position [Term] id: EDAM_data:2217 name: Tumor annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1622 ! Disease annotation [Term] id: EDAM_data:2218 name: Server metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Basic information about a server on the web, such as an SRS server." [http://edamontology.org] namespace: data is_a: EDAM_data:3106 ! System metadata [Term] id: EDAM_data:2219 name: Database field name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a field in a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2220 name: Sequence cluster ID (SYSTERS) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "SYSTERS cluster ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier of a sequence cluster from the SYSTERS database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:2223 name: Ontology metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning a biological ontology." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_data:2235 name: Raw SCOP domain classification comment: These are the parsable data files provided by SCOP. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Raw SCOP domain classification data files." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:2236 name: Raw CATH domain classification comment: These are the parsable data files provided by CATH. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Raw CATH domain classification data files." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:2240 name: Heterogen annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files." [http://edamontology.org] namespace: data is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2242 name: Phylogenetic property values subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Phylogenetic property values data." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0871 ! Phylogenetic character data [Term] id: EDAM_data:2245 name: Sequence set (bootstrapped) comment: Bootstrapping is often performed in phylogenetic analysis. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A collection of sequences output from a bootstrapping (resampling) procedure." [http://edamontology.org] namespace: data is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:2247 name: Phylogenetic consensus tree subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A consensus phylogenetic tree derived from comparison of multiple trees." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0872 ! Phylogenetic tree [Term] id: EDAM_data:2248 name: Schema subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A data schema for organising or transforming data of some type." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2249 name: DTD subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A DTD (document type definition)." [http://edamontology.org] namespace: data is_a: EDAM_data:2248 ! Schema [Term] id: EDAM_data:2250 name: XML Schema subset: bioinformatics subset: data subset: edam synonym: "XSD" EXACT [] created_in: "beta12orEarlier" def: "An XML Schema." [http://edamontology.org] namespace: data is_a: EDAM_data:2248 ! Schema [Term] id: EDAM_data:2251 name: Relax-NG schema subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A relax-NG schema." [http://edamontology.org] namespace: data is_a: EDAM_data:2248 ! Schema [Term] id: EDAM_data:2252 name: XSLT stylesheet subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An XSLT stylesheet." [http://edamontology.org] namespace: data is_a: EDAM_data:2248 ! Schema [Term] id: EDAM_data:2253 name: Data resource definition name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a data type." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1084 ! Data resource definition identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2254 name: OBO file format name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of an OBO file format such as OBO-XML, plain and so on." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2129 ! File format name [Term] id: EDAM_data:2285 name: Gene ID (MIPS) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "MIPS genetic element identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier for genetic elements in MIPS database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2288 name: Sequence identifier (protein) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of protein sequence(s) or protein sequence database entries." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1096 ! Sequence accession (protein) [Term] id: EDAM_data:2289 name: Sequence identifier (nucleic acid) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of nucleotide sequence(s) or nucleotide sequence database entries." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2290 name: EMBL accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "EMBL accession number" EXACT [] synonym: "EMBL ID" EXACT [] synonym: "EMBL identifier" EXACT [] created_in: "beta12orEarlier" def: "An accession number of an entry from the EMBL sequence database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID [Term] id: EDAM_data:2291 name: UniProt ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "UniProt entry name" EXACT [] synonym: "UniProt identifier" EXACT [] synonym: "UniProtKB entry name" EXACT [] synonym: "UniProtKB identifier" EXACT [] created_in: "beta12orEarlier" def: "An identifier of a polypeptide in the UniProt database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2154 ! Sequence name relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2292 name: GenBank accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "GenBank accession number" EXACT [] synonym: "GenBank ID" EXACT [] synonym: "GenBank identifier" EXACT [] created_in: "beta12orEarlier" def: "Accession number of an entry from the GenBank sequence database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID [Term] id: EDAM_data:2293 name: Gramene secondary identifier subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Gramene internal ID" EXACT [] synonym: "Gramene internal identifier" EXACT [] synonym: "Gramene secondary ID" EXACT [] created_in: "beta12orEarlier" def: "Secondary (internal) identifier of a Gramene database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2915 ! Gramene identifier [Term] id: EDAM_data:2294 name: Sequence variation ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of an entry from a database of molecular sequence variation." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2295 name: Gene ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Gene accession" EXACT [] synonym: "Gene code" EXACT [] created_in: "beta12orEarlier" def: "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1025 ! Gene identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:2296 name: Gene name (AceView) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "AceView gene name" EXACT [] created_in: "beta12orEarlier" def: "Name of an entry (gene) from the AceView genes database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:2297 name: Gene ID (ECK) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "E. coli K-12 gene identifier" EXACT [] synonym: "ECK accession" EXACT [] xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK created_in: "beta12orEarlier" def: "Identifier of an E. coli K-12 gene from EcoGene Database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1795 ! Gene ID (EcoGene) [Term] id: EDAM_data:2298 name: Gene ID (HGNC) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "HGNC ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier for a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2299 name: Gene name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1025 ! Gene identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2300 name: Gene name (NCBI) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "NCBI gene name" EXACT [] created_in: "beta12orEarlier" def: "Name of an entry (gene) from the NCBI genes database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:2301 name: SMILES string subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A specification of a chemical structure in SMILES format." [http://edamontology.org] namespace: data is_a: EDAM_data:0846 ! Chemical formula [Term] id: EDAM_data:2302 name: STRING ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an entry from the STRING database of protein-protein interactions." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:2307 name: Virus annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a specific virus." [http://edamontology.org] namespace: data is_a: EDAM_data:2530 ! Organism annotation [Term] id: EDAM_data:2308 name: Virus annotation (taxonomy) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on the taxonomy of a specific virus." [http://edamontology.org] namespace: data is_a: EDAM_data:2307 ! Virus annotation [Term] id: EDAM_data:2309 name: Reaction ID (SABIO-RK) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a biological reaction from the SABIO-RK reactions database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2108 ! Reaction ID [Term] id: EDAM_data:2313 name: Carbohydrate structure report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Annotation on or information derived from one or more specific carbohydrate 3D structure(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:2085 ! Structure report [Term] id: EDAM_data:2314 name: GI number 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: bioinformatics subset: data subset: edam subset: identifiers synonym: "gi number" EXACT [] synonym: "NCBI GI number" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] id: EDAM_data:2315 name: NCBI version 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: bioinformatics subset: data subset: edam subset: identifiers synonym: "accession.version" EXACT [] synonym: "NCBI accession.version" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2362 ! Sequence accession (hybrid) [Term] id: EDAM_data:2316 name: Cell line name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a cell line." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1046 ! Strain name [Term] id: EDAM_data:2317 name: Cell line name (exact) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a cell line." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2316 ! Cell line name [Term] id: EDAM_data:2318 name: Cell line name (truncated) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a cell line." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2316 ! Cell line name [Term] id: EDAM_data:2319 name: Cell line name (no punctuation) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a cell line." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2316 ! Cell line name [Term] id: EDAM_data:2320 name: Cell line name (assonant) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a cell line." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2316 ! Cell line name [Term] id: EDAM_data:2321 name: Enzyme ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Enzyme accession" EXACT [] created_in: "beta12orEarlier" def: "A unique, persistent identifier of an enzyme." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1010 ! Enzyme identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2325 name: REBASE enzyme number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an enzyme from the REBASE enzymes database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:2326 name: DrugBank ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a drug from the DrugBank database." [http://edamontology.org] regex: "DB[0-9]{5}" namespace: identifier is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:2327 name: GI number (protein) 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: bioinformatics subset: data subset: edam subset: identifiers synonym: "protein gi" EXACT [] synonym: "protein gi number" EXACT [] created_in: "beta12orEarlier" def: "A unique identifier assigned to NCBI protein sequence records." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2314 ! GI number [Term] id: EDAM_data:2335 name: Bit score comment: Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system." [http://edamontology.org] namespace: data is_a: EDAM_data:1413 ! Sequence similarity [Term] id: EDAM_data:2336 name: Translation phase specification subset: bioinformatics subset: data subset: edam synonym: "Phase" EXACT [] created_in: "beta12orEarlier" def: "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2534 ! Sequence parameter is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:2337 name: Metadata comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam synonym: "Provenance metadata" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2338 name: Ontology identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Any arbitrary identifier of an ontology." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0582 ! Ontology [Term] id: EDAM_data:2339 name: Ontology concept name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a concept in an ontology." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:3025 ! Ontology concept identifier [Term] id: EDAM_data:2340 name: Genome build identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a build of a particular genome." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2749 ! Genome identifier [Term] id: EDAM_data:2342 name: Pathway or network name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a biological pathway or network." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1082 ! Pathway or network identifier [Term] id: EDAM_data:2343 name: Pathway ID (KEGG) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "KEGG pathway ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a pathway from the KEGG pathway database." [http://edamontology.org] regex: "[a-zA-Z_0-9]{2,3}[0-9]{5}" namespace: identifier is_a: EDAM_data:1154 ! KEGG object identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2344 name: Pathway ID (NCI-Nature) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a pathway from the NCI-Nature pathway database." [http://edamontology.org] regex: "[a-zA-Z_0-9]+" namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2345 name: Pathway ID (ConsensusPathDB) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a pathway from the ConsensusPathDB pathway database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession is_a: EDAM_data:2917 ! ConsensusPathDB identifier [Term] id: EDAM_data:2346 name: Sequence cluster ID (UniRef) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "UniRef cluster id" EXACT [] synonym: "UniRef entry accession" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier of an entry from the UniRef database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:2347 name: Sequence cluster ID (UniRef100) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "UniRef100 cluster id" EXACT [] synonym: "UniRef100 entry accession" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier of an entry from the UniRef100 database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) [Term] id: EDAM_data:2348 name: Sequence cluster ID (UniRef90) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "UniRef90 cluster id" EXACT [] synonym: "UniRef90 entry accession" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier of an entry from the UniRef90 database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) [Term] id: EDAM_data:2349 name: Sequence cluster ID (UniRef50) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "UniRef50 cluster id" EXACT [] synonym: "UniRef50 entry accession" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier of an entry from the UniRef50 database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef) [Term] id: EDAM_data:2353 name: Ontological data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning an ontology." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0582 ! Ontology consider: EDAM_data:2223 ! Ontology metadata [Term] id: EDAM_data:2354 name: RNA family annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a specific RNA family or other group of classified RNA sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:2986 ! Nucleic acid classification [Term] id: EDAM_data:2355 name: RNA family identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an RNA family, typically an entry from a RNA sequence classification database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2354 ! RNA family annotation [Term] id: EDAM_data:2356 name: RFAM accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Stable accession number of an entry (RNA family) from the RFAM database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2355 ! RNA family identifier [Term] id: EDAM_data:2357 name: Protein signature type subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org] namespace: data is_a: EDAM_data:2100 ! Type is_a: EDAM_data:2534 ! Sequence parameter [Term] id: EDAM_data:2358 name: Domain-nucleic acid interaction subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on protein domain-DNA/RNA interaction(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:1567 ! Protein-nucleic acid interaction [Term] id: EDAM_data:2359 name: Domain-domain interaction subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on protein domain-protein domain interaction(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:1565 ! Protein-protein interaction [Term] id: EDAM_data:2360 name: Domain-domain interaction (indirect) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on indirect protein domain-protein domain interaction(s)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2359 ! Domain-domain interaction [Term] id: EDAM_data:2362 name: Sequence accession (hybrid) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of a nucleotide or protein sequence database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1093 ! Sequence accession relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2363 name: 2D PAGE data 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning two-dimensional polygel electrophoresis." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0942 ! 2D PAGE image consider: EDAM_data:2364 ! Experiment annotation (2D PAGE) [Term] id: EDAM_data:2364 name: Experiment annotation (2D PAGE) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel." [http://edamontology.org] namespace: data is_a: EDAM_data:2531 ! Experiment annotation relationship: has_topic EDAM_topic:0121 ! Proteomics [Term] id: EDAM_data:2365 name: Pathway or network accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A persistent, unique identifier of a biological pathway or network (typically a database entry)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1082 ! Pathway or network identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2366 name: Secondary structure alignment subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Alignment of the (1D representations of) secondary structure of two or more molecules." [http://edamontology.org] namespace: data is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:2367 name: ASTD ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an object from the ASTD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2368 name: ASTD ID (exon) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an exon from the ASTD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2367 ! ASTD ID [Term] id: EDAM_data:2369 name: ASTD ID (intron) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an intron from the ASTD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2367 ! ASTD ID [Term] id: EDAM_data:2370 name: ASTD ID (polya) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a polyA signal from the ASTD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2367 ! ASTD ID [Term] id: EDAM_data:2371 name: ASTD ID (tss) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a transcription start site from the ASTD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2367 ! ASTD ID [Term] id: EDAM_data:2372 name: 2D PAGE spot (annotated) subset: bioinformatics subset: data subset: edam synonym: "2D PAGE spot annotation" EXACT [] created_in: "beta12orEarlier" def: "An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel." [http://edamontology.org] namespace: data is_a: EDAM_data:2965 ! 2D PAGE image (annotated) [Term] id: EDAM_data:2373 name: Spot ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a spot from a two-dimensional (protein) gel." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2374 name: Spot serial number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2373 ! Spot ID [Term] id: EDAM_data:2375 name: Spot ID (HSC-2DPAGE) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2373 ! Spot ID [Term] id: EDAM_data:2378 name: Protein-motif interaction subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1565 ! Protein-protein interaction [Term] id: EDAM_data:2379 name: Strain identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1869 ! Organism identifier [Term] id: EDAM_data:2380 name: CABRI accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of an item from the CABRI database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2381 name: Experiment annotation (genotype) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." [http://edamontology.org] namespace: data is_a: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:2382 name: Genotype experiment ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from a database of genotype experiment metadata." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:2381 ! Experiment annotation (genotype) [Term] id: EDAM_data:2383 name: EGA accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the EGA database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2382 ! Genotype experiment ID [Term] id: EDAM_data:2384 name: IPI protein ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a protein entry catalogued in the International Protein Index (IPI) database." [http://edamontology.org] regex: "IPI[0-9]{8}" namespace: identifier is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] id: EDAM_data:2385 name: RefSeq accession (protein) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "RefSeq protein ID" EXACT [] created_in: "beta12orEarlier" def: "Accession number of a protein from the RefSeq database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1098 ! RefSeq accession [Term] id: EDAM_data:2386 name: EPD ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "EPD identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry (promoter) from the EPD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2727 ! Promoter ID [Term] id: EDAM_data:2387 name: TAIR accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the TAIR database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2388 name: TAIR accession (At gene) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an Arabidopsis thaliana gene from the TAIR database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1037 ! TAIR accession (gene) [Term] id: EDAM_data:2389 name: UniSTS accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the UniSTS database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2390 name: UNITE accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the UNITE database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2391 name: UTR accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the UTR database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2392 name: UniParc accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "UniParc ID" EXACT [] synonym: "UPI" EXACT [] created_in: "beta12orEarlier" def: "Accession number of a UniParc (protein sequence) database entry." [http://edamontology.org] regex: "UPI[A-F0-9]{10}" namespace: identifier is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] id: EDAM_data:2393 name: mFLJ/mKIAA number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the Rouge or HUGE databases." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2395 name: Fungi annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a specific fungus." [http://edamontology.org] namespace: data is_a: EDAM_data:2530 ! Organism annotation [Term] id: EDAM_data:2396 name: Fungi annotation (anamorph) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a specific fungus anamorph." [http://edamontology.org] namespace: data is_a: EDAM_data:2395 ! Fungi annotation [Term] id: EDAM_data:2397 name: Nucleic acid features (exon) subset: bioinformatics subset: data subset: edam synonym: "Gene features (exon)" EXACT [] created_in: "beta12orEarlier" def: "An informative report on an exon in a nucleotide sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] id: EDAM_data:2398 name: Protein ID (Ensembl) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Ensembl protein ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier for a protein from the Ensembl database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2610 ! Ensembl ID is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2399 name: Gene annotation (transcript) subset: bioinformatics subset: data subset: edam synonym: "Gene annotation (clone or EST)" EXACT [] synonym: "Gene transcript annotation" EXACT [] created_in: "beta12orEarlier" def: "An informative report on a specific gene transcript, clone or EST." [http://edamontology.org] namespace: data is_a: EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:2400 name: Toxin annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a specific toxin." [http://edamontology.org] namespace: data is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2401 name: Protein report (membrane protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a membrane protein." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1456 ! Protein features (membrane regions) [Term] id: EDAM_data:2402 name: Protein-drug interaction subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Informative report on protein-drug interaction(s) including binding affinity data." [http://edamontology.org] namespace: data is_a: EDAM_data:1566 ! Protein-ligand interaction [Term] id: EDAM_data:2522 name: Map data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning a map of molecular sequence(s)." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1274 ! Map consider: EDAM_data:2019 ! Map attribute [Term] id: EDAM_data:2523 name: Phylogenetic raw data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam synonym: "Phylogenetic data" EXACT [] created_in: "beta12orEarlier" def: "Data concerning phylogeny, typically of molecular sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2524 name: Protein data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning one or more protein molecules." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:2525 name: Nucleic acid data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning one or more nucleic acid molecules." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:2526 name: Article data 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning the scientific literature." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0971 ! Article [Term] id: EDAM_data:2527 name: Parameter subset: bioinformatics subset: data subset: edam synonym: "Parameter" EXACT [] synonym: "Parameter or primitive" EXACT [] synonym: "SIO:000144" EXACT [] synonym: "Tool parameter" EXACT [] synonym: "Tool-specific parameter" EXACT [] created_in: "beta12orEarlier" def: "Typically a simple numerical or string value that controls the operation of a tool." [http://edamontology.org] namespace: data is_a: EDAM_data:0006 ! Data disjoint_from: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2528 name: Molecular data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam synonym: "Molecule-specific data" EXACT [] created_in: "beta12orEarlier" def: "Data concerning a specific type of molecule." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2529 ! Molecule report [Term] id: EDAM_data:2529 name: Molecule report subset: bioinformatics subset: data subset: edam synonym: "Molecular report" EXACT [] created_in: "beta12orEarlier" def: "An informative report on a specific molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2530 name: Organism annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on a specific organism." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2531 name: Experiment annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Annotation on a wet lab experiment, such as experimental conditions." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2533 name: Nucleic acid features (mutation) subset: bioinformatics subset: data subset: edam synonym: "Mutation annotation" EXACT [] created_in: "beta12orEarlier" def: "Annotation on a mutation." [http://edamontology.org] namespace: data is_a: EDAM_data:0918 ! Nucleic acid features (variation) [Term] id: EDAM_data:2534 name: Sequence parameter subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A parameter concerning calculations on molecular sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:2527 ! Parameter [Term] id: EDAM_data:2535 name: Sequence tag profile 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: bioinformatics subset: data subset: edam synonym: "Sequencing-based expression profile" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0928 ! Gene expression profile [Term] id: EDAM_data:2536 name: Mass spectrometry data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning a mass spectrometry measurement." [http://edamontology.org] namespace: data is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:2537 name: Protein structure raw data 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Raw data from experimental methods for determining protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:2538 name: Mutation identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a mutation." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2539 name: Alignment data 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1916 ! Alignment consider: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:2540 name: Data index data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam synonym: "Database index" EXACT [] created_in: "beta12orEarlier" def: "Data concerning an index of data." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0955 ! Data index consider: EDAM_data:0956 ! Data index report [Term] id: EDAM_data:2563 name: Amino acid name (single letter) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Single letter amino acid identifier, e.g. G." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1006 ! Amino acid name [Term] id: EDAM_data:2564 name: Amino acid name (three letter) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Three letter amino acid identifier, e.g. GLY." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1006 ! Amino acid name [Term] id: EDAM_data:2565 name: Amino acid name (full name) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Full name of an amino acid, e.g. Glycine." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1006 ! Amino acid name [Term] id: EDAM_data:2576 name: Toxin identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a toxin." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1086 ! Compound identifier relationship: is_identifier_of EDAM_data:2852 ! Toxin structure [Term] id: EDAM_data:2578 name: ArachnoServer ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a toxin from the ArachnoServer database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2897 ! Toxin accession [Term] id: EDAM_data:2579 name: Expressed gene list subset: bioinformatics subset: data subset: edam synonym: "Gene annotation (expressed gene list)" EXACT [] created_in: "beta12orEarlier" def: "A simple summary of expressed genes." [http://edamontology.org] namespace: data is_a: EDAM_data:2872 ! ID list [Term] id: EDAM_data:2580 name: BindingDB Monomer ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a monomer from the BindingDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2581 name: GO concept name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a concept from the GO ontology." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2339 ! Ontology concept name [Term] id: EDAM_data:2582 name: GO concept ID (biological process) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a 'biological process' concept from the the Gene Ontology." [http://edamontology.org] regex: "[0-9]{7}|GO:[0-9]{7}" namespace: identifier is_a: EDAM_data:1176 ! GO concept ID [Term] id: EDAM_data:2583 name: GO concept ID (molecular function) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a 'molecular function' concept from the the Gene Ontology." [http://edamontology.org] regex: "[0-9]{7}|GO:[0-9]{7}" namespace: identifier is_a: EDAM_data:1176 ! GO concept ID [Term] id: EDAM_data:2584 name: GO concept name (cellular component) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a concept for a cellular component from the GO ontology." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2339 ! Ontology concept name [Term] id: EDAM_data:2586 name: Northern blot image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An image arising from a Northern Blot experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:3108 ! Experimental measurement [Term] id: EDAM_data:2587 name: Blot ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a blot from a Northern Blot." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2588 name: BlotBase blot ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a blot from a Northern Blot from the BlotBase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2587 ! Blot ID [Term] id: EDAM_data:2589 name: Hierarchy subset: bioinformatics subset: data subset: edam synonym: "Hierarchy annotation" EXACT [] created_in: "beta12orEarlier" def: "A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation." [http://edamontology.org] namespace: data is_a: EDAM_data:2987 ! Classification [Term] id: EDAM_data:2590 name: Hierarchy identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from a database of biological hierarchies." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2891 ! Biological model accession [Term] id: EDAM_data:2591 name: Brite hierarchy ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the Brite database of biological hierarchies." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2891 ! Biological model accession [Term] id: EDAM_data:2592 name: Cancer type subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A type (represented as a string) of cancer." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2100 ! Type [Term] id: EDAM_data:2593 name: BRENDA organism ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier for an organism used in the BRENDA database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2908 ! Organism accession [Term] id: EDAM_data:2594 name: UniGene taxon subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "UniGene organism abbreviation" EXACT [] created_in: "beta12orEarlier" def: "The name of a taxon using the controlled vocabulary of the UniGene database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:2595 name: UTRdb taxon subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a taxon using the controlled vocabulary of the UTRdb database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:2596 name: Catalogue identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a catalogue of biological resources." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2597 name: CABRI catalogue name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a catalogue of biological resources from the CABRI database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2596 ! Catalogue identifier [Term] id: EDAM_data:2598 name: Secondary structure alignment metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2083 ! Alignment report [Term] id: EDAM_data:2599 name: Molecular interaction subset: bioinformatics subset: data subset: edam synonym: "Molecular interaction data" EXACT [] created_in: "beta12orEarlier" def: "Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2600 name: Pathway or network subset: bioinformatics subset: data subset: edam synonym: "Network" EXACT [] created_in: "beta12orEarlier" def: "Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network)." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_data:2601 name: Small molecule data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning one or more small molecules." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2602 name: Genotype and phenotype data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0920 ! Genotype/phenotype annotation [Term] id: EDAM_data:2603 name: Microarray data comment: This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 subset: bioinformatics subset: data subset: edam synonym: "Gene expression data" EXACT [] created_in: "beta12orEarlier" def: "Image or hybridisation data for a microarray, typically a study of gene expression." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2605 name: Compound ID (KEGG) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "KEGG compound ID" EXACT [] synonym: "KEGG compound identifier" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier of a chemical compound from the KEGG database." [http://edamontology.org] regex: "C[0-9]+" namespace: identifier is_a: EDAM_data:1154 ! KEGG object identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2606 name: RFAM name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name (not necessarily stable) an entry (RNA family) from the RFAM database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2355 ! RNA family identifier [Term] id: EDAM_data:2608 name: Reaction ID (KEGG) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a biological reaction from the KEGG reactions database." [http://edamontology.org] regex: "R[0-9]+" namespace: identifier is_a: EDAM_data:1154 ! KEGG object identifier is_a: EDAM_data:2108 ! Reaction ID [Term] id: EDAM_data:2609 name: Drug ID (KEGG) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a drug from the KEGG Drug database." [http://edamontology.org] regex: "D[0-9]+" namespace: identifier is_a: EDAM_data:1154 ! KEGG object identifier is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:2610 name: Ensembl ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database." [http://edamontology.org] regex: "ENS[A-Z]*[FPTG][0-9]{11}" namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2611 name: ICD identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a disease from the International Classification of Diseases (ICD) database." [http://edamontology.org] regex: "[A-Z][0-9]+(\\.[-[0-9]+])?" namespace: identifier is_a: EDAM_data:1150 ! Disease ID relationship: is_identifier_of EDAM_data:1622 ! Disease annotation [Term] id: EDAM_data:2612 name: Sequence cluster ID (CluSTr) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CluSTr cluster ID" EXACT [] synonym: "CluSTr ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier of a sequence cluster from the CluSTr database." [http://edamontology.org] regex: "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\\.[0-9])?" namespace: identifier is_a: EDAM_data:1112 ! Sequence cluster ID [Term] id: EDAM_data:2613 name: KEGG Glycan ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND)." [http://edamontology.org] regex: "G[0-9]+" namespace: identifier is_a: EDAM_data:1154 ! KEGG object identifier is_a: EDAM_data:2900 ! Carbohydrate accession [Term] id: EDAM_data:2614 name: TCDB ID comment: OBO file for regular expression. subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "TC number" EXACT [] created_in: "beta12orEarlier" def: "A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins." [http://edamontology.org] regex: "[0-9]+\\.[A-Z]\\.[0-9]+\\.[0-9]+\\.[0-9]+" namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2615 name: MINT ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an entry from the MINT database of protein-protein interactions." [http://edamontology.org] regex: "MINT\\-[0-9]{1,5}" namespace: identifier is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:2616 name: DIP ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an entry from the DIP database of protein-protein interactions." [http://edamontology.org] regex: "DIP[\\:\\-][0-9]{3}[EN]" namespace: identifier is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:2617 name: Signaling Gateway protein ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database." [http://edamontology.org] regex: "A[0-9]{6}" namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2618 name: Protein modification ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a protein modification catalogued in a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2619 name: RESID ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a protein modification catalogued in the RESID database." [http://edamontology.org] regex: "AA[0-9]{4}" namespace: identifier is_a: EDAM_data:2618 ! Protein modification ID [Term] id: EDAM_data:2620 name: RGD ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the RGD database." [http://edamontology.org] regex: "[0-9]{4,7}" namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2621 name: TAIR accession (protein) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a protein sequence from the TAIR database." [http://edamontology.org] regex: "AASequence:[0-9]{10}" namespace: identifier is_a: EDAM_data:1096 ! Sequence accession (protein) is_a: EDAM_data:2387 ! TAIR accession relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:2622 name: Compound ID (HMDB) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "HMDB ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB)." [http://edamontology.org] regex: "HMDB[0-9]{5}" namespace: identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2625 name: LIPID MAPS ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "LM ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry from the LIPID MAPS database." [http://edamontology.org] regex: "LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?" namespace: identifier is_a: EDAM_data:2905 ! Lipid accession [Term] id: EDAM_data:2626 name: PeptideAtlas ID subset: bioinformatics subset: data subset: edam subset: identifiers xref: PDBML:pdbx_PDB_strand_id created_in: "beta12orEarlier" def: "Identifier of a peptide from the PeptideAtlas peptide databases." [http://edamontology.org] regex: "PAp[0-9]{8}" namespace: identifier is_a: EDAM_data:2906 ! Peptide ID [Term] id: EDAM_data:2627 name: Molecular interaction ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a report of molecular interactions from a database (typically)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:2599 ! Molecular interaction [Term] id: EDAM_data:2628 name: BioGRID interaction ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of an interaction from the BioGRID database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2627 ! Molecular interaction ID [Term] id: EDAM_data:2629 name: Enzyme ID (MEROPS) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "MEROPS ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier of a peptidase enzyme from the MEROPS database." [http://edamontology.org] regex: "S[0-9]{2}\\.[0-9]{3}" namespace: identifier is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:2630 name: Mobile genetic element ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a mobile genetic element." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2631 name: ACLAME ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a mobile genetic element from the Aclame database." [http://edamontology.org] regex: "mge:[0-9]+" namespace: identifier is_a: EDAM_data:2630 ! Mobile genetic element ID [Term] id: EDAM_data:2632 name: SGD ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the Saccharomyces genome database (SGD)." [http://edamontology.org] regex: "PWY[a-zA-Z_0-9]{2}\\-[0-9]{3}" namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2633 name: Book ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a book." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2634 name: ISBN subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The International Standard Book Number (ISBN) is for identifying printed books." [http://edamontology.org] regex: "(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)" namespace: identifier is_a: EDAM_data:2633 ! Book ID [Term] id: EDAM_data:2635 name: Compound ID (3DMET) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "3DMET ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a metabolite from the 3DMET database." [http://edamontology.org] regex: "B[0-9]{5}" namespace: identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2636 name: MatrixDB interaction ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of an interaction from the MatrixDB database." [http://edamontology.org] 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_.*)" namespace: identifier is_a: EDAM_data:2627 ! Molecular interaction ID [Term] id: EDAM_data:2637 name: cPath ID comment: These identifiers are unique within the cPath database, however, they are not stable between releases. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2109 ! Identifier (hybrid) is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2638 name: PubChem bioassay ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an assay from the PubChem database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2639 ! PubChem identifier [Term] id: EDAM_data:2639 name: PubChem identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the PubChem database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2641 name: Reaction ID (MACie) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "MACie entry number" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an enzyme reaction mechanism from the MACie database." [http://edamontology.org] regex: "M[0-9]{4}" namespace: identifier is_a: EDAM_data:2108 ! Reaction ID [Term] id: EDAM_data:2642 name: Gene ID (miRBase) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "miRNA ID" EXACT [] synonym: "miRNA identifier" EXACT [] synonym: "miRNA name" EXACT [] created_in: "beta12orEarlier" def: "Identifier for a gene from the miRBase database." [http://edamontology.org] regex: "MI[0-9]{7}" namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2643 name: Gene ID (ZFIN) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier for a gene from the Zebrafish information network genome (ZFIN) database." [http://edamontology.org] regex: "ZDB\\-GENE\\-[0-9]+\\-[0-9]+" namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2644 name: Reaction ID (Rhea) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an enzyme-catalysed reaction from the Rhea database." [http://edamontology.org] regex: "[0-9]{5}" namespace: identifier is_a: EDAM_data:2108 ! Reaction ID [Term] id: EDAM_data:2645 name: Pathway ID (Unipathway) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "upaid" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a biological pathway from the Unipathway database." [http://edamontology.org] regex: "UPA[0-9]{5}" namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2646 name: Compound ID (ChEMBL) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "ChEMBL ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a small molecular from the ChEMBL database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2647 name: LGICdb identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database." [http://edamontology.org] regex: "[a-zA-Z_0-9]+" namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2648 name: Reaction kinetics ID (SABIO-RK) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2309 ! Reaction ID (SABIO-RK) [Term] id: EDAM_data:2649 name: PharmGKB ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] regex: "PA[0-9]+" namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2650 name: Pathway ID (PharmGKB) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] regex: "PA[0-9]+" namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession is_a: EDAM_data:2649 ! PharmGKB ID [Term] id: EDAM_data:2651 name: Disease ID (PharmGKB) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] regex: "PA[0-9]+" namespace: identifier is_a: EDAM_data:1150 ! Disease ID is_a: EDAM_data:2649 ! PharmGKB ID [Term] id: EDAM_data:2652 name: Drug ID (PharmGKB) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org] regex: "PA[0-9]+" namespace: identifier is_a: EDAM_data:2649 ! PharmGKB ID is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:2653 name: Drug ID (TTD) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a drug from the Therapeutic Target Database (TTD)." [http://edamontology.org] regex: "DAP[0-9]+" namespace: identifier is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:2654 name: Target ID (TTD) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a target protein from the Therapeutic Target Database (TTD)." [http://edamontology.org] regex: "TTDS[0-9]+" namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2655 name: Cell type identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of a type or group of cells." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2656 name: NeuronDB ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of a neuron from the NeuronDB database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2893 ! Cell type accession [Term] id: EDAM_data:2657 name: NeuroMorpho ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of a neuron from the NeuroMorpho database." [http://edamontology.org] regex: "[a-zA-Z_0-9]+" namespace: identifier is_a: EDAM_data:2893 ! Cell type accession [Term] id: EDAM_data:2658 name: Compound ID (ChemIDplus) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "ChemIDplus ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of a chemical from the ChemIDplus database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2894 ! Compound accession [Term] id: EDAM_data:2659 name: Pathway ID (SMPDB) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a pathway from the Small Molecule Pathway Database (SMPDB)." [http://edamontology.org] regex: "SMP[0-9]{5}" namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2660 name: BioNumbers ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2662 name: T3DB ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database." [http://edamontology.org] regex: "T3D[0-9]+" namespace: identifier is_a: EDAM_data:2897 ! Toxin accession [Term] id: EDAM_data:2663 name: Carbohydrate identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a carbohydrate." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1086 ! Compound identifier relationship: is_identifier_of EDAM_data:1462 ! Carbohydrate structure relationship: is_identifier_of EDAM_data:2313 ! Carbohydrate structure report [Term] id: EDAM_data:2664 name: GlycomeDB ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the GlycomeDB database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2900 ! Carbohydrate accession [Term] id: EDAM_data:2665 name: LipidBank ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the LipidBank database." [http://edamontology.org] regex: "[a-zA-Z_0-9]+[0-9]+" namespace: identifier is_a: EDAM_data:2905 ! Lipid accession [Term] id: EDAM_data:2666 name: CDD ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a conserved domain from the Conserved Domain Database." [http://edamontology.org] regex: "cd[0-9]{5}" namespace: identifier is_a: EDAM_data:1038 ! Protein domain ID [Term] id: EDAM_data:2667 name: MMDB ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "MMDB accession" EXACT [] created_in: "beta12orEarlier" def: "An identifier of an entry from the MMDB database." [http://edamontology.org] regex: "[0-9]{1,5}" namespace: identifier is_a: EDAM_data:1070 ! Structure ID [Term] id: EDAM_data:2668 name: iRefIndex ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an entry from the iRefIndex database of protein-protein interactions." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:1074 ! Protein interaction ID [Term] id: EDAM_data:2669 name: ModelDB ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of an entry from the ModelDB database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2891 ! Biological model accession [Term] id: EDAM_data:2670 name: Pathway ID (DQCS) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS)." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2671 name: Ensembl ID (Homo sapiens) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division)." [http://edamontology.org] regex: "ENS([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2672 name: Ensembl ID ('Bos taurus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division)." [http://edamontology.org] regex: "ENSBTA([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2673 name: Ensembl ID ('Canis familiaris') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division)." [http://edamontology.org] regex: "ENSCAF([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2674 name: Ensembl ID ('Cavia porcellus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division)." [http://edamontology.org] regex: "ENSCPO([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2675 name: Ensembl ID ('Ciona intestinalis') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division)." [http://edamontology.org] regex: "ENSCIN([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2676 name: Ensembl ID ('Ciona savignyi') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division)." [http://edamontology.org] regex: "ENSCSAV([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2677 name: Ensembl ID ('Danio rerio') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division)." [http://edamontology.org] regex: "ENSDAR([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2678 name: Ensembl ID ('Dasypus novemcinctus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division)." [http://edamontology.org] regex: "ENSDNO([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2679 name: Ensembl ID ('Echinops telfairi') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division)." [http://edamontology.org] regex: "ENSETE([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2680 name: Ensembl ID ('Erinaceus europaeus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division)." [http://edamontology.org] regex: "ENSEEU([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2681 name: Ensembl ID ('Felis catus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division)." [http://edamontology.org] regex: "ENSFCA([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2682 name: Ensembl ID ('Gallus gallus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division)." [http://edamontology.org] regex: "ENSGAL([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2683 name: Ensembl ID ('Gasterosteus aculeatus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division)." [http://edamontology.org] regex: "ENSGAC([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2684 name: Ensembl ID ('Homo sapiens') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division)." [http://edamontology.org] regex: "ENSHUM([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2685 name: Ensembl ID ('Loxodonta africana') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division)." [http://edamontology.org] regex: "ENSLAF([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2686 name: Ensembl ID ('Macaca mulatta') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division)." [http://edamontology.org] regex: "ENSMMU([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2687 name: Ensembl ID ('Monodelphis domestica') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division)." [http://edamontology.org] regex: "ENSMOD([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2688 name: Ensembl ID ('Mus musculus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division)." [http://edamontology.org] regex: "ENSMUS([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2689 name: Ensembl ID ('Myotis lucifugus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division)." [http://edamontology.org] regex: "ENSMLU([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2690 name: Ensembl ID ("Ornithorhynchus anatinus") subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division)." [http://edamontology.org] regex: "ENSOAN([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2691 name: Ensembl ID ('Oryctolagus cuniculus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division)." [http://edamontology.org] regex: "ENSOCU([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2692 name: Ensembl ID ('Oryzias latipes') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division)." [http://edamontology.org] regex: "ENSORL([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2693 name: Ensembl ID ('Otolemur garnettii') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division)." [http://edamontology.org] regex: "ENSSAR([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2694 name: Ensembl ID ('Pan troglodytes') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division)." [http://edamontology.org] regex: "ENSPTR([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2695 name: Ensembl ID ('Rattus norvegicus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division)." [http://edamontology.org] regex: "ENSRNO([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2696 name: Ensembl ID ('Spermophilus tridecemlineatus') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division)." [http://edamontology.org] regex: "ENSSTO([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2697 name: Ensembl ID ('Takifugu rubripes') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division)." [http://edamontology.org] regex: "ENSFRU([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2698 name: Ensembl ID ('Tupaia belangeri') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division)." [http://edamontology.org] regex: "ENSTBE([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2699 name: Ensembl ID ('Xenopus tropicalis') subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division)." [http://edamontology.org] regex: "ENSXET([EGTP])[0-9]{11}" namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2700 name: CATH identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a protein domain (or other node) from the CATH database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1038 ! Protein domain ID relationship: is_identifier_of EDAM_data:1553 ! CATH node [Term] id: EDAM_data:2701 name: CATH node ID (family) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A code number identifying a family from the CATH database." [http://edamontology.org] example: "2.10.10.10" namespace: identifier is_a: EDAM_data:1043 ! CATH node ID relationship: is_identifier_of EDAM_data:1553 ! CATH node [Term] id: EDAM_data:2702 name: Enzyme ID (CAZy) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CAZy ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an enzyme from the CAZy enzymes database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:2704 name: Clone ID (IMAGE) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "I.M.A.G.E. cloneID" EXACT [] synonym: "IMAGE cloneID" EXACT [] created_in: "beta12orEarlier" def: "A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1855 ! Clone ID [Term] id: EDAM_data:2705 name: GO concept ID (cellular compartment) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "GO concept identifier (cellular compartment)" EXACT [] created_in: "beta12orEarlier" def: "An identifier of a 'cellular compartment' concept from the Gene Ontology." [http://edamontology.org] regex: "[0-9]{7}|GO:[0-9]{7}" namespace: identifier is_a: EDAM_data:1176 ! GO concept ID [Term] id: EDAM_data:2706 name: Chromosome name (BioCyc) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a chromosome as used in the BioCyc database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0987 ! Chromosome name [Term] id: EDAM_data:2709 name: CleanEx entry name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a gene expression profile from the CleanEx database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1080 ! Gene expression report ID [Term] id: EDAM_data:2710 name: CleanEx dataset code subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1078 ! Microarray experiment annotation ID [Term] id: EDAM_data:2711 name: Genome metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Provenance metadata or other general information concerning a genome as a whole." [http://edamontology.org] namespace: data is_a: EDAM_data:0855 ! Sequence metadata [Term] id: EDAM_data:2713 name: Protein ID (CORUM) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CORUM complex ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier for a protein complex from the CORUM database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2714 name: CDD PSSM-ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a position-specific scoring matrix from the CDD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1115 ! Sequence profile ID [Term] id: EDAM_data:2715 name: Protein ID (CuticleDB) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CuticleDB ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier for a protein from the CuticleDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2716 name: DBD ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a predicted transcription factor from the DBD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2911 ! Transcription factor accession [Term] id: EDAM_data:2717 name: Oligonucleotide probe annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "General annotation on an oligonucleotide probe." [http://edamontology.org] namespace: data is_a: EDAM_data:3115 ! Microarray annotation relationship: has_topic EDAM_topic:0632 ! Probes and primers [Term] id: EDAM_data:2718 name: Oligonucleotide ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an oligonucleotide from a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2119 ! Nucleic acid identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2719 name: dbProbe ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an oligonucleotide probe from the dbProbe database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2718 ! Oligonucleotide ID [Term] id: EDAM_data:2720 name: Dinucleotide property subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Physicochemical property data for one or more dinucleotides." [http://edamontology.org] namespace: data is_a: EDAM_data:2088 ! DNA base structural data [Term] id: EDAM_data:2721 name: DiProDB ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an dinucleotide property from the DiProDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2718 ! Oligonucleotide ID [Term] id: EDAM_data:2722 name: Protein features (disordered structure) subset: bioinformatics subset: data subset: edam synonym: "Protein structure report (disordered structure)" EXACT [] created_in: "beta12orEarlier" def: "An informative report about disordered structure in a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:2723 name: Protein ID (DisProt) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "DisProt ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier for a protein from the DisProt database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2724 name: Embryo annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Annotation on an embryo or concerning embryological development." [http://edamontology.org] namespace: data is_a: EDAM_data:2530 ! Organism annotation relationship: has_topic EDAM_topic:3065 ! Embryology resources [Term] id: EDAM_data:2725 name: Transcript ID (Ensembl) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Ensembl Transcript ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier for a gene transcript from the Ensembl database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2610 ! Ensembl ID is_a: EDAM_data:2769 ! Transcript ID [Term] id: EDAM_data:2726 name: Inhibitor annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report on one or more small molecules that are enzyme inhibitors." [http://edamontology.org] namespace: data is_a: EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_data:2727 name: Promoter ID subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby:GeneAccessionList created_in: "beta12orEarlier" def: "An identifier of a promoter of a gene that is catalogued in a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2728 name: EST accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an EST sequence." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1855 ! Clone ID [Term] id: EDAM_data:2729 name: COGEME EST ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an EST sequence from the COGEME database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2728 ! EST accession [Term] id: EDAM_data:2730 name: COGEME unisequence ID comment: A unisequence is a single sequence assembled from ESTs. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a unisequence from the COGEME database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2728 ! EST accession [Term] id: EDAM_data:2731 name: Protein family ID (GeneFarm) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "GeneFarm family ID" EXACT [] created_in: "beta12orEarlier" def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2732 name: Family name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a family of organism." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1868 ! Taxon [Term] id: EDAM_data:2733 name: Genus name (virus) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a genus of viruses." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1870 ! Genus name [Term] id: EDAM_data:2734 name: Family name (virus) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a family of viruses." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2732 ! Family name [Term] id: EDAM_data:2735 name: Database name (SwissRegulon) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a SwissRegulon database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:2736 name: Sequence feature ID (SwissRegulon) comment: This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A feature identifier as used in the SwissRegulon database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1015 ! Sequence feature ID [Term] id: EDAM_data:2737 name: FIG ID comment: A FIG ID consists of four parts: a prefix, genome id, locus type and id number. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of gene in the NMPDR database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2738 name: Gene ID (Xenbase) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of gene in the Xenbase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2739 name: Gene ID (Genolist) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of gene in the Genolist database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2740 name: Gene name (Genolist) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Genolist gene name" EXACT [] created_in: "beta12orEarlier" def: "Name of an entry (gene) from the Genolist genes database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1026 ! Gene symbol [Term] id: EDAM_data:2741 name: ABS ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "ABS identifier" EXACT [] created_in: "beta12orEarlier" def: "Identifier of an entry (promoter) from the ABS database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2727 ! Promoter ID [Term] id: EDAM_data:2742 name: AraC-XylS ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a transcription factor from the AraC-XylS database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2911 ! Transcription factor accession [Term] id: EDAM_data:2743 name: Gene name (HUGO) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of an entry (gene) from the HUGO database." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1791 ! Gene name (HGNC) [Term] id: EDAM_data:2744 name: Locus ID (PseudoCAP) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a locus from the PseudoCAP database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:2745 name: Locus ID (UTR) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a locus from the UTR database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID [Term] id: EDAM_data:2746 name: MonosaccharideDB ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier of a monosaccharide from the MonosaccharideDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2898 ! Monosaccharide accession [Term] id: EDAM_data:2747 name: Database name (CMD) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a subdivision of the Collagen Mutation Database (CMD) database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:2748 name: Database name (Osteogenesis) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a subdivision of the Osteogenesis database." [http://edamontology.org] namespace: identifier obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1056 ! Database name [Term] id: EDAM_data:2749 name: Genome identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a particular genome." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2751 name: GenomeReviews ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a particular genome." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2903 ! Genome accession [Term] id: EDAM_data:2752 name: GlycoMap ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2900 ! Carbohydrate accession [Term] id: EDAM_data:2753 name: Carbohydrate conformational map subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A conformational energy map of the glycosidic linkages in a carbohydrate molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:2313 ! Carbohydrate structure report [Term] id: EDAM_data:2754 name: Nucleic acid features (intron) subset: bioinformatics subset: data subset: edam synonym: "Gene features (intron)" EXACT [] created_in: "beta12orEarlier" def: "An informative report on an intron in a nucleotide sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:2755 name: Transcription factor name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a transcription factor." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1009 ! Protein name is_a: EDAM_data:1077 ! Transcription factor identifier [Term] id: EDAM_data:2756 name: TCID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a membrane transport proteins from the transport classification database (TCDB)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2757 name: Pfam domain name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a domain from the Pfam database." [http://edamontology.org] regex: "PF[0-9]{5}" namespace: identifier is_a: EDAM_data:1131 ! Protein family name [Term] id: EDAM_data:2758 name: Pfam clan ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession number of a Pfam clan." [http://edamontology.org] regex: "CL[0-9]{4}" namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2759 name: Gene ID (VectorBase) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "VectorBase ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier for a gene from the VectorBase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2761 name: UTRSite ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1114 ! Sequence motif identifier [Term] id: EDAM_data:2762 name: Sequence motif metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_data:2763 name: Locus annotation subset: bioinformatics subset: data subset: edam synonym: "Locus report" EXACT [] created_in: "beta12orEarlier" def: "An informative report on a particular locus." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0916 ! Gene annotation [Term] id: EDAM_data:2764 name: Protein name (UniProt) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Official name of a protein as used in the UniProt database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1009 ! Protein name [Term] id: EDAM_data:2765 name: Term ID list comment: The concepts 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: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "One or more terms from one or more controlled vocabularies which are annotations on an entity." [http://edamontology.org] namespace: data is_a: EDAM_data:2872 ! ID list [Term] id: EDAM_data:2766 name: HAMAP ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a protein family from the HAMAP database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2767 name: Identifier with metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance." [http://edamontology.org] namespace: data is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:2768 name: Gene symbol annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Annotation about a gene symbol." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2767 ! Identifier with metadata [Term] id: EDAM_data:2769 name: Transcript ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a RNA transcript." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2119 ! Nucleic acid identifier is_a: EDAM_data:2901 ! Molecule accession relationship: is_identifier_of EDAM_data:2399 ! Gene annotation (transcript) [Term] id: EDAM_data:2770 name: HIT ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an RNA transcript from the H-InvDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2769 ! Transcript ID [Term] id: EDAM_data:2771 name: HIX ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of gene cluster in the H-InvDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2772 name: HPA antibody id subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a antibody from the HPA database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2773 name: IMGT/HLA ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2774 name: Gene ID (JCVI) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2775 name: Kinase name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a kinase protein." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1009 ! Protein name [Term] id: EDAM_data:2776 name: ConsensusPathDB entity ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a physical entity from the ConsensusPathDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2917 ! ConsensusPathDB identifier [Term] id: EDAM_data:2777 name: ConsensusPathDB entity name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a physical entity from the ConsensusPathDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2917 ! ConsensusPathDB identifier [Term] id: EDAM_data:2778 name: CCAP strain number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The number of a strain of algae and protozoa from the CCAP database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2912 ! Strain accession [Term] id: EDAM_data:2779 name: Stock number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of stock from a catalogue of biological resources." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2780 name: Stock number (TAIR) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A stock number from The Arabidopsis information resource (TAIR)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2779 ! Stock number [Term] id: EDAM_data:2781 name: REDIdb ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the RNA editing database (REDIdb)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1097 ! Sequence accession (nucleic acid) [Term] id: EDAM_data:2782 name: SMART domain name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a domain from the SMART database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1131 ! Protein family name [Term] id: EDAM_data:2783 name: Protein family ID (PANTHER) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Panther family ID" EXACT [] created_in: "beta12orEarlier" def: "Accession number of an entry (family) from the PANTHER database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2910 ! Protein family accession [Term] id: EDAM_data:2784 name: RNAVirusDB ID comment: Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier for a virus from the RNAVirusDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2785 ! Virus ID [Term] id: EDAM_data:2785 name: Virus ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2908 ! Organism accession is_a: EDAM_data:2913 ! Virus identifier [Term] id: EDAM_data:2786 name: NCBI Genome Project ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a genome project assigned by NCBI." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2903 ! Genome accession [Term] id: EDAM_data:2787 name: NCBI genome accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of a whole genome assigned by the NCBI." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2903 ! Genome accession [Term] id: EDAM_data:2788 name: Sequence profile metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_data:2789 name: Protein ID (TopDB) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "TopDB ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier for a membrane protein from the TopDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2790 name: Gel identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a two-dimensional (protein) gel." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2791 name: Reference map name (SWISS-2DPAGE) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a reference map gel from the SWISS-2DPAGE database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2790 ! Gel identifier [Term] id: EDAM_data:2792 name: Protein ID (PeroxiBase) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "PeroxiBase ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier for a peroxidase protein from the PeroxiBase database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2793 name: SISYPHUS ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the SISYPHUS database of tertiary structure alignments." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1072 ! Structure alignment ID [Term] id: EDAM_data:2794 name: ORF ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of an open reading frame (catalogued in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1893 ! Locus ID is_a: EDAM_data:2795 ! ORF identifier [Term] id: EDAM_data:2795 name: ORF identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of an open reading frame." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) [Term] id: EDAM_data:2796 name: Linucs ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2900 ! Carbohydrate accession [Term] id: EDAM_data:2797 name: Protein ID (LGICdb) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "LGICdb ID" EXACT [] created_in: "beta12orEarlier" def: "Unique identifier for a ligand-gated ion channel protein from the LGICdb database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2798 name: MaizeDB ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of an EST sequence from the MaizeDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2728 ! EST accession [Term] id: EDAM_data:2799 name: Gene ID (MfunGD) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of gene in the MfunGD database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2800 name: Orpha number subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of a disease from the Orpha database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1150 ! Disease ID relationship: is_identifier_of EDAM_data:1622 ! Disease annotation [Term] id: EDAM_data:2802 name: Protein ID (EcID) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier for a protein from the EcID database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2803 name: Clone ID (RefSeq) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "A unique identifier of a cDNA molecule catalogued in the RefSeq database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1098 ! RefSeq accession is_a: EDAM_data:1855 ! Clone ID [Term] id: EDAM_data:2804 name: Protein ID (ConoServer) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Unique identifier for a cone snail toxin protein from the ConoServer database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2805 name: GeneSNP ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a GeneSNP database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2294 ! Sequence variation ID [Term] id: EDAM_data:2812 name: Lipid identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a lipid." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0982 ! Molecule identifier relationship: is_identifier_of EDAM_data:2850 ! Lipid structure relationship: is_identifier_of EDAM_data:2879 ! Lipid structure report [Term] id: EDAM_data:2831 name: Databank subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A flat-file (textual) data archive." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:2832 name: Web portal subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A web site providing data (web pages) on a common theme to a HTTP client." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_data:2835 name: Gene ID (VBASE2) subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "VBASE2 ID" EXACT [] created_in: "beta12orEarlier" def: "Identifier for a gene from the VBASE2 database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2295 ! Gene ID [Term] id: EDAM_data:2836 name: DPVweb ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "DPVweb virus ID" EXACT [] created_in: "beta12orEarlier" def: "A unique identifier for a virus from the DPVweb database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2785 ! Virus ID [Term] id: EDAM_data:2837 name: Pathway ID (BioSystems) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a pathway from the BioSystems pathway database." [http://edamontology.org] regex: "[0-9]+" namespace: identifier is_a: EDAM_data:2365 ! Pathway or network accession [Term] id: EDAM_data:2838 name: Experimental data (proteomics) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning a proteomics experiment." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:3147 ! Experiment annotation (mass spectrometry) [Term] id: EDAM_data:2849 name: Abstract subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An abstract of a scientific article." [http://edamontology.org] namespace: data is_a: EDAM_data:2857 ! Article metadata [Term] id: EDAM_data:2850 name: Lipid structure subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a lipid structure." [http://edamontology.org] namespace: data is_a: EDAM_data:0883 ! Structure [Term] id: EDAM_data:2851 name: Drug structure subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for the (3D) structure of a drug." [http://edamontology.org] namespace: data is_a: EDAM_data:1463 ! Small molecule structure [Term] id: EDAM_data:2852 name: Toxin structure subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for the (3D) structure of a toxin." [http://edamontology.org] namespace: data is_a: EDAM_data:1463 ! Small molecule structure [Term] id: EDAM_data:2854 name: Position-specific scoring matrix subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1354 ! Sequence profile is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:2855 name: Distance matrix subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity." [http://edamontology.org] namespace: data is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:2856 name: Structural distance matrix subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Distances (values representing similarity) between a group of molecular structures." [http://edamontology.org] namespace: data is_a: EDAM_data:2855 ! Distance matrix [Term] id: EDAM_data:2857 name: Article metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Bibliographic data concerning scientific article(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata is_a: EDAM_data:2954 ! Article report relationship: has_topic EDAM_topic:3068 ! Literature and reference [Term] id: EDAM_data:2858 name: Ontology concept comment: This includes any fields from the concept definition such as concept name, definition, comments and so on. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A concept from a biological ontology." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_data:2865 name: Codon usage bias subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:0914 ! Codon usage report [Term] id: EDAM_data:2866 name: Experiment annotation (Northern blot) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "General annotation on a Northern Blot experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:2867 name: Nucleic acid features (VNTR) comment: VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. subset: bioinformatics subset: data subset: edam synonym: "Variable number of tandem repeat polymorphism" EXACT [] synonym: "VNTR annotation" EXACT [] created_in: "beta12orEarlier" def: "Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_data:2868 name: Nucleic acid features (microsatellite) 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: bioinformatics subset: data subset: edam synonym: "Microsatellite annotation" EXACT [] created_in: "beta12orEarlier" def: "Annotation on a microsatellite polymorphism in a DNA sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_data:2869 name: Nucleic acid features (RFLP) comment: An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. subset: bioinformatics subset: data subset: edam synonym: "RFLP annotation" EXACT [] created_in: "beta12orEarlier" def: "Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_data:2870 name: Radiation hybrid map 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: bioinformatics subset: data subset: edam synonym: "RH map" EXACT [] created_in: "beta12orEarlier" def: "A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome." [http://edamontology.org] namespace: data is_a: EDAM_data:1280 ! Physical map [Term] id: EDAM_data:2872 name: ID list subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data." [http://edamontology.org] namespace: data is_a: EDAM_data:2093 ! Data reference [Term] id: EDAM_data:2873 name: Phylogenetic gene frequencies data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Gene frequencies data that may be read during phylogenetic tree calculation." [http://edamontology.org] namespace: data is_a: EDAM_data:1426 ! Phylogenetic continuous quantitative data [Term] id: EDAM_data:2874 name: Sequence set (polymorphic) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:2875 name: DRCAT resource subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An entry (resource) from the DRCAT bioinformatics resource catalogue." [http://edamontology.org] namespace: data is_a: EDAM_data:0948 ! Data resource definition [Term] id: EDAM_data:2877 name: Protein complex subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another." [http://edamontology.org] namespace: data is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:2878 name: Protein structural motif subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:1460 ! Protein structure [Term] id: EDAM_data:2879 name: Lipid structure report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Annotation on or information derived from one or more specific lipid 3D structure(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:2085 ! Structure report [Term] id: EDAM_data:2880 name: Secondary structure image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image of one or more molecular secondary structures." [http://edamontology.org] namespace: data is_a: EDAM_data:2881 ! Secondary structure report [Term] id: EDAM_data:2881 name: Secondary structure report subset: bioinformatics subset: data subset: edam synonym: "Secondary structure-derived report" EXACT [] created_in: "beta12orEarlier" def: "An informative report on general information, properties or features of one or more molecular secondary structures." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2882 name: DNA features subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "DNA sequence-specific feature annotation (not in a feature table)." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:2883 name: Nucleic acid features (RNA features) subset: bioinformatics subset: data subset: edam synonym: "RNA features" EXACT [] created_in: "beta12orEarlier" def: "Features concerning RNA or regions of DNA that encode an RNA molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:2884 name: Plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Biological data that is plotted as a graph of some type." [http://edamontology.org] namespace: data obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2968 ! Image [Term] id: EDAM_data:2885 name: Nucleic acid features (polymorphism annotation) subset: bioinformatics subset: data subset: edam synonym: "Polymorphism annotation" EXACT [] created_in: "beta12orEarlier" def: "Annotation on a polymorphism." [http://edamontology.org] namespace: data is_a: EDAM_data:0918 ! Nucleic acid features (variation) [Term] id: EDAM_data:2886 name: Sequence record (protein) subset: bioinformatics subset: data subset: edam synonym: "Protein sequence record" EXACT [] created_in: "beta12orEarlier" def: "A protein sequence and associated metadata." [http://edamontology.org] namespace: data is_a: EDAM_data:0849 ! Sequence record is_a: EDAM_data:2976 ! Protein sequence [Term] id: EDAM_data:2887 name: Sequence record (nucleic acid) subset: bioinformatics subset: data subset: edam synonym: "Nucleic acid sequence record" EXACT [] synonym: "Nucleotide sequence record" EXACT [] created_in: "beta12orEarlier" def: "A nucleic acid sequence and associated metadata." [http://edamontology.org] namespace: data is_a: EDAM_data:0849 ! Sequence record is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:2888 name: Sequence record full (protein) subset: bioinformatics subset: data subset: edam xref: SO:2000061 created_in: "beta12orEarlier" def: "A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] namespace: data is_a: EDAM_data:2201 ! Sequence record full is_a: EDAM_data:2886 ! Sequence record (protein) [Term] id: EDAM_data:2889 name: Sequence record full (nucleic acid) subset: bioinformatics subset: data subset: edam xref: SO:2000061 created_in: "beta12orEarlier" def: "A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] namespace: data is_a: EDAM_data:2201 ! Sequence record full is_a: EDAM_data:2887 ! Sequence record (nucleic acid) [Term] id: EDAM_data:2891 name: Biological model accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a mathematical model, typically an entry from a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1085 ! Biological model identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2892 name: Cell type name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a type or group of cells." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2655 ! Cell type identifier [Term] id: EDAM_data:2893 name: Cell type accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a type or group of cells (catalogued in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2655 ! Cell type identifier [Term] id: EDAM_data:2894 name: Compound accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Chemical compound accession" EXACT [] synonym: "Small molecule accession" EXACT [] created_in: "beta12orEarlier" def: "Accession of an entry from a database of chemicals." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1086 ! Compound identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2895 name: Drug accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a drug." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0993 ! Drug identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2896 name: Toxin name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Name of a toxin." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:2576 ! Toxin identifier [Term] id: EDAM_data:2897 name: Toxin accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a toxin (catalogued in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2576 ! Toxin identifier [Term] id: EDAM_data:2898 name: Monosaccharide accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a monosaccharide (catalogued in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0996 ! Monosaccharide identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2899 name: Drug name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Common name of a drug." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0990 ! Compound name is_a: EDAM_data:0993 ! Drug identifier [Term] id: EDAM_data:2900 name: Carbohydrate accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of an entry from a database of carbohydrates." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2663 ! Carbohydrate identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2901 name: Molecule accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a specific molecule (catalogued in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0982 ! Molecule identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2902 name: Data resource definition accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a data definition (catalogued in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1084 ! Data resource definition identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2903 name: Genome accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An accession of a particular genome (in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2749 ! Genome identifier [Term] id: EDAM_data:2904 name: Map accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An accession of a map of a molecular sequence (deposited in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2117 ! Map identifier [Term] id: EDAM_data:2905 name: Lipid accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of an entry from a database of lipids." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2812 ! Lipid identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2906 name: Peptide ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a peptide deposited in a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0988 ! Peptide identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2907 name: Protein accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a protein deposited in a database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0989 ! Protein identifier is_a: EDAM_data:2901 ! Molecule accession [Term] id: EDAM_data:2908 name: Organism accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An accession of annotation on a (group of) organisms (catalogued in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1869 ! Organism identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2909 name: Organism name subset: bioinformatics subset: data subset: edam subset: identifiers xref: Moby:BriefOccurrenceRecord xref: Moby:FirstEpithet xref: Moby:InfraspecificEpithet xref: Moby:OccurrenceRecord xref: Moby:Organism_Name xref: Moby:OrganismsLongName xref: Moby:OrganismsShortName created_in: "beta12orEarlier" def: "The name of an organism (or group of organisms)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1869 ! Organism identifier is_a: EDAM_data:2099 ! Name [Term] id: EDAM_data:2910 name: Protein family accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of a protein family (that is deposited in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1075 ! Protein family identifier is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:2911 name: Transcription factor accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Accession of an entry from a database of transcription factors or binding sites." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1077 ! Transcription factor identifier is_a: EDAM_data:2091 ! Accession is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:2912 name: Strain accession subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2379 ! Strain identifier is_a: EDAM_data:2908 ! Organism accession relationship: is_identifier_of EDAM_data:0963 ! Cell line annotation [Term] id: EDAM_data:2913 name: Virus identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1869 ! Organism identifier relationship: is_identifier_of EDAM_data:2307 ! Virus annotation [Term] id: EDAM_data:2914 name: Sequence features metadata subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Metadata on sequence features." [http://edamontology.org] namespace: data is_a: EDAM_data:0855 ! Sequence metadata [Term] id: EDAM_data:2915 name: Gramene identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a Gramene database entry." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1096 ! Sequence accession (protein) [Term] id: EDAM_data:2916 name: DDBJ accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "DDBJ accession number" EXACT [] synonym: "DDBJ ID" EXACT [] synonym: "DDBJ identifier" EXACT [] created_in: "beta12orEarlier" def: "An identifier of an entry from the DDBJ sequence database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID [Term] id: EDAM_data:2917 name: ConsensusPathDB identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "An identifier of an entity from the ConsensusPathDB database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2109 ! Identifier (hybrid) [Term] id: EDAM_data:2925 name: Sequence data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning molecular sequence(s)." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2044 ! Sequence consider: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:2927 name: Codon usage data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning codon usage." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0914 ! Codon usage report consider: EDAM_data:1597 ! Codon usage table [Term] id: EDAM_data:2954 name: Article report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning or derived from the analysis of a scientific article." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2955 name: Sequence report subset: bioinformatics subset: data subset: edam synonym: "Sequence-derived report" EXACT [] created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report [Term] id: EDAM_data:2956 name: Protein secondary structure report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report about the properties or features of one or more protein secondary structures." [http://edamontology.org] namespace: data is_a: EDAM_data:2881 ! Secondary structure report [Term] id: EDAM_data:2957 name: Hopp and Woods plot subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A Hopp and Woods plot of predicted antigenicity of a peptide or protein." [http://edamontology.org] namespace: data is_a: EDAM_data:1534 ! Peptide immunogenicity data [Term] id: EDAM_data:2958 name: Nucleic acid melting curve comment: Shows the proportion of nucleic acid which are double-stranded versus temperature. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] namespace: data is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] id: EDAM_data:2959 name: Nucleic acid probability profile comment: Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] namespace: data is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] id: EDAM_data:2960 name: Nucleic acid temperature profile comment: Plots melting temperature versus base position. subset: bioinformatics subset: data subset: edam synonym: "Melting map" EXACT [] created_in: "beta12orEarlier" def: "A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org] namespace: data is_a: EDAM_data:1583 ! Nucleic acid melting profile [Term] id: EDAM_data:2961 name: Pathway or network (gene regulation) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report typically including a map (diagram) of a gene regulatory network." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks [Term] id: EDAM_data:2965 name: 2D PAGE image (annotated) subset: bioinformatics subset: data subset: edam synonym: "2D PAGE image annotation" EXACT [] created_in: "beta12orEarlier" def: "An informative report on a two-dimensional (2D PAGE) gel." [http://edamontology.org] namespace: data is_a: EDAM_data:0942 ! 2D PAGE image [Term] id: EDAM_data:2966 name: Oligonucleotide probe sets annotation subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:2717 ! Oligonucleotide probe annotation [Term] id: EDAM_data:2967 name: Microarray image subset: bioinformatics subset: data subset: edam synonym: "Gene expression image" EXACT [] created_in: "beta12orEarlier" def: "An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data." [http://edamontology.org] namespace: data is_a: EDAM_data:2603 ! Microarray data is_a: EDAM_data:2968 ! Image relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:2968 name: Image subset: bioinformatics subset: data subset: edam synonym: "SIO:000079" BROAD [] synonym: "SIO:000081" NARROW [] created_in: "beta12orEarlier" def: "Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2969 name: Sequence image subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Image of a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org] namespace: data is_a: EDAM_data:2955 ! Sequence report is_a: EDAM_data:2968 ! Image [Term] id: EDAM_data:2970 name: Protein hydropathy data subset: bioinformatics subset: data subset: edam synonym: "Protein hydropathy report" EXACT [] created_in: "beta12orEarlier" def: "A report on protein properties concerning hydropathy." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:2971 name: Workflow data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning a computational workflow." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0949 ! Workflow metadata consider: EDAM_data:2972 ! Workflow [Term] id: EDAM_data:2972 name: Workflow subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A computational workflow." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2973 name: Secondary structure data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning molecular secondary structure data." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2081 ! Secondary structure consider: EDAM_data:2881 ! Secondary structure report [Term] id: EDAM_data:2974 name: Raw sequence (protein) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A raw protein sequence (string of characters)." [http://edamontology.org] namespace: data is_a: EDAM_data:0848 ! Raw sequence is_a: EDAM_data:2976 ! Protein sequence [Term] id: EDAM_data:2975 name: Raw sequence (nucleic acid) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A raw nucleic acid sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:0848 ! Raw sequence is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:2976 name: Protein sequence subset: bioinformatics subset: data subset: edam synonym: "AminoAcidSequenceInformation" RELATED [] created_in: "beta12orEarlier" def: "One or more protein sequences, possibly with associated annotation." [http://edamontology.org] namespace: data is_a: EDAM_data:2044 ! Sequence [Term] id: EDAM_data:2977 name: Nucleic acid sequence subset: bioinformatics subset: data subset: edam synonym: "NucleotideSequenceInformation" RELATED [] created_in: "beta12orEarlier" def: "One or more nucleic acid sequences, possibly with associated annotation." [http://edamontology.org] namespace: data is_a: EDAM_data:2044 ! Sequence [Term] id: EDAM_data:2978 name: Reaction data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam synonym: "Enzyme kinetics annotation" EXACT [] synonym: "Reaction annotation" EXACT [] created_in: "beta12orEarlier" def: "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:2979 name: Peptide property subset: bioinformatics subset: data subset: edam synonym: "Peptide data" EXACT [] created_in: "beta12orEarlier" def: "Data concerning small peptides." [http://edamontology.org] namespace: data is_a: EDAM_data:2087 ! Molecular property [Term] id: EDAM_data:2980 name: Protein classification comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam synonym: "Protein classification data" EXACT [] created_in: "beta12orEarlier" def: "Data concerning the classification of protein sequences or structures." [http://edamontology.org] namespace: data is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:2987 ! Classification relationship: has_topic EDAM_topic:0595 ! Protein classification [Term] id: EDAM_data:2981 name: Sequence motif data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning specific or conserved pattern in molecular sequences." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1353 ! Sequence motif [Term] id: EDAM_data:2982 name: Sequence profile data comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning models representing a (typically multiple) sequence alignment." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:2983 name: Pathway or network data subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Data concerning a specific biological pathway or network." [http://edamontology.org] namespace: data obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2600 ! Pathway or network consider: EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_data:2984 name: Pathway or network report subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." [http://edamontology.org] namespace: data is_a: EDAM_data:2048 ! Report relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_data:2985 name: Nucleic acid thermodynamic data subset: bioinformatics subset: data subset: edam synonym: "Nucleic acid property (thermodynamic or kinetic)" EXACT [] synonym: "Nucleic acid thermodynamic property" EXACT [] created_in: "beta12orEarlier" def: "A thermodynamic or kinetic property of a nucleic acid molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_data:2986 name: Nucleic acid classification comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam synonym: "Nucleic acid classification data" EXACT [] created_in: "beta12orEarlier" def: "Data concerning the classification of nucleic acid sequences or structures." [http://edamontology.org] namespace: data is_a: EDAM_data:2084 ! Nucleic acid report is_a: EDAM_data:2987 ! Classification relationship: has_topic EDAM_topic:0722 ! Nucleic acid classification [Term] id: EDAM_data:2987 name: Classification comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. subset: bioinformatics subset: data subset: edam synonym: "Classification data" EXACT [] created_in: "beta12orEarlier" def: "Data concerning a classification of molecular sequences, structures or other entities." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_data:2989 name: Protein features (key folding sites) subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "A report on key residues involved in protein folding." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:2991 name: Protein torsion angle data subset: bioinformatics subset: data subset: edam synonym: "Torsion angle data" EXACT [] created_in: "beta12orEarlier" def: "Torsion angle data for a protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:0897 ! Protein property [Term] id: EDAM_data:2992 name: Protein structure image subset: bioinformatics subset: data subset: edam synonym: "Structure image (protein)" EXACT [] created_in: "beta12orEarlier" def: "An image of protein structure." [http://edamontology.org] namespace: data is_a: EDAM_data:1710 ! Structure image is_a: EDAM_data:3153 ! Protein image [Term] id: EDAM_data:2994 name: Phylogenetic character weights subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" def: "Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted." [http://edamontology.org] namespace: data is_a: EDAM_data:2523 ! Phylogenetic raw data [Term] id: EDAM_data:3002 name: Sequence annotation track subset: bioinformatics subset: data subset: edam synonym: "Annotation track" EXACT [] synonym: "Genome annotation track" EXACT [] synonym: "Genome track" EXACT [] synonym: "Genome-browser track" EXACT [] synonym: "Genomic track" EXACT [] created_in: "beta12orEarlier" def: "Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser." [http://edamontology.org] namespace: data is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:3021 name: UniProt accession subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Swiss-Prot entry accession" NARROW [] synonym: "TrEMBL entry accession" NARROW [] synonym: "UniProt accession number" EXACT [] synonym: "UniProt entry accession" EXACT [] synonym: "UniProtKB accession" EXACT [] synonym: "UniProtKB accession number" EXACT [] created_in: "beta12orEarlier" def: "Accession number of a UniProt (protein sequence) database entry." [http://edamontology.org] example: "P43353|Q7M1G0|Q9C199|A5A6J6" 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]" namespace: identifier is_a: EDAM_data:1096 ! Sequence accession (protein) relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_data:3022 name: NCBI genetic code ID subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a genetic code in the NCBI list of genetic codes." [http://edamontology.org] example: "16" regex: "[1-9][0-9]?" namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:3025 name: Ontology concept identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "Identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2858 ! Ontology concept [Term] id: EDAM_data:3026 name: GO concept name (biological process) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a concept for a biological process from the GO ontology." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2339 ! Ontology concept name [Term] id: EDAM_data:3027 name: GO concept name (molecular function) subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" def: "The name of a concept for a molecular function from the GO ontology." [http://edamontology.org] namespace: identifier obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:2339 ! Ontology concept name [Term] id: EDAM_data:3028 name: Taxonomy comment: This is a broad data type and is used a placeholder for other, more specific types. subset: bioinformatics subset: data subset: edam synonym: "Taxonomic data" EXACT [] created_in: "beta12orEarlier" def: "Data concerning the classification, identification and naming of organisms." [http://edamontology.org] namespace: data is_a: EDAM_data:2987 ! Classification relationship: has_topic EDAM_topic:0637 ! Taxonomy [Term] id: EDAM_data:3029 name: Protein ID (EMBL/GenBank/DDBJ) 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: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta13" def: "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2907 ! Protein accession [Term] id: EDAM_data:3031 name: Core data comment: Core data entities typically have a format and may be identified by an accession number. subset: bioinformatics subset: data subset: edam created_in: "beta13" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0006 ! Data [Term] id: EDAM_data:3034 name: Sequence feature identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta13" def: "Name or other identifier of molecular sequence feature(s)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:1255 ! Feature record [Term] id: EDAM_data:3035 name: Structure identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta13" def: "An identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:0883 ! Structure [Term] id: EDAM_data:3036 name: Matrix identifier subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta13" def: "An identifier of an array of numerical values, such as a comparison matrix." [http://edamontology.org] namespace: identifier is_a: EDAM_data:0976 ! Identifier (typed) relationship: is_identifier_of EDAM_data:2082 ! Matrix [Term] id: EDAM_data:3085 name: Protein sequence composition subset: bioinformatics subset: data subset: edam synonym: "Sequence property (protein composition)" EXACT [] created_in: "beta13" def: "A report (typically a table) on character or word composition / frequency of protein sequence(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:1261 ! Sequence composition [Term] id: EDAM_data:3086 name: Nucleic acid sequence composition subset: bioinformatics subset: data subset: edam synonym: "Sequence property (nucleic acid composition)" EXACT [] created_in: "beta13" def: "A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:0912 ! Nucleic acid property is_a: EDAM_data:1261 ! Sequence composition [Term] id: EDAM_data:3101 name: Protein domain classification node subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "A node from a classification of protein structural domain(s)." [http://edamontology.org] namespace: data is_a: EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_data:3102 name: CAS number subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CAS registry number" EXACT [] created_in: "beta13" def: "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:3103 name: ATC code subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta13" 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)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2895 ! Drug accession [Term] id: EDAM_data:3104 name: UNII subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "Unique Ingredient Identifier" EXACT [] created_in: "beta13" def: "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." [http://edamontology.org] namespace: identifier is_a: EDAM_data:1086 ! Compound identifier [Term] id: EDAM_data:3105 name: Geotemporal metadata subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Basic information concerning geographical location or time." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:3106 name: System metadata subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Metadata concerning the software, hardware or other aspects of a computer system." [http://edamontology.org] namespace: data is_a: EDAM_data:2337 ! Metadata [Term] id: EDAM_data:3107 name: Sequence feature name subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta13" def: "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." [http://edamontology.org] namespace: identifier is_a: EDAM_data:2099 ! Name is_a: EDAM_data:3034 ! Sequence feature identifier [Term] id: EDAM_data:3108 name: Experimental measurement 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: bioinformatics subset: data subset: edam synonym: "Experimental measurement data" EXACT [] synonym: "Experimentally measured data" EXACT [] synonym: "Measured data" EXACT [] synonym: "Measurement" EXACT [] synonym: "Measurement data" EXACT [] synonym: "Measurement metadata" NARROW [] synonym: "Raw experimental data" NARROW [] created_in: "beta13" def: "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware." [http://edamontology.org] namespace: data is_a: EDAM_data:3031 ! Core data [Term] id: EDAM_data:3110 name: Raw microarray data comment: Such data as found in Affymetrix CEL or GPR files. subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:3108 ! Experimental measurement is_a: EDAM_data:3117 ! Microarray hybridisation data [Term] id: EDAM_data:3111 name: Processed microarray data comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. subset: bioinformatics subset: data subset: edam synonym: "Gene annotation (expression)" EXACT [] synonym: "Gene expression report" EXACT [] synonym: "Microarray probe set data" EXACT [] created_in: "beta13" def: "Data generated from processing and analysis of probe set data from a microarray experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:0928 ! Gene expression profile is_a: EDAM_data:3117 ! Microarray hybridisation data relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:3112 name: Normalised microarray data comment: This combines data from all hybridisations. subset: bioinformatics subset: data subset: edam synonym: "Gene expression data matrix" EXACT [] synonym: "Gene expression matrix" EXACT [] created_in: "beta13" def: "The final processed (normalised) data for a set of hybridisations in a microarray experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:3117 ! Microarray hybridisation data [Term] id: EDAM_data:3113 name: Sample annotation comment: This might include compound and dose in a dose response experiment. subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Annotation on a biological sample, for example experimental factors and their values." [http://edamontology.org] namespace: data is_a: EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_data:3115 name: Microarray annotation comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Annotation on the array itself used in a microarray experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_data:3116 name: Microarray protocol annotation comment: This might describe e.g. the normalisation methods used to process the raw data. subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Annotation on laboratory and/or data processing protocols used in an microarray experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_data:3117 name: Microarray hybridisation data subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Data concerning the hybridisations measured during a microarray experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:2603 ! Microarray data relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:3118 name: Protein features (topological domains) subset: bioinformatics subset: data subset: edam synonym: "Protein topological domains" EXACT [] created_in: "beta13" def: "Summary of topological domains such as cytoplasmic regions in a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_data:3119 name: Sequence features (compositionally-biased regions) subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report of regions in a molecular sequence that are biased to certain characters." [http://edamontology.org] namespace: data is_a: EDAM_data:1261 ! Sequence composition [Term] id: EDAM_data:3120 name: Protein features (sequence variants) subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features [Term] id: EDAM_data:3122 name: Nucleic acid features (difference and change) subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on features in a nucleic acid sequence that indicate changes to or differences between sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3123 name: Nucleic acid features (expression signal) subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on regions within a nucleic acid sequence containing a signal that alters a biological function." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3125 name: Nucleic acid features (binding) comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on regions of a nucleic acid sequence that bind some other molecule." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3126 name: Nucleic acid features (repeats) 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: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on repetitive elements within a nucleic acid sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features is_a: EDAM_data:1299 ! Sequence features (repeats) [Term] id: EDAM_data:3127 name: Nucleic acid features (replication and recombination) 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: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3128 name: Nucleic acid features (structure) subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3129 name: Protein features (repeats) subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Location of short repetitive subsequences (repeat sequences) in a protein sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:1299 ! Sequence features (repeats) [Term] id: EDAM_data:3130 name: Protein features (motifs) comment: Use this concept if another, more specific concept is not available. subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1277 ! Protein features is_a: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:3131 name: Nucleic acid features (motifs) comment: Use this concept if another, more specific concept is not available. subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features is_a: EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_data:3132 name: Nucleic acid features (d-loop) comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on displacement loops in a mitochondrial DNA sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] id: EDAM_data:3133 name: Nucleic acid features (stem loop) 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: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on stem loops in a DNA sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:3128 ! Nucleic acid features (structure) [Term] id: EDAM_data:3134 name: Nucleic acid features (mRNA features) comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). subset: bioinformatics subset: data subset: edam synonym: "mRNA features" EXACT [] created_in: "beta13" def: "Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules." [http://edamontology.org] namespace: data is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) [Term] id: EDAM_data:3135 name: Nucleic acid features (signal or transit peptide) 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: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on a coding sequence for a signal or transit peptide." [http://edamontology.org] namespace: data is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features) [Term] id: EDAM_data:3137 name: Nucleic acid features (non-coding RNA) subset: bioinformatics subset: data subset: edam synonym: "ncRNA features" EXACT [] synonym: "Non-coding RNA features" EXACT [] created_in: "beta13" def: "Features concerning non-coding or functional RNA molecules, including tRNA and rRNA." [http://edamontology.org] namespace: data is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) [Term] id: EDAM_data:3138 name: Nucleic acid features (transcriptional) 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: bioinformatics subset: data subset: edam created_in: "beta13" def: "Features concerning transcription of DNA into RNA including the regulation of transcription." [http://edamontology.org] namespace: data is_a: EDAM_data:2883 ! Nucleic acid features (RNA features) [Term] id: EDAM_data:3139 name: Nucleic acid features (STS) 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: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on sequence tagged sites (STS) in nucleic acid sequences." [http://edamontology.org] namespace: data is_a: EDAM_data:1276 ! Nucleic acid features [Term] id: EDAM_data:3140 name: Nucleic acid features (immunoglobulin gene structure) subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." [http://edamontology.org] namespace: data is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:3141 name: SCOP class subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Information on a 'class' node from the SCOP database." [http://edamontology.org] namespace: data is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3142 name: SCOP fold subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Information on a 'fold' node from the SCOP database." [http://edamontology.org] namespace: data is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3143 name: SCOP superfamily subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Information on a 'superfamily' node from the SCOP database." [http://edamontology.org] namespace: data is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3144 name: SCOP family subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Information on a 'family' node from the SCOP database." [http://edamontology.org] namespace: data is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3145 name: SCOP protein subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Information on a 'protein' node from the SCOP database." [http://edamontology.org] namespace: data is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3146 name: SCOP species subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "Information on a 'species' node from the SCOP database." [http://edamontology.org] namespace: data is_a: EDAM_data:1554 ! SCOP node [Term] id: EDAM_data:3147 name: Experiment annotation (mass spectrometry) subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "General annotation on a mass spectrometry experiment." [http://edamontology.org] namespace: data is_a: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:3148 name: Gene family annotation subset: bioinformatics subset: data subset: edam created_in: "beta13" 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." [http://edamontology.org] namespace: data is_a: EDAM_data:0916 ! Gene annotation is_a: EDAM_data:2986 ! Nucleic acid classification [Term] id: EDAM_data:3153 name: Protein image subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "An image of a protein." [http://edamontology.org] namespace: data is_a: EDAM_data:0896 ! Protein report [Term] id: EDAM_data:3154 name: Protein alignment subset: bioinformatics subset: data subset: edam created_in: "beta13" def: "An alignment of protein sequences and/or structures." [http://edamontology.org] namespace: data is_a: EDAM_data:0896 ! Protein report is_a: EDAM_data:1916 ! Alignment [Term] id: EDAM_data:3165 name: Experiment annotation (sequencing) subset: bioinformatics subset: data subset: edam created_in: "1.0" def: "Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis." [http://edamontology.org] namespace: data is_a: EDAM_data:2531 ! Experiment annotation relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_data:3181 name: Sequence assembly report subset: bioinformatics subset: data subset: edam created_in: "1.1" def: "An informative report about a DNA sequence assembly." [http://edamontology.org] namespace: data is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:3210 name: Genome index comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. subset: bioinformatics subset: data subset: edam created_in: "1.1" def: "An index of a genome sequence." [http://edamontology.org] namespace: data is_a: EDAM_data:0955 ! Data index [Term] id: EDAM_data:3231 name: Experiment annotation (GWAS) subset: bioinformatics subset: data subset: edam synonym: "Experiment annotation (genome-wide association study)" EXACT [] created_in: "1.1" def: "Metadata on a genome-wide association study (GWAS)." [http://edamontology.org] namespace: data is_a: EDAM_data:2531 ! Experiment annotation [Term] id: EDAM_data:3236 name: Cytoband position comment: Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on. subset: bioinformatics subset: data subset: edam created_in: "1.2" def: "The position of a cytogenetic band in a genome." [http://edamontology.org] namespace: data is_a: EDAM_data:2012 ! Map position [Term] id: EDAM_data:3238 name: Cell type ontology ID subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "CL ID" EXACT [] created_in: "beta12orEarlier" def: "Cell type ontology concept ID." [http://edamontology.org] regex: "CL_[0-9]{7}" namespace: identifier is_a: EDAM_data:1087 ! Ontology concept ID is_a: EDAM_data:2893 ! Cell type accession [Term] id: EDAM_data:3241 name: Kinetic model subset: bioinformatics subset: data subset: edam created_in: "1.2" def: "Mathematical model of a network, that contains biochemical kinetics." [http://edamontology.org] namespace: data is_a: EDAM_data:2600 ! Pathway or network [Term] id: EDAM_format:1196 name: SMILES subset: bioinformatics subset: edam subset: formats xref: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification xref: http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html created_in: "beta12orEarlier" def: "Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation." [http://edamontology.org] documentation: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification documentation: http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html namespace: format is_a: EDAM_format:2035 ! Chemical formula format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1197 name: InChI subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation." [http://edamontology.org] namespace: format is_a: EDAM_format:2035 ! Chemical formula format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1198 name: mf comment: The general MF query format consists of a series of valid atomic symbols, with an optional number or range. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound." [http://edamontology.org] namespace: format is_a: EDAM_format:2035 ! Chemical formula format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1199 name: inchikey comment: An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: format is_a: EDAM_format:2035 ! Chemical formula format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1200 name: smarts subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." [http://edamontology.org] namespace: format is_a: EDAM_format:1196 ! SMILES [Term] id: EDAM_format:1206 name: unambiguous pure subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2094 ! pure is_a: EDAM_format:2096 ! unambiguous sequence [Term] id: EDAM_format:1207 name: nucleotide comment: Non-sequence characters may be used for example for gaps. subset: bioinformatics subset: edam subset: formats synonym: "Nucleotide_sequence" RELATED [] created_in: "beta12orEarlier" def: "Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:1208 name: protein comment: Non-sequence characters may be used for gaps and translation stop. subset: bioinformatics subset: edam subset: formats synonym: "Amino_acid_sequence" RELATED [] created_in: "beta12orEarlier" def: "Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:1209 name: consensus subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for the consensus of two or more molecular sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2095 ! unpure is_a: EDAM_format:2097 ! ambiguous [Term] id: EDAM_format:1210 name: pure nucleotide subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1207 ! nucleotide is_a: EDAM_format:2094 ! pure [Term] id: EDAM_format:1211 name: unambiguous pure nucleotide subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters ." [http://edamontology.org] namespace: format is_a: EDAM_format:1206 ! unambiguous pure is_a: EDAM_format:1207 ! nucleotide [Term] id: EDAM_format:1212 name: dna subset: bioinformatics subset: edam subset: formats synonym: "DNA_sequence" RELATED [] created_in: "beta12orEarlier" def: "Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1207 ! nucleotide [Term] id: EDAM_format:1213 name: rna subset: bioinformatics subset: edam subset: formats synonym: "RNA_sequence" RELATED [] created_in: "beta12orEarlier" def: "Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1207 ! nucleotide [Term] id: EDAM_format:1214 name: unambiguous pure dna subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1206 ! unambiguous pure is_a: EDAM_format:1212 ! dna [Term] id: EDAM_format:1215 name: pure dna subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1210 ! pure nucleotide is_a: EDAM_format:1212 ! dna [Term] id: EDAM_format:1216 name: unambiguous pure rna sequence subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1206 ! unambiguous pure is_a: EDAM_format:1213 ! rna [Term] id: EDAM_format:1217 name: pure rna subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1210 ! pure nucleotide is_a: EDAM_format:1213 ! rna [Term] id: EDAM_format:1218 name: unambiguous pure protein subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1206 ! unambiguous pure is_a: EDAM_format:1208 ! protein [Term] id: EDAM_format:1219 name: pure protein subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1208 ! protein is_a: EDAM_format:2094 ! pure [Term] id: EDAM_format:1228 name: UniGene entry format 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from UniGene." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1247 name: COG sequence cluster format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the COG database of clusters of (related) protein sequences." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1248 name: EMBL feature location subset: bioinformatics subset: edam subset: formats synonym: "Feature location" EXACT [] created_in: "beta12orEarlier" def: "Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database." [http://edamontology.org] namespace: format is_a: EDAM_format:2078 ! Sequence range format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1295 name: quicktandem subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program)." [http://edamontology.org] namespace: format is_a: EDAM_format:2155 ! Sequence features (repeats) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1296 name: Sanger inverted repeats subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program)." [http://edamontology.org] namespace: format is_a: EDAM_format:2155 ! Sequence features (repeats) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1297 name: EMBOSS repeat subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Report format for tandem repeats in a sequence (an EMBOSS report format)." [http://edamontology.org] namespace: format is_a: EDAM_format:2155 ! Sequence features (repeats) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1316 name: est2genome format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on exon-intron structure generated by EMBOSS est2genome." [http://edamontology.org] namespace: format is_a: EDAM_format:2159 ! Gene features (coding region) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1318 name: restrict format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Report format for restriction enzyme recognition sites used by EMBOSS restrict program." [http://edamontology.org] namespace: format is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1319 name: restover format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Report format for restriction enzyme recognition sites used by EMBOSS restover program." [http://edamontology.org] namespace: format is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1320 name: REBASE restriction sites subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Report format for restriction enzyme recognition sites used by REBASE database." [http://edamontology.org] namespace: format is_a: EDAM_format:2158 ! Nucleic acid features (restriction sites) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1332 name: FASTA search results format comment: This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of results of a sequence database search using FASTA." [http://edamontology.org] namespace: format is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1333 name: BLAST results comment: This includes score data, alignment data and summary table. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of results of a sequence database search using some variant of BLAST." [http://edamontology.org] namespace: format is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1334 name: mspcrunch subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of results of a sequence database search using some variant of MSPCrunch." [http://edamontology.org] namespace: format is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1335 name: Smith-Waterman format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of results of a sequence database search using some variant of Smith Waterman." [http://edamontology.org] namespace: format is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1336 name: dhf comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information." [http://edamontology.org] namespace: format is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1337 name: lhf comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information." [http://edamontology.org] namespace: format is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1341 name: InterPro hits format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Results format for searches of the InterPro database." [http://edamontology.org] namespace: format is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1342 name: InterPro protein view report format 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries." [http://edamontology.org] namespace: format is_a: EDAM_format:1341 ! InterPro hits format [Term] id: EDAM_format:1343 name: InterPro match table format 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry." [http://edamontology.org] namespace: format is_a: EDAM_format:1341 ! InterPro hits format [Term] id: EDAM_format:1349 name: HMMER Dirichlet prior subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Dirichlet distribution HMMER format." [http://edamontology.org] namespace: format is_a: EDAM_format:2074 ! Dirichlet distribution format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1350 name: MEME Dirichlet prior subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Dirichlet distribution MEME format." [http://edamontology.org] namespace: format is_a: EDAM_format:2074 ! Dirichlet distribution format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1351 name: HMMER emission and transition subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model." [http://edamontology.org] namespace: format is_a: EDAM_format:2075 ! HMM emission and transition counts format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1356 name: prosite-pattern subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a regular expression pattern from the Prosite database." [http://edamontology.org] namespace: format is_a: EDAM_format:2068 ! Sequence motif format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1357 name: EMBOSS sequence pattern subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an EMBOSS sequence pattern." [http://edamontology.org] namespace: format is_a: EDAM_format:2068 ! Sequence motif format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1360 name: meme-motif subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A motif in the format generated by the MEME program." [http://edamontology.org] namespace: format is_a: EDAM_format:2068 ! Sequence motif format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1366 name: prosite-profile subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Sequence profile (sequence classifier) format used in the PROSITE database." [http://edamontology.org] namespace: format is_a: EDAM_format:2069 ! Sequence profile format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1367 name: JASPAR format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A profile (sequence classifier) in the format used in the JASPAR database." [http://edamontology.org] namespace: format is_a: EDAM_format:2069 ! Sequence profile format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1369 name: MEME background Markov model subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of the model of random sequences used by MEME." [http://edamontology.org] namespace: format is_a: EDAM_format:2072 ! Hidden Markov model format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1370 name: HMMER format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a hidden Markov model representation used by the HMMER package." [http://edamontology.org] namespace: format is_a: EDAM_format:2072 ! Hidden Markov model format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1391 name: HMMER-aln subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "FASTA-style format for multiple sequences aligned by HMMER package to an HMM." [http://edamontology.org] namespace: format is_a: EDAM_format:2200 ! FASTA-like (text) is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1392 name: DIALIGN format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of multiple sequences aligned by DIALIGN package." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1393 name: daf comment: The format is clustal-like and includes annotation of domain family classification information. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1419 name: Sequence-MEME profile alignment subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package." [http://edamontology.org] namespace: format is_a: EDAM_format:2014 ! Sequence-profile alignment format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1421 name: HMMER profile alignment (sequences versus HMMs) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database." [http://edamontology.org] namespace: format is_a: EDAM_format:2014 ! Sequence-profile alignment format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1422 name: HMMER profile alignment (HMM versus sequences) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database." [http://edamontology.org] namespace: format is_a: EDAM_format:2014 ! Sequence-profile alignment format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1423 name: Phylip distance matrix comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of PHYLIP phylogenetic distance matrix data." [http://edamontology.org] namespace: format is_a: EDAM_format:2067 ! Sequence distance matrix format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1424 name: ClustalW dendrogram subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Dendrogram (tree file) format generated by ClustalW." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] id: EDAM_format:1425 name: Phylip tree raw subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] id: EDAM_format:1430 name: Phylip continuous quantitative characters subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "PHYLIP file format for continuous quantitative character data." [http://edamontology.org] namespace: format is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1431 name: Phylogenetic property values format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of phylogenetic property data." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2036 ! Phylogenetic character data format [Term] id: EDAM_format:1432 name: Phylip character frequencies format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "PHYLIP file format for phylogenetics character frequency data." [http://edamontology.org] namespace: format is_a: EDAM_format:2037 ! Phylogenetic continuous quantitative character format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1433 name: Phylip discrete states format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of PHYLIP discrete states data." [http://edamontology.org] namespace: format is_a: EDAM_format:2038 ! Phylogenetic discrete states format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1434 name: Phylip cliques format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of PHYLIP cliques data." [http://edamontology.org] namespace: format is_a: EDAM_format:2039 ! Phylogenetic tree report (cliques) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1435 name: Phylip tree format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Phylogenetic tree data format used by the PHYLIP program." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] id: EDAM_format:1436 name: TreeBASE format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the TreeBASE database of phylogenetic data." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] id: EDAM_format:1437 name: TreeFam format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the TreeFam database of phylogenetic data." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] id: EDAM_format:1445 name: Phylip tree distance format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package." [http://edamontology.org] namespace: format is_a: EDAM_format:2049 ! Phylogenetic tree report (tree distances) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1454 name: dssp 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins)." [http://edamontology.org] namespace: format is_a: EDAM_format:2077 ! Protein secondary structure format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1455 name: hssp subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins)." [http://edamontology.org] namespace: format is_a: EDAM_format:2077 ! Protein secondary structure format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1457 name: Dot-bracket format subset: bioinformatics subset: edam subset: formats synonym: "Vienna RNA format" EXACT [] synonym: "Vienna RNA secondary structure format" EXACT [] created_in: "beta12orEarlier" def: "Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server." [http://edamontology.org] namespace: format is_a: EDAM_format:2076 ! RNA secondary structure format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1458 name: Vienna local RNA secondary structure format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server." [http://edamontology.org] namespace: format is_a: EDAM_format:1457 ! Dot-bracket format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1475 name: PDB database entry format subset: bioinformatics subset: edam subset: formats synonym: "PDB entry format" EXACT [] created_in: "beta12orEarlier" def: "Format of an entry (or part of an entry) from the PDB database." [http://edamontology.org] namespace: format is_a: EDAM_format:2033 ! Tertiary structure format relationship: is_format_of EDAM_data:0883 ! Structure [Term] id: EDAM_format:1476 name: PDB format subset: bioinformatics subset: edam subset: formats synonym: "PDB" EXACT [] created_in: "beta12orEarlier" def: "Entry format of PDB database in PDB format." [http://edamontology.org] namespace: format is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1477 name: mmCIF subset: bioinformatics subset: edam subset: formats synonym: "mmcif" EXACT [] created_in: "beta12orEarlier" def: "Entry format of PDB database in mmCIF format." [http://edamontology.org] namespace: format is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1478 name: PDBML subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of PDB database in PDBML (XML) format." [http://edamontology.org] namespace: format is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:1500 name: Domainatrix 3D-1D scoring matrix format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_format:1504 name: aaindex subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Amino acid index format used by the AAindex database." [http://edamontology.org] namespace: format is_a: EDAM_format:2017 ! Amino acid index format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1511 name: IntEnz enzyme report format 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from IntEnz (The Integrated Relational Enzyme Database)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1512 name: BRENDA enzyme report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the BRENDA enzyme database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1513 name: KEGG REACTION enzyme report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the KEGG REACTION database of biochemical reactions." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1514 name: KEGG ENZYME enzyme report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the KEGG ENZYME database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1515 name: REBASE proto enzyme report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the proto section of the REBASE enzyme database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1516 name: REBASE withrefm enzyme report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the withrefm section of the REBASE enzyme database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1551 name: Pcons report format 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of output of the Pcons Model Quality Assessment Program (MQAP)." [http://edamontology.org] namespace: format is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1552 name: ProQ report format comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of output of the ProQ protein model quality predictor." [http://edamontology.org] namespace: format is_a: EDAM_format:2065 ! Protein structure report (quality evaluation) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1563 name: SMART domain assignment report format 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of SMART domain assignment data." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1568 name: BIND entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the BIND database of protein interaction." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1569 name: IntAct entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the IntAct database of protein interaction." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1570 name: InterPro entry format 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1571 name: InterPro entry abstract format comment: References are included and a functional inference is made where possible. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the textual abstract of signatures in an InterPro entry and its protein matches." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1572 name: Gene3D entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the Gene3D protein secondary database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1573 name: PIRSF entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the PIRSF protein secondary database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1574 name: PRINTS entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the PRINTS protein secondary database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1575 name: Panther Families and HMMs entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the Panther library of protein families and subfamilies." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1576 name: Pfam entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the Pfam protein secondary database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1577 name: SMART entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the SMART protein secondary database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1578 name: Superfamily entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the Superfamily protein secondary database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1579 name: TIGRFam entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the TIGRFam protein secondary database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1580 name: ProDom entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the ProDom protein domain classification database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1581 name: FSSP entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the FSSP database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1582 name: findkm subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: format is_a: EDAM_format:2027 ! Enzyme kinetics report format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1603 name: Ensembl gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of Ensembl genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1604 name: DictyBase gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of DictyBase genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1605 name: CGD gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of Candida Genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1606 name: DragonDB gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of DragonDB genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1607 name: EcoCyc gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of EcoCyc genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1608 name: FlyBase gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of FlyBase genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1609 name: Gramene gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of Gramene genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1610 name: KEGG GENES gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of KEGG GENES genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1611 name: MaizeGDB gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of the Maize genetics and genomics database (MaizeGDB)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1612 name: MGD gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of the Mouse Genome Database (MGD)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1613 name: RGD gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of the Rat Genome Database (RGD)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1614 name: SGD gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of the Saccharomyces Genome Database (SGD)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1615 name: GeneDB gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of the Sanger GeneDB genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1616 name: TAIR gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of The Arabidopsis Information Resource (TAIR) genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1617 name: WormBase gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of the WormBase genomes database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1618 name: ZFIN gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of the Zebrafish Information Network (ZFIN) genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1619 name: TIGR gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format of the TIGR genome database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1620 name: dbSNP polymorphism report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the dbSNP database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1623 name: OMIM entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the OMIM database of genotypes and phenotypes." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1624 name: HGVbase entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a record from the HGVbase database of genotypes and phenotypes." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1625 name: HIVDB entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a record from the HIVDB database of genotypes and phenotypes." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1626 name: KEGG DISEASE entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the KEGG DISEASE database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1627 name: Primer3 primer subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program." [http://edamontology.org] namespace: format is_a: EDAM_format:2061 ! Nucleic acid features (primers) format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1628 name: ABI subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A format of raw sequence read data from an Applied Biosystems sequencing machine." [http://edamontology.org] namespace: format is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:1629 name: mira subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of MIRA sequence trace information file." [http://edamontology.org] namespace: format is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1630 name: CAF subset: bioinformatics subset: edam subset: formats xref: http://www.sanger.ac.uk/resources/software/caf/ created_in: "beta12orEarlier" def: "Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata." [http://edamontology.org] documentation: http://www.sanger.ac.uk/resources/software/caf/ namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2561 ! Sequence assembly format (text) [Term] id: EDAM_format:1631 name: exp subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Sequence assembly project file EXP format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2561 ! Sequence assembly format (text) [Term] id: EDAM_format:1632 name: SCF subset: bioinformatics subset: edam subset: formats xref: http://staden.sourceforge.net/manual/formats_unix_2.html created_in: "beta12orEarlier" def: "Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata." [http://edamontology.org] documentation: http://staden.sourceforge.net/manual/formats_unix_2.html namespace: format is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:1633 name: PHD subset: bioinformatics subset: edam subset: formats xref: http://www.bioperl.org/wiki/PHD_sequence_format created_in: "beta12orEarlier" def: "PHD sequence trace format to store serialised chromatogram data (reads)." [http://edamontology.org] documentation: http://www.bioperl.org/wiki/PHD_sequence_format namespace: format is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1637 name: dat subset: bioinformatics subset: edam subset: formats synonym: "Affymetrix image data file format" EXACT [] created_in: "beta12orEarlier" def: "Format of Affymetrix data file of raw image data." [http://edamontology.org] namespace: format is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2330 ! Textual format relationship: is_format_of EDAM_data:1714 ! Microarray spots image [Term] id: EDAM_format:1638 name: cel subset: bioinformatics subset: edam subset: formats synonym: "Affymetrix probe raw data format" EXACT [] created_in: "beta12orEarlier" def: "Format of Affymetrix data file of information about (raw) expression levels of the individual probes." [http://edamontology.org] namespace: format is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2330 ! Textual format relationship: is_format_of EDAM_data:3110 ! Raw microarray data [Term] id: EDAM_format:1639 name: affymetrix subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [http://edamontology.org] namespace: format is_a: EDAM_format:2172 ! Sequence cluster format (nucleic acid) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1640 name: ArrayExpress entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the ArrayExpress microarrays database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1641 name: affymetrix-exp subset: bioinformatics subset: edam subset: formats synonym: "Affymetrix experimental conditions data file format" EXACT [] created_in: "beta12orEarlier" def: "Affymetrix data file format for information about experimental conditions and protocols." [http://edamontology.org] namespace: format is_a: EDAM_format:2056 ! Microarray experiment data format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1644 name: CHP subset: bioinformatics subset: edam subset: formats synonym: "Affymetrix probe normalised data format" EXACT [] created_in: "beta12orEarlier" def: "Format of Affymetrix data file of information about (normalised) expression levels of the individual probes." [http://edamontology.org] namespace: format is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2330 ! Textual format relationship: is_format_of EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_format:1645 name: EMDB entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the Electron Microscopy DataBase (EMDB)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1647 name: KEGG PATHWAY entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1648 name: MetaCyc entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the MetaCyc metabolic pathways database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1649 name: HumanCyc entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of a report from the HumanCyc metabolic pathways database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1650 name: INOH entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the INOH signal transduction pathways database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1651 name: PATIKA entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the PATIKA biological pathways database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1652 name: Reactome entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the reactome biological pathways database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1653 name: aMAZE entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the aMAZE biological pathways and molecular interactions database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1654 name: CPDB entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the CPDB database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1655 name: Panther Pathways entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the Panther Pathways database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1665 name: Taverna workflow format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of Taverna workflows." [http://edamontology.org] namespace: format is_a: EDAM_format:2032 ! Workflow format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:1666 name: BioModel mathematical model format comment: Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of mathematical models from the BioModel database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1697 name: KEGG LIGAND entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the KEGG LIGAND chemical database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1698 name: KEGG COMPOUND entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the KEGG COMPOUND database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1699 name: KEGG PLANT entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the KEGG PLANT database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1700 name: KEGG GLYCAN entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the KEGG GLYCAN database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1701 name: PubChem entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from PubChem." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1702 name: ChemSpider entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from a database of chemical structures and property predictions." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1703 name: ChEBI entry format comment: ChEBI includes an ontological classification defining relations between entities or classes of entities. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from Chemical Entities of Biological Interest (ChEBI)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1704 name: MSDchem ligand dictionary entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the MSDchem ligand dictionary." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1705 name: HET group dictionary entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the HET group dictionary (HET groups from PDB files)." [http://edamontology.org] namespace: format is_a: EDAM_format:2030 ! Small molecule report format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1706 name: KEGG DRUG entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the KEGG DRUG database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1734 name: PubMed citation subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of bibliographic reference as used by the PubMed database." 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Bibliographic reference format [Term] id: EDAM_format:1737 name: CiteXplore-all subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2848 ! Bibliographic reference format [Term] id: EDAM_format:1739 name: pmc subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Article format of the PubMed Central database." [http://edamontology.org] namespace: format is_a: EDAM_format:2020 ! Article format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1740 name: iHOP text mining abstract format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "iHOP abstract format." [http://edamontology.org] namespace: format is_a: EDAM_format:2021 ! Text mining report format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1741 name: Oscar3 comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Text mining abstract format from the Oscar 3 application." [http://edamontology.org] namespace: format is_a: EDAM_format:2021 ! Text mining report format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1747 name: PDB atom record format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an ATOM record (describing data for an individual atom) from a PDB file." [http://edamontology.org] namespace: format obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1476 ! PDB format [Term] id: EDAM_format:1760 name: CATH chain report format 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of CATH domain classification information for a polypeptide chain." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1761 name: CATH PDB report format 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: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of CATH domain classification information for a protein PDB file." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1782 name: NCBI gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry (gene) format of the NCBI database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1808 name: GeneIlluminator gene report format comment: This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. subset: bioinformatics subset: edam subset: formats xref: Moby:GI_Gene created_in: "beta12orEarlier" def: "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1809 name: BacMap gene card format subset: bioinformatics subset: edam subset: formats xref: Moby:BacMapGeneCard created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1810 name: ColiCard report format subset: bioinformatics subset: edam subset: formats xref: Moby:ColiCard created_in: "beta12orEarlier" def: "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:1861 name: PlasMapper TextMap subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Map of a plasmid (circular DNA) in PlasMapper TextMap format." [http://edamontology.org] namespace: format is_a: EDAM_format:2060 ! Map format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1910 name: newick subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Phylogenetic tree Newick (text) format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] id: EDAM_format:1911 name: TreeCon format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Phylogenetic tree TreeCon (text) format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] id: EDAM_format:1912 name: Nexus format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Phylogenetic tree Nexus (text) format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2556 ! Phylogenetic tree format (text) [Term] id: EDAM_format:1915 name: Format comment: The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. subset: bioinformatics subset: edam subset: formats synonym: "WSIO_compression:004" RELATED [] synonym: "Continuant" BROAD [] synonym: "Data format" EXACT [] synonym: "Data model" BROAD [] synonym: "Exchange format" EXACT [] synonym: "File format" NARROW [] synonym: "File:format" RELATED [] synonym: "http://en.wikipedia.org/wiki/List_of_file_formats" RELATED [] synonym: "http://purl.org/dc/elements/1.1/format" BROAD [] synonym: "IAO:0000098" RELATED [] synonym: "MachineLanguage" RELATED [] synonym: "Perpetuant" RELATED [] synonym: "Quality" BROAD [] synonym: "Quality" RELATED [] synonym: "quality" RELATED [] synonym: "SIO:000612" RELATED [] synonym: "SIO:000618" RELATED [] synonym: "Symbol_structure" RELATED [] created_in: "beta12orEarlier" def: "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere." [http://edamontology.org] namespace: format disjoint_from: EDAM_operation:0004 ! Operation disjoint_from: EDAM_topic:0003 ! Topic [Term] id: EDAM_format:1918 name: Atomic data format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for an individual atom." [http://edamontology.org] namespace: format obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1475 ! PDB database entry format [Term] id: EDAM_format:1919 name: Sequence record format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a molecular sequence record." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0849 ! Sequence record [Term] id: EDAM_format:1920 name: Sequence feature annotation format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for molecular sequence feature information." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1255 ! Feature record [Term] id: EDAM_format:1921 name: Alignment format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for molecular sequence alignment information." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_format:1923 name: acedb subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "ACEDB sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1924 name: clustal sequence format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Clustalw output format." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1982 ! ClustalW format [Term] id: EDAM_format:1925 name: codata subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Codata entry format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1926 name: dbid subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Fasta format variant with database name before ID." [http://edamontology.org] namespace: format is_a: EDAM_format:2200 ! FASTA-like (text) [Term] id: EDAM_format:1927 name: EMBL format subset: bioinformatics subset: edam subset: formats synonym: "EMBL" EXACT [] synonym: "EMBL sequence format" EXACT [] created_in: "beta12orEarlier" def: "EMBL entry format." [http://edamontology.org] namespace: format is_a: EDAM_format:2181 ! EMBL-like (text) is_a: EDAM_format:2206 ! Sequence feature table format (text) [Term] id: EDAM_format:1928 name: Staden experiment format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Staden experiment file format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1929 name: FASTA format subset: bioinformatics subset: edam subset: formats synonym: "FASTA" EXACT [] synonym: "FASTA sequence format" EXACT [] created_in: "beta12orEarlier" def: "FASTA format including NCBI-style IDs." [http://edamontology.org] namespace: format is_a: EDAM_format:2200 ! FASTA-like (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1930 name: FASTQ subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "FASTQ short read format ignoring quality scores." [http://edamontology.org] namespace: format is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1931 name: FASTQ-illumina subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "FASTQ Illumina 1.3 short read format." [http://edamontology.org] namespace: format is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1932 name: FASTQ-sanger subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "FASTQ short read format with phred quality." [http://edamontology.org] namespace: format is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1933 name: FASTQ-solexa subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "FASTQ Solexa/Illumina 1.0 short read format." [http://edamontology.org] namespace: format is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1934 name: fitch program subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Fitch program format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1935 name: gcg subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "GCG sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1936 name: GenBank format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Genbank entry format." [http://edamontology.org] namespace: format is_a: EDAM_format:2205 ! GenBank-like format (text) is_a: EDAM_format:2206 ! Sequence feature table format (text) [Term] id: EDAM_format:1937 name: genpept comment: Currently identical to refseqp format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Genpept protein entry format." [http://edamontology.org] namespace: format is_a: EDAM_format:2205 ! GenBank-like format (text) [Term] id: EDAM_format:1938 name: GFF2-seq subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "GFF feature file format with sequence in the header." [http://edamontology.org] namespace: format is_a: EDAM_format:1974 ! GFF2 is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1939 name: GFF3-seq subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "GFF3 feature file format with sequence." [http://edamontology.org] namespace: format is_a: EDAM_format:1975 ! GFF3 is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1940 name: giFASTA format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "FASTA sequence format including NCBI-style GIs." [http://edamontology.org] namespace: format is_a: EDAM_format:2200 ! FASTA-like (text) [Term] id: EDAM_format:1941 name: hennig86 subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Hennig86 output sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1942 name: ig subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Intelligenetics sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1943 name: igstrict subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Intelligenetics sequence format (strict version)." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1944 name: jackknifer subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Jackknifer interleaved and non-interleaved sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1945 name: mase format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Mase program sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1946 name: mega-seq subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Mega interleaved and non-interleaved sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1947 name: msf subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "GCG MSF (multiple sequence file) file format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1948 name: nbrf subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "NBRF/PIR entry sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2202 ! Sequence record full format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1949 name: nexus-seq subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Nexus/paup interleaved sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1950 name: pdbatom comment: pdb format in EMBOSS. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "PDB sequence format (ATOM lines)." [http://edamontology.org] namespace: format is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1951 name: pdbatomnuc comment: pdbnuc format in EMBOSS. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "PDB nucleotide sequence format (ATOM lines)." [http://edamontology.org] namespace: format is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1952 name: pdbseqresnuc comment: pdbnucseq format in EMBOSS. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "PDB nucleotide sequence format (SEQRES lines)." [http://edamontology.org] namespace: format is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1953 name: pdbseqres comment: pdbseq format in EMBOSS. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "PDB sequence format (SEQRES lines)." [http://edamontology.org] namespace: format is_a: EDAM_format:1475 ! PDB database entry format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1954 name: Pearson format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Plain old FASTA sequence format (unspecified format for IDs)." [http://edamontology.org] namespace: format is_a: EDAM_format:2200 ! FASTA-like (text) [Term] id: EDAM_format:1955 name: phylip sequence format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Phylip interleaved sequence format." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1997 ! Phylip format [Term] id: EDAM_format:1956 name: phylipnon sequence format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Phylip non-interleaved sequence format." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1998 ! Phylipnon [Term] id: EDAM_format:1957 name: raw subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Raw sequence format with no non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:1958 name: refseqp comment: Currently identical to genpept format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Refseq protein entry sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1959 name: selex sequence format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Selex sequence format." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2000 ! selex [Term] id: EDAM_format:1960 name: Staden format subset: bioinformatics subset: edam subset: formats xref: http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html xref: staden created_in: "beta12orEarlier" def: "Staden suite sequence format." [http://edamontology.org] documentation: http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html documentation: "staden" namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1961 name: Stockholm format subset: bioinformatics subset: edam subset: formats xref: Stockholm:format created_in: "beta12orEarlier" def: "Stockholm multiple sequence alignment format (used by Pfam and Rfam)." [http://edamontology.org] documentation: Stockholm:format namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1962 name: strider format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "DNA strider output sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1963 name: UniProtKB format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "UniProtKB entry sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2187 ! UniProt-like (text) [Term] id: EDAM_format:1964 name: plain text format (unformatted) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Plain text sequence format (essentially unformatted)." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1965 name: treecon sequence format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Treecon output sequence format." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2005 ! TreeCon-seq [Term] id: EDAM_format:1966 name: ASN.1 sequence format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "NCBI ASN.1-based sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1967 name: DAS format subset: bioinformatics subset: edam subset: formats synonym: "das sequence format" EXACT [] created_in: "beta12orEarlier" def: "DAS sequence (XML) format (any type)." [http://edamontology.org] namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2552 ! Sequence record format (XML) [Term] id: EDAM_format:1968 name: dasdna comment: The use of this format is deprecated. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "DAS sequence (XML) format (nucleotide-only)." [http://edamontology.org] namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2552 ! Sequence record format (XML) [Term] id: EDAM_format:1969 name: debug-seq subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "EMBOSS debugging trace sequence format of full internal data content." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1970 name: jackknifernon subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Jackknifer output sequence non-interleaved format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) [Term] id: EDAM_format:1971 name: meganon sequence format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Mega non-interleaved output sequence format." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1992 ! meganon [Term] id: EDAM_format:1972 name: NCBI format comment: There are several variants of this. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "NCBI FASTA sequence format with NCBI-style IDs." [http://edamontology.org] namespace: format is_a: EDAM_format:2200 ! FASTA-like (text) [Term] id: EDAM_format:1973 name: nexusnon subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Nexus/paup non-interleaved sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1974 name: GFF2 subset: bioinformatics subset: edam subset: formats xref: http://www.sanger.ac.uk/resources/software/gff/spec.html created_in: "beta12orEarlier" def: "General Feature Format (GFF) of sequence features." [http://edamontology.org] documentation: http://www.sanger.ac.uk/resources/software/gff/spec.html namespace: format is_a: EDAM_format:2305 ! GFF [Term] id: EDAM_format:1975 name: GFF3 subset: bioinformatics subset: edam subset: formats xref: http://sequenceontology.org/resources/gff3.html created_in: "beta12orEarlier" def: "Generic Feature Format version 3 (GFF3) of sequence features." [http://edamontology.org] documentation: http://sequenceontology.org/resources/gff3.html namespace: format is_a: EDAM_format:2305 ! GFF [Term] id: EDAM_format:1976 name: pir subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "PIR feature format." [http://edamontology.org] namespace: format is_a: EDAM_format:2206 ! Sequence feature table format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1977 name: swiss feature subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Swiss-Prot feature format." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1963 ! UniProtKB format [Term] id: EDAM_format:1978 name: DASGFF subset: bioinformatics subset: edam subset: formats synonym: "das feature" EXACT [] synonym: "DASGFF feature" EXACT [] created_in: "beta12orEarlier" def: "DAS GFF (XML) feature format." [http://edamontology.org] namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2553 ! Sequence feature table format (XML) [Term] id: EDAM_format:1979 name: debug-feat subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "EMBOSS debugging trace feature format of full internal data content." [http://edamontology.org] namespace: format is_a: EDAM_format:1920 ! Sequence feature annotation format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:1980 name: EMBL feature subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "EMBL feature format." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1927 ! EMBL format [Term] id: EDAM_format:1981 name: GenBank feature subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Genbank feature format." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1936 ! GenBank format [Term] id: EDAM_format:1982 name: ClustalW format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "ClustalW format for (aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1983 name: debug subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "EMBOSS alignment format for debugging trace of full internal data content." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1984 name: FASTA-aln subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Fasta format for (aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2200 ! FASTA-like (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1985 name: markx0 subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Pearson MARKX0 alignment format." [http://edamontology.org] namespace: format is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1986 name: markx1 subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Pearson MARKX1 alignment format." [http://edamontology.org] namespace: format is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1987 name: markx10 subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Pearson MARKX10 alignment format." [http://edamontology.org] namespace: format is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1988 name: markx2 subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Pearson MARKX2 alignment format." [http://edamontology.org] namespace: format is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1989 name: markx3 subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Pearson MARKX3 alignment format." [http://edamontology.org] namespace: format is_a: EDAM_format:2922 ! markx0 variant [Term] id: EDAM_format:1990 name: match subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alignment format for start and end of matches between sequence pairs." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1991 name: mega subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Mega format for (typically aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2923 ! mega variant [Term] id: EDAM_format:1992 name: meganon subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Mega non-interleaved format for (typically aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2923 ! mega variant [Term] id: EDAM_format:1993 name: msf alignment format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "MSF format for (aligned) sequences." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1947 ! msf [Term] id: EDAM_format:1994 name: nexus alignment format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Nexus/paup format for (aligned) sequences." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1949 ! nexus-seq [Term] id: EDAM_format:1995 name: nexusnon alignment format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Nexus/paup non-interleaved format for (aligned) sequences." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:1973 ! nexusnon [Term] id: EDAM_format:1996 name: pair subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "EMBOSS simple sequence pair alignment format." [http://edamontology.org] namespace: format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:1997 name: Phylip format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Phylip format for (aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2924 ! Phylip format variant [Term] id: EDAM_format:1998 name: Phylipnon subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Phylip non-interleaved format for (aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2924 ! Phylip format variant [Term] id: EDAM_format:1999 name: scores format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alignment format for score values for pairs of sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:2000 name: selex subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "SELEX format for (aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:2001 name: EMBOSS simple format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "EMBOSS simple multiple alignment format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:2002 name: srs format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Simple multiple sequence (alignment) format for SRS." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:2003 name: srspair subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Simple sequence pair (alignment) format for SRS." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] id: EDAM_format:2004 name: T-Coffee format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "T-Coffee program alignment format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:2005 name: TreeCon-seq subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Treecon format for (aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:2006 name: Phylogenetic tree format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a phylogenetic tree." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0872 ! Phylogenetic tree [Term] id: EDAM_format:2013 name: Biological pathway or network format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a biological pathway or network." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2600 ! Pathway or network [Term] id: EDAM_format:2014 name: Sequence-profile alignment format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a sequence-profile alignment." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_format:2015 name: Sequence-profile alignment (HMM) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a sequence-HMM profile alignment." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2014 ! Sequence-profile alignment format [Term] id: EDAM_format:2017 name: Amino acid index format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for an amino acid index." [http://edamontology.org] namespace: format is_a: EDAM_format:3033 ! Matrix format relationship: is_format_of EDAM_data:1501 ! Amino acid index [Term] id: EDAM_format:2020 name: Article format subset: bioinformatics subset: edam subset: formats synonym: "Literature format" EXACT [] created_in: "beta12orEarlier" def: "Data format for a full-text scientific article." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0971 ! Article [Term] id: EDAM_format:2021 name: Text mining report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for an abstract (report) from text mining." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0972 ! Text mining report [Term] id: EDAM_format:2027 name: Enzyme kinetics report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for reports on enzyme kinetics." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2024 ! Enzyme kinetics data [Term] id: EDAM_format:2030 name: Small molecule report format subset: bioinformatics subset: edam subset: formats synonym: "Chemical compound annotation format" EXACT [] created_in: "beta12orEarlier" def: "Format of a report on a chemical compound." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0962 ! Small molecule annotation [Term] id: EDAM_format:2031 name: Gene annotation format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0916 ! Gene annotation [Term] id: EDAM_format:2032 name: Workflow format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a workflow." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2972 ! Workflow [Term] id: EDAM_format:2033 name: Tertiary structure format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a molecular tertiary structure." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:2034 name: Biological model format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a biological model." [http://edamontology.org] namespace: format obsolete_since: "1.2" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2013 ! Biological pathway or network format [Term] id: EDAM_format:2035 name: Chemical formula format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Text format of a chemical formula." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0846 ! Chemical formula [Term] id: EDAM_format:2036 name: Phylogenetic character data format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of raw (unplotted) phylogenetic data." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0871 ! Phylogenetic character data [Term] id: EDAM_format:2037 name: Phylogenetic continuous quantitative character format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of phylogenetic continuous quantitative character data." [http://edamontology.org] namespace: format is_a: EDAM_format:2036 ! Phylogenetic character data format relationship: is_format_of EDAM_data:1426 ! Phylogenetic continuous quantitative data [Term] id: EDAM_format:2038 name: Phylogenetic discrete states format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of phylogenetic discrete states data." [http://edamontology.org] namespace: format is_a: EDAM_format:2036 ! Phylogenetic character data format relationship: is_format_of EDAM_data:1427 ! Phylogenetic discrete data [Term] id: EDAM_format:2039 name: Phylogenetic tree report (cliques) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of phylogenetic cliques data." [http://edamontology.org] namespace: format is_a: EDAM_format:2036 ! Phylogenetic character data format relationship: is_format_of EDAM_data:1428 ! Phylogenetic character cliques [Term] id: EDAM_format:2040 name: Phylogenetic tree report (invariants) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of phylogenetic invariants data." [http://edamontology.org] namespace: format is_a: EDAM_format:2036 ! Phylogenetic character data format relationship: is_format_of EDAM_data:1429 ! Phylogenetic invariants [Term] id: EDAM_format:2045 name: Electron microscopy model format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Annotation format for electron microscopy models." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:2049 name: Phylogenetic tree report (tree distances) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for phylogenetic tree distance data." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1442 ! Phylogenetic tree report (tree distances) [Term] id: EDAM_format:2051 name: Polymorphism report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for sequence polymorphism data." [http://edamontology.org] namespace: format obsolete_since: "1.0" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_format:2052 name: Protein family report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for reports on a protein family." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0907 ! Protein family [Term] id: EDAM_format:2054 name: Molecular interaction format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for molecular interaction data." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2599 ! Molecular interaction [Term] id: EDAM_format:2055 name: Sequence assembly format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for sequence assembly data." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0925 ! Sequence assembly [Term] id: EDAM_format:2056 name: Microarray experiment data format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for microarray experimental data." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_format:2057 name: Sequence trace format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for sequence trace data (i.e. including base call information)." [http://edamontology.org] namespace: format is_a: EDAM_format:1919 ! Sequence record format relationship: is_format_of EDAM_data:0924 ! Sequence trace [Term] id: EDAM_format:2058 name: Gene expression report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for a report on gene expression." [http://edamontology.org] namespace: format is_a: EDAM_format:2031 ! Gene annotation format relationship: is_format_of EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_format:2059 name: Genotype and phenotype annotation format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on genotype / phenotype information." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:2060 name: Map format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a map of (typically one) molecular sequence annotated with features." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1274 ! Map [Term] id: EDAM_format:2061 name: Nucleic acid features (primers) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0922 ! Nucleic acid features (primers) [Term] id: EDAM_format:2062 name: Protein report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report of general information about a specific protein." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0896 ! Protein report [Term] id: EDAM_format:2063 name: Protein report (enzyme) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report of general information about a specific enzyme." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:2064 name: 3D-1D scoring matrix format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [http://edamontology.org] namespace: format is_a: EDAM_format:3033 ! Matrix format relationship: is_format_of EDAM_data:1499 ! 3D-1D scoring matrix [Term] id: EDAM_format:2065 name: Protein structure report (quality evaluation) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on the quality of a protein three-dimensional model." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1539 ! Protein structural quality report [Term] id: EDAM_format:2066 name: Database hits (sequence) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on sequence hits and associated data from searching a sequence database." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0857 ! Database hits (sequence) [Term] id: EDAM_format:2067 name: Sequence distance matrix format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a matrix of genetic distances between molecular sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0870 ! Sequence distance matrix [Term] id: EDAM_format:2068 name: Sequence motif format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a sequence motif." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1353 ! Sequence motif [Term] id: EDAM_format:2069 name: Sequence profile format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a sequence profile." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1354 ! Sequence profile [Term] id: EDAM_format:2072 name: Hidden Markov model format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a hidden Markov model." [http://edamontology.org] namespace: format is_a: EDAM_format:2069 ! Sequence profile format relationship: is_format_of EDAM_data:1364 ! Hidden Markov model [Term] id: EDAM_format:2074 name: Dirichlet distribution format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format of a dirichlet distribution." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1347 ! Dirichlet distribution [Term] id: EDAM_format:2075 name: HMM emission and transition counts format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for the emission and transition counts of a hidden Markov model." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1348 ! HMM emission and transition counts [Term] id: EDAM_format:2076 name: RNA secondary structure format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0880 ! RNA secondary structure record [Term] id: EDAM_format:2077 name: Protein secondary structure format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for secondary structure (predicted or real) of a protein molecule." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0876 ! Protein features (secondary structure) [Term] id: EDAM_format:2078 name: Sequence range format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used to specify range(s) of sequence positions." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1017 ! Sequence range [Term] id: EDAM_format:2094 name: pure subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for molecular sequence with possible unknown positions but without non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:2095 name: unpure subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:2096 name: unambiguous sequence subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:2097 name: ambiguous subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:2155 name: Sequence features (repeats) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used for map of repeats in molecular (typically nucleotide) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1299 ! Sequence features (repeats) [Term] id: EDAM_format:2158 name: Nucleic acid features (restriction sites) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used for report on restriction enzyme recognition sites in nucleotide sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1305 ! Nucleic acid features (restriction sites) [Term] id: EDAM_format:2159 name: Gene features (coding region) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used for report on coding regions in nucleotide sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2031 ! Gene annotation format relationship: is_format_of EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] id: EDAM_format:2170 name: Sequence cluster format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used for clusters of molecular sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_format:2171 name: Sequence cluster format (protein) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used for clusters of protein sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2170 ! Sequence cluster format [Term] id: EDAM_format:2172 name: Sequence cluster format (nucleic acid) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used for clusters of nucleotide sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2170 ! Sequence cluster format [Term] id: EDAM_format:2175 name: Gene cluster format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used for clusters of genes." [http://edamontology.org] namespace: format obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2172 ! Sequence cluster format (nucleic acid) [Term] id: EDAM_format:2181 name: EMBL-like (text) comment: This concept may be used for the many non-standard EMBL-like text formats. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A text format resembling EMBL entry format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2543 ! EMBL-like format [Term] id: EDAM_format:2182 name: FASTQ-like format (text) comment: This concept may be used for non-standard FASTQ short read-like formats. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A text format resembling FASTQ short read format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2545 ! FASTQ-like format [Term] id: EDAM_format:2183 name: EMBLXML subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "XML format for EMBL entries." [http://edamontology.org] namespace: format is_a: EDAM_format:2204 ! EMBL format (XML) [Term] id: EDAM_format:2184 name: cdsxml subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "XML format for EMBL entries." [http://edamontology.org] namespace: format is_a: EDAM_format:2204 ! EMBL format (XML) [Term] id: EDAM_format:2185 name: insdxml subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "XML format for EMBL entries." [http://edamontology.org] namespace: format is_a: EDAM_format:2204 ! EMBL format (XML) [Term] id: EDAM_format:2186 name: geneseq subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Geneseq sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2181 ! EMBL-like (text) [Term] id: EDAM_format:2187 name: UniProt-like (text) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A text sequence format resembling uniprotkb entry format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2547 ! uniprotkb-like format [Term] id: EDAM_format:2188 name: UniProt format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "UniProt entry sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2187 ! UniProt-like (text) [Term] id: EDAM_format:2189 name: ipi subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "ipi sequence format." [http://edamontology.org] namespace: format is_a: EDAM_format:2187 ! UniProt-like (text) [Term] id: EDAM_format:2194 name: medline subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Abstract format used by MedLine database." [http://edamontology.org] namespace: format is_a: EDAM_format:2020 ! Article format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2195 name: Ontology format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format used for ontologies." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0582 ! Ontology [Term] id: EDAM_format:2196 name: OBO format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A serialisation format conforming to the Open Biomedical Ontologies (OBO) model." [http://edamontology.org] namespace: format is_a: EDAM_format:2195 ! Ontology format [Term] id: EDAM_format:2197 name: OWL format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A serialisation format conforming to the Web Ontology Language (OWL) model." [http://edamontology.org] namespace: format is_a: EDAM_format:2195 ! Ontology format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2200 name: FASTA-like (text) comment: This concept may also be used for the many non-standard FASTA-like formats. subset: bioinformatics subset: edam subset: formats synonym: "http://filext.com/file-extension/FASTA" NARROW [] created_in: "beta12orEarlier" def: "A text format resembling FASTA format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2546 ! FASTA-like [Term] id: EDAM_format:2202 name: Sequence record full format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org] namespace: format is_a: EDAM_format:1919 ! Sequence record format relationship: is_format_of EDAM_data:2201 ! Sequence record full [Term] id: EDAM_format:2203 name: Sequence record lite format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: format is_a: EDAM_format:1919 ! Sequence record format relationship: is_format_of EDAM_data:2043 ! Sequence record lite [Term] id: EDAM_format:2204 name: EMBL format (XML) comment: This is a placeholder for other more specific concepts. It should not normally be used for annotation. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "An XML format for EMBL entries." [http://edamontology.org] namespace: format is_a: EDAM_format:2558 ! EMBL-like (XML) [Term] id: EDAM_format:2205 name: GenBank-like format (text) comment: This concept may be used for the non-standard GenBank-like text formats. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A text format resembling GenBank entry (plain text) format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2559 ! GenBank-like format [Term] id: EDAM_format:2206 name: Sequence feature table format (text) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Text format for a sequence feature table." [http://edamontology.org] namespace: format is_a: EDAM_format:2548 ! Sequence feature table format [Term] id: EDAM_format:2210 name: Strain data format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on organism strain data / cell line." [http://edamontology.org] namespace: format obsolete_since: "1.0" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_format:2211 name: CIP strain data format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for a report of strain data as used for CIP database entries." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2243 name: phylip property values subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "PHYLIP file format for phylogenetic property data." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2036 ! Phylogenetic character data format [Term] id: EDAM_format:2303 name: STRING entry format (HTML) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format (HTML) for the STRING database of protein interaction." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2304 name: STRING entry format (XML) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format (XML) for the STRING database of protein interaction." [http://edamontology.org] namespace: format is_a: EDAM_format:2054 ! Molecular interaction format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2305 name: GFF subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "GFF feature format (of indeterminate version)." [http://edamontology.org] namespace: format is_a: EDAM_format:2206 ! Sequence feature table format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2306 name: GTF subset: bioinformatics subset: edam subset: formats xref: format4 xref: http://mblab.wustl.edu/GTF22.html created_in: "beta12orEarlier" def: "Gene Transfer Format (GTF), a restricted version of GFF." [http://edamontology.org] documentation: http://mblab.wustl.edu/GTF22.html namespace: format is_a: EDAM_format:2305 ! GFF [Term] id: EDAM_format:2310 name: FASTA-HTML subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "FASTA format wrapped in HTML elements." [http://edamontology.org] namespace: format is_a: EDAM_format:2331 ! HTML is_a: EDAM_format:2546 ! FASTA-like [Term] id: EDAM_format:2311 name: EMBL-HTML subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "EMBL entry format wrapped in HTML elements." [http://edamontology.org] namespace: format is_a: EDAM_format:2331 ! HTML is_a: EDAM_format:2543 ! EMBL-like format [Term] id: EDAM_format:2322 name: BioCyc enzyme report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the BioCyc enzyme database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2323 name: ENZYME enzyme report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of an entry from the Enzyme nomenclature database (ENZYME)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2328 name: PseudoCAP gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on a gene from the PseudoCAP database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2329 name: GeneCards gene report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on a gene from the GeneCards database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2330 name: Textual format comment: Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). subset: bioinformatics subset: edam subset: formats synonym: "http://filext.com/file-extension/TSV" NARROW [] synonym: "http://filext.com/file-extension/TXT" NARROW [] synonym: "Plain text" NARROW [] synonym: "Tabular format" NARROW [] created_in: "beta12orEarlier" def: "Textual format." [http://edamontology.org] namespace: format is_a: EDAM_format:1915 ! Format [Term] id: EDAM_format:2331 name: HTML subset: bioinformatics subset: edam subset: formats synonym: "http://filext.com/file-extension/HTML" EXACT [] synonym: "Hypertext Markup Language" EXACT [] created_in: "beta12orEarlier" def: "HTML format." [http://edamontology.org] namespace: format is_a: EDAM_format:1915 ! Format relationship: is_format_of EDAM_data:2048 ! Report [Term] id: EDAM_format:2332 name: XML comment: Data in XML format can be serialised into text, or binary format. subset: bioinformatics subset: edam subset: formats synonym: "Extensible Markup Language" EXACT [] synonym: "http://filext.com/file-extension/XML" EXACT [] created_in: "beta12orEarlier" def: "eXtensible Markup Language (XML) format." [http://edamontology.org] namespace: format is_a: EDAM_format:1915 ! Format [Term] id: EDAM_format:2333 name: Binary format comment: Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Binary format." [http://edamontology.org] namespace: format is_a: EDAM_format:1915 ! Format [Term] id: EDAM_format:2334 name: URI format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Typical textual representation of a URI." [http://edamontology.org] namespace: format obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:1047 ! URI [Term] id: EDAM_format:2341 name: NCI-Nature pathway entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "The format of an entry from the NCI-Nature pathways database." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2350 name: Format (typed) comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A broad class of format distinguished by the scientific nature of the data that is identified." [http://edamontology.org] namespace: format is_a: EDAM_format:1915 ! Format [Term] id: EDAM_format:2352 name: BioXSD subset: bioinformatics subset: edam subset: formats synonym: "BioXSD XML format" EXACT [] xref: http://bioxsd.org created_in: "beta12orEarlier" def: "BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more)." [http://edamontology.org] documentation: http://bioxsd.org namespace: format is_a: EDAM_format:1919 ! Sequence record format is_a: EDAM_format:1920 ! Sequence feature annotation format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2555 ! Alignment format (XML) is_a: EDAM_format:2571 ! Raw sequence format relationship: is_format_of EDAM_data:0863 ! Sequence alignment relationship: is_format_of EDAM_data:1255 ! Feature record relationship: is_format_of EDAM_data:2044 ! Sequence [Term] id: EDAM_format:2376 name: RDF format subset: bioinformatics subset: edam subset: formats synonym: "SWO:3000006" EXACT [] created_in: "beta12orEarlier" def: "A serialisation format conforming to the Resource Description Framework (RDF) model." [http://edamontology.org] namespace: format is_a: EDAM_format:2195 ! Ontology format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2532 name: GenBank-HTML subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Genbank entry format wrapped in HTML elements." [http://edamontology.org] namespace: format is_a: EDAM_format:2331 ! HTML is_a: EDAM_format:2559 ! GenBank-like format [Term] id: EDAM_format:2542 name: Protein features (domains) format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a report on protein features (domain composition)." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:2543 name: EMBL-like format comment: This concept may be used for the many non-standard EMBL-like formats. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A format resembling EMBL entry (plain text) format." [http://edamontology.org] namespace: format is_a: EDAM_format:2202 ! Sequence record full format [Term] id: EDAM_format:2545 name: FASTQ-like format comment: This concept may be used for non-standard FASTQ short read-like formats. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A format resembling FASTQ short read format." [http://edamontology.org] namespace: format is_a: EDAM_format:2057 ! Sequence trace format [Term] id: EDAM_format:2546 name: FASTA-like comment: This concept may be used for the many non-standard FASTA-like formats. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A format resembling FASTA format." [http://edamontology.org] namespace: format is_a: EDAM_format:2203 ! Sequence record lite format [Term] id: EDAM_format:2547 name: uniprotkb-like format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A sequence format resembling uniprotkb entry format." [http://edamontology.org] namespace: format is_a: EDAM_format:2202 ! Sequence record full format is_a: EDAM_format:2206 ! Sequence feature table format (text) [Term] id: EDAM_format:2548 name: Sequence feature table format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format for a sequence feature table." [http://edamontology.org] namespace: format is_a: EDAM_format:1920 ! Sequence feature annotation format relationship: is_format_of EDAM_data:1255 ! Feature record [Term] id: EDAM_format:2549 name: OBO subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "OBO ontology text format." [http://edamontology.org] namespace: format is_a: EDAM_format:2196 ! OBO format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:2550 name: OBO-XML subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "OBO ontology XML format." [http://edamontology.org] namespace: format is_a: EDAM_format:2196 ! OBO format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2551 name: Sequence record format (text) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a molecular sequence record." [http://edamontology.org] namespace: format is_a: EDAM_format:1919 ! Sequence record format [Term] id: EDAM_format:2552 name: Sequence record format (XML) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a molecular sequence record." [http://edamontology.org] namespace: format is_a: EDAM_format:1919 ! Sequence record format [Term] id: EDAM_format:2553 name: Sequence feature table format (XML) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "XML format for a sequence feature table." [http://edamontology.org] namespace: format is_a: EDAM_format:2548 ! Sequence feature table format [Term] id: EDAM_format:2554 name: Alignment format (text) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Text format for molecular sequence alignment information." [http://edamontology.org] namespace: format is_a: EDAM_format:1921 ! Alignment format [Term] id: EDAM_format:2555 name: Alignment format (XML) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "XML format for molecular sequence alignment information." [http://edamontology.org] namespace: format is_a: EDAM_format:1921 ! Alignment format [Term] id: EDAM_format:2556 name: Phylogenetic tree format (text) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Text format for a phylogenetic tree." [http://edamontology.org] namespace: format is_a: EDAM_format:2006 ! Phylogenetic tree format [Term] id: EDAM_format:2557 name: Phylogenetic tree format (XML) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "XML format for a phylogenetic tree." [http://edamontology.org] namespace: format is_a: EDAM_format:2006 ! Phylogenetic tree format [Term] id: EDAM_format:2558 name: EMBL-like (XML) comment: This concept may be used for the any non-standard EMBL-like XML formats. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "An XML format resembling EMBL entry format." [http://edamontology.org] namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2543 ! EMBL-like format [Term] id: EDAM_format:2559 name: GenBank-like format comment: This concept may be used for the non-standard GenBank-like formats. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "A format resembling GenBank entry (plain text) format." [http://edamontology.org] namespace: format is_a: EDAM_format:2202 ! Sequence record full format [Term] id: EDAM_format:2560 name: STRING entry format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Entry format for the STRING database of protein interaction." [http://edamontology.org] namespace: format obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_format:2331 ! HTML [Term] id: EDAM_format:2561 name: Sequence assembly format (text) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Text format for sequence assembly data." [http://edamontology.org] namespace: format is_a: EDAM_format:2055 ! Sequence assembly format [Term] id: EDAM_format:2562 name: Amino acid identifier format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Text format (representation) of amino acid residues." [http://edamontology.org] namespace: format obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_data:0994 ! Amino acid identifier [Term] id: EDAM_format:2566 name: completely unambiguous subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a molecular sequence without any unknown positions or ambiguity characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:2567 name: completely unambiguous pure subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:2094 ! pure is_a: EDAM_format:2566 ! completely unambiguous [Term] id: EDAM_format:2568 name: completely unambiguous pure nucleotide subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters ." [http://edamontology.org] namespace: format is_a: EDAM_format:1207 ! nucleotide is_a: EDAM_format:2567 ! completely unambiguous pure [Term] id: EDAM_format:2569 name: completely unambiguous pure dna subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1212 ! dna is_a: EDAM_format:2567 ! completely unambiguous pure [Term] id: EDAM_format:2570 name: completely unambiguous pure rna sequence subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1213 ! rna is_a: EDAM_format:2567 ! completely unambiguous pure [Term] id: EDAM_format:2571 name: Raw sequence format subset: bioinformatics subset: edam subset: formats synonym: "Symbol_sequence" RELATED [] created_in: "beta12orEarlier" def: "Format of a raw molecular sequence (i.e. the alphabet used)." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0848 ! Raw sequence [Term] id: EDAM_format:2572 name: BAM subset: bioinformatics subset: edam subset: formats xref: http://samtools.sourceforge.net/SAM-1.3.pdf created_in: "beta12orEarlier" 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." [http://edamontology.org] documentation: http://samtools.sourceforge.net/SAM-1.3.pdf namespace: format is_a: EDAM_format:1921 ! Alignment format is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:2573 name: SAM 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: bioinformatics subset: edam subset: formats xref: http://samtools.sourceforge.net/SAM-1.3.pdf created_in: "beta12orEarlier" 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." [http://edamontology.org] documentation: http://samtools.sourceforge.net/SAM-1.3.pdf namespace: format is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] id: EDAM_format:2585 name: SBML subset: bioinformatics subset: edam subset: formats xref: http://sbml.org created_in: "beta12orEarlier" def: "Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation." [http://edamontology.org] documentation: http://sbml.org namespace: format is_a: EDAM_format:2013 ! Biological pathway or network format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:2607 name: completely unambiguous pure protein subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org] namespace: format is_a: EDAM_format:1208 ! protein is_a: EDAM_format:2567 ! completely unambiguous pure [Term] id: EDAM_format:2848 name: Bibliographic reference format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a bibliographic reference." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0970 ! Bibliographic reference relationship: is_format_of EDAM_data:2849 ! Abstract [Term] id: EDAM_format:2919 name: Sequence annotation track format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of a sequence annotation track." [http://edamontology.org] namespace: format is_a: EDAM_format:1920 ! Sequence feature annotation format relationship: is_format_of EDAM_data:3002 ! Sequence annotation track [Term] id: EDAM_format:2920 name: Alignment format (pair only) subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:1921 ! Alignment format relationship: is_format_of EDAM_data:1381 ! Sequence alignment (pair) [Term] id: EDAM_format:2921 name: Sequence variation annotation format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Format of sequence variation annotation." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0918 ! Nucleic acid features (variation) [Term] id: EDAM_format:2922 name: markx0 variant subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Some variant of Pearson MARKX alignment format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:2923 name: mega variant subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Some variant of Mega format for (typically aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:2924 name: Phylip format variant subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Some variant of Phylip format for (aligned) sequences." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2551 ! Sequence record format (text) is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_format:3000 name: AB1 comment: AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" 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://edamontology.org] namespace: format is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:3001 name: ACE subset: bioinformatics subset: edam subset: formats xref: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt created_in: "beta12orEarlier" def: "ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards)." [http://edamontology.org] documentation: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt namespace: format is_a: EDAM_format:2055 ! Sequence assembly format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3003 name: BED 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: bioinformatics subset: edam subset: formats xref: format1 created_in: "beta12orEarlier" def: "Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser." [http://edamontology.org] documentation: "format1" namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2919 ! Sequence annotation track format [Term] id: EDAM_format:3004 name: bigBed subset: bioinformatics subset: edam subset: formats xref: format1.5 created_in: "beta12orEarlier" def: "bigBed format for large sequence annotation tracks, similar to textual BED format." [http://edamontology.org] documentation: "format1.5" namespace: format is_a: EDAM_format:2333 ! Binary format is_a: EDAM_format:2919 ! Sequence annotation track format [Term] id: EDAM_format:3005 name: WIG subset: bioinformatics subset: edam subset: formats xref: http://genome.ucsc.edu/goldenPath/help/wiggle.html created_in: "beta12orEarlier" 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." [http://edamontology.org] documentation: http://genome.ucsc.edu/goldenPath/help/wiggle.html namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2919 ! Sequence annotation track format [Term] id: EDAM_format:3006 name: bigWig subset: bioinformatics subset: edam subset: formats xref: format6.1 created_in: "beta12orEarlier" def: "bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format." [http://edamontology.org] documentation: "format6.1" namespace: format is_a: EDAM_format:2333 ! Binary format is_a: EDAM_format:2919 ! Sequence annotation track format [Term] id: EDAM_format:3007 name: PSL subset: bioinformatics subset: edam subset: formats xref: format2 created_in: "beta12orEarlier" def: "PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track." [http://edamontology.org] documentation: "format2" namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2919 ! Sequence annotation track format is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] id: EDAM_format:3008 name: MAF 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: bioinformatics subset: edam subset: formats xref: format5 created_in: "beta12orEarlier" def: "Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth." [http://edamontology.org] documentation: "format5" namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2919 ! Sequence annotation track format [Term] id: EDAM_format:3009 name: 2bit subset: bioinformatics subset: edam subset: formats xref: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD xref: http://jcomeau.freeshell.org/www/genome/2bitformat.html created_in: "beta12orEarlier" def: "2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'." [http://edamontology.org] documentation: http://jcomeau.freeshell.org/www/genome/2bitformat.html namespace: format is_a: EDAM_format:2333 ! Binary format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:3010 name: .nib subset: bioinformatics subset: edam subset: formats xref: format8 created_in: "beta12orEarlier" def: ".nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'." [http://edamontology.org] documentation: "format8" namespace: format is_a: EDAM_format:2333 ! Binary format is_a: EDAM_format:2571 ! Raw sequence format [Term] id: EDAM_format:3011 name: genePred 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: bioinformatics subset: edam subset: formats xref: format9 created_in: "beta12orEarlier" def: "genePred table format for gene prediction tracks." [http://edamontology.org] documentation: "format9" namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2919 ! Sequence annotation track format [Term] id: EDAM_format:3012 name: pgSnp subset: bioinformatics subset: edam subset: formats xref: format10 created_in: "beta12orEarlier" def: "Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser." [http://edamontology.org] documentation: "format10" namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2919 ! Sequence annotation track format [Term] id: EDAM_format:3013 name: axt subset: bioinformatics subset: edam subset: formats xref: http://genome.ucsc.edu/goldenPath/help/axt.html created_in: "beta12orEarlier" def: "axt format of alignments, typically produced from BLASTZ." [http://edamontology.org] documentation: http://genome.ucsc.edu/goldenPath/help/axt.html namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] id: EDAM_format:3014 name: LAV subset: bioinformatics subset: edam subset: formats xref: lav:format.html created_in: "beta12orEarlier" def: "LAV format of alignments generated by BLASTZ and LASTZ." [http://edamontology.org] documentation: lav:format.html namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] id: EDAM_format:3015 name: Pileup subset: bioinformatics subset: edam subset: formats xref: http://samtools.sourceforge.net/pileup.shtml created_in: "beta12orEarlier" 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)." [http://edamontology.org] documentation: http://samtools.sourceforge.net/pileup.shtml namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] id: EDAM_format:3016 name: VCF subset: bioinformatics subset: edam subset: formats xref: http://vcftools.sourceforge.net/specs.html created_in: "beta12orEarlier" def: "Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org] documentation: http://vcftools.sourceforge.net/specs.html namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2921 ! Sequence variation annotation format [Term] id: EDAM_format:3017 name: SRF subset: bioinformatics subset: edam subset: formats xref: http://srf.sourceforge.net/ created_in: "beta12orEarlier" def: "Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive." [http://edamontology.org] documentation: http://srf.sourceforge.net/ namespace: format is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:3018 name: ZTR subset: bioinformatics subset: edam subset: formats xref: http://staden.sourceforge.net/manual/formats_unix_12.html created_in: "beta12orEarlier" def: "ZTR format for storing chromatogram data from DNA sequencing instruments." [http://edamontology.org] documentation: http://staden.sourceforge.net/manual/formats_unix_12.html namespace: format is_a: EDAM_format:2057 ! Sequence trace format is_a: EDAM_format:2333 ! Binary format [Term] id: EDAM_format:3019 name: GVF subset: bioinformatics subset: edam subset: formats xref: http://sequenceontology.org/gvf.html created_in: "beta12orEarlier" def: "Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation." [http://edamontology.org] documentation: http://sequenceontology.org/gvf.html namespace: format is_a: EDAM_format:1975 ! GFF3 is_a: EDAM_format:2921 ! Sequence variation annotation format [Term] id: EDAM_format:3020 name: BCF subset: bioinformatics subset: edam subset: formats xref: http://samtools.sourceforge.net/mpileup.shtml created_in: "beta12orEarlier" def: "BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org] namespace: format is_a: EDAM_format:2333 ! Binary format is_a: EDAM_format:2921 ! Sequence variation annotation format [Term] id: EDAM_format:3033 name: Matrix format subset: bioinformatics subset: edam subset: formats created_in: "beta13" def: "Format of a matrix (array) of numerical values." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2082 ! Matrix [Term] id: EDAM_format:3097 name: Protein domain classification format subset: bioinformatics subset: edam subset: formats created_in: "beta13" def: "Format of data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0900 ! Protein domain classification [Term] id: EDAM_format:3098 name: Raw SCOP domain classification format comment: These are the parsable data files provided by SCOP. subset: bioinformatics subset: edam subset: formats created_in: "beta13" def: "Format of raw SCOP domain classification data files." [http://edamontology.org] namespace: format is_a: EDAM_format:3097 ! Protein domain classification format [Term] id: EDAM_format:3099 name: Raw CATH domain classification format comment: These are the parsable data files provided by CATH. subset: bioinformatics subset: edam subset: formats created_in: "beta13" def: "Format of raw CATH domain classification data files." [http://edamontology.org] namespace: format is_a: EDAM_format:3097 ! Protein domain classification format [Term] id: EDAM_format:3100 name: CATH domain report format 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: bioinformatics subset: edam subset: formats created_in: "beta13" def: "Format of summary of domain classification information for a CATH domain." [http://edamontology.org] namespace: format is_a: EDAM_format:3097 ! Protein domain classification format [Term] id: EDAM_format:3155 name: SBRML subset: bioinformatics subset: edam subset: formats xref: http://www.comp-sys-bio.org/tiki-index.php?page=SBRML created_in: "1.0" def: "Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models." [http://edamontology.org] documentation: http://www.comp-sys-bio.org/tiki-index.php?page=SBRML namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:3166 ! Biological pathway or network report format [Term] id: EDAM_format:3156 name: BioPAX subset: bioinformatics subset: edam subset: formats xref: http://www.biopax.org created_in: "1.0" def: "BioPAX is an exchange format for pathway data, with its data model defined in OWL." [http://edamontology.org] documentation: http://www.biopax.org namespace: format is_a: EDAM_format:2013 ! Biological pathway or network format [Term] id: EDAM_format:3157 name: EBI Application Result XML subset: bioinformatics subset: edam subset: formats xref: http://www.ebi.ac.uk/schema/ApplicationResult.xsd created_in: "1.0" def: "EBI Application Result XML is a format returned by sequence similarity search Web services at EBI." [http://edamontology.org] documentation: http://www.ebi.ac.uk/schema/ApplicationResult.xsd namespace: format is_a: EDAM_format:2066 ! Database hits (sequence) format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2920 ! Alignment format (pair only) [Term] id: EDAM_format:3158 name: PSI MI XML (MIF) subset: bioinformatics subset: edam subset: formats synonym: "MIF" EXACT [] xref: http://www.psidev.info/mif created_in: "1.0" def: "XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI." [http://edamontology.org] documentation: http://www.psidev.info/mif namespace: format is_a: EDAM_format:2054 ! Molecular interaction format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3159 name: phyloXML subset: bioinformatics subset: edam subset: formats xref: http://www.phyloxml.org created_in: "1.0" def: "phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data." [http://edamontology.org] documentation: http://www.phyloxml.org namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2557 ! Phylogenetic tree format (XML) [Term] id: EDAM_format:3160 name: NeXML subset: bioinformatics subset: edam subset: formats xref: http://www.nexml.org created_in: "1.0" def: "NeXML is a standardised XML format for rich phyloinformatic data." [http://edamontology.org] documentation: http://www.nexml.org namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2557 ! Phylogenetic tree format (XML) [Term] id: EDAM_format:3161 name: MAGE-ML subset: bioinformatics subset: edam subset: formats xref: http://www.mged.org/Workgroups/MAGE/mage-ml.html created_in: "1.0" def: "MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org] documentation: http://www.mged.org/Workgroups/MAGE/mage-ml.html namespace: format is_a: EDAM_format:2056 ! Microarray experiment data format is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3162 name: MAGE-TAB subset: bioinformatics subset: edam subset: formats xref: http://www.mged.org/mage-tab created_in: "1.0" def: "MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org] documentation: http://www.mged.org/mage-tab namespace: format is_a: EDAM_format:2056 ! Microarray experiment data format is_a: EDAM_format:2058 ! Gene expression report format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3163 name: GCDML subset: bioinformatics subset: edam subset: formats xref: http://gcdml.gensc.org created_in: "1.0" def: "GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC)." [http://edamontology.org] documentation: http://gcdml.gensc.org namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:3167 ! Experiment annotation format relationship: is_format_of EDAM_data:3165 ! Experiment annotation (sequencing) [Term] id: EDAM_format:3164 name: GTrack subset: bioinformatics subset: edam subset: formats xref: http://www.gtrack.no created_in: "1.0" def: "GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG)." [http://edamontology.org] documentation: http://www.gtrack.no namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2919 ! Sequence annotation track format [Term] id: EDAM_format:3166 name: Biological pathway or network report format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for a report of information derived from a biological pathway or network." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_format:3167 name: Experiment annotation format subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" def: "Data format for annotation on a laboratory experiment." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) [Term] id: EDAM_format:3235 name: Cytoband format comment: Reflects a UCSC Browser DB table. subset: bioinformatics subset: edam subset: formats xref: http://www.broadinstitute.org/software/igv/Cytoband created_in: "1.2" def: "Cytoband format for chromosome cytobands." [http://edamontology.org] documentation: http://www.broadinstitute.org/software/igv/Cytoband namespace: format is_a: EDAM_format:2078 ! Sequence range format is_a: EDAM_format:2330 ! Textual format relationship: is_format_of EDAM_data:3236 ! Cytoband position [Term] id: EDAM_format:3239 name: CopasiML subset: bioinformatics subset: edam subset: formats xref: http://www.copasi.org/tiki-index.php?page_ref_id=128 created_in: "1.2" def: "CopasiML, the native format of COPASI." [http://edamontology.org] documentation: http://www.copasi.org/tiki-index.php?page_ref_id=128 namespace: format is_a: EDAM_format:2013 ! Biological pathway or network format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:3166 ! Biological pathway or network report format [Term] id: EDAM_format:3240 name: CellML subset: bioinformatics subset: edam subset: formats xref: http://www.cellml.org created_in: "1.2" def: "CellML, the format for mathematical models of biological and other networks." [http://edamontology.org] documentation: http://www.cellml.org namespace: format is_a: EDAM_format:2013 ! Biological pathway or network format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_format:3242 name: PSI MI TAB (MITAB) subset: bioinformatics subset: edam subset: formats xref: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README created_in: "1.2" def: "Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI." [http://edamontology.org] documentation: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README namespace: format is_a: EDAM_format:2054 ! Molecular interaction format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3243 name: PSI-PAR subset: bioinformatics subset: edam subset: formats xref: http://www.psidev.info/psi-par created_in: "1.2" def: "Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema." [http://edamontology.org] documentation: http://www.psidev.info/psi-par namespace: format is_a: EDAM_format:3158 ! PSI MI XML (MIF) [Term] id: EDAM_format:3244 name: mzML comment: mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. subset: bioinformatics subset: edam subset: formats xref: http://psidev.info/mzml created_in: "1.2" def: "mzML format for raw spectrometer output data, standardised by HUPO PSI MSS." [http://edamontology.org] documentation: http://psidev.info/mzml namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:3245 ! Mass spectrometry data format [Term] id: EDAM_format:3245 name: Mass spectrometry data format subset: bioinformatics subset: edam subset: formats created_in: "1.2" def: "Format for mass spectrometry data." [http://edamontology.org] namespace: format is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:2536 ! Mass spectrometry data [Term] id: EDAM_format:3246 name: TraML subset: bioinformatics subset: edam subset: formats xref: http://psidev.info/traml created_in: "1.2" def: "TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS." [http://edamontology.org] documentation: http://psidev.info/traml namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:3245 ! Mass spectrometry data format [Term] id: EDAM_format:3247 name: mzIdentML subset: bioinformatics subset: edam subset: formats xref: http://psidev.info/mzidentml created_in: "1.2" def: "mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines." [http://edamontology.org] documentation: http://psidev.info/mzidentml namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:3245 ! Mass spectrometry data format [Term] id: EDAM_format:3248 name: mzQuantML subset: bioinformatics subset: edam subset: formats xref: http://psidev.info/mzquantml created_in: "1.2" def: "mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics." [http://edamontology.org] documentation: http://psidev.info/mzquantml namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:3245 ! Mass spectrometry data format [Term] id: EDAM_format:3249 name: GelML subset: bioinformatics subset: edam subset: formats xref: http://psidev.info/gelml created_in: "1.2" def: "GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS." [http://edamontology.org] documentation: http://psidev.info/gelml namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:3167 ! Experiment annotation format relationship: is_format_of EDAM_data:3147 ! Experiment annotation (mass spectrometry) [Term] id: EDAM_format:3250 name: spML subset: bioinformatics subset: edam subset: formats xref: http://psidev.info created_in: "1.2" def: "spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics." [http://edamontology.org] documentation: http://psidev.info namespace: format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:3167 ! Experiment annotation format relationship: is_format_of EDAM_data:3147 ! Experiment annotation (mass spectrometry) [Term] id: EDAM_format:3252 name: OWL Functional Syntax subset: bioinformatics subset: edam subset: formats created_in: "1.2" def: "A human-readable encoding for the Web Ontology Language (OWL)." [http://edamontology.org] namespace: format is_a: EDAM_format:2197 ! OWL format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3253 name: Manchester OWL Syntax comment: This format was influenced by the OWL Abstract Syntax and the DL style syntax. subset: bioinformatics subset: edam subset: formats created_in: "1.2" def: "A syntax for writing OWL class expressions." [http://edamontology.org] namespace: format is_a: EDAM_format:2197 ! OWL format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3254 name: KRSS2 Syntax comment: This format is used in Protege 4. subset: bioinformatics subset: edam subset: formats created_in: "1.2" def: "A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort"." [http://edamontology.org] namespace: format is_a: EDAM_format:2195 ! Ontology format is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_format:3255 name: Turtle comment: The SPARQL Query Language incorporates a very similar syntax. subset: bioinformatics subset: edam subset: formats created_in: "1.2" def: "The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2376 ! RDF format [Term] id: EDAM_format:3256 name: N-Triples comment: N-Triples should not be confused with Notation 3 which is a superset of Turtle. subset: bioinformatics subset: edam subset: formats created_in: "1.2" def: "A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2376 ! RDF format [Term] id: EDAM_format:3257 name: Notation3 subset: bioinformatics subset: edam subset: formats synonym: "N3" EXACT [] created_in: "1.2" def: "A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind." [http://edamontology.org] namespace: format is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2376 ! RDF format [Term] id: EDAM_format:3261 name: RDF/XML comment: RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. subset: bioinformatics subset: edam subset: formats synonym: "RDF" EXACT [] synonym: "SWO:3000006" EXACT [] created_in: "beta12orEarlier" def: "Resource Description Framework (RDF) XML format." [http://edamontology.org] namespace: format is_a: EDAM_format:2197 ! OWL format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2376 ! RDF format [Term] id: EDAM_format:3262 name: OWL/XML subset: bioinformatics subset: edam subset: formats synonym: "OWL" EXACT [] created_in: "beta12orEarlier" def: "OWL ontology XML serialisation format." [http://edamontology.org] namespace: format is_a: EDAM_format:2197 ! OWL format is_a: EDAM_format:2332 ! XML [Term] id: EDAM_operation:0004 name: Operation subset: bioinformatics subset: edam subset: operations synonym: "Computational method" NARROW [] synonym: "Computational operation" NARROW [] synonym: "Computational procedure" NARROW [] synonym: "Computational subroutine" NARROW [] synonym: "Computational tool" RELATED [] synonym: "Continuant" BROAD [] synonym: "Function" BROAD [] synonym: "Function" BROAD [] synonym: "Function" BROAD [] synonym: "Function" RELATED [] synonym: "Function (programming)" NARROW [] synonym: "Function:(mathematics)" NARROW [] synonym: "http://en.wikipedia.org/wiki/Function_(computer_science)" NARROW [] synonym: "http://en.wikipedia.org/wiki/Subroutine" NARROW [] synonym: "Lambda abstraction" NARROW [] synonym: "Mathematical function" NARROW [] synonym: "Mathematical operation" NARROW [] synonym: "Method" RELATED [] synonym: "WSIO_operation:001" EXACT [] synonym: "Perpetuant" RELATED [] synonym: "Process" RELATED [] synonym: "Process" RELATED [] synonym: "process" RELATED [] synonym: "Quality" RELATED [] synonym: "quality" RELATED [] synonym: "SIO:000017" BROAD [] synonym: "SIO:000649" RELATED [] synonym: "sumo:Function" RELATED [] synonym: "SWO:0000003" RELATED [] created_in: "beta12orEarlier" def: "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state." [http://edamontology.org] namespace: operation disjoint_from: EDAM_topic:0003 ! Topic [Term] id: EDAM_operation:0224 name: Search and retrieval subset: bioinformatics subset: edam subset: operations synonym: "Database retrieval" EXACT [] created_in: "beta12orEarlier" def: "Search or query a data resource and retrieve entries and / or annotation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation relationship: has_output EDAM_data:0006 ! Data relationship: has_topic EDAM_topic:0090 ! Data search and retrieval [Term] id: EDAM_operation:0225 name: Data retrieval (database cross-reference) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Search database to retrieve all relevant references to a particular entity or entry." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0226 name: Annotation comment: This is a broad concept and is used a placeholder for other, more specific concepts. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation relationship: has_input EDAM_data:0582 ! Ontology relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_operation:0227 name: Data indexing subset: bioinformatics subset: edam subset: operations synonym: "Database indexing" EXACT [] created_in: "beta12orEarlier" def: "Generate an index of (typically a file of) biological data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2412 ! Data index processing relationship: has_output EDAM_data:0955 ! Data index [Term] id: EDAM_operation:0228 name: Data index analysis subset: bioinformatics subset: edam subset: operations synonym: "Database index analysis" EXACT [] created_in: "beta12orEarlier" def: "Analyse an index of biological data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2412 ! Data index processing relationship: has_input EDAM_data:0955 ! Data index relationship: has_output EDAM_data:0956 ! Data index report [Term] id: EDAM_operation:0229 name: Annotation retrieval (sequence) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Retrieve basic information about a molecular sequence." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:1813 ! Sequence retrieval [Term] id: EDAM_operation:0230 name: Sequence generation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a molecular sequence by some means." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2121 ! Sequence file processing [Term] id: EDAM_operation:0231 name: Sequence editing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Edit or change a molecular sequence, either randomly or specifically." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2121 ! Sequence file processing is_a: EDAM_operation:3096 ! Editing [Term] id: EDAM_operation:0232 name: Sequence merging subset: bioinformatics subset: edam subset: operations synonym: "Sequence splicing" EXACT [] created_in: "beta12orEarlier" def: "Merge two or more (typically overlapping) molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0231 ! Sequence editing [Term] id: EDAM_operation:0233 name: Sequence conversion subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Convert a molecular sequence from one type to another." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0231 ! Sequence editing [Term] id: EDAM_operation:0234 name: Sequence complexity calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0236 ! Sequence composition calculation relationship: has_output EDAM_data:1259 ! Sequence complexity relationship: has_topic EDAM_topic:0642 ! Low complexity sequences [Term] id: EDAM_operation:0235 name: Sequence ambiguity calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0236 ! Sequence composition calculation relationship: has_output EDAM_data:1260 ! Sequence ambiguity relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] id: EDAM_operation:0236 name: Sequence composition calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate character or word composition or frequency of a molecular sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2403 ! Sequence analysis relationship: has_output EDAM_data:1261 ! Sequence composition relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] id: EDAM_operation:0237 name: Repeat sequence analysis 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Find and/or analyse repeat sequences in (typically nucleotide) sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2403 ! Sequence analysis relationship: has_topic EDAM_topic:0641 ! Repeat sequences [Term] id: EDAM_operation:0238 name: Sequence motif discovery comment: Motifs and patterns might be conserved or over-represented (occur with improbable frequency). subset: bioinformatics subset: edam subset: operations synonym: "Motif discovery" EXACT [] created_in: "beta12orEarlier" def: "Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0253 ! Feature prediction is_a: EDAM_operation:2404 ! Sequence motif processing relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_operation:0239 name: Sequence motif recognition subset: bioinformatics subset: edam subset: operations synonym: "Motif detection" EXACT [] synonym: "Motif recognition" EXACT [] synonym: "Sequence motif detection" EXACT [] created_in: "beta12orEarlier" def: "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0253 ! Feature prediction is_a: EDAM_operation:2404 ! Sequence motif processing relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_operation:0240 name: Sequence motif comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Find motifs shared by molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2404 ! Sequence motif processing is_a: EDAM_operation:2451 ! Sequence comparison relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_operation:0241 name: Transcription regulatory sequence analysis comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] id: EDAM_operation:0242 name: Conserved transcription regulatory sequence identification 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction is_a: EDAM_operation:0438 ! Transcription regulatory element prediction relationship: has_output EDAM_data:1315 ! Gene features (TFBS) [Term] id: EDAM_operation:0243 name: Protein property calculation (from structure) comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. subset: bioinformatics subset: edam subset: operations synonym: "Protein structural property calculation" EXACT [] created_in: "beta12orEarlier" def: "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0250 ! Protein property calculation is_a: EDAM_operation:2406 ! Protein structure analysis relationship: has_output EDAM_data:0897 ! Protein property relationship: has_topic EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_operation:0244 name: Protein flexibility and motion analysis comment: Use this concept 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse flexibility and motion in protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0243 ! Protein property calculation (from structure) is_a: EDAM_operation:2476 ! Molecular dynamics simulation relationship: has_output EDAM_data:1541 ! Protein flexibility or motion report [Term] id: EDAM_operation:0245 name: Protein structural motif recognition 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: bioinformatics subset: edam subset: operations synonym: "Protein structural feature identification" EXACT [] created_in: "beta12orEarlier" def: "Identify or screen for 3D structural motifs in protein structure(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) relationship: has_output EDAM_data:0899 ! Protein features (3D motif) relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces [Term] id: EDAM_operation:0246 name: Protein domain recognition subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) relationship: has_output EDAM_data:0901 ! Protein features (domains) relationship: has_topic EDAM_topic:0736 ! Protein domains and folds [Term] id: EDAM_operation:0247 name: Protein architecture analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2406 ! Protein structure analysis relationship: has_output EDAM_data:0902 ! Protein architecture report [Term] id: EDAM_operation:0248 name: Residue interaction calculation subset: bioinformatics subset: edam subset: operations xref: WHATIF: SymShellFiveXML xref: WHATIF: SymShellOneXML xref: WHATIF: SymShellTenXML xref: WHATIF: SymShellTwoXML xref: WHATIF:ListContactsNormal xref: WHATIF:ListContactsRelaxed xref: WHATIF:ListSideChainContactsNormal xref: WHATIF:ListSideChainContactsRelaxed created_in: "beta12orEarlier" def: "Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0243 ! Protein property calculation (from structure) relationship: has_output EDAM_data:1540 ! Protein residue interactions relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] id: EDAM_operation:0249 name: Torsion angle calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0243 ! Protein property calculation (from structure) relationship: has_output EDAM_data:2991 ! Protein torsion angle data [Term] id: EDAM_operation:0250 name: Protein property calculation comment: This includes methods to render and visualise the properties of a protein sequence. subset: bioinformatics subset: edam subset: operations synonym: "Protein property rendering" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2502 ! Protein data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_input EDAM_data:0897 ! Protein property relationship: has_output EDAM_data:0897 ! Protein property relationship: has_topic EDAM_topic:0123 ! Protein properties [Term] id: EDAM_operation:0252 name: Peptide immunogenicity prediction 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2492 ! Protein interaction prediction is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1534 ! Peptide immunogenicity data relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] id: EDAM_operation:0253 name: Feature prediction subset: bioinformatics subset: edam subset: operations synonym: "Sequence feature detection" EXACT [] synonym: "SO:0000110" RELATED [] created_in: "beta12orEarlier" def: "Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2423 ! Prediction, detection and recognition relationship: has_output EDAM_data:1255 ! Feature record relationship: has_topic EDAM_topic:3072 ! Sequence feature detection [Term] id: EDAM_operation:0254 name: Data retrieval (feature table) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Extract a sequence feature table from a sequence database entry." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0255 name: Feature table query subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Query the features (in a feature table) of molecular sequence(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2453 ! Feature table processing relationship: has_input EDAM_data:1270 ! Sequence feature table relationship: has_input EDAM_data:2201 ! Sequence record full relationship: has_output EDAM_data:1255 ! Feature record [Term] id: EDAM_operation:0256 name: Feature comparison subset: bioinformatics subset: edam subset: operations synonym: "Feature table comparison" EXACT [] synonym: "Sequence feature comparison" EXACT [] created_in: "beta12orEarlier" def: "Compare the feature tables of two or more molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2424 ! Comparison is_a: EDAM_operation:2453 ! Feature table processing relationship: has_input EDAM_data:1270 ! Sequence feature table relationship: has_input EDAM_data:2201 ! Sequence record full [Term] id: EDAM_operation:0257 name: Data retrieval (sequence alignment) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Display basic information about a sequence alignment." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0258 name: Sequence alignment analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse a molecular sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2463 ! Sequence alignment processing is_a: EDAM_operation:2946 ! Alignment analysis relationship: has_input EDAM_data:0863 ! Sequence alignment relationship: has_output EDAM_data:0867 ! Sequence alignment report [Term] id: EDAM_operation:0259 name: Sequence alignment comparison comment: See also 'Sequence profile alignment'. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare (typically by aligning) two molecular sequence alignments." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2424 ! Comparison [Term] id: EDAM_operation:0260 name: Sequence alignment conversion subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3081 ! Sequence alignment editing [Term] id: EDAM_operation:0261 name: Nucleic acid property processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) physicochemical property data of nucleic acids." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0262 ! Nucleic acid property calculation [Term] id: EDAM_operation:0262 name: Nucleic acid property calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_output EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_operation:0264 name: Splice transcript prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2499 ! Splicing analysis relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] id: EDAM_operation:0265 name: Frameshift error detection comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3195 ! Sequencing error detection is_a: EDAM_operation:3202 ! Mutation detection relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:0266 name: Vector sequence detection subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison [Term] id: EDAM_operation:0267 name: Protein secondary structure prediction 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: bioinformatics subset: edam subset: operations synonym: "Secondary structure prediction (protein)" EXACT [] created_in: "beta12orEarlier" def: "Predict secondary structure of protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) is_a: EDAM_operation:2444 ! Protein secondary structure processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:0876 ! Protein features (secondary structure) relationship: has_topic EDAM_topic:0178 ! Protein secondary structure prediction [Term] id: EDAM_operation:0268 name: Protein super-secondary structure prediction comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict super-secondary structure of protein sequence(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0267 ! Protein secondary structure prediction relationship: has_output EDAM_data:0877 ! Protein features (super-secondary) [Term] id: EDAM_operation:0269 name: Transmembrane protein prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0267 ! Protein secondary structure prediction is_a: EDAM_operation:0270 ! Transmembrane protein analysis relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) [Term] id: EDAM_operation:0270 name: Transmembrane protein analysis comment: Use this (or child) concept 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2502 ! Protein data processing relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) relationship: has_topic EDAM_topic:0820 ! Membrane proteins [Term] id: EDAM_operation:0271 name: Structure prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict tertiary structure of a molecular (biopolymer) sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2423 ! Prediction, detection and recognition is_a: EDAM_operation:2465 ! Structure processing relationship: has_output EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0082 ! Structure prediction [Term] id: EDAM_operation:0272 name: Residue interaction prediction comment: Methods usually involve multiple sequence alignment analysis. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0243 ! Protein property calculation (from structure) is_a: EDAM_operation:2506 ! Sequence alignment analysis (protein) relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] id: EDAM_operation:0273 name: Protein interaction raw data analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2949 ! Protein interaction analysis relationship: has_input EDAM_data:0905 ! Protein interaction raw data relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] id: EDAM_operation:0274 name: Protein-protein interaction prediction (from protein sequence) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2464 ! Protein-protein interaction prediction is_a: EDAM_operation:3084 ! Protein function prediction (from sequence) [Term] id: EDAM_operation:0275 name: Protein-protein interaction prediction (from protein structure) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2464 ! Protein-protein interaction prediction is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) [Term] id: EDAM_operation:0276 name: Protein interaction network analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse a network of protein interactions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2445 ! Protein interaction network processing is_a: EDAM_operation:2497 ! Pathway or network analysis is_a: EDAM_operation:2949 ! Protein interaction analysis relationship: has_input EDAM_data:1663 ! Pathway or network (protein-protein interaction) relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_operation:0277 name: Protein interaction network comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more networks of protein interactions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0276 ! Protein interaction network analysis is_a: EDAM_operation:1778 ! Protein function comparison relationship: has_input EDAM_data:1663 ! Pathway or network (protein-protein interaction) [Term] id: EDAM_operation:0278 name: RNA secondary structure prediction comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction is_a: EDAM_operation:2439 ! RNA secondary structure processing relationship: has_output EDAM_data:0880 ! RNA secondary structure record relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_operation:0279 name: Nucleic acid folding analysis subset: bioinformatics subset: edam subset: operations synonym: "Nucleic acid folding" EXACT [] synonym: "Nucleic acid folding modelling" EXACT [] created_in: "beta12orEarlier" def: "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2426 ! Modelling and simulation is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_output EDAM_data:1596 ! Nucleic acid folding report relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_operation:0280 name: Data retrieval (restriction enzyme annotation) subset: bioinformatics subset: edam subset: operations synonym: "Restriction enzyme information retrieval" EXACT [] created_in: "beta12orEarlier" def: "Retrieve information on restriction enzymes or restriction enzyme sites." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:0281 name: Genetic marker identification 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify genetic markers in DNA sequences." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:0282 name: Genetic mapping 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: bioinformatics subset: edam subset: operations synonym: "Genetic map generation" EXACT [] synonym: "Linkage mapping" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2520 ! DNA mapping relationship: has_output EDAM_data:1278 ! Genetic map relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] id: EDAM_operation:0283 name: Linkage analysis 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse genetic linkage." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_output EDAM_data:0927 ! Gene annotation (linkage) relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] id: EDAM_operation:0284 name: Codon usage table generation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate codon usage statistics and create a codon usage table." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2433 ! Codon usage table processing relationship: has_output EDAM_data:1597 ! Codon usage table [Term] id: EDAM_operation:0285 name: Codon usage table comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more codon usage tables." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2433 ! Codon usage table processing is_a: EDAM_operation:2998 ! Nucleic acid comparison [Term] id: EDAM_operation:0286 name: Codon usage analysis subset: bioinformatics subset: edam subset: operations synonym: "synon: Codon usage data analysis" EXACT [] synonym: "synon: Codon usage table analysis" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_input EDAM_data:1597 ! Codon usage table relationship: has_input EDAM_data:2977 ! Nucleic acid sequence relationship: has_output EDAM_data:0914 ! Codon usage report relationship: has_output EDAM_data:1597 ! Codon usage table relationship: has_topic EDAM_topic:0107 ! Codon usage analysis [Term] id: EDAM_operation:0287 name: Base position variability plotting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify and plot third base position variability in a nucleotide sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0286 ! Codon usage analysis relationship: has_output EDAM_data:1263 ! Sequence composition (base position variability) relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] id: EDAM_operation:0288 name: Sequence word comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Find exact character or word matches between molecular sequences without full sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2451 ! Sequence comparison relationship: has_output EDAM_data:0861 ! Sequence alignment (words) [Term] id: EDAM_operation:0289 name: Sequence distance matrix generation subset: bioinformatics subset: edam subset: operations synonym: "Phylogenetic distance matrix generation" EXACT [] created_in: "beta12orEarlier" def: "Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2451 ! Sequence comparison relationship: has_output EDAM_data:0870 ! Sequence distance matrix relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:0290 name: Sequence redundancy removal subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0291 ! Sequence clustering relationship: has_output EDAM_data:2044 ! Sequence relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] id: EDAM_operation:0291 name: Sequence clustering comment: The clusters may be output or used internally for some other purpose. subset: bioinformatics subset: edam subset: operations synonym: "Sequence cluster generation" EXACT [] created_in: "beta12orEarlier" def: "Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2452 ! Sequence cluster processing is_a: EDAM_operation:2995 ! Sequence classification relationship: has_output EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_operation:0292 name: Sequence alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Sequence alignment" EXACT [] synonym: "Sequence alignment computation" EXACT [] synonym: "Sequence alignment generation" EXACT [] created_in: "beta12orEarlier" def: "Align (identify equivalent sites within) molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2463 ! Sequence alignment processing is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:2044 ! Sequence relationship: has_output EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_operation:0293 name: Hybrid sequence alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Hybrid sequence alignment" EXACT [] created_in: "beta12orEarlier" def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0292 ! Sequence alignment construction [Term] id: EDAM_operation:0294 name: Structure-based sequence alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Structure-based sequence alignment" EXACT [] created_in: "beta12orEarlier" def: "Align molecular sequences using sequence and structural information." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0292 ! Sequence alignment construction relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:0295 name: Structure alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Structure alignment" EXACT [] created_in: "beta12orEarlier" def: "Align (superimpose) molecular tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2483 ! Structure comparison is_a: EDAM_operation:2928 ! Alignment construction is_a: EDAM_operation:2952 ! Structure alignment processing relationship: has_output EDAM_data:0886 ! Structure alignment [Term] id: EDAM_operation:0296 name: Sequence profile generation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2413 ! Sequence profile processing is_a: EDAM_operation:2463 ! Sequence alignment processing relationship: has_input EDAM_data:0863 ! Sequence alignment relationship: has_output EDAM_data:1354 ! Sequence profile [Term] id: EDAM_operation:0297 name: Structural (3D) profile generation subset: bioinformatics subset: edam subset: operations synonym: "Structural profile generation" EXACT [] created_in: "beta12orEarlier" def: "Generate some type of structural (3D) profile or template from a structure or structure alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2411 ! Structural (3D) profile processing is_a: EDAM_operation:2465 ! Structure processing is_a: EDAM_operation:2952 ! Structure alignment processing relationship: has_input EDAM_data:0883 ! Structure relationship: has_input EDAM_data:0886 ! Structure alignment relationship: has_output EDAM_data:0889 ! Structural (3D) profile [Term] id: EDAM_operation:0298 name: Sequence profile alignment construction comment: See also 'Sequence alignment comparison'. subset: bioinformatics subset: edam subset: operations synonym: "Sequence profile alignment" EXACT [] created_in: "beta12orEarlier" def: "Align sequence profiles (representing sequence alignments)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2413 ! Sequence profile processing is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:1354 ! Sequence profile relationship: has_output EDAM_data:0868 ! Sequence profile alignment [Term] id: EDAM_operation:0299 name: Structural (3D) profile alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Structural (3D) profile alignment" EXACT [] synonym: "Structural profile alignment" EXACT [] created_in: "beta12orEarlier" def: "Align structural (3D) profiles or templates (representing structures or structure alignments)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2411 ! Structural (3D) profile processing is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:0889 ! Structural (3D) profile relationship: has_output EDAM_data:0890 ! Structural (3D) profile alignment relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] id: EDAM_operation:0300 name: Sequence-profile alignment construction comment: A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: bioinformatics subset: edam subset: operations synonym: "Sequence-profile alignment" EXACT [] created_in: "beta12orEarlier" def: "Align molecular sequence(s) to sequence profile(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2413 ! Sequence profile processing is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:1354 ! Sequence profile relationship: has_output EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_operation:0301 name: Sequence-3D profile alignment construction comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: bioinformatics subset: edam subset: operations synonym: "Sequence-3D profile alignment" EXACT [] created_in: "beta12orEarlier" def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0303 ! Protein fold recognition is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:0889 ! Structural (3D) profile relationship: has_output EDAM_data:0891 ! Sequence-3D profile alignment relationship: has_topic EDAM_topic:0184 ! Threading [Term] id: EDAM_operation:0302 name: Protein threading comment: Use this concept 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: bioinformatics subset: edam subset: operations synonym: "Sequence-structure alignment" EXACT [] created_in: "beta12orEarlier" def: "Align molecular sequence to structure in 3D space (threading)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0303 ! Protein fold recognition is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:1460 ! Protein structure relationship: has_output EDAM_data:0893 ! Sequence-structure alignment relationship: has_topic EDAM_topic:0175 ! Homology modelling relationship: has_topic EDAM_topic:0184 ! Threading [Term] id: EDAM_operation:0303 name: Protein fold recognition 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: bioinformatics subset: edam subset: operations synonym: "Protein domain prediction" EXACT [] synonym: "Protein fold prediction" EXACT [] created_in: "beta12orEarlier" def: "Recognize (predict and identify) known protein structural domains or folds in protein sequence(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) is_a: EDAM_operation:0474 ! Protein structure prediction is_a: EDAM_operation:2997 ! Protein comparison relationship: has_output EDAM_data:0901 ! Protein features (domains) relationship: has_topic EDAM_topic:0184 ! Threading [Term] id: EDAM_operation:0304 name: Data retrieval (metadata and documentation) comment: This includes documentation, general information and other metadata on entities such as databases, database entries and tools. subset: bioinformatics subset: edam subset: operations synonym: "Data retrieval (documentation)" EXACT [] synonym: "Data retrieval (metadata)" EXACT [] created_in: "beta12orEarlier" def: "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2422 ! Data retrieval relationship: has_output EDAM_data:2337 ! Metadata [Term] id: EDAM_operation:0305 name: Literature search subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Query the biomedical and informatics literature." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2421 ! Database search relationship: has_output EDAM_data:0970 ! Bibliographic reference relationship: has_topic EDAM_topic:0217 ! Literature analysis [Term] id: EDAM_operation:0306 name: Text mining subset: bioinformatics subset: edam subset: operations synonym: "Text data mining" EXACT [] created_in: "beta12orEarlier" def: "Process and analyse text (typically the biomedical and informatics literature) to extract information from it." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2947 ! Article analysis relationship: has_input EDAM_data:2048 ! Report relationship: has_output EDAM_data:0972 ! Text mining report relationship: has_topic EDAM_topic:0218 ! Text mining [Term] id: EDAM_operation:0307 name: Virtual PCR subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Perform in-silico (virtual) PCR." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_operation:0308 name: PCR primer design 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: bioinformatics subset: edam subset: operations synonym: "PCR primer prediction" EXACT [] created_in: "beta12orEarlier" def: "Design or predict oligonucleotide primers for PCR and DNA amplification etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2419 ! Primer and probe design relationship: has_input EDAM_data:2977 ! Nucleic acid sequence relationship: has_output EDAM_data:1240 ! PCR primers relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] id: EDAM_operation:0309 name: Microarray probe design subset: bioinformatics subset: edam subset: operations synonym: "Microarray probe prediction" EXACT [] created_in: "beta12orEarlier" def: "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2419 ! Primer and probe design is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_input EDAM_data:2977 ! Nucleic acid sequence relationship: has_output EDAM_data:2717 ! Oligonucleotide probe annotation relationship: has_topic EDAM_topic:0200 ! Microarrays relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] id: EDAM_operation:0310 name: Sequence assembly comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2429 ! Mapping and assembly is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_output EDAM_data:0925 ! Sequence assembly relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] id: EDAM_operation:0311 name: Microarray data standardization and normalization comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Standardize or normalize microarray data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2428 ! Evaluation and validation is_a: EDAM_operation:2495 ! Gene expression data processing relationship: has_input EDAM_data:3117 ! Microarray hybridisation data relationship: has_output EDAM_data:3117 ! Microarray hybridisation data [Term] id: EDAM_operation:0312 name: Sequencing-based expression profile data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) SAGE, MPSS or SBS experimental data." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:0313 name: Gene expression profile clustering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0315 ! Gene expression profile comparison relationship: has_output EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_operation:0314 name: Gene expression profile generation subset: bioinformatics subset: edam subset: operations synonym: "Expression profiling" EXACT [] synonym: "Gene expression profiling" EXACT [] created_in: "beta12orEarlier" def: "Generate a gene expression profile or pattern, for example from microarray data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2435 ! Gene expression profile processing relationship: has_output EDAM_data:0928 ! Gene expression profile [Term] id: EDAM_operation:0315 name: Gene expression profile comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare gene expression profiles or patterns." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0532 ! Gene expression profile analysis is_a: EDAM_operation:2998 ! Nucleic acid comparison relationship: has_output EDAM_data:3111 ! Processed microarray data [Term] id: EDAM_operation:0316 name: Functional profiling subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Interpret (in functional terms) and annotate gene expression data." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0532 ! Gene expression profile analysis [Term] id: EDAM_operation:0317 name: EST and cDNA sequence analysis comment: For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse EST or cDNA sequences." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2403 ! Sequence analysis [Term] id: EDAM_operation:0318 name: Structural genomics target selection comment: Methods will typically navigate a graph of protein families of known structure. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify and select targets for protein structural determination." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2406 ! Protein structure analysis [Term] id: EDAM_operation:0319 name: Protein secondary structure assignment subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assign secondary structure from protein coordinate or experimental data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2444 ! Protein secondary structure processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:0876 ! Protein features (secondary structure) relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] id: EDAM_operation:0320 name: Protein structure assignment subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assign a protein tertiary structure (3D coordinates) from raw experimental data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2459 ! Structure processing (protein) relationship: has_output EDAM_data:1460 ! Protein structure relationship: has_topic EDAM_topic:2226 ! Structure determination [Term] id: EDAM_operation:0321 name: Protein model evaluation 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: bioinformatics subset: edam subset: operations xref: WHATIF: UseFileDB created_in: "beta12orEarlier" def: "Evaluate the quality or correctness a protein three-dimensional model." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0477 ! Protein modelling is_a: EDAM_operation:2428 ! Evaluation and validation relationship: has_output EDAM_data:1539 ! Protein structural quality report relationship: has_topic EDAM_topic:0175 ! Homology modelling relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction relationship: has_topic EDAM_topic:2275 ! Molecular modelling [Term] id: EDAM_operation:0322 name: Protein model refinement 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: bioinformatics subset: edam subset: operations xref: WHATIF: CorrectedPDBasXML created_in: "beta12orEarlier" def: "Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0321 ! Protein model evaluation is_a: EDAM_operation:2425 ! Optimisation and refinement [Term] id: EDAM_operation:0323 name: Phylogenetic tree construction comment: Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. subset: bioinformatics subset: edam subset: operations synonym: "Phylogenetic tree construction" EXACT [] synonym: "Phylogenetic tree generation" EXACT [] created_in: "beta12orEarlier" def: "Construct a phylogenetic tree." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2443 ! Phylogenetic tree processing is_a: EDAM_operation:2995 ! Sequence classification relationship: has_output EDAM_data:0872 ! Phylogenetic tree relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_operation:0324 name: Phylogenetic tree analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2443 ! Phylogenetic tree processing relationship: has_input EDAM_data:0872 ! Phylogenetic tree relationship: has_output EDAM_data:1438 ! Phylogenetic tree report [Term] id: EDAM_operation:0325 name: Phylogenetic tree comparison 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more phylogenetic trees." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0324 ! Phylogenetic tree analysis is_a: EDAM_operation:2424 ! Comparison [Term] id: EDAM_operation:0326 name: Phylogenetic tree editing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Edit a phylogenetic tree." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2443 ! Phylogenetic tree processing is_a: EDAM_operation:3096 ! Editing relationship: has_input EDAM_data:0872 ! Phylogenetic tree relationship: has_output EDAM_data:0872 ! Phylogenetic tree [Term] id: EDAM_operation:0327 name: Phylogenetic footprinting / shadowing 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences) relationship: has_topic EDAM_topic:0194 ! Phylogenomics [Term] id: EDAM_operation:0328 name: Protein folding simulation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Simulate the folding of a protein." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2415 ! Protein folding analysis [Term] id: EDAM_operation:0329 name: Protein folding pathway prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict the folding pathway(s) or non-native structural intermediates of a protein." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2415 ! Protein folding analysis is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) [Term] id: EDAM_operation:0330 name: Protein SNP mapping subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0331 ! Protein modelling (mutation) relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) relationship: has_topic EDAM_topic:2277 ! SNPs [Term] id: EDAM_operation:0331 name: Protein modelling (mutation) comment: Methods might predict silent or pathological mutations. subset: bioinformatics subset: edam subset: operations synonym: "Protein mutation modelling" EXACT [] created_in: "beta12orEarlier" def: "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0477 ! Protein modelling is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_topic EDAM_topic:0130 ! Protein folding and stability relationship: has_topic EDAM_topic:0199 ! Genetic variation [Term] id: EDAM_operation:0332 name: Immunogen design subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Design molecules that elicit an immune response (immunogens)." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0559 ! Peptide immunogen prediction and optimisation [Term] id: EDAM_operation:0333 name: Zinc finger protein domain prediction and optimisation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0420 ! Protein-nucleic acid binding prediction is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_output EDAM_data:1567 ! Protein-nucleic acid interaction relationship: has_topic EDAM_topic:0150 ! Protein design [Term] id: EDAM_operation:0334 name: Enzyme kinetics calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate Km, Vmax and derived data for an enzyme reaction." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:2024 ! Enzyme kinetics data relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions [Term] id: EDAM_operation:0335 name: File reformatting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Reformat a file of data (or equivalent entity in memory)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2409 ! File processing [Term] id: EDAM_operation:0336 name: File validation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Test and validate the format and content of a data file." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2409 ! File processing is_a: EDAM_operation:2428 ! Evaluation and validation [Term] id: EDAM_operation:0337 name: Plotting and rendering subset: bioinformatics subset: edam subset: operations synonym: "Visualisation" EXACT [] created_in: "beta12orEarlier" def: "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation relationship: has_input EDAM_data:0006 ! Data relationship: has_output EDAM_data:2968 ! Image relationship: has_topic EDAM_topic:0092 ! Data visualisation [Term] id: EDAM_operation:0338 name: Sequence database search comment: This excludes direct retrieval methods (e.g. the dbfetch program). subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Search a sequence database by sequence comparison and retrieve similar sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2421 ! Database search relationship: has_output EDAM_data:0857 ! Database hits (sequence) relationship: has_topic EDAM_topic:0159 ! Sequence comparison [Term] id: EDAM_operation:0339 name: Structure database search subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:2996 ! Structure classification relationship: has_output EDAM_data:0885 ! Database hits (structure) relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_operation:0340 name: Protein secondary database search 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: bioinformatics subset: edam subset: operations synonym: "Protein sequence classification" EXACT [] created_in: "beta12orEarlier" def: "Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:3093 ! Sequence screening relationship: has_output EDAM_data:0858 ! Database hits (secondary) relationship: has_topic EDAM_topic:0595 ! Protein classification [Term] id: EDAM_operation:0341 name: Motif database search subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Screen a sequence against a motif or pattern database." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0239 ! Sequence motif recognition is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:3093 ! Sequence screening relationship: has_output EDAM_data:1298 ! Sequence features (motifs) relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_operation:0342 name: Sequence profile database search subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Search a database of sequence profiles with a query sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0300 ! Sequence-profile alignment construction is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:3093 ! Sequence screening relationship: has_output EDAM_data:1298 ! Sequence features (motifs) [Term] id: EDAM_operation:0343 name: Transmembrane protein database search subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Search a database of transmembrane proteins, for example for sequence or structural similarities." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2421 ! Database search [Term] id: EDAM_operation:0344 name: Sequence retrieval (by code) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Query a database and retrieve sequences with a given entry code or accession number." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1813 ! Sequence retrieval [Term] id: EDAM_operation:0345 name: Sequence retrieval (by keyword) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Query a database and retrieve sequences containing a given keyword." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1813 ! Sequence retrieval [Term] id: EDAM_operation:0346 name: Sequence database search (by sequence) subset: bioinformatics subset: edam subset: operations synonym: "Sequence similarity search" EXACT [] created_in: "beta12orEarlier" def: "Search a sequence database and retrieve sequences that are similar to a query sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0338 ! Sequence database search is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:3093 ! Sequence screening [Term] id: EDAM_operation:0347 name: Sequence database search (by motif or pattern) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0239 ! Sequence motif recognition is_a: EDAM_operation:0338 ! Sequence database search relationship: has_input EDAM_data:1353 ! Sequence motif relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_operation:0348 name: Sequence database search (by amino acid composition) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Search a sequence database and retrieve sequences of a given amino acid composition." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0338 ! Sequence database search relationship: has_input EDAM_data:1267 ! Amino acid frequencies relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] id: EDAM_operation:0349 name: Sequence database search (by physicochemical property) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Search a sequence database and retrieve sequences with a specified physicochemical property." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0338 ! Sequence database search [Term] id: EDAM_operation:0350 name: Sequence database search (by sequence using word-based methods) 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: bioinformatics subset: edam subset: operations synonym: "Sequence similarity search (word-based methods)" EXACT [] created_in: "beta12orEarlier" def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0288 ! Sequence word comparison is_a: EDAM_operation:0346 ! Sequence database search (by sequence) [Term] id: EDAM_operation:0351 name: Sequence database search (by sequence using profile-based methods) comment: This includes tools based on PSI-BLAST. subset: bioinformatics subset: edam subset: operations synonym: "Sequence similarity search (profile-based methods)" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0300 ! Sequence-profile alignment construction is_a: EDAM_operation:0346 ! Sequence database search (by sequence) [Term] id: EDAM_operation:0352 name: Sequence database search (by sequence using local alignment-based methods) comment: This includes tools based on the Smith-Waterman algorithm or FASTA. subset: bioinformatics subset: edam subset: operations synonym: "Sequence similarity search (local alignment-based methods) " EXACT [] created_in: "beta12orEarlier" def: "Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0346 ! Sequence database search (by sequence) is_a: EDAM_operation:0493 ! Pairwise sequence alignment construction (local) relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:0353 name: Sequence database search (by sequence using global alignment-based methods) comment: This includes tools based on the Needleman and Wunsch algorithm. subset: bioinformatics subset: edam subset: operations synonym: "Sequence similarity search (global alignment-based methods)" EXACT [] created_in: "beta12orEarlier" def: "Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0346 ! Sequence database search (by sequence) is_a: EDAM_operation:0494 ! Pairwise sequence alignment construction (global) relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:0354 name: Sequence database search (by sequence for primer sequences) comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. subset: bioinformatics subset: edam subset: operations synonym: "Sequence similarity search (primer sequences)" EXACT [] created_in: "beta12orEarlier" def: "Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0346 ! Sequence database search (by sequence) relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] id: EDAM_operation:0355 name: Sequence database search (by molecular weight) subset: bioinformatics subset: edam subset: operations synonym: "Peptide mass fingerprinting" EXACT [] synonym: "Protein fingerprinting" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property) relationship: has_input EDAM_data:0944 ! Peptide mass fingerprint relationship: has_topic EDAM_topic:0123 ! Protein properties relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_operation:0356 name: Sequence database search (by isoelectric point) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property) relationship: has_topic EDAM_topic:0123 ! Protein properties [Term] id: EDAM_operation:0357 name: Structure retrieval (by code) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Query a tertiary structure database and retrieve entries with a given entry code or accession number." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1814 ! Structure retrieval [Term] id: EDAM_operation:0358 name: Structure retrieval (by keyword) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Query a tertiary structure database and retrieve entries containing a given keyword." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1814 ! Structure retrieval [Term] id: EDAM_operation:0359 name: Structure database search (by sequence) subset: bioinformatics subset: edam subset: operations synonym: "Structure retrieval by sequence" EXACT [] created_in: "beta12orEarlier" def: "Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0339 ! Structure database search is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:3093 ! Sequence screening [Term] id: EDAM_operation:0360 name: Structure database search (by structure) subset: bioinformatics subset: edam subset: operations synonym: "Structural similarity search" EXACT [] synonym: "Structure retrieval by structure" EXACT [] created_in: "beta12orEarlier" def: "Search a tertiary structure database and retrieve structures that are similar to a query structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0339 ! Structure database search relationship: has_topic EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_operation:0361 name: Sequence annotation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Annotate a molecular sequence record with terms from a controlled vocabulary." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0226 ! Annotation relationship: has_input EDAM_data:0849 ! Sequence record relationship: has_output EDAM_data:0849 ! Sequence record [Term] id: EDAM_operation:0362 name: Genome annotation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Annotate a genome sequence with terms from a controlled vocabulary." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0361 ! Sequence annotation [Term] id: EDAM_operation:0363 name: Nucleic acid sequence reverse and complement subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate the reverse and / or complement of a nucleotide sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid) [Term] id: EDAM_operation:0364 name: Random sequence generation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a random sequence, for example, with a specific character composition." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0230 ! Sequence generation [Term] id: EDAM_operation:0365 name: Nucleic acid restriction digest subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate digest fragments for a nucleotide sequence containing restriction sites." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0262 ! Nucleic acid property calculation is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid) relationship: has_output EDAM_data:1239 ! Restriction digest relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] id: EDAM_operation:0366 name: Protein sequence cleavage subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2514 ! Sequence generation (protein) is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1238 ! Proteolytic digest relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_operation:0367 name: Sequence mutation and randomization subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0231 ! Sequence editing [Term] id: EDAM_operation:0368 name: Sequence masking comment: For example, SNPs or repeats in a DNA sequence might be masked. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Mask characters in a molecular sequence (replacing those characters with a mask character)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0231 ! Sequence editing relationship: has_input EDAM_data:0851 ! Sequence mask character [Term] id: EDAM_operation:0369 name: Sequence cutting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Cut (remove) characters or a region from a molecular sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0231 ! Sequence editing [Term] id: EDAM_operation:0370 name: Restriction site creation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Create (or remove) restriction sites in sequences, for example using silent mutations." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid) relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] id: EDAM_operation:0371 name: DNA translation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Translate a DNA sequence into protein." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0233 ! Sequence conversion relationship: has_topic EDAM_topic:0108 ! Translation [Term] id: EDAM_operation:0372 name: DNA transcription subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Transcribe a nucleotide sequence into mRNA sequence(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0233 ! Sequence conversion relationship: has_topic EDAM_topic:0110 ! Transcription [Term] id: EDAM_operation:0377 name: Sequence composition calculation (nucleic acid) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate base frequency or word composition of a nucleotide sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0236 ! Sequence composition calculation is_a: EDAM_operation:0262 ! Nucleic acid property calculation [Term] id: EDAM_operation:0378 name: Sequence composition calculation (protein) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate amino acid frequency or word composition of a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0236 ! Sequence composition calculation is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) [Term] id: EDAM_operation:0379 name: Repeat sequence detection subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0237 ! Repeat sequence analysis is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1299 ! Sequence features (repeats) [Term] id: EDAM_operation:0380 name: Repeat sequence organisation analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse repeat sequence organization such as periodicity." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0236 ! Sequence composition calculation is_a: EDAM_operation:0237 ! Repeat sequence analysis [Term] id: EDAM_operation:0383 name: Protein hydropathy calculation (from structure) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0243 ! Protein property calculation (from structure) is_a: EDAM_operation:2574 ! Protein hydropathy calculation [Term] id: EDAM_operation:0384 name: Protein solvent accessibility calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate solvent accessible or buried surface areas in protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0243 ! Protein property calculation (from structure) relationship: has_output EDAM_data:1542 ! Protein solvent accessibility relationship: has_topic EDAM_topic:0137 ! Protein hydropathy [Term] id: EDAM_operation:0385 name: Protein hydropathy cluster calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify clusters of hydrophobic or charged residues in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0383 ! Protein hydropathy calculation (from structure) is_a: EDAM_operation:0393 ! Protein residue cluster calculation [Term] id: EDAM_operation:0386 name: Protein dipole moment calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate whether a protein structure has an unusually large net charge (dipole moment)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1545 ! Protein dipole moment [Term] id: EDAM_operation:0387 name: Protein surface and interior calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0384 ! Protein solvent accessibility calculation relationship: has_output EDAM_data:1543 ! Protein surface report relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces [Term] id: EDAM_operation:0388 name: Binding site prediction (from structure) subset: bioinformatics subset: edam subset: operations synonym: "Ligand-binding and active site prediction (from structure)" EXACT [] created_in: "beta12orEarlier" def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0245 ! Protein structural motif recognition is_a: EDAM_operation:2575 ! Binding site prediction [Term] id: EDAM_operation:0389 name: Protein-nucleic acid binding site analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse RNA or DNA-binding sites in protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2949 ! Protein interaction analysis relationship: has_input EDAM_data:1567 ! Protein-nucleic acid interaction relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions [Term] id: EDAM_operation:0390 name: Protein peeling subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Decompose a structure into compact or globular fragments (protein peeling)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0246 ! Protein domain recognition relationship: has_output EDAM_data:0901 ! Protein features (domains) [Term] id: EDAM_operation:0391 name: Protein distance matrix calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0248 ! Residue interaction calculation relationship: has_output EDAM_data:1546 ! Protein distance matrix [Term] id: EDAM_operation:0392 name: Protein contact map calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) relationship: has_output EDAM_data:1547 ! Protein contact map [Term] id: EDAM_operation:0393 name: Protein residue cluster calculation comment: Cluster of contacting residues might be key structural residues. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate clusters of contacting residues in protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) relationship: has_output EDAM_data:1548 ! Protein residue 3D cluster [Term] id: EDAM_operation:0394 name: Hydrogen bond calculation comment: The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. subset: bioinformatics subset: edam subset: operations xref: WHATIF:HasHydrogenBonds xref: WHATIF:ShowHydrogenBonds xref: WHATIF:ShowHydrogenBondsM created_in: "beta12orEarlier" def: "Identify potential hydrogen bonds between amino acids and other groups." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0248 ! Residue interaction calculation relationship: has_output EDAM_data:1549 ! Protein hydrogen bonds [Term] id: EDAM_operation:0395 name: Residue non-canonical interaction detection subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate non-canonical atomic interactions in protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0248 ! Residue interaction calculation is_a: EDAM_operation:0321 ! Protein model evaluation relationship: has_output EDAM_data:1550 ! Protein non-canonical interactions [Term] id: EDAM_operation:0396 name: Ramachandran plot calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate a Ramachandran plot of a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0249 ! Torsion angle calculation relationship: has_output EDAM_data:1544 ! Ramachandran plot [Term] id: EDAM_operation:0397 name: Ramachandran plot evaluation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse (typically to validate) a Ramachandran plot of a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1844 ! Dihedral angle validation relationship: has_input EDAM_data:1544 ! Ramachandran plot relationship: has_output EDAM_data:1539 ! Protein structural quality report [Term] id: EDAM_operation:0398 name: Protein molecular weight calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate the molecular weight of a protein sequence or fragments." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1519 ! Peptide molecular weights relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_operation:0399 name: Protein extinction coefficient calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict extinction coefficients or optical density of a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1531 ! Protein extinction coefficient [Term] id: EDAM_operation:0400 name: Protein pH-dependent property calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate pH-dependent properties from pKa calculations of a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:0897 ! Protein property relationship: has_topic EDAM_topic:0137 ! Protein hydropathy [Term] id: EDAM_operation:0401 name: Protein hydropathy calculation (from sequence) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Hydropathy calculation on a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2574 ! Protein hydropathy calculation [Term] id: EDAM_operation:0402 name: Protein titration curve plotting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Plot a protein titration curve." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation relationship: has_output EDAM_data:1527 ! Protein titration curve [Term] id: EDAM_operation:0403 name: Protein isoelectric point calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate isoelectric point of a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation relationship: has_output EDAM_data:1528 ! Protein isoelectric point [Term] id: EDAM_operation:0404 name: Protein hydrogen exchange rate calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Estimate hydrogen exchange rate of a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation relationship: has_output EDAM_data:1530 ! Protein hydrogen exchange rate [Term] id: EDAM_operation:0405 name: Protein hydrophobic region calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate hydrophobic or hydrophilic / charged regions of a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) [Term] id: EDAM_operation:0406 name: Protein aliphatic index calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1521 ! Protein aliphatic index [Term] id: EDAM_operation:0407 name: Protein hydrophobic moment plotting comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1520 ! Peptide hydrophobic moment [Term] id: EDAM_operation:0408 name: Protein globularity prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1526 ! Protein globularity [Term] id: EDAM_operation:0409 name: Protein solubility prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict the solubility or atomic solvation energy of a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1524 ! Protein solubility [Term] id: EDAM_operation:0410 name: Protein crystallizability prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict crystallizability of a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence) relationship: has_output EDAM_data:1525 ! Protein crystallizability [Term] id: EDAM_operation:0411 name: Protein signal peptide detection (eukaryotes) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0418 ! Protein signal peptide detection [Term] id: EDAM_operation:0412 name: Protein signal peptide detection (bacteria) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0418 ! Protein signal peptide detection [Term] id: EDAM_operation:0413 name: MHC peptide immunogenicity prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction [Term] id: EDAM_operation:0414 name: Protein feature prediction (from sequence) comment: Methods typically involve scanning for known motifs, patterns and regular expressions. subset: bioinformatics subset: edam subset: operations synonym: "Sequence feature detection (protein)" EXACT [] created_in: "beta12orEarlier" def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2479 ! Protein sequence analysis is_a: EDAM_operation:3092 ! Protein feature prediction [Term] id: EDAM_operation:0415 name: Nucleic acid feature prediction comment: Methods typically involve scanning for known motifs, patterns and regular expressions. subset: bioinformatics subset: edam subset: operations synonym: "Sequence feature detection (nucleic acid)" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0239 ! Sequence motif recognition is_a: EDAM_operation:0253 ! Feature prediction is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:1276 ! Nucleic acid features relationship: has_topic EDAM_topic:3073 ! Nucleic acid feature detection [Term] id: EDAM_operation:0416 name: Epitope mapping comment: Epitope mapping is commonly done during vaccine design. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict antigenic determinant sites (epitopes) in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2429 ! Mapping and assembly is_a: EDAM_operation:3087 ! Protein site detection relationship: has_output EDAM_data:1326 ! Protein features (binding sites) relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] id: EDAM_operation:0417 name: Protein post-translation modification site prediction 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict post-translation modification sites in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3087 ! Protein site detection relationship: has_output EDAM_data:1324 ! Protein features (post-translation modifications) relationship: has_topic EDAM_topic:0601 ! Protein modifications [Term] id: EDAM_operation:0418 name: Protein signal peptide detection comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect or predict signal peptides and signal peptide cleavage sites in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2489 ! Protein subcellular localization prediction is_a: EDAM_operation:3087 ! Protein site detection relationship: has_output EDAM_data:1322 ! Protein features (signal peptides) relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization [Term] id: EDAM_operation:0419 name: Binding site prediction (from sequence) subset: bioinformatics subset: edam subset: operations synonym: "Ligand-binding and active site prediction (from sequence)" EXACT [] created_in: "beta12orEarlier" def: "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2575 ! Binding site prediction is_a: EDAM_operation:3087 ! Protein site detection [Term] id: EDAM_operation:0420 name: Protein-nucleic acid binding prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict RNA and DNA-binding binding sites in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0419 ! Binding site prediction (from sequence) relationship: has_output EDAM_data:1326 ! Protein features (binding sites) [Term] id: EDAM_operation:0421 name: Protein folding site prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2415 ! Protein folding analysis is_a: EDAM_operation:3087 ! Protein site detection relationship: has_output EDAM_data:2989 ! Protein features (key folding sites) [Term] id: EDAM_operation:0422 name: Protein cleavage site prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect or predict cleavage sites (enzymatic or chemical) in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3087 ! Protein site detection relationship: has_output EDAM_data:1323 ! Protein features (cleavage sites) relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_operation:0423 name: Epitope mapping (MHC Class I) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict epitopes that bind to MHC class I molecules." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0416 ! Epitope mapping [Term] id: EDAM_operation:0424 name: Epitope mapping (MHC Class II) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict epitopes that bind to MHC class II molecules." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0416 ! Epitope mapping [Term] id: EDAM_operation:0425 name: Whole gene prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2454 ! Gene and gene component prediction [Term] id: EDAM_operation:0426 name: Gene component prediction comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2454 ! Gene and gene component prediction [Term] id: EDAM_operation:0427 name: Transposon prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1301 ! Nucleic acid features (mobile genetic elements) [Term] id: EDAM_operation:0428 name: PolyA signal detection subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect polyA signals in nucleotide sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1302 ! Nucleic acid features (PolyA signal or site) [Term] id: EDAM_operation:0429 name: Quadruplex formation site detection comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. subset: bioinformatics subset: edam subset: operations synonym: "Quadruplex structure prediction" EXACT [] created_in: "beta12orEarlier" def: "Detect quadruplex-forming motifs in nucleotide sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1303 ! Nucleic acid features (quadruplexes) relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_operation:0430 name: CpG island and isochore detection 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: bioinformatics subset: edam subset: operations synonym: "CpG island and isochores detection" EXACT [] synonym: "CpG island and isochores rendering" EXACT [] created_in: "beta12orEarlier" def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1304 ! Nucleic acid features (CpG island and isochore) relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] id: EDAM_operation:0431 name: Restriction site recognition subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1305 ! Nucleic acid features (restriction sites) relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction [Term] id: EDAM_operation:0432 name: Nucleosome formation or exclusion sequence prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1306 ! Nucleic acid features (nucleosome exclusion sequences) [Term] id: EDAM_operation:0433 name: Splice site prediction comment: Methods might require a pre-mRNA or genomic DNA sequence. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify, predict or analyse splice sites in nucleotide sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1307 ! Nucleic acid features (splice sites) relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] id: EDAM_operation:0434 name: Integrated gene prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict whole gene structure using a combination of multiple methods to achieve better predictions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0425 ! Whole gene prediction [Term] id: EDAM_operation:0435 name: Operon prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Find operons (operators, promoters and genes) in bacteria genes." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0425 ! Whole gene prediction [Term] id: EDAM_operation:0436 name: Coding region prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0426 ! Gene component prediction relationship: has_output EDAM_data:1313 ! Nucleic acid features (coding sequence) [Term] id: EDAM_operation:0437 name: Selenocysteine insertion sequence (SECIS) prediction comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0426 ! Gene component prediction relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_operation:0438 name: Transcription regulatory element prediction 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0426 ! Gene component prediction relationship: has_topic EDAM_topic:0110 ! Transcription relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites [Term] id: EDAM_operation:0439 name: Translation initiation site prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict translation initiation sites, possibly by searching a database of sites." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0436 ! Coding region prediction relationship: has_topic EDAM_topic:0108 ! Translation [Term] id: EDAM_operation:0440 name: Promoter prediction comment: Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0438 ! Transcription regulatory element prediction relationship: has_output EDAM_data:1312 ! Gene features (promoter) [Term] id: EDAM_operation:0441 name: Transcription regulatory element prediction (DNA-cis) 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] id: EDAM_operation:0442 name: Transcription regulatory element prediction (RNA-cis) 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0438 ! Transcription regulatory element prediction [Term] id: EDAM_operation:0443 name: Transcription regulatory element prediction (trans) comment: Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. subset: bioinformatics subset: edam subset: operations synonym: "Functional RNA identification" EXACT [] created_in: "beta12orEarlier" def: "Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0438 ! Transcription regulatory element prediction relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_operation:0444 name: Matrix/scaffold attachment site prediction 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0438 ! Transcription regulatory element prediction relationship: has_output EDAM_data:1308 ! Nucleic acid features (matrix/scaffold attachment sites) [Term] id: EDAM_operation:0445 name: Transcription factor binding site prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict transcription factor binding sites in DNA sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0440 ! Promoter prediction relationship: has_output EDAM_data:1315 ! Gene features (TFBS) [Term] id: EDAM_operation:0446 name: Exonic splicing enhancer prediction 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict exonic splicing enhancers (ESE) in exons." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0440 ! Promoter prediction relationship: has_output EDAM_data:2397 ! Nucleic acid features (exon) relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] id: EDAM_operation:0447 name: Sequence alignment quality evaluation comment: Evaluation might be purely sequence-based or use structural information. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Evaluate molecular sequence alignment accuracy." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2428 ! Evaluation and validation [Term] id: EDAM_operation:0448 name: Sequence alignment analysis (conservation) comment: Use this concept 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0258 ! Sequence alignment analysis relationship: has_output EDAM_data:1415 ! Sequence alignment report (site conservation) [Term] id: EDAM_operation:0449 name: Sequence alignment analysis (site correlation) comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse correlations between sites in a molecular sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0258 ! Sequence alignment analysis relationship: has_output EDAM_data:1416 ! Sequence alignment report (site correlation) [Term] id: EDAM_operation:0450 name: Sequence alignment analysis (chimeric sequence detection) 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detects chimeric sequences (chimeras) from a sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] id: EDAM_operation:0451 name: Sequence alignment analysis (recombination detection) comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] id: EDAM_operation:0452 name: Sequence alignment analysis (indel detection) comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify insertion, deletion and duplication events from a sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) [Term] id: EDAM_operation:0453 name: Nucleosome formation potential prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict nucleosome formation potential of DNA sequences." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0432 ! Nucleosome formation or exclusion sequence prediction [Term] id: EDAM_operation:0455 name: Nucleic acid thermodynamic property calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0262 ! Nucleic acid property calculation relationship: has_output EDAM_data:2985 ! Nucleic acid thermodynamic data [Term] id: EDAM_operation:0456 name: Nucleic acid melting profile plotting comment: A melting profile is used to visualise and analyse partly melted DNA conformations. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate and plot a DNA or DNA/RNA melting profile." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0262 ! Nucleic acid property calculation relationship: has_output EDAM_data:1583 ! Nucleic acid melting profile [Term] id: EDAM_operation:0457 name: Nucleic acid stitch profile plotting comment: A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate and plot a DNA or DNA/RNA stitch profile." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting relationship: has_output EDAM_data:1587 ! Nucleic acid stitch profile [Term] id: EDAM_operation:0458 name: Nucleic acid melting curve plotting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate and plot a DNA or DNA/RNA melting curve." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting relationship: has_output EDAM_data:2958 ! Nucleic acid melting curve [Term] id: EDAM_operation:0459 name: Nucleic acid probability profile plotting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate and plot a DNA or DNA/RNA probability profile." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting relationship: has_output EDAM_data:2959 ! Nucleic acid probability profile [Term] id: EDAM_operation:0460 name: Nucleic acid temperature profile plotting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate and plot a DNA or DNA/RNA temperature profile." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting relationship: has_output EDAM_data:2960 ! Nucleic acid temperature profile [Term] id: EDAM_operation:0461 name: Nucleic acid curvature calculation comment: This includes properties such as. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate curvature and flexibility / stiffness of a nucleotide sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0262 ! Nucleic acid property calculation relationship: has_output EDAM_data:0912 ! Nucleic acid property relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:0463 name: microRNA detection subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) relationship: has_output EDAM_data:1310 ! Nucleic acid features (microRNA) [Term] id: EDAM_operation:0464 name: tRNA gene prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0425 ! Whole gene prediction relationship: has_topic EDAM_topic:0663 ! tRNA [Term] id: EDAM_operation:0465 name: siRNA binding specificity prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_operation:0467 name: Protein secondary structure prediction (integrated) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0468 name: Protein secondary structure prediction (helices) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict helical secondary structure of protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0469 name: Protein secondary structure prediction (turns) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict turn structure (for example beta hairpin turns) of protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0470 name: Protein secondary structure prediction (coils) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0471 name: Protein secondary structure prediction (disulfide bonds) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict cysteine bonding state and disulfide bond partners in protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_operation:0472 name: GPCR prediction subset: bioinformatics subset: edam subset: operations synonym: "G protein-coupled receptor (GPCR) prediction" EXACT [] created_in: "beta12orEarlier" def: "Predict G protein-coupled receptors (GPCR)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0269 ! Transmembrane protein prediction is_a: EDAM_operation:0473 ! GPCR analysis [Term] id: EDAM_operation:0473 name: GPCR analysis subset: bioinformatics subset: edam subset: operations synonym: "G protein-coupled receptor (GPCR) analysis" EXACT [] created_in: "beta12orEarlier" def: "Analyse G-protein coupled receptor proteins (GPCRs)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0270 ! Transmembrane protein analysis relationship: has_output EDAM_data:1456 ! Protein features (membrane regions) relationship: has_topic EDAM_topic:0820 ! Membrane proteins [Term] id: EDAM_operation:0474 name: Protein structure prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict tertiary structure (backbone and side-chain conformation) of protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0271 ! Structure prediction is_a: EDAM_operation:2459 ! Structure processing (protein) is_a: EDAM_operation:2479 ! Protein sequence analysis is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:1460 ! Protein structure relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction [Term] id: EDAM_operation:0475 name: Nucleic acid structure prediction comment: Methods might identify thermodynamically stable or evolutionarily conserved structures. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict tertiary structure of DNA or RNA." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0271 ! Structure prediction is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:2519 ! Structure processing (nucleic acid) is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:1459 ! Nucleic acid structure relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_operation:0476 name: Ab initio structure prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict tertiary structure of protein sequence(s) without homologs of known structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0474 ! Protein structure prediction relationship: has_topic EDAM_topic:0174 ! Ab initio structure prediction [Term] id: EDAM_operation:0477 name: Protein modelling 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: bioinformatics subset: edam subset: operations synonym: "Comparative modelling" EXACT [] synonym: "Homology modelling" EXACT [] synonym: "Homology structure modelling" EXACT [] synonym: "Protein structure comparative modelling" EXACT [] created_in: "beta12orEarlier" def: "Build a three-dimensional protein model based on known (for example homologs) structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0474 ! Protein structure prediction is_a: EDAM_operation:2406 ! Protein structure analysis is_a: EDAM_operation:2426 ! Modelling and simulation relationship: has_topic EDAM_topic:0175 ! Homology modelling [Term] id: EDAM_operation:0478 name: Protein docking 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0477 ! Protein modelling is_a: EDAM_operation:2492 ! Protein interaction prediction relationship: has_output EDAM_data:1461 ! Protein-ligand complex relationship: has_output EDAM_data:2877 ! Protein complex relationship: has_topic EDAM_topic:0177 ! Molecular docking [Term] id: EDAM_operation:0479 name: Protein modelling (backbone) comment: Methods might require a preliminary C(alpha) trace. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Model protein backbone conformation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0477 ! Protein modelling [Term] id: EDAM_operation:0480 name: Protein modelling (side chains) comment: Methods might use a residue rotamer library. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0477 ! Protein modelling [Term] id: EDAM_operation:0481 name: Protein modelling (loops) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Model loop conformation in protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0477 ! Protein modelling [Term] id: EDAM_operation:0482 name: Protein-ligand docking comment: Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. subset: bioinformatics subset: edam subset: operations synonym: "Virtual ligand screening" EXACT [] created_in: "beta12orEarlier" def: "Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0478 ! Protein docking relationship: has_output EDAM_data:1461 ! Protein-ligand complex relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] id: EDAM_operation:0483 name: Structured RNA prediction and optimisation subset: bioinformatics subset: edam subset: operations synonym: "Nucleic acid folding family identification" EXACT [] synonym: "RNA inverse folding" EXACT [] created_in: "beta12orEarlier" def: "Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2425 ! Optimisation and refinement is_a: EDAM_operation:3095 ! Nucleic acid design relationship: has_output EDAM_data:1234 ! Sequence set (nucleic acid) relationship: has_topic EDAM_topic:2953 ! Nucleic acid design [Term] id: EDAM_operation:0484 name: SNP detection comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. subset: bioinformatics subset: edam subset: operations synonym: "Single nucleotide polymorphism detection" EXACT [] created_in: "beta12orEarlier" def: "Find single nucleotide polymorphisms (SNPs) between sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:0415 ! Nucleic acid feature prediction is_a: EDAM_operation:3202 ! Mutation detection relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) [Term] id: EDAM_operation:0485 name: Radiation Hybrid Mapping subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2944 ! Physical mapping relationship: has_output EDAM_data:2870 ! Radiation hybrid map [Term] id: EDAM_operation:0486 name: Functional mapping comment: This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Map the genetic architecture of dynamic complex traits." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0282 ! Genetic mapping [Term] id: EDAM_operation:0487 name: Haplotype inference comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. 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: bioinformatics subset: edam subset: operations synonym: "Haplotype mapping" EXACT [] synonym: "Haplotype reconstruction" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0283 ! Linkage analysis relationship: has_output EDAM_data:1863 ! Haplotype map [Term] id: EDAM_operation:0488 name: Linkage disequilibrium calculation 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0283 ! Linkage analysis relationship: has_output EDAM_data:1634 ! Gene annotation (linkage disequilibrium) [Term] id: EDAM_operation:0489 name: Genetic code prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict genetic code from analysis of codon usage data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0286 ! Codon usage analysis is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:1598 ! Genetic code [Term] id: EDAM_operation:0490 name: Dotplot plotting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Draw a dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0288 ! Sequence word comparison is_a: EDAM_operation:0565 ! Sequence alignment rendering relationship: has_output EDAM_data:0862 ! Dotplot [Term] id: EDAM_operation:0491 name: Pairwise sequence alignment construction comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: bioinformatics subset: edam subset: operations synonym: "Pairwise sequence alignment" EXACT [] created_in: "beta12orEarlier" def: "Align exactly two molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0292 ! Sequence alignment construction relationship: has_output EDAM_data:1381 ! Sequence alignment (pair) [Term] id: EDAM_operation:0492 name: Multiple sequence alignment construction 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: bioinformatics subset: edam subset: operations synonym: "Multiple sequence alignment" EXACT [] created_in: "beta12orEarlier" def: "Align two or more molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0292 ! Sequence alignment construction [Term] id: EDAM_operation:0493 name: Pairwise sequence alignment construction (local) comment: Local alignment methods identify regions of local similarity. subset: bioinformatics subset: edam subset: operations synonym: "Local pairwise sequence alignment construction" EXACT [] synonym: "Pairwise sequence alignment (local)" EXACT [] created_in: "beta12orEarlier" def: "Locally align exactly two molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction [Term] id: EDAM_operation:0494 name: Pairwise sequence alignment construction (global) comment: Global alignment methods identify similarity across the entire length of the sequences. subset: bioinformatics subset: edam subset: operations synonym: "Global pairwise sequence alignment construction" EXACT [] synonym: "Pairwise sequence alignment (global)" EXACT [] created_in: "beta12orEarlier" def: "Globally align exactly two molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction [Term] id: EDAM_operation:0495 name: Multiple sequence alignment construction (local) comment: Local alignment methods identify regions of local similarity. subset: bioinformatics subset: edam subset: operations synonym: "Local multiple sequence alignment construction" EXACT [] synonym: "Multiple sequence alignment (local)" EXACT [] created_in: "beta12orEarlier" def: "Locally align two or more molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] id: EDAM_operation:0496 name: Multiple sequence alignment construction (global) comment: Global alignment methods identify similarity across the entire length of the sequences. subset: bioinformatics subset: edam subset: operations synonym: "Global multiple sequence alignment construction" EXACT [] synonym: "Multiple sequence alignment (global)" EXACT [] created_in: "beta12orEarlier" def: "Globally align two or more molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] id: EDAM_operation:0497 name: Multiple sequence alignment construction (constrained) subset: bioinformatics subset: edam subset: operations synonym: "Constrained multiple sequence alignment construction" EXACT [] synonym: "Multiple sequence alignment (constrained)" EXACT [] created_in: "beta12orEarlier" def: "Align two or more molecular sequences with user-defined constraints." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] id: EDAM_operation:0498 name: Multiple sequence alignment construction (consensus) subset: bioinformatics subset: edam subset: operations synonym: "Consensus multiple sequence alignment construction" EXACT [] synonym: "Multiple sequence alignment (consensus)" EXACT [] created_in: "beta12orEarlier" def: "Align two or more molecular sequences using multiple methods to achieve higher quality." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] id: EDAM_operation:0499 name: Multiple sequence alignment construction (phylogenetic tree-based) comment: This is supposed to give a more biologically meaningful alignment than standard alignments. subset: bioinformatics subset: edam subset: operations synonym: "Multiple sequence alignment (phylogenetic tree-based)" EXACT [] synonym: "Phylogenetic tree-based multiple sequence alignment construction" EXACT [] created_in: "beta12orEarlier" def: "Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0492 ! Multiple sequence alignment construction relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:0500 name: Secondary structure alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Secondary structure alignment" EXACT [] created_in: "beta12orEarlier" def: "Align molecular secondary structure (represented as a 1D string)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0294 ! Structure-based sequence alignment construction is_a: EDAM_operation:2482 ! Secondary structure processing is_a: EDAM_operation:2931 ! Secondary structure comparison relationship: has_output EDAM_data:2366 ! Secondary structure alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:0501 name: Protein secondary structure alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Protein secondary structure alignment" EXACT [] synonym: "Secondary structure alignment (protein)" EXACT [] created_in: "beta12orEarlier" def: "Align protein secondary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0500 ! Secondary structure alignment construction is_a: EDAM_operation:2488 ! Protein secondary structure comparison relationship: has_output EDAM_data:0878 ! Secondary structure alignment (protein) [Term] id: EDAM_operation:0502 name: RNA secondary structure alignment construction subset: bioinformatics subset: edam subset: operations synonym: "RNA secondary structure alignment" EXACT [] synonym: "Secondary structure alignment (RNA)" EXACT [] created_in: "beta12orEarlier" def: "Align RNA secondary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0500 ! Secondary structure alignment construction is_a: EDAM_operation:2439 ! RNA secondary structure processing relationship: has_input EDAM_data:0880 ! RNA secondary structure record relationship: has_output EDAM_data:0881 ! Secondary structure alignment (RNA) [Term] id: EDAM_operation:0503 name: Pairwise structure alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Pairwise structure alignment" EXACT [] created_in: "beta12orEarlier" def: "Align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:0504 name: Multiple structure alignment construction comment: This includes methods that use an existing alignment. subset: bioinformatics subset: edam subset: operations synonym: "Multiple structure alignment" EXACT [] created_in: "beta12orEarlier" def: "Align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:0505 name: Structure alignment (protein) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Align protein tertiary structures." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:0506 name: Structure alignment (RNA) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Align RNA tertiary structures." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:0507 name: Pairwise structure alignment construction (local) comment: Local alignment methods identify regions of local similarity, common substructures etc. subset: bioinformatics subset: edam subset: operations synonym: "Local pairwise structure alignment construction" EXACT [] synonym: "Pairwise structure alignment (local)" EXACT [] created_in: "beta12orEarlier" def: "Locally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0503 ! Pairwise structure alignment construction [Term] id: EDAM_operation:0508 name: Pairwise structure alignment construction (global) comment: Global alignment methods identify similarity across the entire structures. subset: bioinformatics subset: edam subset: operations synonym: "Global pairwise structure alignment construction" EXACT [] synonym: "Pairwise structure alignment (global)" EXACT [] created_in: "beta12orEarlier" def: "Globally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0503 ! Pairwise structure alignment construction [Term] id: EDAM_operation:0509 name: Multiple structure alignment construction (local) comment: Local alignment methods identify regions of local similarity, common substructures etc. subset: bioinformatics subset: edam subset: operations synonym: "Local multiple structure alignment construction" EXACT [] synonym: "Multiple structure alignment (local)" EXACT [] created_in: "beta12orEarlier" def: "Locally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0504 ! Multiple structure alignment construction [Term] id: EDAM_operation:0510 name: Multiple structure alignment construction (global) comment: Global alignment methods identify similarity across the entire structures. subset: bioinformatics subset: edam subset: operations synonym: "Global multiple structure alignment construction" EXACT [] synonym: "Multiple structure alignment (global)" EXACT [] created_in: "beta12orEarlier" def: "Globally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0504 ! Multiple structure alignment construction [Term] id: EDAM_operation:0511 name: Sequence profile alignment construction (pairwise) comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: bioinformatics subset: edam subset: operations synonym: "Pairwise sequence profile alignment construction" EXACT [] synonym: "Sequence profile alignment (pairwise)" EXACT [] created_in: "beta12orEarlier" def: "Align exactly two molecular profiles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0298 ! Sequence profile alignment construction [Term] id: EDAM_operation:0512 name: Sequence profile alignment construction (multiple) subset: bioinformatics subset: edam subset: operations synonym: "Multiple sequence profile alignment construction" EXACT [] synonym: "Sequence profile alignment (multiple)" EXACT [] created_in: "beta12orEarlier" def: "Align two or more molecular profiles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0298 ! Sequence profile alignment construction [Term] id: EDAM_operation:0513 name: Structural (3D) profile alignment construction (pairwise) comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. subset: bioinformatics subset: edam subset: operations synonym: "Pairwise structural (3D) profile alignment construction" EXACT [] synonym: "Structural (3D) profile alignment (pairwise)" EXACT [] created_in: "beta12orEarlier" def: "Align exactly two molecular Structural (3D) profiles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction [Term] id: EDAM_operation:0514 name: Structural (3D) profile alignment construction (multiple) subset: bioinformatics subset: edam subset: operations synonym: "Multiple structural (3D) profile alignment construction" EXACT [] synonym: "Structural (3D) profile alignment (multiple)" EXACT [] created_in: "beta12orEarlier" def: "Align two or more molecular 3D profiles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction [Term] id: EDAM_operation:0515 name: Data retrieval (tool metadata) subset: bioinformatics subset: edam subset: operations synonym: "Data retrieval (tool annotation)" EXACT [] synonym: "Tool information retrieval" EXACT [] created_in: "beta12orEarlier" def: "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) relationship: has_output EDAM_data:0958 ! Tool metadata [Term] id: EDAM_operation:0516 name: Data retrieval (database metadata) subset: bioinformatics subset: edam subset: operations synonym: "Data retrieval (database annotation)" EXACT [] synonym: "Database information retrieval" EXACT [] created_in: "beta12orEarlier" def: "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) relationship: has_output EDAM_data:0957 ! Database metadata [Term] id: EDAM_operation:0517 name: PCR primer design (for large scale sequencing) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict primers for large scale sequencing." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0308 ! PCR primer design relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:0518 name: PCR primer design (for genotyping polymorphisms) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0308 ! PCR primer design [Term] id: EDAM_operation:0519 name: PCR primer design (for gene transcription profiling) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict primers for gene transcription profiling." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0308 ! PCR primer design relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] id: EDAM_operation:0520 name: PCR primer design (for conserved primers) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict primers that are conserved across multiple genomes or species." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0308 ! PCR primer design [Term] id: EDAM_operation:0521 name: PCR primer design (based on gene structure) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict primers based on gene structure, promoters, exon-exon junctions etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0308 ! PCR primer design relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] id: EDAM_operation:0522 name: PCR primer design (for methylation PCRs) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict primers for methylation PCRs." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0308 ! PCR primer design [Term] id: EDAM_operation:0523 name: Sequence assembly (mapping assembly) comment: The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Sequence assembly by combining fragments using an existing backbone sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:0524 name: Sequence assembly (de-novo assembly) comment: De-novo assemblers are much slower and more memory intensive than mapping assemblers. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Sequence assembly by combining fragments into a new, previously unknown sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:0525 name: Sequence assembly (genome assembly) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Sequence assembly capable on a very large scale such as assembly of whole genomes." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:0526 name: Sequence assembly (EST assembly) comment: Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Sequence assembly for EST sequences (transcribed mRNA)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:0527 name: Tag mapping comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. subset: bioinformatics subset: edam subset: operations synonym: "Tag to gene assignment" EXACT [] created_in: "beta12orEarlier" def: "Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2436 ! Gene expression profile annotation relationship: has_output EDAM_data:0936 ! Sequence tag profile (with gene assignment) [Term] id: EDAM_operation:0528 name: SAGE data processing subset: bioinformatics subset: edam subset: operations synonym: "Serial analysis of gene expression data processing" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) serial analysis of gene expression (SAGE) data." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:0529 name: MPSS data processing subset: bioinformatics subset: edam subset: operations synonym: "Massively parallel signature sequencing data processing" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) massively parallel signature sequencing (MPSS) data." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:0530 name: SBS data processing subset: bioinformatics subset: edam subset: operations synonym: "Sequencing by synthesis data processing" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) sequencing by synthesis (SBS) data." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:0531 name: Heat map generation 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a heat map of gene expression from microarray data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering relationship: has_output EDAM_data:1636 ! Heat map [Term] id: EDAM_operation:0532 name: Gene expression profile analysis subset: bioinformatics subset: edam subset: operations synonym: "Functional profiling" EXACT [] created_in: "beta12orEarlier" def: "Analyse one or more gene expression profiles, typically to interpret them in functional terms." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2435 ! Gene expression profile processing relationship: has_input EDAM_data:0928 ! Gene expression profile [Term] id: EDAM_operation:0533 name: Gene expression profile pathway mapping subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0532 ! Gene expression profile analysis is_a: EDAM_operation:2497 ! Pathway or network analysis relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_operation:0534 name: Protein secondary structure assignment (from coordinate data) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assign secondary structure from protein coordinate data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0319 ! Protein secondary structure assignment is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) [Term] id: EDAM_operation:0535 name: Protein secondary structure assignment (from CD data) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assign secondary structure from circular dichroism (CD) spectroscopic data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0319 ! Protein secondary structure assignment relationship: has_input EDAM_data:0939 ! Protein circular dichroism (CD) spectroscopic data [Term] id: EDAM_operation:0536 name: Protein structure assignment (from X-ray crystallographic data) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0320 ! Protein structure assignment relationship: has_input EDAM_data:0937 ! Protein X-ray crystallographic data [Term] id: EDAM_operation:0537 name: Protein structure assignment (from NMR data) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0320 ! Protein structure assignment relationship: has_input EDAM_data:0938 ! Protein NMR data [Term] id: EDAM_operation:0538 name: Phylogenetic tree construction (data centric) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Construct a phylogenetic tree from a specific type of data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0323 ! Phylogenetic tree construction [Term] id: EDAM_operation:0539 name: Phylogenetic tree construction (method centric) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Construct a phylogenetic tree using a specific method." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0323 ! Phylogenetic tree construction [Term] id: EDAM_operation:0540 name: Phylogenetic tree construction (from molecular sequences) comment: Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Phylogenetic tree construction from molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) is_a: EDAM_operation:2403 ! Sequence analysis [Term] id: EDAM_operation:0541 name: Phylogenetic tree construction (from continuous quantitative characters) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Phylogenetic tree construction from continuous quantitative character data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) relationship: has_input EDAM_data:1426 ! Phylogenetic continuous quantitative data [Term] id: EDAM_operation:0542 name: Phylogenetic tree construction (from gene frequencies) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Phylogenetic tree construction from gene frequency data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) relationship: has_input EDAM_data:2873 ! Phylogenetic gene frequencies data relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] id: EDAM_operation:0543 name: Phylogenetic tree construction (from polymorphism data) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) relationship: has_topic EDAM_topic:0199 ! Genetic variation [Term] id: EDAM_operation:0544 name: Phylogenetic species tree construction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences) [Term] id: EDAM_operation:0545 name: Phylogenetic tree construction (parsimony methods) comment: This includes evolutionary parsimony (invariants) methods. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0546 name: Phylogenetic tree construction (minimum distance methods) comment: This includes neighbor joining (NJ) clustering method. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0547 name: Phylogenetic tree construction (maximum likelihood and Bayesian methods) 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0548 name: Phylogenetic tree construction (quartet methods) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0549 name: Phylogenetic tree construction (AI methods) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric) [Term] id: EDAM_operation:0550 name: Sequence alignment analysis (phylogenetic modelling) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify a plausible model of DNA substitution that explains a DNA sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2426 ! Modelling and simulation is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid) relationship: has_output EDAM_data:1439 ! DNA substitution model relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:0551 name: Phylogenetic tree analysis (shape) subset: bioinformatics subset: edam subset: operations synonym: "Phylogenetic tree topology analysis" EXACT [] created_in: "beta12orEarlier" def: "Analyse the shape (topology) of a phylogenetic tree." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0324 ! Phylogenetic tree analysis relationship: has_output EDAM_data:1440 ! Phylogenetic tree report (tree shape) [Term] id: EDAM_operation:0552 name: Phylogenetic tree bootstrapping subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0324 ! Phylogenetic tree analysis is_a: EDAM_operation:2428 ! Evaluation and validation relationship: has_output EDAM_data:1441 ! Phylogenetic tree report (tree evaluation) [Term] id: EDAM_operation:0553 name: Phylogenetic tree analysis (gene family prediction) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict families of genes and gene function based on their position in a phylogenetic tree." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0324 ! Phylogenetic tree analysis relationship: has_output EDAM_data:0916 ! Gene annotation relationship: has_topic EDAM_topic:0194 ! Phylogenomics [Term] id: EDAM_operation:0554 name: Phylogenetic tree analysis (natural selection) 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0324 ! Phylogenetic tree analysis [Term] id: EDAM_operation:0555 name: Phylogenetic tree construction (consensus) comment: Methods typically test for topological similarity between trees using for example a congruence index. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more phylogenetic trees to produce a consensus tree." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0323 ! Phylogenetic tree construction is_a: EDAM_operation:0325 ! Phylogenetic tree comparison [Term] id: EDAM_operation:0556 name: Phylogenetic sub/super tree detection subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more phylogenetic trees to detect subtrees or supertrees." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0325 ! Phylogenetic tree comparison [Term] id: EDAM_operation:0557 name: Phylogenetic tree distances calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more phylogenetic trees to calculate distances between trees." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0325 ! Phylogenetic tree comparison relationship: has_output EDAM_data:1442 ! Phylogenetic tree report (tree distances) [Term] id: EDAM_operation:0558 name: Phylogenetic tree annotation subset: bioinformatics subset: edam subset: operations synonym: "CDAOAnnotation" RELATED [] created_in: "beta12orEarlier" def: "Annotate a phylogenetic tree with terms from a controlled vocabulary." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0226 ! Annotation is_a: EDAM_operation:0326 ! Phylogenetic tree editing [Term] id: EDAM_operation:0559 name: Peptide immunogen prediction and optimisation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict and optimise peptide ligands that elicit an immunological response." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_output EDAM_data:1460 ! Protein structure relationship: has_topic EDAM_topic:0150 ! Protein design relationship: has_topic EDAM_topic:0804 ! Immunoinformatics [Term] id: EDAM_operation:0560 name: DNA vaccine prediction and optimisation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict or optimise DNA to elicit (via DNA vaccination) an immunological response." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2425 ! Optimisation and refinement is_a: EDAM_operation:3095 ! Nucleic acid design relationship: has_topic EDAM_topic:0804 ! Immunoinformatics relationship: has_topic EDAM_topic:2953 ! Nucleic acid design [Term] id: EDAM_operation:0561 name: Sequence reformatting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Reformat (a file or other report of) molecular sequence(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0335 ! File reformatting is_a: EDAM_operation:2121 ! Sequence file processing [Term] id: EDAM_operation:0562 name: Sequence alignment reformatting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Reformat (a file or other report of) molecular sequence alignment(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0335 ! File reformatting is_a: EDAM_operation:2122 ! Sequence alignment file processing [Term] id: EDAM_operation:0563 name: Codon usage table reformatting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Reformat a codon usage table." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0335 ! File reformatting is_a: EDAM_operation:2433 ! Codon usage table processing relationship: has_input EDAM_data:1597 ! Codon usage table relationship: has_output EDAM_data:1597 ! Codon usage table [Term] id: EDAM_operation:0564 name: Sequence rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise, format or render a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 ! Sequence relationship: has_output EDAM_data:2969 ! Sequence image [Term] id: EDAM_operation:0565 name: Sequence alignment rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise, format or print a molecular sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2463 ! Sequence alignment processing relationship: has_input EDAM_data:0863 ! Sequence alignment relationship: has_output EDAM_data:1711 ! Sequence alignment image [Term] id: EDAM_operation:0566 name: Sequence cluster rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise, format or render sequence clusters." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2452 ! Sequence cluster processing relationship: has_input EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_operation:0567 name: Phylogenetic tree rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise or plot a phylogenetic tree." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2443 ! Phylogenetic tree processing relationship: has_output EDAM_data:0872 ! Phylogenetic tree [Term] id: EDAM_operation:0568 name: RNA secondary structure rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2439 ! RNA secondary structure processing relationship: has_input EDAM_data:0880 ! RNA secondary structure record [Term] id: EDAM_operation:0569 name: Protein secondary structure rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Render and visualise protein secondary structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2444 ! Protein secondary structure processing relationship: has_input EDAM_data:0876 ! Protein features (secondary structure) [Term] id: EDAM_operation:0570 name: Structure rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2465 ! Structure processing relationship: has_input EDAM_data:0883 ! Structure relationship: has_output EDAM_data:1710 ! Structure image [Term] id: EDAM_operation:0571 name: Microarray data rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise microarray data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2435 ! Gene expression profile processing relationship: has_input EDAM_data:3117 ! Microarray hybridisation data relationship: has_output EDAM_data:2967 ! Microarray image [Term] id: EDAM_operation:0572 name: Protein interaction network rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify and analyse networks of protein interactions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2445 ! Protein interaction network processing is_a: EDAM_operation:3083 ! Pathway or network rendering relationship: has_input EDAM_data:1663 ! Pathway or network (protein-protein interaction) [Term] id: EDAM_operation:0573 name: Map rendering subset: bioinformatics subset: edam subset: operations synonym: "DNA map rendering" EXACT [] created_in: "beta12orEarlier" def: "Render and visualise a DNA map." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) is_a: EDAM_operation:2521 ! Map data processing relationship: has_input EDAM_data:1274 ! Map [Term] id: EDAM_operation:0574 name: Sequence motif rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Render a sequence with motifs." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0564 ! Sequence rendering [Term] id: EDAM_operation:0575 name: Restriction map rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise restriction maps in DNA sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0431 ! Restriction site recognition is_a: EDAM_operation:0573 ! Map rendering relationship: has_output EDAM_data:1289 ! Restriction map [Term] id: EDAM_operation:0577 name: DNA linear map rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Draw a linear maps of DNA." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0573 ! Map rendering [Term] id: EDAM_operation:0578 name: DNA circular map rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Draw a circular maps of DNA, for example a plasmid map." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0573 ! Map rendering [Term] id: EDAM_operation:0579 name: Operon rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise operon structure etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0573 ! Map rendering relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] id: EDAM_operation:1768 name: Nucleic acid folding family identification subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify folding families of related RNAs." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0483 ! Structured RNA prediction and optimisation [Term] id: EDAM_operation:1769 name: Nucleic acid folding energy calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0279 ! Nucleic acid folding analysis [Term] id: EDAM_operation:1774 name: Annotation retrieval comment: Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Retrieve existing annotation (or documentation), typically annotation on a database entity." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:1777 name: Protein function prediction comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict general functional properties of a protein." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2414 ! Protein function analysis is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_topic EDAM_topic:2276 ! Protein function prediction [Term] id: EDAM_operation:1778 name: Protein function comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare the functional properties of two or more proteins." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2414 ! Protein function analysis is_a: EDAM_operation:2997 ! Protein comparison relationship: has_topic EDAM_topic:1775 ! Protein function analysis [Term] id: EDAM_operation:1780 name: Sequence submission subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Submit a molecular sequence to a database." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 ! Sequence relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition [Term] id: EDAM_operation:1781 name: Gene regulatory network analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse a known network of gene regulation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2496 ! Gene regulatory network processing is_a: EDAM_operation:2497 ! Pathway or network analysis relationship: has_input EDAM_data:2961 ! Pathway or network (gene regulation) [Term] id: EDAM_operation:1812 name: Data loading subset: bioinformatics subset: edam subset: operations synonym: "Data submission" EXACT [] synonym: "Database submission" EXACT [] xref: WHATIF:UploadPDB created_in: "beta12orEarlier" def: "Prepare or load a user-specified data file so that it is available for use." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2409 ! File processing relationship: has_input EDAM_data:0842 ! Identifier [Term] id: EDAM_operation:1813 name: Sequence retrieval comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. subset: bioinformatics subset: edam subset: operations synonym: "Data retrieval (sequences)" EXACT [] created_in: "beta12orEarlier" def: "Query a sequence data resource (typically a database) and retrieve sequences and / or annotation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2422 ! Data retrieval is_a: EDAM_operation:2446 ! Sequence processing relationship: has_output EDAM_data:2044 ! Sequence [Term] id: EDAM_operation:1814 name: Structure retrieval comment: This includes direct retrieval methods but not those that perform calculations on the sequence or structure. subset: bioinformatics subset: edam subset: operations xref: WHATIF:DownloadPDB xref: WHATIF:EchoPDB created_in: "beta12orEarlier" def: "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2422 ! Data retrieval is_a: EDAM_operation:2465 ! Structure processing relationship: has_output EDAM_data:0883 ! Structure [Term] id: EDAM_operation:1816 name: Surface rendering comment: A dot has three coordinates (x,y,z) and (typically) a color. subset: bioinformatics subset: edam subset: operations xref: WHATIF:GetSurfaceDots created_in: "beta12orEarlier" def: "Calculate the positions of dots that are homogeneously distributed over the surface of a molecule." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0570 ! Structure rendering is_a: EDAM_operation:2462 ! Protein surface calculation [Term] id: EDAM_operation:1817 name: Protein atom surface calculation (accessible) comment: Waters are not considered. subset: bioinformatics subset: edam subset: operations xref: WHATIF:AtomAccessibilitySolvent xref: WHATIF:AtomAccessibilitySolventPlus created_in: "beta12orEarlier" def: "Calculate the solvent accessibility ('accessible surface') for each atom in a structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2460 ! Protein atom surface calculation [Term] id: EDAM_operation:1818 name: Protein atom surface calculation (accessible molecular) comment: Waters are not considered. subset: bioinformatics subset: edam subset: operations xref: WHATIF:AtomAccessibilityMolecular xref: WHATIF:AtomAccessibilityMolecularPlus created_in: "beta12orEarlier" def: "Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2460 ! Protein atom surface calculation [Term] id: EDAM_operation:1819 name: Protein residue surface calculation (accessible) comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). subset: bioinformatics subset: edam subset: operations xref: WHATIF:ResidueAccessibilitySolvent created_in: "beta12orEarlier" def: "Calculate the solvent accessibility ('accessible surface') for each residue in a structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] id: EDAM_operation:1820 name: Protein residue surface calculation (vacuum accessible) comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). subset: bioinformatics subset: edam subset: operations xref: WHATIF:ResidueAccessibilityVacuum created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] id: EDAM_operation:1821 name: Protein residue surface calculation (accessible molecular) comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). subset: bioinformatics subset: edam subset: operations xref: WHATIF:ResidueAccessibilityMolecular created_in: "beta12orEarlier" def: "Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] id: EDAM_operation:1822 name: Protein residue surface calculation (vacuum molecular) comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). subset: bioinformatics subset: edam subset: operations xref: WHATIF:ResidueAccessibilityVacuumMolecular created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2461 ! Protein residue surface calculation [Term] id: EDAM_operation:1823 name: Protein surface calculation (accessible molecular) subset: bioinformatics subset: edam subset: operations xref: WHATIF:TotAccessibilityMolecular created_in: "beta12orEarlier" def: "Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2462 ! Protein surface calculation [Term] id: EDAM_operation:1824 name: Protein surface calculation (accessible) subset: bioinformatics subset: edam subset: operations xref: WHATIF:TotAccessibilitySolvent created_in: "beta12orEarlier" def: "Calculate the solvent accessibility ('accessible surface') for a structure as a whole." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2462 ! Protein surface calculation [Term] id: EDAM_operation:1825 name: Backbone torsion angle calculation subset: bioinformatics subset: edam subset: operations xref: WHATIF:ResidueTorsionsBB created_in: "beta12orEarlier" def: "Calculate for each residue in a protein structure all its backbone torsion angles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] id: EDAM_operation:1826 name: Full torsion angle calculation subset: bioinformatics subset: edam subset: operations xref: WHATIF:ResidueTorsions created_in: "beta12orEarlier" def: "Calculate for each residue in a protein structure all its torsion angles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] id: EDAM_operation:1827 name: Cysteine torsion angle calculation subset: bioinformatics subset: edam subset: operations xref: WHATIF:CysteineTorsions created_in: "beta12orEarlier" def: "Calculate for each cysteine (bridge) all its torsion angles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] id: EDAM_operation:1828 name: Tau angle calculation comment: Tau is the backbone angle N-Calpha-C (angle over the C-alpha). subset: bioinformatics subset: edam subset: operations xref: WHATIF:ShowTauAngle created_in: "beta12orEarlier" def: "For each amino acid in a protein structure calculate the backbone angle tau." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0249 ! Torsion angle calculation [Term] id: EDAM_operation:1829 name: Cysteine bridge detection subset: bioinformatics subset: edam subset: operations xref: WHATIF:ShowCysteineBridge created_in: "beta12orEarlier" def: "Detect cysteine bridges (from coordinate data) in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM_operation:1830 name: Free cysteine detection comment: A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. subset: bioinformatics subset: edam subset: operations xref: WHATIF:ShowCysteineFree created_in: "beta12orEarlier" def: "Detect free cysteines in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM_operation:1831 name: Metal-bound cysteine detection subset: bioinformatics subset: edam subset: operations xref: WHATIF:ShowCysteineMetal created_in: "beta12orEarlier" def: "Detect cysteines that are bound to metal in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment [Term] id: EDAM_operation:1832 name: Residue contact calculation (residue-nucleic acid) subset: bioinformatics subset: edam subset: operations xref: WHATIF:HasNucleicContacts xref: WHATIF:ShowProteiNucleicContacts created_in: "beta12orEarlier" def: "Calculate protein residue contacts with nucleic acids in a structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0245 ! Protein structural motif recognition is_a: EDAM_operation:0389 ! Protein-nucleic acid binding site analysis is_a: EDAM_operation:2950 ! Residue contact calculation [Term] id: EDAM_operation:1834 name: Residue contact calculation (residue-metal) subset: bioinformatics subset: edam subset: operations xref: WHATIF:HasMetalContacts xref: WHATIF:HasMetalContactsPlus created_in: "beta12orEarlier" def: "Calculate protein residue contacts with metal in a structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0388 ! Binding site prediction (from structure) is_a: EDAM_operation:2950 ! Residue contact calculation [Term] id: EDAM_operation:1835 name: Residue contact calculation (residue-negative ion) subset: bioinformatics subset: edam subset: operations xref: WHATIF:HasNegativeIonContacts xref: WHATIF:HasNegativeIonContactsPlus created_in: "beta12orEarlier" def: "Calculate ion contacts in a structure (all ions for all side chain atoms)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2950 ! Residue contact calculation [Term] id: EDAM_operation:1836 name: Residue bump detection subset: bioinformatics subset: edam subset: operations xref: WHATIF:ShowBumps created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection [Term] id: EDAM_operation:1837 name: Residue symmetry contact calculation comment: A symmetry contact is a contact between two atoms in different asymmetric unit. subset: bioinformatics subset: edam subset: operations xref: WHATIF:SymmetryContact created_in: "beta12orEarlier" def: "Calculate the number of symmetry contacts made by residues in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] id: EDAM_operation:1838 name: Residue contact calculation (residue-ligand) subset: bioinformatics subset: edam subset: operations xref: WHATIF:ShowDrugContacts xref: WHATIF:ShowDrugContactsShort xref: WHATIF:ShowLigandContacts created_in: "beta12orEarlier" def: "Calculate contacts between residues and ligands in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0388 ! Binding site prediction (from structure) is_a: EDAM_operation:2950 ! Residue contact calculation [Term] id: EDAM_operation:1839 name: Salt bridge calculation comment: Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. subset: bioinformatics subset: edam subset: operations xref: WHATIF:HasSaltBridge xref: WHATIF:HasSaltBridgePlus xref: WHATIF:ShowSaltBridges xref: WHATIF:ShowSaltBridgesH created_in: "beta12orEarlier" def: "Calculate (and possibly score) salt bridges in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] id: EDAM_operation:1841 name: Rotamer likelihood prediction comment: Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. subset: bioinformatics subset: edam subset: operations 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 created_in: "beta12orEarlier" def: "Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0480 ! Protein modelling (side chains) [Term] id: EDAM_operation:1842 name: Proline mutation value calculation subset: bioinformatics subset: edam subset: operations xref: WHATIF:ProlineMutationValue created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0331 ! Protein modelling (mutation) [Term] id: EDAM_operation:1843 name: Residue packing validation subset: bioinformatics subset: edam subset: operations xref: WHATIF: PackingQuality created_in: "beta12orEarlier" def: "Identify poorly packed residues in protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection [Term] id: EDAM_operation:1844 name: Dihedral angle validation subset: bioinformatics subset: edam subset: operations xref: WHATIF: ImproperQualityMax xref: WHATIF: ImproperQualitySum created_in: "beta12orEarlier" def: "Identify for each residue in a protein structure any improper dihedral (phi/psi) angles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0321 ! Protein model evaluation [Term] id: EDAM_operation:1845 name: PDB file sequence retrieval subset: bioinformatics subset: edam subset: operations xref: WHATIF: PDB_sequence created_in: "beta12orEarlier" def: "Extract a molecular sequence from a PDB file." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0344 ! Sequence retrieval (by code) [Term] id: EDAM_operation:1846 name: HET group detection 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: bioinformatics subset: edam subset: operations xref: WHATIF: HETGroupNames created_in: "beta12orEarlier" def: "Identify HET groups in PDB files." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1838 ! Residue contact calculation (residue-ligand) [Term] id: EDAM_operation:1847 name: DSSP secondary structure assignment subset: bioinformatics subset: edam subset: operations xref: WHATIF: ResidueDSSP created_in: "beta12orEarlier" def: "Determine for residue the DSSP determined secondary structure in three-state (HSC)." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data) [Term] id: EDAM_operation:1848 name: Structure reformatting subset: bioinformatics subset: edam subset: operations xref: WHATIF: PDBasXML created_in: "beta12orEarlier" def: "Reformat (a file or other report of) tertiary structure data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0335 ! File reformatting is_a: EDAM_operation:2234 ! Structure file processing [Term] id: EDAM_operation:1850 name: Protein cysteine and disulfide bond assignment subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assign cysteine bonding state and disulfide bond partners in protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data) relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis [Term] id: EDAM_operation:1913 name: Residue validation 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: bioinformatics subset: edam subset: operations xref: WHATIF: UseResidueDB created_in: "beta12orEarlier" def: "Identify poor quality amino acid positions in protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0321 ! Protein model evaluation [Term] id: EDAM_operation:1914 name: Structure retrieval (water) subset: bioinformatics subset: edam subset: operations xref: WHATIF:MovedWaterPDB created_in: "beta12orEarlier" def: "Query a tertiary structure database and retrieve water molecules." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1814 ! Structure retrieval [Term] id: EDAM_operation:2008 name: siRNA duplex prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict siRNA duplexes in RNA." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans) relationship: has_output EDAM_data:2169 ! Nucleic acid features (siRNA) relationship: has_topic EDAM_topic:3060 ! Regulatory RNA [Term] id: EDAM_operation:2089 name: Sequence alignment refinement subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Refine an existing sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2425 ! Optimisation and refinement [Term] id: EDAM_operation:2120 name: Listfile processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2409 ! File processing [Term] id: EDAM_operation:2121 name: Sequence file processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2409 ! File processing is_a: EDAM_operation:2446 ! Sequence processing [Term] id: EDAM_operation:2122 name: Sequence alignment file processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2409 ! File processing is_a: EDAM_operation:2463 ! Sequence alignment processing [Term] id: EDAM_operation:2123 name: Small molecule data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) physicochemical property data for small molecules." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2222 name: Data retrieval (ontology annotation) subset: bioinformatics subset: edam subset: operations synonym: "Ontology information retrieval" EXACT [] created_in: "beta12orEarlier" def: "Search and retrieve documentation on a bioinformatics ontology." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2224 name: Data retrieval (ontology concept) subset: bioinformatics subset: edam subset: operations synonym: "Ontology retrieval" EXACT [] created_in: "beta12orEarlier" def: "Query an ontology and retrieve concepts or relations." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2233 name: Representative sequence identification subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0291 ! Sequence clustering relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] id: EDAM_operation:2234 name: Structure file processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Perform basic (non-analytical) operations on a file of molecular tertiary structural data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2409 ! File processing is_a: EDAM_operation:2465 ! Structure processing [Term] id: EDAM_operation:2237 name: Data retrieval (sequence profile) comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Query a profile data resource and retrieve one or more profile(s) and / or associated annotation." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2238 name: Statistical calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Perform a statistical data operation of some type, e.g. calibration or validation." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2239 name: 3D-1D scoring matrix generation comment: A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0243 ! Protein property calculation (from structure) is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:1499 ! 3D-1D scoring matrix relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] id: EDAM_operation:2241 name: Transmembrane protein rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0270 ! Transmembrane protein analysis is_a: EDAM_operation:0569 ! Protein secondary structure rendering relationship: has_input EDAM_data:1456 ! Protein features (membrane regions) relationship: has_output EDAM_data:2992 ! Protein structure image [Term] id: EDAM_operation:2246 name: Demonstration subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "An operation performing purely illustrative (pedagogical) purposes." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_operation:2264 name: Data retrieval (pathway or network) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Query a biological pathways database and retrieve annotation on one or more pathways." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2265 name: Data retrieval (identifier) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Query a database and retrieve one or more data identifiers." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2284 name: Nucleic acid density plotting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate a density plot (of base composition) for a nucleotide sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0377 ! Sequence composition calculation (nucleic acid) [Term] id: EDAM_operation:2403 name: Sequence analysis subset: bioinformatics subset: edam subset: operations synonym: "Sequence analysis (general)" EXACT [] created_in: "beta12orEarlier" def: "Analyse one or more known molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 ! Sequence relationship: has_output EDAM_data:2955 ! Sequence report relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_operation:2404 name: Sequence motif processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) molecular sequence motifs." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] id: EDAM_operation:2405 name: Protein interaction data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) protein interaction data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2502 ! Protein data processing relationship: has_topic EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_operation:2406 name: Protein structure analysis subset: bioinformatics subset: edam subset: operations synonym: "Structure analysis (protein)" EXACT [] created_in: "beta12orEarlier" def: "Analyse protein tertiary structural data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2459 ! Structure processing (protein) is_a: EDAM_operation:2480 ! Structure analysis relationship: has_input EDAM_data:1460 ! Protein structure relationship: has_output EDAM_data:0897 ! Protein property [Term] id: EDAM_operation:2407 name: Annotation processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2408 name: Sequence feature analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse features in molecular sequences." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0253 ! Feature prediction [Term] id: EDAM_operation:2409 name: File processing subset: bioinformatics subset: edam subset: operations synonym: "Data file processing" EXACT [] synonym: "File handling" EXACT [] synonym: "Report handling" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] id: EDAM_operation:2410 name: Gene expression analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse gene expression and regulation data." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:2411 name: Structural (3D) profile processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles [Term] id: EDAM_operation:2412 name: Data index processing subset: bioinformatics subset: edam subset: operations synonym: "Database index processing" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) an index of (typically a file of) biological data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2409 ! File processing [Term] id: EDAM_operation:2413 name: Sequence profile processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) some type of sequence profile." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_operation:2414 name: Protein function analysis comment: This is a broad concept and is used a placeholder for other, more specific concepts. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2502 ! Protein data processing relationship: has_output EDAM_data:0896 ! Protein report [Term] id: EDAM_operation:2415 name: Protein folding analysis comment: This is a broad concept and is used a placeholder for other, more specific concepts. subset: bioinformatics subset: edam subset: operations synonym: "Protein folding modelling" EXACT [] created_in: "beta12orEarlier" def: "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2426 ! Modelling and simulation is_a: EDAM_operation:2502 ! Protein data processing relationship: has_output EDAM_data:0903 ! Protein folding report relationship: has_topic EDAM_topic:0130 ! Protein folding and stability [Term] id: EDAM_operation:2416 name: Protein secondary structure analysis subset: bioinformatics subset: edam subset: operations synonym: "Secondary structure analysis (protein)" EXACT [] created_in: "beta12orEarlier" def: "Analyse known protein secondary structure data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2444 ! Protein secondary structure processing relationship: has_input EDAM_data:0876 ! Protein features (secondary structure) relationship: has_output EDAM_data:2956 ! Protein secondary structure report [Term] id: EDAM_operation:2417 name: Physicochemical property data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) data on the physicochemical property of a molecule." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2419 name: Primer and probe design subset: bioinformatics subset: edam subset: operations synonym: "Primer and probe prediction" EXACT [] created_in: "beta12orEarlier" def: "Predict oligonucleotide primers or probes." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) is_a: EDAM_operation:3095 ! Nucleic acid design relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] id: EDAM_operation:2420 name: Analysis and processing subset: bioinformatics subset: edam subset: operations synonym: "Calculation" EXACT [] synonym: "Computation" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) data of a specific type, for example applying analytical methods." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2421 name: Database search 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: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0224 ! Search and retrieval is_a: EDAM_operation:2424 ! Comparison relationship: has_output EDAM_data:2080 ! Database hits [Term] id: EDAM_operation:2422 name: Data retrieval subset: bioinformatics subset: edam subset: operations synonym: "Information retrieval" BROAD [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0224 ! Search and retrieval relationship: has_input EDAM_data:0842 ! Identifier [Term] id: EDAM_operation:2423 name: Prediction, detection and recognition subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict, recognise, detect or identify some properties of a biomolecule." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2424 name: Comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more things to identify similarities." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2425 name: Optimisation and refinement subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Refine or optimise some data model." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2426 name: Modelling and simulation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Model or simulate some biological entity or system." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation relationship: has_topic EDAM_topic:2275 ! Molecular modelling [Term] id: EDAM_operation:2427 name: Data handling subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Perform basic operations on some data or a database." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2428 name: Evaluation and validation subset: bioinformatics subset: edam subset: operations synonym: "Validation and standardisation" EXACT [] created_in: "beta12orEarlier" def: "Validate or standardise some data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:2429 name: Mapping and assembly comment: This is a broad concept and is used a placeholder for other, more specific concepts. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation relationship: has_topic EDAM_topic:0102 ! Mapping relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] id: EDAM_operation:2430 name: Design subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Design a biological entity (typically a molecular sequence or structure) with specific properties." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) [Term] id: EDAM_operation:2432 name: Microarray data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) microarray data." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:2433 name: Codon usage table processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a codon usage table." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0286 ! Codon usage analysis [Term] id: EDAM_operation:2434 name: Data retrieval (codon usage table) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Retrieve a codon usage table and / or associated annotation." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2435 name: Gene expression profile processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a gene expression profile." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:2436 name: Gene expression profile annotation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Annotate a gene expression profile with concepts from an ontology of gene functions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0226 ! Annotation is_a: EDAM_operation:0532 ! Gene expression profile analysis relationship: has_output EDAM_data:0928 ! Gene expression profile [Term] id: EDAM_operation:2437 name: Gene regulatory network prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict a network of gene regulation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2496 ! Gene regulatory network processing is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:2961 ! Pathway or network (gene regulation) [Term] id: EDAM_operation:2438 name: Pathway or network processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate, analyse or handle a biological pathway or network." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_operation:2439 name: RNA secondary structure processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) RNA secondary structure data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2482 ! Secondary structure processing is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment [Term] id: EDAM_operation:2440 name: Structure processing (RNA) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) RNA tertiary structure data." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2519 ! Structure processing (nucleic acid) [Term] id: EDAM_operation:2441 name: RNA structure prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict RNA tertiary structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0475 ! Nucleic acid structure prediction relationship: has_output EDAM_data:1465 ! RNA structure record [Term] id: EDAM_operation:2442 name: DNA structure prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict DNA tertiary structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0475 ! Nucleic acid structure prediction relationship: has_output EDAM_data:1464 ! DNA structure [Term] id: EDAM_operation:2443 name: Phylogenetic tree processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a phylogenetic tree." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:2444 name: Protein secondary structure processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) protein secondary structure data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2482 ! Secondary structure processing is_a: EDAM_operation:2502 ! Protein data processing relationship: has_topic EDAM_topic:0694 ! Protein secondary structure [Term] id: EDAM_operation:2445 name: Protein interaction network processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a network of protein interactions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2405 ! Protein interaction data processing is_a: EDAM_operation:2438 ! Pathway or network processing relationship: has_topic EDAM_topic:3044 ! Protein interaction networks [Term] id: EDAM_operation:2446 name: Sequence processing subset: bioinformatics subset: edam subset: operations synonym: "Sequence processing (general)" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) one or more molecular sequences and associated annotation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2447 name: Sequence processing (protein) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a protein sequence and associated annotation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2446 ! Sequence processing is_a: EDAM_operation:2502 ! Protein data processing [Term] id: EDAM_operation:2448 name: Sequence processing (nucleic acid) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a nucleotide sequence and associated annotation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2446 ! Sequence processing is_a: EDAM_operation:2501 ! Nucleic acid data processing [Term] id: EDAM_operation:2451 name: Sequence comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more molecular sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2424 ! Comparison relationship: has_input EDAM_data:2044 ! Sequence relationship: has_output EDAM_data:2955 ! Sequence report relationship: has_topic EDAM_topic:0159 ! Sequence comparison [Term] id: EDAM_operation:2452 name: Sequence cluster processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a sequence cluster." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] id: EDAM_operation:2453 name: Feature table processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a sequence feature table." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:1270 ! Sequence feature table relationship: has_input EDAM_data:2201 ! Sequence record full relationship: has_output EDAM_data:1255 ! Feature record relationship: has_topic EDAM_topic:0160 ! Sequence sites and features [Term] id: EDAM_operation:2454 name: Gene and gene component prediction subset: bioinformatics subset: edam subset: operations synonym: "Gene finding" EXACT [] created_in: "beta12orEarlier" def: "Detect, predict and identify genes or components of genes in DNA sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) relationship: has_topic EDAM_topic:0109 ! Gene finding [Term] id: EDAM_operation:2456 name: GPCR classification subset: bioinformatics subset: edam subset: operations synonym: "G protein-coupled receptor (GPCR) classification" EXACT [] created_in: "beta12orEarlier" def: "Classify G-protein coupled receptors (GPCRs) into families and subfamilies." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0473 ! GPCR analysis is_a: EDAM_operation:2995 ! Sequence classification relationship: has_output EDAM_data:0907 ! Protein family [Term] id: EDAM_operation:2457 name: GPCR coupling selectivity prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict G-protein coupled receptor (GPCR) coupling selectivity." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0473 ! GPCR analysis is_a: EDAM_operation:2492 ! Protein interaction prediction is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) relationship: has_output EDAM_data:0896 ! Protein report [Term] id: EDAM_operation:2459 name: Structure processing (protein) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a protein tertiary structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2465 ! Structure processing is_a: EDAM_operation:2502 ! Protein data processing relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure [Term] id: EDAM_operation:2460 name: Protein atom surface calculation comment: Waters are not considered. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate the solvent accessibility for each atom in a structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] id: EDAM_operation:2461 name: Protein residue surface calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate the solvent accessibility for each residue in a structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] id: EDAM_operation:2462 name: Protein surface calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate the solvent accessibility of a structure as a whole." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0387 ! Protein surface and interior calculation [Term] id: EDAM_operation:2463 name: Sequence alignment processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a molecular sequence alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2951 ! Alignment processing relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:2464 name: Protein-protein interaction prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify or predict protein-protein interactions, interfaces, binding sites etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2492 ! Protein interaction prediction relationship: has_output EDAM_data:1565 ! Protein-protein interaction relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions [Term] id: EDAM_operation:2465 name: Structure processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a molecular tertiary structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2466 name: Map annotation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Annotate a DNA map of some type with terms from a controlled vocabulary." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0226 ! Annotation is_a: EDAM_operation:2521 ! Map data processing relationship: has_input EDAM_data:1274 ! Map relationship: has_output EDAM_data:1274 ! Map [Term] id: EDAM_operation:2467 name: Data retrieval (protein annotation) subset: bioinformatics subset: edam subset: operations synonym: "Protein information retrieval" EXACT [] created_in: "beta12orEarlier" def: "Retrieve information on a protein." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2468 name: Data retrieval (phylogenetic tree) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Retrieve a phylogenetic tree from a data resource." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2469 name: Data retrieval (protein interaction annotation) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Retrieve information on a protein interaction." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2470 name: Data retrieval (protein family annotation) subset: bioinformatics subset: edam subset: operations synonym: "Protein family information retrieval" EXACT [] created_in: "beta12orEarlier" def: "Retrieve information on a protein family." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2471 name: Data retrieval (RNA family annotation) subset: bioinformatics subset: edam subset: operations synonym: "RNA family information retrieval" EXACT [] created_in: "beta12orEarlier" def: "Retrieve information on an RNA family." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2472 name: Data retrieval (gene annotation) subset: bioinformatics subset: edam subset: operations synonym: "Gene information retrieval" EXACT [] created_in: "beta12orEarlier" def: "Retrieve information on a specific gene." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2473 name: Data retrieval (genotype and phenotype annotation) subset: bioinformatics subset: edam subset: operations synonym: "Genotype and phenotype information retrieval" EXACT [] created_in: "beta12orEarlier" def: "Retrieve information on a specific genotype or phenotype." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2422 ! Data retrieval [Term] id: EDAM_operation:2474 name: Protein architecture comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare the architecture of two or more protein structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0247 ! Protein architecture analysis is_a: EDAM_operation:2488 ! Protein secondary structure comparison relationship: has_output EDAM_data:0902 ! Protein architecture report [Term] id: EDAM_operation:2475 name: Protein architecture recognition subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify the architecture of a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0247 ! Protein architecture analysis is_a: EDAM_operation:2996 ! Structure classification is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:0902 ! Protein architecture report [Term] id: EDAM_operation:2476 name: Molecular dynamics simulation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2423 ! Prediction, detection and recognition is_a: EDAM_operation:2426 ! Modelling and simulation is_a: EDAM_operation:2480 ! Structure analysis relationship: has_output EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0082 ! Structure prediction relationship: has_topic EDAM_topic:0176 ! Molecular dynamics [Term] id: EDAM_operation:2478 name: Nucleic acid sequence analysis subset: bioinformatics subset: edam subset: operations synonym: "Sequence analysis (nucleic acid)" EXACT [] created_in: "beta12orEarlier" def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) relationship: has_input EDAM_data:2977 ! Nucleic acid sequence relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:2479 name: Protein sequence analysis subset: bioinformatics subset: edam subset: operations synonym: "Sequence analysis (protein)" EXACT [] created_in: "beta12orEarlier" def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2447 ! Sequence processing (protein) relationship: has_input EDAM_data:2976 ! Protein sequence relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis [Term] id: EDAM_operation:2480 name: Structure analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse known molecular tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2465 ! Structure processing relationship: has_input EDAM_data:0883 ! Structure relationship: has_output EDAM_data:2085 ! Structure report relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_operation:2481 name: Nucleic acid structure analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse nucleic acid tertiary structural data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2480 ! Structure analysis is_a: EDAM_operation:2519 ! Structure processing (nucleic acid) relationship: has_input EDAM_data:1459 ! Nucleic acid structure relationship: has_output EDAM_data:0912 ! Nucleic acid property [Term] id: EDAM_operation:2482 name: Secondary structure processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a molecular secondary structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_operation:2483 name: Structure comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more molecular tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2424 ! Comparison is_a: EDAM_operation:2480 ! Structure analysis relationship: has_topic EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_operation:2485 name: Helical wheel rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Render a helical wheel representation of protein secondary structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0569 ! Protein secondary structure rendering relationship: has_output EDAM_data:2162 ! Helical wheel [Term] id: EDAM_operation:2486 name: Topology diagram rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Render a topology diagram of protein secondary structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0569 ! Protein secondary structure rendering relationship: has_output EDAM_data:2992 ! Protein structure image [Term] id: EDAM_operation:2487 name: Protein structure comparison comment: Methods might identify structural neighbors, find structural similarities or define a structural core. subset: bioinformatics subset: edam subset: operations synonym: "Structure comparison (protein)" EXACT [] created_in: "beta12orEarlier" def: "Compare protein tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2459 ! Structure processing (protein) is_a: EDAM_operation:2483 ! Structure comparison is_a: EDAM_operation:2997 ! Protein comparison relationship: has_input EDAM_data:1460 ! Protein structure relationship: has_output EDAM_data:0897 ! Protein property [Term] id: EDAM_operation:2488 name: Protein secondary structure comparison subset: bioinformatics subset: edam subset: operations synonym: "Protein secondary structure" EXACT [] synonym: "Secondary structure comparison (protein)" EXACT [] created_in: "beta12orEarlier" def: "Compare protein secondary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2416 ! Protein secondary structure analysis is_a: EDAM_operation:2931 ! Secondary structure comparison is_a: EDAM_operation:2997 ! Protein comparison relationship: has_input EDAM_data:0876 ! Protein features (secondary structure) [Term] id: EDAM_operation:2489 name: Protein subcellular localization prediction comment: The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. subset: bioinformatics subset: edam subset: operations synonym: "Protein targeting prediction" EXACT [] created_in: "beta12orEarlier" def: "Predict the subcellular localization of a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) is_a: EDAM_operation:3084 ! Protein function prediction (from sequence) relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization [Term] id: EDAM_operation:2490 name: Residue contact calculation (residue-residue) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate contacts between residues in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2950 ! Residue contact calculation [Term] id: EDAM_operation:2491 name: Hydrogen bond calculation (inter-residue) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify potential hydrogen bonds between amino acid residues." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0394 ! Hydrogen bond calculation is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue) [Term] id: EDAM_operation:2492 name: Protein interaction prediction subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict the interactions of proteins with other molecules." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2405 ! Protein interaction data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:0906 ! Protein interaction [Term] id: EDAM_operation:2493 name: Codon usage data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) codon usage data." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:0286 ! Codon usage analysis [Term] id: EDAM_operation:2495 name: Gene expression data processing subset: bioinformatics subset: edam subset: operations synonym: "Gene expression (microarray) data processing" EXACT [] synonym: "Microarray data processing" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) gene expression (typically microarray) data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0200 ! Microarrays relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] id: EDAM_operation:2496 name: Gene regulatory network processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a network of gene regulation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2438 ! Pathway or network processing relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks [Term] id: EDAM_operation:2497 name: Pathway or network analysis subset: bioinformatics subset: edam subset: operations synonym: "Network analysis" EXACT [] synonym: "Pathway analysis" EXACT [] created_in: "beta12orEarlier" def: "Analyse a known biological pathway or network." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2438 ! Pathway or network processing relationship: has_input EDAM_data:2600 ! Pathway or network relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_operation:2498 name: Sequencing-based expression profile data analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:2499 name: Splicing analysis subset: bioinformatics subset: edam subset: operations synonym: "Splicing modelling" EXACT [] created_in: "beta12orEarlier" def: "Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2426 ! Modelling and simulation is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:1307 ! Nucleic acid features (splice sites) relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] id: EDAM_operation:2500 name: Microarray raw data analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse raw microarray data." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2495 ! Gene expression data processing [Term] id: EDAM_operation:2501 name: Nucleic acid data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) nucleic acid sequence or structural data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_operation:2502 name: Protein data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) protein sequence or structural data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_topic EDAM_topic:0078 ! Protein analysis [Term] id: EDAM_operation:2503 name: Sequence data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) molecular sequence data." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2446 ! Sequence processing [Term] id: EDAM_operation:2504 name: Structural data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) molecular structural data." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2465 ! Structure processing [Term] id: EDAM_operation:2505 name: Text processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) text." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2506 name: Sequence alignment analysis (protein) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2502 ! Protein data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_input EDAM_data:1384 ! Sequence alignment (protein) relationship: has_topic EDAM_topic:0741 ! Protein sequence alignment [Term] id: EDAM_operation:2507 name: Sequence alignment analysis (nucleic acid) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2501 ! Nucleic acid data processing is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_input EDAM_data:1383 ! Sequence alignment (nucleic acid) relationship: has_topic EDAM_topic:0740 ! Nucleic acid sequence alignment [Term] id: EDAM_operation:2508 name: Nucleic acid sequence comparison subset: bioinformatics subset: edam subset: operations synonym: "Sequence comparison (nucleic acid)" EXACT [] created_in: "beta12orEarlier" def: "Compare two or more nucleic acid sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:2998 ! Nucleic acid comparison [Term] id: EDAM_operation:2509 name: Protein sequence comparison subset: bioinformatics subset: edam subset: operations synonym: "Sequence comparison (protein)" EXACT [] created_in: "beta12orEarlier" def: "Compare two or more protein sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2479 ! Protein sequence analysis is_a: EDAM_operation:2997 ! Protein comparison [Term] id: EDAM_operation:2510 name: DNA back-translation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Back-translate a protein sequence into DNA." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0233 ! Sequence conversion relationship: has_topic EDAM_topic:0108 ! Translation [Term] id: EDAM_operation:2511 name: Sequence editing (nucleic acid) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Edit or change a nucleic acid sequence, either randomly or specifically." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0231 ! Sequence editing is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) [Term] id: EDAM_operation:2512 name: Sequence editing (protein) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Edit or change a protein sequence, either randomly or specifically." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0231 ! Sequence editing is_a: EDAM_operation:2447 ! Sequence processing (protein) [Term] id: EDAM_operation:2513 name: Sequence generation (nucleic acid) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a nucleic acid sequence by some means." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0230 ! Sequence generation is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:2514 name: Sequence generation (protein) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a protein sequence by some means." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0230 ! Sequence generation is_a: EDAM_operation:2447 ! Sequence processing (protein) relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis [Term] id: EDAM_operation:2515 name: Sequence rendering (nucleic acid) comment: Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise, format or render a nucleic acid sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0564 ! Sequence rendering is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:2516 name: Sequence rendering (protein) comment: Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise, format or render a protein sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0564 ! Sequence rendering is_a: EDAM_operation:2447 ! Sequence processing (protein) [Term] id: EDAM_operation:2518 name: Nucleic acid structure comparison subset: bioinformatics subset: edam subset: operations synonym: "Structure comparison (nucleic acid)" EXACT [] created_in: "beta12orEarlier" def: "Compare nucleic acid tertiary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2481 ! Nucleic acid structure analysis is_a: EDAM_operation:2483 ! Structure comparison is_a: EDAM_operation:2998 ! Nucleic acid comparison [Term] id: EDAM_operation:2519 name: Structure processing (nucleic acid) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) nucleic acid tertiary structure data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2465 ! Structure processing is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis [Term] id: EDAM_operation:2520 name: DNA mapping subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a map of a DNA sequence annotated with positional or non-positional features of some type." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2429 ! Mapping and assembly is_a: EDAM_operation:2521 ! Map data processing relationship: has_output EDAM_data:1274 ! Map [Term] id: EDAM_operation:2521 name: Map data processing subset: bioinformatics subset: edam subset: operations synonym: "DNA map data processing" EXACT [] created_in: "beta12orEarlier" def: "Process (read and / or write) a DNA map of some type." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2501 ! Nucleic acid data processing relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage [Term] id: EDAM_operation:2574 name: Protein hydropathy calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0250 ! Protein property calculation relationship: has_output EDAM_data:2970 ! Protein hydropathy data relationship: has_topic EDAM_topic:0137 ! Protein hydropathy [Term] id: EDAM_operation:2575 name: Binding site prediction subset: bioinformatics subset: edam subset: operations synonym: "Ligand-binding and active site prediction" EXACT [] created_in: "beta12orEarlier" def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2492 ! Protein interaction prediction relationship: has_output EDAM_data:1325 ! Protein features (active sites) relationship: has_output EDAM_data:1326 ! Protein features (binding sites) relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] id: EDAM_operation:2871 name: Sequence tagged site (STS) mapping 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: bioinformatics subset: edam subset: operations synonym: "Sequence mapping" EXACT [] created_in: "beta12orEarlier" def: "Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2944 ! Physical mapping relationship: has_output EDAM_data:1279 ! Sequence map [Term] id: EDAM_operation:2928 name: Alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Alignment" EXACT [] created_in: "beta12orEarlier" def: "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2951 ! Alignment processing relationship: has_output EDAM_data:1916 ! Alignment [Term] id: EDAM_operation:2929 name: Protein fragment weight comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0398 ! Protein molecular weight calculation is_a: EDAM_operation:2930 ! Protein property comparison [Term] id: EDAM_operation:2930 name: Protein property comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare the physicochemical properties of two or more proteins (or reference data)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2997 ! Protein comparison relationship: has_output EDAM_data:0897 ! Protein property [Term] id: EDAM_operation:2931 name: Secondary structure comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more molecular secondary structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2424 ! Comparison relationship: has_input EDAM_data:2081 ! Secondary structure relationship: has_output EDAM_data:2881 ! Secondary structure report relationship: has_topic EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_operation:2932 name: Hopp and Woods plotting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a Hopp and Woods plot of antigenicity of a protein." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction [Term] id: EDAM_operation:2934 name: Microarray cluster textual view rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise gene clusters with gene names." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2935 name: Microarray wave graph rendering 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: bioinformatics subset: edam subset: operations synonym: "Microarray cluster temporal graph rendering" EXACT [] created_in: "beta12orEarlier" def: "Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2936 name: Microarray dendrograph rendering subset: bioinformatics subset: edam subset: operations synonym: "Microarray checks view rendering" EXACT [] synonym: "Microarray view rendering" EXACT [] created_in: "beta12orEarlier" def: "Generate a dendrograph of raw, preprocessed or clustered microarray data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2937 name: Microarray proximity map rendering subset: bioinformatics subset: edam subset: operations synonym: "Microarray distance map rendering" EXACT [] created_in: "beta12orEarlier" def: "Generate a plot of distances (distance matrix) between genes." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2938 name: Microarray tree or dendrogram view rendering subset: bioinformatics subset: edam subset: operations synonym: "Microarray 2-way dendrogram rendering" EXACT [] synonym: "Microarray matrix tree plot rendering" EXACT [] created_in: "beta12orEarlier" def: "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2939 name: Microarray principal component rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2940 name: Microarray scatter plot rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a scatter plot of microarray data, typically after principal component analysis." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2941 name: Whole microarray graph view rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise gene expression data where each band (or line graph) corresponds to a sample." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2942 name: Microarray tree-map rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise gene expression data after hierarchical clustering for representing hierarchical relationships." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2943 name: Microarray Box-Whisker plot rendering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0571 ! Microarray data rendering [Term] id: EDAM_operation:2944 name: Physical mapping subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2520 ! DNA mapping relationship: has_output EDAM_data:1280 ! Physical map relationship: has_topic EDAM_topic:0102 ! Mapping [Term] id: EDAM_operation:2945 name: Analysis comment: For non-analytical operations, see the 'Processing' branch. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Apply analytical methods to existing data of a specific type." [http://edamontology.org] namespace: operation obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2946 name: Alignment analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse an existing alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2951 ! Alignment processing relationship: has_input EDAM_data:1916 ! Alignment relationship: has_output EDAM_data:2083 ! Alignment report [Term] id: EDAM_operation:2947 name: Article analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse a body of scientific text (typically a full text article from a scientific journal.)" [http://edamontology.org] namespace: operation is_a: EDAM_operation:2505 ! Text processing relationship: has_input EDAM_data:0971 ! Article relationship: has_output EDAM_data:2954 ! Article report relationship: has_topic EDAM_topic:0217 ! Literature analysis [Term] id: EDAM_operation:2948 name: Molecular interaction analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_operation:2949 name: Protein interaction analysis subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2405 ! Protein interaction data processing relationship: has_output EDAM_data:0906 ! Protein interaction [Term] id: EDAM_operation:2950 name: Residue contact calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate contacts between residues and some other group in a protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0248 ! Residue interaction calculation [Term] id: EDAM_operation:2951 name: Alignment processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:2952 name: Structure alignment processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) a molecular tertiary (3D) structure alignment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2951 ! Alignment processing relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] id: EDAM_operation:2962 name: Codon usage bias calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate codon usage bias." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0286 ! Codon usage analysis relationship: has_output EDAM_data:2865 ! Codon usage bias [Term] id: EDAM_operation:2963 name: Codon usage bias plotting subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Generate a codon usage bias plot." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2962 ! Codon usage bias calculation relationship: has_output EDAM_data:1600 ! Codon usage bias plot [Term] id: EDAM_operation:2964 name: Codon usage fraction calculation subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0286 ! Codon usage analysis relationship: has_output EDAM_data:1602 ! Codon usage fraction difference [Term] id: EDAM_operation:2990 name: Classification subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation relationship: has_output EDAM_data:2987 ! Classification [Term] id: EDAM_operation:2993 name: Molecular interaction data processing subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Process (read and / or write) molecular interaction data." [http://edamontology.org] namespace: operation obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_operation:2995 name: Sequence classification subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assign molecular sequence(s) to a group or category." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2990 ! Classification [Term] id: EDAM_operation:2996 name: Structure classification subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Assign molecular structure(s) to a group or category." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2480 ! Structure analysis is_a: EDAM_operation:2990 ! Classification [Term] id: EDAM_operation:2997 name: Protein comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more proteins (or some aspect) to identify similarities." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2424 ! Comparison [Term] id: EDAM_operation:2998 name: Nucleic acid comparison subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Compare two or more nucleic acids to identify similarities." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2424 ! Comparison [Term] id: EDAM_operation:3023 name: Prediction, detection and recognition (protein) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict, recognise, detect or identify some properties of proteins." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2423 ! Prediction, detection and recognition [Term] id: EDAM_operation:3024 name: Prediction, detection and recognition (nucleic acid) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Predict, recognise, detect or identify some properties of nucleic acids." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2423 ! Prediction, detection and recognition [Term] id: EDAM_operation:3080 name: Structure editing subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2234 ! Structure file processing is_a: EDAM_operation:3096 ! Editing relationship: has_input EDAM_data:0883 ! Structure [Term] id: EDAM_operation:3081 name: Sequence alignment editing subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2122 ! Sequence alignment file processing is_a: EDAM_operation:3096 ! Editing [Term] id: EDAM_operation:3083 name: Pathway or network rendering subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Render (visualise) a biological pathway or network." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2438 ! Pathway or network processing relationship: has_input EDAM_data:2600 ! Pathway or network [Term] id: EDAM_operation:3084 name: Protein function prediction (from sequence) comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Predict general (non-positional) functional properties of a protein from analysing its sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:1777 ! Protein function prediction is_a: EDAM_operation:2479 ! Protein sequence analysis is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_topic EDAM_topic:2276 ! Protein function prediction [Term] id: EDAM_operation:3087 name: Protein site detection subset: bioinformatics subset: edam subset: operations synonym: "name: Sequence motif recognition (protein)" EXACT [] created_in: "beta13" def: "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0239 ! Sequence motif recognition is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) [Term] id: EDAM_operation:3088 name: Protein property calculation (from sequence) subset: bioinformatics subset: edam subset: operations created_in: "beta13" 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." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0250 ! Protein property calculation is_a: EDAM_operation:2479 ! Protein sequence analysis [Term] id: EDAM_operation:3090 name: Protein feature prediction (from structure) subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Predict, recognise and identify positional features in proteins from analysing protein structure." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2406 ! Protein structure analysis is_a: EDAM_operation:3092 ! Protein feature prediction [Term] id: EDAM_operation:3092 name: Protein feature prediction subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0253 ! Feature prediction is_a: EDAM_operation:2502 ! Protein data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:1277 ! Protein features relationship: has_topic EDAM_topic:3074 ! Protein feature detection [Term] id: EDAM_operation:3093 name: Sequence screening subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2995 ! Sequence classification [Term] id: EDAM_operation:3094 name: Protein interaction network prediction subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Predict a network of protein interactions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2445 ! Protein interaction network processing relationship: has_output EDAM_data:1663 ! Pathway or network (protein-protein interaction) [Term] id: EDAM_operation:3095 name: Nucleic acid design subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Design (or predict) nucleic acid sequences with specific chemical or physical properties." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3096 name: Editing subset: bioinformatics subset: edam subset: operations created_in: "beta13" def: "Edit, convert or otherwise change a data entity, either randomly or specifically." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0004 ! Operation [Term] id: EDAM_operation:3180 name: Sequence assembly evaluation subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Evaluate a DNA sequence assembly, typically for purposes of quality control." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2425 ! Optimisation and refinement is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_input EDAM_data:0925 ! Sequence assembly relationship: has_output EDAM_data:3181 ! Sequence assembly report relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] id: EDAM_operation:3182 name: Genome alignment construction subset: bioinformatics subset: edam subset: operations synonym: "Genome alignment" EXACT [] created_in: "1.1" def: "Align two or more (tpyically huge) molecular sequences that represent genomes." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0292 ! Sequence alignment construction [Term] id: EDAM_operation:3183 name: Localized reassembly subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Reconstruction of a sequence assembly in a localised area." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0310 ! Sequence assembly [Term] id: EDAM_operation:3184 name: Sequence assembly rendering subset: bioinformatics subset: edam subset: operations synonym: "Assembly rendering" EXACT [] synonym: "Assembly visualisation" EXACT [] synonym: "Sequence assembly visualisation" EXACT [] created_in: "1.1" def: "Render and visualise a DNA sequence assembly." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) [Term] id: EDAM_operation:3185 name: Base-calling subset: bioinformatics subset: edam subset: operations synonym: "Base calling" EXACT [] synonym: "Phred base calling" EXACT [] synonym: "Phred base-calling" EXACT [] created_in: "1.1" def: "Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:3186 name: Bisulfite mapping comment: Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. subset: bioinformatics subset: edam subset: operations synonym: "Bisulfite sequence alignment" EXACT [] synonym: "Bisulfite sequence mapping" EXACT [] created_in: "1.1" def: "The mapping of methylation sites in a DNA (genome) sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2944 ! Physical mapping [Term] id: EDAM_operation:3187 name: Sequence contamination filtering subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_operation:3189 name: Trim ends comment: For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Trim sequences (typically from an automated DNA sequencer) to remove misleading ends." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3192 ! Sequence trimming [Term] id: EDAM_operation:3190 name: Trim vector subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3192 ! Sequence trimming [Term] id: EDAM_operation:3191 name: Trim to reference subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3192 ! Sequence trimming [Term] id: EDAM_operation:3192 name: Sequence trimming subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Cut (remove) the end from a molecular sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0369 ! Sequence cutting [Term] id: EDAM_operation:3194 name: Genome feature comparison comment: Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Compare the features of two genome sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0256 ! Feature comparison [Term] id: EDAM_operation:3195 name: Sequencing error detection subset: bioinformatics subset: edam subset: operations synonym: "Short read error correction" EXACT [] synonym: "Short-read error correction" EXACT [] created_in: "beta12orEarlier" def: "Detect errors in DNA sequences generated from sequencing projects)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:3196 name: Genotyping comment: Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3197 ! Genetic variation analysis [Term] id: EDAM_operation:3197 name: Genetic variation analysis comment: Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. subset: bioinformatics subset: edam subset: operations synonym: "Genetic variation annotation" EXACT [] synonym: "Sequence variation analysis" EXACT [] created_in: "1.1" def: "Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison relationship: has_output EDAM_data:0918 ! Nucleic acid features (variation) [Term] id: EDAM_operation:3198 name: Oligonucleotide alignment construction comment: The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. subset: bioinformatics subset: edam subset: operations synonym: "Oligonucleotide alignment" EXACT [] synonym: "Oligonucleotide mapping" EXACT [] synonym: "Read alignment" EXACT [] synonym: "Read mapping" EXACT [] synonym: "Short oligonucleotide alignment" EXACT [] synonym: "Short read alignment" EXACT [] synonym: "Short read mapping" EXACT [] synonym: "Short sequence read mapping" EXACT [] created_in: "1.1" def: "Align short oligonucleotide sequences (reads) to a larger (genomic) sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0292 ! Sequence alignment construction [Term] id: EDAM_operation:3199 name: Split read mapping subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3198 ! Oligonucleotide alignment construction [Term] id: EDAM_operation:3200 name: DNA barcoding subset: bioinformatics subset: edam subset: operations synonym: "Sample barcoding" EXACT [] created_in: "1.1" def: "Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:3201 name: SNP calling comment: Operations usually score confidence in the prediction or some other statistical measure of evidence. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0484 ! SNP detection [Term] id: EDAM_operation:3202 name: Mutation detection subset: bioinformatics subset: edam subset: operations synonym: "Polymorphism detection" EXACT [] created_in: "1.1" def: "Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3197 ! Genetic variation analysis [Term] id: EDAM_operation:3203 name: Chromatogram visualisation subset: bioinformatics subset: edam subset: operations synonym: "Chromatogram viewing" EXACT [] created_in: "1.1" def: "Visualise, format or render an image of a Chromatogram." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0337 ! Plotting and rendering [Term] id: EDAM_operation:3204 name: Methylation analysis subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Determine cytosine methylation states in nucleic acid sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:3205 name: Methylation calling subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Determine cytosine methylation status of specific positions in a nucleic acid sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3204 ! Methylation analysis [Term] id: EDAM_operation:3206 name: Methylation level analysis (global) subset: bioinformatics subset: edam subset: operations synonym: "Global methylation analysis" EXACT [] created_in: "1.1" def: "Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3205 ! Methylation calling [Term] id: EDAM_operation:3207 name: Methylation level analysis (gene-specific) comment: Many different techniques are available for this. subset: bioinformatics subset: edam subset: operations synonym: "Gene-specific methylation analysis" EXACT [] created_in: "1.1" def: "Measure the level of methyl cytosines in specific genes." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3205 ! Methylation calling [Term] id: EDAM_operation:3208 name: Genome rendering subset: bioinformatics subset: edam subset: operations synonym: "Genome browsing" EXACT [] synonym: "Genome viewing" EXACT [] synonym: "Genome visualisation" EXACT [] synonym: "Genome visualization" EXACT [] created_in: "1.1" def: "Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) [Term] id: EDAM_operation:3209 name: Genome comparison subset: bioinformatics subset: edam subset: operations synonym: "Genomic region matching" EXACT [] created_in: "1.1" def: "Compare the sequence or features of two or more genomes, for example, to find matching regions." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison [Term] id: EDAM_operation:3211 name: Genome indexing comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Generate an index of a genome sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0227 ! Data indexing relationship: has_output EDAM_data:3210 ! Genome index [Term] id: EDAM_operation:3212 name: Genome indexing (Burrows-Wheeler) comment: The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Generate an index of a genome sequence using the Burrows-Wheeler algorithm." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3211 ! Genome indexing [Term] id: EDAM_operation:3213 name: Genome indexing (suffix arrays) comment: A suffix array consists of the lexicographically sorted list of suffixes of a genome. subset: bioinformatics subset: edam subset: operations synonym: "suffix arrays" EXACT [] created_in: "1.1" def: "Generate an index of a genome sequence using a suffix arrays algorithm." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3211 ! Genome indexing [Term] id: EDAM_operation:3214 name: Spectrum analysis subset: bioinformatics subset: edam subset: operations synonym: "Mass spectrum analysis" EXACT [] synonym: "Spectral analysis" EXACT [] created_in: "1.1" def: "Analyse a spectrum from a mass spectrometry (or other) experiment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2420 ! Analysis and processing [Term] id: EDAM_operation:3215 name: Peak detection subset: bioinformatics subset: edam subset: operations synonym: "Peak finding" EXACT [] created_in: "1.1" def: "Identify peaks in a spectrum from a mass spectrometry experiment." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3214 ! Spectrum analysis relationship: has_input EDAM_data:0943 ! Mass spectrometry spectra [Term] id: EDAM_operation:3216 name: Scaffolding comment: Scaffold may be positioned along a chromosome physical map to create a "golden path". subset: bioinformatics subset: edam subset: operations synonym: "Scaffold construction" EXACT [] created_in: "1.1" def: "Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2429 ! Mapping and assembly is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3217 name: Scaffold gap completion comment: Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2429 ! Mapping and assembly is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3218 name: Sequencing quality control subset: bioinformatics subset: edam subset: operations synonym: "Analyse raw sequence data from a sequencing pipeline and identify problems." EXACT [] synonym: "Sequencing QC" EXACT [] created_in: "1.1" def: "Raw sequence data quality control." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2428 ! Evaluation and validation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3219 name: Read pre-processing comment: This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. subset: bioinformatics subset: edam subset: operations synonym: "Sequence read pre-processing" EXACT [] created_in: "1.1" def: "Pre-process sequence reads to ensure (or improve) quality and reliability." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3221 name: Species frequency estimation subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_topic EDAM_topic:3174 ! Metagenomics [Term] id: EDAM_operation:3222 name: Peak calling comment: Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). subset: bioinformatics subset: edam subset: operations synonym: "Protein binding peak detection" EXACT [] created_in: "1.1" def: "Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:3223 name: Differential expression analysis comment: Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. subset: bioinformatics subset: edam subset: operations synonym: "Differentially expressed gene identification" EXACT [] created_in: "1.1" def: "Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0315 ! Gene expression profile comparison [Term] id: EDAM_operation:3224 name: Gene set testing comment: Gene sets can be defined beforehand by biological function, chromosome locations and so on. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2435 ! Gene expression profile processing [Term] id: EDAM_operation:3225 name: Variant classification comment: Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:2995 ! Sequence classification [Term] id: EDAM_operation:3226 name: Variant prioritization comment: Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3227 name: Variant mapping comment: Methods often utilise a database of aligned reads. subset: bioinformatics subset: edam subset: operations synonym: "Variant calling" EXACT [] created_in: "1.1" def: "Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3197 ! Genetic variation analysis [Term] id: EDAM_operation:3228 name: Structural variation discovery comment: Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3197 ! Genetic variation analysis [Term] id: EDAM_operation:3229 name: Exome analysis comment: Exome sequencing is considered a cheap alternative to whole genome sequencing. subset: bioinformatics subset: edam subset: operations synonym: "Exome sequence analysis" EXACT [] synonym: "Targeted exome capture" EXACT [] created_in: "1.1" def: "Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3230 name: Read depth analysis subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3232 name: Gene expression QTL analysis subset: bioinformatics subset: edam subset: operations synonym: "eQTL profiling" EXACT [] synonym: "expression QTL profiling" EXACT [] synonym: "expression quantitative trait loci profiling" EXACT [] created_in: "1.1" def: "Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0532 ! Gene expression profile analysis relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] id: EDAM_operation:3233 name: Copy number estimation comment: Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). subset: bioinformatics subset: edam subset: operations synonym: "Transcript copy number estimation" EXACT [] created_in: "1.1" def: "Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis [Term] id: EDAM_operation:3237 name: Primer removal subset: bioinformatics subset: edam subset: operations created_in: "1.1" def: "Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products)." [http://edamontology.org] namespace: operation is_a: EDAM_operation:0369 ! Sequence cutting is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid) [Term] id: EDAM_operation:3258 name: Transcriptome assembly subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Infer a transcriptome sequence by analysis of short sequence reads." [http://edamontology.org] namespace: operation is_a: EDAM_operation:2429 ! Mapping and assembly is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_output EDAM_data:0925 ! Sequence assembly relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] id: EDAM_operation:3259 name: Transcriptome assembly (de novo) subset: bioinformatics subset: edam subset: operations synonym: "de novo transcriptome assembly" EXACT [] created_in: "beta12orEarlier" def: "Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3258 ! Transcriptome assembly [Term] id: EDAM_operation:3260 name: Transcriptome assembly (mapping) subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" def: "Infer a transcriptome sequence by mapping short reads to a reference genome." [http://edamontology.org] namespace: operation is_a: EDAM_operation:3258 ! Transcriptome assembly [Term] id: EDAM_topic:0003 name: Topic subset: bioinformatics subset: edam subset: topics synonym: "Area_of_Research" RELATED [] synonym: "Category" RELATED [] synonym: "Continuant" BROAD [] synonym: "Method" RELATED [] synonym: "Perpetuant" RELATED [] synonym: "Quality" BROAD [] synonym: "Quality" RELATED [] synonym: "quality" RELATED [] synonym: "sumo:FieldOfStudy" RELATED [] created_in: "beta12orEarlier" def: "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other." [http://edamontology.org] namespace: topic [Term] id: EDAM_topic:0077 name: Nucleic acid analysis subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D017422" NARROW [] synonym: "http://purl.bioontology.org/ontology/MSH/D017423" NARROW [] synonym: "Nucleic acid bioinformatics" EXACT [] synonym: "Nucleic acid informatics" EXACT [] synonym: "Nucleic acids" EXACT [] created_in: "beta12orEarlier" def: "Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0078 name: Protein analysis subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D020539" NARROW [] synonym: "Protein bioinformatics" EXACT [] synonym: "Protein informatics" EXACT [] synonym: "Proteins" EXACT [] created_in: "beta12orEarlier" def: "Processing and analysis of protein data, typically molecular sequence and structural data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0079 name: Metabolites comment: This concept excludes macromolecules such as proteins and nucleic acids. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0154 ! Small molecules is_a: EDAM_topic:3172 ! Metabolomics [Term] id: EDAM_topic:0080 name: Sequence analysis subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D017421" EXACT [] synonym: "Sequences" EXACT [] xref: BioCatalogue:Sequence Analysis created_in: "beta12orEarlier" def: "Processing and analysis of molecular sequences (monomer composition of polymers) including related concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0081 name: Structure analysis comment: This includes related concepts such as structural properties, alignments and structural motifs. subset: bioinformatics subset: edam subset: topics synonym: "Computation structural biology" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D015394" RELATED [] synonym: "Structural bioinformatics" EXACT [] created_in: "beta12orEarlier" def: "Processing and analysis of molecular secondary or tertiary (3D) structure, typically of proteins and nucleic acids." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0082 name: Structure prediction subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the prediction of molecular (secondary or tertiary) structure." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_topic:0083 name: Alignment subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0182 ! Sequence alignment consider: EDAM_topic:0183 ! Structure alignment consider: EDAM_topic:0184 ! Threading [Term] id: EDAM_topic:0084 name: Phylogenetics 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: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D010802" NARROW [] synonym: "Phylogenetic clocks, dating and stratigraphy" EXACT [] synonym: "Phylogenetic simulation" EXACT [] xref: BioCatalogue:Phylogeny xref: BioCatalogue:Statistical Robustness created_in: "beta12orEarlier" def: "Topic concerning the study of evolutionary relationships amongst organisms; phylogenetic trees, gene transfer, mode of selection / evolution etc." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0085 name: Functional genomics subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the study of gene or protein functions and their interactions." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:0089 name: Ontology comment: This includes the annotation of entities (typically biological database entries) with concepts from a controlled vocabulary. subset: bioinformatics subset: edam subset: topics synonym: "Applied ontology" NARROW [] synonym: "Ontologies" EXACT [] xref: BioCatalogue:Ontology Lookup xref: BioCatalogue:Ontology created_in: "beta12orEarlier" def: "Topic concerning ontologies, controlled vocabularies, structured glossary or other related resource." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:0090 name: Data search and retrieval comment: This includes, for example, search, query and retrieval of molecular sequences and associated data. subset: bioinformatics subset: edam subset: topics synonym: "Data retrieval" EXACT [] xref: BioCatalogue:Data Retrieval xref: BioCatalogue:Identifier Retrieval xref: BioCatalogue:Image Retrieval xref: BioCatalogue:Sequence Retrieval xref: BioCatalogue:Structure Retrieval created_in: "beta12orEarlier" def: "Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0091 name: Data handling subset: bioinformatics subset: edam subset: topics synonym: "Data types, processing and visualisation" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D016247" NARROW [] created_in: "beta12orEarlier" def: "Topic for the generic management of biological data including basic handling of files and databases, datatypes, workflows and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0092 name: Data visualisation subset: bioinformatics subset: edam subset: topics synonym: "Data plotting" EXACT [] synonym: "Data rendering" EXACT [] synonym: "Data rendering and visualisation" EXACT [] created_in: "beta12orEarlier" def: "Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0094 name: Nucleic acid thermodynamics comment: This includes the study of thermal and conformational properties including DNA or DNA/RNA denaturation (melting). subset: bioinformatics subset: edam subset: topics synonym: "DNA melting" EXACT [] synonym: "Nucleic acid denaturation" EXACT [] synonym: "Nucleic acid physicochemistry" EXACT [] synonym: "Nucleic acid properties" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the study of the thermodynamic properties of a nucleic acid." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0097 name: Nucleic acid structure analysis subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "The processing and analysis of nucleic acid (secondary or tertiary) structural data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0077 ! Nucleic acid analysis is_a: EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_topic:0099 name: RNA subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning RNA sequences and structures." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3042 ! Nucleic acid sequences [Term] id: EDAM_topic:0100 name: Nucleic acid restriction subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis is_a: EDAM_topic:0821 ! Enzymes and reactions [Term] id: EDAM_topic:0102 name: Mapping subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the mapping of complete (typically nucleotide) sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0107 name: Codon usage analysis subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0110 ! Transcription [Term] id: EDAM_topic:0108 name: Translation subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the translation of mRNA into protein." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0109 name: Gene finding 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: bioinformatics subset: edam subset: topics synonym: "Gene discovery" EXACT [] synonym: "Gene prediction" EXACT [] xref: BioCatalogue:Gene Prediction created_in: "beta12orEarlier" def: "Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3073 ! Nucleic acid feature detection [Term] id: EDAM_topic:0110 name: Transcription subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Transcription Factors created_in: "beta12orEarlier" def: "Topic concerning the transcription of DNA into mRNA." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0111 name: Promoters subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Promoter Prediction created_in: "beta12orEarlier" def: "Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins)." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0749 ! Transcription factors and regulatory sites [Term] id: EDAM_topic:0112 name: Nucleic acid folding subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the folding (in 3D space) of nucleic acid molecules." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0173 ! Nucleic acid structure prediction [Term] id: EDAM_topic:0114 name: Gene structure and RNA splicing comment: This includes splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. subset: bioinformatics subset: edam subset: topics synonym: "Gene structure" EXACT [] synonym: "RNA splicing" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0747 ! Nucleic acid sites and features is_a: EDAM_topic:3062 ! Genetic organisation [Term] id: EDAM_topic:0121 name: Proteomics 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: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D040901" EXACT [] synonym: "Protein expression" EXACT [] xref: BioCatalogue:Proteomics created_in: "beta12orEarlier" def: "Topic concerning the study of whole proteomes of organisms." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0122 name: Structural genomics subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Structural Genomics created_in: "beta12orEarlier" def: "Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0622 ! Genomics is_a: EDAM_topic:2226 ! Structure determination [Term] id: EDAM_topic:0123 name: Protein properties subset: bioinformatics subset: edam subset: topics synonym: "Protein physicochemistry" EXACT [] created_in: "beta12orEarlier" def: "Topic for the study of the physical and biochemical properties of peptides and proteins." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0639 ! Protein sequence analysis [Term] id: EDAM_topic:0128 name: Protein interactions comment: This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Protein Interaction created_in: "beta12orEarlier" def: "Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." [http://edamontology.org] namespace: topic is_a: EDAM_topic:1775 ! Protein function analysis is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0130 name: Protein folding and stability subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0133 name: Two-dimensional gel electrophoresis subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning two-dimensional gel electrophoresis image and related data." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0121 ! Proteomics [Term] id: EDAM_topic:0134 name: Mass spectrometry subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning mass spectrometry and related data." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0121 ! Proteomics [Term] id: EDAM_topic:0135 name: Protein microarrays subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning protein microarray data." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0121 ! Proteomics consider: EDAM_topic:0200 ! Microarrays [Term] id: EDAM_topic:0137 name: Protein hydropathy subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0123 ! Protein properties [Term] id: EDAM_topic:0140 name: Protein targeting and localization subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2225 ! Protein databases is_a: EDAM_topic:2276 ! Protein function prediction [Term] id: EDAM_topic:0141 name: Protein cleavage sites and proteolysis subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0639 ! Protein sequence analysis [Term] id: EDAM_topic:0143 name: Protein structure comparison comment: Use this concept for methods that are exclusively for protein structure. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the comparison of two or more protein structures." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0698 ! Protein tertiary structure consider: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:0144 name: Protein residue interaction analysis subset: bioinformatics subset: edam subset: topics synonym: "Protein residue interactions" EXACT [] created_in: "beta12orEarlier" def: "The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0147 name: Protein-protein interactions subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning protein-protein interactions, protein complexes, protein functional coupling etc." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_topic:0148 name: Protein-ligand interactions subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Ligand Interaction created_in: "beta12orEarlier" def: "Topic concerning protein-ligand (small molecule) interactions." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_topic:0149 name: Protein-nucleic acid interactions subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning protein-DNA/RNA interactions." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0128 ! Protein interactions [Term] id: EDAM_topic:0150 name: Protein design subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0172 ! Protein structure prediction [Term] id: EDAM_topic:0151 name: G protein-coupled receptors (GPCR) subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning G-protein coupled receptors (GPCRs)." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0820 ! Membrane proteins [Term] id: EDAM_topic:0152 name: Carbohydrates subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning carbohydrates, typically including structural information." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:0153 name: Lipids subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning lipids and their structures." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:0154 name: Small molecules comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. subset: bioinformatics subset: edam subset: topics synonym: "CHEBI:23367" RELATED [] created_in: "beta12orEarlier" def: "Topic concerning small molecules of biological significance, typically including structural information." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:0156 name: Sequence editing subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0080 ! Sequence analysis consider: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0157 name: Sequence composition analysis subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0158 name: Sequence motifs subset: bioinformatics subset: edam subset: topics synonym: "Motifs" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0594 ! Sequence classification [Term] id: EDAM_topic:0159 name: Sequence comparison comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Nucleotide Sequence Similarity xref: BioCatalogue:Protein Sequence Similarity created_in: "beta12orEarlier" def: "Topic concerning the comparison of two or more molecular sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0160 name: Sequence sites and features subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0163 name: Sequence database search comment: The query is a sequence-based entity such as another sequence, a motif or profile. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence)." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0159 ! Sequence comparison [Term] id: EDAM_topic:0164 name: Sequence clustering comment: This includes systems that generate, process and analyse sequence clusters. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0159 ! Sequence comparison [Term] id: EDAM_topic:0166 name: Protein structural motifs and surfaces comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. subset: bioinformatics subset: edam subset: topics synonym: "Protein structural features" EXACT [] synonym: "Protein structural motifs" EXACT [] synonym: "Protein surfaces" EXACT [] synonym: "Structural motifs" EXACT [] created_in: "beta12orEarlier" def: "Topic 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0698 ! Protein tertiary structure [Term] id: EDAM_topic:0167 name: Structural (3D) profiles subset: bioinformatics subset: edam subset: topics synonym: "Structural profiles" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:0172 name: Protein structure prediction subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Protein Structure Prediction created_in: "beta12orEarlier" def: "Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0082 ! Structure prediction is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0173 name: Nucleic acid structure prediction subset: bioinformatics subset: edam subset: topics synonym: "Nucleic acid folding" EXACT [] synonym: "RNA/DNA structure prediction" EXACT [] xref: BioCatalogue:Nucleotide Secondary Structure xref: BioCatalogue:Nucleotide Structure Prediction xref: BioCatalogue:Nucleotide Tertiary Structure created_in: "beta12orEarlier" def: "Topic concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0082 ! Structure prediction is_a: EDAM_topic:0097 ! Nucleic acid structure analysis [Term] id: EDAM_topic:0174 name: Ab initio structure prediction subset: bioinformatics subset: edam subset: topics synonym: "de novo protein structure prediction" EXACT [] created_in: "beta12orEarlier" def: "Topic 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0082 ! Structure prediction [Term] id: EDAM_topic:0175 name: Homology modelling subset: bioinformatics subset: edam subset: topics synonym: "Comparative modelling" EXACT [] created_in: "beta12orEarlier" def: "Topic for the modelling of the three-dimensional structure of a protein using known sequence and structural data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2275 ! Molecular modelling [Term] id: EDAM_topic:0176 name: Molecular dynamics comment: This includes resources concerning flexibility and motion in protein and other molecular structures. subset: bioinformatics subset: edam subset: topics synonym: "Molecular flexibility" EXACT [] synonym: "Molecular motions" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2275 ! Molecular modelling [Term] id: EDAM_topic:0177 name: Molecular docking subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic for modelling the structure of proteins in complex with small molecules or other macromolecules." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2275 ! Molecular modelling [Term] id: EDAM_topic:0178 name: Protein secondary structure prediction subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Protein Secondary Structure created_in: "beta12orEarlier" def: "Topic concerning the prediction of secondary or supersecondary structure of protein sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0172 ! Protein structure prediction is_a: EDAM_topic:0694 ! Protein secondary structure [Term] id: EDAM_topic:0179 name: Protein tertiary structure prediction subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Protein Tertiary Structure created_in: "beta12orEarlier" def: "Topic concerning the prediction of tertiary structure of protein sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0172 ! Protein structure prediction is_a: EDAM_topic:0698 ! Protein tertiary structure [Term] id: EDAM_topic:0180 name: Protein fold recognition subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0172 ! Protein structure prediction [Term] id: EDAM_topic:0182 name: Sequence alignment 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: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D016415" EXACT [] xref: BioCatalogue:Nucleotide Multiple Alignment xref: BioCatalogue:Nucleotide Pairwise Alignment xref: BioCatalogue:Nucleotide Sequence Alignment xref: BioCatalogue:Protein Multiple Alignment xref: BioCatalogue:Protein Pairwise Alignment xref: BioCatalogue:Protein Sequence Alignment created_in: "beta12orEarlier" def: "Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0159 ! Sequence comparison is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0183 name: Structure alignment comment: This includes the generation, storage, analysis, rendering etc. of structure alignments. subset: bioinformatics subset: edam subset: topics synonym: "Structure alignment generation" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:1770 ! Structure comparison is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:0184 name: Threading subset: bioinformatics subset: edam subset: topics synonym: "Sequence-structure alignment" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0180 ! Protein fold recognition [Term] id: EDAM_topic:0188 name: Sequence profiles and HMMs comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0594 ! Sequence classification [Term] id: EDAM_topic:0191 name: Phylogeny reconstruction comment: Currently too specific for the topic sub-ontology (but might be unobsoleted). subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Evolutionary Distance Measurements xref: BioCatalogue:Tree Inference created_in: "beta12orEarlier" def: "Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_topic:0194 name: Phylogenomics subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0084 ! Phylogenetics is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:0195 name: Virtual PCR subset: bioinformatics subset: edam subset: topics synonym: "PCR" EXACT [] synonym: "Polymerase chain reaction" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning simulated polymerase chain reaction (PCR)." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_topic:0196 name: Sequence assembly subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3168 ! Sequencing [Term] id: EDAM_topic:0199 name: Genetic variation subset: bioinformatics subset: edam subset: topics synonym: "DNA variation" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D014644" EXACT [] synonym: "Mutation and polymorphism" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning DNA sequence variation (mutation and polymorphism) data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0625 ! Genotype and phenotype is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0200 name: Microarrays subset: bioinformatics subset: edam subset: topics synonym: "DNA microarrays" NARROW [] synonym: "http://purl.bioontology.org/ontology/MSH/D046228" NARROW [] xref: BioCatalogue:Microarrays created_in: "beta12orEarlier" def: "Topic concerning microarrays, for example, to process microarray data or design probes and experiments." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0607 ! Laboratory resources [Term] id: EDAM_topic:0202 name: Pharmacoinformatics subset: bioinformatics subset: edam subset: topics synonym: "Computational pharmacology" EXACT [] created_in: "beta12orEarlier" def: "Topic for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2258 ! Chemoinformatics [Term] id: EDAM_topic:0203 name: Transcriptomics alt_id: topic_0197 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: bioinformatics subset: edam subset: topics synonym: "Expression profiling" EXACT [] synonym: "Gene expression analysis" EXACT [] synonym: "Gene expression profiling" EXACT [] synonym: "Gene expression resources" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D015870" RELATED [] created_in: "beta12orEarlier" def: "Topic concerning primarily raw or processed gene (mRNA) expression (typically microarray) data, including the analysis of gene expression levels, by identifying, quantifying or comparing mRNA transcripts and the interpretation (in functional terms) of gene expression data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:0204 name: Gene regulation subset: bioinformatics subset: edam subset: topics synonym: "Gene regulation resources" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning primarily the regulation of gene expression." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:0208 name: Pharmacogenomics subset: bioinformatics subset: edam subset: topics synonym: "Pharmacogenetics" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0202 ! Pharmacoinformatics is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:0209 name: Drug design 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: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the design of drugs or potential drug compounds." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0202 ! Pharmacoinformatics [Term] id: EDAM_topic:0210 name: Fish comment: The resource may be specific to a fish, a group of fish or all fish. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2820 ! Vertebrates [Term] id: EDAM_topic:0211 name: Flies comment: The resource may be specific to a fly, a group of flies or all flies. subset: bioinformatics subset: edam subset: topics synonym: "Fly" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2819 ! Invertebrates [Term] id: EDAM_topic:0213 name: Mice or rats comment: The resource may be specific to a group of mice / rats or all mice / rats. subset: bioinformatics subset: edam subset: topics synonym: "Mouse or rat" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3048 ! Mammals [Term] id: EDAM_topic:0215 name: Worms comment: The resource may be specific to a worm, a group of worms or all worms. subset: bioinformatics subset: edam subset: topics synonym: "Worm" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2819 ! Invertebrates [Term] id: EDAM_topic:0217 name: Literature analysis subset: bioinformatics subset: edam subset: topics synonym: "Literature search and analysis" EXACT [] synonym: "Literature sources" EXACT [] xref: BioCatalogue: Document Discovery xref: BioCatalogue: Literature retrieval created_in: "beta12orEarlier" def: "The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3068 ! Literature and reference [Term] id: EDAM_topic:0218 name: Text mining subset: bioinformatics subset: edam subset: topics synonym: "Text data mining" EXACT [] xref: BioCatalogue:Document Clustering xref: BioCatalogue:Document Similarity xref: BioCatalogue:Named Entity Recognition xref: BioCatalogue:Text Mining created_in: "beta12orEarlier" def: "Topic concerning the analysis of the biomedical and informatics literature." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0217 ! Literature analysis [Term] id: EDAM_topic:0219 name: Annotation subset: bioinformatics subset: edam subset: topics synonym: "Ontology annotation" EXACT [] xref: BioCatalogue:Genome Annotation xref: BioCatalogue:Ontology Annotation created_in: "beta12orEarlier" def: "Topic for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:0220 name: Data processing and validation comment: This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. subset: bioinformatics subset: edam subset: topics synonym: "Data file handling" EXACT [] synonym: "File handling" EXACT [] synonym: "Report handling" EXACT [] synonym: "Report processing" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning basic manipulations of files or reports of generic biological data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0221 name: Sequence annotation subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Annotate a molecular sequence." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0219 ! Annotation [Term] id: EDAM_topic:0222 name: Genome annotation subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Genome Annotation created_in: "beta12orEarlier" def: "Annotate a genome." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0219 ! Annotation consider: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:0593 name: NMR subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning raw NMR data." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:2226 ! Structure determination [Term] id: EDAM_topic:0594 name: Sequence classification comment: Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the classification of molecular sequences based on some measure of their similarity." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0595 name: Protein classification subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0078 ! Protein analysis is_a: EDAM_topic:0594 ! Sequence classification is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:0598 name: Sequence motif or profile comment: This includes comparison, discovery, recognition etc. of sequence motifs. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0158 ! Sequence motifs consider: EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_topic:0601 name: Protein modifications comment: EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) subset: bioinformatics subset: edam subset: topics synonym: "GO:0006464" RELATED [] synonym: "MOD:00000" RELATED [] synonym: "Protein post-translational modification" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning protein chemical modifications, e.g. post-translational modifications." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0123 ! Protein properties is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0602 name: Pathways, networks and models alt_id: topic_3076 subset: bioinformatics subset: edam subset: topics synonym: "Network or pathway analysis" EXACT [] xref: BioCatalogue:Pathway Retrieval xref: BioCatalogue:Pathways created_in: "beta13" def: "Topic concerning biological pathways, networks and other models, including their construction and analysis." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2259 ! Systems biology is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:0605 name: Informatics subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0606 name: Literature data resources subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3068 ! Literature and reference is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:0607 name: Laboratory resources subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:0608 name: Cell culture resources subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning general cell culture or data on a specific cell lines." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0607 ! Laboratory resources [Term] id: EDAM_topic:0610 name: Ecoinformatics subset: bioinformatics subset: edam subset: topics synonym: "Computational ecology" EXACT [] synonym: "Ecological informatics" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D004777" RELATED [] created_in: "beta12orEarlier" def: "Topic concerning the application of information technology to the ecological and environmental sciences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0611 name: Electron microscopy subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning electron microscopy data." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:2226 ! Structure determination [Term] id: EDAM_topic:0612 name: Cell cycle subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the cell cycle including key genes and proteins." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:2229 ! Cell biology resources [Term] id: EDAM_topic:0613 name: Peptides and amino acids subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0154 ! Small molecules [Term] id: EDAM_topic:0616 name: Organelle genes and proteins subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3078 ! Gene and protein resources [Term] id: EDAM_topic:0617 name: Ribosomal genes and proteins subset: bioinformatics subset: edam subset: topics synonym: "Ribosome genes and proteins" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning ribosomes, typically of ribosome-related genes and proteins." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0616 ! Organelle genes and proteins [Term] id: EDAM_topic:0618 name: Scents subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "A database about scents." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0154 ! Small molecules [Term] id: EDAM_topic:0620 name: Drugs and targets subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the structures of drugs, drug target, their interactions and binding affinities." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0154 ! Small molecules is_a: EDAM_topic:0202 ! Pharmacoinformatics [Term] id: EDAM_topic:0621 name: Genome, proteome and model organisms comment: General information on or more organisms, genomes (including molecular sequences and map, genes and annotation) and proteomes may be included. subset: bioinformatics subset: edam subset: topics synonym: "Genome map" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the genome, proteome or other information about a specific organism, such as a model organism, or group of organisms." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0121 ! Proteomics is_a: EDAM_topic:0622 ! Genomics is_a: EDAM_topic:0625 ! Genotype and phenotype [Term] id: EDAM_topic:0622 name: Genomics subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D023281" EXACT [] xref: BioCatalogue:Functional Genomics xref: BioCatalogue:Genomics created_in: "beta12orEarlier" def: "Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0623 name: Genes, gene family or system subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning particular gene(s), gene system or groups of genes." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2816 ! Gene resources is_a: EDAM_topic:3052 ! Sequence clusters and classification [Term] id: EDAM_topic:0624 name: Chromosomes subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning chromosomes." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3062 ! Genetic organisation [Term] id: EDAM_topic:0625 name: Genotype and phenotype subset: bioinformatics subset: edam subset: topics synonym: "Genotype and phenotype resources" EXACT [] synonym: "Genotyping" EXACT [] created_in: "beta12orEarlier" def: "Topic 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:0629 name: Gene expression and microarray subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0200 ! Microarrays consider: EDAM_topic:0203 ! Transcriptomics [Term] id: EDAM_topic:0632 name: Probes and primers subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D015335" RELATED [] created_in: "beta12orEarlier" def: "Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0607 ! Laboratory resources is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0634 name: Disease resources subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning diseases." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0625 ! Genotype and phenotype [Term] id: EDAM_topic:0635 name: Specific protein resources subset: bioinformatics subset: edam subset: topics synonym: "Specific protein" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning a particular protein, protein family or other group of proteins." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0637 name: Taxonomy subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning organism classification, identification and naming." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:0639 name: Protein sequence analysis subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Protein Sequence Analysis created_in: "beta12orEarlier" def: "Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0078 ! Protein analysis is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0640 name: Nucleic acid sequence analysis subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Nucleotide Sequence Analysis created_in: "beta12orEarlier" def: "Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0077 ! Nucleic acid analysis is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0641 name: Repeat sequences subset: bioinformatics subset: edam subset: topics synonym: "Repeat sequence" EXACT [] xref: BioCatalogue:Repeats created_in: "beta12orEarlier" def: "Topic concerning the repetitive nature of molecular sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0157 ! Sequence composition analysis is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0642 name: Low complexity sequences subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0157 ! Sequence composition analysis is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:0644 name: Proteome subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning a specific proteome including protein sequences and annotation." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0654 name: DNA comment: The DNA sequences might be coding or non-coding sequences. subset: bioinformatics subset: edam subset: topics synonym: "DNA analysis" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning DNA sequences and structure, including processes such as methylation and replication." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0077 ! Nucleic acid analysis is_a: EDAM_topic:3042 ! Nucleic acid sequences [Term] id: EDAM_topic:0655 name: mRNA, EST or cDNA database subset: bioinformatics subset: edam subset: topics synonym: "mRNA, EST or cDNA" EXACT [] synonym: "Transcriptome" EXACT [] synonym: "Transcriptome database" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning data resources for messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0099 ! RNA [Term] id: EDAM_topic:0659 name: Functional and non-coding RNA comment: For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). subset: bioinformatics subset: edam subset: topics synonym: "Functional RNA" EXACT [] synonym: "Non-coding RNA" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning functional or non-coding RNA sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0099 ! RNA [Term] id: EDAM_topic:0660 name: rRNA subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning one or more ribosomal RNA (rRNA) sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] id: EDAM_topic:0663 name: tRNA subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning one or more transfer RNA (tRNA) sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] id: EDAM_topic:0694 name: Protein secondary structure comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. subset: bioinformatics subset: edam subset: topics synonym: "Protein secondary structure analysis" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning protein secondary structure or secondary structure alignments." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0697 name: RNA structure and alignment subset: bioinformatics subset: edam subset: topics synonym: "RNA alignment" EXACT [] synonym: "RNA structure" EXACT [] synonym: "RNA structure alignment" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning RNA secondary or tertiary structure and alignments." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0183 ! Structure alignment [Term] id: EDAM_topic:0698 name: Protein tertiary structure subset: bioinformatics subset: edam subset: topics synonym: "Protein tertiary structure analysis" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning protein tertiary structures." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0722 name: Nucleic acid classification subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning nucleic acid classification (typically sequence classification)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0077 ! Nucleic acid analysis is_a: EDAM_topic:0594 ! Sequence classification is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:0724 name: Protein families comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. subset: bioinformatics subset: edam subset: topics synonym: "Protein secondary" EXACT [] synonym: "Protein sequence classification" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning primarily proteins that have been classified as members of a protein family (or other grouping)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2225 ! Protein databases is_a: EDAM_topic:3052 ! Sequence clusters and classification [Term] id: EDAM_topic:0736 name: Protein domains and folds subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Domains created_in: "beta12orEarlier" def: "Topic concerning protein tertiary structural domains and folds." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0698 ! Protein tertiary structure is_a: EDAM_topic:0724 ! Protein families [Term] id: EDAM_topic:0740 name: Nucleic acid sequence alignment subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning nucleotide sequence alignments." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0182 ! Sequence alignment is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:0741 name: Protein sequence alignment comment: A sequence profile typically represents a sequence alignment. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning protein sequence alignments." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0182 ! Sequence alignment is_a: EDAM_topic:0639 ! Protein sequence analysis [Term] id: EDAM_topic:0747 name: Nucleic acid sites and features subset: bioinformatics subset: edam subset: topics synonym: "Nucleic acid features" EXACT [] synonym: "Nucleic acid functional sites" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning positional features such as functional sites in nucleotide sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0160 ! Sequence sites and features is_a: EDAM_topic:3042 ! Nucleic acid sequences [Term] id: EDAM_topic:0748 name: Protein sites and features subset: bioinformatics subset: edam subset: topics synonym: "Protein functional sites" EXACT [] synonym: "Protein sequence features" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning positional features such as functional sites in protein sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0160 ! Sequence sites and features is_a: EDAM_topic:3043 ! Protein sequences [Term] id: EDAM_topic:0749 name: Transcription factors and regulatory sites 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. subset: bioinformatics subset: edam subset: topics synonym: "Transcription factor and binding site" EXACT [] synonym: "Transcription factors" EXACT [] synonym: "Transcriptional regulatory sites" EXACT [] created_in: "beta12orEarlier" def: "Topic 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0110 ! Transcription is_a: EDAM_topic:0204 ! Gene regulation is_a: EDAM_topic:0635 ! Specific protein resources is_a: EDAM_topic:0747 ! Nucleic acid sites and features is_a: EDAM_topic:3062 ! Genetic organisation is_a: EDAM_topic:3073 ! Nucleic acid feature detection [Term] id: EDAM_topic:0751 name: Phosphorylation sites subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning protein phosphorylation and phosphorylation sites in protein sequences." [http://edamontology.org] namespace: topic obsolete_since: "1.0" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0601 ! Protein modifications consider: EDAM_topic:0748 ! Protein sites and features [Term] id: EDAM_topic:0753 name: Metabolic pathways subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning metabolic pathways." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0602 ! Pathways, networks and models is_a: EDAM_topic:3172 ! Metabolomics [Term] id: EDAM_topic:0754 name: Signaling pathways subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning signaling pathways." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_topic:0767 name: Protein and peptide identification comment: This includes the results of any methods that separate, characterize and identify expressed proteins. subset: bioinformatics subset: edam subset: topics synonym: "Peptide identification and proteolysis" EXACT [] synonym: "Proteomics data" EXACT [] synonym: "Proteomics data resources" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0121 ! Proteomics is_a: EDAM_topic:0639 ! Protein sequence analysis is_a: EDAM_topic:2225 ! Protein databases [Term] id: EDAM_topic:0769 name: Workflows subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning biological or biomedical analytical workflows or pipelines." [http://edamontology.org] namespace: topic obsolete_since: "1.0" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_topic:0770 name: Data types and objects subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning structuring data into basic types and (computational) objects." [http://edamontology.org] namespace: topic obsolete_since: "1.0" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:0771 name: Biological models comment: This includes databases of models and methods to construct or analyse a model. subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Model Creation created_in: "beta12orEarlier" def: "Topic concerning mathematical or other models of biological processes." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_topic:0779 name: Mitochondrial genes and proteins subset: bioinformatics subset: edam subset: topics synonym: "Mitochondria genes and proteins" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning mitochondria, typically of mitochondrial genes and proteins." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0616 ! Organelle genes and proteins [Term] id: EDAM_topic:0780 name: Plants comment: The resource may be specific to a plant, a group of plants or all plants. subset: bioinformatics subset: edam subset: topics synonym: "Plant" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:0781 name: Viruses comment: The resource may be specific to a virus, a group of viruses or all viruses. subset: bioinformatics subset: edam subset: topics synonym: "Virus" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:0782 name: Fungi comment: The resource may be specific to a fungus, a group of fungi or all fungi. subset: bioinformatics subset: edam subset: topics synonym: "Fungal" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:0783 name: Pathogens comment: The resource may be specific to a pathogen, a group of pathogens or all pathogens. subset: bioinformatics subset: edam subset: topics synonym: "Pathogen" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:0786 name: Arabidopsis subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning Arabidopsis-specific data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0780 ! Plants [Term] id: EDAM_topic:0787 name: Rice subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning rice-specific data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0780 ! Plants [Term] id: EDAM_topic:0796 name: Genetic mapping and linkage subset: bioinformatics subset: edam subset: topics synonym: "Genetic linkage" EXACT [] synonym: "Linkage mapping" EXACT [] created_in: "beta12orEarlier" 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0102 ! Mapping [Term] id: EDAM_topic:0797 name: Comparative genomics subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Comparative Genomics created_in: "beta12orEarlier" def: "Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:0798 name: Mobile genetic elements subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3062 ! Genetic organisation [Term] id: EDAM_topic:0803 name: Human disease subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0634 ! Disease resources [Term] id: EDAM_topic:0804 name: Immunoinformatics subset: bioinformatics subset: edam subset: topics synonym: "Computational immunology" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D007120" RELATED [] synonym: "http://purl.bioontology.org/ontology/MSH/D007125" RELATED [] created_in: "beta12orEarlier" def: "Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0820 name: Membrane proteins subset: bioinformatics subset: edam subset: topics synonym: "Transmembrane proteins" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning a protein or region of a protein that spans a membrane." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0635 ! Specific protein resources [Term] id: EDAM_topic:0821 name: Enzymes and reactions subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0635 ! Specific protein resources [Term] id: EDAM_topic:1770 name: Structure comparison comment: This might involve comparison of secondary or tertiary (3D) structural information. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the comparison of two or more molecular structures." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_topic:1775 name: Protein function analysis subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic for the study of protein function." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0078 ! Protein analysis [Term] id: EDAM_topic:1811 name: Prokaryotes and archae comment: The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. subset: bioinformatics subset: edam subset: topics synonym: "Prokaryote and archae" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:2225 name: Protein databases subset: bioinformatics subset: edam subset: topics synonym: "Protein data resources" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning protein data resources." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0078 ! Protein analysis is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:2226 name: Structure determination subset: bioinformatics subset: edam subset: topics synonym: "Raw structural data analysis" EXACT [] synonym: "Structural assignment" EXACT [] synonym: "Structural determination" EXACT [] synonym: "Structure assignment" EXACT [] created_in: "beta12orEarlier" def: "Topic 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0081 ! Structure analysis [Term] id: EDAM_topic:2229 name: Cell biology resources subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning cells, such as key genes and proteins involved in the cell cycle." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3070 ! Biological science resources [Term] id: EDAM_topic:2230 name: Classification subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:2232 name: Lipoproteins subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning lipoproteins (protein-lipid assemblies)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0635 ! Specific protein resources [Term] id: EDAM_topic:2257 name: Phylogeny visualisation subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Tree Display created_in: "beta12orEarlier" def: "Visualise a phylogeny, for example, render a phylogenetic tree." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_topic:2258 name: Chemoinformatics subset: bioinformatics subset: edam subset: topics synonym: "Chemical informatics" EXACT [] synonym: "Cheminformatics" EXACT [] synonym: "Computational chemistry" EXACT [] xref: BioCatalogue:Chemoinformatics created_in: "beta12orEarlier" def: "Topic for the application of information technology to chemistry." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2259 name: Systems biology subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D049490" EXACT [] synonym: "Systems:biology" EXACT [] xref: BioCatalogue:Systems Biology created_in: "beta12orEarlier" def: "Topic concerning the holistic modelling and analysis of biological systems and the interactions therein." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2269 name: Biostatistics subset: bioinformatics subset: edam subset: topics synonym: "Biometrics" EXACT [] synonym: "Biometry" EXACT [] synonym: "http://en.wikipedia.org/wiki/Biostatistics" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D056808" EXACT [] xref: BioCatalogue:Biostatistics created_in: "beta12orEarlier" def: "Topic for the application of statistical methods to biological problems." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:2271 name: Structure database search comment: The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure)." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:2275 name: Molecular modelling subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. " [http://edamontology.org] namespace: topic is_a: EDAM_topic:0082 ! Structure prediction is_a: EDAM_topic:0172 ! Protein structure prediction [Term] id: EDAM_topic:2276 name: Protein function prediction subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Function Prediction created_in: "beta12orEarlier" def: "Topic concerning the prediction of functional properties of a protein." [http://edamontology.org] namespace: topic is_a: EDAM_topic:1775 ! Protein function analysis [Term] id: EDAM_topic:2277 name: SNPs 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: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0199 ! Genetic variation [Term] id: EDAM_topic:2278 name: Transmembrane protein prediction subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Predict transmembrane domains and topology in protein sequences." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0178 ! Protein secondary structure prediction consider: EDAM_topic:0820 ! Membrane proteins [Term] id: EDAM_topic:2280 name: Nucleic acid structure comparison comment: Use this concept for methods that are exclusively for nucleic acid structures. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0097 ! Nucleic acid structure analysis consider: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:2640 name: Cancer subset: bioinformatics subset: edam subset: topics synonym: "Cancer resources" EXACT [] created_in: "beta12orEarlier" def: "Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0634 ! Disease resources [Term] id: EDAM_topic:2661 name: Toxins and targets subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning structural and associated data for toxic chemical substances." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0154 ! Small molecules is_a: EDAM_topic:2840 ! Toxicoinformatics [Term] id: EDAM_topic:2807 name: Tool topic subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2809 name: Study topic subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2811 name: Nomenclature subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning biological nomenclature (naming), symbols and terminology." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:2813 name: Disease genes and proteins subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning the genes, gene variations and proteins involved in one or more specific diseases." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0634 ! Disease resources is_a: EDAM_topic:3078 ! Gene and protein resources [Term] id: EDAM_topic:2814 name: Protein structure analysis alt_id: topic_3040 subset: bioinformatics subset: edam subset: topics synonym: "Protein structure" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning protein secondary or tertiary structural data and/or associated annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0078 ! Protein analysis is_a: EDAM_topic:0081 ! Structure analysis is_a: EDAM_topic:2225 ! Protein databases is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:2815 name: Humans comment: The resource may be specific to a human, a group of humans or all humans. subset: bioinformatics subset: edam subset: topics synonym: "Human" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3048 ! Mammals [Term] id: EDAM_topic:2816 name: Gene resources subset: bioinformatics subset: edam subset: topics synonym: "Gene database" EXACT [] synonym: "Gene resource" EXACT [] created_in: "beta12orEarlier" def: "Informatics resource (typically a database) primarily focussed on genes." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3053 ! Genetics is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:2817 name: Yeast subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0782 ! Fungi [Term] id: EDAM_topic:2818 name: Eukaryotes comment: The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. subset: bioinformatics subset: edam subset: topics synonym: "Eukaryote" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0621 ! Genome, proteome and model organisms [Term] id: EDAM_topic:2819 name: Invertebrates comment: The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:2820 name: Vertebrates comment: The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. subset: bioinformatics subset: edam subset: topics synonym: "Vertebrate" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:2821 name: Unicellular eukaryotes comment: The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. subset: bioinformatics subset: edam subset: topics synonym: "Unicellular eukaryote" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2818 ! Eukaryotes [Term] id: EDAM_topic:2826 name: Protein structure alignment subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning protein secondary or tertiary structure alignments." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0183 ! Structure alignment is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:2828 name: X-ray crystallography subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning X-ray crystallography data." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:2226 ! Structure determination [Term] id: EDAM_topic:2829 name: Ontologies, nomenclature and classification subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D002965" NARROW [] created_in: "beta12orEarlier" def: "Topic 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2830 name: Immunity genes, immunoproteins and antigens comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." subset: bioinformatics subset: edam subset: topics synonym: "Immunoproteins and immunopeptides" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning immunity-related genes, proteins and their ligands." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0804 ! Immunoinformatics is_a: EDAM_topic:3078 ! Gene and protein resources [Term] id: EDAM_topic:2839 name: Molecules subset: bioinformatics subset: edam subset: topics synonym: "CHEBI:23367" RELATED [] created_in: "beta12orEarlier" def: "Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true [Term] id: EDAM_topic:2840 name: Toxicoinformatics subset: bioinformatics subset: edam subset: topics synonym: "Computational toxicology" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the adverse effects of chemical substances on living organisms." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2258 ! Chemoinformatics [Term] id: EDAM_topic:2842 name: High-throughput sequencing subset: bioinformatics subset: edam subset: topics synonym: "Next-generation sequencing" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [http://edamontology.org] namespace: topic obsolete_since: "beta13" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:3168 ! Sequencing [Term] id: EDAM_topic:2844 name: Structural clustering subset: bioinformatics subset: edam subset: topics synonym: "Structure classification" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." [http://edamontology.org] namespace: topic is_a: EDAM_topic:1770 ! Structure comparison [Term] id: EDAM_topic:2846 name: Gene regulatory networks subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic concerning gene regulatory networks." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0204 ! Gene regulation is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_topic:2847 name: Disease (specific) subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Informatics resources dedicated to one or more specific diseases (not diseases in general)." [http://edamontology.org] namespace: topic obsolete_since: "beta12orEarlier" !is_a: ObsoleteClass ! Obsolete concept (EDAM) is_obsolete: true consider: EDAM_topic:0634 ! Disease resources [Term] id: EDAM_topic:2953 name: Nucleic acid design subset: bioinformatics subset: edam subset: topics created_in: "beta12orEarlier" def: "Topic for the design of nucleic acid sequences with specific conformations." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0077 ! Nucleic acid analysis [Term] id: EDAM_topic:3032 name: Primer or probe design subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:3038 name: Structure databases subset: bioinformatics subset: edam subset: topics synonym: "Structure data resources" EXACT [] created_in: "beta13" def: "Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0081 ! Structure analysis is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:3039 name: Nucleic acid structure subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3038 ! Structure databases [Term] id: EDAM_topic:3041 name: Sequence databases subset: bioinformatics subset: edam subset: topics synonym: "Sequence data" EXACT [] synonym: "Sequence data resource" EXACT [] synonym: "Sequence data resources" EXACT [] created_in: "beta13" def: "Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0080 ! Sequence analysis is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:3042 name: Nucleic acid sequences subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:3043 name: Protein sequences subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Protein Sequence Analysis created_in: "beta13" def: "Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2225 ! Protein databases is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:3044 name: Protein interaction networks subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning protein-protein interaction networks." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0147 ! Protein-protein interactions is_a: EDAM_topic:0602 ! Pathways, networks and models [Term] id: EDAM_topic:3047 name: Molecular biology reference subset: bioinformatics subset: edam subset: topics xref: BioCatalogue: Document Discovery xref: BioCatalogue: Literature retrieval created_in: "beta13" def: "Topic concerning general molecular biology information extracted from the literature." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0606 ! Literature data resources [Term] id: EDAM_topic:3048 name: Mammals subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2820 ! Vertebrates [Term] id: EDAM_topic:3050 name: Biodiversity subset: bioinformatics subset: edam subset: topics synonym: "Biodiversity data resource" EXACT [] synonym: "Biodiversity data resources" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D044822" EXACT [] created_in: "beta13" def: "Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0610 ! Ecoinformatics [Term] id: EDAM_topic:3052 name: Sequence clusters and classification comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. subset: bioinformatics subset: edam subset: topics synonym: "Sequence clusters" EXACT [] synonym: "Sequence families" EXACT [] created_in: "beta13" def: "Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3041 ! Sequence databases [Term] id: EDAM_topic:3053 name: Genetics subset: bioinformatics subset: edam subset: topics synonym: "Genetics data resources" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D005823" EXACT [] created_in: "beta13" def: "Topic concerning the study of genes, genetic variation and heredity in living organisms." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:3055 name: Quantitative genetics subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3053 ! Genetics [Term] id: EDAM_topic:3056 name: Population genetics subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3053 ! Genetics [Term] id: EDAM_topic:3060 name: Regulatory RNA comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA)." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] id: EDAM_topic:3061 name: Documentation and help subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning documentation and getting help." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3068 ! Literature and reference [Term] id: EDAM_topic:3062 name: Genetic organisation subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning the structural and functional organisation of genes and other genetic elements." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:3063 name: Medical informatics resources subset: bioinformatics subset: edam subset: topics synonym: "Biomedical informatics" EXACT [] synonym: "Clinical informatics" EXACT [] synonym: "Health and disease" EXACT [] synonym: "Health informatics" EXACT [] synonym: "Healthcare informatics" EXACT [] created_in: "beta13" def: "Topic for the application of information technology to health, disease and biomedicine." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0607 ! Laboratory resources [Term] id: EDAM_topic:3064 name: Developmental biology resources subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning how organisms grow and develop." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3070 ! Biological science resources [Term] id: EDAM_topic:3065 name: Embryology resources subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3064 ! Developmental biology resources [Term] id: EDAM_topic:3067 name: Anatomy resources subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning the structures of living organisms." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3070 ! Biological science resources [Term] id: EDAM_topic:3068 name: Literature and reference subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D011642" RELATED [] created_in: "beta13" def: "Topic concerning the scientific literature, reference information and documentation." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:3070 name: Biological science resources subset: bioinformatics subset: edam subset: topics synonym: "Phenotype resource" EXACT [] created_in: "beta13" def: "Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3071 ! Biological data resources [Term] id: EDAM_topic:3071 name: Biological data resources subset: bioinformatics subset: edam subset: topics synonym: "Biological data resource" EXACT [] synonym: "Biological databases" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D030541" NARROW [] created_in: "beta13" 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." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:3072 name: Sequence feature detection subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D058977" RELATED [] created_in: "beta13" def: "Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:3073 name: Nucleic acid feature detection subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning the detection of positional features such as functional sites in nucleotide sequences." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis is_a: EDAM_topic:3072 ! Sequence feature detection [Term] id: EDAM_topic:3074 name: Protein feature detection subset: bioinformatics subset: edam subset: topics created_in: "beta13" def: "Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0639 ! Protein sequence analysis is_a: EDAM_topic:3072 ! Sequence feature detection [Term] id: EDAM_topic:3075 name: Biological system modelling subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Model Analysis xref: BioCatalogue:Model Execution created_in: "beta13" def: "Topic for modelling biological systems in mathematical terms." [http://edamontology.org] namespace: topic is_a: EDAM_topic:2259 ! Systems biology [Term] id: EDAM_topic:3077 name: Data acquisition and deposition subset: bioinformatics subset: edam subset: topics synonym: "Database submission" EXACT [] created_in: "beta13" def: "Topic concerning the acquisition and deposition of biological data." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0091 ! Data handling [Term] id: EDAM_topic:3078 name: Gene and protein resources subset: bioinformatics subset: edam subset: topics synonym: "Genes and proteins resources" EXACT [] created_in: "beta13" def: "Topic concerning specific genes and their encoded proteins or a related group of such genes and proteins." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0623 ! Genes, gene family or system is_a: EDAM_topic:0635 ! Specific protein resources [Term] id: EDAM_topic:3168 name: Sequencing subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D059014" NARROW [] created_in: "1.1" def: "Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] id: EDAM_topic:3169 name: ChIP-seq subset: bioinformatics subset: edam subset: topics synonym: "Chip seq" EXACT [] synonym: "Chip sequencing" EXACT [] synonym: "Chip-sequencing" EXACT [] created_in: "1.1" def: "Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0128 ! Protein interactions is_a: EDAM_topic:3168 ! Sequencing [Term] id: EDAM_topic:3170 name: RNA-Seq comment: This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. subset: bioinformatics subset: edam subset: topics synonym: "RNA-seq" EXACT [] synonym: "Small RNA-Seq" EXACT [] synonym: "Small RNA-seq" EXACT [] synonym: "Whole transcriptome shotgun sequencing" EXACT [] synonym: "WTSS" EXACT [] created_in: "1.1" def: "A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. " [http://edamontology.org] namespace: topic is_a: EDAM_topic:0203 ! Transcriptomics is_a: EDAM_topic:3168 ! Sequencing [Term] id: EDAM_topic:3171 name: DNA methylation subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D019175" EXACT [] created_in: "1.1" def: "Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0654 ! DNA [Term] id: EDAM_topic:3172 name: Metabolomics subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D055432" EXACT [] created_in: "1.1" def: "Topic concerning the study of metabolites and the chemical processes they are involved in, especially the systematic study of the chemical fingerprints of specific cellular processes." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:3173 name: Epigenomics comment: Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. subset: bioinformatics subset: edam subset: topics synonym: "Epigenetics" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D057890" EXACT [] created_in: "1.1" def: "A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:3174 name: Metagenomics subset: bioinformatics subset: edam subset: topics synonym: "Community genomics" EXACT [] synonym: "Ecogenomics" EXACT [] synonym: "Environmental genomics" EXACT [] synonym: "http://purl.bioontology.org/ontology/MSH/D056186" EXACT [] created_in: "1.1" def: "Topic concerning the study of genetic material recovered from environmental samples." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0610 ! Ecoinformatics is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_topic:3175 name: Structural variation subset: bioinformatics subset: edam subset: topics synonym: "Genomic structural variation" EXACT [] created_in: "1.1" def: "Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0199 ! Genetic variation is_a: EDAM_topic:0624 ! Chromosomes [Term] id: EDAM_topic:3176 name: DNA packaging subset: bioinformatics subset: edam subset: topics synonym: "http://purl.bioontology.org/ontology/MSH/D042003" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0624 ! Chromosomes is_a: EDAM_topic:0654 ! DNA [Term] id: EDAM_topic:3177 name: DNA-Seq subset: bioinformatics subset: edam subset: topics synonym: "DNA-seq" EXACT [] created_in: "1.1" def: "A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements." [http://edamontology.org] namespace: topic is_a: EDAM_topic:3168 ! Sequencing [Term] id: EDAM_topic:3178 name: RNA-Seq alignment subset: bioinformatics subset: edam subset: topics synonym: "RNA-seq alignment" EXACT [] created_in: "beta12orEarlier" def: "Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_topic:3179 name: ChIP-on-chip subset: bioinformatics subset: edam subset: topics synonym: "ChIP-chip" EXACT [] created_in: "1.1" def: "Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions." [http://edamontology.org] namespace: topic is_a: EDAM_topic:0128 ! Protein interactions is_a: EDAM_topic:3168 ! Sequencing [Typedef] id: has_format name: has format comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. subset: bioinformatics subset: edam subset: relations synonym: "has-quality" RELATED [] synonym: "OBI:0000298" RELATED [] def: "'A has_format B' defines for the subject A, that it has the object B as its data format." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: false transitive_over: OBO_REL:is_a domain: EDAM_data:0006 ! Data range: EDAM_format:1915 ! Format [Typedef] id: has_function name: has function comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. subset: bioinformatics subset: edam subset: relations synonym: "has-quality" RELATED [] synonym: "has_function" EXACT [] synonym: "OBI:0000306" NARROW [] synonym: "OBO_REL:bearer_of" RELATED [] def: "'A has_function B' defines for the subject A, that it has the object B as its function." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: true transitive_over: OBO_REL:is_a range: EDAM_operation:0004 ! Operation [Typedef] id: has_identifier name: has identifier comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. subset: bioinformatics subset: edam subset: relations def: "'A has_identifier B' defines for the subject A, that it has the object B as its identifier." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: false transitive_over: OBO_REL:is_a domain: EDAM_data:0006 ! Data range: EDAM_data:0842 ! Identifier [Typedef] id: has_input name: has input comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. subset: bioinformatics subset: edam subset: relations synonym: "has_input" EXACT [] synonym: "OBI:0000293" NARROW [] synonym: "OBO_REL:has_participant" RELATED [] def: "'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: true transitive_over: OBO_REL:is_a domain: EDAM_operation:0004 ! Operation range: EDAM_data:0006 ! Data [Typedef] id: has_output name: has output comment: Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. subset: bioinformatics subset: edam subset: relations synonym: "has_output" EXACT [] synonym: "OBI:0000299" NARROW [] synonym: "OBO_REL:has_participant" RELATED [] def: "'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: true transitive_over: OBO_REL:is_a domain: EDAM_operation:0004 ! Operation range: EDAM_data:0006 ! Data [Typedef] id: has_topic name: has topic comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. subset: bioinformatics subset: edam subset: relations synonym: "has-quality" RELATED [] synonym: "hasTopic" RELATED [] synonym: "IAO:0000136" RELATED [] synonym: "OBI:0000298" RELATED [] def: "'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B)." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: true transitive_over: OBO_REL:is_a range: EDAM_topic:0003 ! Topic [Typedef] id: is_format_of name: is format of comment: Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. subset: bioinformatics subset: edam subset: relations synonym: "inherent-in" RELATED [] synonym: "OBO_REL:quality_of" RELATED [] def: "'A is_format_of B' defines for the subject A, that it is a data format of the object B." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: false transitive_over: OBO_REL:is_a domain: EDAM_format:1915 ! Format range: EDAM_data:0006 ! Data inverse_of: has_format ! has format [Typedef] id: is_function_of name: is function of comment: Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. subset: bioinformatics subset: edam subset: relations synonym: "http://wsio.org/is_function_of" EXACT [] synonym: "inherent-in" RELATED [] synonym: "OBO_REL:function_of" NARROW [] synonym: "OBO_REL:inheres_in" RELATED [] def: "'A is_function_of B' defines for the subject A, that it is a function of the object B." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: true transitive_over: OBO_REL:is_a domain: EDAM_operation:0004 ! Operation inverse_of: has_function ! has function [Typedef] id: is_identifier_of name: is identifier of comment: Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. subset: bioinformatics subset: edam subset: relations def: "'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: false transitive_over: OBO_REL:is_a domain: EDAM_data:0842 ! Identifier range: EDAM_data:0006 ! Data inverse_of: has_identifier ! has identifier [Typedef] id: is_input_of name: is input of comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. subset: bioinformatics subset: edam subset: relations synonym: "http://wsio.org/is_input_of" EXACT [] synonym: "OBI:0000295" NARROW [] synonym: "OBO_REL:participates_in" RELATED [] def: "'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: true transitive_over: OBO_REL:is_a domain: EDAM_data:0006 ! Data range: EDAM_operation:0004 ! Operation inverse_of: has_input ! has input [Typedef] id: is_output_of name: is output of comment: Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. subset: bioinformatics subset: edam subset: relations synonym: "http://wsio.org/is_output_of" EXACT [] synonym: "OBI:0000312" NARROW [] synonym: "OBO_REL:participates_in" RELATED [] def: "'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: true transitive_over: OBO_REL:is_a domain: EDAM_data:0006 ! Data range: EDAM_operation:0004 ! Operation inverse_of: has_output ! has output [Typedef] id: is_topic_of name: is topic of comment: Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. subset: bioinformatics subset: edam subset: relations synonym: "inherent-in" RELATED [] synonym: "OBO_REL:quality_of" RELATED [] def: "'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B)." [http://edamontology.org] is_anti_symmetric: false is_reflexive: false is_symmetric: false is_cyclic: true transitive_over: OBO_REL:is_a domain: EDAM_topic:0003 ! Topic inverse_of: has_topic ! has topic